patrick ch14 p1

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Patrick Patrick An Introduction to Medicinal An Introduction to Medicinal

ChemistryChemistry 3/e 3/e

Chapter 14Chapter 14

COMBINATORIAL COMBINATORIAL CHEMISTRYCHEMISTRY

Part 1: Sections 14.1 – 14.4Part 1: Sections 14.1 – 14.4

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ContentsContents

Part 1: Sections 14.1 – 14.4

1. Definition2. Solid Phase Techniques

2.1. Advantages 2.2. Requirements 2.3. Examples of Solid Supports (2 slides)2.4. Anchor or linker

2.4.1. Merrifield resin for peptide synthesis (chloromethyl group)

2.4.2. Wang resin (2 slides)2.4.3. Rink resin (2 slides)2.4.4. Dihydropyran resin (2 slides)

3. Parallel Synthesis3.1. Houghton’s Tea Bag Procedure 3.2. Automated parallel synthesis (2 slides)3.3. Automated parallel synthesis of all 27 tripeptides from 3 amino

acids (2 slides)4. Mixed Combinatorial Synthesis (21 slides)

[41 slides]

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1. DEFINITION1. DEFINITION

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

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

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

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

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2. SOLID PHASE TECHNIQUES2. SOLID PHASE TECHNIQUES

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

2.1 Advantages2.1 Advantages • Specific reactants can be bound to specific beadsSpecific reactants can be bound to specific beads• Beads can be mixed and reacted in the same reaction vesselBeads can be mixed and reacted in the same reaction vessel• Products formed are distinctive for each bead and physically distinct Products formed are distinctive for each bead and physically distinct • Excess reagents can be used to drive reactions to completionExcess reagents can be used to drive reactions to completion• Excess reagents and by products are easily removedExcess reagents and by products are easily removed• Reaction intermediates are attached to bead and do not need to be Reaction intermediates are attached to bead and do not need to be

isolated and purifiedisolated and purified• Individual beads can be separated to isolate individual productsIndividual beads can be separated to isolate individual products• Polymeric support can be regenerated and re-used after cleaving the Polymeric support can be regenerated and re-used after cleaving the

productproduct• Automation is possibleAutomation is possible

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2. 2. SOLID PHASE TECHNIQUESSOLID PHASE TECHNIQUES

2.2 Requirements2.2 Requirements

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

• An anchor or linkerAn anchor or linker• A bond linking the substrate to the linker. The bond must be A bond linking the substrate to the linker. The bond must be

stable to the reaction conditions used in the synthesisstable to the reaction conditions used in the synthesis• A means of cleaving the product from the linker at the endA means of cleaving the product from the linker at the end• Protecting groups for functional groups not involved in the Protecting groups for functional groups not involved in the

synthesissynthesis

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2.3 Examples of Solid Supports2.3 Examples of Solid Supports • Partially cross-linked polystyrene beads hydrophobic in naturePartially cross-linked polystyrene beads hydrophobic in nature

causes problems in peptide synthesis due to peptide foldingcauses problems in peptide synthesis due to peptide folding

• Sheppard’s polyamide resin - more polarSheppard’s polyamide resin - more polar

• Tentagel resin - similar environment to ether or THFTentagel resin - similar environment to ether or THF

• Beads, pins and functionalised glass surfacesBeads, pins and functionalised glass surfaces

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Starting material,reagents and solvent

Swelling

Linkers


2.32.3 • Beads must be able to swell in the solvent used, and remain Beads must be able to swell in the solvent used, and remain

stablestable• Most reactions occur in the bead interiorMost reactions occur in the bead interior

Resin bead

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2.4 Anchor or linker2.4 Anchor or linker

• A molecular moiety which is covalently attached to the solid A molecular moiety which is covalently attached to the solid support, and which contains a reactive functional groupsupport, and which contains a reactive functional group

• Allows attachment of the first reactantAllows attachment of the first reactant

• The link must be stable to the reaction conditions in the The link must be stable to the reaction conditions in the synthesis but easily cleaved to release the final compoundsynthesis but easily cleaved to release the final compound

• Different linkers are available depending on the functional Different linkers are available depending on the functional group to be attached and the desired functional group on the group to be attached and the desired functional group on the productproduct

• Resins are named to define the linker e.g.Resins are named to define the linker e.g. MerrifieldMerrifield

WangWang

RinkRink

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Deprotection

O

aa1aa2aa3

O

aan NH2

2.4.1 Merrifield resin for peptide synthesis (chloromethyl group)2.4.1 Merrifield resin for peptide synthesis (chloromethyl group)

O

O

R

NHBoc

H

O

O

R

NH2

H

HO2C NHBoc

R2H

coupling

O

O

R

NH

H

O

NHBoc

R2H

= resin bead

Cl HO2C NHBoc

R H+

Linker

HF

OH

aa1aa2aa3 aanHO2C NH2

Peptide

Release from solid support

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Linking functional groupO

OH

Wang Resin

2.4.2 Wang resin2.4.2 Wang resin

Linker

OH

Bead Linker

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peptidesynthesis

O Caa1aa2aa3

O

aan NH2

TFAcleavage

OH

aa1aa2aa3 aan NH2HO2C

Fmoc =

O

O

2.4.2 Wang resin2.4.2 Wang resin

OH

Carboxylic Carboxylic acidacid


HO2C NH(Fmoc)

R H

+ O C NH(Fmoc)

R H

O

O C NH2

R H

O

piperidine

deprotection

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Linking functional group

O

NH2

OMe

OMeRink resin

2.4.3 Rink resin2.4.3 Rink resin

Linker

Bead Linker

NH2

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further modifications

2.4.3 Rink resin2.4.3 Rink resin


PrimaryPrimaryamideamide

NH

C

O

RBead Linker

NH2 HO2C R+

NH

C

O

R'TFA

H2N C

O

R'

cleavage

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Linking functional group

O

dihydropyranderivatised resin

O

2.4.4 Dihydropyran resin2.4.4 Dihydropyran resin

Linker

BeadO

Linker

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BeadO

Linker

ROH

PPts O ORfurther modifications

O OR'

TFA

R'HO

2.4.4 Dihydropyran resin2.4.4 Dihydropyran resin

AlcoholAlcohol

AlcoholAlcohol

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3. Parallel Synthesis3. Parallel SynthesisAimsAims

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

• The identity of each structure is knownThe identity of each structure is known

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

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• Each tea bag contains beads and is labelledEach tea bag contains beads and is labelled

• Separate reactions are carried out on each tea bagSeparate reactions are carried out on each tea bag

• Combine tea bags for common reactions or work up Combine tea bags for common reactions or work up proceduresprocedures

• A single product is synthesised within each teabagA single product is synthesised within each teabag

• Different products are formed in different teabagsDifferent products are formed in different teabags

• Economy of effort - e.g. combining tea bags for workupsEconomy of effort - e.g. combining tea bags for workups

• Cheap and possible for any labCheap and possible for any lab

• Manual procedure and is not suitable for producing large Manual procedure and is not suitable for producing large quantities of different productsquantities of different products

3. Parallel Synthesis3. Parallel Synthesis3.1 Houghton’s Tea Bag Procedure3.1 Houghton’s Tea Bag Procedure

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3. Parallel Synthesis3. Parallel Synthesis3.2 Automated parallel synthesis3.2 Automated parallel synthesis

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3. Parallel Synthesis3. Parallel Synthesis3.2 Automated parallel synthesis3.2 Automated parallel synthesis

Wells

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

• Use beads or pins for solid phase supportUse beads or pins for solid phase support

• Reactions and work ups are carried out automaticallyReactions and work ups are carried out automatically

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

• Different product obtained per vesselDifferent product obtained per vessel

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3. Parallel Synthesis3. Parallel Synthesis3.3 Automated parallel synthesis of all 27 tripeptides from 3 amino acids3.3 Automated parallel synthesis of all 27 tripeptides from 3 amino acids

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27 TRIPEPTIDES

27 VIALS

3. Parallel Synthesis3. Parallel Synthesis3.3 Automated parallel synthesis of all 27 tripeptides from 3 amino acids3.3 Automated parallel synthesis of all 27 tripeptides from 3 amino acids

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4. Mixed Combinatorial Synthesis4. Mixed Combinatorial SynthesisAimsAims

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

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

• Useful for finding a lead compoundUseful for finding a lead compound

• Capable of synthesising large numbers of compounds quicklyCapable of synthesising large numbers of compounds quickly

• Each mixture is tested for activity as the mixtureEach mixture is tested for activity as the mixture

• Inactive mixtures are stored in combinatorial librariesInactive mixtures are stored in combinatorial libraries

• Active mixtures are studied further to identify active Active mixtures are studied further to identify active componentcomponent

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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

4. Mixed Combinatorial Synthesis4. Mixed Combinatorial SynthesisThe Mix and Split MethodThe Mix and Split Method

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

ExampleExample - Synthesis of all possible dipeptides using 5 amino acids- Synthesis of all possible dipeptides using 5 amino acids

•Standard methods would involve 25 separate syntheses Standard methods would involve 25 separate syntheses

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combine

Gly

Ala

Phe

Val

Ser

Gly

Ala

Phe

Val

Ser

+

+

+

+

+

Gly

Ala

Phe

Val

Ser

Split

Gly

Ala

Phe

Val

Ser

Gly

Ala

Phe

Val

Ser

Gly

Ala

Phe

Val

Ser

Gly

Ala

Phe

Val

Ser

Gly

Ala

Phe

Val

Ser

Gly Ala Phe Val Ser

Gly

Ala

Phe

Val

Ser

Gly

Gly

Gly

Gly

Gly

Gly

Ala

Phe

Val

Ser

Ser

Ser

Ser

Ser

Ser

Gly

Ala

Phe

Val

Ser

Ala

Ala

Ala

Ala

Ala

Gly

Ala

Phe

Val

Ser

Val

Val

Val

Val

Val

Gly

Ala

Phe

Val

Ser

Phe

Phe

Phe

Phe

Phe

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Synthesis of all possible tripeptides using 3 amino acidsSynthesis of all possible tripeptides using 3 amino acids


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1©MIXMIX


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1©MIXMIX


1©SPLITSPLIT


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