Hugo Kubinyi, www.kubinyi.

de

Combinatorial
Chemistry
Technology

Hugo Kubinyi
Germany

E-Mail kubinyi@t-online.de
HomePage www.kubinyi.de

Hugo Kubinyi, www.kubinyi.de

Combinatorial Diversity in Nature

20 natural amino acids yield
400 dipeptides
8,000 tripeptides ...
64,000,000 hexapeptides and, in principle,
10400 proteins with MW ≈ 30 kD
100 chemically modified amino acids yield
e.g. 1,000,000,000,000 hexapeptides,

and ... 4 nucleic bases encode all organisms !

Hugo Kubinyi, www.kubinyi.de

Number of organic molecules with MW < 500

(C, H, O, N, P, S, F, Cl, Br, I)

1 000 000 000 000 000 000 000 000 000 000
000 000 000 000 000 000 000 000 000 000
000 000 000 000 000 000 000 000 000 000
000 000 000 000 000 000 000 000 000 000

or more or less ....

Hugo Kubinyi, www.kubinyi.de

Principles of Combinatorial Chemistry

Combinatorial Chemistry generates a multitude of

chemically related (”congeneric”) compounds,
so-called ”combinatorial libraries"

In the last years, combinatorial chemistry in drug

research changed more and more to automated
parallel synthesis and parallel purification.
Hugo Kubinyi, www.kubinyi.de

O
Classical organic OMe
NH2 HN
synthesis: O
CH3 + = CH3
OMe
Cl

1 educt x 1 educt = 1 product

Combinatorial synthesis: O O
R1 NH2 + = R1
Cl R2 N R2
e.g. 50 educts x 20 educts = H
1,000 products

Multistep combinatorial e.g. 50 x 20 x 20 educts =

synthesis: 20,000 products

Multicomponent reaction (e.g. Ugi reaction): O R2 H

N
R1-NH2 + R2-CHO + R3-NC + R4-COOH = R4 N R3
R1 O
e.g. 50 x 20 x 5 x 200 educts = 1 million products

Hugo Kubinyi, www.kubinyi.de

Combinatorial Library
R5 R4O
R6 R
N 9
*N
* R10
R7 R3
R8 R1 R2

Building blocks with 68 different residues in 10

positions (R1 - R10 are 5, 10, 10, 4, 2, 5, 5, 2, 5, and 20
residues) generate a library of 20 million different
compounds. Consideration of both steric centers (*)
increases this number by a factor of four, i.e. to
80 million different compounds.
Hugo Kubinyi, www.kubinyi.de

Solid Phase Synthesis: Beads

Cross-linked polystyrene
(1.0-1.5% divinylbenzene)
Cl
Ph

Cl
Ph Ph Ph Ph

Ph
Ph Ph Ph

Ph Cl
Ph
Ph Ph
Functionalization Ph
of the beads by Ph

chloromethylation
and further chemical
reactions Ph Cl

Hugo Kubinyi, www.kubinyi.de

Tentagel Beads (Polystyrene, Grafted with Polyoxy-

ethylene), Rapp Polymers, Tübingen, Germany
Hugo Kubinyi, www.kubinyi.de

The Principle of Solid Phase Synthesis

immobilization

bead
scaffold with
(40-80 µm)
functional groups
and linker

cleavage

three-step
synthesis
immobilized product product

Hugo Kubinyi, www.kubinyi.de

The Combination of Scaffolds and Building Blocks

3 building blocks A1-A3

and
3 building blocks B1-B3

yield 9 products
A1B1 – A3B3 .

In the same manner,

10 x 10 x 10 building
blocks yield 1,000
products A1B1C1 –
A10B10C10 .
Hugo Kubinyi, www.kubinyi.de

A
B
C "Split and
Combine"
A B C
Method for
Library
Synthesis
A C
B

A A A B B B C C C
A B C A B C A B C

A C
B

Hugo Kubinyi, www.kubinyi.de

A
B
C 3 Mixtures
with 9 different
A A A B B B C C C
A A A A A A A A A
compounds in
A B C A B C A B C
each reaction
vessel
A A A B B B C C C
B B B B B B B B B
A B C A B C A B C

A A A B B B C C C
C C C C C C C C C
A B C A B C A B C
Hugo Kubinyi, www.kubinyi.de

Linkers: Merrifield and Wang linkers

Cl Merrifield resin

OH
O Wang resin
("Wang linker")

R (several steps)
O
O O RCOOH
50% TFA
(product)

Hugo Kubinyi, www.kubinyi.de

Linkers: a) Merrifield Peptide Synthesis

Cl Boc-NHCHR1COO- R1
H NHBoc
SN2 O
O

1) HCl / CH3COOH
O NHBoc
R1
2) Boc-NHCHR2COO- / DCCI H N H R2
O H
O

50% TFA O NH2

R1
H N H R2 Dipeptide
HO H
O
Hugo Kubinyi, www.kubinyi.de

Other linkers

OH NHFmoc
O OMe O OMe

Rink acid protected

linker OMe Rink amide
linker OMe

NHFmoc
O
Cl
protected O
Trityl Sieber
linker linker

Hugo Kubinyi, www.kubinyi.de

Safety catch linkers

OO OO
S OR S OR S + R-OH
base
stable labile

O
R OH-
N product-COOH
H N Product
S
OO O product-CONR1R2
HNR1R2
R = H: stable
+ CH2N2 → R = CH3: labile
 Hugo Kubinyi, www.kubinyi.de

Traceless (safety catch) linker

H Cu(OAc)2
N H
N N
O H R + N2 +
O
stable NH2 R

Polymer-supported solution phase syntheses

Polymeric reagents

reagent
C
A+B A-B

Hugo Kubinyi, www.kubinyi.de

Solid Phase-Supported Synthesis of (±)-Epibatidine

NMe2
1. NMe3BH4 4.
O OH
OTBS
2. NMe3RuO4 NO2
Cl 5.
Cl N 3. NMe3OH Cl N
+ MeNO2 6. NMe3BH4

7. Mesyl-Cl
OH NH NH
Cl
N N
H N
8. NMe3BH4 H
NO2
Cl N basic
(±) 9. Et2N N-tBu N epimerization
P Cl
N N 85% (±)-Epibatidine
(±) endo
(exo:endo = 3:1)
R. J. Booth and J. C. Hodges, J. Am. Chem. Soc. 119, 4882-4886 (1997)
Hugo Kubinyi, www.kubinyi.de

Solid Phase-Supported Synthesis of (±)-Oxomaritidine

and (±)-Epimaritidine
NH2
1. HO
OH N N
NMe3+ RuO4- CHO
HO
(F3CCO)2O
CH2Cl2 2. NMe3+ BH4-MeO N
OMe OMe H
MeOH 99 %
OMe 100 % OMe MeO
90 %
O
HO O
MeO
NEt3+ HCO3-
I(OCOCX3)2
N
MeO X = H or F MeOH MeO
N MeO
(±)-Oxomaritidine
MeO O CF3 F3CCH2OH N
100 %
MeO H2 / Pd / C
CF3
70 % MeOH
O
NMe3+ BH4- 95 %
S. V. Ley et al., (±)-Epimaritidine OH CuSO4 or NiCl2 O
J. Chem. Soc. MeO MeOH
MeO
Perkin Trans. 1,
N 90 % N
1251-1252 (1999) MeO MeO

Hugo Kubinyi, www.kubinyi.de

Polymeric scavengers for building blocks, side

products and reagents

X
A + excess B A-B + B A-B + X-B

reagent
C X
A+B A-B + C A-B + X-C

X
A+B A-B + side A-B + X-D
product D
Hugo Kubinyi, www.kubinyi.de

Scavenger Reagents: Ion Exchange Resins,

Polymeric Acids and Bases, Isocyanates, etc.
NHNH2
O O
N
Me +
O
COOH
NCO
1 equivalent 1.2 equivalents

Me O Me

1. Cl O N
N
N 2. R-NH2 N

3. NCO +

COOH CONHR
HN CH2CH2N(CH2CH2NH2)2

Hugo Kubinyi, www.kubinyi.de

Resin capture strategy

reagent
C X cleavage
A+B A-B + C + X-A-B A-B
side product D
Resin capture with an ion exchange resin
- NH3/MeOH
SO3
-
H2N-R SO3 H3N+-R H2N-R
(Amberlite ion exchange resin)

Catch and release strategy

reagent
C X-A
B1 + B2 B+C+ [ X-A-B ] A-B
side product D
 Hugo Kubinyi, www.kubinyi.de

Catch and release strategy, using a traceless linker

R1 R1 R1

Susuki
coupling release
R3 R3 R3

B
R2 O O R2 R2

Si
NH Me
O Me

Hugo Kubinyi, www.kubinyi.de

Milestones in the History of Multicomponent Reactions

A. Strecker (1850) C N
NH3 + HCN + RCHO
R NH2
H
Cl O O N
A. R. Hantzsch (1890) R1
R2
NH3 + R1 +H OR
O R2 COOR

O O O
P. Biginelli (1893) HN
R3
R1-CHO + H2N NH2 + R2 R1 NH

R2 R3
C. Mannich (1912) R4
H R2 R3 R4
CH2O + R1R2NH + R3 N H
O R1
O
Hugo Kubinyi, www.kubinyi.de

O R2
M. Passerini (1921) H
N
R1NC + R2CHO + R3COOH R3 O R1
O O
H. T. Bucherer (1934)
HN NH
HCN + NH3 + CO2 + RCHO
O R

O O R1
F. Asinger (1958) S
R4 R4
NH3 + R1 R2 + R3 R2
N
SH
R3

O R2
I. Ugi (1959) R1NH2 + R2CHO H
N
+ R3NC + R4COOH R4 N R3
R1 O

Hugo Kubinyi, www.kubinyi.de

Complex Molecules from Multicomponent

OSi(iPr)
Reactions
3 Ar
O CHO NC
+ + +
NH

O
OH
H2N HOOC

O
O
N
4 steps e.g. N
H H
O
O Br
H H N

S. L. Schreiber, Science 287, 1964-1969 (2000)

L. Weber, Drug Discov. today 7, 143-147 (2002)
 Hugo Kubinyi, www.kubinyi.de

The Generation of Scaffold Diversity

O OH NH2
N H2NHN
NH

N NC
NH O OMe

NH2 CHO
HN
O
N N
HN NC
(Me)2N
O N
MeO O
OMe O COSH

L. Weber, Drug Discov. today 7, 143-147 (2002)

Hugo Kubinyi, www.kubinyi.de

The Generation of Scaffold Diversity

R1 N C
+
+ R2 O + R3 NH2 Three component
Ugi reaction
R NHR H H
N MeOOC N O
N
R R
N N N N R
H NHR R
O COOEt O
NHR
N N R
RHN H
N O N R
N R N O N R N
N R H
R O
R R N NHR
R
O NHR
HN R O
N N
C R
N R N
NHR
O N
N NHR
NHR H O O
O R
L. Weber, QSAR Comb. Sci. 24, 809-823 (2005)
 Hugo Kubinyi, www.kubinyi.de

Increasing Diversity of Combinatorial Libraries

O O
S H N S
S S R1
2

H2N H2N N
R1 H
N N O N
N
H N R1 O
O
R2 R2 O H
R2

R2
O O
R1
N N
H2N R1 H 2N
N
N O
F HN
O R2
R3 N
H
N O2
O
R1
O R2 N
N H2N
N S
H2 N R3
N
R2
R1 O
O O
R1
S N courtesy of Drs.
H2N R3 H2 N
N N O M. Mann, W. Sauer,
R1 O O R2 Serono, Geneva ©

Hugo Kubinyi, www.kubinyi.de

References
Bunin BA, The Combinatorial Index, Academic Press, San Diego,
1998. 350 pp, $ 80.
Terrett NK, Combinatorial Chemistry. Oxford University Press,
New York, 1998. 186 pp, $ 29 (in German 264 pp, EUR 29).
Jung G, Combinatorial Chemistry, Wiley-VCH, Weinheim, 1999.
601 pp, EUR 149.
Beck-Sickinger AG and Weber P, Combinatorial Strategies in
Biology and Chemistry, Wiley, 2002. 179 pp, $ 35 (in German EUR 20).
Bannwarth W and Felder E, Combinatorial Chemistry, Wiley-VCH,
Weinheim, 2000. 430 pp, EUR 149.
Seneci P, Solid-Phase Synthesis and Combinatorial Technologies,
Wiley-Interscience, New York, 2000. 637 pp, $ 115.
Ghose AK and Viswanadhan VN, Combinatorial Library Design and
Evaluation: Principles. Software Tools, and Applications in Drug
Discovery, Marcel Dekker, New York, 2001. 631 pp, $ 195.
Nicolaou KC, Hanko R and Hartwig W, Handbook of Combinatorial
Chemistry. Drugs, Catalysts, Materials, Wiley-VCH, Weinheim,
2002. 1114 pp, EUR 389.