Medical Chemistry

1. Combinatorial SynthesisCombinatorial SynthesisCombinatorial SynthesisCombinatorial Synthesis

2. Combinatorial chemistry in
medicinal chemistry

3.  Solid phase techniques
 Protecting groups and synthetic strategy
 Methods of parallel synthesis
 Isolating the active component in a mixture:
deconvolution
 Structure determination of the active Structure determination of the active
compound(s)
 Limitations of combinatorial synthesis
Ref: An introduction to medicinal chemistry, G. L. Patrick,
3rd Edition.

4. 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
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• 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

5. Solid phase techniques

6. Solid phase technique
Protecting groups and
synthetic strategy
 Fmoc/t-Bu strategy
http://www.sigmaaldrich.com
/img/assets/22080/Solid_ph
ase_syn_schem_SMALL.gif

7. Solid phase techniques

8. Solid phase techniques

9. Mixed combinatorial synthesis
 Combinatorial or compound libraries

10.  The mix and split method
Mixed combinatorial synthesis

11.  The mix and split method
Mixed combinatorial synthesis

12. Mixed combinatorial synthesis
 The mix and split method

13. Automated Parallel synthesis
Houghton’s teabag procedure

14. • 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
Parallel Synthesis
Houghton’s Tea Bag Procedure
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

15. Isolating the active component in a
mixture: deconvolution
 Micromanipulation: colour reaction
 Recursive deconvolution

16.  Sequential
release

17. SOLID PHASE TECHNIQUES
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• 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

18. SOLID PHASE TECHNIQUES
Examples of Solid Supports
• Partially cross-linked polystyrene beads hydrophobic in natur
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

19. SOLID PHASE TECHNIQUES
• Beads must be able to swell in the solvent used, and remain
stable
• Most reactions occur in the bead interior
Starting material,
reagents and solvent
Swelling
Linkers
Resin bead

20. Resin beads
•Cross-linked, insoluble, solvent swellable polymeric
materials, inert to the conditions of synthesis
•80-200 µm
• Preparation:-
1. Addition and dispersion of an organic phase of monomer and
cross-linker in an aqueous solutioncross-linker in an aqueous solution
2. Dissolvation of a free radical initiator in the organic mixture
3. Raising of temperature starts polymerisation to form resin
beads
4. Collection of resin beads by filtration and washing of unreacted
monomers and the aqueous phase

21. A. Cross-linked polystyrene
Lightly cross-linked gel type
polystyrene (GPS) has been most
widely used due to its common
availability and inexpensive cost
which are functionalised with
chloromethyl-, aminomethyl- etc.chloromethyl-, aminomethyl- etc.
They absorb large relative volumes of
organic solvents (swelling) and
changed to a solvent-swollen gel,
where the reactive sites are accessed
by diffusion of reactants.

22. A. Cross-linked polystyrene
• First used by Merrifield
• Gel type polymer made from cross-linked polystyrene
• 1% divinylbenzene is added to styrene to link
polystyrene chain together.
• Can not be used with highly electrophilic reagents
• Reaction condition has to be below 130 oC• Reaction condition has to be below 130 oC

23. B. Polyamide resins
• N,N-dimethylacrylamide as backbone, cross-linked with N,N`-
bisacryloylethylenediamine, functionalised through N-acryloyl-N`-Boc-
b-alaninylhexamethylenediamine.
• Swells in polar solvent, limited in less polar solvent.
•Sheppard designed polyacrylamide polymers for peptide synthesis as it
was expected that these polymers would more closely mimic the
properties of the peptide chains themselves and have greatly improved
solvation properties in polar, aprotic solvents (e.g. DMF, or N-methyl
pyrrolidinone).

24. C. Controlled pore glass
• Macropourous polymers with rigid open pores to permit
a ready and continuous solvent flow
• Glass-derived bead material
• Compatible to any type of solvent
• Stable in aggressive reagents and extremes of pressure
and temperature.and temperature.
• Used for combinatorial synthesis of peptides and
oligonucleotides.

25. D. Tentagel resin
• Polystyrene glycol attached to cross-linked
polystyrene through ether link
• Prepared by the polymerisation of ethylene
oxide on cross-linked polystyrene (derivatised
with tetraethylene glycol to give polyethylene
glycol chains) long flexible chains that terminate
with a reactive site spatially separated from the
more rigid polystyrene backbone.more rigid polystyrene backbone.
• TGR carry polyethylen glycol chains of about (3 kDa), 70 – 80% of
resin weight
• The hydrophilic nature of the resin facilitate release of product in
aqueous environment
• Benefits of the soluble polyethylene glycol support with the
insolubility and handling characteristics of the polystyrene bead. These
beads display relatively uniform swelling in a variety of solvents from
medium to high polarity ranging from toluene to water.

26. E. Magnetic beads
• Nitration of polydivinylbenzene and reduction of
nitrogroup with ferrous sulfate hexahydrate results in
production of ferrous ferric ions within the bead.
• These ions are converted into magnetic crystals by
addition of concentrated NH4OH solution and gentle
heating.heating.
• The beads contain 24 – 32% iron by wight.
• The beads are used for synthesis of protected dipeptide
like Fmoc-Phe-Ala-OH.

27. SOLID PHASE TECHNIQUES
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• 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
Wang
Rink

28. Linkers
• Regenerate the originally linked functionality (-OH or -
COOH)
• Convert from one functional group to another (-COOH to
–CONH2)
• Totally remove the functionality on cleavage.
• Types:-• Types:-
A. Carboxylic acid linker
B. Carboxamide linker
C. Alcohol linker
D. Amine linker
E. Traceless linker
F. Light cleavable linker

29. A. Carboxylic acid linker
•The first linking group used for peptide synthesis bears the name of
the father of solid phase synthesis.
• Merrifield resin is cross-linked polystyrene functionalised with a
chloromethyl group. The carbonyl group is attached by the
nucleophilic displacement of the chloride with a cesium carboxylate
salt in DMF.
• Cleavage to regenerate the carboxylic acid is usually achieved byCleavage to regenerate the carboxylic acid is usually achieved by
hydrogen fluoride.

30. A. Carboxylic acid linker
• The second class of linker used for carboxylic acid is the Wang
linker. This linker is generally attached to cross-linked polystyrene,
TentaGel and polyacrylamide to form Wang resin.
• It was designed for the synthesis of peptide carboxylic acids using
the Fmoc-protection strategy, and due to the activated benzyl
alcohol design, the carboxylic acid product can be cleaved with TFA.
• A more acid-labile form of the Wang resin has been developed. The
SASRIN resin has the same structure as the Wang linker but with the
addition of a methoxy group to stabilise the carbonium ion formed
during acid catalysed cleavage.

31. B. Carboxamide linker
• The Wang ester linker can be cleaved with ammonia to generate primary
carboxamide, but this is a difficult reaction, that is very slow with sterically
hundred amino acids such as valine. A prolonged treatment with ammonia
could lead to a racemisation of chiral peptides.
• Chemists developed a linking group that would generate carboxamide in
mild acidic conditions. The first developed was the methylbenzhydrylamine
(MBHA) linker on polystyrene for improved synthesis of peptides using the
Boc protection strategy.
• Cleavage of Wang Ester linker with ammonia generates carboxamides.

32. B. Carboxamide linker
•The rink linker is now preferred for generating primary
carboxamide on solid phase. The greater acid sensitivity in this
linker is due to the two additional electron donating methoxy
group. In the generation of primary carboxamide, the starting
material is attached to the linker as a carboxylic acid and after
synthetic modification is cleaved from the resin with TFA.

33. C. Alcohol linker
• A hydroxyl linker based on the tetrahydropyranyl (THP) protecting
group has been developed by Thompson and Ellmann. All type of
alcohols readily add to dihydropyran and the resulting THP protecting
group is stable to strong base, but easily cleaved with acid. This linker
is attached to a Merrifield resin.
Na salt of
Hydroxymethyl
85% in water
15 minHydroxymethyl
dihydropyran
15 min
•The trityl group is a good acid-
labile protecting group for a lot of
heteroatoms. The trityl group has
been used to anchor alcohols in the
synthesis of a library of β-
mercaptoketones.

34. D. Amine linker
•Carbamates linker has been used for the synthesis of a combinatorial
library of 576 polyamines prepared in the search of inhibitors of
trypanosomal parasitic infections.
• Two linkers were investigated. 1. based on hydroxymethylbenzoic
acid, and 2. an electron-donating group has been added 2. The last
one allowed cleavage by TFA while the first one could be cleaved with
strong acidic conditions.
• Amine bearing linkers used for preparation of library of polyamine
trypanothione reductase inhibitor

35. E. Traceless linker
• In some case, the starting materials are loaded onto the resin in
one form, such as carboxylic acid, and cleaved in another form; a
carboxamide. This is perfect when the target compound requires
the released function.
•These linkers show non-specific function after cleavage. Traceless
linkers are so called because an examination of the final compound
reveals no trace of the point of linkage to the solid phase
• Sulfide linker as traceless linker

36. F. Light cleavable linker
• O-nitrobenzyl resin- slow cleavage rates (12 - 24h)

37. Deprotection
Merrifield resin for peptide synthesis (chloromethyl group)
O
O
R
NHBoc
H
O
O
HO2C NHBoc
R2
H
O
O
O
= resin bead
Cl HO2C NHBoc
R H
+
Linker
O
aa1aa2aa3
O
aan NH2
R
NH2
H
coupling
R
NH
H
NHBoc
R2
H
HF
OH
aa1aa2aa3 aanHO2C NH2
Peptide
Release from
solid support

38. O
OH
Wang Resin
Wang resin
OH
Bead Linker

39. peptide
synthesis
O C
O
Wang resin
OH
Carboxylic
acid
HO2C NH(Fmoc)
R H
+ O C NH(Fmoc)
R H
O
O C NH2
O
piperidine
deprotection
O C
aa1aa2aa3 aan NH2
TFA
cleavage
OH
aa1aa2aa3 aan NH2HO2C
Fmoc =
O
O
Carboxylic
acid
O C NH2
R H

40. O
NH2
OMe
OMe
Rink resin
Rink resin
Bead Linker
NH2

41. further modifications
Rink resin
Carboxylic
acid
Primary
amide
N
H
C
O
RBead Linker
NH2 HO2C R+
amide
N
H
C
O
R'
TFA
H2N C
O
R'
cleavage

42. O
dihydropyran
derivatised resin
O
Dihydropyran resin
Bead
O
Linker

43. Bead
O
Linker
ROH
PPts O OR
further
O O
R'
Dihydropyran resin
Alcohol
further
modifications
TFA
R'HO
Alcohol

44. Double cleavable linker

45. Examples: HIV protease inhibitors

46. Examples: heterocycles

48. Structure determination of active compound(s)
• Tagging

49. Tagging