Perspective

pubs.acs.org/jmc

Applications of Fluorine in Medicinal Chemistry

Eric P. Gillis,*,† Kyle J. Eastman,† Matthew D. Hill,† David J. Donnelly,‡ and Nicholas A. Meanwell†
†
Department of Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford,
Connecticut 06492, United States
‡
Discovery Chemistry Platforms, PET Radiochemical Synthesis, Bristol-Myers Squibb Research and Development, P.O. Box 4000,
Princeton, New Jersey 08543, United States

ABSTRACT: The role of fluorine in drug design and development is

expanding rapidly as we learn more about the unique properties associated
with this unusual element and how to deploy it with greater sophistication.
The judicious introduction of fluorine into a molecule can productively
influence conformation, pKa, intrinsic potency, membrane permeability,
metabolic pathways, and pharmacokinetic properties. In addition, 18F has
been established as a useful positron emitting isotope for use with in vivo
imaging technology that potentially has extensive application in drug
discovery and development, often limited only by convenient synthetic
accessibility to labeled compounds. The wide ranging applications of fluorine in
drug design are providing a strong stimulus for the development of new
synthetic methodologies that allow more facile access to a wide range of
fluorinated compounds. In this review, we provide an update on the effects of the strategic incorporation of fluorine in drug
molecules and applications in positron emission tomography.

■ INTRODUCTION
Fluorine has been exploited extensively in drug design and
development, with broader incorporation limited largely by
synthetic accessibility.1 As synthetic methodology to introduce
fluorine has evolved, allowing deployment in ever increasing and
more sophisticated settings, this enigmatic element continues to
enchant as we learn more about its unique properties not only
within the halogen series but also within the limited number of
elements that are commonly incorporated into drug molecules.2
Fluorine is also emerging as one of the most prominent atoms
in the application of positron emission tomography (PET)
due to the favorable half-life of the 18F isotope (109.8 min)
when compared to 11C (20.4 min) and 124I (4.2 days), and new
synthetic methodology is considerably enhancing its utility,
particularly for central nervous system (CNS) drug discovery.3 In
this review, we provide an overview of some of the tactical
applications of fluorine in the design and optimization of drug
candidates with an emphasis on studies published since the last
update in the Journal of Medicinal Chemistry.1f
available for hyperconjugative donation. In aliphatic systems,
a combination of these effects produces a strong preference
for vicinal functionality to align gauche to fluorine, where this
influence is of sufficient magnitude to find practical application in
the design of drugs and organocatalysts.5 The calculated energies
of stabilization for several fluoroethane derivatives that demon-
strate this “gauche effect” are presented in Table 1 with comment
on what is considered to be the origin(s) of the phenomenon:
hyperconjugative electron donation by an adjacent C−H bond
into low lying C−F σ* orbitals, C−F···H−X interactions, and/or
dipole and electrostatic interactions.5b The application of these
effects as potential probes of conformational preferences in
drug design and drug−target interactions is beginning to be more
fully appreciated, and a number of examples that take advantage
of this phenomenon in a productive fashion have been described.
Illustrative examples of each mode of influence are provided
below.
(a) Fluorine−Fluorine Interactions. Vicinally fluorinated
alkanes adopt a gauche conformation stabilized by reinforcing

■ FLUORINE AS A CONFORMATIONAL CONTROL

ELEMENT
Fluorine can play an important and unique role in influencing
molecular conformation. From the perspective of steric effects,
the influence of fluorine is anticipated to be marginal; fluorine
is a small atom with a van der Waals radius of 1.47 Å, close to
the 1.20 Å value for hydrogen.1a,4 However, the high electro-
negativity of fluorine (3.98 on the Pauling electronegativity scale
compared to 2.20 for H, 3.44 for O, and 2.55 for C) results in a
highly polarized C−F bond which presents both a strong dipole
moment (μ C−F = 1.41 D) and a low lying C−F σ* orbital
hyperconjugative interactions in which the low-lying C−F σ*
orbitals accept electron density from adjacent C−H σ bonds.
This phenomenon in isolation is modest in magnitude, calculated
to be worth 0.8 kcal/mol, but is still sufficient to influence
conformation (Figure 1).4b,5b,6 For example, the (±)-erythro
and (±)-threo isomers of 9,10-difluorostearic acid, 1 and 2,
respectively, differ only by the absolute configuration at C-9, yet
(±)-threo-isomer 2 melts at a temperature almost 20 °C higher
than (±)-erythro-isomer 1.6,7 This has been attributed to 2 more
Received: February 13, 2015

© XXXX American Chemical Society A DOI: 10.1021/acs.jmedchem.5b00258

J. Med. Chem. XXXX, XXX, XXX−XXX
Journal of Medicinal Chemistry Perspective

Table 1. Calculated Energy Differences between the gauche- and anti-Isomers of Select X-Substituted Fluoroethane Derivatives

X stabilization energy (kcal/mol) underlying interaction

F 0.5−1.0 C(F)−H σ to C−F σ* hyperconjugation
OH 1.0−2.0 hyperconjugation and an intramolecular C−F to O−H electrostatic interaction
NH2 0.9−1.0 intramolecular C−F H-bonding
NH3+ 5.8 electrostatic interaction between F δ− and NH3+ δ+ dipoles
OAc 1.6 hyperconjugation of C(OAc)−H σ bond to C−F σ*
NHAc 1.8 electrostatic interaction between C−F δ− and N−H δ+

Figure 1. Conformational preferences of 1,2- and 1,3-difluoroalkanes.

readily adopting a stable and elongated form that is favored by a

gauche interaction between the two F atoms. This form deploys
the two alkyl moieties in an antiperiplanar arrangement which
minimizes unfavorable steric interactions. In contrast, when
the fluorine atoms of 1 adopt either of two possible gauche
arrangements, the alkyl side chains are also gauche to one
another. As a consequence, unfavorable steric interactions
between the alkyl side chains destabilize both conformations,
while the alternative arrangement places the alkyl groups in a
more favorable antiperiplanar relationship but the fluorine atoms
are also antiperiplanar, unable to take advantage of the gauche
effect. To assess their conformational mobility, the Langmuir
isotherms for material deposited from a CHCl3 solution onto
ultrapure H2O were measured, with the expanded nature of the
curve for 1 indicating conformational disorder in contrast to 2
which behaved analogously to the parent unsubstituted acid.7
The overall result is that 1 exhibits no strong conformational
preference, leading to structural disorder that is reflected in the
lower melting point.
1,3-Difluoroalkane motifs prefer to adopt a conformation that
minimizes dipole−dipole interactions between the C−F bonds,
with the lowest energy form depicted in Figure 1 and favored
by 2.7−3.3 kcal/mol.4b,5b,8 The combination of 1,2- and 1,3- Figure 2. Solid state structure of 3 (structure drawn with PyMol).
difluoro interactions can exert considerable conformational
control, as exemplified by the hexafluoroalkanes 3 and 4. The
former adopts a helical conformation in both solution and the
solid state which minimizes unfavorable dipole−dipole inter-
actions between the 1,3-difluoro motifs while maximizing gauche
interactions between the vicinal fluorine atoms (Figure 2).6,9 The
same effects underlie the preference for an extended con-
formation with 4 stabilized by 3 out of 5 possible gauche F−F
arrangements.
The judicious deployment of CF2 moieties in alkyl chains can
be exploited to bias conformation, as exemplified by palmitic acid
derivatives 5−7. These derivatives exhibit considerably different
melting points as determined by differential scanning calorim-
etry. Difluorinated palmitic acid 5 melts at 62.9 °C, comparable In contrast, acid 6 failed to crystallize but the amorphous material
to the 62.5 °C melting point of the unsubstituted progenitor and melted at 69 °C while crystalline 7 exhibited a melting point of
suggestive of limited influence of fluorination on conformation. 89.9 °C.10 In the solid state, 7 adopted an extended anti-zigzag
B DOI: 10.1021/acs.jmedchem.5b00258
J. Med. Chem. XXXX, XXX, XXX−XXX
Journal of Medicinal Chemistry
conformation that was attributed to a favorable alignment of the
dipoles associated with the carbon to fluorine bonds and a
minimization of unfavorable steric interactions between the CF2
moiety.10 The amorphous noncrystalline nature of 6 was
considered to be a function of repulsive effects between the
dipoles of the 1,3-disposed C−F moieties that cannot adequately
be satisfied in a single low energy conformation, resulting in
disorder of the alkyl chain such that a preferred conformation
could not be determined.
The relevance of the fluorine gauche effect in a more complex
setting is exemplified by difluoro-substituted analogs 9−12 of
unguisin A (8), a macrocyclic heptapeptide isolated from the
marine fungus Emericella unguis that incorporates γ-aminobutyric
acid (GABA) as one of the amino acid residues (Figure 3).11 The
Figure 3. Unguisin A and the four macrocycle analogues 9−12
containing difluoro GABA elements.
four stereoisomers 13−16 of the GABA analog 2,3-difluoro-4-
aminobutyric acid have been studied in isolation as modulators
of the GABA receptors GABAA, GABAB, and GABAC.12 As
analyzed by nuclear magnetic resonance (NMR) spectroscopy
and molecular modeling, the preferred conformations of 13 and
14 are those in which the gauche preferences of both fluorine
atoms are fully realized.12a The GABA element of unguisin
A has been shown to exhibit conformational disorder based
on analysis of NMR spectral data; thus, GABA analogs 13−16
were incorporated into unguisin A in order to explore the
effect of their intrinsic conformational preferences on the
overall secondary structure of 8. 1H NMR spectra of the four
difluorinated analogs 9−12 were recorded at a range of
temperatures, and the 3JH,H and 3JH,F values were measured.11c
C DOI: 10.1021/acs.jmedchem.5b00258
Perspective
For syn-di-F analogue 9 the coupling constants were consistent
with a gauche relationship between the two F atoms but with
disorder between the two possible conformers. For the syn-
isomer 10, the J values were of a higher magnitude, indicative of
an extended structure for the GABA element in which a gauche
arrangement between the two F atoms is strongly preferred. The
two anti-isomers 11 and 12, similar to 9, favor a gauche
relationship between the two fluorine atoms but with
considerable disorder between the two possible conformers.
The interaction of fluorine with amide N−H functionality is
discussed below; however, in analogs 9−12 this interaction was
not detected, presumably because of geometric constraints
imposed by the macrocyclic ring structure. Molecular modeling
of the five compounds, in which the low energy conformations
were aligned with the 1H NMR data, indicated that while 8
preferred an overall flat topography, the four difluorinated
analogs 9−12 behaved quite differently. Compound 9 exhibited a
fully planar geometry, while 10 demonstrated more pucker than
8 and adopted a conformation that is distinct from 9. In contrast,
11 and 12 adopted highly compressed and puckered structures
that, while similar to each other, are distinct relative to 9 and 10.
The structural similarity of 9 and 10 parallels the similar effect of
13 and 14 on GABAA receptor activity. An explanation for these
findings is that while the two anti-isomers 11 and 12 can populate
two similarly low energy conformations, a single low energy
conformer is strongly preferred for each of the two syn-isomers 9
and 10.11c
(b) Fluorine−OH and Fluorine−O Interactions. It has
been known for some time that fluoroalcohols such as 2-
fluoroethanol (17, Figure 4) prefer, by 1−2 kcal/mol, a
conformation in which fluorine lies gauche to oxygen, a
phenomenon that has largely been attributed to a C−F···H−O
hydrogen bond.5e,f,g13 However, the role of a stabilizing C−F···
H−O interaction appears nuanced, and the significance of C−F
hydrogen-bonding remains a topic of some debate (vida
infra).14,15 Recent density functional theory (DFT) calculations
and natural bond order (NBO) analysis performed at a high level
of theory suggest that σ CH → σ* CF and σ CH → σ* CO
hyperconjugation is the dominant force underlying the
fluorohydrin gauche effect and that any contribution from a
favorable C−F···H−O interaction is electrostatic in nature.16
J. Med. Chem. XXXX, XXX, XXX−XXX
Journal of Medicinal Chemistry Perspective

Figure 4. Energy-minimized conformations of 17 and 18.

Accordingly, the preferred conformer remains the gauche form

even when the hydroxyl group is replaced by an OMe group. It
has also been calculated that for each of the four most populated
conformers of 3-fluoro-1,2-propanediol (18) all heteroatoms lie
gauche and a hydroxyl proton approaches fluorine.17 As indicated
by DFT calculations and multidimensional NMR, in this system
hyperconjugation from σCH and σCC into σ*CO and σ*CF appears
to be the dominant influence.17
Alternatively, under certain circumstances the C−F···H−O
interaction can be of sufficient strength to significantly reduce the
ability of an alcohol to act as a H-bond donor. It is notable that
this influence more than counteracts the enhanced acidity due to

the proximal electron-withdrawing fluorine atom.18 This is most

strikingly exemplified by cis-disposed 3-fluorocyclohexanol 20,
one of the series of fluorinated alcohols 19−22 designed to
systematically explore this phenomenon. In contrast to 19, fluoro
analog 20 weakly donates a H-bond to N-methylpyrrolidinone in
CCl4, measured as a negative pKAHY where pKAHY is a measure of
the H-bonding potential of a functional group and is distinct
from pKa.18 The reduced H-bond donating effect of the alcohol
in 20 is strongly dependent on the dihedral angle of the
fluorohydrin and is maximal at 180°. The effect of fluorine on the
H-bond donating properties of the O−H in vicinal fluorohydrin
22 is more modest compared to the hydrogen analog 21,
reflecting both the altered dihedral angle and the less than ideal
1,5 geometric relationship between the fluorine and hydrogen
atoms.
The importance of the fluorohydrin gauche effect in drug
design is highlighted in the design of fluoro analogs of the HIV-1
protease inhibitor indinavir (23) and its hydroxy epimer (24).
All four of the possible fluorinated diastereomers (25−28) were
prepared and tested for potency in a HIV-1 protease inhibition
assay.19 These data revealed profiles that are complex, an
anticipated outcome based on the multiple influences of F: an
effect on the acidity of the OH, conformational preferences,
steric interactions, and solvation. The syn,syn diastereomer 25
fully preserved the potent inhibitory activity of 23 while the
anti,anti diastereomer 26 was 10-fold weaker. For the epi-
indinavir series, the syn,anti analog 27 was 8-fold more potent
than its progenitor 24 while the anti,syn analog 28 was 36-fold
weaker than 24. A careful analysis of the 1H−1H and 1H−19F
coupling constants of this series revealed that the syn,syn and
syn,anti analogs 25 and 27, respectively, fully reproduced the
extended conformation observed crystallographically with 23
bound to HIV-1 protease, a conformation favored by a gauche
relationship between the fluorine and OH substituents.19
Diastereomers 26 and 28 were more conformationally mobile
and populated additional conformers, a potential reason for
their weaker protease inhibitory potency relative to the
progenitors.
D DOI: 10.1021/acs.jmedchem.5b00258
The conformational bias of alkyl aryl ethers is also influenced
by fluorine substitution. The low energy conformation of anisole
(29), favored by ∼3 kcal/mol, is that in which the OMe moiety is
close to coplanar with the phenyl ring (Figure 5).20 The planar
conformation is stabilized by an interaction between the aryl ring
π system and oxygen lone pair electrons which rehybridize to
facilitate orbital overlap, overcoming the inherent allylic 1,3
Figure 5. Geometry associated with the low energy conformation of 29.
strain.21 However, this conformational preference can be
perturbed by introducing ortho substituents that disfavor a
planar topology because of increased allylic 1,3 strain.20c,22
α-Fluorination provides access to this same orthogonal arrange-
ment but with a smaller substituent size while also reducing the
potential for CYP 450-mediated dealkylation.1a,23 The prefer-
ence for the CF3O moiety to align orthogonal to the plane of the
aromatic ring, calculated to be favored by ∼0.5 kcal/mol, is
attributed to weakened oxygen lone pair donation into the
aromatic π orbitals;1a,24 this conformational preference is also
observed with difluoroalkoxy moieties.23d,e
A role for the conformational mobility of fluorinated alkyl
phenyl ethers in the expression of biological activity was explored
in an analog of the cholesterol ester transfer protein (CETP)
inhibitor 30. The tetrafluoro-substituted ether 31 demonstrated
an 8-fold increase in inhibitory potency relative to 30, a gain
hypothesized to be due, in part, to the ability of this substituent to
adopt a more orthogonal projection of the CF2HCF2O moiety.25
J. Med. Chem. XXXX, XXX, XXX−XXX
Journal of Medicinal Chemistry
This hypothesis stimulated the design of a series of compounds
in which alternative substituents were examined. Improved
potency was observed with the furan analog 32, with modeling
studies suggesting a nonplanar confirmation analogous to that
hypothesized for 31. However, this may not provide a definitive
explanation, since differences between the available torsion
angles and electron distribution between the two substituents
were noted.25
(c) Conformational Bias Induced by Fluorine−
Ammonium Interactions. Fluorine interacts strongly with
ammonium species to favor a gauche stereochemical relationship.
Of potential importance in drug design, this interaction is
believed to be governed by a favorable electrostatic interaction
between the electronegative fluorine atom and the positively
charged ammonium moiety.4a,5b,g For 2-fluoroethylammonium
species, the gauche conformation is preferred by 5.8 kcal/mol; for
the neutral amine form this bias is only ∼1 kcal/mol.4a,5b,g In
3-fluoro-N-methylpiperidinium (33) these effects are manifested
as an overwhelming conformational bias that populates only the
two conformers in which fluorine is axial, with the equatorial
N−CH3 strongly preferred over the more sterically congested
axial N−CH3 (Figure 6).26
Figure 6. Structure and conformational preferences of 33.
Figure 7. Structures and conformational preferences of 35 and 36.
E DOI: 10.1021/acs.jmedchem.5b00258
Perspective
The synthesis of fluorinated analogs of the neurotransmitter
GABA (34) designed to take advantage of the fluorine-
ammonium gauche effect was explored as an approach to
providing tool molecules with which to probe stereochemical
preferences in biological recognition (Figure 7).11,12,27 (R)-3-
Fluoro-γ-aminobutyric acid (35, (R)-3F-GABA) and its
enantiomer 36 ((S)-3F-GABA) were prepared in optically
pure form in which the zwitterionic nature of the progenitor
is maintained at neutral pH, a consequence of reduced amine
basicity combined with a more acidic carboxylic acid moiety.27a
Analogous to 34, both 35 and 36 adopt an extended conformation
in solution and the more stable conformers are those in which the
fluorine and NH3+ are in a gauche relationship (Figure 7).27a This
analysis suggests that conformer A is disfavored for 35, while
conformer C is disfavored for 36. Although less potent than 34,
both 35 and 36 activated a cloned human GABAA receptor with
comparable potency, a result that suggested that conformer B, in
which the NH3+ and CH2CO2− moieties are in an antiperiplanar
relationship, is recognized by the GABAA receptor.27a,b Neither
compound was a substrate for GABA aminotransferase, but 35
was a 10-fold more potent inhibitor of this enzyme than 36.27b
Moreover, GABA aminotransferase catalyzed the elimination of
HF from 35 with over 10-fold greater efficiency than for 36.
These data, in conjunction with modeling studies, suggested that
conformer C is preferentially recognized by this enzyme.27b
Fluorine analogs of the glutamate mimic N-methyl-D-aspartate
(NMDA, 37) also provide an illustration of the influence of the
fluorine−ammonium gauche effect on biological activity. NMDA
is an agonist at the GluN2A and GluN2B receptors that are
activated by glutamic acid (38). The preferred conformational
relationship between the amine and acid moieties that is
recognized by these proteins was studied using the two 3-F
substituted diastereomers 39 and 40.27e The 1H and 19F NMR
spectra of 39 were consistent with this molecule adopting
conformer A in solution (Figure 8). In contrast, data for 40
indicated that conformer C was not appreciably populated, but
the experimental data failed to discriminate between conformers
A and B.27e DFT calculations indicated that conformer B, found
in the single crystal X-ray structure, is more stable than
conformer A. In Xenopus laevis oocytes expressing GluN2A and
GluN2B glutamate receptors, 39 evoked currents indicative of
J. Med. Chem. XXXX, XXX, XXX−XXX
Journal of Medicinal Chemistry
Figure 8. Structures and conformational analysis of 39 and 40.
agonist activity, although the effects of this molecule were less
than that observed with NMDA, while 40 was inactive. Since
only 39 was capable of activating these two glutamate receptors,
the preferred conformation was concluded to be that represented
by conformer A in Figure 8. This result is consistent with the
X-ray cocrystal structure of 37 bound to the highly homologous
GluN2D receptor.27e
(d) Conformational Effects between Fluorine and
Amides. The introduction of a fluorine atom proximal to an
amide moiety can influence molecular conformation in a
topologically dependent fashion. Capsaicin (41), a constituent
of peppers that is an agonist of the transient receptor potential
cation channel subfamily V member 1 (TRPV1) protein, is a
potentially useful vehicle to study this phenomenon in relation to
receptor recognition.28 The two enantiomers of α-fluoro
capsaicin (42) were prepared in optically pure form and
evaluated for agonist activity at the TRPV1 receptor. It was
predicted based on the calculated rotamer energies summarized
in Figure 10 that the trans conformation would be favored by
6 kcal/mol over the gauche conformation and by 8 kcal/mol over
the cis conformer.28,29 The trans conformer is stabilized by both a
favorable dipole−dipole interaction between the C−F and
CO bonds and a productive electrostatic interaction between
the electronegative fluorine atom and the electropositive amide
N−H. Through-space interactions involving fluorine, denoted
herein with a red arrow (Figure 9), are a topic of ongoing debate
and may generally be described as multipolar in nature (vida
infra). In practice, both enantiomers performed similarly as
agonists of the TRPV1 receptor, leading to the conclusion that
the receptor-bound form is that in which the side chains extend in
the same plane as the amide and the aryl ring (conformation A,
Figure 9) rather than projecting orthogonally (conformation B,
Figure 9).
The conformation of anilides can be influenced by
introduction of a fluorine atom ortho to the anilide N−H. This
phenomenon has been used to understand the preferred
topology of 43, a potent spiroindane-based antagonist of the
calcitonin gene-related peptide (CGRP) receptor that holds
potential as a therapeutic for the prevention of migraine
F DOI: 10.1021/acs.jmedchem.5b00258
Perspective
Figure 9. Potential bound conformers of the two enantiomers of 42.
Figure 10. Calculated relative energy levels of conformational isomers
of α-fluoroamides.
attacks.30 Although 43 exhibited reasonable oral bioavailability,
the pharmacokinetic profile of more potent derivatives was less
than optimal, with poor oral absorption attributed to a high polar
surface area (PSA). In an attempt to address this problem,
attention was focused on the design of isosteres of the central
amide moiety that would offer reduced PSA as a means of
facilitating oral absorption.30a A torsion plot indicated a
preference for the amide and spiroindane core moieties to be
coplanar with the lowest calculated energies observed at 0° and
180°, leading to two topologically distinct conformations. In
order to investigate the optimal binding topology, a fluorine
atom was introduced independently at each of the two positions
ortho to the N−H. In this way, complementary topologies that
are preferred by ∼3 kcal/mol are underpinned by a combination
of repulsive steric and electrostatic interactions between the
CO and fluorine atom and an attractive electrostatic
association between the N−H and fluorine. The isomers 44
and 45 demonstrated a 10-fold difference in CGRP receptor
affinity, where the extended conformation represented by 44 is
favored by the receptor, confirmed by the synthesis of fused ring
compounds constrained to unambiguous topology.31
The role of 4-(R)-hydroxyproline (4R-Hyp, 47) in enhancing
the thermal stability of collagen, the major structural protein in
connective tissue, has been clarified through studies based on the
J. Med. Chem. XXXX, XXX, XXX−XXX
Journal of Medicinal Chemistry
proline analogs 4-(R)-fluoroproline (48) and 4-(S)-fluoropro-
line (49).13f,g,32 The thermal stability of the characteristic triple
helix polypeptide structure of collagen, where each peptide chain
comprises repetitive sequences of X-Y-Gly (where X is often
proline (46) and Y is frequently either 46 or 47), was originally
attributed to a network of H-bond interactions between the
4R-Hyp hydroxyl moiety and bridging water molecules.13f,33
However, studies with 48 and 49 have led to the conclusion that
the effect of hydroxylation of 46 on the structure of collagen has
its origin in a stereoelectronic phenomenon associated with the
electron-withdrawing properties of the hydroxyl substituent and
the effect that this modification exerts on the conformational
preference of the pyrrolidine ring.14,32
The circular dichroism (CD) spectrum of (46-48-Gly)10 is
identical to the CD spectra of the collagen-based polypeptides
(46-46-Gly)10 and (46-47-Gly)10, consistent with this polypep-
tide also adopting a triple-helix structure where both substituted
proline moieties adopt a Cγ-exo pucker.32f However, molecular
modeling studies of (46-46-Gly)10 have suggested that the first
proline prefers to adopt a Cγ-endo pucker, leading to the
hypothesis that installing 49 at this position would promote triple
helix formation while 48 would not.32h,34 This postulate has been
confirmed experimentally with the preparation of (49-46-Gly)10,
which assembles into a triple helix structure, and (48-46-Gly)10,
which does not.32h,i 4,4-Difluoroproline (50) does not substitute
for 47 in collagen-related peptides, since it does not induce
conformational bias.14
DFT calculations indicate that N-acetylproline methyl ester
(51) inherently favors the Cγ-endo conformation by 0.41 kcal/mol,
resulting in a 2:1 ratio at room temperature, while the 4R-Hyp
derivative 52 prefers the Cγ-exo conformation by 0.48 kcal/mol
(Figure 11).32c,d For N-acetyl-4-(R)-fluoroproline methyl ester (53)
the Cγ-exo conformation is preferred by 0.48 kcal/mol, mimicking
4R-Hyp; for N-acetyl-4-(S)-fluoroproline methyl ester (54) the
Cγ-endo conformation is more stable by 0.61 kcal/mol.32c,d,j The
Cγ-endo conformation is also the preferred conformer of proline
and is observed in the single crystal X-ray structure of Boc-4-(S)-
fluoroproline.32j
The effects of fluorine on the conformation of proline can
include the establishment of a favorable gauche interaction be-
tween the fluorine and the N−CO moiety that also influences
G DOI: 10.1021/acs.jmedchem.5b00258
Perspective
Figure 11. Conformational preferences of N-acetylproline derivatives
51−54.
the conformation of the amide bond. The Cγ-exo pucker that is
favored by 53 allows the amide CO lone pair of electrons to
donate into the π* orbital of the ester carbonyl (n → π* interac-
tion). This stabilizes the trans (Z) isomer and pyramidalizes the
ester moiety, thereby inducing incipient chirality in a
functionality that is typically planar and achiral.34,35 In contrast,
the Cγ-endo conformation preferred by 54 weakens this
interaction considerably, leading to a higher population of the
cis (E) amide topology. This effect is observed in the single crystal
X-ray structures of N-acetyl-4R-Hyp and N-acetyl-4S-Hyp and
related compounds.35
The structure−activity relationships (SARs) associated with
inhibitors of the serine proteases dipeptidyl dipeptidase IV
(DPP-4) and fibroblast activation protein (FAP) provide striking
examples of the importance of fluorine absolute stereochemistry
on inhibitory potency in the context of proline derivatives.39 In
the DPP-4 inhibitor series 55−58, 4-(S)-isomer 56 is over
450-fold more potent than 4-(R)-isomer 57, while the difluoro
homologue 58 demonstrated potency comparable to both
56 and the unsubstituted parent 55 (Table 2).38a This
Table 2. SAR Associated with Isoleucine-Based Inhibitors of
DPP-4
compd R R′ DPP-4 IC50 (nM)
55 H H 1.5
56 H F 0.6
57 F H 290
58 F F 0.8
structure−activity pattern is reproduced in the series of FAP
inhibitors 59−62 where the 4-(S)-isomer 60 is over 300-fold
more potent than its 4-(R)-enantiomer 61 (Table 3).38b The
significant inhibitory activity in each series associated with the
difluoro analogs 58 and 62 indicates an absence of fluorine-
derived steric interference in the S1 pocket of the enzymes to
which the pyrrolidine moiety binds.38b It is hypothesized that the
4-(R)- and 4-(S)-fluorine atoms preferentially stabilize a single
conformational pucker of the pyrrolidine ring, presumably the
Cγ-endo by analogy with 53 and 54, since both proline and its
J. Med. Chem. XXXX, XXX, XXX−XXX
Journal of Medicinal Chemistry
Table 3. SAR Associated with FAP Inhibitors
compd R R′ FAP IC50 (nM)
59 H H 10.3
60 H F 3.3
61 F H 1000
62 F F 3.2
4,4-difluoro analog exhibit only a limited conformational
preference for an Cγ-exo- or Cγ-endo-pucker.13g
Studies of 3-fluoroprolinamide derivatives 63 and 64 also
revealed conformational bias as a consequence of the 3-fluorine
substitution and which are the reverse of those preferred by
4-fluorine substitution (Figure 12). In the solid state both
amide moieties adopt the (Z)-trans configuration; however, the
conformation of the pyrrolidine rings is distinct.36 In each case
the pyrrolidine ring is stabilized by a gauche interaction between
the F atom, which adopts an axial orientation, and the amide
moiety (Figure 12). For 63 the Cγ-exo:Cγ-endo pucker ratio was
predicted to be 2:1 and, consistent with this, 63 crystallized in the
Cγ-exo conformation. In this case the preference for the Cγ-exo
conformation is influenced by unfavorable steric and electronic
interactions between the F atom and the ester moiety. For 64
the Cγ-endo conformation prevailed in solution to the extent
of 97% based on the ≤1 Hz coupling constant measured
between the C-2 and C-3 protons in the 1H NMR spectrum.
These conformational preferences were expressed when 63 and
64 were incorporated into short polypeptides.32e,36,37
(e) Conformational Bias Induced by Fluorine in
Nucleoside Analogs. The small size of fluorine has encouraged
its introduction into the ribose ring of nucleoside analogs where
its effects on conformational preferences have been extensively
explored.23b,c,39 These effects are prominent but complex, dictated
by the interplay of several influences: anomeric effects, gauche
interactions, dipole−dipole interactions, the antiperiplanar
effect, and interactions between the F atom and the base.40 As
a consequence, the outcome on conformation is dependent on the
particular substitution pattern of an individual nucleoside analog.
Ribose analogs with 2′-fluoro substitution in an α-config-
uration favor a north conformation, while conformational bias
with a 2′-fluoro-β configuration is more varied and less stringent.40
Figure 12. Structure and solid state conformation of 3-fluoroproline derivatives 63 and 64 and the predicted equilibria.
H DOI: 10.1021/acs.jmedchem.5b00258
Perspective
With a 2′-fluoro α-configuration, the fluorinated nucleoside analog
65 (Figure 13) is unable to sample the south conformation
Figure 13. Preferred conformations of fluorinated nucleoside analogs
65−67.
that is thought to be predominantly recognized by HIV-1 re-
verse transcriptase.4b,40−42 Consistent with this, the adenosine
derivative 65 is inactive as an inhibitor of HIV-1 replication
in cell culture, although poor phosphorylation to the triphos-
phate cannot be ruled out as a contributory factor. In con-
trast, the β-configured 2′-fluoro isomer 66 exhibits a strong
preference for the south pucker, and this is reinforced by the 3′-
α-F substituent in 67. Both compounds inhibit HIV-1 replication
in cell culture, with measured EC50 values of 4.4 μM for 66 and
0.72 μM for 67.4b,41c,43 The 2′-α-fluororibose derivatives 68 and
69 also strongly favor a north conformation, with both gauche
and anomeric effects contributing to the conformational stability
of 68.44 On the basis of DFT calculations, the C-4′ aminomethyl
derivative 69 is predicted to adopt a north conformation that is
stabilized by both a gauche effect and an intramolecular C−H to
fluorine interaction, suggested to be a H-bond, from one of the
protons of the aminomethylene moiety (Figure 14). In contrast,
the 2′-OMe analog of 69 is predicted to prefer a south
conformation, while the 2′-OH variant prefers the north pucker
but is flexible enough to adopt the south conformation.44b The
introduction of a 2′-β-fluoro substituent to both 70 and 72
enhances the preference for a north pucker; the population of
this conformation for 70, 71, 72, and 73 is 58%, 100%, 28%, and
J. Med. Chem. XXXX, XXX, XXX−XXX
Journal of Medicinal Chemistry
Figure 14. 2′-α-F ribose derivatives 68 and 69 and the intramolecular
C−F···H interaction considered to contribute to the stability of the
north conformation of 69.
Figure 15. Compound 79 and its north and south conformers.
58%, respectively.41b,c It is postulated that for 73, an intra-
molecular interaction between the 2′-flourine atom and the C−H
of the purine C-8 atom may influence the ribose ring confor-
mation.45 The 2′,3′-difluorouridine derivative 74 exhibits a bias
toward the south conformation such that in solution this pucker
represents ∼80% of the equilibrium conformer population.41b,c
The effect of 3′-fluoro substitution on ribose ring
conformation has also been studied in the context of 75−78.
The 3′-α-fluorothymidine derivative 75 adopts the south
conformation in solution to the extent of 95% and 97% in
CD3OD and DMSO, respectively. This preference also applies to
the 2′-H, 2′-OH, 2′-NH2, and 2′-N3 homologues with alternative
base moieties, where this pucker is preferred to an extent of
≥94%.46 3′-β-Fluorouridine 76 prefers the north pucker almost
exclusively based on NMR analysis, although ab initio
calculations suggest that the south conformation should be
more stable. Difluorinated nucleoside analogs 77 and 78 prefer a
north conformation in both the single crystal X-ray structures
and in solution. Analog 77 is considered to be stabilized by a
weak F···H interaction between the C-3′-F and the C-6 H of the
base. The observation that 78 samples the south conformation
I DOI: 10.1021/acs.jmedchem.5b00258
Perspective
more readily than 77 has been attributed to an unfavorable
interaction between the C-6 aza and 3′-fluorine atoms.41c
The effects of fluorine substitution on ribose conformational
preferences in nucleoside analogs may be muted in more
complex settings, as illustrated by a study of clevudine (79,
L-FMAU), a 2′-β-fluoro nucleoside analog in the L-ribose series
(Figure 15). Clevudine (79) potently inhibits hepatitis B virus
(HBV) replication in cell culture (EC50 = 100 nM) by virtue of
being metabolized in cells to the 5′-triphosphate that is a potent
inhibitor of the HBV DNA polymerase.47 In the single crystal
X-ray structure, 79 adopts a south pucker due to favorable gauche
effects between the 2′-fluorine and ring oxygen atoms, as well as
between the 3′-OH and ring oxygen atom, a conformation that
places the fluorine and OH in an antiperiplanar relationship.
Although this conformation is thought to be the more stable,
docking of the triphosphate of 79 in a model of the HBV
polymerase active site suggested that the north pucker would be
preferred by the enzyme. This observation prompted a
computational study using Monte Carlo methodology which
revealed that the south and north conformations of the
triphosphate of 78 have similar energies and that in this case
altering the ribose ring pucker would incur only a minimal
energetic cost.48 While this change in conformation was
postulated to be able to occur when bound to the acitve site of
HBV polymerase because of an inherent flexibility, the modeling
studies suggested that the unique conformational aspects of the
triphosphate of 78 would prevent it from being incorporated into
the growing DNA chain because the 5′-triphosphate moiety
would not be presented in a geometry that would allow an
efficient reaction with the 3′-OH of the primer strand. Thus, the
triphosphate of 78 was predicted to bind to the active site in
conjunction with a conformational change that allows it to
effectively interfere with access of the natural substrate.
■ APPLICATIONS OF THE ELECTRON-WITHDRAWING
PROPERTIES OF FLUORINE
Because of its strong electronegativity, fluorine is a powerful tool
for modulating the pKa of proximal functionality and the electron
density of aromatic and heteroaromatic rings.1c,i,49 The pKa of an
ionizable center in a drug molecule changes the lipophilicity
profile (because of the pH dependence of the distribution
coefficient, D), which influences solubility, permeability, and
protein binding. Changes in pKa can manifest as changes in
potency, selectivity, toxicity, and pharmacokinetic (PK) proper-
ties including absorption, distribution, metabolism, and excretion
(ADME).50 Strategic deployment of fluorine can be guided by a
generalized set of rules used to predict the effect of fluorine on
the pKa of proximal functionality.
(a) Fluorine in Aliphatic Systems. In simple linear systems
the influence of successive fluorine substitution is additive, as
summarized by the data presented in Table 4. For example, each
fluorine substitution in ethylamine reduces the pKa by 1.6−1.7
units. CF3CH2NH2 is so weakly basic that this moiety has been
exploited as an amide isostere in both peptidometics and small
molecules.51 The influence of fluorine on amine basicity decreases
as carbon homologation increases the distance between the fluorine
atom and the amine, with estimates of the effect summarized in
Table 5.51b,c There is a −1.7 pKa unit change for each fluorine atom
introduced to the β-carbon while the effect is muted to differences
of −0.7, −0.3, and −0.1 pKa units at the γ-, δ-, and ε-carbon atoms,
respectively, which provides for a precise means of modulating the
basicity of an alkylamine.
J. Med. Chem. XXXX, XXX, XXX−XXX
Journal of Medicinal Chemistry Perspective

Table 4. Effect of Proximal Fluorine Substitution on the pKa of Acids, Alcohols, and Amines
acid pKa alcohol pKa amine pKa
CH3CO2H 4.8 CH3CH2OH 15.9 CH3CH2NH2 10.7
CH2FCO2H 2.6 (CH3)2CHOH 17.1 CH2FCH2NH2 9.0
CHF2CO2H 1.3 (CH3)3COH 19.0 CHF2CH2NH2 7.3
CF3CO2H 0.5 CF3CH2OH 12.4 CF3CH2NH2 5.7
CH3CH2CO2H 4.9 (CF3)2CHOH 9.3
CF3CH2CO2H 3.1 (CF3)3COH 5.4
C6H5CO2H 4.2 C6H5OH 10.0
C6F5CO2H 1.7 C6F5OH 5.5

Table 5. Effect of Carbon Chain Homologation on Basicity of

Fluorinated Amines

n position ΔpKa
1 β-F −1.7
2 γ-F −0.7
3 δ-F −0.3
4 ε-F −0.1

Analogous to aliphatic amines, the influence of fluorine on the

basicity of unstrained cyclic amines is generally additive in nature
but with the added consideration that the electron-withdrawing
effect of the σ-acceptor is exerted in both directions around
the connectivity of the ring. The predicted and experimental
effects for piperidine are summarized in Table 6.51a Thus,

Table 6. Calculated and Experimental Effects of Fluorine
Substitution on the pKa of Piperidine
3-fluoropiperidine is predicted to be a weaker base than
piperidine by 2.0 pKa units based on Δ of −1.7 exerted via the
proximal β-fluorine atom bonding network and an additional Δ
of −0.3 induced by the δ-disposed F atom; this predicted value is
close to the measured difference of −1.8 pKa units. In this case,
the difference between predicted and experimental values may
be attributed to the conformational preferences discussed earlier
in which the fluorine atom adopts an axial disposition in the
protonated form but prefers an equatorial projection when the
amine is unprotonated.26a In the axial orientation, the dipole of
the C−F bond is aligned in an antiparallel fashion with the N+−H
bond, stabilizing the protonated state and resulting in a higher
measured pKa than predicted; equatorially oriented fluorine
atoms in a piperidine ring lower amine pKa more significantly.
This phenomenon has been exploited in drug design.52
An example of the effects of F substitution on basicity is
provided by the kinesin spindle protein (KSP) inhibitor 80.52
This KSP inhibitor was explored as a potential treatment
for taxane-refractory solid tumors, but P-glycoprotein (P-gp)
efflux of the compound limited its efficacy.52b Structure−activity
studies revealed that recognition by the transporter was
J DOI: 10.1021/acs.jmedchem.5b00258
minimized if the pKa of the piperidine was between 6.5 and
8.0, prompting an examination of electron-withdrawing sub-
stituents designed to reduce the basicity of the N atom to within
the targeted range. The cyclopropyl- and the β-fluoroethyl-
substituted compounds 81 and 82, respectively, met the targeted
basicity criteria but 81 was associated with time-dependent
CYP 450 inhibition, a known liability of cyclopropylamines,
while 82 liberated the highly toxic fluoroacetic acid in vivo as
the result of metabolic N-dealkylation.53 The solution to
this problem was to install the fluorine atom in the piperidine
ring, and the more basic (pKa = 7.6) axial isomer MK-0731 (83)
was ultimately selected for clinical evaluation over the less
basic (pKa = 6.6) equatorial homologue 84.52b In a related series
of compounds, in which the amine moiety was appended to
the C-2 carbon of the dihydropyrrole ring, the problem of P-gp
efflux was also resolved by attenuating the basic nature of the
molecule (Table 7). In this case, two fluorine atoms β to the
amine provided the optimal combination of properties,
demonstrated by the SAR associated with 85−88.54 A pKa of
7 minimized P-gp efflux while maintaining potency, a
compromise exemplified by the two complementary topologies
represented by 86 and 88.
A similar strategy was adopted in a quest for selective
inhibitors of platelet-derived growth factor receptor (PDGFR), a
member of the receptor tyrosine kinase inhibitor class 3 family.55
The enzyme exists in two forms, PDGFRα and PDGFRβ,
encoded by different genes. Inhibitors of PDGFRβ were sought
in an effort to provide tools to illuminate the role of the enzyme
in tumor growth, angiogenesis, and fibrosis. Guided by a
homology model of the kinase, the piperidine 89 was identified
as a refined lead with an IC50 of 3 nM against PDGFRβ in
a cell-based assay, 10-fold selectivity over KDR and >100-fold
over cKit and cFMS. However, despite apparently good passive
J. Med. Chem. XXXX, XXX, XXX−XXX
Journal of Medicinal Chemistry
Table 7. Potency, Physical Properties, and Off-Target
Activities of the KSP Inhibitors 85−88
permeability and aqueous solubility (>1 mg/mL), the compound
showed poor exposure in the rat following oral dosing, which
was attributed to a combination of a moderate metabolic
clearance rate (clearance of 33 mL min−1 kg−1 following a 1 mpk
intravenous (iv) dose) and P-gp efflux, with a ratio of
5.7 determined in vitro. Attention was focused on attenuating
the basicity of the piperidine to reduce P-gp recognition,
and trans (equatorial fluorine) and cis (axial fluorine)
derivatives 90 and 91, respectively, were prepared in racemic
form. Interestingly, in this example there was little difference
between the measured pKa values of the equatorial and
axially disposed isomers. In contrast to predictions based
on precedent, the passive permeability of both 90 and 91
was reduced but both exhibited a reduced efflux ratio and
slightly lower iv clearance (24 and 28 mL min−1 kg−1,
respectively) in the rat. The trans isomer 90 offered a 2- to
3-fold improved area under the curve (AUC) following oral
dosing to rats, while the AUC for the cis isomer was similar to
the parent molecule.55
Poor brain penetration attributed to P-gp efflux was found
with the α7 nicotinic acetylcholine receptor agonist 92, a com-
pound of interest for treating the cognitive deficits and negative
symptoms of schizophrenia.56 Attenuation of the basicity of the
K DOI: 10.1021/acs.jmedchem.5b00258
Perspective
quinuclidine ring was accomplished with fluorinated analog 93;
this structural modification altered the efflux ratio in the desired
direction but at the expense of markedly reduced intrinsic
potency toward the receptor.
As part of an examination of the SARs associated with
piperazine 94 as a 5HT1D agonist with potential utility for the
relief of migraine attacks, piperidine 95 was prepared and found
to possess a similar in vitro profile (Figure 16A).52a However,
while 94 was rapidly absorbed in rats, 95 was associated with
poor oral bioavailability attributed to increased basicity, which
prompted synthesis of 4-F-piperidine 96. This compound
(Ymax = 58%) largely recapitulated the in vitro profile of 95,
which is a partial agonist at 5HT1D receptor (Ymax = 63%). The
pKa of 96 is similar to that of piperazine 94, and this compound
exhibited much improved absorption in the rat compared to 95.
Interestingly, on the basis of the similarity of calculated elec-
trostatic potential contours of 4-fluoro-1,4-dimethylpiperidine
and 1,4-dimethylpiperazine, an isosteric relationship between the
rings was suggested a priori in which the electron density of
fluorine mimics the lone pair of electrons on the piperazine N
atom (Figure 16B). However, other factors appear to underlie
the SARs associated with this series of 5HT1D agonists.
Attenuating the basicity of nitrogen atoms is also a useful tactic
for reducing inhibition of the cardiac K+ channel encoded by the
human ether-a-go-go-related gene (hERG). This has been
demonstrated in a series of 4-aminopiperidine-based bacterial
topoisomerase inhibitors, exemplified by 97, that demon-
strated activity toward Staphylococcus aureus (S. aureus) and
Mycobacterium tuberculosis (Mtb).57 In this exercise, attention
was focused on modulating the more basic secondary amine
(pKa = 8.27) by introducing fluorine at the 3 position of the
piperidine ring. Introduction of the fluorine at the 3 position
would also affect the tertiary amine which has a measured pKa
of 5.75. This was indeed the case, with the axial fluorine-
containing cis-3R,4S isomer 98 exhibiting much reduced
basicity at both amines and attenuated hERG inhibition.
The cis-3S,4R isomer 99 presented a similar profile. One
enantiomer of the trans isomer, in which the fluorine is
equatorially disposed, showed a further reduction in the pKa
values for both amines (pKa of 6.66 and 4.07) and a 3-fold
reduced affinity for hERG compared to the progenitor 97. The
3-fluoropiperidine moiety was subsequently incorporated into
the related compound 100 which focused on amplifying the
Mtb inhibition observed with 97.57c
Replacing the 4′-OH of neomycin (101) with fluorine was
explored as an approach to avoiding 4′-OH modification by
O-adenyltransferase (ANT(4′)) enzymes as well as for its
potential to protect the adjacent 3′-OH against modification by
O-phosphotransferase (APH(3′)) enzymes.58 These pathways
have developed in bacteria to negate the activity of the
aminoglycoside class of antibiotic. The synthetic approach was
designed to access the equatorial and axial isomers 102 and 103,
respectively, both of which demonstrated activity comparable to
J. Med. Chem. XXXX, XXX, XXX−XXX
Journal of Medicinal Chemistry Perspective

Figure 16. (A) Structure−activity relationships and physical property data associated with 5HT1D agonists 94−96. (B) Proposed structural mimicry
between N-benzylpiperazine and N-benzyl-4-fluoropiperidine.

101 in susceptible S. aureus, Klebsiella pneumonia (K. pneumonia),

and Escherichia coli (E. coli). This result indicates that substi-
tution was accommodated by the A-site of the bacterial 30S
ribosomal subunit. As anticipated from the structural change,
protection against two forms of ANT(4′) was observed, with
axial F isomer 103 retaining activity toward two strains of
Pseudomonas aeruginosa expressing APH(3′), while both 101 and
102 were inactive.58 This observation was attributed to the
lower nucleophilicity of the 4′-OH in 103 which reduced the
propensity for phosphate transfer, a strategy that was preserved
in the amide derivative 104. An X-ray cocrystal structure of 104
bound to the bacterial ribosome 30S subunit A site revealed a
binding mode analogous to that of the 4′-equatorial hydroxyl
compound. Similar to the contacts made by the 4′-H in the
4′-OH prototype, the axial fluorine atom of 104 was in close
contact with C-2, N-3, and C-4 of guanosine 1491.58 The dis-
tances between the fluorine atom and C-2, N-3, and C-4 are 2.7 Å,
2.6 Å, and 2.8 Å, respectively. These are less than the sum of the
van der Waals radii which for the individual atoms are 1.47 Å for F,
1.7 Å for C, and 1.55 Å for N.
It is believed that the kidney toxicity associated with
aminoglycosides is related to the number of basic amine groups
that mediate binding to the ribosomal A site; however, these
basic amines are an essential element of the antibacterial phar-
macophore.59 The modified aminoglycoside antibiotic 3′,4′,-
3‴,4‴-tetradeoxyneomycin (105) and its N1-(S)-hydroxyami-
nobutyric amide derivative 106 exhibit improved antibacterial
activity compared to the hydroxylated progenitor. This benefit
is due to an absence of hydroxyl substituents which, as part
of resistance pathways discussed above, are targeted by modi-
fying enzymes for acetylation.59 The introduction of electron-
withdrawing substituents proximal to the hydroxylated butyr-
amide provided an opportunity to modulate the pKa of the
terminal amine in an effort to achieve a balance between
antibacterial activity and avoidance of renal toxicity. Hydroxy-
lated analog 107, monofluoro analog 108, and difluoro analog
109 provided a successive reduction of the amine pKa of up to
3 log10. All three compounds demonstrated minimum inhibitory
concentration (MIC) levels against resistant strains which were
superior to 105 but comparable to 106.59 However, difluoro
derivative 109 was 2-fold less toxic toward the HK2 human
kidney cell line, suggestive of improved tolerance, while 107 and
108 were comparable to 106 in this assay.
(b) Fluorine in Aromatic/Heteroaromatic Systems. that can provide important insight into SAR, modulate the physical
Substitution of aromatic and heteroaromatic rings with electron- properties of other substituents, and potentially interfere with
withdrawing substituents is a common practice in drug discovery oxidative metabolic processes.60−62 Although fluorine is frequently
L DOI: 10.1021/acs.jmedchem.5b00258
J. Med. Chem. XXXX, XXX, XXX−XXX
Journal of Medicinal Chemistry
deployed as an aryl substituent, its high inductive electron-
withdrawing effect (σF = 0.45) is counterbalanced by a resonance
component (σR = −0.39), resulting in a net para-effect (σP) of 0.06
(Table 8, entry 1). As a result, fluorine as an aryl substituent
demonstrates an overall electron-withdrawing effect that is less
than chlorine (Table 8, entry 2).60 However, in systems such as
CF3 where π-resonance is not possible the inductive electron-
withdrawing effect of fluorine can exert a powerful influence on
substituents. This is exemplified by comparison of the matched pairs
CH3/CF3 (Table 8, entries 1 and 6), P(O)(CH2CH2CH3)2/
P(O)(CF2CF2CF3)2 (Table 8, entries 4 and 23), SO2CH3/
SO2CF3 (Table 8, entries 11 and 17), and SO2CH2CH3/
SO2CF2CF3 (Table 8, entries 13 and 18) where the σP values
differ by 0.71, 0.60, 0.24, and 0.35, respectively. These
modifications are accompanied by significant increases in
lipophilicity in the cases of CF3 (0.74) and SO2CF3 (2.18).
Interestingly, the poly-fluorinated sulfonated sulfilimine
(Table 8, entry 24) and sulfoximine (Table 8, entry 25) are the
most powerful electron-withdrawing substituents described to
M DOI: 10.1021/acs.jmedchem.5b00258
Perspective
date and are referred to as super acceptor groups.61 The utility
of the SF5 moiety (entry 10), stereochemically distinct from CF3,
is increasing as new synthetic methods address its installation
(vide infra).61b,c
The inductive effects of fluorine on the acidity of phenol
(pKa = 9.81) are significant. For example, 2,6-difluorophenol
(pKa = 7.12) performs as a lipophilic isostere of a carboxylic acid
in analogs of GABA (34), where additional functional mimicry
was anticipated because of similarity between C−F and the
CO moiety of the acid.63 Both 110 and 111 are competitive
inhibitors of GABA aminotransferase with measured Ki values of
11 and 6.3 mM, respectively.63 This concept was subsequently
extended to inhibitors of rat lens aldose reductase where a 2,6-
difluorophenol effectively substituted for an acetic acid moiety.
This is exemplified by comparison of the prototype 112 with 113,
and 114 with 115−119. Potency was increased in each matched
pair and could be further enhanced in the sulfonamide series
115−119.64
The acidity of phenolic functionality in drug candidates can be
optimized for target binding through incorporation of fluorine.
The introduction of a fluorine atom ortho to the para-disposed
phenol of 17β-hydroxysteroid dehydrogenase 1 (17β-HSD1)
inhibitor 120, which emerged from a systematic study of bis-
phenols, afforded inhibitor 121 (Table 9).65 This compound
demonstrated enhanced potency and selectivity for the enzyme
versus 17β-HSD2, an enzyme that catalyzes the reverse reaction,
the oxidation of estradiol. This phenol moiety is considered to
mimic the phenol of estrogen which forms H-bonding
interactions with Glu282 and His221 in the active site of the
enzyme. An alternative binding mode for 121 was also postulated
based on a docking experiment, one in which 121 binds to a site
between the steroid and cofactor binding sites and interacts with
the nicotinamide moiety.65c In this series, the introduction of a
second fluorine atom at the other ortho position gave 122 which
J. Med. Chem. XXXX, XXX, XXX−XXX
Journal of Medicinal Chemistry

■
Perspective

Table 8. Hammett Substituent Constants Describing the IMPACT OF FLUORINATION ON DRUG POTENCY,
Electron-Withdrawing Properties of Fluorinated Substituents PERMEABILITY, METABOLISM, AND
in Aromatic/Heteroaromatic Rings1e,60,61 PHARMACOKINETIC PROPERTIES
The strategic incorporation of fluorine to improve drug potency
has become increasingly prevalent in recent decades.1a,b,f,66
Fluorine substitution can enhance potency and impact target
selectivity by affecting pKa, modulating conformation, hydrophobic
interactions and lipophilicity, or a combination of these
properties.1i Fluorine has also been used as a tool to address
issues associated with drug metabolism.62 Fluorine substitution
as a direct replacement for a labile hydrogen atom/s (e.g.,
Ar−H → Ar−F, CH3 → CF3) can reduce metabolism including
when installed on an aromatic group that is prone to oxidation
(e.g., electron-rich phenyl rings). Fluorine is frequently included
in bioisosteres of carbonyl-containing moieties. Additionally,
fluorine can modulate lipophilicity and restrict conformation,
which may afford improved metabolic stability. Although the
strategic introduction of fluorine has been used to overcome
issues associated with metabolic stability, there are occasions
where it may be detrimental. These include changes in primary
pharmacology due to increased lipophilicity and adjustments of
pharmacokinetic properties. In order to overcome these
limitations, pharmacological activity and metabolic stability are
typically optimized in parallel.
(a) Influence of Fluorine on Potency. Human kinesin Eg5
is an attractive target for the treatment of cancer due to its role in
establishing bipolar spindles. Inhibition of this enzyme causes
mitotic arrest, which triggers cell apoptosis in certain tumors.
The dihydropyrimidine-2(1H)-thione derivative monastrol
(123) was identified as an allosteric inhibitor of the ATPase
activity of Eg5, with activity residing in the (S)-enantiomer and
drug−target interactions confirmed by solving an X-ray structure
of the cocrystal.67 Efforts toward expanding the SAR associated
with 123 led to the identification of a closely related series of
5-aroyl dihydydropyrimidine derivatives demonstrating superior
potency for which enzyme inhibitory activity surprisingly resided
in the (R)-enantiomer. The prototype of this series was (R)-
mon97 (124), and optimization afforded fluorastrol (125) as a
compound with 5-fold improved growth inhibition toward five
tumor and nontumor cell lines.68 X-ray cocrystal structures
obtained from racemic 124 and 125 with human Eg5 contained
only the (R)-isomers bound to the enzyme.69 Some differences in
the dispositions between 123 and 124 in the binding pocket of
the enzyme were noted. For 124, the key interactions are
established by the N-3-H of the dihydropyrimidine ring which
forms a H-bond with the main chain carbonyl moiety of Gly117,
Table 9. SARs Associated with Potency and Selectivity for
the thioxo moiety which interacts with Glu118, and the phenol
17β-HSD1 Inhibitors 120−122
O−H which engages the protein via H-bonding to the main chain
carbonyl of Glu118, the main chain amino moiety of Ala133 and
side chain nitrogen atom of Arg119.68,69 Difluoro homologue
125 binds in the same orientation, but the 2-thioxo moiety
projects into the solvent-exposed region of the protein and inter-
acts with two H2O molecules (Figure 17).68a The pyrimidine
17β-HSD1 IC50 17β-HSD2 IC50 selectivity N-3-H engages the carbonyl oxygen atom of Gly117, and the
compd R R′ (nM) (nM) factor phenol interacts with Glu118, Arg119, Ala133 in a similar fashion
120 H H 69 1950 28 to 124. The enhanced potency of 125 appears to be a function of
121 F H 8 940 118 three multipolar interactions involving the aryl-4-fluoro atom:
122 F F 56 312 6 one to the guanidinium side chain of Arg221, one with the
backbone carbonyl moiety of Gly217, and one with the amide of
exhibited reduced potency and selectivity, suggesting that the Ala218.68a Furthermore, it was hypothesized that sandwich π−π
acidity of the phenol may have an optimal range for binding to stacking of the fluorinated phenyl ring with the salt bridge formed
the enzyme. between Glu116 and Arg221 (not shown in Figure 17) is
N DOI: 10.1021/acs.jmedchem.5b00258
J. Med. Chem. XXXX, XXX, XXX−XXX
Journal of Medicinal Chemistry Perspective

enhanced because of the electron-withdrawing effect of the two

fluorine atoms and the interactions of the 4′-fluorine with the
protein.

Figure 18. Interactions of the 4-fluorobenzyl moiety of 128 with

thrombin.

A survey of X-ray crystal structures in the Cambridge Structural

A systematic fluorine scan was used to establish SARs
associated with 126, an inhibitor of thrombin probed as a
racemate. Specifically, aryl substituents of the N-benzylimide
moiety were surveyed, with the data on select compounds
presented in Table 10.70 The results highlighted the positive
effect of a 4-fluoro substituent, with 128 exhibiting 5-fold
enhanced potency over progenitor 126 and the 3-fluoro isomer
127. An X-ray cocrystal of 128 with the enzyme showed a close
contact between the fluorine atom and both the CO carbon of
Asn98 (3.5 Å, F approaches CO at an angle of 96°) and the
α-C-H of this residue (2.1 Å at an angle of 157°) (Figure 18).
Database (CSD) and the Protein Data Bank (PDB) found that
a close interaction of fluorine with an amide carbonyl is not
uncommon; the C−F to CO angle typically lies between 100°
and 140°, where a smaller angle is associated with a closer contact
distance. The energy of this interaction has been estimated to
range from 0.2 to 0.38 kcal mol−1.70c In the context of a related
but intrinsically more potent series evaluated in racemic form, the
introduction of a 4-fluoro substituent provided 131 as the most
potent thrombin inhibitor (Ki = 5 nM). However, although 131
is 13-fold more potent than its unsubstituted hydrogen analog
130, the 4-chloro (132) and 4-methoxy (133) homologues also
demonstrate enhanced potency. X-ray cocrystals of 132 and 133
indicate that these substituents are not sufficiently close to the
Asn98 CO to establish productive interactions, suggesting that
the enhancement in potency observed with 131 is not the result
of a productive fluorine to CO interaction.70d

The capacity of covalently bound fluorine to act as a H-bond

acceptor is controversial and an issue of continuing debate.14,15
Although this type of interaction is considered to be weak in
nature, numerous instances of C−F···H−X close contacts have
Figure 17. Key drug−target interactions between 125 and Eg5. been observed crystallographically, and searches of the PDB
and CSD have played a prominent role in efforts to describe
Table 10. SARs Associated with Substituted N-Benzylimide- the character of C−F···H−X contacts.1b,14,15,71 However, a
Based Thrombin Inhibitors predictive model for F···H contact distance has remained elusive.
Model systems have also been used to gain insight into the
underlying mechanics of the C−F···H−X interaction, with some
cases supportive of a role for fluorine as a weak hydrogen-bond
acceptor (HBA).15,72 Nuances in the interpretation of NMR
1H
JF,H(X) coupling, infrared (IR) vibrational shifts, and computa-
tional modeling complicate study of this weak interaction.71d,73
It is generally agreed that the HBA capacity of fluorine is
significantly weaker than that of oxygen, and it is often difficult to
separate the role of C−F···H−X bonding from other more
compd R R′ R″ Ki (μM) dominant forces. Fluorine to hydrogen interactions are described
126 H H H 0.27 in the literature as either hydrogen bonding or multipolar in
127 F H H 0.360 nature. In deference to the ambiguity around fluorine and
128 H F H 0.057 H-bonding, we have chosen to depict fluorine to hydrogen
129 F H F 0.590 contacts as multipolar interactions, marked as a red arrow.
O DOI: 10.1021/acs.jmedchem.5b00258
J. Med. Chem. XXXX, XXX, XXX−XXX
Journal of Medicinal Chemistry Perspective

Figure 19. Factor VIIa inhibitor 134, noting interactions observed in the X-ray cocrystal structure, and its progenitor 135.

An aryl C−F moiety has been explored as a lipophilic isostere the pKa of the aniline N−H by an estimated 3 units, thereby
of a pyridone carbonyl moiety in the context of factor VIIa and strengthening the interaction with Gly216. The gem-difluoro
thrombin inhibitors (Figure 19).74 The fluorophenyl derivative substituents may be regarded as mimics of the shape and dipole
134 was designed as a factor VIIa inhibitor based on the potent of the sulfone oxygen atoms.75b Similar SARs were observed
activity associated with the pyridone 135. A cocrystal structure in the analogous series of aminopyrazinone-based thrombin
revealed the anticipated close contact between the fluorine atom inhibitors summarized in Table 11.75d
of 134 and the N−H of Gly216.74,75 The distance between the
fluorine atom of 134 and the nitrogen atom of Gly216 in the
X-ray cocrystal structure was measured to be 3.4 Å, an identical
distance to that between the aniline nitrogen atom of 134 and the
carbonyl oxygen of Gly216.74a
A similar tactic was successful in the design of thrombin
inhibitors based on the prototype 136 (RWJ-445167), a potent
compound (Ki = 4 nM) that advanced into clinical evaluation but
suffered from unacceptably low exposure following oral dosing.75
This compound engages Gly216 of thrombin via the sulfonamide
N−H (H-bond donor (HBD)) and the pyridone CO (HBA).
The fluorophenyl derivatives 137 and 138 were designed as more
lipophilic inhibitors in an effort to address the poor bioavailability
observed with 136. Both compounds are potent inhibitors of
thrombin, with Ki values measured as 8.6 nM for 137 and 1.2 nM
for 138. X-ray cocrystal data for these compounds indicated a
close contact between the aryl fluorine atom and the backbone Table 11. SARs Associated with the Series of Thrombin
nitrogen atom of Gly216, in both cases measured as 3.17 Å; based Inhibitors 141−145
on a N−H bond length of 1.03 Å, a F···H distance of 2.14 Å was
calculated.75b,c

compd X R thrombin Ki (nM)

141 CH H 0.8
142 CH F 0.1
143 CH CH3 1.1
144 N H 0.27
145 N F 0.042

The principle of engaging the N−H of Gly216 of factor Xa by a

The gem-difluoroethyl moiety markedly influences potency in
the chloro-substituted series of thrombin inhibitors represented
by 137. Replacing the gem-difluoroethyl moiety with either a
gem-dimethyl or a cyclopropyl ring, compounds 139 and 140,
respectively, resulted in a 7-fold decrease in thrombin inhibition.
Replacing the pyridine of 137 with a phenyl reduced potency by a
similar amount.75 In this context, the gem-difluoroethyl moiety
not only blocks metabolism at the benzylic position but functions
as a lipophilic isostere of the sulfonamide moiety of 136.
The inductive electron withdrawal by the fluorine atoms reduces
P DOI: 10.1021/acs.jmedchem.5b00258
fluorine atom in an inhibitor was extended to the design of
fluoro-substituted indazole derivatives, represented by 147 as an
optimized compound (Ki = 15.9 nM).76 In this molecule, the
fused fluorophenyl ring substitutes for the pyrazole carboxamide
moiety found in razaxaban (146).76 The importance of the
fluorine substituent was established via the matched-pairs
analysis compiled in Table 12. A 60-fold improvement in
potency was measured for 149 and 151 compared to 148 and
150, respectively, which represents an energy difference of
∼2.4 kcal mol−1. An X-ray cocrystal of factor Xa-bound 147
confirmed a close interaction between the C-7 fluorine atom and
the backbone N−H of Gly216. The measured F···N distance
J. Med. Chem. XXXX, XXX, XXX−XXX
Journal of Medicinal Chemistry
of 2.90 Å is within H-bonding range and is comparable to the
3.04 Å contact observed between the Gly216 N−H and the
carboxamide oxygen of 146.76
Table 12. SARs Associated with the Series of Indazole-Based
Factor Xa Inhibitors 148−151
compd X n factor Xa Ki (nM)
148 H 1 >14400
149 F 1 223
150 H 2 6850
151 F 2 124
A high-throughput screening campaign identified indole-2-
carboxylic acid derivative 152 as a moderately potent inhibitor of
hepatitis C virus (HCV) NS5B polymerase (IC50 = 0.9 μM) that
was, however, inactive in a cell-based replicon assay.77 A cocrystal
of 152 with the polymerase revealed that drug−target association
was dominated by hydrophobic interactions and that the
carboxylic acid did not establish specific contacts with the
enzyme. Interestingly, the fluorine atom appeared to engage the
N−H of Tyr448 with a 2.6 Å distance between the fluorine atom
of 152 and the nitrogen atom (Figure 20). The carbon atom
adjacent to fluorine approached the carbonyl oxygen of Ile447
with a distance of just 2.9 Å, less than the sum of the van der
Waals radii and suggestive of a productive interaction. The
importance of the F···H−N interaction was underscored by an
extensive SAR survey that established the importance of the
fluorine atom and its regiochemistry. This is emphasized by
comparing the matched pairs 153 and 154 which reflect a 40-fold
Figure 20. Key interactions between 152 and HCV NS5B polymerase.
Q DOI: 10.1021/acs.jmedchem.5b00258
Perspective
difference in potency. Although this initial survey failed to
identify compounds that were significantly more potent, the
observation of the F···H−N interaction inspired the design of a
series of compounds in which C−F was replaced by a carbonyl
moiety, a powerful H-bond acceptor. Pyridone 155 inhibited
HCV NS5B with an IC50 of 17 nM and prevented replication of
an HCV genotype 1b replicon with EC50 = 300 nM. X-ray
cocrystal data for an analogue confirmed an H-bond between the
pyridone CO and the backbone N−H of Tyr448.77
The MAP kinase 1 (MEK1) inhibitor 156 is noncompetitive
with ATP, and in the X-ray cocrystal structure of the ternary
complex the molecule occupied a pocket adjacent to the
adenosine triphosphate (ATP) binding site. In this structure
the glycol moiety lies close to the MgATP phosphates.78 The
conformation of the molecule was oriented via an intramolecular
H-bond between the aniline N−H and the adjacent amide
carbonyl. This arrangement projected the iodophenyl moiety
orthogonal to the plane of the core and established a halogen
bond between the iodine atom and the carbonyl of Val127. The
4-fluoro atom of the benzamide established close contacts with
the N−H moieties of Ser212 and Val211, interactions described
as H-bonds (Figure 21).78 Optimization of 156 led to
CH4987655 (RO4987655, 157), a selective MEK1 inhibitor
(IC50 = 5.2 nM), in which the steric bulk added at the 5 position
of the benzamide is designed to block hydrolysis of the amide
moiety and improve orally bioavailability. Compound 157
demonstrated slow dissociation kinetics from the enzyme and
potent antitumor activity in vivo, alone or in combination, and
was selected for clinical evaluation.78d The X-ray cocrystal of the
ternary complex of 157 with MEK1 and adenylylimidodiphos-
phate revealed binding interactions similar to 156; the
benzamide 4-fluoro atom is proximal to the backbone NHs of
Val211 and Ser212. An alternative path of optimization explored
replacement of the C−F bond with an amide carbonyl. This
ultimately afforded 158, which inhibits MEK1 with IC50 = 38 nM.
X-ray cocrystal data with a prototype molecule suggested inhi-
bitor interaction with the NHs of Val211 and Ser212.78a,b
Aromatic fluorides are common structural elements in inhibitors
of DPP-4, the serine protease that degrades glucaogon-like peptide
J. Med. Chem. XXXX, XXX, XXX−XXX
Journal of Medicinal Chemistry Perspective

Figure 21. Key drug−target interactions between 156 and MEK1 and the structures of analogs 157 and 158.

Figure 22. Key interactions between 159 and DPP-4.

1 (GLP-1), and cocrystal structures have revealed close

interactions between the fluorine atoms and H-bond donors of
the enyzme.79,80 The 2,4,5-trifluorophenyl moiety of sitagliptin
(159) is an important structural element that conferred an
improved safety profile compared to the 2,5-difluoro homo-
logue.80b The 2,4,5-trifluorophenyl ring occupies the S1 subsite of
the enzyme, and the 2-fluoro atom is close to the side chain
N-Hs of Arg125 and Asn710, with the distance between this
fluorine atom and the nitrogen atom of Asn710 measured as
3.2 Å (Figure 22).80a,k The primary amine of 159 forms salt bridges
with Glu205 and Glu206 in the S2 pocket, the amide oxygen atom inhibitory constants were similar.80h An X-ray cocrystal structure
engages Tyr547 via the intermediacy of a water molecule, and the of an analogue of 165 confirmed the proximity of the aryl fluorine
pyrazolopyridine heterocycle occupies an extended S2 site, atom to the side chains of Asn710 and Arg125.80h
stacking against Phe347 with both of the vicinal triazole nitrogen
atoms interacting with H2O molecules. The SARs around the
fluorophenyl moiety are consistent with a role in drug−target
interactions based on the imperfect comparison of 160 and 161
where the absence of the 2-fluorine results in an approximate 5-fold
erosion of potency.80a
The 2,5-difluorophenyl moiety is preserved in more refined
molecules including omarigliptin (163), a long acting compound
with PK properties suitable for once-weekly dosing in humans, Interestingly, 167 is representative of a related series of DPP-4
and its predecessor 162.80k,l An X-ray cocrystal structure of inhibitors based on α-amino acid derivatives that bound to the
fluoroomarigliptin (164) revealed similar interactions between enzyme with a reversed binding mode compared to the β-amino
the 2-fluoro atom and the enzyme.80l derivatives described above with the pyrrolidine ring occupying
That the 2-fluorophenyl moiety can function as a surrogate for the S1 pocket.80b,h The fluoroolefin 168 was examined as a
a more conventional H-bond acceptor is illustrated by the potential isostere of the amide moiety of 167 as part of a probe of
comparable inhibitory potency exhibited by 165 and the amide the selectivity and PK properties of this molecule.80e The matched
166, one of a series of three matched pairs where the DPP-4 pair of analogues 167 and 168 exhibit similar DPP-4 inhibitory
R DOI: 10.1021/acs.jmedchem.5b00258
J. Med. Chem. XXXX, XXX, XXX−XXX
Journal of Medicinal Chemistry
activity, establishing an effective isosteric relationship between
the fluoroolefin and the amide, with a cocrystal of the more
potent homologue 169 revealing that both series bound to the
enzyme in similar modes. In the X-ray cocrystal structure, the
fluorine atom of 169 interacted with the side chain N-Hs of both
Asn710 and Arg125, interactions described as H-bonding in
nature.80e
The introduction of an R-methyl substituent at C-8 of the
triazolopyrazine moiety of 159 afforded 170 which demonstrated
4-fold improved DPP-4 inhibitory potency with activity sensitive
to the absolute configuration at this center, since the S-isomer
was 20-fold weaker.80c Expansion of this substituent to benzyl
(171) and 4-fluorobenzyl (172) moieties resulted in further
gains in potency that exhibited heightened sensitivity to the
chirality at C-8. The high potency of 172 was attributed to an
interaction between the 4-fluorophenyl and Ser630 mediated by
a water molecule and described as H-bonding in nature based on
an X-ray cocrystal structure of 172 with DPP-4.80c
A gem-difluoromethyl moiety was conceived as a functional
replacement for the ketone carbonyl in V-10,367 (173), a
compound that mimics the FKBP12-binding portion of FK506
and exhibits neurotrophic activity in vitro.81 The difluoroamide
174 inhibits FKBP12-mediated rotamase activity with a Ki of
19 nM, comparable in potency to 173. An X-ray cocrystal of 173
with FKBP12 indicated that the ketone oxygen atom engaged the
Tyr26 hydroxyl group through an electrostatic interaction at a
distance of 3.4 Å. With 174, this ketone functionality is absent
but one of the F atoms approximates the carbonyl-Tyr26
hydroxyl interaction with the distance between the F and phenol
oxygen atom determined to be 3.18 Å. This was described as at
least an electrostatic and possibly a H-bonding interaction, while
the other fluorine atom was within van der Waals contact of two
hydrogen atoms of Phe36, with distances measured as 3.0 and
3.3 Å, respectively.81
Fluoroacetic acid (175) is a naturally occurring toxin produced
predominantly in the plant kingdom but that is also synthesized
by the soil microbe Streptomyces cattleya (S. cattleya).82 Con-
version of fluoroacetate to (−)-erythro-2-fluorocitrate (2R,3R)
(176) in mammals leads to potent inhibition of the enzyme
S DOI: 10.1021/acs.jmedchem.5b00258
Perspective
aconitase, a component of the tricarboxylic acid cycle.62a,83 A
dose of 2−10 mg/kg in humans is lethal, with a lowest observed
effect level of 0.1 mg/kg.62a As a defensive posture to prevent the
entry of fluoroacetate into its own citric acid (Krebs) cycle,
S. cattleya expresses a fluoroacetyl-CoA-specific thioesterase (FIK)
that hydrolyzes fluoroacetyl-CoA with a one-million-fold
selectivity over acetyl-CoA. The differences in rate for the two
substrates (Kcat/KM = 5 × x107 vs 30 M−1 s−1) represent a
remarkable discrimination between substrates that differ by a
single fluorine for hydrogen substitution in such a small
molecule. Initial explanations for the selectivity were derived
from X-ray cocrystal data which suggested several influencing
factors: enzyme recognition via close interactions of the fluorine
atom with the N-Hs of Gly69 and Arg120; enhanced
electrophilicity of fluoroacetate compared to acetate; restricted
access of H2O to the active site; and reduced interaction between
the CO moiety and the enzyme (Figure 23). However, more
recent studies of the process have observed a kinetic isotope
effect only for the (R)-H atom of fluoroacetic acid. This suggests
that the basis for selectivity resides in the catalytic activity of the
enzyme, where abstraction of the (R)-H to afford a ketene
intermediate occurs 104-fold more rapidly in fluoroacetate than
acetate.84
(b) Influence of Fluorine on Permeability. Permeability
(Pe), the ability of a molecule to pass through a cell or cellular
membrane, is a major consideration during the process of lead
optimization of orally bioavailable compounds.85 Drug and
metabolite permeability plays a significant role in ADME, in
addition to affecting other considerations such as toxicity, clinical
dosing, and formulations. Permeability is typically measured as
the rate (10−6 cm/s) at which a molecule is passively diffused or
actively transported (uptake/efflux) across membranes. Passive
permeability is most affected by two parameters: molecular size
(increase correlates with decreased Pe) and lipophilicity (increase
correlates with increased Pe). However, active transport is organ
specific and considerably more difficult to predict. Fluorine is
often used to influence permeability by way of modulation of
lipophilicity, association with pendent H-bond donors, or
reduction of amine basicity. Most orally administered drugs
have log P values, a common measure of lipophilicity of
between 1 and 5.86 The log P of a neutral molecule is typically
increased upon the addition of an aryl or vinyl fluorine but,
conversely, often decreases with alkyl fluorination.87 Mono-
fluorination of a terminal alkyl methyl group typically leads
to a larger reduction in lipophilicity than trifluorination, while
difluorination is predicted to have a similar effect on log P as
monofluorination.87b These effects are primarily due to participa-
tion of arylfluorines in resonance electron donation and the large
dipole associated with carbon−fluorine bonds in fluoroalkanes.87b
J. Med. Chem. XXXX, XXX, XXX−XXX
Journal of Medicinal Chemistry
Figure 23. Interactions of 175 in the fluoroacetyl-CoA-specific thioesterase active site.
For amine-containing molecules, the log D may increase upon the
introduction of proximal fluorine atoms if basicity is reduced.
Permeability across a confluent Caco-2 cell layer for the
two closely related series of factor Xa inhibitors 177−180 and
181−183 was found to be improved via fluorine substitution
of the hydrogen atom ortho to the anilide N−H, although
the differences between 179 and 180 are small (Table 13).88
Table 13. Effect on Caco-2 Permeability of Substituents Ortho
to an Anilide in Two Series of Factor Xa Inhibitors
The increase in permeability observed for fluoro-substituted
compounds 178, 180, and 182, compared to their matched
partners 177, 179, and 181, may be due to an electrostatic
interaction between the fluorine atom and pendent N−H that
effectively masks its H-bond donor properties, thereby
enhancing membrane permeability.15a,89 Lending support to
this hypothesis, the permeability of the ortho-nitrile 183 is
significantly reduced compared to both 181 and 182. This is
presumably a reflection of the increased H-bond donor capacity
of the N−H that cannot be satisfied in an intramolecular fashion
because of the geometrical constraints associated with the linear
nitrile substituent. However, an effect of the increased PSA
associated with this substituent may be a contributory factor.
Anilides and benzamides are common motifs in drug design
and are particularly prevalent in kinase inhibitors. Fluorine sub-
stitution has been studied as a tool to improve the permeability of
these chemotypes. In a matched-pairs analysis of this phenome-
non, 12 of 27 pairs of anilide derivatives (Figure 24A) exhibited
effective parallel artificial membrane permeability assay (PAMPA)
permeability that improved by ≥0.3 log10 cm s−1 when the ortho-
hydrogen atom was replaced by a fluorine atom. The same
substitution in benzamides (Figure 24B) improved permeability in
9 of 15 cases.15a This effect was not considered to be a function of
lipophilicity since the meta-fluoro isomers did not demonstrate
enhanced permeability. In 6 of the 42 cases examined, permeability
T DOI: 10.1021/acs.jmedchem.5b00258
Perspective
was not affected, while a reduction was observed in 3 of 42 cases. For
the remaining 12 examples, permeability was increased by only 0.1
or 0.2 log10 cm s−1, not considered significant by the authors for the
purpose of discussion. Since this study was conducted on a relatively
small number of examples, it was suggested that although it cannot
be concluded definitively that an ortho-fluorine atom will enhance
permeability, it would nevertheless be a useful strategy to explore.
A useful strategy to address a range of developability problems,
including membrane permeability and CNS penetration, is to
introduce intramolecular H-bonds or electrostatic interactions.
This approach was explored in the context of improving the
delivery of β-site amyloid precursor protein cleaving enzyme 1
(BACE-1) inhibitors (Table 14).90,91 Prototype BACE-1
Table 14. Enzyme Inhibition, Porcine Renal Epithelial
(LLC-PK1) Cell Permeability, and Efflux Ratios for the Series
of BACE-1 Inhibitors 184−187
inhibitor 184 was subject to efficient efflux by cell lines
expressing either rat or human P-gp which contributed to the
low brain levels attained by this compound following oral admin-
istration to rats.91 Hydrogen-bonding plays a role in compound
recognition by P-gp, and to address this problem focus was
placed on perturbing the electronics of the acetamide N−H.91,92
Analogues 185−187 all demonstrated improved efflux ratios,
where the two fluorinated derivatives 186 and 187 performed as
effectively as MeO-substituted 184.91
Passive membrane permeability and P-gp efflux ratios were
improved by an analogous tactical approach applied to a series of
CNS-penetrant bradykinin B1 antagonists that were explored as
potential agents for the relief of pain (Table 15).93 The introduc-
tion of fluorine atoms into the acetamide moiety of 188 resulted
in compounds 189−191 which demonstrated improved profiles.
J. Med. Chem. XXXX, XXX, XXX−XXX
Journal of Medicinal Chemistry Perspective

Table 15. Bradykinin B1 Binding, Passive Permeability, P-gp Efflux Ratios in LLC-PK1 Cells, and H-Bond Strength for the Series
of Aminocyclopropanecarboxamide-Based Antagonists 188−191

passive permeability Papp P-gp efflux ratio in LLC-PK1

compd R hBK1 Ki (nM) (10−6 cm/s) cells expressing human MDR1 HBA (log) strength of CO
188 CH3 0.93 21 8.6 2.12
189 CHF2 0.40 311 3.2 1.63
190 CF3 0.57 28 2.3 1.39
191 CF3CF2 1.6 31 1.4 1.35

This was attributed to a reduction in the strength of the terminal
amide carbonyl to function as an H-bond acceptor, although an
intramolecular interaction between the fluorine atoms and the
N−H may also contribute.
The N-terminal amide N−H of the tachykinin hNK2 receptor
antagonist 192 was deemed critical for potency but was believed
to contribute to the observed poor membrane permeability
assessed in Caco-2 cells (Table 16).94 The introduction of a
Table 16. Human NK2 Receptor Binding Affinity and
Permeability in Caco-2 and PAMPA Assays for the Series of
Antagonists 192−196 Derived from Phenylalanine
halogen atom at the ortho-position, designed to interact with the
N−H, resulted in improved permeability in both a PAMPA and
Caco-2 cell layer assay. Although chloro-substituted analog 193
offered an advantage over the prototype, fluoro derivative 194
was found to be superior. By way of comparison, the ortho-
fluorine substituent in 194 improved permeability similarly to
pyridine 196, which exhibits 2- to 3-fold higher transit in both
assays compared to its matched pair, the phenyl derivative 195.94
The principle of introducing a fluorine proximal to an N−H to
improve permeability was also effective in a series of amino-
isoindole-based BACE-1 inhibitors exemplified by prototype 197
(Table 17).95 The physical properties associated with the
embedded amidine moiety of this chemotype impeded effective
CNS penetration, resulting in poor reduction of β-amyloid
peptides in mouse brain. The introduction of a fluorine atom at
C-4 afforded 198, which exhibited modestly improved potency
toward BACE-1 but demonstrated markedly changed physical
properties. While the pKa of 198 is 8.4, this is reduced to 7.1 for
the prototype 197, which is associated with an increase in the
log D (determined by liquid chromatography). These changes
were associated with increased Caco-2 cell permeability and a
reduced efflux ratio, effects attributed to the formation of a weak
interaction between the amidine NH2 and fluorine moieties
characterized as a H-bond. Calculations indicated a less negative
solvation energy for 198 compared to isomers where the fluorine
is located meta or para to the amidine moiety. This results in an
overall effect that was interpreted as shielding of the polar amine
moiety from solvent. Interestingly, the resolved S-isomer of 198
displayed improved permeability over the racemate (Papp =
22 × 10−6 cm/s) and an efflux ratio of 1.9. This compound
demonstrated robust lowering of β-amyloid peptides in the brain
of C57BL/6 mice following oral administration.
(c) Influence of Fluorine on Metabolism and PK
Properties. In part because of the strength of the C−F bond,
fluorine is often used to overcome issues associated with poor
metabolic stability, where it may be deployed as the direct

Table 17. Enzyme Inhibition, Physical Property Attributes, and Caco-2 Cell Permeability Properties of BACE-1 Inhibitors 197
and 198

Papp apical to basolateral through efflux ratio Papp(B−A)/Papp(A−B)

compd R BACE-1 IC50 (nM) pKa log D Caco-2 cells (10−6 cm/s) in Caco-2 cells
197 H 500 8.4 0.7 3.4 12
198 F 158 7.1 0.9 12 3.1

U DOI: 10.1021/acs.jmedchem.5b00258
J. Med. Chem. XXXX, XXX, XXX−XXX
Journal of Medicinal Chemistry Perspective

replacement for a metabolically labile H atom in both aromatic Table 19. Effects on Potency and Metabolic Stability of
(Ar−H → Ar−F) and aliphatic settings (CH3 → CHF2, CF3).62a,96 Replacing CH3 by CF3 in the tert-Butyl Substituents of NK1
In addition, electron-rich phenyl and heterocyclic rings or olefins (202, 203) and TRPV1 (204, 205) Receptor Antagonists
that are prone to oxidation may exhibit enhanced metabolic sta-
bility after the installation of fluorine atoms or fluorine-containing
substituents. Fluorine has been used as an isostere of the carbonyl
moiety that eliminates susceptibility to reductive processes and may
improve metabolic stability due to the effect of fluorine on
modulating lipophilicity and restricting conformation.
The judicious deployment of a fluorinated substituent in
the triazolopyrazine moiety of the DPP-4 inhibitor 159 was
instrumental in the identification of compounds with oral
bioavailability (Table 18).80a,b,m The ethyl-substituted analog

Table 18. SARs and PK Associated with Analogues of 159

IC50 for Cl in the rat oral

inhibition of (mLmin−1 kg−1)a bioavailability in
compd R′ DPP-4 (nM) the rat (%)a
199 Et 37 70 2
200 CF2H 29 66 39
201 CF2CF3 71 58 61
159 CF3 18 60 76 The same structural modification was examined in the context
a
Dose is 1 mpk iv; 2 mpk po. of the endothelin antagonist bosentan (210) and the CCR9
antagonist vercirnon (212).99b In each case, the metabolic stabi-
lity of the Cp-CF3 derivatives 211 and 213 in RLM was increased,
199 showed poor bioavailability in the rat, a deficiency that was
with clearance declining from 37 to <10 μM min−1 mg−1 for 210
improved by fluorination of this substituent (200, 201, 159),
to 211 and from 34 to 20 μM min−1 mg−1 for 212 to 213.
with the CF3 of 159 providing the most improvement.80a,b
However, the effect of this modification on metabolic stability in
The CF3 moiety has emerged as a prominent structural ele-
mouse and human liver microsomes was more modest.99b
ment in several approaches aimed at improving the metabolic
stability of alkyl groups. Replacing a single CH3 of a tert-butyl
substituent with a CF3 group in neurokinin 1 (NK1, substance P)
receptor antagonist 202, a compound explored for its potential to
treat depression or induce analgesia, afforded 203. The same
change in TRPV1 receptor antagonist 204 afforded 205. In both
cases this change led to improved metabolic stability in human
liver microsomes without a significant effect on potency (Table 19).97
A similar tactic was effective in identifying inhibitors of V-RAF
murine sarcoma viral oncogene homologue B1 (BRAF) V600E
kinase with improved pharmacokinetic properties. In this context
the fluoro-substituted analog 207 (CEP-32496) was superior to
206 and was advanced into clinical trials.98 The trifluoromethyl-
cyclopropyl (Cp-CF3) moiety may also serve as an advantageous
replacement for tert-butyl, as demonstrated in a series of matched
pairs in which these groups were compared as substituents of an
aromatic ring.99 In studies of compound stability in human
(HLM) and rat liver microsomal (RLM) preparations, the
Cp-CF3 substituent provided superior metabolic stability relative
to tert-butyl and conferred enhanced RLM and HLM stability in
each of six biphenylamide matched pairs. The utility of the
Cp-CF3 moiety as an amine substituent was probed in the
context of finasteride (208), a compound that is subject to
oxidative degradation at both the tert-butyl moiety and the The cathepsin K inhibitor odanacatib (214), a molecule in
core and exhibited a t1/2 of 63 min in HLM. The Cp-CF3 phase 3 clinical trials for the treatment of osteoporosis, provides
derivative (209) exhibited an improved t1/2 of 114 min, an overall an example of fluorination playing multiple roles in improving
modest improvement but that is significant because other metabolic stability.51d,100 The introduction of a fluorine atom
sites of the molecule remain prone to metabolic modification.99a to the leucine moiety blocked hydroxylative metabolism at this
V DOI: 10.1021/acs.jmedchem.5b00258
J. Med. Chem. XXXX, XXX, XXX−XXX
Journal of Medicinal Chemistry Perspective

site. In addition, the design of this molecule takes advantage

of the trifluoroethlyamine moiety as an amide isostere that resists
proteolysis. The difluoroethylamine moiety performs similarly
but with the advantage of sufficiently increased basicity
(by almost 1 log unit) to allow the formation of stable salts
with strong acids that included hydrochloric acid, sulfuric acid,
and methanesulfonic acid. As a result, 215 exhibits improved
pharmaceutics properties compared to poorly soluble 214,
which translated into improved oral bioavailability from a
suspension formulation.101

The CETP inhibitor 216, identified after optimization of a

screening lead, exhibited good potency in a binding assay (IC50 = Table 20. Potency and PK Profiles of the 11β-HSD Inhibitors
20 nM) and in a human whole plasma assay (EC50 = 1.6 μM) but 220−223 in the Rata
suffered from poor metabolic stability with just 9%, 8%, and 10%
remaining after incubation in human, mouse, and rat liver
microsomes, respectively.101 The gem-difluoro homologue 217
exhibited improved intrinsic activity in both assays and was
considerably more stable in all three liver microsomal prepara-
tions. However, this structural modification provided inadequate
protection against oxidative metabolism in the related ether
derivative 218. This deficiency was overcome by excising a portion IC50 human Cl
of the cyclopentane ring to afford 219, a compound with the compd R R′ 11β-HSD (nM) (mL min−1 kg−1) t1/2 (h) F (%)
optimal combination of CETP inhibition and metabolic stability.101 220 H H NR 81 0.3 27
The systematic introduction of fluorine atoms to the 221 F H 5 11 1.5 100
cyclobutane ring of the 11β-HSD1 inhibitor 220 was examined 222 H F 22 NR NR NR
in an effort to interfere with a facile hydroxylation process 223 F F 35 NR NR NR
occurring at this site that promotes rapid in vivo clearance from a
NR = not reported.
mouse plasma (data summarized in Table 20).102 Relative to
220, the anti (relative to the triazole) monofluoro derivative 221
exhibited lower clearance, an enhanced half-life, and increased for further structural modification with the series of fluoro-
oral bioavailability. Of the fluorinated derivatives, 221 provided substituted derivates 225−227 emerging as compounds of
the best enzyme inhibition, 4-fold better than 222 and 7-fold interest. All three compounds demonstrated improved oral PK
improved over the gem-difluoro analogue 223, but the PK profiles in the rat. However, further modification by perdeutera-
profiles of 222 and 223 were not disclosed. tion of the methylene adjacent to the isothiazole was required to
The Aurora kinase inhibitor 224 is a promising potential provide a compound that combined targeted antitumor
cancer therapeutic that competes with ATP and exhibits potent properties with oral bioavailability.
inhibition of both the Aurora A (IC50 ≤ 4 nM) and B (IC50 ≤ Fluorinated pyrrolidines are a common heterocyclic element
13 nM) enzymes that inhibit histone H3 phosphorylation in DPP-4 inhibitors, but some caution is advisible based on the
(phos-HH3) in a cell-based assay, a marker of Aurora B inhibition observation that incubation of tritiated 228 in RLM revealed
(Table 21).103 However, this compound exhibited poor oral metabolic activation to reactive species that were detected as
bioavailability in the rat due to a combination of poor absorption protein-covalent adducts (Figure 25).104 A detailed analysis of
and rapid metabolism with the AUC reported as zero μM·h. the metabolism of 228 identified GSH adducts of the unsaturated
Metabolite identification studies using radiolabeled material aldehydes which arise from α-hydroxylation and elimination
revealed that N-dealkylation of the amine moiety, which was of HF. This observation was supported by the trapping of
known to project into solvent when bound to the enzyme, was two aldehyde analogs as their semicarbazide derivatives.104 This
the primary clearance pathway. This finding provided a focus metabolic pathway may not always be operative, dependent upon
W DOI: 10.1021/acs.jmedchem.5b00258
J. Med. Chem. XXXX, XXX, XXX−XXX
Journal of Medicinal Chemistry
Figure 24. Parent structures used in matched-pairs analysis of ortho-
fluoro-substituted anilides (A) and benzamides (B).
Table 21. Structures of the Aurora Kinase Inhibitors 224−227
and the Associated in Vitro and in Vivo Profiling Data
context, since detailed studies of the 3,3-difluoropyrrolidine
derivatives 229 and 230 (PF-00734200) do not appear to
undergo metabolic activation in this fashion.105 However, the
HIV-1 nucleotide-competing reverse transcriptase inhibitor
231 exhibits a short half-life in rat and human liver microsomes,
with the 3,3-difluoropyrrolidine identified as the metabolically
labile site, although the degradation pathway was not explicitly
determined.106
The metabolic lability of aryl alkyl ethers can also be improved
by fluorination, exemplified by the robust stability of some 2,2,2-
trifluoroethoxy ethers in RLM, although the antiarrhythmic
agent flecainide (232) is subject to oxidative dealkylation at the
least sterically hindered ether.107,108 An interesting but perhaps
underutilized application of fluorine to resolve problematic
metabolism is in the context of the benzodioxole moiety. This is a
prevalent structural element in natural products that presents
challenges in drug discovery due to the potential for mechanism-
dependent inhibition of CYP 450 enzymes and subsequent
generation of catechols.109 CYP 450 enzymes oxidize the
methylene to a carbene that binds tightly to the Fe atom and
forms a slowly dissociating metabolic-intermediate (MI)
complex that exhibits a characteristic absorption maximum at
455 nm.110 This phenomenon is a potential source of drug−drug
interactions and is exemplified by paroxetine (233), a compound
Figure 25. Metabolic activation pathway for the 3-fluoropyrrolidine element of 228.
X DOI: 10.1021/acs.jmedchem.5b00258
Perspective
for which deuteration (i.e., CTP-347, 234) modulated this
process.109,111 Moreover, this metabolic pathway ultimately
produces a catechol, which can be oxidized to a chemically
reactive ortho-quinone.110 Fluorination of the benzodioxole
methylene has been explored as a mitigation strategy, but details
of the result of this modification on metabolic activation and
metabolism are not well documented.112 Nevertheless, this
moiety is beginning to attract attention as a drug motif and is
most prominently represented by lumacaftor (235) which is
being investigated clinically for the treatment of cystic fibrosis.113
The difluorobenzodioxole element in the camptothecin analogue
BMS-286309 (236) was designed with a specific focus on
improving the metabolic stability associated with the benzodiox-
ole moiety. This compound demonstrated improved pharmaco-
kinetic properties in the rat compared to irinotecan (237) and
was >100-fold more potent in mouse distal-site tumor models.112
Fluorination of a benzodioxole methylene was also used to
probe the role of metabolites of MDMA (238), a commonly
abused drug known as ecstasy, in the expression of
psychotomimetic effects and toxicity.114 The difluoro analogues
of 238 and MDA (240), 239 and 241, respectively, were
designed to avoid oxidation of the benzodioxole methylene.
However, while DFMDA (239) exhibited serotonin transporter
(SERT) affinity between that of 238 and 240, neither 239
(dosed up to 120 mg) nor 241 (dosed up to 250 mg) showed a
significant physiological effect in humans at doses that both 238
and 240 showed activity.114
The lactone moiety of the quinoline-based alkaloid
camptothecin (242), considered to be critical for antitumor activity,
is subject to hydrolytic ring opening under physiological conditions
which limits its therapeutic utility.115 Replacing the lactone CO
J. Med. Chem. XXXX, XXX, XXX−XXX
Journal of Medicinal Chemistry Perspective

natural product. The β-fluoro-substituted derivative 244 demon-

strated greatly improved hydrolytic stability following incubation in
H2O at 37 °C and pH 7.4 (96% of 244 remained after 6 h compared
to just 43% of 242).115

■ SF5 FUNCTIONAL GROUP

The SF5 moiety offers interesting properties and an unusual
shape that are of potential advantage in drug design, but
applications have been limited, largely a function of poor
synthetic accessibility.116 Lack of awareness may also play a role
despite the fact that SF5 data were included in the Craig plot of σ
constants versus π values for aromatic ring substituents.117
Recent advances in the introduction of SF5 into building blocks
and molecules are beginning to change both perceptions and
awareness of this moiety, and SF5 is being exploited more
frequently in drug optimization campaigns. DSM-265 (246), an
inhibitor of Plasmodium falciparum (Pf) dihydroorotate dehy-
drogenase (DHODH), is the first SF5-containing molecule to
enter clinical trials, where it is undergoing evaluation for its
potential as an antimalarial agent.118

The lipophilicity and electron-withdrawing properties of the

SF5 moiety are both characterized as higher than those of CF3 but
but with lipophilicity less than tert-butyl.99a For example, in the
context of 210 which has a measured log D of 0.99, the log D
values of the SF5 and CF3 analogues are 0.37 and 0.14,
respectively, a trend recapitulated with 212.99a However, the
shape of SF5 is markedly different, offering octahedral geometry
and a larger size (>2-fold) when compared to tetrahedral CF3,
although it is still two-fold smaller than a tert-butyl substituent
(Table 23).99b The electron density patterns of the two moieties
also differ, with SF5 presenting a pyramidal shape while CF3
displays an inverted cone.
with an isosteric C−F moiety was explored as a potential solution to
this problem with both the α-fluoro (243) and β-fluoro (244) Table 23. Comparison of the Physical Chemistry Attributes of
derivatives prepared. The potency of 244 toward a series of tumor CF3 and SF5
cell lines in vitro was superior to 243 but inferior to 242 (Table 22).
This was remedied by the cyclohexyl-substituted homologue 245 attribute CF3 SF5
that demonstrated in vitro antitumor properties comparable to the σP 0.54 0.68
σR 0.12 0.11
Table 22. In Vitro Antitumor Activity of 242−245 in Three σI 1.09 0.55
Cell Lines π 1.09 1.51
electronegativity 3.36 3.65
pKa of anilinium ion 2.94 2.37
van der Waals volume (cm3 mol−1) 20.5 49.2 (calcd)

These properties can translate into differences in biological

activity as illustrated by the matched pairs of cannabinoid recep-
tor B1 ligands 247 and 248 where the SF5 derivative is 2-fold
more potent than the CF3 analogue, a consistent observation in
this series.61c,119 Direct comparisons of SF5 with CF3 have also
compd A549 IC50 (μM) MDA-MB-435 IC50 (μM) HCT-116 IC50 (μM) been made in the serotonin reuptake inhibitors and receptor
242 0.65 0.45 0.07 modulators fluoxetine (249), fenfluramine (251), and norfen-
243 46.2 >100 50.91 fluramine (253).120 In the matched pair 249 and 250, the latter
244 9.95 58.33 6.35 demonstrated reduced binding to 5HT2a and 5HT2c receptors
245 0.71 0.41 0.07 compared to 249 with no effect on the affinity for the 5HT2b
Y DOI: 10.1021/acs.jmedchem.5b00258
J. Med. Chem. XXXX, XXX, XXX−XXX
Journal of Medicinal Chemistry Perspective

subtype. However, substitution of CF3 by SF5 in the fenflur- cytotoxicity compared to 262 and other analogues, while retaining
amine series produced more pronounced effects with 252 ex- good membrane permeability.122
hibiting an almost 10-fold increased affinity for 5HT2b and
5HT6 receptors compared to 251 while affinity for the 5HT2c
receptor was also increased but more modestly.120 Interestingly,
this observation did not extend to the norfenfluramine matched
pair, since the receptor binding profile of 254 was similar to 253.

A matched pairs analysis compared the effect on biological

potency and developability parameters of analogues of the
endothelin antagonist 210 and the CCR9 antagonist 212 in
which the tert-butyl substituent of each was replaced with several
moieties including the SF5 and CF3, compounds 264−267.99b In
the series based on 210, the CF3 (264) and SF5 (265) analogues
performed similarly as endothelin A antagonists but were 10-fold
less potent than 210. In the CCR-9 antagonists, biological assay
at a concentration of 50 nM revealed comparabale activity for
210, 266, and 267. In both series, the SF5 and CF3 substituents
conferred improved metabolic stability compared to the tert-
butyl prototype.

In a series of thymidine phosphorylase inhibitors, the SF5

analog 256 exhibited a modest 3-fold potency advantage over the
CF3 homologue 255. However, in a series of dopamine D3
antagonists based on a triazole chemotype, compounds
257−260 which are racemic, no significant differences were
seen in hERG inhibition nor the overall profiles at the D2 and D3
receptors (Table 24).121 The calculated PSA for the four

Table 24. Functional Dopamine D2 and D3 pKi, hERG IC50,

PSA, and ACD log D Data for 257−260 Although not yet explored in the context of drug design, alkyl
SF5 derivatives have been shown by experimental and theoretical
methods to exert an effect on conformational preferences
that has been attributed to a combination of steric and
stereoelectronic effects.123 In alcohols substituted at the
β-position with fluorinated moieties, an SF5 showed a higher
dopamine D2 dopamine D3 hERG PSA ACD barrier to rotation than fluorinated methyl substituents. An SF5
compd R functional pKi functional pKi pIC50 (Å2) log D substituent also influences the conformation of alkyl chains in a
257 3-CF3 7.5 9.3 5.5 60 1.8 fashion that reflects a volume that is smaller than that of a tert-
butyl moiety.

■
258 3-SF5 6.9 8.9 6.0 60 2.5
259 4-CF3 6.9 9.3 6.0 60 21
260 4-SF5 6.8 9.1 6.3 60 2.5 FLUORINE IN POSITRON EMISSION TOMOGRAPHY
The three pillars of survival for a drug in phase 2 clinical trials
compounds was identical, but the calculated log D of the SF5 have been defined as (1) the demonstration of exposure of a drug
derivatives was higher than the CF3 analogues, reflecting their candidate at the target site of action over a desired period
individual π coefficients. of time, (2) the determination of the binding of a drug to its
In an analysis of the effects of aryl substituent variation in pharmacological target based on its mode of action, and (3) the
the series of trypanothione reductase inhibitors 261−263, expression of a pharmacological effect that is commensurate with
explored as potential antiprotozoal agents, the SF5 derivative the demonstrated target exposure and target binding.124 Positron
263 performed similarly to the CF3 analogue, and both offered emission tomography (PET) imaging has been viewed as a
a modest advantage over tert-butyl analog 261.122 This SAR was useful, noninvasive translational technique that has the potential
rationalized by the modeling of 263 in the active site of the enzyme to assess target engagement, particularly in the CNS, providing
and attributed to a combination of size and electronic effects insight into the first two pillars described above, in cases where a
on the aryl ring. However, 263 demonstrated 2-fold reduced suitable and effective labeled ligand can be developed.3e,f,125
Z DOI: 10.1021/acs.jmedchem.5b00258
J. Med. Chem. XXXX, XXX, XXX−XXX
Journal of Medicinal Chemistry
There is considerable value in determining that a specific
molecular target is being adequately interrogated by a drug
candidate in vivo in situations where measuring a pharmacody-
namic effect is not straightforward. Determining target engage-
ment allows a level of rational decision making with respect to
identifying doses to explore in efficacy studies or assessing the
potential of a molecule and its intrinsic mechanism to affect a
particular disease state. For example, the demonstration of target
engagement in the absence of the anticipated pharmacological
effect may invalidate the underlying hypothesis allowing early
termination of a drug candidate. Molecular imaging tools may
increase the speed at which a drug reaches clinical trials, provide
information about the safety profile, and enrich the potential
treatment population, all issues of considerable interest in the
drug discovery and development process.126
Molecular imaging is a term used for the combination of
imaging technologies that provide both anatomic and functional
information around a biological target. By combining techniques
like X-ray or magnetic resonance imaging (MRI), which provide
anatomical information, with functional imaging techniques such
as PET, we now have the ability to monitor biological processes
in living systems at the molecular level. PET has been described
as a new kind of “precision pharmacology”.126 PET ligands
confer the ability to quantitatively monitor in vivo molecular
events in real time, which can address several questions that are
critical to the drug discovery process in humans.126 This includes
target engagement, dose−receptor occupancy relationships,
metabolism, biodistribution, and the use of PET radioligands
as biomarkers for patient enrichment strategies, thereby enabling
personalized medicine treatment and offering more effective
clinical trials.126
PET imaging involves the synthetic incorporation of short-
lived radionuclides into biologically active molecules, and once
inside the body, decay of the radioisotope emits a positron that
travels a short distance until it combines with an electron in an
event described as annihilation. This generates two photons each
with an energy of 511 keV that travel collinearly in opposite
directions. Detection of the γ radiation generated during the
annihilation allows for well-defined images at the molecular level
as a function of time. The radioactive isotope of fluorine, [18F]-
fluorine, is particularly suited to the development of PET ligands
due in part to its 109.7 min half-life. This half-life permits time
for multistep syntheses with incorporation of 18F into complex
molecules while offering the convenience of same-day imaging.
[18F]-Fluorine has low positron energy, traveling only short
distances before annihilation occurs, which affords better
spatial resolution for imaging than other PET radionuclides
while offering lower overall radiation exposure to a patient.127
Several factors are of importance to the design of effective PET
ligands in general, and some are associated more specifically with
the use of [18F]-fluorine.3g,128 Fundamentally, the ligand under
consideration must have functionality that facilitates incorpo-
ration of a labeled atom. Syntheses are typically designed
specifically for late-stage introduction in deference to the short
half-lives of PET radionuclides. Introduction of fluorine often
presents a significant synthetic challenge, although the demand
for [18F]-fluorinated ligands has, in part, stimulated the develop-
ment of new methodology and the design of prosthetic moieties
for label incorporation as a frequently utilized option.129 With
respect to ligand pharmacology, high potency and selectivity
(typically >100-fold) toward the target of interest are paramount,
with affinity constants in the low to subnanomolar range
preferred. Adequate metabolic stability is also of importance,
AA
Perspective
particularly with respect to the labeling element. Given that the
PET detector does not distinguish the source of the signal, in vivo
generation of labeled metabolites has the potential to confuse the
interpretation of results. For CNS applications, the PET tracer
must offer good blood−brain barrier penetration with low
nonspecific binding if the signal-to-noise ratio is to be practically
useful. For the latter, physical properties play a significant role
with less lipophilic compounds associated with lower nonspecific
binding. For good CNS penetration a log P between 1.5 and
2.5 or a log D of 1−3 appears to be optimal. However, predicting
the performance of PET tracers remains a challenge despite the
development of methods to assess the nonspecific affinity of
candidate molecules.3g,128
[18F]-Fluorine is produced most commonly in a cyclotron, and
although it has become the most widely used PET imaging
radionuclide, generating [18F]-labeled radioligands in high
specific activity can present significant synthetic chemistry
challenges. One factor is the microscale nature of the synthesis,
where [18F]-fluoride is the limiting reagent, typically present in
only pico- to nanomolar concentrations while the labeling
precursor is used in large excess. This can lead to low
radiochemical yields due to competing side reactions, which
are not always seen with the corresponding nonradioactive (19F)
model reaction. The term radiochemical yield (RCY) commonly
refers to the isolated amount of purified labeled compound
divided by the amount of radioactivity originally present at the
start of the synthesis. Preparative expediency is of the essence
given the challenge associated with the half-life of [18F].
Successful synthesis of a useful PET radioligand requires
generation of the [18F] source, most typically fluoride, followed
by its incorporation into the molecule under investigation,
purification, and formulation for iv injection into a living animal.
The entire preparative processes must be completed in less
than 3 h. With these unique challenges, methodologies that
incorporate [18F]-fluorine into a molecule rapidly, efficiently,
and as late in the synthetic pathway as possible have gene-
rated a significant amount of published research over the past
decade.129 This section will summarize some the recent advances in
radiochemical synthetic approaches to incorporate [18F]-fluorine
into important drugs, druglike molecules, and PET radio-
ligands used to answer key questions in drug discovery and
development.
[18F]-Fluorine is generated in a cyclotron yielding either
[ F]-fluoride or [18F]-fluorine gas ([18F]-F2). [18F]-Fluoride is
18
produced by proton bombardment of liquid isotopically enriched
[18O]-H2O via the 18O(p,n)18F nuclear reaction.127 The [18F]-
fluoride produced in this fashion must be further processed to
provide a species capable of incorporating 18F into molecules.
Since fluoride is poorly nucleophilic because of its high solvation
in water, it is separated from the [18O]-H2O and any metal
impurities generated from the cyclotron target by use of a
quaternary ammonium chloride polymer (QMA) or Chromafix
PS-HCO3 (filled with quaternary ammonium bicarbonate
polymers) anion exchange resin cartridge. The [18F]-fluoride is
eluted from the resin cartridge with an alkali carbonate in
CH3CN/H2O and mixed with a phase transfer catalyst like
Kryptofix 2.2.2 (K.2.2.2) or a crown ether. Alternatively,
[18F]-fluoride can be eluted from the resin cartridge with
tetrabutylammonium hydroxide to generate [18F]-tetrabutylam-
monium fluoride ([18F]-TBAF). The final step is an azeotropic
drying process to remove any residual water from the elution
mixture. A recently developed method reduces byproducts and
preparation time, thereby increasing the overall radiochemical
DOI: 10.1021/acs.jmedchem.5b00258
J. Med. Chem. XXXX, XXX, XXX−XXX
Journal of Medicinal Chemistry
Scheme 1. Synthesis of 269
yields by using ionic liquids (tetrabutylammonium methanesul-
fonate or 1-butyl-3-methylimidazolium triflate) dissolved in
MeOH to release [18F]-fluoride from a Chromafix PS-HCO3
polymer cartridge.130 In this process, azeotropic drying requires
only 1 min, resulting in a 10% increase of available radioactivity
for subsequent [18F]-fluorine labeling. A second approach relies
upon trapping aqueous [18F]-fluoride on a strong anion-
exchange cartridge and then eluting the radionuclide with an
anhydrous solution of [K.2.2.2]OH− in CH3CN which can be
used directly for nucleophilic fluorination reactions without
azeotropic drying, facilitating the automated production of
[18F]-labeled products.131
[18F]-F2(g) is obtained from the nuclear reaction of 18O-
(p,n)18F through the addition of F2 (0.2%) to an enriched
[18O]O2 gas target.127 The specific activity (SA) for the “in-
target” protocol is in the range of 27 mCi/mmol (1 GBq/mmol),
which is significantly lower than the specific activities reached
using [18F]-fluoride which can be as high as 150 Ci/μmol
(5500 GBq/μmol).132 SA is defined as the amount of isolated
activity of a purified [18F] PET tracer divided by the mass (or
molar amount) of the total sum of all radioactive and
nonradioactive species present within that isolated PET tracer.133
When PET imaging studies are performed, the amount of
radioactivity to be administered is fixed within a range to ensure
high quality images are obtained. Thus, the SA determines the
molar amount of PET radioligand that has been delivered during
these imaging studies. In some applications, the [18F] radio-
pharmaceutical may be a toxic molecule or is being used to visualize
a low density receptors in the brain.134 In these cases, obtaining a
[18F] product in high SA is key to obtaining a high quality PET
image without producing a pharmacodynamic effect, toxicological
event, or saturating the target of interest. Improvements that allow
the generation of [18F]-F2(g) with a higher SA have focused on
a “post-target” method using [18F]-fluoromethane to produce
[18F]-F2(g) via an electrical discharge chamber using a 18F/19F
exchange reaction and a low amount of the F2 carrier gas. High
SA [18F]-fluoromethane can be produced by nucleophilic
substitution of CH3I with [18F]-fluoride, and this “post-target”
synthesis generates [18F]-F2(g) with specific activities up to
15 Ci/μmol (555 GBq/μmol).135
(a) Aromatic Nucleophilic Fluorination Using [18F]-
Fluoride. The generation of high specific activity [18F]-fluoride
and [18F]-F2(g) has facilitated an increase in the design and
application of 18F-labeled PET radioligands procured via
either nucleophilic or electrophilic fluorination processes. Fluo-
rinated arenes are a widely used motif in drug design, and
methods to label aromatic rings with [18F] offer convenient
access to PET ligands. Nucleophilic fluorination of aromatic
rings typically involves the displacement of a leaving group
facilitated either by an electron-deficient substituent attached
to the aromatic ring or, more commonly, by an exogenous cata-
lyst. Numerous important [18F]-PET radioligands and [18F]-
labeled drugs have been produced using the latter approach,
and these methodologies dominate the literature with good
progress made recently toward developing processes to label
unactivated and electron-rich aromatic systems.129,136−144
AB
Perspective
The most common procedures are summarized in Figure 26,
although not all of these have been exemplified using [18F]-
fluoride, and some may require additional optimization for
successful application.129
(b) Nucleophilic Fluorination of Alkyl Groups. The
incorporation of [18F]-fluorine at a specific aliphatic position on a
molecule has traditionally been accomplished via a nucleophilic
displacement of a halide or sulfonate using [18F]-fluoride in a
polar aprotic solvent such as DMSO, DMF, or acetonitrile.129e,145
Numerous useful [18F]-PET radioligands have been generated using
this approach, with the clinically approved [18F]-florbetapir (269),
marketed as Amyvid, a representative example (Scheme 1). [18F]-
Florbetapir is the first Food and Drug Administration (FDA)
approved PET tracer for quantifying amyloid plaque burden in
humans during therapy or as a patient enrichment biomarker
for designing more effective clinical trials.146 The synthesis of
269 involves a two-step process in which the tosyl group of 268 is
displaced by [18F]-flouride at elevated temperature using
K.2.2.2/[18F]KF followed by removal of the Boc protecting
group.147 Improved methods for aliphatic nucleophilic fluorina-
tion with [18F]-fluoride include the use of microwave, ionic
liquids, the inclusion of tertiary alcohols, and the use of fluorous
solid-phase methods that allows rapid purification of [18F]-
labeled products.148
The enantioslective preparation of [18F]-fluorohydrins, via
epoxide ring opening using the chiral catalysts [18F]-(R,R)-
(salen)CoF and [18F]-(R,R,R,R)-(linked salen)Co2OTsF, com-
prises an effective approach to several clinically validated PET
radioligands that can be prepared under mild conditions (MeCN,
50 °C, 20 min).149 These conditions are compatible with base-
sensitive functional groups, epimerizable stereocenters, and
nitrogen-rich motifs, as exemplified by the enantioselective
[18F]-labeling of [18F]-(S)-THK-5105 (270), a potential PET
ligand for assessing tau pathology, and [18F]-FETNIM (271),
a promising PET radioligand for quantifying tumor hypoxia
in vivo.150 This type of process opens up an avenue to explore
the relationship between stereochemistry and imaging proper-
ties of important PET radioligands, an area unexplored because
of the difficulty of chiral [18F]-fluorination reactions.
A late-stage process for the direct [18F]-labeling of benzylic
C−H bonds using [18F]-fluoride exploits a Mn(salen)OTs
species as a fluoride transfer catalyst. This process has enabled
the radiolabeling of drug molecules and common chemical
intermediates that can be used as building blocks to generate
[18F]-labeled tracers.150c [18F]-labeled compounds can be
prepared in radiochemical yields (RCY) ranging from 20% to
72% in 10 min without the need for preactivation of the labeling
precursor. The facility of this process provides a translational
DOI: 10.1021/acs.jmedchem.5b00258
J. Med. Chem. XXXX, XXX, XXX−XXX
Journal of Medicinal Chemistry
Figure 26. Processes for the nucleophilic fluorination of arenes and heteroarenes.
method to label PET radioligands for human use. Eight druglike
molecules have been derivatized with an [18F]-label including
ibuprofen methyl ester (272), an analog of celecoxib (274), and a
protected form of enalaprilat (276) to afford 273, 275, and 277,
respectively (Scheme 2).150c
A simple one step nucleophilic radiosynthesis of monolabeled
[18F]-trifluoromethyl derivatives with high specific activity has
been developed based on the reaction of difluorovinyl-function-
alized precursors 278 with [18F]-fluoride using standard K.2.2.2
conditions (Scheme 3a).151 This procedure affords a mixture of
two 18F-labeled products, an isotopic exchange with the 2,2,-
difluorovinylethyltosylate precursor 279, and the desired [18F]-
2-fluoro-2-2-trifluoroethyltosylate (280) which predominates by
a ratio of 10:1. This method has been used to synthesize [18F]-
lansoprazole (283), a promising PET ligand for imaging the tau
pathway in Alzheimer’s disease.152 The difluorovinyl precursor
281 was treated with [18F]-fluoride to afford 283 along with the
[18F]-labeled starting material 282 in a combined 14%
radiochemical yield, sufficient for exploration of 283 as a
AC
Perspective
potential tau imaging agent (Scheme 3b). Axn alternative
procedure with broad application to the preparation of aryl and
heteroaryl [18F]-trifluoromethyl derivatives relies upon the Cu-
catalyzed cross-coupling reaction of aryl and heteroaryl iodides
with methyl 2-chloro-2,2-difluoroacetate and [18F]-fluoride.153
The preparation of [18F]-labeled fluoxetine (285) from the
iodide 284 depicted in Scheme 4 is representative of the process.
A related process utilizes CHF2I as the source of the 18FCF2−
and converts iodophenyl derivatives 286 into labeled CF3
compounds 287 (Scheme 5). This process is tolerant of
a wide range of functionality. Although 4-iodophenol gave
a poor yield, this problem is solved by protection as the
benzyloxy ether.154
(c) Electrophilic Fluorination of Arenes. Although many
sources of nucleophilic fluorine exist, fewer sources of electro-
philic fluorine are available. Selectfluor (288) is one of the most
reactive electrophilic fluorination reagents and is safe, nontoxic,
and easy to handle.155 As such, 288 represents a significant
advance in preparative organofluorine chemistry. The preparation
DOI: 10.1021/acs.jmedchem.5b00258
J. Med. Chem. XXXX, XXX, XXX−XXX
Journal of Medicinal Chemistry Perspective

Scheme 2. Direct [18F]-Labeling of Benzylic C−H Bonds

Scheme 3. Conversion of Difluorovinyl Functionality to the [18F]-Trifluoromethyl Group

Scheme 4. Preparation of 285

Scheme 6. Preparation of 290 from 289

Scheme 5. Cu-Catalyzed Cross Coupling of Phenyl Iodides

(286) Employing CHF2I as the [18F]CF2− Source

of [18F]-Selectfluor bis(triflate) (290) from 289 has been

accomplished using high specific activity [18F]-F2g providing a
useful electrophilic [18F]-fluorination agent (Scheme 6).156 This
reagent was used to convert 291 to [18F]-6-fluoro-L-DOPA
(292) of high specific activity, an important PET radioligand
of use in understanding the dopaminergic pathway in human
AD DOI: 10.1021/acs.jmedchem.5b00258
J. Med. Chem. XXXX, XXX, XXX−XXX
Journal of Medicinal Chemistry Perspective

Scheme 7. Preparation of 292 from 291

Scheme 8. Palladium-Mediated Synthesis of 296

Scheme 9. Nickel-Mediated Synthesis of 300

imaging studies in patients with Parkinson’s disease, schizo- Scheme 10. Preparation of 302 from 301
phrenia, and brain tumors (Scheme 7).157
An alternative approach to the use of 290 for electrophilic
[18F]-fluorinations exploits palladium(IV) and nickel(II) com-
plexes where the reactivity of [18F]-fluoride is inverted, allowing
it to react in an electrophilic manifold.158 The first step of
the palladium process is capture of the [18F]-fluoride as the
[18F]-palladium(IV) species 294 derived from 293. This species
AE DOI: 10.1021/acs.jmedchem.5b00258
J. Med. Chem. XXXX, XXX, XXX−XXX
Journal of Medicinal Chemistry
Scheme 11. Preparation of the [18F]-Labeled Exendin Analog 305
Scheme 12. Preparation of 306 for IEDDA Conjugation
acts as a source of electrophilic [ 18 F]-fluorine, which
subsequently undergoes oxidative transfer of fluorine to a
palladium(II) aryl complex 295. This yields a [18F]-Pd(IV)
fluoride species that undergoes reductive elimination of C−18F,
thereby generating the [18F]-labeled aryl fluoride derivative,
exemplified by the synthesis of [18F]-paroxetine 296 (Scheme 8).
This methodology has been translated onto a commercially
available automated synthesis unit that has produced quantities
of [18F]-labeled PET radioligands suitable for use in imaging
studies. This process allows [18F]-labeling at positions of a
molecule that have typically been difficult to access.159 In the
nickel-based process, a one-step oxidative [18F]-fluorination of
aromatic rings is accomplished using [18F]-fluoride, 18-crown-6,
an activated nickel complex, and a hypervalent iodine oxidant. This
process can be carried out at ambient temperature and pressure, is
typically complete after only 1 min, and generates the targeted aryl
fluoride products in modest radiochemical yields (13−58%).158
A translational application of this chemistry is exemplified by the
Scheme 13. Labeling of a Bombesin Derivative 310 Mediated by 309
AF
Perspective
synthesis of [18F]-MDL-100907 (300, volinanserin), a promising
new PET radioligand for labeling the 5HT2a receptor, from 297
through the intermediacy of 298 which is used to alkylate the
piperidine 299 (Scheme 9).160
(d) Synthetic Methods for the [18F]-Labeling of Bio-
logics. The increase in the application of biologics-based drugs
has stimulated considerable interest in methods for the
introduction of 18F into these molecules with a focus on the
use of chemical reactions that are bioorthogonal in nature.161
Compared to more typical 124I-labeling, the use of 18F offers the
advantage of same day imaging and reduced dosimetry.
However, the direct incorporation of [18F]-fluoride into bio-
logic constructs suffers from a major limitation based on the harsh
reaction conditions (high organic solvent concentrations, high
temperatures, high pH, etc.) that are required for currently
available fluorination processes. To overcome this limitation,
several [18F]-labeled prosthetic groups have been designed that
take advantage of either random lysine conjugation or site-specific
conjugation using [18F]-substituted maleimides, oximes, fluo-
roproprionates, or click chemistry approaches.162
One highly efficient bioorthogonal ligation approach relies
upon an inverse electron demand Diels−Alder reaction
(IEDDA) between 1,2,4,5-tetrazines and strained cycloalkenes,
including transcyclooctenes and cyclopropene derivatives.163
These reactions exhibit very fast kinetics with rate constants of
DOI: 10.1021/acs.jmedchem.5b00258
J. Med. Chem. XXXX, XXX, XXX−XXX
Journal of Medicinal Chemistry
Scheme 14. Staudinger Ligation Using 313
approximately 20 000 M−1 s−1 in MeOH at 25 °C and have been
used successfully in live cell imaging. [18F]-trans-Cyclooctene
302 ([18F]-TCO), prepared from 301, has been developed for
use in bioorthogonal ligations (Scheme 10). Several biologics
agents have been labeled with 18F by reacting [18F]-TCO
with biomolecules that have been preassembled to contain
a tetrazine. The preparation of the exendin analog 304 from
303 by an IEDDA with 302 is illustrative of this process
which provides a useful agent for imaging pancreatic β-cells
(Scheme 11).164
The poor metabolic stability of 302 prevents its application
toward in vivo labeling of tetrazine-derived macromolecules.
This problem is addressed by the design of a [18F]-labeled
tetrazine with favorable pharmacokinetics that has application as
a versatile tool for pretargeted PET imaging using in vivo click
chemistry derivatization.165 The design relies upon the use of
[18F]-3,6-dialkyltetrazine 306, prepared from 305 as depicted in
Scheme 12, which was generated in 18% radiochemical yield.
Tetrazine 306 was found to be stable in vitro in human plasma
at 37 °C for 12 h and in vivo in rodents, with approximately
85% of the molecule remaining intact 120 min after injection.165
This reagent offers considerable potential to conduct an IEDDA
reaction with a pretargeted biologic containing either trans-
cyclooctene or cyclopropene in a living animal.
Scheme 15. Derivatization of an O-Alkylated Hydroxylamine Derivative with 318
AG
Perspective
Another approach to introducing 18F into biomolecules
uses strain-promoted, copper-free click chemistry to conjugate
[ 18 F]-norbornene derivative 309 ([18F]-NFB), prepared
from the established prosthetic peptide labeling compound
[ 18 F]-N-succinimidyl-4-fluorobenzoate (308, [ 18 F]-SFB),
which in turn is obtained from 307, to a tetrazine species
(Scheme 13).166,167 Compound 309 was cyclized with a tetrazine-
functionalized derivative of bombesin (TT-BBN, 310), a 14-
residue neurotransmitter that targets the gastrin-releasing peptide
receptor (GRPR) that is overexpressed in human prostate cancer
(Scheme 13).168 Compound 309 is frequently employed in rapid
and high-yielding click chemistry reactions conducted under mild
conditions in the absence of copper, making it an attractive option for
radiolabeling of protein and antibody fragments with 18F.
One mild and effective procedure for introducing 18F into
both biomolecules and small molecules relies upon a traceless
Staudinger ligation using [18F]-fluoroethylazide (313) which
reacts with a diphenylphosphine derivative 312 to afford a
β-fluoroamide derivative 316 and the thiol side product 317 via
the intermediacy of 314 and 315, as depicted in Scheme 14.169
This process is attractive, since it results in a native amide bond
without inclusion of the phosphine oxide in the final product
and can be used to introduce a [18F]-fluoroethylamide under
catalyst-free conditions in short reaction times and with high
radiochemical yields.
Commercially available 2-[18F]-fluoro-2-deoxy-D-glucose
(318) is widely used in assessing the metabolic status of a
range of organs, including the brain, lungs, heart, and tumor cells.
Tumor cells, having high metabolic demand, accumulate 318
which is recognized as glucose by the transporter.170 In its acyclic
form, 318 presents an aldehyde that readily reacts with
DOI: 10.1021/acs.jmedchem.5b00258
J. Med. Chem. XXXX, XXX, XXX−XXX
Journal of Medicinal Chemistry
Scheme 16. Silicon-, Boron-, and Aluminum-Based Reagents for [18F]-Fluorine Incorporation
O-alkylated hydroxylamines to afford an oxime. This reactivity
has been exploited to label biologics, exemplified by the
conjugation of the cyclic RGD peptide 319 in a simple, single
step radiosynthesis to afford 320 (Scheme 15).171 This
represents a novel and useful method for the labeling of biologics
without the need for an on-site cyclotron.
Several prosthetic moieties based on silicon-, boron-, and
aluminum-based reagents that take advantage of [18F]-fluoride
reactivity have been devised (Scheme 16).172 These reagents
allow [18F]-fluorine to be introduced under mild conditions in a
single step using preassembled precursors, an attractive feature
because they offer a final “kitlike” procedure for radiolabeling
biologic products via a simple GMP synthesis.173 By use of this
methodology, a prepackaged sterile, lyophilized protein kit can
be mixed with [18F]-fluoride to generate the final PET
radioligands suitable for human use.173
■ CONCLUSION
Over the past two decades our understanding of the unique and
enigmatic properties of fluorine has deepened considerably.
This has led to more sophisticated and creative approaches to the
deployment of this element in the design of drug candidates. The
introduction of fluorine into a molecule can affect a range of
properties of critical importance to drug design. Mastering when
and how to install this element in the context of a complex
organic molecule, where the resulting effects may be somewhat
cryptic in nature rather than simply additive, has the potential to
lead to refined drug candidates. This may offer greater probability
of compound success in an arena where failure in development is
a far too common event.
In this review we have captured some of the creative
applications of fluorine in drug design, many of which have
been made possible by the emerging understanding of the
fundamental attributes of this element. Although fluorine is a
prominent element in marketed drugs and development
candidates, its prevalence is very likely limited by issues
associated with an incomplete understanding of how to
productively deploy this atom to the greatest effect and the
difficulty of synthetic access to fluorinated building blocks. This
is particularly the case for prosthetic groups like the SF5 moiety
which is of contemporary interest. In addition to the importance
of fluorine in drug design, the 18F isotope is established as an
appealing and useful positron emitter that offers considerable
AH
Perspective
utility in both a preclinical and clinical setting where labeled
ligands provide useful tools for understanding drug disposition
and evaluating drug−target engagement. Taken together, these
developments are providing a strong impetus to develop
new synthetic methodologies that are facilitating a broader
deployment of fluorine in drug design. This in turn is providing
opportunity to further clarify the nuanced role of this element in
ever more complex settings. We anticipate that our under-
standing of the organic and medicinal chemistry of fluorine will
continue to evolve and will contribute to the design and
development of important future drugs to address the considerable
unmet medical need that remains in human health.
■ AUTHOR INFORMATION
Corresponding Author
*E-mail: eric.gillis@bms.com.
Notes
The authors declare no competing financial interest.
Biographies
Eric P. Gillis received his Ph.D. degree from the University of Illinois at
UrbanaChampaign under the supervision of Professor Martin Burke.
His graduate studies focused on the development of MIDA boronates
for iterative cross-coupling, slow-release cross-coupling, and automated
small molecule synthesis. In 2010 he joined Bristol-Myers Squibb where
he is a member of the Department of Discovery Chemistry.
Kyle J. Eastman received his Ph.D. degree from The Pennsylvania State
University under the tutelage of Professor Ken Feldman. His graduate
studies focused on mechanism of action studies of a diazoparaquinone
family of natural products as well as natural product synthesis.
Kyle subsequently joined the laboratories of Professor Phil Baran at
The Scripps Research Institute in La Jolla, CA, where he directed efforts
toward method development and natural product synthesis of indole
containing architectures. He joined Bristol-Myers Squibb in 2008 where
he is a medicinal chemist in the Department of Discovery Chemistry.
Matthew D. Hill received his Ph.D. in Organic Chemistry in 2008 from
The Massachusetts Institute of Technology (MIT) under the
supervision of Professor Mohammad Movassaghi. In the course of his
graduate studies Matthew developed several new methodologies for the
preparation of azaheterocycles. Prior research includes the synthesis of
phorbol analogues under the supervision of Professor Mark McMills at
Ohio University and work on age-related macular degeneration with
Professor Koji Nakanishi at Columbia University, NY. Currently a
DOI: 10.1021/acs.jmedchem.5b00258
J. Med. Chem. XXXX, XXX, XXX−XXX
Journal of Medicinal Chemistry
member of Discovery Chemistry at Bristol-Myers Squibb, Matthew has
experience in neuroscience and oncology-focused medicinal chemistry.
David J. Donnelly received his Ph.D. degree from the State University
of New York at Buffalo under the supervision of Professor Michael Detty
and conducted postdoctoral studies in radiopharmaceutical production
at the University of Michigan in collaboration with Professor Michael
Kilbourn. He joined Bristol-Myers Squibb in 2007 where he is a member
of the PET radiochemistry synthesis group within the Discovery
Chemistry Platforms department.
Nicholas A. Meanwell received his Ph.D. degree from the University of
Sheffield, Sheffield, England, under the supervision of Dr. D. Neville
Jones and conducted postdoctoral studies at Wayne State University,
Detroit, MI, in collaboration with Professor Carl R. Johnson. He joined
Bristol-Myers Squibb in 1982 where he has supervised teams that have
advanced clinical candidates in several areas of antiviral drug discovery,
including BMY-433771, an inhibitor of respiratory syncytial virus fusion,
the HIV-1 attachment inhibitor BMS-626529 that is being developed as
the prodrug BMS-663068, the HCV NS3 protease inhibitor asunaprevir
and the HCV NS5A inhibitor daclatasvir, both of which are approved in
Japan for the treatment HCV genotype 1b infection.
■
ACKNOWLEDGMENTS
We thank Carolyn Weigelt for stimulating discussions and Brett
R. Beno for assistance with some of the graphics.
■ ABBREVIATIONS USED
17β-HSD, 17β-hydroxysteroid dehydrogenase; ADME, absorp-
tion, distribution, metabolism, and excretion; ATP, adenosine
triphosphate; AUC, area under the curve; BACE, β-site amyloid
precursor protein cleaving enzyme; CD, circular dichroism;
CETP, cholesterol ester transfer protein; CGRP, calcitonin gene-
related peptide; CNS, central nervous system; Cp-CF3,
trifluoromethylcyclopropyl; CSD, Cambridge Structural Data-
base; CYP 450, cytochrome P450; DHODH, dihydroorotate
dehydrogenase; FAP, fibroblast activation protein; DFT, density
functional theory; DPP-4, dipeptidy peptidase IV; FDA, Food
and Drug Administration; GABA, γ-aminobutyric acid; GLP-1,
glucagon-like peptide 1; GSH, glutathione; HBV, hepatitis B
virus; HIV-1, human immunodeficiency virus 1; hERG, human
ether-a-go-go-related gene; HLM, human liver microsome; IR,
infrared; iv, intravenous; HBA, hydrogen-bond acceptor; HBD,
H-bond donor; HCV, hepatitis C virus; 4R-Hyp, 4-(R)-
hydroxyproline; IEDDA, inverse electron demand Diels−Alder
reaction; iv, intravenous; KSP, kinesin spindle protein; MEK1,
MAP kinase 1; MIC, minimum inhibitory concentration; MRI,
magnetic resonance imaging; Mtb, Mycobacterium tuberculosis;
NBO, natural bond order; NK1, neurokinin 1 or substance P; NMDA,
N-methyl-D-aspartate; NMR, nuclear magnetic resonance;
PAMPA, parallel artificial membrane permeability assay;
PDGFR, platelet-derived growth factor receptor; PDB, Protein
Data Bank; Pe, permeability; PET, positron emission tomography;
P-gp, P-glycoprotein; phos-HH3, histone H3 phosphorylation; PK,
pharmacokinetic; PSA, polar surface area; QMA, quaternary
ammonium chloride polymer; RCY, radiochemical yield; RLM, rat
liver microsome; rt, room temperature; SA, specific activity; SAR,
structure−activity relationship; SERT, serotonin transporter; TBAF,
tetrabutylammonium fluoride; TCO, trans-cyclooctene; TRPV1,
transient receptor potential cation channel subfamily V member 1
■
REFERENCES
(1) (a) Böhm, H. J.; Banner, D.; Bendels, S.; Kansy, M.; Kuhn, B.;
Müller, K.; Obst-Sander, U.; Stahl, M. Fluorine in medicinal chemistry.
AI
Perspective
ChemBioChem 2004, 5, 637−643. (b) Müller, K.; Faeh, C.; Diederich, F.
Fluorine in pharmaceuticals: looking beyond intuition. Science 2007,
317, 1881−1886. (c) Shah, P.; Westwell, A. D. The role of fluorine in
medicinal chemistry. J. Enzyme Inhib. Med. Chem. 2007, 22, 527−540.
(d) Bégué, J. P.; Bonnet-Delpon, D. Bioorganic and Medicinal Chemistry
of Fluorine; Wiley: Hoboken, NJ, 2007; pp 1−365. (e) Purser, S.; Moore,
P. R.; Swallow, S.; Gouverneur, V. Fluorine in medicinal chemistry.
Chem. Soc. Rev. 2008, 37, 320−330. (f) Hagmann, W. K. The many roles
for fluorine in medicinal chemistry. J. Med. Chem. 2008, 51, 4359−4369.
(g) Yamazaki, T.; Taguchi, T.; Ojima, I. Unique properties of fluorine
and their relevance to medicinal chemistry and chemical biology. In
Fluorine in Medicinal Chemistry and Chemical Biology; Ojima, I., Ed.;
Wiley-Blackwell, Chichester, U.K., 2009; pp 1−46. (h) Wang, J.;
Sánchez-Roselló, M.; Aceña, J. L.; del Pozo, C.; Sorochinsky, A. E.;
Fustero, S.; Soloshonok, V. A.; Liu, H. Fluorine in pharmaceutical
industry: fluorine-containing drugs introduced to the market in the last
decade (2001−2011). Chem. Rev. 2014, 114, 2432−2506. (i) Eastman,
K. J.; Gillis, E. P.; Meanwell, N. A. Tactical applications of fluorine in
drug design and development. Fluorine in Heterocyclic Chemistry, Volume
1, 5-Membered Heterocycles and Macrocycles; Nenajdenko, V., Ed.;
Springer International: Cham, Switzerland, 2014; pp 1−54. (j) Nenaj-
denko, V. G.; Muzalevskiy, V. M.; Shastin, A. V. Polyfluorinated ethanes
as versatile fluorinated C2-building blocks for organic synthesis. Chem.
Rev. 2015, 115, 973−1050. (k) Alonso, C.; Martínez de Marigorta, E.;
Rubiales, G.; Palacios, F. Carbon trifluoromethylation reactions of
hydrocarbon derivatives and heteroarenes. Chem. Rev. 2015, 115, 1847−
1935.
(2) (a) Ahrens, T.; Kohlmann, J.; Ahrens, M.; Braun, T.
Functionalization of fluorinated molecules by transition-metal-mediated
C−F bond activation to access fluorinated building blocks. Chem. Rev.
2015, 115, 931−972. (b) Yang, X.; Wu, T.; Phipps, R. J.; Toste, F. D.
Advances in catalytic enantioselective fluorination, mono-, di-, and
trifluoromethylation, and trifluoromethylthiolation reactions. Chem.
Rev. 2015, 115, 826−870. (c) Liang, T.; Neumann, C. N.; Ritter, T.
Introduction of fluorine and fluorine-containing functional groups.
Angew. Chem., Int. Ed. 2013, 52, 8214−8264. (d) Champagne, P. A.;
Desroches, J.; Hamel, J.-D.; Vandamme, M.; Paquin, J.-F. Monofluori-
nation of organic compounds: 10 years of innovation. Chem. Rev. 2015,
115 DOI: 10.1021/cr500706a.
(3) (a) Le Bars, D. Fluorine-18 and medical imaging: radiopharma-
ceuticals for positron emission tomography. J. Fluorine Chem. 2006, 127,
1488−1493. (b) Miller, P. W.; Long, N. J.; Vilar, R.; Gee, A. D. Synthesis
of 11C, 18F, 15O, and 13N radiolabels for positron emission tomography.
Angew. Chem., Int. Ed. 2008, 47, 8998−9033. (c) Alauddin, M. M.
Positron emission tomography (PET) imaging with 18F-based radio-
tracers. Am. J. Nucl. Med. Mol. Imaging 2012, 2, 55−76. (d) Ametamey, S.
M.; Honer, M.; Schubiger, P. A. Molecular imaging with PET. Chem.
Rev. 2008, 108, 1501−1516. (e) Piel, M.; Vernaleken, I.; Rösch, F.
Positron emission tomography in CNS drug discovery and drug
monitoring. J. Med. Chem. 2014, 57, 9232−9258. (f) Honer, M.; Gobbi,
L.; Martarello, L.; Comley, R. A. Radioligand development for molecular
imaging of the central nervous system with positron emission
tomography. Drug Discovery Today 2014, 19, 1936−1944. (g) Zhang,
L.; Villalobos, A. Recent advances in the development of PET and
SPECT tracers for brain imaging. Annu. Rep. Med. Chem. 2012, 47, 105−
119. (h) Li, Z.; Conti, P. S. Radiopharmaceutical chemistry for positron
emission tomography. Adv. Drug Delivery Rev. 2010, 62, 1031−1051.
(4) (a) O’Hagan, D. Understanding organofluorine chemistry. An
introduction to the C-F bond. Chem. Soc. Rev. 2008, 37, 308−319.
(b) Hunter, L. The C−F bond as a conformational tool in organic and
biological chemistry. Beilstein J. Org. Chem. 2010, 6, 38.
(5) (a) Zimmer, L. E.; Sparr, C.; Gilmour, R. Fluorine conformational
effects in organocatalysis: an emerging strategy for molecular design.
Angew. Chem., Int. Ed. 2011, 50, 11860−11871. (b) Buissonneaud, D. Y.;
van Mourik, T.; O’Hagan, D. A DFT study on the origin of the fluorine
gauche effect in substituted fluoroethanes. Tetrahedron 2010, 66, 2196−
2202. (c) Abraham, R. J.; Chambers, E. J.; Thomas, W. A.
Conformational analysis. Part 22. An NMR and theoretical investigation
of the gauche effect in fluoroethanols. J. Chem. Soc., Perkin Trans. 2 1994,
DOI: 10.1021/acs.jmedchem.5b00258
J. Med. Chem. XXXX, XXX, XXX−XXX
Journal of Medicinal Chemistry
949−955. (d) Abraham, R. J.; Smith, T. A. D.; Thomas, W. A.
Conformational analysis. Part 28. OH···F hydrogen bonding and the
conformation of trans-2-fluorocyclohexanol. J. Chem. Soc., Perkin Trans.
2 1996, 9, 1949−1955. (e) Dixon, D. A.; Smart, B. E. Conformational
energies of 2-fluoroethanol and 2-fluoroacetaldehyde enol: strength of
the internal hydrogen bond. J. Phys. Chem. 1991, 95, 1609−1612.
(f) Briggs, C. R. S.; Allen, M. J.; O’Hagan, D.; Tozer, D. J.; Slawin, A. M.
Z.; Goeta, A. E.; Howard, J. A. K. The observation of a large gauche
preference when 2-fluoroethylamine and 2-fluoroethanol become
protonated. Org. Biomol. Chem. 2004, 2, 732−740. (g) Bakke, J. M.;
Bjerkeseth, L. H.; Rønnow, T. E. C. L.; Steinsvoll, K. The conformation
of 2-fluoroethanolIs intramolecular hydrogen bonding important? J.
Mol. Struct. 1994, 321, 205−214.
(6) O’Hagan, D. Organofluorine chemistry: synthesis and conforma-
tion of vicinal fluoromethylene motifs. J. Org. Chem. 2012, 77, 3689−
3699.
(7) Tavasli, M.; O’Hagan, D.; Pearson, C.; Petty, M. C. The fluorine
gauche effect. Langmuir isotherms report the relative conformational
stability of (±)-erythro- and (±)-threo-9,10-difluorostearic acids. Chem.
Commun. 2002, 1226−1227.
(8) Wu, D.; Tian, A.; Sun, H. Conformational properties of 1,3-
difluoropropane. J. Phys. Chem. A 1998, 102, 9901−9905.
(9) Hunter, L.; Kirsch, P.; Slawin, A. M. Z.; O’Hagan, D. Synthesis and
structure of stereoisomeric multivicinal hexafluoroalkanes. Angew.
Chem., Int. Ed. 2009, 48, 5457−5460.
(10) Wang, Y.; Callejo, R.; Slawin, A. M. Z.; O’Hagan, D. The
difluoromethylene (CF2) group in aliphatic chains: synthesis and
conformational preference of palmitic acids and nonadecane containing
CF2 groups. Beilstein J. Org. Chem. 2014, 10, 18−25.
(11) (a) Hunter, L.; Chung, J. H. Total synthesis of unguisin A. J. Org.
Chem. 2011, 76, 5502−5505. (b) Hunter, L.; Butler, S.; Ludbrook, S. B.
Solid phase synthesis of peptides containing backbone-fluorinated
amino acids. Org. Biomol. Chem. 2012, 10, 8911−8918. (c) Hu, X. G.;
Thomas, D. S.; Griffith, R.; Hunter, L. Stereoselective fluorination alters
the geometry of a cyclic peptide: exploration of backbone-fluorinated
analogues of unguisin A. Angew. Chem., Int. Ed. 2014, 53, 6176−6179.
(12) (a) Hunter, L.; Jolliffe, K. A.; Jordan, M. J. T.; Jensen, P.;
MacQuart, R. B. Synthesis and conformational analysis of α,β-difluoro-
γ-amino acid derivatives. Chem.Eur. J. 2011, 17, 2340−2343.
(b) Yamamoto, I.; Jordan, M. J. T.; Gavande, N.; Doddareddy, M. R.;
Chebib, M.; Hunter, L. The enantiomers of syn-2,3-difluoro-4-
aminobutyric acid elicit opposite responses at the GABA C receptor.
Chem. Commun. 2012, 48, 829−831.
(13) (a) Abraham, R. J.; Chambers, E. J.; Thomas, W. A.
Conformational analysis. Part 22. An NMR and theoretical investigation
of the gauche effect in fluoroethanols. J. Chem. Soc., Perkin Trans. 2 1994,
949−955. (b) Wiberg, K. B.; Murcko, M. A. Rotational barriers: Part 3.
2-Haloethanols. J. Mol. Struct.: THEOCHEM 1988, 163, 1−17.
(c) Hagen, K.; Hedberg, K. Conformational analysis. III. Molecular
structure and composition of 2-fluoroethanol as determined by electron
diffraction. J. Am. Chem. Soc. 1973, 95, 8263−8266. (d) Huang, J.;
Hedberg, K. Conformational analysis. 13. 2-Fluoroethanol. An
investigation of the molecular structure and conformational composi-
tion at 20, 156, and 240 °C. Estimate of the anti-gauche energy
difference. J. Am. Chem. Soc. 1989, 111, 6909−6913. (e) Buckton, K. S.;
Azrak, R. G. Microwave spectrum and intramolecular hydrogen bonding
in 2-fluoroethanol. J. Chem. Phys. 1970, 52, 5652−5655. (f) Jenkins, C.
L.; Raines, R. T. Insights on the conformational stability of collagen. Nat.
Prod. Rep. 2002, 19, 49−59. (g) Shoulders, M. D.; Kamer, K. J.; Raines,
R. T. Origin of the stability conferred upon collagen by fluorination.
Bioorg. Med. Chem. Lett. 2009, 19, 3859−3862.
(14) (a) Dunitz, J. D.; Taylor, R. Organic fluorine hardly ever accepts
hydrogen bonds. Chem.Eur. J. 1997, 3, 89−98. (b) Dunitz, J. D.
Organic fluorine: odd man out. ChemBioChem 2004, 5, 614−621.
(15) (a) Dalvit, C.; Vulpetti, A. Intermolecular and intramolecular
hydrogen bonds involving fluorine atoms: implications for recognition,
selectivity, and chemical properties. ChemMedChem 2012, 7, 262−272.
(b) Schneider, H.-J. Hydrogen bonds with fluorine. Studies in solution,
in gas phase and by computations, conflicting conclusions from
AJ
Perspective
crystallographic analyses. Chem. Sci. 2012, 3, 1381−1394. (c) Cham-
pagne, P. A.; Desroches, J.; Paquin, J.-F. Organic fluorine as a hydrogen-
bond acceptor: recent examples and applications. Synthesis 2015, 47,
306−322. (d) Dalvit, C.; Invernizzi, C.; Vulpetti, A. Fluorine as a
hydrogen-bond acceptor: experimental evidence and computational
calculations. Chem.Eur. J. 2014, 20, 11058−11068.
(16) Souza, F. R.; Freitas, M. P. Conformational analysis and
intramolecular interactions in 2-haloethanols and their methyl ethers.
Comput. Theor. Chem. 2011, 964, 155−159.
(17) Andrade, L. A. F.; Silla, J. M.; Duarte, C. J.; Rittnerb, R.; Freitas, M.
P. The preferred all-gauche conformations in 3-fluoro-1,2-propanediol.
Org. Biomol. Chem. 2013, 11, 6766−6771.
(18) Graton, J.; Wang, Z.; Brossard, A.-M.; Gonçalves Monteiro, D.; Le
Questel, J.-Y.; Linclau, B. An unexpected and significantly lower
hydrogen-bond-donating capacity of fluorohydrins compared to
nonfluorinated alcohols. Angew. Chem., Int. Ed. 2012, 51, 6176−6180.
(19) Myers, A. G.; Barbay, J. K.; Zhong, B. Asymmetric synthesis of
chiral organofluorine compounds: use of nonracemic fluoroiodoacetic
acid as a practical electrophile and its application to the synthesis of
monofluoro hydroxyethylene dipeptide isosteres within a novel series of
HIV protease inhibitors. J. Am. Chem. Soc. 2001, 123, 7207−7219.
(20) (a) Hehre, W. J.; Radom, L.; Pople, J. A. Molecular orbital theory
of the electronic structure of organic compounds. XII. Conformations,
stabilities, and charge distributions in monosubstituted benzenes. J. Am.
Chem. Soc. 1972, 94, 1496−1504. (b) Hummel, W.; Huml, K.; Bürgi, H.-
B. Conformational flexibility of the methoxyphenyl group studied by
statistical analysis of crystal structure data. Helv. Chim. Acta 1988, 71,
1291−1302. (c) Brameld, K. A.; Kuhn, B.; Reuter, D. C.; Stahl, M. Small
molecule conformational preferences derived from crystal structure
data. A medicinal chemistry focused analysis. J. Chem. Inf. Model. 2008,
48, 1−24.
(21) Johnson, F. Allylic strain in six-membered rings. Chem. Rev. 1968,
68, 375−413.
(22) Anderson, G. M.; Kollman, P. A.; Domelsmith, L. N.; Houk, K. N.
Methoxy group nonplanarity in o-dimethoxybenzenes. Simple
predictive models for conformations and rotational barriers in
alkoxyaromatics. J. Am. Chem. Soc. 1979, 101, 2344−2352.
(23) (a) Leroux, F.; Jeschke, P.; Schlosser, M. α-Fluorinated ethers,
thioethers, and amines: anomerically biased species. Chem. Rev. 2005,
105, 827−856. (b) Leroux, F. R.; Manteau, B.; Vors, J. P.; Pazenok, S.
Trifluoromethyl etherssynthesis and properties of an unusual
substituent. Beilstein J. Org. Chem. 2008, 4, 13 DOI: 10.3762/
bjoc.4.13. (c) Manteau, B.; Pazenok, S.; Vors, J. P.; Leroux, F. R. New
trends in the chemistry of α-fluorinated ethers, thioethers, amines and
phosphines. J. Fluorine Chem. 2010, 131, 140−158. (d) Horne, D. B.;
Bartberger, M. D.; Kaller, M. R.; Monenschein, H.; Zhong, W.;
Hitchcock, S. A. Synthesis and conformational analysis of α,α-
difluoroalkyl heteroaryl ethers. Tetrahedron Lett. 2009, 50, 5452−
5455. (e) Xing, L.; Blakemore, D. C.; Narayanan, A.; Unwalla, R.;
Lovering, F.; Denny, R. A.; Zhou, H.; Bunnage, M. E. Fluorine in drug
design: a case study with fluoroanisoles. ChemMedChem 2015, 10, 715−
726.
(24) Klocker, J.; Karpfen, A.; Wolschann, P. On the structure and
torsional potential of trifluoromethoxybenzene: an ab initio and density
functional study. Chem. Phys. Lett. 2003, 367, 566−575.
(25) (a) Massa, M. A.; Spangler, D. P.; Durley, R. C.; Hickory, B. S.;
Connolly, D. T.; Witherbee, B. J.; Smith, M. E.; Sikorski, J. A. Novel
heteroaryl replacements of aromatic 3-tetrafluoroethoxy substituents in
trifluoro-3-(tertiaryamino)-2-propanols as potent inhibitors of choles-
teryl ester transfer protein. Bioorg. Med. Chem. Lett. 2001, 11, 1625−
1628. (b) Reinhard, E. J.; Wang, J. L.; Durley, R. C.; Fobian, Y. M.;
Grapperhaus, M. L.; Hickory, B. S.; Massa, M. A.; Norton, M. B.; Promo,
M. A.; Tollefson, M. B.; Vernier, W. F.; Connolly, D. T.; Witherbee, B. J.;
Melton, M. A.; Regina, K. J.; Smith, M. E.; Sikorski, J. A. Discovery of a
simple picomolar inhibitor of cholesteryl ester transfer protein. J. Med.
Chem. 2003, 46, 2152−2168.
(26) (a) Lankin, D. C.; Chandrakumar, N. S.; Rao, S. N.; Spangler, D.
P.; Snyder, J. P. Protonated 3-fluoropiperidines: an unusual fluoro
directing effect and a test for quantitative theories of solvation. J. Am.
DOI: 10.1021/acs.jmedchem.5b00258
J. Med. Chem. XXXX, XXX, XXX−XXX
Journal of Medicinal Chemistry
Chem. Soc. 1993, 115, 3356−3357. (b) Snyder, J. P.; Chandrakumar, N.
S.; Sato, H.; Lankin, D. C. The unexpected diaxial orientation of cis-3,5-
difluoropiperidine in water: a potent CF···NH charge-dipole effect. J.
Am. Chem. Soc. 2000, 122, 544−545. (c) Sun, A.; Lankin, D. C.;
Hardcastle, K.; Snyder, J. P. 3-Fluoropiperidines and N-methyl-3-
fluoropiperidinium salts: the persistence of axial fluorine. Chem.Eur. J.
2005, 11, 1579−1591.
(27) (a) Deniau, G.; Slawin, A. M. Z.; Lebl, T.; Chorki, F.; Issberner, J.
P.; van Mourik, T.; Heygate, J. M.; Lambert, J. J.; Etherington, L. A.;
Sillar, K. T.; O’Hagan, D. Synthesis, conformation and biological
evaluation of the enantiomers of 3-fluoro-γ-aminobutyric acid ((R)- and
(S)-3F-GABA): an analogue of the neurotransmittter GABA.
ChemBioChem 2007, 8, 2265−2274. (b) Clift, M. D.; Ji, H.; Deniau,
G. P.; O’Hagan, D.; Silverman, R. B. Enantiomers of 4-amino-3-
fluorobutanoic acid as substrates for γ-aminobutyric acid amino-
transferase. Conformational probes for GABA binding. Biochemistry
2007, 46, 13819−13828. (c) Yamamoto, I.; Deniau, G. P.; Gavande, N.;
Chebib, M.; Johnston, G. A. R.; O’Hagan, D. Agonist responses of (R)-
and (S)-3-fluoro-γ-aminobutyric acids suggest an enantiomeric fold for
GABA binding to GABAC receptors. Chem. Commun. 2011, 47, 7956−
7958. (d) Crittenden, D. L.; Chebib, M.; Jordan, M. J. T. A quantitative
structure-activity relationship investigation into agonist binding at
GABAC receptors. J. Mol. Struct.: THEOCHEM 2005, 755, 81−89.
(e) Chia, P. W.; Livesey, M. R.; Slawin, A. M. Z.; Van Mourik, T.; Wyllie,
D. J. A.; O’Hagan, D. 3-Fluoro-N-methyl-D-aspartic acid (3F-NMDA)
stereoisomers as conformational probes for exploring agonist binding at
NMDA receptors. Chem.Eur. J. 2012, 18, 8813−8819.
(28) (a) Winkler, M.; Moraux, T.; Khairy, H. A.; Scott, R. H.; Slawin, A.
M. Z.; O’Hagan, D. Synthesis and vanilloid receptor (TRPV1) activity of
the enantiomers of α-fluorinated capsaicin. ChemBioChem 2009, 10,
823−828. (b) Yang, F.; Xiao, X.; Cheng, W.; Yang, W.; Yu, P.; Song, Z.;
Yarov-Yarovoy, V.; Zheng, J.Structural mechanism underlying capsaicin
binding and activation of the TRPV1 ion channel. Nature Chem. Biol.
2015, in press. DOI: 10.1038/nchembio.1835
(29) (a) Peddie, V.; Butcher, R. J.; Robinson, W. T.; Wilce, M. C. J.;
Traore, D. A. K.; Abell, A. D. Synthesis and conformation of fluorinated
β-peptidic compounds. Chem.Eur. J. 2012, 18, 6655−6662.
(b) O’Hagan, D.; Bilton, C.; Howard, J. A. K.; Knight, L.; Tozer, D. J.
The preferred conformation of N-β-fluoroethylamides. Observation of
the fluorine amide gauche effect. J. Chem. Soc., Perkin Trans. 2 2000,
605−607. (c) O’Hagan, D.; Rzepa, H. S. Some influences of fluorine in
bioorganic chemistry. Chem. Commun. 1997, 645−652.
(30) (a) Bell, I. M.; Bednar, R. A.; Fay, J. F.; Gallicchio, S. N.;
Hochman, J. H.; McMasters, D. R.; Miller-Stein, C.; Moore, E. L.;
Mosser, S. D.; Pudvah, N. T.; Quigley, A. G.; Salvatore, C. A.; Stump, C.
A.; Theberge, C. R.; Wong, B. K.; Zartman, C. B.; Zhang, X. F.; Kane, S.
A.; Graham, S. L.; Vacca, J. P.; Williams, T. M. Identification of novel,
orally bioavailable spirohydantoin CGRP receptor antagonists. Bioorg.
Med. Chem. Lett. 2006, 16, 6165−6169. (b) Bonomo, S.; Tosco, P.;
Giorgis, M.; Lolli, M.; Fruttero, R. The role of fluorine in stabilizing the
bioactive conformation of dihydroorotate dehydrogenase inhibitors. J.
Mol. Model. 2013, 19, 1099−1107.
(31) Stump, C. A.; Bell, I. M.; Bednar, R. A.; Fay, J. F.; Gallicchio, S. N.;
Hershey, J. C.; Jelley, R.; Kreatsoulas, C.; Moore, E. L.; Mosser, S. D.;
Quigley, A. G.; Roller, S. A.; Salvatore, C. A.; Sharik, S. S.; Theberge, C.
R.; Zartman, C. B.; Kane, S. A.; Graham, S. L.; Selnick, H. G.; Vacca, J. P.;
Williams, T. M. Identification of potent, highly constrained CGRP
receptor antagonists. Bioorg. Med. Chem. Lett. 2010, 20, 2572−2576.
(32) (a) Improta, R.; Mele, F.; Crescenzi, O.; Benzi, C.; Barone, V.
Understanding the role of stereoelectronic effects in determining
collagen stability. 2. A quantum mechanical/molecular mechanical study
of (proline-proline-glycine)n polypeptides. J. Am. Chem. Soc. 2002, 124,
7857−7865. (b) Hinderaker, M. P.; Raines, R. T. An electronic effect on
protein structure. Protein Sci. 2003, 12, 1188−1194. (c) Park, S.;
Radmer, R. J.; Klein, T. E.; Pande, V. S. A new set of molecular
mechanics parameters for hydroxyproline and its use in molecular
dynamics simulations of collagen-like peptides. J. Comput. Chem. 2005,
26, 1612−1616. (d) DeRider, M. L.; Wilkens, S. J.; Waddell, M. J.;
Bretscher, L. E.; Weinhold, F.; Raines, R. T.; Markley, J. L. Collagen
AK
Perspective
stability: insights from NMR spectroscopic and hybrid density
functional computational investigations of the effect of electronegative
substituents on prolyl ring conformations. J. Am. Chem. Soc. 2002, 124,
2497−2505. (e) Hodges, J. A.; Raines, R. T. Stereoelectronic and steric
effects in the collagen triple helix: toward a code for strand association. J.
Am. Chem. Soc. 2005, 127, 15923−15932. (f) Holmgren, S. K.; Taylor,
K. M.; Bretscher, L. E.; Raines, R. T. Code for collagen’s stability
deciphered. Nature 1998, 392, 666−667. (g) Bretscher, L. E.; Jenkins, C.
L.; Taylor, K. M.; DeRider, M. L.; Raines, R. T. Conformational stability
of collagen relies on a stereoelectronic effect. J. Am. Chem. Soc. 2001,
123, 777−778. (h) Hodges, J. A.; Raines, R. T. Stereoelectronic effects
on collagen stability: the dichotomy of 4-fluoroproline diastereomers. J.
Am. Chem. Soc. 2003, 125, 9262−9263. (i) Doi, M.; Nishi, Y.; Uchiyama,
S.; Nishiuchi, Y.; Nakazawa, T.; Ohkubo, T.; Kobayashi, Y. Character-
ization of collagen model peptides containing 4-fluoroproline; (4(S)-
fluoroproline-Pro-Gly)10 forms a triple helix, but (4(R)-fluoroproline-
Pro-Gly)10 does not. J. Am. Chem. Soc. 2003, 125, 9922−9923. (j) Doi,
M.; Nishi, Y.; Kiritoshi, N.; Iwata, T.; Nago, M.; Nakano, H.; Uchiyama,
S.; Nakazawa, T.; Wakamiya, T.; Kobayashi, Y. Simple and efficient
syntheses of Boc- and Fmoc-protected 4(R)- and 4(S)-fluoroproline
solely from 4(R)-hydroxyproline. Tetrahedron 2002, 58, 8453−8459.
(k) Raines, R. T. 2005 Emil Thomas Kaiser award. Protein Sci. 2006, 15,
1219−1225.
(33) Bella, J.; Brodsky, B.; Berman, H. M. Hydration structure of a
collagen peptide. Structure 1995, 3, 893−906.
(34) Hodges, J. A.; Raines, R. T. Energetics of an n → π* interaction
that impacts protein structure. Org. Lett. 2006, 8, 4695−4697.
(35) Choudhary, A.; Newberry, R. W.; Raines, R. T. n →π*
interactions engender chirality in carbonyl groups. Org. Lett. 2014, 16,
3421−3423.
(36) Kim, W.; Hardcastle, K. I.; Conticello, V. P. Fluoroproline flip-
flop: regiochemical reversal of a stereoelectronic effect on peptide and
protein structures. Angew. Chem., Int. Ed. 2006, 45, 8141−8145.
(37) Kitamoto, T.; Ozawa, T.; Abe, M.; Marubayashi, S.; Yamazaki, T.
Incorporation of fluoroprolines to proctolin: study on the effect of a
fluorine atom toward peptidic conformation. J. Fluorine Chem. 2008,
129, 286−293.
(38) (a) Fukushima, H.; Hiratate, A.; Takahashi, M.; Saito, M.;
Munetomo, E.; Kitano, K.; Saito, H.; Takaoka, Y.; Yamamoto, K.
Synthesis and structure-activity relationships of potent 3- or 4-
substituted-2-cyanopyrrolidine dipeptidyl peptidase IV inhibitors.
Bioorg. Med. Chem. 2004, 12, 6053−6061. (b) Jansen, K.; Heirbaut,
L.; Verkerk, R.; Cheng, J. D.; Joossens, J.; Cos, P.; Maes, L.; Lambeir, A.
M.; De Meester, I.; Augustyns, K.; Van Der Veken, P. Extended
structure-activity relationship and pharmacokinetic investigation of (4-
quinolinoyl)glycyl-2-cyanopyrrolidine inhibitors of fibroblast activation
protein (FAP). J. Med. Chem. 2014, 57, 3053−3074.
(39) (a) Liu, P.; Sharon, A.; Chu, C. K. Fluorinated nucleosides:
synthesis and biological implication. J. Fluorine Chem. 2008, 129, 743−
766. (b) Qiu, X.-L.; Xu, X.-H.; Qing, F.-L. Recent advances in the
synthesis of fluorinated nucleosides. Tetrahedron 2010, 66, 789−843.
(40) Thibaudeau, C.; Acharya, P.; Chattopadhyaya, J. Stereoelectronic
Effects in Nucelosides and Nucleotides and Their Structural Implications,
2nd ed.; Uppsala University Press: Uppsala, Sweden, 2005.
(41) (a) Barchi, J. J., Jr; Jeong, L. S.; Siddiqui, M. A.; Marquez, V. E.
Conformational analysis of the complete series of 2′ and 3′
monofluorinated dideoxyuridines. J. Biochem. Biophys. Methods 1997,
34, 11−29. (b) Seela, F.; Chittepu, P. 6-Azauracil or 8-aza-7-
deazaadenine nucleosides and oligonucleotides: the effect of 2′-fluoro
substituents and nucleobase nitrogens on conformation and base
pairing. Org. Biomol. Chem. 2008, 6, 596−607. (c) Barchi, J. J., Jr.; Karki,
R. G.; Nicklaus, M. C.; Siddiqui, M. A.; George, C.; Mikhailopulo, I. A.;
Marquez, V. E. Comprehensive structural studies of 2′,3′-difluorinated
nucleosides: comparison of theory, solution, and solid state. J. Am. Chem.
Soc. 2008, 130, 9048−9057. (d) Watts, J. K.; Damha, M. J. 2′F-
Arabinonucleic acids (2′F-ANA)history, properties, and new
frontiers. Can. J. Chem. 2008, 86, 641−656.
(42) (a) Blandin, M.; Son, T. D.; Catlin, J. C.; Guschlbauer, W.
Nucleoside conformations. 16. Nuclear magnetic resonance and circular
DOI: 10.1021/acs.jmedchem.5b00258
J. Med. Chem. XXXX, XXX, XXX−XXX
Journal of Medicinal Chemistry
dichroism studies on pyrimidine-2′-fluoro-2′-deoxyribonucleosides.
Biochim. Biophys. Acta 1974, 361, 249−256. (b) Sivets, G. G.;
Kalinichenko, E. N.; Mikhailopulo, I. A. Synthesis and conformational
analysis of 1′- and 3′-substituted 2-deoxy-2-fluoro-D-ribofuranosyl
nucleosides. Helv. Chim. Acta 2007, 90, 1818−1836. (c) Marquez, V.
E.; Tseng, C. K. H.; Mitsuya, H.; Aoki, S.; Kelley, J. A.; Ford, H., Jr.;
Roth, J. S.; Broder, S.; Johns, D. G.; Driscoll, J. S. Acid-stable 2′-fluoro
purine dideoxynucleosides as active agents against HIV. J. Med. Chem.
1990, 33, 978−985. (d) Van Roey, P.; Salerno, J. M.; Chu, C. K.;
Schinazi, R. F. Correlation between preferred sugar ring conformation
and activity of nucleoside analogues against human immunodeficiency
virus. Proc. Natl. Acad. Sci. U.S.A. 1989, 86, 3929−3933.
(43) (a) Marquez, V. E.; Tseng, C. K. H.; Kelley, J. A.; Mitsuya, H.;
Broder, S.; Roth, J. S.; Driscoll, J. S. 2′,3′-Dideoxy-2′-fluoro-ara-A. An
acid-stable purine nucleoside active against human immunodeficiency
virus (HIV). Biochem. Pharmacol. 1987, 36, 2719−2722. (b) Graul, A.;
Silvestre, J.; Castaner, J. Lodenosine. Anti-HIV, reverse transcriptase
inhibitor. Drugs Future 1998, 23, 1176−1189. (c) Sivets, G. G.;
Kalinichenko, E. N.; Mikhailopulo, I. A.; Detorio, M. A.; McBrayer, T.
R.; Whitaker, T.; Schinazi, R. F. Synthesis and antiviral activity of purine
2′,3′-dideoxy-2′,3′-difluoro-D-arabinofuranosyl nucleosides. Nucleosides,
Nucleotides Nucleic Acids 2009, 28, 519−536.
(44) (a) Martínez-Montero, S.; Deleavey, G. F.; Kulkarni, A.; Martín-
Pintado, N.; Lindovska, P.; Thomson, M.; González, C.; Götte, M.;
Damha, M. J. Rigid 2′,4′-difluororibonucleosides: synthesis, conforma-
tional analysis, and incorporation into nascent RNA by HCV
polymerase. J. Org. Chem. 2014, 79, 5627−5635. (b) Gore, K. R.;
Harikrishna, S.; Pradeepkumar, P. I. Influence of 2′-fluoro versus 2′-O-
methyl substituent on the sugar puckering of 4′-C-aminomethyluridine.
J. Org. Chem. 2013, 78, 9956−9962.
(45) Anzahaee, M. Y.; Watts, J. K.; Alla, N. R.; Nicholson, A. W.; Damha,
M. J. Energetically important C-H···F-C pseudohydrogen bonding in
water: evidence and application to rational design of oligonucleotides with
high binding affinity. J. Am. Chem. Soc. 2011, 133, 728−731.
(46) Mikhailopulo, I. A.; Pricota, T. I.; Sivets, G. G.; Altona, C. 2′-
Chloro-2′,3′-dideoxy-3′-fluoro-D-ribonucleosides: synthesis, stereospe-
cificity, some chemical transformations, and conformational analysis. J.
Org. Chem. 2003, 68, 5897−5908.
(47) Hui, C. K.; Lau, G. K. K. Clevudine for the treatment of chronic
hepatitis B virus infection. Expert Opin. Invest. Drugs 2005, 14, 1277−
1284.
(48) Chong, Y.; Chu, C. K. Understanding the unique mechanism of L-
FMAU (clevudine) against hepatitis B virus: molecular dynamics
studies. Bioorg. Med. Chem. Lett. 2002, 12, 3459−3462.
(49) Alabugin, I. V.; Zeidan, T. A. Stereoelectronic effects and general
trends in hyperconjugative acceptor ability of σ bonds. J. Am. Chem. Soc.
2002, 124, 3175−3185.
(50) (a) Meanwell, N. A. Improving drug candidates by design: a focus
on physicochemical properties as a means of improving compound
disposition and safety. Chem. Res. Toxicol. 2011, 24, 1420−1456.
(b) Hopkins, A. L.; Keserü, G. M.; Leeson, P. D.; Rees, D. C.; Reynolds,
C. H. The role of ligand efficiency metrics in drug discovery. Nat. Rev.
Drug Discovery 2014, 13, 105−121. (c) Ritchie, T. J.; Macdonald, S. J. F.
How drug-like are “ugly” drugs: do drug-likeness metrics predict ADME
behaviour in humans? Drug Discovery Today 2014, 19, 489−495.
(d) Wager, T. T.; Kormos, B. L.; Brady, J. T.; Will, Y.; Aleo, M. D.;
Stedman, D. B.; Kuhn, M.; Chandrasekaran, R. Y. Improving the odds of
success in drug discovery: choosing the best compounds for in vivo
toxicology studies. J. Med. Chem. 2013, 56, 9771−9779. (e) Tarcsay, A.;
Keserú, G. M. Contributions of molecular properties to drug
promiscuity. J. Med. Chem. 2013, 56, 1789−1795. (f) Yusof, I.; Segall,
M. D. Considering the impact drug-like properties have on the chance of
success. Drug Discovery Today 2013, 18, 659−666.
(51) (a) Morgenthaler, M.; Schweizer, E.; Hoffmann-Röder, A.;
Benini, F.; Martin, R. E.; Jaeschke, G.; Wagner, B.; Fischer, H.; Bendels,
S.; Zimmerli, D.; Schneider, J.; Diederich, F.; Kansy, M.; Müller, K.
Predicting and tuning physicochemical properties in lead optimization:
amine basicities. ChemMedChem 2007, 2, 1100−1115. (b) Sani, M.;
Volonterio, A.; Zanda, M. The trifluoroethylamine function as peptide
AL
Perspective
bond replacement. ChemMedChem 2007, 2, 1693−1700. (c) Jagodzin-
ska, M.; Huguenot, F.; Candiani, G.; Zanda, M. Assessing the
bioisosterism of the trifluoromethyl group with a protease probe.
ChemMedChem 2009, 4, 49−51. (d) Gauthier, J. Y.; Chauret, N.;
Cromlish, W.; Desmarais, S.; Duong, L. T.; Falgueyret, J. P.; Kimmel, D.
B.; Lamontagne, S.; Léger, S.; LeRiche, T.; Li, C. S.; Massé, F.; McKay,
D. J.; Nicoll-Griffith, D. A.; Oballa, R. M.; Palmer, J. T.; Percival, M. D.;
Riendeau, D.; Robichaud, J.; Rodan, G. A.; Rodan, S. B.; Seto, C.;
Thérien, M.; Truong, V. L.; Venuti, M. C.; Wesolowski, G.; Young, R.
N.; Zamboni, R.; Black, W. C. The discovery of odanacatib (MK-0822),
a selective inhibitor of cathepsin K. Bioorg. Med. Chem. Lett. 2008, 18,
923−928.
(52) (a) Van Niel, M. B.; Collins, I.; Beer, M. S.; Broughton, H. B.;
Cheng, S. K. F.; Goodacre, S. C.; Heald, A.; Locker, K. L.; MacLeod, A.
M.; Morrison, D.; Moyes, C. R.; O’Connor, D.; Pike, A.; Rowley, M.;
Russell, M. G. N.; Sohal, B.; Stanton, J. A.; Thomas, S.; Verrier, H.; Watt,
A. P.; Castro, J. L. Fluorination of 3-(3-(piperidin-1-yl)propyl)indoles
and 3-(3-(piperazin-1-yl)propyl)indoles gives selective human 5-
HT(1D) receptor ligands with improved pharmacokinetic profiles. J.
Med. Chem. 1999, 42, 2087−2104. (b) Cox, C. D.; Coleman, P. J.;
Breslin, M. J.; Whitman, D. B.; Garbaccio, R. M.; Fraley, M. E.; Buser, C.
A.; Walsh, E. S.; Hamilton, K.; Schaber, M. D.; Lobell, R. B.; Tao, W.;
Davide, J. P.; Diehl, R. E.; Abrams, M. T.; South, V. J.; Huber, H. E.;
Torrent, M.; Prueksaritanont, T.; Li, C.; Slaughter, D. E.; Mahan, E.;
Fernandez-Metzler, C.; Yan, Y.; Kuo, L. C.; Kohl, N. E.; Hartman, G. D.
Kinesin spindle protein (KSP) inhibitors. 9. Discovery of (2S)-4-(2,5-
difluorophenyl)-N-[(3R,4S)-3-fluoro-1-methylpiperidin-4-yl]-2-(hy-
droxymethyl)-N-methyl-2-phenyl-2,5-dihydro-1H-pyrrole-1-carboxa-
mide (MK-0731) for the treatment of taxane-refractory cancer. J. Med.
Chem. 2008, 51, 4239−4252.
(53) (a) Cerny, M. A.; Hanzlik, R. P. Cyclopropylamine inactivation of
cytochromes P450: role of metabolic intermediate complexes. Arch.
Biochem. Biophys. 2005, 436, 265−275. (b) Goncharov, N. V.; Jenkins,
R. O.; Radilov, A. S. Toxicology of fluoroacetate: a review, with possible
directions for therapy research. J. Appl. Toxicol. 2006, 26, 148−161.
(54) Cox, C. D.; Breslin, M. J.; Whitman, D. B.; Coleman, P. J.;
Garbaccio, R. M.; Fraley, M. E.; Zrada, M. M.; Buser, C. A.; Walsh, E. S.;
Hamilton, K.; Lobell, R. B.; Tao, W.; Abrams, M. T.; South, V. J.; Huber,
H. E.; Kohl, N. E.; Hartman, G. D. Kinesin spindle protein (KSP)
inhibitors. Part V: discovery of 2-propylamino-2,4-diaryl-2,5-dihydro-
pyrroles as potent, water-soluble KSP inhibitors, and modulation of their
basicity by β-fluorination to overcome cellular efflux by P-glycoprotein.
Bioorg. Med. Chem. Lett. 2007, 17, 2697−2702.
(55) Hicken, E. J.; Marmsater, F. P.; Munson, M. C.; Schlachter, S. T.;
Robinson, J. E.; Allen, S.; Burgess, L. E.; Delisle, R. K.; Rizzi, J. P.;
Topalov, G. T.; Zhao, Q.; Hicks, J. M.; Kallan, N. C.; Tarlton, E.; Allen,
A.; Callejo, M.; Cox, A.; Rana, S.; Klopfenstein, N.; Woessner, R.;
Lyssikatos, J. P. Discovery of a novel class of imidazo[1,2-a]pyridines
with potent PDGFR activity and oral bioavailability. ACS Med. Chem.
Lett. 2014, 5, 78−83.
(56) McDonald, I. M.; Mate, R. A.; Zusi, F. C.; Huang, H.; Post-
Munson, D. J.; Ferrante, M. A.; Gallagher, L.; Bertekap, R. L., Jr; Knox,
R. J.; Robertson, B. J.; Harden, D. G.; Morgan, D. G.; Lodge, N. J.;
Dworetzky, S. I.; Olson, R. E.; Macor, J. E. Discovery of a novel series of
quinolone α7 nicotinic acetylcholine receptor agonists. Bioorg. Med.
Chem. Lett. 2013, 23, 1684−1688.
(57) (a) Reck, F.; Alm, R.; Brassil, P.; Newman, J.; Dejonge, B.;
Eyermann, C. J.; Breault, G.; Breen, J.; Comita-Prevoir, J.; Cronin, M.;
Davis, H.; Ehmann, D.; Galullo, V.; Geng, B.; Grebe, T.; Morningstar,
M.; Walker, P.; Hayter, B.; Fisher, S. Novel N-linked aminopiperidine
inhibitors of bacterial topoisomerase type II: broad-spectrum
antibacterial agents with reduced hERG activity. J. Med. Chem. 2011,
54, 7834−7847. (b) Reck, F.; Alm, R. A.; Brassil, P.; Newman, J. V.;
Ciaccio, P.; McNulty, J.; Barthlow, H.; Goteti, K.; Breen, J.; Comita-
Prevoir, J.; Cronin, M.; Ehmann, D. E.; Geng, B.; Godfrey, A. A.; Fisher,
S. L. Novel N-linked aminopiperidine inhibitors of bacterial topoisomer-
ase type II with reduced pKa: antibacterial agents with an improved
safety profile. J. Med. Chem. 2012, 55, 6916−6933. (c) Hameed, P. S.;
Patil, V.; Solapure, S.; Sharma, U.; Madhavapeddi, P.; Raichurkar, A.;
DOI: 10.1021/acs.jmedchem.5b00258
J. Med. Chem. XXXX, XXX, XXX−XXX
Journal of Medicinal Chemistry
Chinnapattu, M.; Manjrekar, P.; Shanbhag, G.; Puttur, J.; Shinde, V.;
Menasinakai, S.; Rudrapatana, S.; Achar, V.; Awasthy, D.; Nandishaiah,
R.; Humnabadkar, V.; Ghosh, A.; Narayan, C.; Ramya, V. K.; Kaur, P.;
Sharma, S.; Werngren, J.; Hoffner, S.; Panduga, V.; Kumar, C. N. N.;
Reddy, J.; Kumar, K. N. M.; Ganguly, S.; Bharath, S.; Bheemarao, U.;
Mukherjee, K.; Arora, U.; Gaonkar, S.; Coulson, M.; Waterson, D.;
Sambandamurthy, V. K.; De Sousa, S. M. Novel N-linked amino-
piperidine-based gyrase inhibitors with improved hERG and in vivo
efficacy against mycobacterium tuberculosis. J. Med. Chem. 2014, 57,
4889−4905.
(58) Hanessian, S.; Saavedra, O. M.; Vilchis-Reyes, M. A.; Maianti, J. P.;
Kanazawa, H.; Dozzo, P.; Matias, R. D.; Serio, A.; Kondo, J. Synthesis,
broad spectrum antibacterial activity, and X-ray co-crystal structure of
the decoding bacterial ribosomal A-site with 4′-deoxy-4′-fluoro
neomycin analogs. Chem. Sci. 2014, 5, 4621−4632.
(59) Maianti, J. P.; Kanazawa, H.; Dozzo, P.; Matias, R. D.; Feeney, L.
A.; Armstrong, E. S.; Hildebrandt, D. J.; Kane, T. R.; Gliedt, M. J.;
Goldblum, A. A.; Linsell, M. S.; Aggen, J. B.; Kondo, J.; Hanessian, S.
Toxicity modulation, resistance enzyme evasion, and A-site X-ray
structure of broad-spectrum antibacterial neomycin analogs. ACS Chem.
Biol. 2014, 9, 2067−2073.
(60) (a) Hansch, C.; Leo, A.; Unger, S. H.; Kim, K. H.; Nikaitani, D.;
Lien, E. J. Aromatic substituent constants for structure-activity
correlations. J. Med. Chem. 1973, 16, 1207−1216. (b) Hansch, C.;
Leo, A.; Taft, R. W. A survey of Hammett substituent constants and
resonance and field parameters. Chem. Rev. 1991, 91, 165−195.
(c) Iwasa, J.; Fujita, T.; Hansch, C. Substituent constants for aliphatic
functions obtained from partition coefficients. J. Med. Chem. 1965, 8,
150−153.
(61) (a) Rouxel, C.; Le Droumaguet, C.; Macé, Y.; Clift, S.; Mongin,
O.; Magnier, E.; Blanchard-Desce, M. Octupolar derivatives function-
alized with superacceptor peripheral groups: synthesis and evaluation of
the electron-withdrawing ability of potent unusual groups. Chem.Eur.
J. 2012, 18, 12487−12497. (b) Yagupolskii, L. M. Aromatic compounds
with new fluorine-containing substituents. J. Fluorine Chem. 1987, 36,
1−28. (c) Altomonte, S.; Zanda, M. Synthetic chemistry and biological
activity of pentafluorosulphanyl (SF5) organic molecules. J. Fluorine
Chem. 2012, 143, 57−93.
(62) (a) Park, B. K.; Kitteringham, N. R.; O’Neill, P. M. Metabolism of
fluorine-containing drugs. Annu. Rev. Pharmacool. Toxicol. 2001, 41,
443−470. (b) Gleeson, P.; Bravi, G.; Modi, S.; Lowe, D. ADMET rules
of thumb II: a comparison of the effects of common substituents on a
range of ADMET parameters. Bioorg. Med. Chem. 2009, 17, 5906−5919.
(c) Dossetter, A. G. A statistical analysis of in vitro human microsomal
metabolic stability of small phenyl group substituents, leading to
improved design sets for parallel SAR exploration of a chemical series.
Bioorg. Med. Chem. 2010, 18, 4405−4414.
(63) Qiu, J.; Stevenson, S. H.; O’Beirne, M. J.; Silverman, R. B. 2,6-
Difluorophenol as a bioisostere of a carboxylic acid: bioisosteric
analogues of γ-aminobutyric acid. J. Med. Chem. 1999, 42, 329−332.
(64) (a) Nicolaou, I.; Zika, C.; Demopoulos, V. J. [1-(3,5-Difluoro-4-
hydroxyphenyl)-1H-pyrrol-3-yl]phenylmethanone as a bioisostere of a
carboxylic acid aldose reductase inhibitor. J. Med. Chem. 2004, 47,
2706−2709. (b) Alexiou, P.; Demopoulos, V. J. A diverse series of
substituted benzenesulfonamides as aldose reductase inhibitors with
antioxidant activity: design, synthesis, and in vitro activity. J. Med. Chem.
2010, 53, 7756−7766. (c) Kotsampasakou, E.; Demopoulos, V. J.
Synthesis of derivatives of the keto-pyrrolyl-difluorophenol scaffold:
some structural aspects for aldose reductase inhibitory activity and
selectivity. Bioorg. Med. Chem. 2013, 21, 869−873.
(65) (a) Bey, E.; Marchais-Oberwinkler, S.; Kruchten, P.; Frotscher,
M.; Werth, R.; Oster, A.; Algül, O.; Neugebauer, A.; Hartmann, R. W.
Design, synthesis and biological evaluation of bis(hydroxyphenyl) azoles
as potent and selective non-steroidal inhibitors of 17β-hydroxysteroid
dehydrogenase type 1 (17β-HSD1) for the treatment of estrogen-
dependent diseases. Bioorg. Med. Chem. 2008, 16, 6423−6435. (b) Bey,
E.; Marchais-Oberwinkler, S.; Negri, M.; Kruchten, P.; Oster, A.; Klein,
T.; Spadaro, A.; Werth, R.; Frotscher, M.; Birk, B.; Hartmann, R. W.
New insights into the SAR and binding modes of bis(hydroxyphenyl)-
AM
Perspective
thiophenes and -benzenes: influence of additional substituents on 17β-
hydroxysteroid dehydrogenase type 1 (17β-HSD1) inhibitory activity
and selectivity. J. Med. Chem. 2009, 52, 6724−6743. (c) Bey, E.;
Marchais-Oberwinkler, S.; Werth, R.; Negri, M.; Al-Soud, Y. A.;
Kruchten, P.; Oster, A.; Frotscher, M.; Birk, B.; Hartmann, R. W. Design,
synthesis, biological evaluation and pharmacokinetics of bis-
(hydroxyphenyl) substituted azoles, thiophenes, benzenes, and aza-
benzenes as potent and selective nonsteroidal inhibitors of 17β-
hydroxysteroid dehydrogenase type 1 (17β-HSD1). J. Med. Chem. 2008,
51, 6725−6739.
(66) (a) Kirk, K. L. Selective fluorination in drug design and
development: an overview of biochemical rationales. Curr. Top. Med.
Chem. 2006, 6, 1447−1456. (b) Lou, Y.; Sweeney, Z. K.; Kuglstatter, A.;
Davis, D.; Goldstein, D. M.; Han, X.; Hong, J.; kocer, B.; Kondru, R. K.;
Litman, R.; McIntosh, J.; Sarma, K.; Suh, J.; Taygerly, J.; Owens, T. D.
Finding the perfect spot for fluorine: improving potency up to 40-fold
during a rational fluorine scan of Bruton’s tyrosine kinase (BTK)-
inhibitor scaffold. Bioorg. Med. Chem. Lett. 2015, 25, 367−371. (c) Deng,
X.; Kokkonda, S.; El Mazouni, F.; White, J.; Burrows, J. N.; Kaminsky,
W.; Charman, S. A.; Matthews, D.; Rathod, P. K.; Phillips, M. A.
Fluorine modulates species selectivity in the triazolopyrimidine class of
Plasmodium falciparum didhydroorotate dehydrogenase inhibitors. J.
Med. Chem. 2014, 57, 5381−5394. (d) Boehringer, M.; Fischer, H.;
Hennig, M.; Hunziker, D.; Huwyler, J.; Kuhn, B.; Loeffer, B. M.;
Luebbers, T.; Mattei, P.; Narquizian, R.; Sebokova, E.; Sprecher, U.;
Wessel, H. P. Aryl- and heteroaryl-substituted aminobenzo[a]-
quinolizines as dipeptidyl peptidase IV inhibitors. Bioorg. Med. Chem.
Lett. 2010, 20, 1106−1108.
(67) (a) Mayer, T. U.; Kapoor, T. M.; Haggarty, S. J.; King, R. W.;
Schreiber, S. L.; Mitchison, T. J. Small molecule inhibitor of mitotic
spindle bipolarity identified in a phenotype-based screen. Science 1999,
286, 971−974. (b) Maliga, Z.; Kapoor, T. M.; Mitchison, T. J. Evidence
that monastrol is an allosteric inhibitor of the mitotic kinesin Eg5. Chem.
Biol. 2002, 9, 989−996.
(68) (a) Kristal Kaan, H. Y.; Ulaganathan, V.; Rath, O.; Prokopcová,
H.; Dallinger, D.; Kappe, C. O.; Kozielski, F. Structural basis for
inhibition of Eg5 by dihydropyrimidines: stereoselectivity of antimitotic
inhibitors enastron, dimethylenastron and fluorastrol. J. Med. Chem.
2010, 53, 5676−5683. (b) Prokopcová, H.; Dallinger, D.; Uray, G.;
Kaan, H. Y. K.; Ulaganathan, V.; Kozielski, F.; Laggner, C.; Kappe, C. O.
Structure-activity relationships and molecular docking of novel
dihydropyrimidine-based mitotic Eg5 inhibitors. ChemMedChem
2010, 5, 1760−1769.
(69) Garcia-Saez, I.; DeBonis, S.; Lopez, R.; Trucco, F.; Rousseau, B.;
Thuéry, P.; Kozielski, F. Structure of human Eg5 in complex with a new
monastrol-based inhibitor bound in the R configuration. J. Biol. Chem.
2007, 282, 9740−9747.
(70) (a) Olsen, J. A.; Banner, D. W.; Seiler, P.; Sander, U. O.; D’Arcy,
A.; Stihle, M.; Müller, K.; Diederich, F. A fluorine scan of thrombin
inhibitors to map the fluorophilicity/fluorophobicity of an enzyme
active site: evidence for C-F···CO interactions. Angew. Chem., Int. Ed.
2003, 42, 2507−2511. (b) Olsen, J. A.; Banner, D. W.; Seiler, P.;
Wagner, B.; Tschopp, T.; Obst-Sander, U.; Kansy, M.; Müller, K.;
Diederich, F. Fluorine interactions at the thrombin active site: protein
backbone fragments H-Cα-CO comprise a favorable C-F environ-
ment and interactions of C-F with electrophiles. ChemBioChem 2004, 5,
666−675. (c) Hof, F.; Scofield, D. M.; Schweizer, W. B.; Diederich, F. A
weak attractive interaction between organic fluorine and an amide
group. Angew. Chem., Int. Ed. 2004, 43, 5056−5059. (d) Schweizer, E.;
Hoffmann-Röder, A.; Olsen, J. A.; Seiler, P.; Obst-Sander, U.; Wagner,
B.; Kansy, M.; Banner, D. W.; Diederich, F. Multipolar interactions in
the D pocket of thrombin: large differences between tricyclic imide and
lactam inhibitors. Org. Biomol. Chem. 2006, 4, 2364−2375.
(71) (a) Van Den Berg, J. A.; Seddon, K. R. Critical evaluation of C-H···
X hydrogen bonding in the crystalline state. Cryst. Growth Des. 2003, 3,
643−661. (b) Carosati, E.; Sciabola, S.; Cruciani, G. Hydrogen bonding
interactions of covalently bonded fluorine atoms: from crystallographic
data to a new angular function in the GRID force field. J. Med. Chem.
2004, 47, 5114−5125. (c) D’Oria, E.; Novoa, J. J. On the hydrogen bond
DOI: 10.1021/acs.jmedchem.5b00258
J. Med. Chem. XXXX, XXX, XXX−XXX
Journal of Medicinal Chemistry
nature of the C-HF interactions in molecular crystals. An exhaustive
investigation combining a crystallographic database search and ab initio
theoretical calculations. CrystEngComm 2008, 10, 423−436. (d) Zhou,
P.; Zou, J.; Tian, F.; Shang, Z. Fluorine bondingHow does it work in
protein-ligand interactions? J. Chem. Inf. Model. 2009, 49, 2344−2355.
(72) (a) Ouvrard, C.; Berthelot, M.; Laurence, C. The first basicity
scale of fluoro-, chloro-, bromo- and iodo-alkanes: some cross-
comparisons with simple alkyl derivatives of other elements. J. Chem.
Soc., Perkin Trans. 2 1999, 1357−1362. (b) Laurence, C.; Berthelot, M.
Observations on the strength of hydrogen bonding. Perspect. Drug
Discovery Des. 2000, 18, 39−60. (c) Laurence, C.; Brameld, K. A.;
Graton, J.; Le Questel, J. Y.; Renault, E. The pKBHX database: toward a
better understanding of hydrogen-bond basicity for medicinal chemists.
J. Med. Chem. 2009, 52, 4073−4086.
(73) (a) Dunitz, J. D.; Gavezzotti, A. Molecular recognition in organic
crystals: directed intermolecular bonds or nonlocalized bonding? Angew.
Chem., Int. Ed. 2005, 44, 1766−1787. (b) Joseph, J.; Jemmis, E. D. Red-,
blue-, or no-shift in hydrogen bondsa unified explanation. J. Am.
Chem. Soc. 2007, 129, 4620−4632. (c) Cormanich, R. A.; Moreira, M.
A.; Freitas, M. P.; Ramalho, T. C.; Anconi, C. P. A.; Rittner, R.;
Contreras, R. H.; Tormena, C. F. 1hJFH coupling in 2-fluorophenol
revisited: is intramolecular hydrogen bond responsible for this long-
range coupling? Magn. Reson. Chem. 2011, 49, 763−767. (d) Fonseca, T.
A. O.; Ramalho, T. C.; Freitas, M. P. F···HO intramolecular hydrogen
bond as the main transmission mechanism for 1hJF,H(O) coupling
constant in 2′-fluoroflavonol. Magn. Reson. Chem. 2012, 50, 551−556.
(e) Struble, M. D.; Strull, J.; Patel, K.; Siegler, M. A.; Lectka, T.
Modulating “jousting” C−F···H−C interactions with a bit of hydrogen
bonding. J. Org. Chem. 2014, 79, 1−6. (f) Struble, M. D.; Kelly, C.;
Siegler, M. A.; Lectka, T. Search for a strong, virtually “no-shift”
hydrogen bond: a cage molecule with an exceptional OH···F interaction.
Angew. Chem., Int. Ed. 2014, 53, 8924−8928.
(74) (a) Parlow, J. J.; Stevens, A. M.; Stegeman, R. A.; Stallings, W. C.;
Kurumbail, R. G.; South, M. S. Synthesis and crystal structures of
substituted benzenes and benzoquinones as tissue factor VIIa inhibitors.
J. Med. Chem. 2003, 46, 4297−4312. (b) Parlow, J. J.; Kurumbail, R. G.;
Stegeman, R. A.; Stevens, A. M.; Stallings, W. C.; South, M. S. Design,
synthesis, and crystal structure of selective 2-pyridone tissue factor VIIa
inhibitors. J. Med. Chem. 2003, 46, 4696−4701. (c) Parlow, J. J.;
Kurumbail, R. G.; Stegeman, R. A.; Stevens, A. M.; Stallings, W. C.;
South, M. S. Synthesis and X-ray crystal structures of substituted
fluorobenzene and benzoquinone inhibitors of the tissue factor VIIa
complex. Bioorg. Med. Chem. Lett. 2003, 13, 3721−3725.
(75) (a) Maryanoff, B. E.; McComsey, D. F.; Costanzo, M. J.; Yabut, S.
C.; Lu, T.; Player, M. R.; Giardino, E. C.; Damiano, B. P. Exploration of
potential prodrugs of RWJ-445167, an oxyguanidine-based dual
inhibitor of thrombin and factor Xa. Chem. Biol. Drug Des. 2006, 68,
29−36. (b) Lee, L.; Kreutter, K. D.; Pan, W.; Crysler, C.; Spurlino, J.;
Player, M. R.; Tomczuk, B.; Lu, T. 2-(2-Chloro-6-fluorophenyl)-
acetamides as potent thrombin inhibitors. Bioorg. Med. Chem. Lett. 2007,
17, 6266−6269. (c) Kreutter, K. D.; Lu, T.; Lee, L.; Giardino, E. C.;
Patel, S.; Huang, H.; Xu, G.; Fitzgerald, M.; Haertlein, B. J.; Mohan, V.;
Crysler, C.; Eisennagel, S.; Dasgupta, M.; McMillan, M.; Spurlino, J. C.;
Huebert, N. D.; Maryanoff, B. E.; Tomczuk, B. E.; Damiano, B. P.;
Player, M. R. Orally efficacious thrombin inhibitors with cyanofluor-
ophenylacetamide as the P2 motif. Bioorg. Med. Chem. Lett. 2008, 18,
2865−2870. (d) Burgey, C. S.; Robinson, K. A.; Lyle, T. A.; Sanderson,
P. E. J.; Lewis, S. D.; Lucas, B. J.; Krueger, J. A.; Singh, R.; Miller-Stein,
C.; White, R. B.; Wong, B.; Lyle, E. A.; Williams, P. D.; Coburn, C. A.;
Dorsey, B. D.; Barrow, J. C.; Stranieri, M. T.; Holahan, M. A.; Sitko, G.
R.; Cook, J. J.; McMasters, D. R.; McDonough, C. M.; Sanders, W. M.;
Wallace, A. A.; Clayton, F. C.; Bohn, D.; Leonard, Y. M.; Detwiler, T. J.,
Jr.; Lynch, J. J., Jr.; Yan, Y.; Chen, Z.; Kuo, L.; Gardell, S. J.; Shafer, J. A.;
Vacca, J. P. Metabolism-directed optimization of 3-aminopyrazinone
acetamide thrombin inhibitors. Development of an orally bioavailable
series containing P1 and P3 pyridines. J. Med. Chem. 2003, 46, 461−473.
(76) Lee, Y. K.; Parks, D. J.; Lu, T.; Thieu, T. V.; Markotan, T.; Pan, W.;
McComsey, D. F.; Milkiewicz, K. L.; Crysler, C. S.; Ninan, N.; Abad, M.
C.; Giardino, E. C.; Maryanoff, B. E.; Damiano, B. P.; Player, M. R. 7-
AN
Perspective
Fluoroindazoles as potent and selective inhibitors of factor Xa. J. Med.
Chem. 2008, 51, 282−297.
(77) Anilkumar, G. N.; Lesburg, C. A.; Selyutin, O.; Rosenblum, S. B.;
Zeng, Q.; Jiang, Y.; Chan, T. Y.; Pu, H.; Vaccaro, H.; Wang, L.; Bennett,
F.; Chen, K. X.; Duca, J.; Gavalas, S.; Huang, Y.; Pinto, P.; Sannigrahi,
M.; Velazquez, F.; Venkatraman, S.; Vibulbhan, B.; Agrawal, S.;
Butkiewicz, N.; Feld, B.; Ferrari, E.; He, Z.; Jiang, C. K.; Palermo, R.
E.; McMonagle, P.; Huang, H. C.; Shih, N. Y.; Njoroge, G.; Kozlowski, J.
A. I. Novel HCV NS5B polymerase inhibitors: discovery of indole 2-
carboxylic acids with C3-heterocycles. Bioorg. Med. Chem. Lett. 2011, 21,
5336−5341.
(78) (a) Ohren, J. F.; Chen, H.; Pavlovsky, A.; Whitehead, C.; Zhang,
E.; Kuffa, P.; Yan, C.; McConnell, P.; Spessard, C.; Banotai, C.; Mueller,
W. T.; Delaney, A.; Omer, C.; Sebolt-Leopold, J.; Dudley, D. T.; Leung,
I. K.; Flamme, C.; Warmus, J.; Kaufman, M.; Barrett, S.; Tecle, H.;
Hasemann, C. A. Structures of human MAP kinase kinase 1 (MEK1)
and MEK2 describe novel noncompetitive kinase inhibition. Nat. Struct.
Mol. Biol. 2004, 11, 1192−1197. (b) Wallace, M. B.; Adams, M. E.;
Kanouni, T.; Mol, C. D.; Dougan, D. R.; Feher, V. A.; O’Connell, S. M.;
Shi, L.; Halkowycz, P.; Dong, Q. Structure-based design and synthesis of
pyrrole derivatives as MEK inhibitors. Bioorg. Med. Chem. Lett. 2010, 20,
4156−4158. (c) Adams, M. E.; Wallace, M. B.; Kanouni, T.; Scorah, N.;
O’Connell, S. M.; Miyake, H.; Shi, L.; Halkowycz, P.; Zhang, L.; Dong,
Q. Design and synthesis of orally available MEK inhibitors with potent
in vivo antitumor efficacy. Bioorg. Med. Chem. Lett. 2012, 22, 2411−
2414. (d) Isshiki, Y.; Kohchi, Y.; Iikura, H.; Matsubara, Y.; Asoh, K.;
Murata, T.; Kohchi, M.; Mizuguchi, E.; Tsujii, S.; Hattori, K.; Miura, T.;
Yoshimura, Y.; Aida, S.; Miwa, M.; Saitoh, R.; Murao, N.; Okabe, H.;
Belunis, C.; Janson, C.; Lukacs, C.; Schück, V.; Shimma, N. Design and
synthesis of novel allosteric MEK inhibitor CH4987655 as an orally
available anticancer agent. Bioorg. Med. Chem. Lett. 2011, 21, 1795−
1801.
(79) Razgulin, A. V.; Mecozzi, S. Binding properties of aromatic
carbon-bound fluorine. J. Med. Chem. 2006, 49, 7902−7906.
(80) (a) Kim, D.; Wang, L.; Beconi, M.; Eiermann, G. J.; Fisher, M. H.;
He, H.; Hickey, G. J.; Kowalchick, J. E.; Leiting, B.; Lyons, K.; Marsilio,
F.; McCann, M. E.; Patel, R. A.; Petrov, A.; Scapin, G.; Patel, S. B.; Sinha
Roy, R.; Wu, J. K.; Wyvratt, M. J.; Zhang, B. B.; Zhu, L.; Thornberry, N.
A.; Weber, A. E. (2R)-4-Oxo-4-[3-(trifluoromethyl)-5,6-dihydro[1,2,4]-
triazolo[4,3-a]pyrazin-7(8H)-yl]-1-(2,4,5-trifluorophenyl)butan-2-
amine: a potent, orally active dipeptidyl peptidase IV inhibitor for the
treatment of type 2 diabetes. J. Med. Chem. 2005, 48, 141−151.
(b) Thornberry, N. A.; Weber, A. E. Discovery of JANUVIA
(sitagliptin), a selective dipeptidyl peptidase IV inhibitor for the
treatment of type 2 diabetes. Curr. Top. Med. Chem. 2007, 7, 557−568.
(c) Kim, D.; Kowalchick, J. E.; Brockunier, L. L.; Parmee, E. R.;
Eiermann, G. J.; Fisher, M. H.; He, H.; Leiting, B.; Lyons, K.; Scapin, G.;
Patel, S. B.; Petrov, A.; Pryor, K. D.; Sinha Roy, R.; Wu, J. K.; Zhang, X.;
Wyvratt, M. J.; Zhang, B. B.; Zhu, L.; Thornberry, N. A.; Weber, A. E.
Discovery of potent and selective dipeptidyl peptidase IV inhibitors
derived from β-aminoamides bearing substituted triazolopiperidines. J.
Med. Chem. 2008, 51, 589−602. (d) Xu, J.; Wei, L.; Mathvink, R. J.;
Edmondson, S. D.; Eiermann, G. J.; He, H.; Leone, J. F.; Leiting, B.;
Lyons, K. A.; Marsilio, F.; Patel, R. A.; Patel, S. B.; Petrov, A.; Scapin, G.;
Wu, J. K.; Thornberry, N. A.; Weber, A. E. Discovery of potent, selective,
and orally bioavailable oxadiazole-based dipeptidyl peptidase IV
inhibitors. Bioorg. Med. Chem. Lett. 2006, 16, 5373−5377. (e) Edmond-
son, S. D.; Wei, L.; Xu, J.; Shang, J.; Xu, S.; Pang, J.; Chaudhary, A.; Dean,
D. C.; He, H.; Leiting, B.; Lyons, K. A.; Patel, R. A.; Patel, S. B.; Scapin,
G.; Wu, J. K.; Beconi, M. G.; Thornberry, N. A.; Weber, A. E.
Fluoroolefins as amide bond mimics in dipeptidyl peptidase IV
inhibitors. Bioorg. Med. Chem. Lett. 2008, 18, 2409−2413. (f) Biftu,
T.; Feng, D.; Qian, X.; Liang, G.-B.; Kieczykowski, G.; Eiermann, G.; He,
H.; Leiting, B.; Lyons, K.; Petrov, A.; Sinha-Roy, R.; Zhang, B.; Scapin,
G.; Patel, S.; Gao, Y.-D.; Singh, S.; Wu, J.; Zhang, X.; Thornberry, N. A.;
Weber, A. E. (3R)-4-[(3R)-3-Amino-4-(2,4,5-trifluorophenyl)-
butanoyl]-3-(2,2,2-trifluoroethyl)-1,4-diazepan-2-one, a selective dipep-
tidyl peptidase IV inhibitor for the treatment of type 2 diabetes. Bioorg.
Med. Chem. Lett. 2007, 17, 49−52. (g) Liang, G.-B.; Qian, X.; Feng, D.;
DOI: 10.1021/acs.jmedchem.5b00258
J. Med. Chem. XXXX, XXX, XXX−XXX
Journal of Medicinal Chemistry
Biftu, T.; Eiermann, G.; He, H.; Leiting, B.; Lyons, K.; Petrov, A.; Sinha-
Roy, R.; Zhang, B.; Wu, J.; Zhang, X.; Thornberry, N. A.; Weber, A. E.
Optimization of 1,4-diazepan-2-one containing dipeptidyl peptidase IV
inhibitors for the treatment of type 2 diabetes. Bioorg. Med. Chem. Lett.
2007, 17, 1903−1907. (h) Liang, G.-B.; Qian, X.; Biftu, T.; Singh, S.;
Gao, Y.-D.; Scapin, G.; Patel, S.; Leiting, B.; Patel, R.; Wu, J.; Zhang, X.;
Thornberry, N. A.; Weber, A. E. Discovery of new binding elements in
DPP-4 inhibition and their applications in novel DPP-4 inhibitor design.
Bioorg. Med. Chem. Lett. 2008, 18, 3706−3710. (i) Biftu, T.; Scapin, G.;
Singh, S.; Feng, D.; Becker, J. W.; Eiermann, G.; He, H.; Lyons, K.; Patel,
S.; Petrov, A.; Sinha-Roy, R.; Zhang, B.; Wu, J.; Zhang, X.; Doss, G. A.;
Thornberry, N. A.; Weber, A. E. Rational design of a novel, potent, and
orally bioavailable DPP-4 inhibitor by application of molecular modeling
and X-ray crystallography of sitagliptin. Bioorg. Med. Chem. Lett. 2007,
17, 3384−3387. (j) Gao, Y.-D.; Feng, D.; Sheridan, R. P.; Scapin, G.;
Patel, S. B.; Wu, J. K.; Zhang, X.; Sinha-Roy, R.; Thornberry, N. A.;
Weber, A. E.; Biftu, T. Modeling assisted rational design of novel, potent,
and selective pyrrolopyrimidine DPP-4 inhibitors. Bioorg. Med. Chem.
Lett. 2007, 17, 3877−3879. (k) Biftu, T.; Qian, X.; Chen, P.; Feng, D.;
Scapin, G.; Gao, Y.-D.; Cox, J.; Sinha Roy, R.; Eiermann, G.; He, H.;
Lyons, K.; Salituro, G.; Patel, S.; Petrov, A.; Xu, F.; Xu, S. S.; Zhang, B.;
Caldwell, C.; Wu, J. K.; Lyons, K.; Weber, A. E. Novel tetrahydropyran
analogs as dipeptidyl peptidase IV inhibitors: profile of clinical candidate
(2R,3S,5R)-2-(2,5-difluorophenyl)-5-[2-(methylsulfonyl)-2,6-
dihydropyrrolo[3,4-c]pyrazol-5(4H)-yl]tetrahydro-2H-pyran-3-amine
(23). Bioorg. Med. Chem. Lett. 2013, 23, 5361−5366. (l) Biftu, T.; Sinha-
Roy, R.; Chen, P.; Qian, X.; Feng, D.; Kuethe, J. T.; Scapin, G.; Gao, Y.
D.; Yan, Y.; Krueger, D.; Bak, A.; Eiermann, G.; He, J.; Cox, J.; Hicks, J.;
Lyons, K.; He, H.; Salituro, G.; Tong, S.; Patel, S.; Doss, G.; Petrov, A.;
Wu, J.; Xu, S. S.; Sewall, C.; Zhang, X.; Zhang, B.; Thornberry, N. A.;
Weber, A. E. Omarigliptin (MK-3102): a novel long-acting DPP-4
inhibitor for once-weekly treatment of type 2 diabetes. J. Med. Chem.
2014, 57, 3205−3212. (m) Kim, D.; Kowalchick, J. E.; Edmondson, S.
D.; Mastracchio, A.; Xu, J.; Eiermann, G. J.; Leiting, B.; Wu, J. K.; Pryor,
K. D.; Patel, R. A.; He, H.; Lyons, K. A.; Thornberry, N. A.; Weber, A. E.
Triazolopiperazine-amides as dipeptidyl peptidase IV inhibitors: close
analogs of JANUVIA (sitagliptin phosphate). Bioorg. Med. Chem. Lett.
2007, 17, 3373−3377.
(81) Dubowchik, G. M.; Vrudhula, V. M.; Dasgupta, B.; Ditta, J.; Chen,
T.; Sheriff, S.; Sipman, K.; Witmer, M.; Tredup, J.; Vyas, D. M.;
Verdoorn, T. A.; Bollini, S.; Vinitsky, A. 2-Aryl-2,2-difluoroacetamide
FKBP12 ligands: synthesis and X-ray structural studies. Org. Lett. 2001,
3, 3987−3990.
(82) Harper, D. B.; O’Hagan, D. The fluorinated natural products. Nat.
Prod. Rep. 1994, 11, 123−133.
(83) Lauble, H.; Kennedy, M. C.; Emptage, M. H.; Beinert, H.; Stout,
C. D. The reaction of fluorocitrate with aconitase and the crystal
structure of the enzyme-inhibitor complex. Proc. Natl. Acad. Sci. U.S.A.
1996, 93, 13699−13703.
(84) (a) Weeks, A. M.; Chang, M. C. Y. Catalytic control of enzymatic
fluorine specificity. Proc. Natl. Acad. Sci. U.S.A. 2012, 109, 19667−
19672. (b) Weeks, A. M.; Keddie, N. S.; Wadoux, R. D. P.; O’Hagan, D.;
Chang, M. C. Y. Molecular recognition of fluorine impacts substrate
selectivity in the fluoroacetyl-CoA thioesterase FlK. Biochemistry 2014,
53, 2053−2063.
(85) Fagerholm, U. The role of permeability in drug ADME/PK,
interactions and toxicity, and the permeability-based classification system
(PCS). Burger’s Medicinal Chemistry and Drug Discovery, 7th ed.;
Abraham, D. J.; Rotella, D. P., Eds.; Wiley: New York, 2010; pp 367−380.
(86) Lennernäs, H.; Abrahamsson, B. The use of biopharmaceutic
classification of drugs in drug discovery and development: current status
and future extension. J. Pharm. Pharmacol. 2005, 57, 273−285.
(87) (a) Smart, B. E. Fluorine substituent effects (on bioactivity). J.
Fluorine Chem. 2001, 109, 3−11. (b) Huchet, Q. A.; Kuhn, B.; Wagner,
B.; Fischer, H.; Kansy, M.; Zimmerli, D.; Carreira, E. M.; Müller, K. On
the polarity of partially fluorinated methyl groups. J. Fluorine Chem.
2013, 152, 119−128.
(88) (a) Pinto, D. J. P.; Orwat, M. J.; Wang, S.; Fevig, J. M.; Quan, M.
L.; Amparo, E.; Cacciola, J.; Rossi, K. A.; Alexander, R. S.; Smallwood, A.
AO
Perspective
M.; Luettgen, J. M.; Liang, L.; Aungst, B. J.; Wright, M. R.; Knabb, R. M.;
Wong, P. C.; Wexler, R. R.; Lam, P. Y. S. Discovery of 1-[3-
(aminomethyl)phenyl]-N-[3-fluoro-2′-(methylsulfonyl)-[1,1′-biphen-
yl]-4-yl]-3-(trifluoromethyl)-1H-pyrazole-5-carboxamide (DPC423), a
highly potent, selective, and orally bioavailable inhibitor of blood
coagulation factor Xa. J. Med. Chem. 2001, 44, 566−578. (b) Quan, M.
L.; Lam, P. Y. S.; Han, Q.; Pinto, D. J. P.; He, M. Y.; Li, R.; Ellis, C. D.;
Clark, C. G.; Teleha, C. A.; Sun, J. H.; Alexander, R. S.; Bai, S.; Luettgen,
J. M.; Knabb, R. M.; Wong, P. C.; Wexler, R. R. Discovery of 1-(3′-
aminobenzisoxazol-5′-yl)-3-trifluoromethyl-N-[2-fluoro-4-[(2′-
dimethylaminomethyl)imidazol-1-yl]phenyl]-1H-pyrazole-5-carboxya-
mide hydrochloride (razaxaban), a highly potent, selective, and orally
bioavailable factor Xa inhibitor. J. Med. Chem. 2005, 48, 1729−1744.
(89) (a) Chopra, D.; Row, T. N. G. Evaluation of the interchangeability
of C-H and C-F groups: Insights from crystal packing in a series of
isomeric fluorinated benzanilides. CrystEngComm 2008, 10, 54−67.
(b) Nayak, S. K.; Kishore Reddy, M.; Row, T. N. G.; Chopra, D. Role of
Hetero-halogen (F···X, X = Cl, Br, and I) or homo-halogen (X···X, X =
F, Cl, Br, and I) interactions in substituted benzanilides. Cryst. Growth
Des. 2011, 11, 1578−1596.
(90) Kuhn, B.; Mohr, P.; Stahl, M. Intramolecular hydrogen bonding in
medicinal chemistry. J. Med. Chem. 2010, 53, 2601−2611.
(91) (a) Weiss, M. M.; Williamson, T.; Babu-Khan, S.; Bartberger, M.
D.; Brown, J.; Chen, K.; Cheng, Y.; Citron, M.; Croghan, M. D.; Dineen,
T. A.; Esmay, J.; Graceffa, R. F.; Harried, S. S.; Hickman, D.; Hitchcock,
S. A.; Horne, D. B.; Huang, H.; Imbeah-Ampiah, R.; Judd, T.; Kaller, M.
R.; Kreiman, C. R.; La, D. S.; Li, V.; Lopez, P.; Louie, S.; Monenschein,
H.; Nguyen, T. T.; Pennington, L. D.; Rattan, C.; San Miguel, T.;
Sickmier, E. A.; Wahl, R. C.; Wen, P. H.; Wood, S.; Xue, Q.; Yang, B. H.;
Patel, V. F.; Zhong, W. Design and preparation of a potent series of
hydroxyethylamine containing β-secretase inhibitors that demonstrate
robust reduction of central β-amyloid. J. Med. Chem. 2012, 55, 9009−
9024. (b) Dineen, T. A.; Weiss, M. M.; Williamson, T.; Acton, P.; Babu-
Khan, S.; Bartberger, M. D.; Brown, J.; Chen, K.; Cheng, Y.; Citron, M.;
Croghan, M. D.; Dunn, R. T.; Esmay, J.; Graceffa, R. F.; Harried, S. S.;
Hickman, D.; Hitchcock, S. A.; Horne, D. B.; Huang, H.; Imbeah-
Ampiah, R.; Judd, T.; Kaller, M. R.; Kreiman, C. R.; La, D. S.; Li, V.;
Lopez, P.; Louie, S.; Monenschein, H.; Nguyen, T. T.; Pennington, L.
D.; San Miguel, T.; Sickmier, E. A.; Vargas, H. M.; Wahl, R. C.; Wen, P.
H.; Whittington, D. A.; Wood, S.; Xue, Q.; Yang, B. H.; Patel, V. F.;
Zhong, W. Design and synthesis of potent, orally efficacious
hydroxyethylamine derived β-site amyloid precursor protein cleaving
enzyme (BACE1) inhibitors. J. Med. Chem. 2012, 55, 9025−9044.
(c) Kaller, M. R.; Harried, S. S.; Albrecht, B.; Amarante, P.; Babu-Khan,
S.; Bartberger, M. D.; Brown, J.; Brown, R.; Chen, K.; Cheng, Y.; Citron,
M.; Croghan, M. D.; Graceffa, R.; Hickman, D.; Judd, T.; Kriemen, C.;
La, D.; Li, V.; Lopez, P.; Luo, Y.; Masse, C.; Monenschein, H.; Nguyen,
T.; Pennington, L. D.; Miguel, T. S.; Sickmier, E. A.; Wahl, R. C.; Weiss,
M. M.; Wen, P. H.; Williamson, T.; Wood, S.; Xue, M.; Yang, B.; Zhang,
J.; Patel, V.; Zhong, W.; Hitchcock, S. A potent and orally efficacious,
hydroxyethylamine-based inhibitor of β-secretase. ACS Med. Chem. Lett.
2012, 3, 886−891.
(92) (a) Hitchcock, S. A. Structural modifications that alter the P-
glycoprotein efflux properties of compounds. J. Med. Chem. 2012, 55,
4877−4895. (b) Desai, P. V.; Raub, T. J.; Blanco, M. J. How hydrogen
bonds impact P-glycoprotein transport and permeability. Bioorg. Med.
Chem. Lett. 2012, 22, 6540−6548.
(93) Kuduk, S. D.; Di Marco, C. N.; Chang, R. K.; Wood, M. R.;
Schirripa, K. M.; Kim, J. J.; Wai, J. M. C.; DiPardo, R. M.; Murphy, K. L.;
Ransom, R. W.; Harrell, C. M.; Reiss, D. R.; Holahan, M. A.; Cook, J.;
Hess, J. F.; Sain, N.; Urban, M. O.; Tang, C.; Prueksaritanont, T.;
Pettibone, D. J.; Bock, M. G. Development of orally bioavailable and
CNS penetrant biphenylaminocyclopropane carboxamide bradykinin
B1 receptor antagonists. J. Med. Chem. 2007, 50, 272−282.
(94) Ettorre, A.; D’Andrea, P.; Mauro, S.; Porcelloni, M.; Rossi, C.;
Altamura, M.; Catalioto, R. M.; Giuliani, S.; Maggi, C. A.; Fattori, D.
HNK2 receptor antagonists. The use of intramolecular hydrogen
bonding to increase solubility and membrane permeability. Bioorg. Med.
Chem. Lett. 2011, 21, 1807−1809.
DOI: 10.1021/acs.jmedchem.5b00258
J. Med. Chem. XXXX, XXX, XXX−XXX
Journal of Medicinal Chemistry
(95) Swahn, B.-M.; Kolmodin, K.; Karlström, S.; von Berg, S.;
Söderman, P.; Holenz, J.; Berg, S.; Lindström, J.; Sundström, M.; Turek,
D.; Kihlström, J.; Slivo, C.; Andersson, L.; Pyring, D.; Rotticci, D.;
Ö hberg, L.; Kers, A.; Bogar, K.; von Kieseritzky, F.; Bergh, M.; Olsson,
L.-L.; Janson, J.; Eketjäll, S.; Georgievska, B.; Jeppsson, F.; Fälting, J.
Design and synthesis of β-site amyloid precursor protein cleaving
enzyme (BACE1) inhibitors with in vivo brain reduction of β-amyloid
peptides. J. Med. Chem. 2012, 55, 9346−9361.
(96) Park, K. B.; Kitteringham, N. R. Effects of fluorine substitution on
drug metabolism: pharmacological and toxicological implications. Drug
Metab. Rev. 1994, 26, 605−643.
(97) Tanaka, H.; Shishido, Y. Synthesis of aromatic compounds
containing a 1,1-dialkyl-2-trifluoromethyl group, a bioisostere of the tert-
alkyl moiety. Bioorg. Med. Chem. Lett. 2007, 17, 6079−6085.
(98) Rowbottom, M. W.; Faraoni, R.; Chao, Q.; Campbell, B. T.; Lai,
A. G.; Setti, E.; Ezawa, M.; Sprankle, K. G.; Abraham, S.; Tran, L.; Struss,
B.; Gibney, M.; Armstrong, R. C.; Gunawardane, R. N.; Nepomuceno,
R. R.; Valenta, I.; Hua, H.; Gardner, M. F.; Cramer, M. D.; Gitnick, D.;
Insko, D. E.; Apuy, J. L.; Jones-Bolin, S.; Ghose, A. K.; Herbertz, T.;
Ator, M. A.; Dorsey, B. D.; Ruggeri, B.; Williams, M.; Bhagwat, S.; James,
J.; Holladay, M. W. Identification of 1-(3-(6,7-dimethoxyquinazolin-4-
yloxy)phenyl)-3-(5-(1,1, 1-trifluoro-2-methylpropan-2-yl)isoxazol-3-
yl)urea hydrochloride (CEP-32496), a highly potent and orally
efficacious inhibitor of V-RAF murine sarcoma viral oncogene
homologue B1 (BRAF) V600E. J. Med. Chem. 2012, 55, 1082−1105.
(99) (a) Barnes-Seeman, D.; Jain, M.; Bell, L.; Ferreira, S.; Cohen, S.;
Chen, X. H.; Amin, J.; Snodgrass, B.; Hatsis, P. Metabolically stable tert-
butyl replacement. ACS Med. Chem. Lett. 2013, 4, 514−516.
(b) Westphal, M. W.; Wolfstädter, B. T.; Plancher, J.-M.; Gatfield, J.;
Carreira, E. M. Evaluation of tert-butyl isosteres: case studies of
physicochemical and pharmacokinetic properties, efficacies, and
activities. ChemMedChem 2015, 10, 461−469.
(100) (a) Black, W. C.; Bayly, C. I.; Davis, D. E.; Desmarais, S.;
Falgueyret, J. P.; Léger, S.; Chun, S. L.; Massé, F.; McKay, D. J.; Palmer,
J. T.; Percival, M. D.; Robichaud, J.; Tsou, N.; Zamboni, R.
Trifluoroethylamines as amide isosteres in inhibitors of cathepsin K.
Bioorg. Med. Chem. Lett. 2005, 15, 4741−4744. (b) Isabel, E.; Mellon, C.;
Boyd, M. J.; Chauret, N.; Deschênes, D.; Desmarais, S.; Falgueyret, J. P.;
Gauthier, J. Y.; Khougaz, K.; Lau, C. K.; Léger, S.; Levorse, D. A.; Li, C.
S.; Massé, F.; David Percival, M.; Roy, B.; Scheigetz, J.; Thérien, M.;
Truong, V. L.; Wesolowski, G.; Young, R. N.; Zamboni, R.; Cameron
Black, W. Difluoroethylamines as an amide isostere in inhibitors of
cathepsin K. Bioorg. Med. Chem. Lett. 2011, 21, 920−923.
(101) Miller, M. M.; Liu, Y.; Jiang, J.; Johnson, J. A.; Kamau, M.;
Nirschl, D. S.; Wang, Y.; Harikrishnan, L.; Taylor, D. S.; Chen, A. Y. A.;
Yin, X.; Seethala, R.; Peterson, T. L.; Zvyaga, T.; Zhang, J.; Huang, C. S.;
Wexler, R. R.; Poss, M. A.; Lawrence, R. M.; Adam, L. P.; Salvati, M. E.
Identification of a potent and metabolically stable series of fluorinated
diphenylpyridylethanamine-based cholesteryl ester transfer protein
inhibitors. Bioorg. Med. Chem. Lett. 2012, 22, 6503−6508.
(102) Zhu, Y.; Olson, S. H.; Graham, D.; Patel, G.; Hermanowski-
Vosatka, A.; Mundt, S.; Shah, K.; Springer, M.; Thieringer, R.; Wright,
S.; Xiao, J.; Zokian, H.; Dragovic, J.; Balkovec, J. M. Phenylcyclobutyl
triazoles as selective inhibitors of 11β-hydroxysteroid dehydrogenase
type I. Bioorg. Med. Chem. Lett. 2008, 18, 3412−3416.
(103) Kerekes, A. D.; Esposite, S. J.; Doll, R. J.; Tagat, J. R.; Yu, T.;
Xiao, Y.; Zhang, Y.; Prelusky, D. B.; Tevar, S.; Gray, K.; Terracina, G. A.;
Lee, S.; Jones, J.; Liu, M.; Basso, A. D.; Smith, E. B. Aurora kinase
inhibitors based on the imidazo[1,2-a]pyrazine core: fluorine and
deuterium incorporation improve oral absorption and exposure. J. Med.
Chem. 2011, 54, 201−210.
(104) Xu, S.; Zhu, B.; Teffera, Y.; Pan, D. E.; Caldwell, C. G.; Doss, G.;
Stearns, R. A.; Evans, D. C.; Beconi, M. G. Metabolic activation of
fluoropyrrolidine dipeptidyl peptidase-IV inhibitors by rat liver
microsomes. Drug Metab. Dispos. 2005, 33, 121−130.
(105) (a) Edmondson, S. D.; Mastracchio, A.; Mathvink, R. J.; He, J.;
Harper, B.; Park, Y. J.; Beconi, M.; Di Salvo, J.; Eiermann, G. J.; He, H.;
Leiting, B.; Leone, J. F.; Levorse, D. A.; Lyons, K.; Patel, R. A.; Patel, S.
B.; Petrov, A.; Scapin, G.; Shang, J.; Roy, R. S.; Smith, A.; Wu, J. K.; Xu,
AP
Perspective
S.; Zhu, B.; Thornberry, N. A.; Weber, A. E. (2S,3S)-3-Amino-4-(3,3-
difluoropyrrolidin-1-yl)-N,N-dimethyl-4-oxo-2-(4-[1,2,4]triazolo[1,5-
a]-pyridin-6-ylphenyl)butanamide: a selective α-amino amide dipep-
tidyl peptidase IV inhibitor for the treatment of type 2 diabetes. J. Med.
Chem. 2006, 49, 3614−3627. (b) Sharma, R.; Sun, H.; Piotrowski, D.
W.; Ryder, T. F.; Doran, S. D.; Dai, H.; Prakash, C. Metabolism,
excretion, and pharmacokinetics of (3,3-difluoropyrrolidin-1- yl)-
((2S,4S)-4-(4-(pyrimidin-2-yl)piperazin-1-yl)pyrrolidin-2-yl)-
methanone, a dipeptidyl peptidase inhibitor, in rat, dog and human.
Drug Metab. Dispos. 2012, 40, 2143−2161.
(106) Tremblay, M.; Bethell, R. C.; Cordingley, M. G.; Deroy, P.;
Duan, J.; Duplessis, M.; Edwards, P. J.; Faucher, A. M.; Halmos, T.;
James, C. A.; Kuhn, C.; Lacoste, J. E.; Lamorte, L.; Laplante, S. R.;
Malenfant, É.; Minville, J.; Morency, L.; Morin, S.; Rajotte, D.; Salois, P.;
Simoneau, B.; Tremblay, S.; Sturino, C. F. Identification of benzofurano-
[3,2-d]pyrimidin-2-ones, a new series of HIV-1 nucleotide-competing
reverse transcriptase inhibitors. Bioorg. Med. Chem. Lett. 2013, 23,
2775−2780.
(107) (a) Irurre, J., Jr.; Casas, J.; Messeguer, A. Resistance to the 2,2,2-
trifluoroethoxy aryl moiety to the cytochrome P-450 metabolism in rat
liver microsomes. Bioorg. Med. Chem. Lett. 1993, 3, 179−182.
(b) Williams, S. J.; Zammit, S. C.; Cox, A. J.; Shackleford, D. M.;
Morizzi, J.; Zhang, Y.; Powell, A. K.; Gilbert, R. E.; Krum, H.; Kelly, D. J.
3′,4′-Bis-difluoromethoxycinnamoylanthranilate (FT061): an orally-
active antifibrotic agent that reduces albuminuria in a rat model of
progressive diabetic nephropathy. Bioorg. Med. Chem. Lett. 2013, 23,
6868−6873.
(108) McQuinn, R. L.; Quarfoth, G. J.; Johnson, J. D. Biotransforma-
tion and elimination of 14C-flecainide acetate in humans. Drug Metab.
Dispos. 1984, 12, 414−420.
(109) (a) Harbeson, S. L.; Tung, R. D. Deuterium in drug discovery
and development. Annu. Rep. Med. Chem. 2011, 46, 403−417. (b) Gant,
T. G. Using deuterium in drug discovery: leaving the label in the drug. J.
Med. Chem. 2014, 57, 3595−3611.
(110) Kalgutkar, A. S.; Gardner, I.; Obach, R. S.; Shaffer, C. L.;
Callegari, E.; Henne, K. R.; Mutlib, A. E.; Dalvie, D. K.; Lee, J. S.; Nakai,
Y.; O’Donnell, J. P.; Boer, J.; Harriman, S. P. A comprehensive listing of
bioactivation pathways of organic functional groups. Curr. Drug Metab.
2005, 6, 161−225.
(111) Bertelsen, K. M.; Venkatakrishnan, K.; Von Moltke, L. L.;
Obach, R. S.; Greenblatt, D. J. Apparent mechanism-based inhibition of
human CYP2D6 in vitro by paroxetine: comparison with fluoxetine and
quinidine. Drug Metab. Dispos. 2003, 31, 289−293.
(112) Rose, W. C.; Marathe, P. H.; Jang, G. R.; Monticello, T. M.;
Balasubramanian, B. N.; Long, B.; Fairchild, C. R.; Wall, M. E.; Wani, M.
C. Novel fluoro-substituted camptothecins: in vivo antitumor activity,
reduced gastrointestinal toxicity and pharmacokinetic characterization.
Cancer Chemother. Pharmacol. 2006, 58, 73−85.
(113) Van Goor, F.; Hadida, S.; Grootenhuis, P. D. J.; Burton, B.; Stack,
J. H.; Straley, K. S.; Decker, C. J.; Miller, M.; McCartney, J.; Olson, E. R.;
Wine, J. J.; Frizzell, R. A.; Ashlock, M.; Negulescu, P. A. Correction of
the F508del-CFTR protein processing defect in vitro by the
investigational drug VX-809. Proc. Natl. Acad. Sci. U.S.A. 2011, 108,
18843−18848.
(114) (a) Trachsel, D.; Hadorn, M.; Baumberger, F. Synthesis of fluoro
analogues of 3,4-(methylenedioxy)amphetamine (MDA) and its
derivatives. Chem. Biodiversity 2006, 3, 326−336. (b) Trachsel, D.
Fluorine in psychedelic phenethylamines. Drug Test. Anal. 2012, 4,
577−590.
(115) Miao, Z.; Zhu, L.; Dong, G.; Zhuang, C.; Wu, Y.; Wang, S.; Guo,
Z.; Liu, Y.; Wu, S.; Zhu, S.; Fang, K.; Yao, J.; Li, J.; Sheng, C.; Zhang, W.
A new strategy to improve the metabolic stability of lactone: discovery of
(20S,21S)-21-fluorocamptothecins as novel, hydrolytically stable
topoisomerase I inhibitors. J. Med. Chem. 2013, 56, 7902−7910.
(116) Savoie, P. R.; Welch, J. T. Preparation and utility of organic
pentafluorosulfanyl-containing compounds. Chem. Rev. 2015, 115,
1130−1190.
DOI: 10.1021/acs.jmedchem.5b00258
J. Med. Chem. XXXX, XXX, XXX−XXX
Journal of Medicinal Chemistry
(117) Craig, P. N. Interdependence between physical parameters and
selection of substituent groups for correlation studies. J. Med. Chem.
1971, 14, 680−684.
(118) (a) Coteron, J. M.; Marco, M.; Esquivias, J.; Deng, X.; White, K.
L.; White, J.; Koltun, M.; El Mazouni, F.; Kokkonda, S.; Katneni, K.;
Bhamidipati, R.; Shackleford, D. M.; Angulo-Barturen, I.; Ferrer, S. B.;
Jiménez-Díaz, M. B.; Gamo, F. J.; Goldsmith, E. J.; Charman, W. N.;
Bathurst, I.; Floyd, D.; Matthews, D.; Burrows, J. N.; Rathod, P. K.;
Charman, S. A.; Phillips, M. A. Structure-guided lead optimization of
triazolopyrimidine-ring substituents identifies potent Plasmodium
falciparum dihydroorotate dehydrogenase inhibitors with clinical
candidate potential. J. Med. Chem. 2011, 54, 5540−5561. (b) Deng,
X.; Kokkonda, S.; El Mazouni, F.; White, J.; Burrows, J. N.; Kaminsky,
W.; Charman, S. A.; Matthews, D.; Rathod, P. K.; Phillips, M. A.
Fluorine modulates species selectivity in the triazolopyrimidine class of
Plasmodium falciparum dihydroorotate dehydrogenase inhibitors. J. Med.
Chem. 2014, 57, 5381−5394.
(119) Altomonte, S.; Baillie, G. L.; Ross, R. A.; Riley, J.; Zanda, M. The
pentafluorosulfanyl group in cannabinoid receptor ligands: synthesis
and comparison with trifluoromethyl and tert-butyl analogues. RSC Adv.
2014, 4, 20164−20176.
(120) Welch, J. T.; Lim, D. S. The synthesis and biological activity of
pentafluorosulfanyl analogs of fluoxetine, fenfluramine, and norfenflur-
amine. Bioorg. Med. Chem. 2007, 15, 6659−6666.
(121) (a) Micheli, F.; Andreotti, D.; Braggio, S.; Checchia, A. A specific
and direct comparison of the trifluoromethyl and pentafluorosulfanyl
groups on the selective dopamine D3 antagonist 3-(3-{[4-methyl-5-(4-
methyl-1,3-oxazol-5-yl)-4H-1,2,4-triazol-3-yl]thio}propyl)-1-phenyl-3-
azabicyclo[3.1.0]hexane template. Bioorg. Med. Chem. Lett. 2010, 20,
4566−4568. (b) Sun, L.; Bera, H.; Chui, W. K. Synthesis of
pyrazolo[1,5-a][1,3,5]triazine derivatives as inhibitors of thymidine
phosphorylase. Eur. J. Med. Chem. 2013, 65, 1−11. (c) Sun, L.; Li, J.;
Bera, H.; Dolzhenko, A. V.; Chiu, G. N. C.; Chui, W. K. Fragment-based
approach to the design of 5-chlorouracil-linked-pyrazolo[1,5-a][1,3,5]-
triazines as thymidine phosphorylase inhibitors. Eur. J. Med. Chem. 2013,
70, 400−410.
(122) Stump, B.; Eberle, C.; Schweizer, W. B.; Kaiser, M.; Brun, R.;
Krauth-Siegel, R. L.; Lentz, D.; Diederich, F. Pentafluorosulfanyl as a
novel building block for enzyme inhibitors: trypanothione reductase
inhibition and antiprotozoal activities of diarylamines. ChemBioChem
2009, 10, 79−83.
(123) (a) Savoie, P. R.; Higashiya, S.; Lin, J. H.; Wagle, D. V.; Welch, J.
T. Conformational impact of pentafluorosulfanylation on acyclic
aliphatic molecules. J. Fluorine Chem. 2012, 143, 281−286. (b) Savoie,
P. R.; Welch, J. M.; Higashiya, S.; Welch, J. T. Control of hydroxyl group
conformation by the pentafluorosulfanyl group. J. Fluorine Chem. 2013,
148, 1−5.
(124) Morgan, P.; Van Der Graaf, P. H.; Arrowsmith, J.; Feltner, D. E.;
Drummond, K. S.; Wegner, C. D.; Street, S. D. A. Can the flow of
medicines be improved? Fundamental pharmacokinetic and pharmaco-
logical principles toward improving phase II survival. Drug Discovery
Today 2012, 17, 419−424.
(125) Mullard, A. Molecular imaging as a de-risking tool: coming into
focus? Nat. Rev. Drug Discovery 2013, 12, 251−252.
(126) (a) Matthews, P. M.; Rabiner, E. A.; Passchier, J.; Gunn, R. N.
Positron emission tomography molecular imaging for drug develop-
ment. Br. J. Clin. Pharmacol. 2012, 73, 175−186. (b) Cook, D.; Brown,
D.; Alexander, R.; March, R.; Morgan, P.; Satterthwaite, G.; Pangalos, M.
N. Lesssons learned from the fate of AstraZeneca’s drug pipeline: a five-
dimensional framework. Nat. Rev. Drug Discovery 2014, 13, 419−431.
(127) Kilbourn, M. R. Fluorine-18 Labeling of Radiopharmaceuticals;
National Academy Press: Washington, DC, 1990.
(128) Van de Bittner, G. C.; Ricq, E. L.; Hooker, J. M. A philosophy for
CNS radiotracer design. Acc. Chem. Res. 2014, 47, 3127−3134.
(129) (a) Liang, T.; Neumann, C. N.; Ritter, T. Introduction of
fluorine and fluorine-containing functional groups. Angew. Chem., Int.
Ed. 2013, 52, 8214−8264. (b) Tredwell, M.; Gouverneur, V. 18F
Labeling of arenes. Angew. Chem., Int. Ed. 2012, 51, 11426−11437.
(c) Pretze, M.; Pietzsch, D.; Mamat, C. Recent trends in bioorthogonal
AQ
Perspective
click-radiolabeling reactions using fluorine-18. Molecules 2013, 18,
8618−8665. (d) Way, J.; Bouvet, V.; Wuest, F. Synthesis of 4-
[18F]fluorohalobenzenes and palladium-mediated cross-coupling reac-
tions for the synthesis of 18F-labeled radiotracers. Curr. Org. Chem. 2013,
17, 2138−2152. (e) Littich, R.; Scott, P. J. H. Novel strategies for
fluorine-18 radiochemistry. Angew. Chem., Int. Ed. 2012, 51, 1106−1109.
(f) Laverman, P.; McBride, W. J.; Sharkey, R. M.; Goldenberg, D. M.;
Boerman, O. C. Al18F labeling of peptides and proteins. J. Labelled
Compd. Radiopharm. 2014, 57, 219−223. (g) Brooks, A. F.; Topczewski,
J. J.; Ichiishi, N.; Sanford, M. S.; Scott, P. J. H. Late-stage
[18F]fluorination: new solutions to old problems. Chem. Sci. 2014, 5,
4545−4553. (h) Cole, E. L.; Stewart, M. N.; Littich, R.; Hoareau, R.;
Scott, P. J. H. Radiosyntheses using fluorine-18: the art and science of
late stage fluorination. Curr. Top. Med. Chem. 2014, 14, 875−900.
(i) Kim, D. W.; Jeong, H.-J.; Lim, S. T.; Sohn, M.-H. Recent trends in the
nucleophilic [18F]-radiolabeling method with no-carrier-added [18F]-
fluoride. Nucl. Med. Mol. Imaging 2010, 44, 25−32. (j) Li, Z.; Conti, P. S.
Radiopharmaceutical chemistry for positron emission tomography. Adv.
Drug Delivery Rev. 2010, 62, 1031−1051. (k) O’Hagan, D.; Deng, H.
Enzymatic fluorination and biotechnological developments of the
fluorinase. Chem. Rev. 2015, 115, 634−649.
(130) Seo, J.-W.; Lee, B.-S.; Lee, S.-J.; Oh, S.-J.; Chi, D.-Y. Fast and easy
drying method for the preparation of activated [18F]fluoride using
polymer cartridge. Bull. Korean Chem. Soc. 2011, 32, 71−76.
(131) Wessmann, S. H.; Henriksen, G.; Wester, H. J. Cryptate-
mediated nucleophilic 18F-fluorination without azeotropic drying.
Nuklearmedizin 2012, 51, 1−8.
(132) (a) Snyder, S. E.; Kilbourn, M. R. Chemistry of fluorine-18 radio-
pharmaceuticals. In Handbook of Radiopharmaceuticals : Radiochemistry
and Applications; Welch, M. J., Redvanly, C. S., Eds.; John Wiley & Sons Ltd.:
New York, 2003; pp 195−227. (b) Bailey, D. L., Townsend, D. W., Valk, P.
E., Maisey, M. N., Eds. Positron Emission Tomography: Basic Sciences;
Springer: New York, 2005.
(133) (a) De Goeij, J. J. M.; Bonardi, M. L. How do we define the
concepts specific activity, radioactive concentration, carrier, carrier-free
and no-carrier-added? J. Radioanal. Nucl. Chem. 2005, 263, 13−18.
(b) Bonardi, M. L.; Birattari, C.; Groppi, F.; Gini, L.; Mainardi, H. S. C.
Cyclotron production and quality control of “high specific activity”
radionuclides in “no-carrier-added” form for radioanalytical applications
in the life sciences. J. Radioanal. Nucl. Chem. 2004, 259, 415−419.
(134) (a) Mick, I.; Myers, J.; Stokes, P. R. A.; Erritzoe, D.; Colasanti, A.;
Bowden-Jones, H.; Clark, L.; Gunn, R. N.; Rabiner, E. A.; Searle, G. E.;
Waldman, A. D.; Parkin, M. C.; Brailsford, A. D.; Nutt, D. J.; Lingford-
Hughes, A. R. Amphetamine induced endogenous opioid release in the
human brain detected with [11C]carfentanil PET: replication in an
independent cohort. Int. J. Neuropsychopharmacol. 2014, 17, 2069−
2074. (b) Kilbourn, M. R.; Hockley, B.; Lee, L.; Sherman, P.; Quesada,
C.; Frey, K. A.; Koeppe, R. A. Positron emission tomography imaging of
(2R,3R)-5-[18F]fluoroethoxybenzovesamicol in rat and monkey brain: a
radioligand for the vesicular acetylcholine transporter. Nucl. Med. Biol.
2009, 36, 489−493. (c) Orbay, H.; Hong, H.; Zhang, Y.; Cai, W.
Positron emission tomography imaging of atherosclerosis. Theranostics
2013, 3, 894−902.
(135) (a) Bergman, J.; Solin, O. Fluorine-18-labeled fluorine gas for
synthesis of tracer molecules. Nucl. Med. Biol. 1997, 24, 677−683.
(b) Bergman, J.; Solin, O. Fluorine-18-labeled fluorine gas for synthesis
of tracer molecules. Nucl. Med. Biol. 1997, 24, 677−683.
(136) Okamura, N.; Furumoto, S.; Harada, R.; Tago, T.; Yoshikawa,
T.; Fodero-Tavoletti, M.; Mulligan, R. S.; Villemagne, V. L.; Akatsu, H.;
Yamamoto, T.; Arai, H.; Iwata, R.; Yanai, K.; Kudo, Y. Novel 18F-labeled
arylquinoline derivatives for noninvasive imaging of tau pathology in
Alzheimer disease. J. Nucl. Med. 2013, 54, 1420−1427.
(137) (a) Watson, D. A.; Su, M.; Teverovskiy, G.; Zhang, Y.; García-
Fortanet, J.; Kinzel, T.; Buchwald, S. L. Formation of ArF from
LPdAr(F): catalytic conversion of aryl triflates to aryl fluorides. Science
2009, 325, 1661−1664. (b) Noël, T.; Maimone, T. J.; Buchwald, S. L.
Accelerating palladium-catalyzed C-F bond formation: use of a
microflow packed-bed reactor. Angew. Chem., Int. Ed. 2011, 50, 8900−
8903. (c) Lee, H. G.; Milner, P. J.; Buchwald, S. L. An improved catalyst
DOI: 10.1021/acs.jmedchem.5b00258
J. Med. Chem. XXXX, XXX, XXX−XXX
Journal of Medicinal Chemistry
system for the Pd-catalyzed fluorination of (hetero)aryl triflates. Org.
Lett. 2013, 15, 5602−5605.
(138) (a) Tang, P.; Wang, W.; Ritter, T. Deoxyfluorination of phenols.
J. Am. Chem. Soc. 2011, 133, 11482−11484. (b) Sladojevich, F.; Arlow, S.
I.; Tang, P.; Ritter, T. Late-stage deoxyfluorination of alcohols with
PhenoFluor. J. Am. Chem. Soc. 2013, 135, 2470−2473.
(139) Chun, J.-H.; Morse, C. L.; Chin, F. T.; Pike, V. W. No-carrier-
added [18F]fluoroarenes from the radiofluorination of diaryl sulfoxides.
Chem. Commun. 2013, 49, 2151−2153.
(140) Ye, Y.; Schimler, S. D.; Hanley, P. S.; Sanford, M. S. Cu(OTf)2-
mediated fluorination of aryltrifluoroborates with potassium fluoride. J.
Am. Chem. Soc. 2013, 135, 16292−16295.
(141) Fier, P. S.; Hartwig, J. F. Copper-mediated fluorination of aryl
iodides. J. Am. Chem. Soc. 2012, 134, 10795−10798.
(142) (a) Ichiishi, N.; Canty, A. J.; Yates, B. F.; Sanford, M. S. Cu-
catalyzed fluorination of diaryliodonium salts with KF. Org. Lett. 2013,
15, 5134−5137. (b) Ichiishi, N.; Brooks, A. F.; Topczewski, J. J.;
Rodnick, M. E.; Sanford, M. S.; Scott, P. J. H. Copper-catalyzed
[18F]fluorination of (mesityl)(aryl)iodonium salts. Org. Lett. 2014, 16,
3224−3227.
(143) Rotstein, B. H.; Stephenson, N. A.; Vasdev, N.; Liang, S. H.
Spirocyclic hypervalent iodine(III)-mediated radiofluorination of non-
activated and hindered aromatics. Nat. Commun. 2014, 5, 4365
DOI: 10.1038/ncomms5365.
(144) Tredwell, M.; Preshlock, S. M.; Taylor, N. J.; Gruber, S.; Huiban,
M.; Passchier, J.; Mercier, J.; Genicot, C.; Gouverneur, V. A general
copper-mediated nucleophilic 18F fluorination of arenes. Angew. Chem.,
Int. Ed. 2014, 53, 7751−7755.
(145) Welch, M. J., Redvanly, C. S.; Eds. Handbook of Radiopharma-
ceuticals: Radiochemistry and Applications; John Wiley & Sons Ltd.: New
York, 2003.
(146) (a) Choi, S. R.; Golding, G.; Zhuang, Z.; Zhang, W.; Lim, N.;
Hefti, F.; Benedum, T. E.; Kilbourn, M. R.; Skovronskyhank, D.; Kung,
H. F. Preclinical properties of 18F-AV-45: a PET agent for Aβ plaques in
the brain. J. Nucl. Med. 2009, 50, 1887−1894. (b) Zhang, W.; Oya, S.;
Kung, M. P.; Hou, C.; Maier, D. L.; Kung, H. F. F-18 stilbenes as PET
imaging agents for detecting β-amyloid plaques in the brain. J. Med.
Chem. 2005, 48, 5980−5988. (c) Wong, D. F.; Rosenberg, P. B.; Zhou,
Y.; Kumar, A.; Raymont, V.; Ravert, H. T.; Dannals, R. F.; Nandi, A.;
Brasic, J. R.; Ye, W.; Hilton, J.; Lyketsos, C.; Kung, H. F.; Joshi, A. D.;
Skovronsky, D. M.; Pontecorvo, M. J. In vivo imaging of amyloid
deposition in Alzheimer disease using the radioligand 18F-AV-45
(flobetapir F 18). J. Nucl. Med. 2010, 51, 913−920. (d) Clark, C. M.;
Schneider, J. A.; Bedell, B. J.; Beach, T. C.; Bilker, W. B.; Mintun, M. A.;
Pontecorvo, M. J.; Hefti, F.; Carpenter, A. P.; Flitter, M. L.;
Krautkramer, M. J.; Kung, H. F.; Coleman, R. E.; Doraiswamy, P. M.;
Fleisher, A. S.; Sabbagh, M. N.; Sadowsky, C. H.; Reiman, P. E. M.;
Zehntner, S. P.; Skovronsky, D. M. Use of florbetapir-PET for imaging
β-amyloid pathology. JAMA, J. Am. Med. Assoc. 2011, 305, 275−283.
(147) Hayashi, K.; Tachibana, A.; Tazawa, S.; Mizukawa, Y.; Osaki, K.;
Morimoto, Y.; Zochi, R.; Kurahashi, M.; Aki, H.; Takahashi, K.
Preparation and stability of ethanol-free solution of [18F]florbetapir
([18F]AV-45) for positron emission tomography amyloid imaging. J.
Labelled Compd. Radiopharm. 2013, 56, 295−300.
(148) (a) Belanger, A. P.; Pandey, M. K.; DeGrado, T. R. Microwave-
assisted radiosynthesis of [18F]fluorinated fatty acid analogs. Nucl. Med.
Biol. 2011, 38, 435−441. (b) Kim, D. W.; Jeong, H. J.; Lim, S. T.; Sohn,
M. H. Recent trends in the nucleophilic [18F]-radiolabeling method with
no-carrier-added [18F]fluoride. Nucl. Med. Mol. Imaging 2010, 44, 25−
32. (c) Kim, D. W.; Ahn, D. S.; Oh, Y. H.; Lee, S.; Kil, H. S.; Oh, S. J.;
Lee, S. J.; Kim, J. S.; Ryu, J. S.; Moon, D. H.; Chi, D. Y. A new class of SN2
reactions catalyzed by protic solvents: facile fluorination for isotopic
labeling of diagnostic molecules. J. Am. Chem. Soc. 2006, 128, 16394−
16397. (d) Zhang, W.; Curran, D. P. Synthetic applications of fluorous
solid-phase extraction (F-SPE). Tetrahedron 2006, 62, 11837−11865.
(e) Bejot, R.; Fowler, T.; Carroll, L.; Boldon, S.; Moore, J. E.; Declerck,
J.; Gouverneur, V. Fluorous synthesis of 18F radiotracers with the
[18F]fluoride ion: nucleophilic fluorination as the detagging process.
Angew. Chem., Int. Ed. 2009, 48, 586−589.
AR
Perspective
(149) Graham, T. J.; Lambert, R. F.; Ploessl, K.; Kung, H. F.; Doyle, A.
G. Enantioselective radiosynthesis of positron emission tomography
(PET) tracers containing [18F]fluorohydrins. J. Am. Chem. Soc. 2014,
136, 5291−5294.
(150) (a) Yang, D. J.; Wallace, S.; Cherif, A.; Li, C.; Gretzer, M. B.;
Kim, E. E.; Podoloff, D. A. Development of F-18-labeled fluoroery-
thronitroimidazole as a PET agent for imaging tumor hypoxia. Radiology
1995, 194, 795−800. (b) Kurihara, H.; Honda, N.; Kono, Y.; Arai, Y.
Radiolabelled agents for PET imaging of tumor hypoxia. Curr. Med.
Chem. 2012, 19, 3282−3289. (c) Huang, X.; Liu, W.; Ren, H.;
Neelamegam, R.; Hooker, J. M.; Groves, J. T. Late stage benzylic C-H
fluorination with [18F]fluoride for PET imaging. J. Am. Chem. Soc. 2014,
136, 6842−6845.
(151) Riss, P. J.; Aigbirhio, F. I. A simple, rapid procedure for
nucleophilic radiosynthesis of aliphatic [18F]trifluoromethyl groups.
Chem. Commun. 2011, 47, 11873−11875.
(152) Fawaz, M. V.; Brooks, A. F.; Rodnick, M. E.; Carpenter, G. M.;
Shao, X.; Desmond, T. J.; Sherman, P.; Quesada, C. A.; Hockley, B. G.;
Kilbourn, M. R.; Albin, R. L.; Frey, K. A.; Scott, P. J. H. High affinity
radiopharmaceuticals based upon lansoprazole for PET imaging of
aggregated tau in Alzheimer’s disease and progressive supranuclear
palsy: synthesis, preclinical evaluation, and lead selection. ACS Chem.
Neurosci. 2014, 5, 718−730.
(153) Huiban, M.; Tredwell, M.; Mizuta, S.; Wan, Z.; Zhang, X.;
Collier, T. L.; Gouverneur, V.; Passchier, J. A broadly applicable
[18F]trifluoromethylation of aryl and heteroaryl iodides for PET
imaging. Nat. Chem. 2013, 5, 941−944.
(154) Ruhl, T.; Rafique, W.; Lien, V. T.; Riss, P. J. Cu(I)-mediated 18F-
trifluoromethylation of arenes: rapid synthesis of 18F-labeled trifluor-
omethyl arenes. Chem. Commun. 2014, 50, 6056−6059.
(155) Nyffeler, P. T.; Durón, S. G.; Burkart, M. D.; Vincent, S. P.;
Wong, C.-H. Selectfluor: mechanistic insight and applications. Angew.
Chem., Int. Ed. 2005, 44, 192−212.
(156) Teare, H.; Robins, E. G.; Kirjavainen, A.; Forsback, S.; Sandford,
G.; Solin, O.; Luthra, S. K.; Gouverneur, V. Radiosynthesis and
evaluation of [18F]selectfluor bis(triflate). Angew. Chem., Int. Ed. 2010,
49, 6821−6824.
(157) (a) Stenhagen, I. S. R.; Kirjavainen, A. K.; Forsback, S. J.;
Jorgensen, C. G.; Robins, E. G.; Luthra, S. K.; Solin, O.; Gouverneur, V.
[18F]Fluorination of an arylboronic ester using [18F]selectfluor
bis(triflate): application to 6-[18F]fluoro-L-DOPA. Chem. Commun.
2013, 49, 1386−1388. (b) Kumakura, Y.; Cumming, P. PET studies of
cerebral levodopa metabolism: a review of clinical findings and modeling
approaches. Neuroscientist 2009, 15, 635−650. (c) Calabria, F.;
Chiaravalloti, A.; Di Pietro, B.; Grasso, C.; Schillaci, O. Molecular
imaging of brain tumors with 18F-DOPA PET and PET/CT. Nucl. Med.
Commun. 2012, 33, 563−570.
(158) (a) Lee, E.; Kamlet, A. S.; Powers, D. C.; Neumann, C. N.;
Boursalian, G. B.; Furuya, T.; Choi, D. C.; Hooker, J. M.; Ritter, T. A
fluoride-derived electrophilic late-stage fluorination reagent for PET
imaging. Science 2011, 334, 639−642. (b) Lee, E.; Hooker, J. M.; Ritter,
T. Nickel-mediated oxidative fluorination for PET with aqueous [18F]
fluoride. J. Am. Chem. Soc. 2012, 134, 17456−17458. (c) Campbell, M.
G.; Ritter, T. Late-stage fluorination: from fundamentals to application.
Org. Process Res. Dev. 2014, 18, 474−480.
(159) Kamlet, A. S.; Neumann, C. N.; Lee, E.; Carlin, S. M.; Moseley,
C. K.; Stephenson, N.; Hooker, J. M.; Ritter, T. Application of
palladium-mediated 18F-fluorination to PET radiotracer development:
overcoming hurdles to translation. PLoS One 2013, 8, e59187.
(160) Ren, H.; Wey, H.-Y.; Strebl, M.; Neelamegam, R.; Ritter, T.;
Hooker, J. M. Synthesis and imaging validation of [18F]MDL100907
enabled by Ni-mediated fluorination. ACS Chem. Neurosci. 2014, 5,
611−615.
(161) (a) Prescher, J. A.; Bertozzi, C. R. Chemistry in living systems.
Nat. Chem. Biol. 2005, 1, 13−21. (b) Sletten, E. M.; Bertozzi, C. R.
Bioorthogonal chemistry: fishing for selectivity in a sea of functionality.
Angew. Chem., Int. Ed. 2009, 48, 6974−6998.
(162) (a) Olberg, D. E.; Hjelstuen, O. K. Labeling strategies of peptides
with 18F for positron emission tomography. Curr. Top. Med. Chem. 2010,
DOI: 10.1021/acs.jmedchem.5b00258
J. Med. Chem. XXXX, XXX, XXX−XXX
Journal of Medicinal Chemistry Perspective

10, 1669−1679. (b) Wu, Z.; Kandeel, F. 18F-labeled proteins. Curr. (173) (a) McBride, W. J.; Sharkey, R. M.; Karacay, H.; Souza, C. A.;
Pharm. Biotechnol. 2010, 11, 572−580. (c) Bejot, R.; Gouverneur, V. 18F- Rossi, E. A.; Laverman, P.; Chang, C.-H.; Boerman, O. C.; Goldenberg,
Radionuclide chemistry. Mol. Med. Med. Chem. 2012, 6, 335−382. D. M. A novel method of 18F radiolabeling for PET. J. Nucl. Med. 2009,
(163) Blackman, M. L.; Royzen, M.; Fox, J. M. Tetrazine ligation: fast 50, 991−998. (b) Hausner, S. H.; Bauer, N.; Sutcliffe, J. L. In vitro and in
bioconjugation based on inverse-electron-demand Diels−Alder reac- vivo evaluation of the effects of aluminum [18F]fluoride radiolabeling on
tivity. J. Am. Chem. Soc. 2008, 130, 13518−13519. an integrin αvβ6-specific peptide. Nucl. Med. Biol. 2014, 41, 43−50.
(164) (a) Wild, D.; Wicki, A.; Mansi, R.; Behe, M.; Keil, B.; Bernhardt, (c) Liu, Z.; Li, Y.; Lozada, J.; Wong, M. Q.; Greene, J.; Lin, K. S.; Yapp,
P.; Christofori, G.; Ell, P. J.; Macke, H. R. Exendin-4-based D.; Perrin, D. M. Kit-like 18F-labeling of RGD-19F-arytrifluroborate in
radiopharmaceuticals for glucagonlike peptide-1 receptor PET/CT high yield and at extraordinarily high specific activity with preliminary in
and SPECT/CT. J. Nucl. Med. 2010, 51, 1059−1067. (b) Kiesewetter, vivo tumor imaging. Nucl. Med. Biol. 2013, 40, 841−849.
D. O.; Gao, H.; Ma, Y.; Niu, G.; Quan, Q.; Guo, N.; Chen, X. 18F-
Radiolabeled analogs of exendin-4 for PET imaging of GLP-1 in
insulinoma. Eur. J. Nucl. Med. Mol. Imaging 2012, 39, 463−473. (c) Wu,
H.; Liang, S.; Liu, S.; Pan, Y.; Cheng, D.; Zhang, Y. 18F-Radiolabeled
GLP-1 analog exendin-4 for PET/CT imaging of insulinoma in small
animals. Nucl. Med. Commun. 2013, 34, 701−708. (d) Wu, Z.; Nair, I.;
Omori, K.; Scott, S.; Todorov, I.; Kandeel, F.; Liu, S.; Conti, P. S.; Li, Z.;
Shively, J. E. 64Cu Labeled sarcophagine exendin-4 for microPET
imaging of glucagon like peptide-1 receptor expression. Theranostics
2014, 4, 770−777.
(165) Denk, C.; Svatunek, D.; Filip, T.; Wanek, T.; Lumpi, D.;
Fröhlich, J.; Kuntner, C.; Mikula, H. Development of a 18F-labeled
tetrazine with favorable pharmacokinetics for bioorthogonal PET
imaging. Angew. Chem., Int. Ed. 2014, 53, 9655−9659.
(166) Knight, J. C.; Richter, S.; Wuest, M.; Way, J. D.; Wuest, F.
Synthesis and evaluation of an 18F-labelled norbornene derivative for
copper-free click chemistry reactions. Org. Biomol. Chem. 2013, 11,
3817−3825.
(167) (a) Marik, J.; Sutcliffe, J. L. Fully automated preparation of n.c.a.
4-[18F]fluorobenzoic acid and N-succinimidyl 4-[18F]fluorobenzoate
using a Siemens/CTI chemistry process control unit (CPCU). Appl.
Radiat. Isot. 2007, 65, 199−203. (b) Ackermann, U.; Yeoh, S. D.;
Sachinidis, J. I.; Poniger, S. S.; Scott, A. M.; Tochon-Danguy, H. J. A
simplified protocol for the automated production of succinimidyl 4-
[18F]fluorobenzoate on an IBA Synthera module. J. Labelled Compd.
Radiopharm. 2011, 54, 671−673.
(168) Gonzalez, N.; Moody, T. W.; Igarashi, H.; Ito, T.; Jensen, R. T.
Bombesin-related peptides and their receptors: recent advances in their
role in physiology and disease states. Curr. Opin. Endocrinol., Diabetes
Obes. 2008, 15, 58−64.
(169) Carroll, L.; Boldon, S.; Bejot, R.; Moore, J. E.; Declerck, J.;
Gouverneur, V. The traceless Staudinger ligation for indirect 18F-
radiolabelling. Org. Biomol. Chem. 2011, 9, 136−140.
(170) Pauwels, E. K. J. 18F-Labeled fluorodeoxyglucose for PET
imaging: the working mechanism and its clinical implication. Drugs
Future 2001, 26, 659−668.
(171) (a) Wuest, F.; Hultsch, C.; Berndt, M.; Bergmann, R. Direct
labelling of peptides with 2-[18F]fluoro-2-deoxy-D-glucose ([18F]FDG).
Bioorg. Med. Chem. Lett. 2009, 19, 5426−5428. (b) Namavari, M.;
Cheng, Z.; Zhang, R.; De, A.; Levi, J.; Hoerner, J. K.; Yaghoubi, S. S.;
Syud, F. A.; Gambhir, S. S. A novel method for direct site-specific
radiolabeling of peptides using [18F]FDG. Bioconjugate Chem. 2009, 20,
432−436. (c) Hultsch, C.; Schottelius, M.; Auernheimer, J.; Alke, A.;
Wester, H.-J. 18F-Fluoroglucosylation of peptides, exemplified on
cyclo(RGDfK). Eur. J. Nucl. Med. Mol. Imaging 2009, 36, 1469−1474.
(172) (a) Ting, R.; Harwig, C.; Auf Dem Keller, U.; McCormick, S.;
Austin, P.; Overall, C. M.; Adam, M. J.; Ruth, T. J.; Perrin, D. M. Toward
[18F]-labeled aryltrifluoroborate radiotracers: in vivo positron emission
tomography imaging of stable aryltrifluoroborate clearance in mice. J.
Am. Chem. Soc. 2008, 130, 12045−12055. (b) Auf Dem Keller, U.;
Bellac, C. L.; Li, Y.; Lou, Y.; Lange, P. F.; Ting, R.; Harwig, C.;
Kappelhoff, R.; Dedhar, S.; Adam, M. J.; Ruth, T. J.; Bénard, F.; Perrin,
D. M.; Overall, C. M. Novel matrix metalloproteinase inhibitor
[18F]marimastat-aryltrifluoroborate as a probe for in vivo positron
emission tomography imaging in cancer. Cancer Res. 2010, 70, 7562−
7569. (c) Liu, Z.; Li, Y.; Lozada, J.; Pan, J.; Lin, K.-S.; Schaffer, P.; Perrin,
D. M. Rapid, one-step, high yielding 18F-labeling of an aryltrifluor-
oborate bioconjugate by isotope exchange at very high specific activity. J.
Labelled Compd. Radiopharm. 2012, 55, 491−496.

AS DOI: 10.1021/acs.jmedchem.5b00258
J. Med. Chem. XXXX, XXX, XXX−XXX