combinatoral chemistry

1Progressive Education Society’s College of

Pharmacy, Yamunanagar Nigdi Pune-411044

COMBINATORIAL CHEMISTRY

A seminar on

Submitted to

Savitribai Phule Pune UniversityFor The First Semister Seminar

Under the guidance ofMr. P. N. Sable

(Assistant Professor)Department of Pharmaceutical Chemistry

byMiss. S.F.Pimple

M. Pharmacy( Pharmaceutical Chemistry)Sem – I, Roll No.:-CH102

2

Contents

1. Introduction 1.1. Definition

1.2. History 2. Solid Phase Techniques

2.1. Advantages 2.2. Requirements 2.3. Examples of Solid Supports2.4. Anchor or linker 2.4.1. Merrifield resin for peptide synthesis

(chloromethyl group)2.4.2. Wang resin2.4.3. Rink resin 2.4.4. Dihydropyran resin

3. Parallel Synthesis3.1. Houghton’s Tea Bag Procedure 3.2. Automated parallel synthesis 3.3. Automated parallel synthesis of all 27

tripeptides from 3 amino acids4. Mixed Combinatorial Synthesis 5. Applications

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1. INTRODUCTION

1.1. Definition

• The automated synthesis of a large number of compounds in a short time period using a defined reaction route and a large variety of reactants

• Normally carried out on small scale using solid phase synthesis and automated synthetic machines

Parallel synthesis • Single product formed in each reaction vessel• Useful for SAR and drug optimisation

Synthesis of mixtures• Mixtures of compounds formed in each reaction vessel• Useful for finding lead compounds

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1.2. History

Bruce MerrifieldBorn July 21, 19211984 Nobel Prize in Chemistry

A little history of solid-phase synthesis

Year198419851986

1986-901988

19901991

1991

1992

1992-93

MilestonesLimited peptide library with the multipin technologyLimited peptide library using tea bagIterative approach on solid phase peptide library screening using the multi-pin synthesisDevelopment of Polynucleotide library methodsIntroduction of the split synthesis method on synthesizing a limited library of solution peptideLight directed parallel peptide synthesis of library of 1024 peptide onclipSuccessful application of the filamentous phage displayed peptide library method on a huge library of peptidesIntroduction of the one bead compound concept and successful application of this concept to a huge bead bound peptide librarySuccessful application of the iterative approch on a huge solution phase peptide librarySynthesis of a limited benzodiazepine based small molecule library development of encoading methods for the one-bead-one compound non-peptide library

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2. SOLID PHASE TECHNIQUES

• Reactants are bound to a polymeric surface and modified whilst still attached. Final product is released at the end of the synthesis

2.1. Advantages

• 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 re-used after cleaving

the product• Automation is possible

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2.2. Requirements

• A resin bead or a functionalised surface to act as a solid support

• An anchor or linker

• A bond linking the substrate to the linker. The bond must be stable to the reaction conditions used in the synthesis

• A means of cleaving the product from the linker at the end

• Protecting groups for functional groups not involved in the synthesis

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2.3. Examples of Solid Supports • Partially cross-linked polystyrene beads hydrophobic in nature

causes problems in peptide synthesis due to peptide folding

• Sheppard’s polyamide resin - more polar

• Tentagel resin - similar environment to ether or THF

• Beads, pins and functionalised glass surfaces

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Starting material,reagents and solvent

Swelling

Linkers


2.3.• Beads must be able to swell in the solvent used, and

remain stable.

• Most reactions occur in the bead interior

Resin bead

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2.4. 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 produc

• Resins are named to define the linker e.g. 1. Merrifield2. Wang 3. Rink

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2.4.1. Merrifield resin for peptide synthesis (chloromethyl group)

= resin bead Linking functional group

Cl HO2C NHBoc

R H+

Linker

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Linking functional groupO

OH

Wang Resin

2.4.2 . Wang resin

Linker

OH

Bead Linker

12

Linking functional group

O

NH2

OMe

OMeRink resin

2.4.3. Rink resin

Linker

Bead Linker

NH2

13

Linking functional group

O

dihydropyranderivatised resin

O

2.4.4. Dihydropyran resin

Linker

BeadO

Linker

14

3. Parallel Synthesis

Aims

• To use a standard synthetic route to produce a range of analogues, with a different analogue in each reaction vessel, tube or well

• The identity of each structure is known

• Useful for producing a range of analogues for SAR or drug optimisation

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• Each tea bag contains beads and is labelled• Separate reactions are carried out on each tea bag• Combine tea bags for common reactions or work up

procedures• A single product is synthesised within each teabag• Different products are formed in different teabags• Economy of effort - e.g. combining tea bags for workups• Cheap and possible for any lab• Manual procedure and is not suitable for producing large

quantities of different products


3.1. Houghton’s Tea Bag Procedure 22

16AUTOMATED SYNTHETIC MACHINES


3.2. Automated parallel synthesis

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3.2. Automated parallel synthesis Wells

• Automated synthesisers are available with 42, 96 or 144 reaction vessels or wells

• Use beads or pins for solid phase support

• Reactions and work ups are carried out automatically

• Same synthetic route used for each vessel, but different reagents

• Different product obtained per vessel

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ETC


3.3. Automated parallel synthesis of all 27 tripeptides from 3 amino acids

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27 TRIPEPTIDES

27 VIALS


3.3. Automated parallel synthesis of all 27 tripeptides from 3 amino acids

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Advantages

No deconvolution is required.

No risk of synergistic effects leading to false positive results during screening.

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4. Mixed Combinatorial Synthesis

Aims

• To use a standard synthetic route to produce a large variety of different analogues where each reaction vessel or tube contains a mixture of products

• The identities of the structures in each vessel are not known with certainty

• Useful for finding a lead compound• Capable of synthesising large numbers of compounds quickly• Each mixture is tested for activity as the mixture• Inactive mixtures are stored in combinatorial libraries• Active mixtures are studied further to identify active

component

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Glycine (Gly)Alanine (Ala)Phenylalanine (Phe)Valine (Val)Serine (Ser)

25 separateexperiments

Gly-GlyGly-AlaGly-PheGly-ValGly-Ser

Ala-GlyAla-AlaAla-PheAla-ValAla-Ser

Phe-GlyPhe-AlaPhe-PhePhe-ValPhe-Ser

Val-GlyVal-AlaVal-PheVal-ValVal-Ser

Ser-GlySer-AlaSer-PheSer-ValSer-Ser


The Mix and Split Method

•Combinatorial procedure involves five separate syntheses using a mix and split strategy

Example - Synthesis of all possible dipeptides using 5 amino acids

•Standard methods would involve 25 separate syntheses

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combine

Gly

AlaPhe

Val

Ser

Gly

Ala

Phe

Val

Ser

+

+

+

+

+

Gly

Ala

Phe

Val

Ser

Split

Gly

AlaPhe

Val

Ser

Gly

AlaPhe

Val

Ser

Gly

AlaPhe

Val

Ser

Gly

AlaPhe

Val

Ser

Gly

AlaPhe

Val

Ser

Gly Ala Phe Val Ser

Gly

AlaPhe

Val

Ser

Gly

Gly

Gly

Gly

Gly

Gly

AlaPhe

Val

Ser

Ser

Ser

Ser

Ser

Ser

Gly

AlaPhe

Val

Ser

Ala

Ala

Ala

Ala

Ala

Gly

AlaPhe

Val

Ser

Val

Val

Val

Val

Val

Gly

AlaPhe

Val

Ser

Phe

Phe

Phe

Phe

Phe

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Synthesis of all possible tripeptides using 3 amino acids



25



26



27

MIX



28

SPLIT



29



30



31



32

MIX



33

SPLIT



34



35



36



37

No. of Tripeptides

9 9 9



38

No. of Tripeptides

9 9 9

27 Tripeptides 3 Vials



39

TEST MIXTURES FOR ACTIVITY



40

Synthesis each tripeptide and test



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20 AMINO ACIDS HEXAPEPTIDES

34 MILLION PRODUCTS

(1,889,568 hexapeptides / vial)

etc.



etc.

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Large libraries are readily available.Advantages

DisadvantagesComplex mixtures are formed.

Deconvolution or tagging is required.

Synergistic effect may be observed during screening, leading to false positive.

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Limitations of combinatorial synthesis Formation of “by-product” (unexpected product) lead to error.

So many beads are required for combinatorial chemistry.

Probability of finding of sample is very less.

It require practical details of weight and volume.

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Applications

Combinatorial lead optimization of dihyrofolate reductase inhibitor

Synthesis of peptoidsCombinatorial lead optimization of Neuropeptide-FF antagonistGeneration of benzodiazepine libraryCombinatorial lead optimization of Histamine H3 receptor antagonist

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Case study

“Solid-phase synthetic approach to pH-independent rhodamine type fluorophores”

L. Brulikova, et.al; Organic & Biomolecular Chemistry, The Royal Society of Chemistry 20xx, J . Name., 2013, 1 – 3.

Procedure:- Solid-phase synthesis

Linkers :- Wang resin

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Conclusion Combinatorial chemistry field has advanced rapidly over past ten years. This method has been considered as a most important advancement in medicinal chemistry and is widely exploited by pharmaceutical industries in drug discovery. Combinatorial chemistry is a process for integration of synthesis and screening. Combinatorial chemistry can now be applied to various new drug target development from our recent understanding of the molecular basis of disease. By considering all aspects it is understandable that this method will definitely become helpful to mankind in development of new drugs and lead molecule at lower expenses.

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References1. Eric M. Gordon, Combinatorial Chemistry and Molecular Diversity In Drug

Discovery, weley liss publication (1998),

2. Patrick Bultinck, Computational Medicinal Chemistry for Drug Discovery, dekkar publication, Page No. 617-634.

3. Mike S. Lee, Integrated Stratergies for Drug Discovery Using Mass Spectroscopy, wiley interscience publication (2006), Page No.231-255.

4. Filvio Gualfieri, New Trends in Synthetic Medicinal Chemistry, wiley VCH publication, 7th volume (2000), Page No.39-77.

5. Richard B. Silverman, The Organic Chemistry of Drug Design and Drug Action, Elsevier publication, 2nd edition (2005), Page No. 34-77.

6. Stanislav Miertus, Giorgio Fassina and P. F. Seneci, Concepts Of Combinatorial Chemistry and Combinatorial Technologies, Chem. Listy issue-94, Refer·ty, 2000, Page No.1104 – 1110.

7. Arpad Furka, Combinatorial Chemistry Principles and Techniques, published by arpad furka in electronic form budapest, 2007, Page No. 1-199.

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9. Xiaoyuan Chen & Sanjiv S Gambhir, Significance of One-bead-one-compound Combinational Chemistry, Nature Chemical Biology, volume 2, issue 7, 2006, Page No. 351-352.

10.Burkhard König, Combinatorial Chemistry and Synthesis on Solid Support, University of Regensburg, Page No.1-151.

11.Sandra Fonseca, Abel Rosado et.al., Molecular Locks and Keys: The Role of Small Molecules in Phytohormone Research, Frontiers in Plant Science, volume 5, issue-709, 2014, Page No.1-17.

12.S. N. Pandeya and D. Thakkar, Advances in Contemporary Research Combinatory Chemistry -A Novel Method in Drug Discovery and its Application, Indian Journal of Chemistry, volume B44, 2005, Page No. 335-348.

13.A. G. Orrillo, A. M. Escalante et al., Dithioacetal Exchange :A New Reversible Reaction for Dynamic Combinatorial Chemistry, Chem. Eur.J., , volume 22, 2016, Page No. 6746 –6749.

14.A. J. Dyson, Barbara Kirchner et.al., Combining Quantum Chemistry with Mechanistic Simulations to Determine Liquid Properties, Chemistry at The University of Basel, Chimia, volume 5, issue-53, 1999, Page No. 205-206.

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