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Fragment-based tailoring of compoundlibraries for high-throughput docking and
screening
Peter [email protected]
Caflisch Lab
236th ACS National Meeting, Philadelphia, August 18, 2008 – p.1/28
Acknowledgements[Acknowledgements ]
� Amedeo Caflisch, Marco Cecchini, Andrea Cavalli, Stefan
Jelakovic, Shaheen Ahmed, Francesco Rao, Enrico Guarnera,
Riccardo Pellarin, Steffi Muff, Raffaele Curcio, Dariusz Ekonomiuk,
Pietro Alfarano
� The Dockers
� Catherine Berset Kipouros, Stephan Audétat, Urs
Lüthi, Alcide Barberis
236th ACS National Meeting, Philadelphia, August 18, 2008 – p.2/28
Acknowledgements[Acknowledgements ]
� Amedeo Caflisch, Marco Cecchini, Andrea Cavalli, Stefan
Jelakovic, Shaheen Ahmed, Francesco Rao, Enrico Guarnera,
Riccardo Pellarin, Steffi Muff, Raffaele Curcio, Dariusz Ekonomiuk,
Pietro Alfarano
� The Dockers
� Catherine Berset Kipouros, Stephan Audétat, Urs
Lüthi, Alcide Barberis
236th ACS National Meeting, Philadelphia, August 18, 2008 – p.2/28
Acknowledgements[Acknowledgements ]
� Amedeo Caflisch, Marco Cecchini, Andrea Cavalli, Stefan
Jelakovic, Shaheen Ahmed, Francesco Rao, Enrico Guarnera,
Riccardo Pellarin, Steffi Muff, Raffaele Curcio, Dariusz Ekonomiuk,
Pietro Alfarano
� The Dockers
� Catherine Berset Kipouros, Stephan Audétat, Urs
Lüthi, Alcide Barberis
236th ACS National Meeting, Philadelphia, August 18, 2008 – p.2/28
Outline[Outline ]
� Fragment-based Docking
�DAIM
� SEED
� FFLD
� Anchor-based Library Tailoring
� Concept
� Application to EphB4
236th ACS National Meeting, Philadelphia, August 18, 2008 – p.3/28
Fragments?[Fragments? ]
“A fragment is a fragment is a fragment.”
236th ACS National Meeting, Philadelphia, August 18, 2008 – p.4/28
DAIM–SEED–FFLD[DAIM–SEED–FFLD ]
DAIM
N
H
ON
F
FF
F
FF
O
N
O N
N
H
H
DAIM SEED FFLD
J Med Chem. 2006;49:7384-92 Proteins. 1999;37:88-105 Biol Chem. 2001;382:1365-72
Proteins. 2001;42:256-68 J Comput Chem. 2004;25:412-22
236th ACS National Meeting, Philadelphia, August 18, 2008 – p.5/28
DAIM | Decomposition And Identification ofMolecules
236th ACS National Meeting, Philadelphia, August 18, 2008 – p.6/28
DAIM: decomposition[DAIM: decomposition ]
DAIM identifies fragments in a four-step process:
1. identification of rings.
236th ACS National Meeting, Philadelphia, August 18, 2008 – p.7/28
DAIM: decomposition[DAIM: decomposition ]
DAIM identifies fragments in a four-step process:
1. identification of rings.
2. definition of initial fragments: atoms connected by “unbreakable”
bonds (double, triple, aromatic, amidic, terminal, ring).
236th ACS National Meeting, Philadelphia, August 18, 2008 – p.7/28
DAIM: decomposition (2)[DAIM: decomposition (2) ]
H
F
F
F
F
F F
HN
NH
O
N
ON
+N
O
H
236th ACS National Meeting, Philadelphia, August 18, 2008 – p.8/28
DAIM: decomposition[DAIM: decomposition ]
DAIM identifies fragments in a four-step process:
1. identification of rings.
2. definition of initial fragments: atoms connected by “unbreakable”
bonds (double, triple, aromatic, amidic, terminal, ring).
3. reconnection of functional groups.
236th ACS National Meeting, Philadelphia, August 18, 2008 – p.9/28
DAIM: decomposition (3)[DAIM: decomposition (3) ]
+N
O
HH
F
F
F
F
F F
HN
NH
O
N
ON
236th ACS National Meeting, Philadelphia, August 18, 2008 – p.10/28
DAIM: decomposition[DAIM: decomposition ]
DAIM identifies fragments in a four-step process:
1. identification of rings.
2. definition of initial fragments: atoms connected by “unbreakable”
bonds (double, triple, aromatic, amidic, terminal, ring).
3. reconnection of functional groups.
4. completion of valences.
236th ACS National Meeting, Philadelphia, August 18, 2008 – p.11/28
Possible triplet combinations[Possible triplet combinations ]
CH4
CH4
CH4
FF
F
F FF
O
N
H
H
HN
NO
N
+N
O
H
We need 3 fragments [ ],
but there are 9 to choose from
→
(93
)
= 9!3!(9−3)! = 84
possible combinations
236th ACS National Meeting, Philadelphia, August 18, 2008 – p.12/28
Chemical richness ρχ[Chemical richness ρχ ]
6 1 0 0 0 0 0 0 0 0 2 1 6 7 0.545298614
vectorsDonor
H
H
H
HH
H H
W4/1000amSHalNAtoms
CO P ar Acceptor
N
236th ACS National Meeting, Philadelphia, August 18, 2008 – p.13/28
Chemical richness ρχ[Chemical richness ρχ ]
6 1 0 0 0 0 0 0 0 0 2 1 6 7 0.545298614
vectorsDonor
H
H
H
HH
H H
W4/1000amSHalNAtoms
CO P ar Acceptor
N
DAIM uses the fingerprint to choose fragments based on the chemical
richness ρχ = ∑i fi and to calculate the octanol/water partition coeffi-
cient (CLogP).
236th ACS National Meeting, Philadelphia, August 18, 2008 – p.13/28
Docking performance: DAIM↔ random[Docking performance: DAIM↔ random ]
84565656120358484205684351020561204204165165441201203520202084102010101056
1hte1b6l
1ets1ppc
1uvs1dbm1dwc1hwr
1ett1bmn1etr2dbl
1ejn7upj
3tmn1atl
1aoe1pph
2tsc1ela
1fkg1c83
1c841mcj
1mnc1hgh
1nnb1nsc
1nsd5tln
1xig4hmg
1tpp2acs2xis
1hgj
0 0.2 0.4 0.6 0.8 1relative number of cases with RMSD below 2Å
0 0.2 0.4 0.6 0.8 1relative rank of the DAIM triplet
tripletsn
below 2Å above 2Å
DAIM rank
n
Using the DAIM triplet re-sults in at least one poseclose to the X-ray structure in20/36 cases. The probabilityto be below 2 Å at least 20times through random selec-tion of triplets is < 0.28%.
J Med Chem. 2006;49:7384-92
236th ACS National Meeting, Philadelphia, August 18, 2008 – p.14/28
SEED | Solvation Energy for ExhaustiveDocking
236th ACS National Meeting, Philadelphia, August 18, 2008 – p.15/28
SEED[SEED ]
236th ACS National Meeting, Philadelphia, August 18, 2008 – p.16/28
SEED (II)[SEED (II) ]
236th ACS National Meeting, Philadelphia, August 18, 2008 – p.17/28
SEED (III)[SEED (III) ]
236th ACS National Meeting, Philadelphia, August 18, 2008 – p.18/28
ALTA | Anchor-based Library Tailoring
236th ACS National Meeting, Philadelphia, August 18, 2008 – p.19/28
ALTA[ALTA ]
12
5
Selection basedon target structure
3
6
Flexible ligand docking
4
Pool of fragmentsPool of compounds
Decomposition
Fragment docking
AIMDAIMD
top−ranking Screening with
fragments
AIMD
Subset of compounds
Candidate fragments
Fragment ranking
Final ranking (LIECE)
AIMDAIMD
AIMD
236th ACS National Meeting, Philadelphia, August 18, 2008 – p.20/28
Application: EphB4
236th ACS National Meeting, Philadelphia, August 18, 2008 – p.21/28
Introduction[ Introduction ]
EphB4
� belongs to the largest family of receptor tyrosine kinases.
� corresponding transmembrane ligand: ephrinB2.
� probably involved in the control of interaction of endothelial cells
→ role in angiogenesis and tumorangiogenesis.
� elevated expression levels in prostate cancer.
236th ACS National Meeting, Philadelphia, August 18, 2008 – p.22/28
EphB4 structure[EphB4 structure ]
236th ACS National Meeting, Philadelphia, August 18, 2008 – p.23/28
Statistics[Statistics ]
ρχ1353335513
52351205
30
7
21418
8849
9960
docked a second time
fragments selected
forming 2HBs
fragments
molecules docked
1 or 2 HB
tested
show some inhibitoryactivity on EphB4
728202total library size
more rings, min1 acce, 1 dono, 1 or
#1: IC50 1.36 µM∗
#2: IC50 76 µM
#3: 20% @ 4.6 µM
#4-7:
15-40% @ 125 µM∗has been developed into a series of in-
hibitors with IC50s between 1 and 50 µM
Proteins. 2008;73:11-18
236th ACS National Meeting, Philadelphia, August 18, 2008 – p.24/28
The hits[The hits ]
enzymatic assays cell-based assay
compound structure MW IC50 IC50 IC50 CHO predicted ∆G
[Da] [µM] [µM] [µM] % [kcal·mol−1]
1
H2N
N
N
O
O
OS
H
H
349 76 n.d. n.d. n.d. −8.8
2-8OO
O
N N
NN
R
HN
R=
2 –(CH2)4OH 353 1.4, 1.8 6.8 5.6, 7.9 neg. −11.0
3 –(CH2)3CH3 337 1.5, 1.5 8.3 n.d. neg. −10.7
4 –(CH2)2CH3 323 1.9 n.d. n.d. neg.
5 ortho-methoxy-phenyl 387 27 n.d. n.d. 14% @ 20 µM
6 –(CH2)3OCH3 353 50 n.d. n.d. 28% @ 20 µM
7 –(CH2)2Ph 385 30% @ 14 µMe n.d. n.d. 34% @ 20 µM
8 –(CH2)2-meta-methylphenyl 399 29% @ 5 µMe n.d. n.d. 14% @ 20 µM
236th ACS National Meeting, Philadelphia, August 18, 2008 – p.25/28
Fragment- vs. compound pose[Fragment- vs. compound pose ]
236th ACS National Meeting, Philadelphia, August 18, 2008 – p.26/28
CPU time requirements[CPU time requirements ]
ALTA hours
DAIM 2
SEED (fragments) 2200
substructure search 1000
docking (DSF) 3300
Σ 6500
Docking only hours
DAIM 2
SEED 10000
FFLD 119000
Σ 129000
236th ACS National Meeting, Philadelphia, August 18, 2008 – p.27/28
CPU time requirements[CPU time requirements ]
ALTA hours
DAIM 2
SEED (fragments) 2200
substructure search 1000
docking (DSF) 3300
Σ 6500
Docking only hours
DAIM 2
SEED 10000
FFLD 119000
Σ 129000
factor of 20!
236th ACS National Meeting, Philadelphia, August 18, 2008 – p.27/28
Conclusions[Conclusions ]
�DAIM can generate chemically sensible molecular fragments and
rank them according to their suitability to serve as anchors in
docking
� ALTA is a technique to tailor docking libraries on the fly by
selecting molecules based on the suitability of their fragments for
a given binding site. This reduces computation time while
preserving diversity.
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