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Combinatorial Chemistry

INTRODUCTION

Combinatorial chemistry is a technique through which large numbers of structurally distinct molecules
may be synthesized at a time and submitted for high throughput screening (HTS) assay. Combinatorial
chemistry is one of the recent methodologies developed by researchers in the pharmaceutical industry to
reduce the time and costs associated with producing successful and competitive new drugs. By accelerating
the process of biologically active compounds, this method is having a profound effect on all the branches
of chemistry, especially on drug discovery. Through the rapidly evolving technology of combinatorial
chemistry, it is now possible to produce compound libraries to screen for novel bioactivities. This powerful
new technology has begun to help pharmaceutical companies to fi nd novel drug candidates quickly, save
significant money in preclinical development costs, and ultimately change their fundamental approach to
drug discovery.
The aim of this chapter is to provide a basic introduction to the field of combinatorial chemistry
describing the development of major techniques and applications.

Principles of Combinatorial Chemistry

The key of combinatorial chemistry is that a large $ %
range of analogues are synthesized using the same
reaction conditions and the same reaction vessels. $ %
In this way, the organic chemist can synthesize
hundreds or thousands of compounds at one time $ %
instead of preparing only a few by a traditional $
methodology. For example, compound A would $ %
have been reacted with compound B to give prod-
uct AB, which would have been isolated after reac-
tion, work up, and purification.
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 Combinatorial Chemistry 67

In contrast to this approach, combinatorial chemistry offers the potential to make every combination of a
compound A1 to An with compound B1 to Bn.
The range of combinatorial techniques is highly diverse, and these products could be made individu-
ally in a parallel or in mixtures, using either solution or solid-phase techniques. Whatever be the technique
used, the common denominator is that productivity has been amplified beyond the levels that have been
routine for the last hundred years.

COMBINATORIAL COMPOUND LIBRARIES

The origin of combinatorial chemistry lies in the use of solid supports for peptide synthesis. By coupling
the growing peptide to a solid support, such as a polystyrene bead, it is possible to use excess reagents and
so ensure that the reaction proceeds to completion. Any excess reagent is simply washed away. In the origi-
nal applications of solid-phase chemistry to peptide synthesis the goal was generally the synthesis of a single
molecular target. A key breakthrough was the recognition that this methodology could be used to generate
large numbers of molecules using a scheme known as split–mix technique. This technique starts with a set of
reagents (which we may also refer to as monomers), each of which is coupled to the solid support. These are
then mixed together and divided into equal-sized aliquots for reaction with the second reagent. The products
from this reaction are reacted with the third reagent, and so on. If the number of reagents at each step are
n1, n2, n3, etc., then the total number of molecules produced is the product is n1n2n3. The size of the library,
thus, increases exponentially with the number of reagents—hence the use of the term ‘combinatorial’.
The original split-mix method is capable of producing extremely large libraries, but it does suffer from
some drawbacks. A particular limitation is that due to the various mixing stages the identity of the product
on each bead is unknown (except for the fi nal reagent). It is important to note, however, that each bead
contains just one discrete chemical entity. In the recent years, many progress has subsequently been made
in the technology for automated synthesis and purification since the first reports were published. These
developments have enabled many of the limitations of the early combinatorial techniques to be overcome,
making automated synthesis methods a common place in both industrial and academic laboratories.

Combinatorial Synthesis on Solid Phase

In 1963, Merrifield pioneered the solid phase synthesis (SPS) work, which earned him a nobel prize.
Merrifield’s SPS concept was first applied for a developed biopolymer, recently it has spread in every field
where organic synthesis is involved. Nowadays, many academic laboratories and pharmaceutical compa-
nies focused on the development of the technologies and chemistry suitable for SPS. This resulted in the
impressive outbreak of combinatorial chemistry, which profoundly changed the approach to new drugs,
new catalyst, or new natural discovery.
The utilization of solid support for the organic synthesis relies on three interconnected requirements.
These are as follows:
1. A cross-linked, insoluble polymeric material should be inert to the condition of synthesis.
2. The linking substrate (linker) to the solid phase that permits selective cleavage of some or all the
products from the solid support during synthesis for analysis of the extent of reaction (s) and ulti-
mately to give the final product of interest.
3. The chemical protection strategy must allow selective protection and deprotection of reactive groups.
68 Drug Design

ADVANTAGES AND DISADVANTAGES OF SOLID SUPPORT REAGENTS

Advantages
• Solid-supported reagents are easily removed from reactions by fi ltration.
• Excess reagents can be used to drive reactions to completion without introducing difficulties in
purification.
• Recycling of recovered reagents is economical, environmentally-sound, and efficient.
• Ease of handling is especially important when dealing with expensive or time-intensive catalysts,
which can be incorporated into flow reactors and automated processes.
• Finely tune chemical properties by altering choice of support and its preparation.
• Toxic, explosive, and noxious reagents are often more safely handled when contained on solid support.
• Reagents on solid-support react differently, mostly more selectively, than their unbound counterparts.
Disadvantages
• Some reagents may not interact well with solid support.
• Ability to recycle reagents on solid support is not assured.
• Reactions may run more slowly due to diffusional constraints.
• Polymeric support materials can be very expensive to prepare.
• Stability of the support material can be poor under harsh reaction conditions.
• Side reactions with the polymer support itself may occur.

Resins for SPS

In solid phase synthesis, resin supports for SPS include spherical beads of lightly cross-linked gel type poly-
styrene (GPS) (1%–2% divinylbenzene) and poly(styrene-oxyethylene) graft copolymers, which are func-
tionalized to allow attachment of linkers and substrate molecules. Each of these materials has advantages
and disadvantages, depending on the particular application. There are several types of resins available for
different type of reactions, which has been mentioned in Table 5.1.

Table 5.1 Types of resins and reactions.

Protecting Deprotecting
Type of Resin Chemical Structure of Resin Group Reagent
2&+

Rink amide resin 2 2&+ Fmoc 95% TFA

5
1
+
2

(Continued)
 Combinatorial Chemistry 69

Table 5.1 (Continued)

Protecting Deprotecting
Type of Resin Chemical Structure of Resin Group Reagent
&+

MBHA resin 2 Boc HF, TFMSA

5
1
+

4-Sulfamylbutyryl AM 2 2 2 2 1. TMS-CHN2
resin 6 Fmoc 2. RSH/
5 1 1
+ + NaSPhcat

2
Sieber Amide resin 1 Fmoc 95% TFA
5
+
2

2
DHP HM resin Fmoc 95% TFA

1
HMBA-AM resin + Fmoc NaBH4/EtOH
5 2

2
2
+&2 2
4-(4-Formyl-3- 1
methoxyphenoxy) + Fmoc 95% TFA
5 1
butyryl AM resin
2 5
Brominated PPOA resin 2 Boc NaOH/
2 Dioxane
2 &+ 1
+
5 2
2

(Continued)
70 Drug Design

Table 5.1 (Continued)

Protecting Deprotecting
Type of Resin Chemical Structure of Resin Group Reagent
12

NaOH/
Oxime resin Boc
Dioxane
5 2 1

2
1% TFA in
2-Chlorotrityl chloride 5 2 Fmoc DCM, AcOH/
resin
DCM/TFE

2
2
1
+ 1% TFA in
HMPB-AM resin 2
Fmoc
5 DCM

2 2&+

5 2
Merrifield resin Boc HF/TFMSA
2
2

5 2 2
PAM resins Boc HF/TFMSA
1
+
2

5 2
Wang resin Fmoc 95% TFA
2

1 ROH/DIPEA/
HMBA-AM resin +
5 2 DMF