in silico small molecule discovery
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in silico small molecule discovery Sales Target gene Discove r hit Hit to lead Optimise lead Clinical Target gene identified with a viable assay High throughpu t screen in silico
description
in silico small molecule discovery. Sales. Hit to lead. Optimise lead. Target gene. Discover hit. Clinical. Target gene identified with a viable assay . High throughput screen. i n silico. Case 1 – receptor structure known. Novel in silico hits ~ 100. dock - PowerPoint PPT Presentation
Transcript of in silico small molecule discovery
in silico small molecule discovery
SalesTargetgene
Discoverhit
Hit tolead
Optimiselead
Clinical
Target gene identified with a viable assay
High throughput screen
in silico
Case 1 – receptor structure known
Novel in silico hits~ 100
ComputerDatabase ofMolecules100,000 +
dock moleculesinto receptor
Secondary assay? hits
IC50 < 10 µM
How successful is this method?
• From Shoichet’s group on target – protein tyrosine phosphate 1B
• None of the in silico hits found by HTS• But unpredictable - other systems yielding < 1%
Method Compounds tested
Hits with IC50 < 10µ M Hit rate
High throughput screening (HTS)
400,000 6 0.001%
In silico docking 365 from docking
18 5%
How does one get the receptor structure?
• X-ray structure available already at RCSB databank
• Set up a structure determination
• Predict structure
Cloning Recombinant protein Expression
Protein purification –
mg quantities
Protein crystalsElectron density map
X-ray diffraction patternProtein structure
Crystallization
X-ray crystallography pipeline
Prediction protein structure by homology
Query sequence
Matchedfold
Match sequence against library of known folds
Phyre- www.sbg.bio.ic.ac.uk
Phyre and predecessor 3DPSSM > 1,000 citations
Case 2: Ligand activity data available
Novel in silico hits
database
Observed activity Structure-activity rules
Screen
INDDExTM –A logic-based method
• Muggleton & Sternberg developed a logic-based strategy
• Method now incorporated into INDDEx within an Imperial spin-out Equinox Pharma
• INDDEx designed to exploit availability of active and inactive data on a at least c. 5 but ideally more ligands
Logic-rules lead to new chemotypes
C D7Å
AB B C
Fragment B is bonded to fragment C
Fragment C is bonded tofragment D
AB C D
7Å
INDDEx can learn complex rule from simpler facts Fragment A is 7Å from fragment B which is bondedto fragment C which is bonded to fragment D
Fragment A is 7Å from fragment B
Rules can be understood by chemists
Standard programs:
Activity = 0.45 LogP + 0.56667 Lumo +1.65 V
AB C D
7Å
ILP rule:In an active molecule:Fragment A is 7Å from fragment B which is bondedto fragment C which is bonded to fragment D
Chemistrt a
Blind trial of hit discovery on GPCR-1 Data from literature
250 novel in silico hits
Order
Observed activity- From Literature
157 Compounds30 Verified in vitro hitsNEW CHEMOTYPES Test
Cerep
in silico at Equinox
Equinox outsourced wet chemistry and biology
INDDEx
GPCR-1: training set
Distribution of 686 training molecules collected from public domain
ActivesInactives
GPCR Target 1 hits for optimatisation
4.7M molecules in Zinc database
400,000 drug like molecules
500 in silico hits
250 hits & new chemotypes
157 tested for inhibition
76 actives
39 for IC50
30 confirmed
30 chemotypes
30
GPCR-1: results of primary screening
Number of in silico hits: 157 (10µM concentration)Number of actives: 76 Number of inactives: 81Primary screen success rate = 48%
10 919 22
16
81
010
2030
4050
6070
8090
Num
ber o
f hits
>70% 60%-70% 50%-60% 40%-50% 30%-40% <30%
Percent of specific binding
CB1 results - primary screening
True hitsFalse hits
GPCR-1: new chemotypes
Distribution of hits based on their diversity (Tanimoto coefficients)
8
14
8
0
2
4
6
8
10
12
14
Num
ber o
f hits
<0.60 0.60-0.70 0.70-0.75
Tanimoto coefficient
CB1 results - new chemotype
New chemotype
Chemistrt a
INDDEx
Equinox hit discovery on GPCR-2 - Data from BioPrint (Cerep)
250 novel in silico hits
Order
Observed activity- From BioPrint
94 Compounds28 Verified in vitro hitsTest
Cerep
in silico at Equinox
Equinox outsources wet chemistry and biology
Confirmed hit rate of in silico predictions on secondary screen c. 35%
Target 1 Target 2In silco hits 157 94Primary screen hits(>30% binding at 10µM)
76 42
No. compounds tested for IC50 39 28IC50 results (<12µM) 30 28Estimated secondary hits if all primary hits tested
40 42
Estimated hit rate = estimated secondary hitsIn silico hits
38/157 = 24 %
42 /94= 45 %
Comparative hit rates
Company / approach Target Hit Rate Technology
INDDEx GPCR 1 & 2 + unknown target
35 % Ligand-based
Structure-based Multiple targets Average< 2% Docking into 3D
structure
High throughput Multiple targets Average 0.001% Experimental
screening
Concluding remarks
• If protein structure available can initiative an in silico screening approach to find hits.– Success rate generally <.2%– X-ray structure determination requires mgs of material– Prediction of structure if sequence identity > 50%
• If structure- activity data available then in silico methods can yield far better hit rates c. 35%
• in silco methods complement high throughput and can find different hits
In silico small molecule discovery
• Michael Sternberg, Ata Amini, Paul Freemont & Michael Sternberg
• Imperial Collge Lond– www.sbg.bio.ic.ac.uk & www.doc.ic.ac.uk/~shm– www.equinoxpharma.com
