53 105 Combinatorial Chemistry: molecular diversity "Synthesis and Applications of Small Molecule Libraries." Thompson, L. A.; Ellman, J. A. Chem. Rev. 1996, 96, 555-600. "Design, Synthesis, and Evaluation of Small-Molecule Libraries.” Ellman, J. A. Acc. Chem. Res. 1996, 29, 132 -143. Combinatorial Chemistry, Nicholas K. Terrett, Oxford University Press, London, 1998 pharmaceutical industry- drug discovery Lead Cmpd optimization (synthesis) Drug 10 years $ 400 - 800 million $ $ $ Lead identification: literature (open & patent) nature (natural products) Careful optimization of a lead structure via chemical synthesis “methyl-ethyl-butyl-futile game” Number of marketable drugs per compounds that undergo preliminary biological testing 1 10,000 Rational drug design Combinatorial chemistry 106 Peptides: poor bioavailability, poor transport, easily metabolized: poor drug candidates. However, they are the natural substrates for many enzymes and receptors (drug targets) and have well-defined conformations: excellent lead compounds Enzymes: converts a substrate to a distinct product Receptor: binds a ligand (no reaction), causing a chain of physio- chemical events leading to a pharmacological response. Agonist: substance that interacts (binds) with a receptor and elicits an observable response Antagonist: substances inhibits the affect of an agonist, but has no biological activity of its own
19
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53
105
Combinatorial Chemistry: molecular diversity"Synthesis and Applications of Small Molecule Libraries."
Thompson, L. A.; Ellman, J. A. Chem. Rev. 1996, 96, 555-600. "Design, Synthesis, and Evaluation of Small-Molecule Libraries.”
Ellman, J. A. Acc. Chem. Res. 1996, 29, 132 -143.Combinatorial Chemistry, Nicholas K. Terrett, Oxford University Press, London, 1998
pharmaceutical industry- drug discovery LeadCmpd
optimization
(synthesis)Drug
10 years
$ 400 - 800million
$ $ $
Lead identification: literature (open & patent)nature (natural products)
Careful optimization of a lead structure via chemical synthesis“methyl-ethyl-butyl-futile game”
Number of marketable drugs per compounds that undergo preliminary biological testing
110,000
Rational drug designCombinatorial chemistry
106
Peptides: poor bioavailability, poor transport, easily metabolized:poor drug candidates.
However, they are the natural substrates for many enzymes and receptors (drug targets) and have well-defined conformations: excellent lead compounds
Enzymes: converts a substrate to a distinct productReceptor: binds a ligand (no reaction), causing a chain of physio-
chemical events leading to a pharmacological response.
Agonist: substance that interacts (binds) with a receptor and elicitsan observable response
Antagonist: substances inhibits the affect of an agonist, but has no biological activity of its own
54
107
Example of molecular diversity:tetra-peptide: H2N-A-B-C-D-CO2H
consider only the 20 natural amino acids (L-series)204 = 160,000 different tetra-peptides !
now include the 19 D-amino acids (20 L + 19 D = 39)394 = 2.3 million different tetra-peptides !!
now include 20 unnatural amino acids594 = 12 million different tetra-peptides !!!!
Combinatorial chemistry: method by which a family (library) of related compounds (structurally & synthetically) can be prepared andevaluated (screened)
For multi-step synthesis, one must use solid-phase synthetic approachin order to expedite purification of intermediates
108
Split synthesis (mixture libraries)
A
B
C
A
B
C
A
B
C
A
B
C
A
B
C
A
B
C
A
B
C
D
D
D
E
E
E
F
F
F
combine, mix,split
Ecombine, mix,split
A
B
C
D
F
55
109
G
A
B
C
D
D
D
A
B
C
E
E
E
A
B
C
F
F
F
A
B
C
D
D
D
A
B
C
E
E
E
A
B
C
F
F
F
A
B
C
D
D
D
A
B
C
E
E
E
A
B
C
F
F
F
A
B
C
D
D
D
A
B
C
E
E
E
A
B
C
F
F
F
G
G
G
G
G
G
G
G
G
A
B
C
D
D
D
A
B
C
E
E
E
A
B
C
F
F
F
H
H
H
H
H
H
H
H
H
A
B
C
D
D
D
A
B
C
E
E
E
A
B
C
F
F
F
I
I
I
I
I
I
I
I
I
H
I
Split synthesis (con’t)
110
Why not?
Reactivity of the coupling reaction may be different and this could bias the library
Split synthesis approach, all compounds are equally represented
(each coupling is individually controlled)
A,B,C
A
B
C
D,E,F
A
B
C
A
B
C
A
B
C
D
D
D
E
E
E
F
F
F
G,H, Ietc
56
111
Deconvolution of the libraryvia biological activity and sub-library re-synthesis
G
A
B
C
D
D
D
A
B
C
E
E
E
A
B
C
F
F
F
G
G
G
G
G
G
G
G
G
A
B
C
D
D
D
A
B
C
E
E
E
A
B
C
F
F
F
H
H
H
H
H
H
H
H
H
A
B
C
D
D
D
A
B
C
E
E
E
A
B
C
F
F
F
I
I
I
I
I
I
I
I
I
H
I
G H I
Biological activity of the library
select library H
112
A
B
C
D
D
D
A
B
C
E
E
E
A
B
C
F
F
F
H
H
H
H
H
H
H
H
H
H
H
E-H F-H
Biological activity of the library
select library D-H
A
B
C
A
B
C
A
B
C
D
D
D
E
E
E
F
F
F
H
D-H
A
B
C
D H
D H
D H
A D H
B D H
C D H
B-D-H C-D-H
Biological activity of the library
select library C-D-H
A-D-H
Lead Cmpd
57
113
Problems:• deconvolution of the library can be labor intensive• can be fooled by low concentrations of highly active
compounds• activity is dependent upon the compound and its
concentration• activity observed is the the combined activity of the entire
library
Advantage:• can synthesize a very large number of compounds very
quickly and relatively easily depending on thechemistry.
114
Encoded Libraries
A
B
C
1
2
3
A
1
B
2
C
3
A
1
B
2
C
3
A
1
B
2
C
3
A
1
B
2
C
3
A
1
B
2
C
3
A
1
B
2
C
3
D
D
D
4
4
4
E
E
E
5
5
5
6
6
6
F
F
F
combine, mix,split
1) D2) 4
1) E2) 5
1) F2) 6
combine, mix,split
58
115
Encoded libaries (con’t)
Cleave the marker and analyze the code. Each uniquemarker codes for a unique peptide sequence
1) G2) 7
1) H2) 8
1) I2) 9
A
1
B
2
C
3
D
D
D
4
4
4
A
1
B
2
C
3
E
E
E
5
5
5
A
1
B
2
C
3
6
6
6
F
F
F
A
1
B
2
C
3
D
D
D
4
4
4
A
1
B
2
C
3
E
E
E
5
5
5
A
1
B
2
C
3
6
6
6
F
F
F
A
1
B
2
C
3
D
D
D
4
4
4
A
1
B
2
C
3
E
E
E
5
5
5
A
1
B
2
C
3
6
6
6
F
F
F
A
1
B
2
C
3
D
D
D
4
4
4
A
1
B
2
C
3
E
E
E
5
5
5
A
1
B
2
C
3
6
6
6
F
F
F
G
G
G
G
G
G
G
G
G
7
7
77
7
77
7
7
A
1
B
2
C
3
D
D
D
4
4
4
A
1
B
2
C
3
E
E
E
5
5
5
A
1
B
2
C
3
6
6
6
F
F
F
H
H
H
H
H
H
H
H
H
8
8
88
8
88
8
8
A
1
B
2
C
3
D
D
D
4
4
4
A
1
B
2
C
3
E
E
E
5
5
5
A
1
B
2
C
3
6
6
6
F
F
F
I
I
I
I
I
I
I
I
I
9
9
99
9
99
9
9
CODE: 1= A2= B3= C
4= D5= E6= F
7= G8= H9= I
116
OHHO
1) linker- AA1-NH-FMOC
2) linker-code1-NH-BOCOOlinker linker AA1
HN FMOCcode 1NHBOC
libraryCode (1-10%)
library region and coding region must be orthogonally protected
1) piperidine2) add AA 2
OOlinker linker AA1
HN AA2
code 1NHBOCHN FMOC
1) H+2)add code 2
OOlinker linker AA1
HN AA2
code 1NHCode 2HN FMOC
HNBOC
Synthesis of an encoded library
59
117
CyN
N
Cx
O
CO2H
BOC
sub-library tag
pool tag
C7H15N
N
CH3
O
CO2H
BOC
C7H15N
N
C2H5
O
CO2H
BOC
C7H15N
N
C3H7
O
CO2H
BOC
C8H17N
N
CH3
O
CO2H
BOC
C8H17N
N
C2H5
O
CO2H
BOC
C8H17N
N
C3H7
O
CO2H
BOC
C9H19N
N
CH3
O
CO2H
BOC
C9H19N
N
C2H5
O
CO2H
BOC
C9H19N
N
C3H7
O
CO2H
BOC
Reading the codeC7H15
N
N
C3H7
O
CO2HO
C8H17N
N
C2H5
O
O
C9H19N
HN
CH3
O hydrolyzeand analyze C9H19
NH
CH3 C7H15NH
C3H7 C8H17NH
C2H5+ +
selectively remove the code from the resin
118
“On-Bead” Assay for Receptor Binding using a Fluorescently Labeled Receptor
Beads
1) Add labeled receptor labelled with fluorescent tag2) allow to bind to ligands on the beads
3) wash to remove unbound receptor
60
119
Spatially Addressable, Parallel Synthesis
A
B
C
A
B
C
A
B
C
A
B
C
D
D
D
D E F
E
E
E
F
F
F
120
Spatially Addressable, Parallel Synthesis (con’t)
A
B
C
A
B
C
A
B
C
A
B
C
D
D
D
G I
E
E
E
F
F
F
H
G
G
GH
H
H I
I
I
61
121
Spatially addressable, parallel libraries
Advantage:• synthesizing pure compounds, no need to deconvolute
Amino Acid Modifications: changes (restricts) conformational degrees of freedom of the peptide
CO2H
NH2
L-Phenylalanine
CO2H
NH2H3C
CO2H
NH2!-C alkylation
CO2H
NH
CO2H
HNCH3
!-N alkylation
CO2H
NH2
CO2H
NH2
CO2H
NH2
H2N CO2H
n
unnatural AA's
66
131
Dipeptide analogues
HN
NH
HN
R
O
O
R
R
O
HN
NH
NH
R
O
O
n
HN
NH
N
R
O
O R
On
O
Bridge two neighboring AA residues
N
Ph
HO2C
CO2H
H
O
Asp-Arg-Val-Tyr-Ile-His-Pro-Phe-His-Leu
angiotensin I angiotensin IIACE
ACE Inhibitor
132
Transition state analoguesfor a protease:
HN
NH
HN
R
O
O
R
R
Oprotease H
NNH
HN
R
O
OH
R
R
O
Nu
Nu= H2O, -OH, -SH, -CO2H
HN
NH
H2N
R
O
O
R
R
O
Nu
HN
NH
R
O
O
R
OH
H2O
+ Nu:
H2N
OH O
OH
Statine
NH
HO O
HN
O
HN
HN
NH
R
O
HHB:
Transition State
HN
H O
H
active site
water
NH
OH O
HN
Statine
NH
OH O
RHN
OH
NH
OH O
RHN
NH
O
P
O
RHN
O_
+
67
133
TS analoges via combinatorial synthesis
O AA1 AA2 AAn NH2
OBr NHBoc
R
(iPr)2NHO AA1 AA2 AAn
HN
O
R
NHBOC
O AA1 AA2 AAn
HN
O
R
NH AAn-1 AAz
HO AA1 AA2 AAn
HN
OH
R
NH AAn-1 AAz
NaBH4
NH2
1:1 mixture of stereoisomers
134
Peptide Backbone Modifications: Increase biological half-lifeRetro-Inverso Isomers: Change from L- to D-amino acids
and inverse N to C sequence
NH
HN
NH
HN
NH
HN
NH
HN
OH
H2N
O
H2NOC
CONH2
O
NH
O
O
O
O
NH
N
O
O
O
SCH3
Natural
HN
NH
HN
NH
HN
NH
HN
NH
NH2
H2N
H2NOC
CONH2
HN
NH
N
O
SCH3
O
O
O
O
O
O
O
O
Retro-Inverso isomer
Interesting idea, but the retro-inverso isomers usually showed much weaker binding. However, they were significantly more resistant to enzymatic digestion.
68
135
Amide Bond Isosteres:
Secondary Structure Mimics: main 2° structures: α-helix, β-sheet, β-turns, γ-turns
α-helix mimic
NH
O
NH
O
_
+
F
H
O
F
OH
F
O
F
OH
FF F
HOH2O
NH
R O
HN
NH
O R O
NH
R
HN
O
R
NH
OH
HN
O
groups responsible for biological activity Replace with a
non-peptide scaffold
136
Vasoactive Intestinal Peptide (VIP): 28 AA helical peptide. Bronchodilator- asthma treatment “α-helical Peptidomimetic for Vasoactive Intestinal Peptide (VIP)” G. L. Olson et al. J. Med. Chem. 1993, 36 (21), 3039-3049.
“Ala-scan” determine which residues are needed for binding
Leu
Tyr
NH2
CONH2
His
Asp
Tyr
Phe
Replace withscaffold
12.32 Å
S
N
HN O
O
Scaffold
12.99 Å
69
137
Ter-phenyl as an α-helix mimic
a
b
c
d
e
f
g
a (i)b
(i+1)
c(i+2)
d (i+3)
e (i+4)
f(i+5)
g (i+6)
a’ (i+7)
138
“stapled” α-helices
CO2H
NHFMOC
n
H3C
70
139
β-amino acids
β-Sheet mimics
N
N
O
N
HH
NO
HO
O
NHH
HN
O
N
O
HH
N
R
OH
O
H2N
!-amino acid
OH
O
H2N
"-amino acid
OH
O
H2N
R
oligomeric "-amino acidwill fold into a helical structurewith 3 AA's per turn