BioSolveIT. A Combinatorial Docking Approach for Dealing with Protonation and Tautomer Ambiguities

Transcription

1 BioSolveIT Biology Problems Solved using Information Technology A Combinatorial Docking Approach for Dealing with Protonation and Tautomer Ambiguities Ingo Dramburg BioSolve IT Gmb An der Ziegelei Sankt Augustin Germany

2 verview Motivation, current state Automatic protonation during docking Benchmarking the method utlook: Isosteric replacement Conclusions 2

3 A drug design workflow Phase I: Building a receptor model split Ligand Protein preparation preparation D C K X-Ray structure (PDB) min. RMSD docked complex Receptor model 3

4 A drug design workflow Phase II: Building a screening model preparation Receptor model Ligand Ligand Compounds D C K docked complexes enrichment maximize active inactive activity data 4

5 preparation A drug design workflow Phase III: Virtual screening Screening model Ligand Ligand Compounds D C K docked complexes hits biol.assay lead optimize similarity leadlike 10 5 compds compounds 10 n compounds 5

6 Ambiguities in X-ray structures Gln,Asn,is are flippable Glu-,Asp-,Lys+,is,(Arg+,Cys,Tyr) are titrateable Glu - Asp must take this into account C + Valid receptor model Lys + is Arg + S Tyr Cys 6

7 Ambiguities in compound libraries Virtual compound libraries differ Sources (vendor, in house,...) File-formats (ML2, SDF, SMILES, PDB,...) Conformations (stereo isomers,...) Protonation, tautomers (neutral, charged) Which protonation state is the right one? ? compounds

8 Typical data preparation steps 1. Complex-structure: separate protein and ligand 2. Protein preparation structure validty ions, water, cofactor handling protonation states for titratable sites atomtypes (interaction properties) 3. Ligand preparation structure validity protonation state atomtypes (interaction properties) 8

9 The BioSolveIT tool family Permute FTrees Molecular Similarity SMARTS engine Comb. I/ Flexible Library Cheminf. Superpos. FlexS (Clib) Protein Ensembles Docking FlexX/E Ingo Dramburg BioSolve IT Gmb 26-Apr-04 9

10 Protein preparation FlexE: Ensemble of multiple conformations common structure -orientation protonation Claussen et al., J.Mol.Biol.(2001)308;

11 Ligand preparation SMARTS rules FlexX Molecule Structure Atoms (Chemical element) SYBYL, ML2 Connectivity Table Atomic Coordinates (3D) Atom Types (SYBYL,ML2) Formal Charges ydrogens Postprocessing Basic I/ SDF SMILES PDB 11

12 SMILE S and be SMART S Line notation for molecule and subgraph description Initially developed by Daylight Inc. SMILES Molecule (Unique description of molecules) SMILES CC(=) (acetic acid) 3 C SMARTS Subgraph (complex description of substructures) SMARTS [P,S,C](=[D1])[D1] ( acidic groups) R R S R R Weininger D., J. Chem. Inf. Comp. Sci. (1988)28;31-36 P R 12

13 Subgraph Matching FlexX SMART S engine Property assignment (aromaticity, atomtypes, charges,...) Descriptor assignment (interaction-types, torsion angles,...) Structure checking (valences, bondtypes) Structure transformation (similar to SMIRKS) Structure initialisation/correction (PDB setup, bondtypes, valences) Adjustment of ambiguities (mesomerism, tautomerism,...) Chemical modifications, reactions Combinatorial structure manipulation: Permutation Permutation of protonation states Generation of close analoges 13

14 Structure transformation old-substructure >> new-substructure C(=) >> C(:[-0.5):[-0.5;0] formal charges C(=) >> C(=)[-] (de)protonation CCC >> =CC=C bondtypes 2 CCCCCC(=) 2 C(=) >> C(-[]). reduction 2 C(=) >> C(=)CC 2 + *C(=) >> *.C(-[]) addition CCCC >> 1CCCC1 disconnect ring closure 14

15 Automatic complex preparation FLEX/RECEPTR> pdbinfo 1dwd 1dwd LIGAD MID-*-1-*, # (APAP SEE REMARK S1) 1dwd PEPTIDE *-*-*-I # (Residues: 11) 1dwd PEPTIDE *-*-*- # (Residues: 258) 1dwd PEPTIDE *-*-*-L # (Residues: 29) FLEX/LIGAD> frompdb 1dwd MID-*-1-* Extract residue(s) as ligand FLEX/RECEPTR> read 1dwd.pdb 6.5 y a) Read pdb-file as receptor with default settings (generic.rdf) b) Use FlexE module to find optimal protonation FLEX/DCKIG> complex all Perform a complete docking run 15

16 Combinatorial structure manipulation Group identification X R3 R3 R2 Combinatorial Library X R2 X R1 Decomposition R1 Core Scaffold Transformation of R-groups Combinatorial docking compounds

17 Simple tranformation rules Rule 1: C(=[D1])[D1] >> C(=); C(=)[-] R1 Core R1 R1 X X R3 - X Rule 2: [D2] >> [];[2+] R2 X R1 R2 X R2 + 2 X R3 R3 R2 X R3 2 + X X 17

18 The complete picture Rules: Rules: C(=) >> C(=); C(=)[-] [D2] >> [2]; [3+]... Solutions: 1. Protein-Ligand Complex SMARTS engine I/ Permute Comb. Library Module compounds ensemble Docking FlexE module FlexX n. 18

19 Benchmarking: A Dataset XXL Dataset from PDB: ~20000 complexes Protein constraints X-Ray structures from PDB Resolution < 3.5 A o DA/RA Ligand constraints MW nly C,,,P,S,F,Cl,Br,I o pure C compounds Max. 10 rot. Bonds, max. ring size 9 on-covalent on-cofactor (242 ET groups, freq. > 10) 2300 selected complexes Sadowski J.,Buning C.,Claussen., (2004), in preparation 19

20 Redocking comparison Generic dataset (2300 complexes) Automatic complex setup Redocking with default settings (6.5 A around ligand as site, no water or cofactors included, chemscore) Ligand is used in two states neutral state default protonation Protonation selected by unified protein model Datasets prepared by hand: Flex200 Kramer et. al. 1) (200 complexes) Astex issink et. al. 2) (305 complexes) 1) Kramer et al., Proteins (1999) 37: ) issink et al., Proteins (2002) 49:

21 RMSD of docking solutions (any rank) % 100,00 80,00 60,00 40,00 20,00 0,00 RMSD flex200 Astex neutral 1,00 1,50 2,00 2,50 3, default 1324 <

22 RMSD of solutions on rank 1 % 70,00 60,00 50,00 40,00 30,00 20,00 10,00 0,00 RMSD flex200 Astex neutral 1,00 1,50 2,00 2,50 3, default 676 < 2.0! 22

23 Permutation Complexes with titratable ligand: 634 RMSD on rank 1 <= 2.0 is a hit without permutation lig.setup # hits PDB2300 neutral % PDB2300 charged % Permutation of isomers increases with hitrate permutation by ~5% independent of initial settings lig.setup # hits PDB2300 neutral % PDB2300 charged % 23

24 utlook: Isosteric replacement Substituition ([CD1,$(c)] >> X) F,Cl,Br,I,CF 3, 2, C 3,C 2 5,isoprop.,t-butyl -,-S,- 2,-C 2,-Me, (Me) 2 Rings: Insertions (*[CD2]* >> X) -C 2 -,--,--,-C 2 4 -,-C 3 6 -,... -CC 2 -, -C-,-C-,... >C=, >C=S, >C=, >C=, >C=-,... 24

25 Example: β-phenylethylamine family C Dopamin Ephedrin ctopamin Me Metoprolol C 3 C 3 2 C 3 C 3 2 Atenolol C 3 Cl 2 Cl Clenbuterol C 3 C 3 C 3 Salbutamol C 3 C 3 C 3 C 3 Fenoterol Terbutalin 25

26 Conclusions FlexX can perform automatic docking successfully Reasonable solution for ~3/4 of selected complexes in pdb Manual setup not always beats automatism Impossible for screening of large datasets Significant increase of top ranked solutions with permutation of isomers (~5 %) Combinatorial docking is fast (5-10x faster than sequential docking of all isomers) Extension of method allows generation and docking of close analogues on the fly 26

27 Acknowledgements AstraZeneca J. Sadowski MPI Saarbrücken A. Kämper BioSolve IT. Claussen M. Gastreich M. Lilienthal C. Lemmen ThanxX for your attention. 27