Combinatorial chemistry
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Combinatorial Chemistry. Advanced Medicinal Chemistry ( Pharm 5219): Section A. Md. Saifuzzaman Assoc. Professor [email protected] Ref.: An Introduction to Medicinal Chemistry , 3 rd ed. 2005, G.L.Patrick , Oxford University press. The Solid support.

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Combinatorial Chemistry

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Combinatorial chemistry

Combinatorial Chemistry

Advanced Medicinal Chemistry

(Pharm 5219): Section A

Md. Saifuzzaman

Assoc. Professor

[email protected]

Ref.: An Introduction to Medicinal Chemistry, 3rd ed. 2005, G.L.Patrick, Oxford University press


The solid support

The Solid support

Earliest form of resin (used by Merrifield) – polystyrene beads – styrene cross-linked with 1% divinylbenzene.

Derivatized with a chloromethyl group (anchor/linker) – amino acids can be coupled via an ester group.

This ester group is stable to reaction conditions but cleaved at end of synthesis using acids (e.g., HF).


The solid support1

The Solid support

Disadvantages of polystyrene beads

Growing peptide chain is hydrophobic, so not solvated and folds itself & forms internal H bonds

thus, hinders access of further amino acids to growing chain


The solid support2

The Solid support

Therefore, more polar solid phages – developed e.g., Sheppard’s polyamide.

For non-peptides, Tentagel resin

80% polyethylene glycol grafted to cross-linked polystyrene

Provides ether or tetrahydrofuran like environment.


Solid support

Solid support

Beads should be capable of swelling in solvent

Most reactions in solid phase synthesis take place in interior of beads rather than surface.

Each bead - a polymer and swelling involves unfolding of the polymer chains so that solvent and reagents can move between the chains into the core of polymer.


Solid support1

Solid support

Besides bead, pins – designed to maximize surface area, maximize amount of compounds linked to solid support.

Functionalized glass surfaces – suitable for oligoneucleotide synthesis.


Anchor linker

Anchor / Linker

A molecular unit covalently attached to polymer chain making up solid support

Contains a reactive functional group with which starting material can react and attach to the resin

Resulting link – stable to reaction conditions but cleavable to release final product

Most linkers – in interior of polymer beads, so swelling is important.


Anchor linker1

Anchor / Linker

Choice of linkers depends on…..

Functional group present on starting material

Functional group to be present on final product upon release


Anchor linker2

Anchor / Linker

Resins of different linkers have different names

Wang resin – has a linker suitable for attachment and release of carboxylic acids

Rink resin – for attachment of carboxylic acids and release of carboxamides

Dihydropyran-derivatized resin – suitable for attachment and release of alcohols


Anchor linker3

Anchor / Linker

Wang resin –

Used in peptide synthesis where N-protected amino acid – linked to resin by means of ester link.

Ester link – remains stable to coupling and deprotection steps in synthesis and cleaved using trifluoroacetic acid (TFA) to release final product.


Anchor linker4

Anchor / Linker

Rink resin –

Attach starting material (with carboxylic acid) via amide link

When reaction is complete, treatment with TFA releases final product with primary amide group.


Anchor linker5

Anchor / Linker

Dihydropyran-derivatized resin–

Attach primary & secondary alcohols in presence of pyridinium 4-toluenesulfonate (PPts) in dichloromethane.

Upon completion of reaction, cleavage using TFA.


Combinatorial chemistry

Combinatorial synthesis with aDihydropyran-derivatized resin


Protecting groups

Protecting groups

Important functional groups (not involved in reaction) – should be protected

Selection is extremely important

Should be stable in reaction condition but capable of being removed under mild conditions after synthesis


Boc benzyl protection strategy

Boc/benzyl protection strategy

N-terminus of each amino acid – protected by a tert-butyloxycarbonyl (Boc) group

After adding a.a. with growing peptide chain, Boc group is removed with TFA to free up amino group

Next protected a.a. = coupled on to the chain

Bond connecting new peptide to linker – stable to TFA, so remains unaffected by synthesis; but susceptible to strong acid and after synthesis, HF – used to release peptide


Boc benzyl protection strategy1

Boc/benzyl protection strategy

  • An amide that is less stable than the protein amide is formed and then removed

  • The tert-butoxycarbonyl amide (BOC) protecting group is introduced with di-tert-butyl dicarbonate

  • Removed by brief treatment with trifluoroacetic acid

21


Boc benzyl protection strategy2

Boc/benzyl protection strategy

Functional groups on a.a. residues – to be protected during synthesis (that protecting group has to be stable to TFA)

Benzyl-type groups – stable to TFA but susceptible to HF


Boc benzyl protection strategy3

Boc/benzyl protection strategy

So, HF both releases final peptide & deprotects residues

Disadvantage of using HF:

nasty chemical

dissolves glass

so use Teflon equipment

too harsh condition – decomposition of peptide

serious health risk (HF on skin!!!!)


Fmoc t bu strategy

Fmoc/t-Bu strategy

9-fluorenylmethoxycarbonyl (Fmoc) group – for terminal amino group – removed using mild base (e.g., piperidine)

Functional groups on a.a. residues – to be protected with t-butyl group – can be removed by TFA

Orthogonal strategy – base for removing Fmoc & acid for t-butyl


Fmoc t bu strategy1

Fmoc/t-Bu strategy

Link to resin – susceptible to TFA, no need to use HF

Both peptide cleavage & functional group deprotection simultaneously


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