Structural modification of organic compounds by chemical synthesis to

develop new antimicrobials.

J.C. Espinoza-Hicks, A. Camacho-Dvila and G.V. Nevrez-Moorilln
1
School of Chemical Sciences, Autonomous University of Chihuahua. Circuito Universitario s/n. Nuevo Campus
Universitario. Chihuahua, Chih., 31125 Mexico
1

One of the focal problems in Public Health related to infectious diseases is the development of bacterial resistance to
commonly used chemotherapeutic agents, with the consequent difficulties on treatment. The search for new therapeutic
options has led to the discovery of new bioactive compounds derived from natural sources, including molecules from
plants, or metabolites from microorganisms. Chemical organic synthesis has allowed the modification of known antibiotics
to enhance its biological activity. On the other hand, synthesis has also provided novel structures of biologically active
molecules that may be used for the development of novel molecules that may target sites different to those present in
natural compounds. A brief account on the developments in synthesis applied to novel chemotherapeutic agents is
presented.
Keywords QSAR; Organic synthesis; Diversed orientes synthesis; ADMET.

Nowadays there is a major concern on the fight against microbial infections and intoxications, mainly because of the
development of resistance by the pathogens such as virus and bacteria, with the consequent reduction on the activity of
chemotherapeutic agents actually in use. As a consequence of this problem, there has been an increase on the search of
novel therapeutic agents. A good example is the focus on solving the AIDS problem, which was considered as a mortal
disease for more than 30 years, but with the development of novel therapeutic molecules, it is now considered as a
controllable disease and the life expectancy for an HIV(+) patient goes beyond 20 years. All of this has prompted the
search for the discovery and development of novel bioactive compounds based on natural sources (plants and
microorganisms). On the other hand, the area of organic synthesis has focused on the modification of already existing
compounds, as well as on the development of novel molecules with sites of action different to the ones previously
known.
The advances in the areas of biology, chemistry and physics has prompted the development of novel disciplines such
as molecular biology, proteomics, metabolomics and genomics which has influenced the development of novel
therapeutics methods and stimulated other areas such as medicinal chemistry.
The area of medicinal chemistry is related to the study, development, identification and interpretation of mechanism
of action of biologically active compounds. All of these objectives require a multidisciplinary approach for the
development of novel drugs such as antimicrobial agents. This approach evaluates novel antibacterial agents possessing
new modes of action and/or new chemical structures or scaffolds possessing potent antibacterial activity, especially
against those strains of pathogens that are resistant to currently available antibacterial drugs.
Unfortunately, only two truly novel chemical entities (NCE) have been approved by the Food and Drug
Administration (FDA) in the last 20 years; both are oxazolidinones, including Linezolid and a lipopeptide named
Daptomycin. This reflects the shifting of many large pharmaceutical companies away from the area of infectious
diseases that has resulted in the appearance of multi-drug resistant strains of previously treatable infections. Despite this
tendency, some pharmaceutical companies have begun to refocus their efforts on small synthetic molecules as well as in
the search for molecules derived from natural sources found in plants of tropical forests and organisms found in the
deep sea environment.
1. Use of organic synthesis in the development of novel drugs.
Organic synthesis plays a major role in the development of novel drugs, due to the possibility of modifying the
chemical structure of naturally active biological compounds and therefore, their biological activity. The basic idea for
the development of biologically active compounds evolves from the hypothesis that the active molecule binds to an
active site of an enzyme or protein with the consequent response in form of certain biological activity. Chemical
modifications on the active molecules may result in an increase, decrease or modification of the biological response.
From this basic idea, a broad range of different structures can be derived, leading to the development of better and more
effective therapeutic agents.
It is also helpful to focus on the development and synthesis of novel chemical structures not based in natural
compounds that may show novel biological activities. The basis of these developments is the interaction between the
novel compounds and novel sites of action, such as enzymes or receptors. All this can be combined with genetic and
metabolic studies for a better understanding on the possible mechanism of action.
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Generally, the process of drug discovery requires the availability of high quality compounds that can be assayed
against multiple biological targets, in terms of efficacy and safety. The development of new drugs, including new
antibiotics, requires a strong interaction between different areas of research, but is especially challenging in terms of the
requirements of safety dictated by health regulating agencies.
In order to accelerate the discovery of novel molecules, the area of organic synthesis has developed novel
methodologies for the rapid preparation of multiple molecules. Among these methodologies, combinational synthesis
based on privileged structures, chemical synthesis based on rational design and diverse oriented synthesis stand out as
the main tools used today towards the discovery and development of structurally novel molecules with biological
activity.
2. Combinatorial synthesis based on privileged structures.
One of the more traditional ways of drug development is based on the description of privileged structures; these can be
defined as the chemical structures containing a specific skeleton which is responsible for the known biological activity.
A privileged structure is obtained from the information gathered from reports for the same biological activity found in
different compounds.
This methodology is based on the principles that structural modifications on the chemical skeleton can derive in
physicochemical changes such as solubility, polarity, acidity, but still maintains the part responsible for the biological
activity (privileged structure). This modification can then result in an increase in the biological activity as compared
with the unmodified structure, although this may also result in a reduction on the biological activity.
Examples of privileged structures are the purines which are an important component of the DNA molecule; therefore,
many proteins contain binding sites to these molecules. An example of this interaction is found in molecules used as
antivirals such as acyclovir (2) and abacavir (1) which are used against viral diseases including as herpes and HIV.
These structures have been used as a scaffold for the development of molecules with novel activities. Advances on the
structural modification of this type of compounds has allowed the development of molecules with the capacity to bind
to the heat shock protein Hsp90, that in the case of compound 3, have shown antiproliferative activity against breast
cancer cells lines (MCF-7) [1].
N
N
N
N
H
2
N
OH
NH
N
N
N
N
OH
O
OH
H
2
N
1
2
N
N
N
N
Cl
F
OMe
OMe MeO
NH
2
3

Fig.1 Privileged structures purines such as precursors of combinatorial synthesis.

Many of the compounds that have been studied have demonstrated good biological activity. Like purines, there are a
great variety of antimicrobial compounds that has been modified in a similar way using as privileged structures
scaffolds such as benzimidazoles, imidazoles and benzofurans. With the identification of this kind of structures it is
possible to describe studies like structure-activity relationship (SAR) based on the structural modification of privileged
compounds.
2.1 QSAR studies
One of the main tools for the development of biological active compounds are the SAR studies, where the main
objective in this kind of studies is the description of the effect of the introduction or removal of different functional
groups attached to the privileged structure. In SAR studies, the main objective is to describe the quantitative effect of
certain functional groups on the biological activity of the studied compounds (QSAR); these analysis can be done with
the assistance of computational methods also known as in silico studies. Derived from the results of these studies, it has
been possible to describe which functional groups may help to increase biological activity of already known chemical
compounds.
QSAR also gives valuable information about the sections or functional groups on the chemical structure that should
be present or cant be removed because their presence is required for biological activity; these studies can be described
starting from the interaction between protein and the compounds.
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From QSAR studies, it has been possible to develop new molecules with novel activities, for example the
development of quinolones, which are based on the discovery of nalidixic acid 2. From this structure by QSAR studies
it could be possible to modify two molecules, which showed weak activity and lead to the development of fourth
generation quinolones possessing a wider spectral of biological activity (figure 2). Compounds such as ciprofloxacin 6
shown in Figure 2 are one of the major prescribed therapeutic antimicrobial nowadays employed against bacterial
strains that have multirresistance to conventional antibiotics [2].
N
O
COOH
Cl
N N
O
COOH
H
3
C
N
N N
O
COOH
N
HN
N
O
COOH F
N
O
COOH
N
HN
F
N N
HN
O
COOH F
N
N
O
COOH F
O
1
Naldixic acid
2
Pipedimic acid
3
Flumequin
4
Norfloxacin
5
Ciprofloxacin
6
Ofloxacin
7

Fig. 2 Chemical evolution of quinolones through SAR.

Another type of antimicrobial molecules subjected to QSAR studies are chalcones, which are secondary metabolites
of a wide variety of plants and are precursors of flavonoids, known to be important antioxidants. For chalcones, there
are a great number of reports of QSAR that demonstrate that the substitution of the chalcone scaffold with groups such
as hydroxyl, prenyl and methoxyl radicals, have shown an increase on their biological activity. For example,
licochalcone A (Figure 3) has shown good antimicrobial activity against Gram positive bacteria [3].
O
HO OH
O

Fig. 3 Chemical structure of the Licochalcone A.
3. Synthesis based on rational design.
Besides privileged structures for the development of novel drugs, another useful tool in the development of new
therapeutic agents is known as named rational design. In this approach, the design of the drug is based on the
knowledge of the mechanism of action of a specific compound. Before entering in the molecular design process, it is
necessary to know the exact mechanism of action as well as the proteins involved in this process.
The advances in molecular biology techniques and genetic sequencing has allowed a better knowledge of the
genomic structure of a great variety of microorganisms; the potential use of this information has generated new
expectancies on drug design, because using the information about specific proteins on specific pathogenic
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microorganisms, it could be possible to propose novel compounds possessing the ability to bind to vital proteins and
enzymes required for the microorganism survival, to inhibit or retard microbial growth [4].
Rational design can be carried out through the following steps:
- Identification of the molecular target (enzyme, protein or receptor).
- Validation of the molecular target. This can be done through molecular studies of genetic Knock-down type,
were the gene that codifies for the analyzed protein or enzyme is blocked and is noticed if this proteins or
enzyme are required for the microorganism survival.
- Search for a lead structure. In these studies, the binding of the molecule with their specific receptor are done in
silico, in order to find the type of interaction between the studied molecule and the receptor functional groups.
- Lead optimization. When a molecule with an optical biological activity is developed through the previous
steps, the evaluation of Absorption, Distribution, Metabolism, Excretion and Toxicology (ADMET) are carried
out in order to obtain a lead that can be directed to clinical studies.
The required preliminary knowledge for the development of novel drugs through rational drug design takes longer
times than the other studies, being the critical points the physicochemical properties of each of the studied molecules
that are reflected on the ADMET. Therefore, an excellent lead may result in a failure if does not fulfill the ADMET
studies.
Studies by some pharmaceutical companies such as GlaxoSmithKline have resulted in a low rate of novel active
targets against pathogenic microorganisms, as well as low activities of the designed compounds towards the target
identified structures. This has prompted further in depth investigation in order to increase the number of target
molecules, as well as studies to optimize the physicochemical characteristics for each designed compound [5].
4. Diversity oriented synthesis (DOS).
This approach has been developed very recently; it derives from the need of chemical structural diversity to obtain
bioactive compounds. The previous mentioned approaches are based on a known structure possessing the biological
activity and the modifications are made on non-essential functionalities. In these approaches, molecular diversity is
reduced to known molecular skeletons restricting the chemical space.
DOS tries to restrict the lack of structural skeletons through the forward synthetic design of structurally complex and
varied compounds. This approach has allowed the development of libraries with structurally small molecules containing
diverse biological activities [6].
In this type of design the diversity can be generated mainly through the use of tandem or domino reactions. In this,
the product of an initial reaction is the substrate for the following reaction and so on.
A collection of diversity oriented compounds can be achieved by different strategies such as:
I.Through the generation of structurally diverse scaffolds containing additional attachment sites (Skeletal diversity).
II.Through the incorporation of diverse functional groups around a specific skeleton.
III.Incorporating stereochemical elements that allow different sterical interactions with the target (stereochemical
diversity) [4].
An example of DOS that incorporates diverse functional groups in to a specific skeleton in the synthesis of alpha-
amino acids, is found in the Ugi multicomponent reaction (Figure 4) between the scaffold compound (1) and benzyl
isocyanide (3) with a variety of aldehydes (2a to 2f) to generate the bicyclic compound 4 which by a series of
transformations produces different substituted alpha amino acids (7a to 7f) [7].
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O
N
H
2
Bn
CO
2
R-CHO
NC
O
N
O
R
O
O
MeOH, rt
N
O
NHBn
O
O R
HCl, Dioxane, rt
N
H
R
O
NHBn
Toluene, reflux
H
2
N
NHBn
O
R
Pd black, formic acid, MeOH, rt
1
2
3
4
5
6
7a - 7f
2a R= i-Pr
2b R= i-Bu
2c R= Et
2d R= 3-MeO-Ph
2e R= 4-Cl-Ph
2f R= Bn

Fig. 4 Generation of diversity through Ugi multicomponent reaction to obtain alpha amino acids (modified from [7]).
5. Structural Hybrids
Another approach to the development of novel antimicrobial agents which is based on a totally different strategy is
based in the simultaneous administration of two different antimicrobial agents. For example, the drug Augmentin is a
combination of the antimicrobials amoxicillin (a -lactamic) and clavulanic acid (a -lactamase inhibitor). This
combination causes the inhibition of the -lactamase by the clavulanic acid which in -lactamic resistant bacteria
inactivates the amoxicillin -lactamic ring responsible for the activity. This combination is used to treat some skin
infections [8].
Although in the example used, both molecules are used in combination, there is also another approach whereby two
molecules of different antibiotics are joined together through a chemical reaction to obtain a single molecule. This is
called a hybrid. The advantage of this approach is that the combination of two active molecules may result in a hybrid
possessing better biological activity or even more that could be active to microorganisms that are resistant to both
antibiotics [9-10].
Although at the present time there is a not commercially available hybrid antibiotic, this approach is widely
investigated, because joining two different antibiotics may result in a good drug candidate. As an example of this
approach, the joining of the antibiotics linezolid and ciprofloxacin results in a series of hybrids that are joined through
different linkers to obtain compounds with interesting probed activity [11]. In figure 5, different structural hybrids of
the fluoroquinolone antibiotics family with other antimicrobial agents are presented. These possess some interesting
activities against several pathogenic bacteria such as S. aureus MRSA and B. anthracis [12].

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Fig. 5 Hybrids molecules of ciprofloxacin.
6. Conclusions.
As can be seen, the importance of organic synthesis in the development of novel drug agents has dramatically increased
in the recent years. The advances in novel approaches and methodologies such as combinatorial synthesis, diversity
oriented synthesis, as well as the development of novel synthetic transformations has allowed an increase in the
diversity of biologically active molecules. It is expected that this will result in the development not only of novel
antimicrobial agents but also in novel anticancer or antiviral drugs.
The need for development of new chemotherapeutic agents is of special importance for developing and
underdeveloped countries, and the identification of new molecules is a task that needs the input of several disciplines, in
order to get the best result. Microorganisms are very effective in developing resistance strategies for the therapeutic
drugs used, with the consequent increase in multiresistant strains; against the enemy, we all need to be together, and
organic synthesis can provide valuable input into the warfare against pathogens.
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N
O
HO
O
F
N
N
F
N
O
NHAc
1
N N
OH
O O
N
N
O
N
N
F
OCH
3
NH
2
H
2
N
OCH
3
N
OH
O O
N
N
H
N
F
O OH
F
N
OH O
N
OH
O
OH
2
3
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[10] Viegas C, Danuello A, Bolzani V, Barreiro E, Manssour C.A, Molecular hybridization: A Useful Tool in the Design of new
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175 FORMATEX 2011
Science against microbial pathogens: communicating current research and technological advances
A. Mndez-Vilas (Ed.) _______________________________________________________________________________