Review On Combinatorial Chemistry and Drug Discovery

Patel Ravindra

Finding of novel drug is a complex process.

Historically,
the main source of biologically active compounds used in drug discovery
programs has been natural products, isolated from plant, animal or fermentation
sources.

Combinatorial chemistry is one of the important new methodologies
developed by researchers in the pharmaceutical industry to reduce the time and
costs associated with producing effective and competitive new drugs.Through
the rapidly evolving technology of combi-chemistry, it is now possible to
produce chemical libraries to screen for novel bioactivities.

Introduction

This powerful new
technology has begun to help pharmaceutical companies to find new drug
candidates quickly, save significant money in preclinical development costs and
ultimately change their fundamental approach to drug discovery(1). The main
objective of combinatorial chemistry is synthesis of arrays of chemical or
biological compounds called libraries. These libraries are screened to identify
useful components, such as drug candidates. Synthesis and screening are often
treated as separate tasks because they require different conditions,
instrumentation, and scientific expertise. Synthesis involves the development
of new chemical reactions to produce the compounds, while screening aims to
identify the biological effect of these compounds, such as strong binding to
proteins and other biomolecular targets (2). With this technique, the migration
times of the ligand-receptor pair are significantly longer than the unreactive
ligands, and can be interrogated by electrospray mass spectrometry. The mass
spectrometric method often provides a direct structural identification of the
ligand, either by determination of its molecular weight or by collision-induced
dissociation experiments. In the latter case, the molecular ion is selected by
a primary mass spectrometer and is driven into a region of high-pressure inert
gas for fragmentation. The fragment ions are then used to reconstruct the
original molecular structure. This direct approach to screening and assaying
has the advantage that the screening is carried out in solution rather than on
a solid support, and it avoids steric problems associated with resin-bound
molecules. At present the approach seems limited to libraries of about 1000
compounds because of interference from unbound ligands, and limited by
sensitivity issues. New strategies using mass spectrometry may eliminate this
limit. (3)(4)

Principle

Combinatorial chemistry is a technique by which large
numbers of structurally distinct molecules may be synthesized in a time and
submitted for pharmacological assay. The key of combinatorial chemistry is that
a large range of analogues is synthesized using the same reaction conditions,
the same reaction vessels. In this way, the chemist can synthesis many hundreds
or thousands of compounds in one time instead of preparing only a few by simple
methodology.

In contrast to this approach, combinatorial chemistry offers
the potential to make every combination of compound A1 to An with compound B1
to Bn.

The range
of combinatorial techniques is highly diverse, and these products could be made
individually in a parallel or in mixtures, using either solution or solid phase
techniques. Whatever the technique used the common denominator is that
productivity has been amplified beyond the levels that have been routine for
the last hundred years.( 5)

Method Of Synthesis

I.

Combinatorial Synthesis On Solid-Phase

The use of solid support for organic synthesis relies on
three interconnected requirements:

A cross linked, insoluble polymeric material that is inert
to the condition of synthesis;

Some means of linking the substrate to this solid phase that
permits selective cleavage of some or the entire product from the solid support
during synthesis for analysis of the extent of reaction(s), and ultimately to
give the final product of interest.

A chemical protection strategy to allow selective protection
and deprotection of reactive groups.

Several series of chemical reactions that can be used to
synthesis proteins have been reported. The direction of synthesis is opposite
to that used in the cell. The intended carboxy terminal amino acid is anchored
to a solid support. Then, the next amino acid is coupled to the first one. In
order to prevent further chain growth at this point, the amino acid, which is
added, has its amino group blocked. After the coupling step, the block is
removed from the primary amino group and the coupling reaction is repeated with
the next amino acid. The process continues until the peptide or protein is
completed. Then, the molecule is cleaved from the solid support and any groups
protecting amino acid side chains are removed. Finally, the peptide or protein
is purified to remove partial products and products containing errors. (6)(7)

II.

Combinatorial Synthesis In Solution

Despite the focus on the use of solid-phase techniques for
the synthesis of combinatorial libraries, there have been few examples where
libraries have successfully been made and screened in solution.

The benefit of preparing libraries on resin beads has been
explained as offering advantages in handling, especially where a need to
separate excess reagents from the reaction products is attached to the resin.
In most of case a simple filtration effects a rapid purification and the
product are ready to further synthetic transformation. But it should be
remember that using solid phase chemistry brings several disadvantages as well.
Clearly the range of chemistry available on solid phase is limited and it is
difficult to monitor the progress of reaction when the substrate and product
are attached to the solid phase.

Indeed some groups have expressed a preference for solution
libraries because there is no prior requirement to develop workable solid phase
coupling and linking techniques. The difficulty in purifying large number of
compounds without sophisticated automated processes.(8)

III.

Parallel Solution Phase Synthesis

Manual or automated approaches can be used for the parallel
preparation of tens to hundreds of analogues of a biologically active
substrate. The products are synthesised using reliable coupling and functional
group interconversion chemistry and are progressed to screening after removal
of solvent and volatile by-products. Parallel and orthodox synthesis is
compared below.

Orthodox synthesis usually involves a multistep sequence,
e.g. from A through to the final product D, which is purified and fully
characterised before screening. The next analogue is then designed, guided by
the biological activity of the previous compound, prepared, and then screened.
This process is repeated to optimise both activity and selectivity.

In contrast parallel analogue synthesis involves reaction of
a substrate S with multiple reactants, R1, R2, R3 … Rn, to produce a compound
library of n individual products SR1, SR2, SR3 … SRn. The library is screened,
usually without purification, and with only minimal characterisation of the
individual compounds, using a rapid throughput screening technique. Panlabs
have recently disclosed an interest in making large number of compounds as
individual components using parallel, reliable solution chemistry. Reactions
are pushed to completion by the use of excess quantities of the reactive
reagent, and are isolated by solvent - solvent extraction. There is no further
purification, and thus they prefer to describe these samples as "reaction
products". (9)

Application

Combinatorial chemistry is one of the important new
methodologies developed by academics and researchers in the pharmaceutical,
agrochemical, and biotechnology industries to reduce the time and costs
associated with producing effective, marketable, and competitive new drugs.
Simply put, scientists use combinatorial chemistry to create large populations
of molecules, or libraries, that can be screened efficiently

en masse

.
By producing larger, more diverse compound libraries, companies increase the
probability that they will find novel compounds of significant therapeutic and
commercial value. The field represents a convergence of chemistry and biology,
made possible by fundamental advances in miniaturization, robotics, and
receptor development. And not surprisingly, it has also captured the attention
of every major player in the pharmaceutical, biotechnology, and agrochemical
arena.

While combinatorial chemistry can be explained simply, its
application can take a variety of forms, each requiring a complex interplay of classical
organic synthesis techniques, rational drug design strategies, robotics, and
scientific information management. This article will provide a basic overview
of existing approaches to combinatorial chemistry, and will outline some of the
unique information management problems that it generates. Combinatorial chemistry is a promising new field that stands
to revolutionize the chemical industry, and demands completely new scientific
information management solutions. Combinatorial chemists will be able to meet
their goals if they can find ways to plan libraries quickly, produce libraries
that better interrogate biological assays, and learn from past screening
results. Using software that can orchestrate the planning, building, screening,
and interpretation of synthesized libraries, combinatorial chemistry programs
will begin to realize their promise of minimizing the time and cost associated
with bringing new molecular entities to market. (10)

Solid Support Combinatorial Chemistry In Lead Discovery And Sar Optimization

The widespread acceptance and use of high throughput
screening technologies for the purposes of drug discovery and development has
created an unprecedented demand for small organic molecules. The requirements
for (i) large numbers of diverse and novel chemical entities and (ii) methods
to rapidly optimize the compounds or 'hits' found by screening may not be met
by medicinal chemistry teams employing traditional synthetic methods.
Alternatively, combinatorial chemistry in solution or on solid support, is
being developed to increase the efficiency of organic syntheses. Furthermore,
successful applications of such methods leading to the discovery of therapeutic
candidates have been reported [11].

The Ontogen Approach

Hardware and software platforms have been designed and
developed to significantly increase the number of compounds that a synthetic
organic/ medicinal chemist can prepare in a given period of time. Thus,
libraries of compounds can be created for biological screening and perform medicinal
chemistry optimization strategies ultimately leading to compounds for human
clinical trials (12)

The synthesis of complex small molecules on solid
support using different organic reactions such as multi-step sequential
substitution reactions, multi-component condensation reactions and
pharmacophore modifying reactions has been accomplished (13)

a) Sequentials ubstitution,

b) Multi-component condensation array (MCCA),

c) Pharmacophore transformation

In this fashion complex, diverse, non-peptide, chemical
compound libraries such as:

• beta-lactams;
• hydantoin imides and thioimides;
• imidazoles;
• N-acyl-alpha-amino amides, esters, acids;
• oxazoles;
• phosphonates (alpha-hydroxy, alpha-amino,
  alpha-acylamino);
• phosphinates;
• pyrroles;
• tetra-substituted 5 membered ring lactams;
• tetra-substituted 6 membered ring lactams and
• tetrazoles.

are synthesized on solid support using a wide range of
organic transformations including:

• acylations;
• aldol condensations;
• alkylations;
• Claisen couplings;
• Heck reactions;
• heterocycle forming reactions such as
  condensations, dipolar cycloadditions, annulations, etc.;
• Michael additions;
• Mitsunobu couplings;
• multicomponent condensation reactions
  and
• reductions.

The final products are cleaved into a standard 96 well
microtiter plate, one compound per well. Each plate can be directly submitted
for high throughput screening as well as quantitative and semi-quantitative analysis
in order to assess purity, identity and yield of each compound synthesized.(14)

Design Of Pharmacophore

The design of the pharmacophore basis of a particular
library is driven by the nature of the biological target of interest. The
following types of information are considered, if available:(15)

1. The biology of the target enzyme or
   receptor;
2. The nature of substrate;
3. The mechanism of target-substrate
   interaction;
4. Related literature information;
5. 3-D structural information;

In general, the method of synthesis is designed to allow
full control over each of the individual substituents. This is accomplished
through the selection of the starting materials or inputs (charge, electron
withdrawing/donating, hydrogen bond donor/acceptor, hydrophobicity, steric
bulk, etc.). In general the inputs are chosen to be commercially available. On
occasion, inputs are synthesized for specific cases, fully aware that input
synthesis has the potential to dramatically reduce the efficiencies of the
combinatorial approach.(16)

Conclusion

Combinatorial chemistry
is a technology for creating molecules en masse and testing them rapidly for
desirable properties-continues to branch out rapidly. One-molecule-at-a-time
discovery strategies, many researchers see combinatorial chemistry as a better
way to discover new drugs, catalysts, and materials. Compared with conventional
one-molecule-at-a-time discovery strategies, many researchers see combinatorial
chemistry as a better way to discover new drugs, catalysts, and materials. It is a method for reacting a small number of chemicals to
produce simultaneously a very large number of compounds, called libraries,
which are screened to identify useful products such as drug candidates and a
method in which very large numbers of chemical entities are synthesized by
condensing a small number of reagents together in all combinations defined by a
small set of reactions.

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About Authors:

Patel Ravindra

Student B.Pharm Final Year, Smriti College of Pharmaceutical Education, Indore MP India

Dwivedi Sumeet

Student B.Pharm Final Year, Smriti College of Pharmaceutical Education, Indore MP India

Pandey Deepak

Student B.Pharm Final Year, Smriti College of Pharmaceutical Education, Indore MP India

Shrivastava Satyaendra

Lecturer,Shri Rawatpura College , Durg (C.G.) India