Tautomers - Advanced Databases for in-silico Screening?
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Transcript of Tautomers - Advanced Databases for in-silico Screening?
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Tautomers - Advanced Databases for in-silico Screening ?
Frank Oellien, 18th CIC Workshop 2004, Boppard
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Overview
• Motivation for tautomers in screening data sets
• Tautomer enumeration approach
• Workflow
• Examples for ‘enhanced’ Database Search
• Results for ‘enhanced’ Database Search
• Summary and Future Tasks
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Biological Relevance of Tautomers
Targets: Bacteria, Arthropods, and ParasitesVariance for physiological pH expected – not static values !
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Ambiguities in Proteins and Ligands
Proteins (X-Ray structures)• Flexibility (e.g. Gln, Asn)• Ionisation states (e.g. Glu, Asp)• Tautomerism (e.g. His)
Ligands (Compound Libraries)• Conformations• Ionization states• Stereo centers• Tautomers
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Software: Virtual Screening
Types of Virtual Screening Software• High-throughput Docking of ligands into
protein X-Ray structures (Gold, FlexX)• DB for pharmacophore search (Catalyst,
Unity)
Current VS software applications adress:• Conformations• Ionization states• Stereo centers• Tautomers
X (exception FlexX 2004)
X
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Biological Relevance of Tautomers
Tautomeric states of ligands can be relevant for biological interactions
• Derivates of tetrazole, triazole, thiazole, pyrazole, iminopyrimidine, …
• Brandstetter et al., MMP-8-InhibitorsJ. Biol. Chem. 276, 2001, 17405-12.
• Pospisil et al., Ligands of herpesviral thymidine kinases, Helvet. Chim. Acta 85, 2002, 3237-50.
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Software: Tautomer Generation
Tautomer Generation Applications• Agent 2.0 (ETH Zurich- Switzerland)• QUAC PAC 1.1 (OpenEyes)• StereoPlex (Tripos)
• no extensions by the means of user-defined rules• no tautomer-sensitive duplicate check
Aim: Easily extensible and scriptable software thatallows the integration and automation of tautomergeneration in our existing screening workflow.
CACTVS: Chemical data management system
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Tautomer enumeration
• C core library, Tcl command layer• Main command:
ens transform $eh $tlist <direction> <reactionmode> <flags> <overlapmode> <excludelist> <maxtautomers> <timeout>
tlist: Transformation definition - SMIRKS line notation
[#1:1][O:2][C:3]#[N:4]>>[O:2]=[C:3]=[N:4][#1:1]
• preferred tautomer forms• tautomer sensitive duplicate check• 21 pre-defined rules (up to 1,11-H-shifts)• user-defined tautomer sets
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Examples
Only 2 transformation rules are needed (1,3 and 1,5-H-shift)
N
NH
NH
N
NH2
O
NH
N N
NH
NH2
O
NH
NH
N
NH
NH
O
N
NH
N
NH
NH2
O
N
N N
NH
NH2
OH
N
NH
N
NH
NH
OH
N
NH
N
N
NH2
OH
NH
N N
N
NH2
OH
NH
NH
N
N
NH
OH
NH
N NH
N
NH2
O
NH
NH
NH
N
NH
O
NH
N NH
N
NH
OH
N
N NH
N
NH2
OH
N
NH
NH
N
NH
OH
NH
N N
NH
NH
OH
1 2 3 4 5
6 7 8 9 10
11 12 13 14 15
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0
200000
400000
600000
800000
1000000
1200000
1400000
Maybridge Specs TimTec VitasM AsinexPlatinum
AsinexGold
ChemDiv
no tautom ers with tautom ers
Database Expansion
x2,7
x3,5
x3,2
x3,6
x3,0
x3,6
x3,4
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Tautomer Enumeration - Benchmark
Platform: SGI Fuel R1400 / 600 MHz, 1 GB RAM
Performance depends on• nature of the compounds• number of tautomers
SupplierDB Compounds/min MultiplierMaybridge Screening > 150 2,5Asinex Platinum > 250 2,9VitasM (in-hose Stock) > 560 3Tripos Leadscreen > 1400 2,2
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Tautomeric Fingerprintsa) Asinex (Platinum Collection)
0
20
40
60
80
100
1 4 7 10 13 16 20 24 28 34 39 46 52 69 115No of tautomer forms
Taut
omer
freq
uenc
y
0
10
20
30
40
50
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 20 21
b) Specs (Screening Collection)
0
20
40
60
80
100
1 9 17 25 33 41 49 57 65 74 84 95 108 125 149 182 210 348 742No of tautomer forms
Taut
omer
freq
uenc
y
0
10
20
30
40
50
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21
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Virtual Screening Workflow @ Intervet
2D / 3DStructure DB
(MDL)
Specific 3DDatabases
(Catalyst, Unity)
TautomerGeneration
Pre-Processing
Tautomer-sensitiveDuplicate check
Data Analysis Virtual
Screening
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Example I - MMP-8 (PDB Entry Code: 1JJ9)
Matrix Metalloproteinase Inhibitor: 8-Barbiturate
H. Brandstetter et al., MMP-8-InhibitorsJ. Biol. Chem.276, 2001, p 17405-12.
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http://home.t-online.de/home/kubinyi/dd-18.pdf
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Example I – MMP-8 Pharmacophore from X-RAY
Matrix Metalloproteinase Inhibitor: 8-Barbiturate
H-Bond Donor: greenH-Bond Acceptor: magentaHydrophobic aliphatic: blueRing Aromatic: brown
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Example I – MMP-8 Testdatabase
993 molecules selected from NCI 2000 Database (Catalyst Version)
2D / 3DStructure DB
(NCI 2000)
Divers CompoundSelection (Cerius 2 4.9)
TautomerGeneration (CACTVS)
3DDatabase(Catalyst,
No Tautomers)
3DDatabase(Catalyst,
with tautomers)
1536 compounds including5 8-Barbiturate Tautomers
994 compounds including8-Barbiturate (X-RAY) *
* Knowledge of stable tautomeric form is needed as prerequisite.
Default conditions for Catalyst database building – exception: max conformers 150
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Example I – MMP-8 Search on Testdatabase
Questions:• Covergage of the suggested tautomeric states for the 8-
barbiturate by our workflow ? • Conformer generation of Catalyst resemble X-Ray ?• Fit value significant for X-Ray and also conformers ?• Signal to noise relationship – fit values of other hits ?
3DDatabase(Catalyst,
No Tautomers)
3DDatabase(Catalyst,
WithTautomers)
1536 compounds including5 8-Barbiturate Tautomers
994 compounds including8-Barbiturate (X-RAY)
Exotic luxury or useful effort
?
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Example I – MMP-8 Results
Best Search – no tautomers:• 29 compounds found• 8-barbiture acid found in database, but scores less significant (BestFit 3.2)• 8-barbiture tautomer form (X-ray) BestFit 7.2 (AV= 3.0 SD = 1.7) • second best scored hit show BestFit 6.2• only 3 hits score higher then BestFit 4• best non X-Ray conformer scores BestFit 6.3
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Example I – MMP-8 Results
Best Search - with tautomers:• 30 compounds found (22 unique, 8 tautomeric duplicates) • 8-barbiture BestFit 7.2 (AV= 2.0 SD = 1.5)• second best scored hit show BestFit 5.5• only 3 hits score higher then BestFit 4• non tautomeric 8-barbiture scores BestFit 3.2• 60 % Overlap between both search results (all top scoring hits incommon)
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Example I – MMP-8 Summary
• Significant better fit value and hit separation in case of a database search including tautomers
• X-ray structure closely resembled • Number unique hits reduced• Significant more structures have to be
converted – time consuming aspectCritical aspect:• Hit rate (unique hits) is lower for database
including tautomers (?)• X-ray structure or known physiological
conditions in the protein appear to be important for sensitive pharmacophore searches
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Example II - CDK of Eimeria tenella
Cyclin Dependent Kinase – Homology Model based on Sequence Analysis
C. Beyer et. al.Oral & Poster Presentation at the 18. Darmstädter Molecular Modelling Workshop 2004
J.H. Kinnaird et al.International Journal for Parasitology 34, 2004, 683–692
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Qualitative pharmacophore model derived from human CDK2 best selective inhibitors – prefilter for docking libraries
H-Bond Donor: greenH-Bond Acceptor: magentaHydrophobic: blueRing Aromatic: brown
Feature mappingof pharmacophorehypothesis with CDK2 selective molecules
Example II - CDK of Eimeria tenella - hiphop
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993 molecules selected from NCI 2000 Database (Catalyst Version) plus 123 known human CDK1/2 inhibitors. 93 ligands show activity against CDK2.
3DDatabase(Catalyst,
No Tautomers)
3DDatabase(Catalyst,
WithTautomers)
2368 compounds including837 CDK1/2 inhibitor tautomers *
*733 CDK2 inhibitor tautomers
1116 compounds including123 CDK1/2 known inhibitors
Example II - CDK of Eimeria tenella - database
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A) Search results without tautomers:• best hypothesis finds 55.5 % of the CDK2 known• Inhibitors (AV 39.8 % SD 9.5 %) • Best selective (selectivity higher 4 included)• Number of hits 81
B) Search results with tautomers:• best hypothesis finds 72.2. % of the CDK2 known• Inhibitors (AV 66.4 % SD 10.0 %) • Best selective (selectivity higher 4 included)• Number of unique hits 61 • Overlap of best hypo search in A) with results in B) 93 %
Example II - CDK of Eimeria tenella - Results
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Example II - CDK of Eimeria tenella - Results
A) Search results without tautomers:• GH Score 0.54 for best pharmacophore model
B) Search results with tautomers:• GH Score 0.77 for best pharmacophore model of A)
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• Number of true hits better in case of tautomers • High overlap among top scoring ligands for both searchesRemark: SBF models under way
Critical aspect:• Number of unique hits is reduced by using tautomer databases
• All kinds of tautomeric states are considered.
Example II - CDK of Eimeria tenella - Summary
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• Modifications of tautomeric rules• Automatisation of database building workflow
• Implementation of defined Ionisations• Further investigations with examples
Future Tasks
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AcknowledgementsDr. J. Cramer, C. Bayer Dr. J. Schröder, PD Dr. P. SelzerIntervet Innovation GmbH
Dr. W.-D. IhlenfeldtΧemistry GmbH
Dr. O. SacherMolecular Networks GmbH
Dr. T. HidakaTakeda Pharmaceutical Ltd.
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Who we are ...
Paul SelzerRichard Marhöfer
Jörg SchröderJörg Cramer
Andreas Rohwer
BIOCHEMINFORMATICS
Carsten Beyer
Andreas Krasky
Anette Klinger
Frank Oellien
Kristin Engels Hon Tran