The Combinatorial Chemistry is a scientific method in which a very large number of chemical entities are synthesized by condensing a small number of chemical compounds together in all combinations defined by a small set of chemical reactions.

1. PREPARED BY: GUIDED BY:
SUNIL YADAV Prof. Mahesh Kumar Kataria
M.Pharm HOD Department of Pharmaceutics.
Seth G. L. Bihani S. D. College of Technical Education
Institute of Pharmaceutical Sciences & Drug Research, Sri Ganganagar, Rajasthan 1

2. Combinatorial chemistry
 Combinatorial chemistry (Combichem) is a collection of techniques which
allow for the synthesis of multiple compounds at the same time.
Conventional Reaction: A + B AB
Combinatorial Chemistry: A1- n + B1- n A1- n B1- n
 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.
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3. Need for Combichem
Problems with Traditional/Conventional Synthesis:
 1 chemist 1 molecule
 Can only make one molecule at a time.
 Each synthesis very time consuming.
 Multistep synthesis have loss at each step.
 Purification of products very time-consuming between steps.
 Yields can be low and produces very few molecules at a time for testing.
 Slower lead generation.
 Hundreds of molecules in a month are generated.
 High risk of failure.
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4. Need for Combichem
Benefits with Combinatorial Synthesis:
 1 chemist multiple molecules
 Can make multiple molecules at a time.
 The time & cost associated with the generation & analysis of each
individual molecule is significantly less when compared to the time & cost
of an individual synthesis.
 Yields can be high and produces many molecules at a time for testing.
 Faster lead generation.
 Thousands of molecules in a month are generated.
 Low risk of failure.
 Multiple molecules synthesized at a time.
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5. Definition of Combichem
 Combinatorial chemistry may be defined as the systematic and repetitive,
covalent connection of a set of different “building blocks” of varying
structures to each other to yield a large array of diverse molecular entities.
 Combinatorial chemistry encompasses many strategies and processes for
the rapid synthesis of large, organized collections of compounds called
libraries. The collection is then tested for the biological activity. Finally the
active compound is identified and made in quantity as a single compound.
 Thus the combinatorial chemistry approach has two phases:
1. Making a library.
2. Finding the active compound
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6. History of Combichem
 Although combinatorial chemistry has only really been taken up by the
industries since the 1990s, its roots can be seen as far back as the 1960s
when a researcher at Rockefeller University, Bruce Merrifield, developed a
way to make peptides by solid-phase synthesis.
 Bruce Merrifield won the Nobel prize in chemistry in 1984 for his work on
solid-phase synthesis. During this time, automated peptide synthesizer
technology was in its infancy, and the preparation of individual peptides
was a challenge.
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7. History of Combichem
 The field in its modern dimensions only began to take shape in the 1980s,
when in 1984, research scientist H. Mario Geysen his coworker developed
a technique for synthesizing peptides on pin-shaped solid supports and in
1985, Richard Houghten developed a technique for creating peptide
libraries in tiny mesh "tea bags" by solid-phase parallel synthesis.
 Another early pioneer was Dr. Árpád Furka (considered to be one of the
fathers of combinatorial synthesis) who introduced the commonly used
split-and-pool method in 1988, which is used to prepare millions of new
peptides in only a couple of days and also for synthesizing organic
libraries.
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8. Principle of Combichem
 To prepare a large number of different compounds at the same time Instead
of synthesizing compounds in a conventional one at a time manner and
then to identify the most promising compound for further development by
high throughput screening (HTS).
 In combinatorial synthesis different compounds are generated
simultaneously under identical reaction conditions in a systematic manner,
so that ideally the products of all possible combinations of a given set of
starting materials (termed building blocks) will be obtained at once. The
collection of these finally synthesized compounds is referred to as a
combinatorial library. The library is then screened for useful properties and
the active compounds are identified.
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9. Principle of Combichem
 Example:
A + B AB (A) Conventional approach
A1 - n + B1 - n A1 – n B1 – n or (B) Combinatorial approach
A1 B1 A1B1 A1B2 A1Bn
A2 B2 A2B1 A2B2 A2Bn
An Bn AnB1 AnB2 AnBn
(A) In a conventional synthesis one starting material A reacts with one reagent
B resulting in one product AB.
(B) In a combinatorial synthesis different building blocks of type A (A1-An)
are treated simultaneously with different building blocks of type B (B1-Bn)
according to combinatorial principles, each starting material A reacts
separately with all reagents B resulting in a combinatorial library A1-nB1-n.
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10. Types of Combichem
 Combinatorial chemistry is of two types:
 SOLID PHASE COMBINATORIAL CHEMISTRY
(Compound library synthesized on solid phase such as resin bead)
 SOLUTION PHASE COMBINATORIAL CHEMISTRY
(Compound library synthesized in solvent in the reaction flask)
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11. Solid phase Combichem
STEPS:
 Attach the starting molecule to an inert solid/resin bead.
 Addition of excess of reagents to the solution.
 Separation of products (attached to resin beads) by simple filteration.
 Cleavage & isolation of products from the beads.
REQUIREMENTS:
 Solid support (Resin beads)
 An anchor or linker.
 A bond linking the substrate to the linker.
 A means of cleaving the product from the linker at the end.
 Protecting groups
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12. Solid phase Combichem
EXAMPLES OF SOLID SUPPORTS:
 Partially cross-linked polystyrene beads: Polystyrene is cross linked
with divinyl benzene, hydrophobic in nature, causes problems in peptide
synthesis due to peptide folding.
 Sheppard’s polyamide resin - more polar.
 Tentagel resin - similar environment to ether
 Beads, pins and functionalised glass surfaces
CHARACTERISTICS OF SOLID SUPPORT:
 Beads must be able to swell in the solvent used, and remain stable.
 Most reactions occur in the bead interior.
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Resin bead Swelling
Linkers
Starting material,
reagents and solvent

13. Solid phase Combichem
ANCHOR OR LINKER:
 A molecular moiety which is covalently attached to the solid support,
and which contains a reactive functional group.
 Allows attachment of the first reactant.
 The link must be stable to the reaction conditions in the synthesis but
easily cleaved to release the final compound.
 Different linkers are available depending on the functional group to be
attached and the desired functional group on the product.
 Resins are named to define the linker e.g.
 Merrifield resin
 Wang resin
 Rink amide resin
 Photolabile anchors
 Traceless anchors
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14. Solid phase Combichem
PROTECTING GROUPS:
 A protecting group is reversibly attached to the functional group to
convert it to a less reactive form.
 When the protection is no longer needed, the protecting group is cleaved
and the original functionality is restored.
 protecting group to be stable under the expected reaction conditions and
to be cleavable - if possible-at mild reaction conditions.
 Some of the protecting groups most widely used in peptide synthesis
are:
 Benzyl carbonyl (Z) group
 t-butoxy carbonyl (Boc) group
 9-fluorenyl methoxy carbonyl (Fmoc) group
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15. Solid phase Combichem
ADVANTAGES OF SOLID PHASE SYNTHESIS:
 Specific reactants can be bound to specific beads.
 Beads can be mixed and reacted in the same reaction vessel.
 Products formed are distinctive for each bead and physically
distinct.
 Excess reagents can be used to drive reactions to completion.
 Excess reagents and by products are easily removed.
 Reaction intermediates are attached to bead and do not need to be
isolated and purified.
 Individual beads can be separated to isolate individual products.
 Polymeric support can be regenerated and reused after cleaving
the product.
 Automation is possible
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16. Solid phase Combichem
DISADVANTAGES OF SOLID PHASE SYNTHESIS:
 Not all syntheses can be done solid phase.
 Some molecules don’t attach well to beads
 Some chemistry just doesn’t work in this fashion
 Removal of product from bead, can be damaging to product if not
careful
 Typically, kinetics not the same.
 Reaction rates can be slower
 Difficult to monitor the progress of reaction when the substrate and
product are attached to the solid phase.
 Assessment of the purity of the resin attached intermediates is also
difficult.
 Purifying the final product after cleavage from the resin also proves to
be a challenge.
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17. Solution phase Combichem
 All chemical reactions are conducted simultaneously, preferably in well-
ordered sets (arrays) of reaction vessels in solution.
 Soluble polymer are used as support for the product.
Limitation
 when numbers of reagents are taken together in a solution
 it can result in several side reactions and
 Lead to polymerization giving a tarry mass.
Rectification
 A new approach is developed in which all chemical structure
combinations are prepared separately, in parallel on a giving building
block using an automated robotic apparatus.
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18. Combinatorial techniques
 There are mainly two combinatorial techniques:
 SPLIT & MIX SYNTHESIS/PORTIONING-MIXING SYNTHESIS
(One bead-one compound library)
 PARALLEL SYNTHESIS
(One vessel-one Compound library)
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19. Split and mix synthesis
 Good to generate large libraries.
 Resin beads are split into
different vessels.
 Then reacted, shuffled, and
split again.
 1000 compund library prepared
from 10 building blocks in each
step  30 reaction steps.
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20. Split and mix synthesis
ADVANTAGES OF SPLIT & MIX SYNTHESIS:
 Only few reaction vessels are required.
 Large libraries (up to 105 compounds) can be quickly generated.
DISADVANTAGES OF SPLIT & MIX SYNTHESIS:
 Large amount of resin beads are required.
 The amount of synthesized product is small.
 Complex mixtures are formed.
 Deconvolution or tagging required.
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21. Parallel synthesis
 Each compound is synthesized
in specific reaction vessel.
 Each starting material is
reacted with each building
block separately.
 Then product is split into
portions, reacted with different
buildind block separately again.
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22. Parallel synthesis
ADVANTAGES OF PARALLEL SYNTHESIS:
 It creates compounds individually & in its own vessels.
 Identity of products are already known.
 Each compound is substantially pure in its location.
DISADVANTAGES OF PARALLEL SYNTHESIS:
 Applicable only for medium libraries.
 Large amount of vessels required.
 Large number of reactions to be performed.
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23. Screening methods
 Screening is the process of determining whether compounds in a
chemical library have a desired chemical or biological activity, without
necessarily identifying the precise chemical nature of the compound(s)
being screened.
 METHODS OF SCREENING OF COMBICHEM LIBRARIES:
 Test mixture in solution
 Test individual compounds in solution
 Test compounds on the bead
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24. Encoding methods
 The process of identification of active compound in a mixture of
compounds is known as Encoding.
 METHODS OF ENCODING OF COMBICHEM LIBRARIES:
 Positional encoding (iterative resynthesis and rescreening)
 Chemical encoding (Tagging)
 Electronic encoding
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25. Positional Encoding
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26. Chemical Encoding
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SUNIL YADAV
Email – Sunilkamalyadav@gmail.com