Combinatorial Chemistry

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• Combinatorial Chemistry

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• The Split-Pool Synthesis Strategy

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• One bead - one substance concept

• Each bead contains only one sort of product
  (50-200 pmol concentration)
• Product can be screened either on bead or after
  cleavage from bead
• Single beads can be spotted in microtiter plates
  or immobilized and screened individually

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• How can we find the active component(s) of the
  library?

• Deconvolution (iterative or parallel)
• Microsequencing
• Tag-based encoding methods

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Iterative Deconvolution
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Parallel Deconvolution (Positional Scanning)
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Microsequencing of peptides by Edman degradation
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Tag-based encoding methods
Encoding principle

• each individual bead contains an encoding tag

• each tag uniquely encodes the building blocks
  on the bead

Encoding tags in use

• DNA (analysis by PCR)

• Peptides (analysis by Edman degradation)

• Haloaromatic groups (suitable for "binary code")

• Secondary amides (suitable for "binary code")

• Radiofrequency transponders

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Chemical encoding tags for solid-phase synthesis
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Example of chemical "binary code" (taken from
Ohlmeyer et al. PNAS 90, 1993, 10922-10926)
Binary translation table Ser (S) 001 Ile
(I) 010 Lys (K) 011 Leu (L) 100 Gln (Q)
101 Glu (E) 110 Asp (D) 111
Sequence E Q K L I
S Binary Code 110 101 011 100 010 001
Tags T18 ... T1
"1" in binary code means "tag is present" "0" in
binary code means "tag is absent"
Peptide Sequence E Q K L I S Tag
Sequence T18 T17 T15 T13 T11 T10 T9 T5 T1
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Tag analysis by electron capture GC (taken from
Ohlmeyer et al. PNAS 90, 1993, 10922-10926)
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Encoding by Radiofrequency chips

• Synthesis by Spit-and-Pool principle
• Polymer beads are located in a microreactor
  vessel
• Each microreactor vessel contains one
  semi-conductor chip
• Unique radiofrequency signals can be recorded
  and detected

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IRORI Kan - , Chiron Pin Technology
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Biopolymers used in Combinatorial Chemistry
vinyl. Sulfonyl- peptides
Peptides
vinyl. Peptides
Peptoids
Oligo-carbamates
Oligosulfones
Oligo- ureas
Oligosulfoxides
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Phage-display libraries

• Bacteriophages can produce desired peptides
• DNA which encodes peptides is inserted in phage
  genome

DNA
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• Non-polymeric combinatorial libraries
• Since biopolymers are often not "drug-like",
  efforts have been made to synthesize single,
  "drug-like" molecules combinatorially
• Solid-phase or solution phase synthesis is
  possible for a wide variety of organic reactions
• Automation support synthesis

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• Some examples...

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• Automation

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Solid phase-combinatorial chemistry to prepare
single compounds
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Schematic representation of a reaction block for
solid-phase synthesis
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Solution-phase combinatorial chemistry
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Automation I
Synthesis robot for solid-phase chemistry A
Reactor block B/C Reagent supplies D Robot
arm with pipetting needles
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Automation II
Reactor block for solid or solution phase
synthesis A Reaction vessels B Teflon
device C Pipetting needles
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Automation III
"Igel" multipipetting synthesizer for solution
phase chemistry
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• Combinatorial Chemistry is more than just large
  numbers!
• systematic variation of substituents on a
  common template
• is a key feature of combinatorial chemistry

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• The systematic variation of substituents
• is ideally suited to explore SAR patterns of
  hits found
• in combichem libraries

Variations in R1
Variations in R2