AN APPROACH TO SEMI FLEXIBLE DOCKING: A case study of the enzymatic reaction catalysed by terpenoid cyclases DIMACS, 13 June 2005 Vladimir Sobolev Weizmann Institute of Science

1. Approach to molecular docking and definition of surface complementarity AN APPROACH TO SEMI FLEXIBLE DOCKING: A case study of the enzymatic reaction catalysed by terpenoid cyclases 2. Modeling first two steps of enzymatic reaction catalysed by terpenoid cyclases

1. Approach to molecular docking and definition of surface complementarity AN APPROACH TO SEMI FLEXIBLE DOCKING: A case study of the enzymatic reaction catalysed by terpenoid cyclases 2. Modeling first two steps of enzymatic reaction catalysed by terpenoid cyclases

Where is the binding site located?What is the ligand orientation? Relevant Questions for Docking Two Major Algorithmic Issues in Molecular Docking: 2. Search procedure 1. Scoring function

CF = S l - S i - E r S l = surface area of legitimate atomic contacts S i = surface area of illegitimate atomic contacts E r = a repulsion term Complementarity Function for molecular docking

Definition of Contact Surface Between Atoms R a,R b ~ Å; R w = 1.4 Å Thus, contact appears from R ab ~ 6 Å contact surface of atom A with B is the surface area of sphere A that penetrates sphere B.

Definition of Contact Surface Between Atoms In both cases R ab is the same, while in second case there is no contact between atoms A and B

Atomic Classes IHydrophilicN or O that donate or accept a hydrogen bond (e.g., O of OH group of Ser or Thr) IIAcceptorN or O that only accept a hydrogen bond (e.g., O of peptide group) IIIDonorN that only donates a hydrogen bond (e.g., N of peptide group) IVHydrophobicCl, Br, I and C atoms not in aromatic rings and not covalently bonded to N or O VAromaticC atoms in aromatic rings VINeutralS, F, P, and metal atoms; C atoms covalently bonded to one or more atoms of class I or two or more atoms of class II or III VIINeutral-donorC atoms that are covalently bonded to only one atom of class III VIIINeut.-acceptorC atoms that are covalently bonded to only one atom of class II

Legitimacy (for each pair of contacts) Atomic class IIIIII IVV VI VII VIII IHydrophilic IIAcceptor IIIDonor IVHydrophobic VAromatic VINeutral VIINeutral-donor VIIINeutral-acceptor Hydrophilic Accepto r Donor Hydrophobic Aromatic Neutral Neutral-donor Neutral-acceptor

CF = S l - S i - E r S l = surface area of legitimate atomic contacts S i = surface area of illegitimate atomic contacts E r = a repulsion term Complementarity Function for molecular docking

Input coordinates, size of search cube, number of initial ligand positions (N), and number of best positions kept (M) Generate random ligand position and orientation in the search cube n = 1 n = n+1 Maximize complementarity function (CF) Keep not more than M best maxima Does n equal N? Yes No. Optimize H-bond lengths for every M structure obtained Cluster maxima Calculate and list contacts for the position with highest complementarity Calculate and list normalized complementarity (CF) following atom substitution Satisfactory CF position found? Yes No Neglect steric clash for a user defined number of residues Flow Chart of LIGIN Program

Critical Assessment of Techniques for Protein Structure Prediction Our Results

1. Approach to molecular docking and definition of surface complementarity AN APPROACH TO SEMI FLEXIBLE DOCKING: A case study of the enzymatic reaction catalysed by terpenoid cyclases 2. Modeling first two steps of enzymatic reaction catalysed by terpenoid cyclases

Chemical scheme of the substrate (farmecyl diphosphate (FFP)

Terpenoid cyclases may produce a large number of products from a single substrate. Steele et al., 1998

Chemical scheme of the substrate (farmecyl diphosphate (FFP)

Flowchart describing semi flexible docking

Results of the semi flexible docking for the first stage

Residues forming contacts with the leading structure Res.Dist. Å Sur f Å 2 Res.Dist. Å Surf Å 2 Arg Tyr Trp Leu Ile Cys Ile Ile Ser Val Asp Tyr Asp Asp Thr Tyr Thr

Docking prediction for WT pocket and three mutants. Blue - predicted structure; green - experimental one WTV516G Y520GV440G

OPP Contribution for the complementarity function of all groups of 4 adjacent carbons.

OPP Contribution for the complementarity function of all groups of 4 adjacent carbons. NCarbon AtomsCOMPLEMENTARITY 1C10 C11 C12 C C9 C10 C11 C C3 C4 C14 C5102 4C6 C7 C8 C985 5C3 C4 C5 C681 6C4 C5 C6 C781 7C5 C6 C7 C880 8C9 C10 C11 C1578 9C2 C3 C4 C C7 C8 C9 C C8 C9 C10 C C5 C6 C7 C C2 C3 C4 C551 14C6 C7 C8 C C7 C8 C13 C949

Scheme for the prediction of the second step of the reaction

Analysis of the results of the “second stage” reaction model KN Compl. Max. Compl. Contacts with (C1)Cluster Thr402a Tyr520, Asp444b Tyr404, Thr403, Thr402c Tyr520, Asp444d Trp273e Trp273f Trp273e Trp273g Tyr404h Trp273e Trp273e

List of super-groups clustered according to the interaction with carbocation C1 Super-grope number Group letters Contacts with C1 1e, f, gTrp273 2b, dTyr520, Asp44, Asp525 3c, hTyr404, Thr403, Thr402 4aThr402

Two candidates for amino acids involved in stabilising the reaction intermediate

Summary 1. Docking algorithm was described 2. First two steps of enzymatic reaction catalysed by terpenoid cyclases were modeled. There is already experimental data confirming correctness of the first step model. While modeling second step in the large extent speculative

ACKNOWLEDGMENTS Meir Edelman (WIS) Eran Eyal (WIS) Gert Vriend (EMBL) Rebecca Wade (EMBL)

AN APPROACH TO SEMI FLEXIBLE DOCKING: A case study of the enzymatic reaction catalysed by terpenoid cyclases DIMACS Workshop, 12 June 2005 Vladimir Sobolev Weizmann Institute of Science