BIOINF 4371 Drug Design 1 Oliver Kohlbacher & Jens Krüger

Transcription

1 BIOINF 4371 Drug Design 1 Oliver Kohlbacher & Jens Krüger Winter 2013/ Docking Part IV: Receptor Flexibility

2 Overview Receptor flexibility Types of flexibility Implica5ons for docking Examples FlexE Flexibility model Algorithmic ideas Results 1

3 Receptor Flexibility Not only the ligand is flexible, but also the receptor Protein flexibility can be essen5al to func5on Allostery: binding at one binding site induces shape change (and thus ac5vity difference) in a second binding site (allosteric regula5on) Induced fit: binding site is not complementary to the ligand itself, but can assume a conforma5on that is complementary Different levels of protein flexibility and different types of mo5on are possible Dis5nct changes of the protein backbone Changes on the side chain level only 2

4 Side- Chain Flexibility Every protein has an inherent flexibility that is implied by the degrees of rota5on of the rotatable single bonds Molecular dynamics simula5ons can reveal these degrees of freedom For most proteins the backbone remains rela5vely stable while the side chains move Example: MD simulation of BPTI (PDB: 4PTI) 3

5 Domain Movements A specific case of backbone flexibility is the mo5on of domains rela5ve to each other Specific (flexible) parts of the backbone (loops) can serve as hinges (hinge bending) or can enable a transla5on of domains rela5ve to each other (shearing) Both can be induced by ligand binding/dissocia5on Nature Reviews Drug Discovery 2, doi: /nrd1129 4

6 Flexibility Calmodulin Example Calmodulin wraps itself around its substrate by introducing a kink into the helix joining the two globular head domains (extreme case of backbone un/refolding going beyond simple hinge bending) PDB: 1CTR/1CLL 5

7 Example: nachr Channel Nico5nic acetylcholine receptors (nachr) gate ion flux upon binding of acetylcholine nachr channels are essen5al for neuronal signal transduc5on at the synap5c clew Their role is to enable the crea5on of a new ac5on poten5al upon binding of acetylcholin nachr channels are pentamers consis5ng of various subunits being essen5al for their role of func5on 6

8 EssenTal Dynamics nachr 7

9 CNG Channel Cyclic nucleo5de- gated (CNG) channel gate ion flux upon binding of cyclic nucleo5des CNG channels are significant for sensory transduc5on and cellular development Their func5on is based on either a depolariza5on or hyperpolariza5on event upon binding of cgmp or camp CNG channels are tetramers consis5ng of various subunits being essen5al for their role of func5on 8

10 CNG Channel Topology kindly provided by S. Schünke 9

11 Cyclic NucleoTde Binding Domain 10

12 Binding Mode 11

13 InteracTons 12

14 Protein Flexibilty 13

15 Energy Landscape 14

16 Docking Problems Scoring func5ons are ge`ng beaer and beaer, but s5ll have problems with numerous interac5on types and target classes Par5cularly problema5c are Entropic contributons SolvaTon Explicit water molecules The contribu5ons of these interac5ons to the overall binding free energy are owen substan5al, however, they are s5ll difficult to model 15

17 Docking Problems Another problem is the fact that most docking codes consider the receptor as rigid For many binding sites this is a reasonable approxima5on Some proteins, however, show significant structural changes upon binding (e.g., in the case of allostery) In these cases, current docking algorithms are unable to iden5fy sufficient chemical and geometric complementarity between receptor and ligand Although there are approaches for large- scale structural changes from protein- protein docking, these are rather experimental 16

18 Rigid vs. Flexible Rigid Docking The first docking algorithms treat both receptor and ligand as rigid objects Search best placement of the ligand to the receptor 6 DOFs in search (3 x transla5on, 3 x rota5on) Flexible Docking Ligand has addi5onal internal (torsional) DOFs More DOFs = larger search space = more difficult Receptor is kept rigid Flexible Docking to Flexible Receptors Treat the receptor or parts of the receptor (side chains) as flexible Problem: Dozens of side chains lining the binding site ) large number of addi5onal DOFs, HUGE search space 17

19 Induced Fit Comparison of the unbound receptor (blue) and bound complex (red) reveals structural changes upon binding (here: MTX/DHFR, PDB: 1DF7/1DG8) 18

20 Side- Chain Flexibility Individual side chains in the ac5ve site can flip upon binding This allows for adapta5on of the binding site to a specific ligand If such a ligand is docked into a crystal structure of the receptor bound to another receptor, there may be no geometric complementarity General Approach Determine which side chains are flexible Experimentally: which side- chain conforma5ons are assumed in different crystal structures Theore5cally: which conforma5ons are energe5cally feasible Include side chains in pose genera5on Include all possible side chain conforma5ons and treat them similar to ligand flexibility 19

21 FlexE Approach Same scoring func5on as FlexX Include flexible receptor side chains Side chain conforma5ons are obtained from different crystal structures Standard case in structure- based drug design: pharmaceu5cal industry usually produces crystals containing different ligands These structures contain a subset of all possible side- chain conforma5ons Different structures are combined into a unified representa5on Dock into this unified structure and include flexible side chains 20

22 Semi- Flexible Docking: FlexE FlexE represents receptor as an ensemble of different conformatons Claussen et al., J. Mol. Biol. (2001), 308,

23 Simplified Protein RepresentaTon Backbone rather rigid Backbones can be superimposed Kabsch algorithm (DD2) produces op5mal solu5on Consider conforma5on of backbone and side chain of an individual Cluster all conforma5ons (complete linkage) Iden5fy representa5ve conforma5ons for all clusters All conforma5ons can be represented like this Claußen et al., J. Mol. Biol. (2001), 308,

24 CompaTbility A piece of backbone or side chain in a specific conforma5on is being called a component Two components are incompatble, if they cannot be realized together Three types of incompa5bility Logical: alterna5ves of the same sub- structure (e.g., different conforma5ons of the same residue) Geometric: two components overlap geometrically Structural: components have to match without distor5ng bond lengths (e.g., in strongly divergent loop regions) 23

25 CompaTbility Graph Compa5bility graph contains nodes for components, edges for incompa5bili5es Claussen et al., J. Mol. Biol. (2001), 308,

26 CompaTbility Graph Exactly one node has to be selected from every connected component A valid receptor structure is completely disconnected subgraph (independent set) Claussen et al., J. Mol. Biol. (2001), 308,

27 Algorithm Incremental construc5on Mul5- greedy algorithm just as in FlexX For each(!) par5al ligand pose, the algorithms determines the op5mal receptor structure Requires to find the independent set yielding the best energy To this end, enumerate all independent sets This can be done using a variant of the Bron- Kerbosch algorithm Finding the independent sets is actually the most 5me- cri5cal step of the algorithm 26

28 Results Complexity Worst case exponen5al run 5me Search can be sped up with heuris5cs Run5mes Significantly slower than FlexX But faster than a series of docking runs against the individual crystal structures Test set For 83% of all known complexes, FlexE found a pose with RMSD < 2 Å 27

29 Comparison FlexX- FlexE Cross- docking of aldose reductase (AR) Three structures of AR with different ligands Docking of each ligand into each (rigid!) receptor structure Merging: joining the best solu5ons of each individual FlexX docking run Claussen et al., J. Mol. Biol. (2001), 308,

30 Aldose Reductase Side- chain conforma5ons vary visibly between the three inhibitors FlexE iden5fies the correct binding mode for all three of them RMSD below 1 Å in all three cases Claussen et al., J. Mol. Biol. (2001), 308,

31 References Original Papers FlexE Claussen H, Buning C, Rarey M, Lengauer T. FlexE: efficient molecular docking considering protein structure varia5ons. J Mol Biol Apr 27;308(2): Books [HSRF] H.- D. Höltje, W. Sippl, D. Rognan, G. Folkers: Molecular Modeling Basic Principles and Applica5ons, 2nd ed., Wiley, 2003 [Lea] Andrew Leach: Molecular Modelling: Principles and Applica5ons, 2nd ed., Pren5ce Hall, 2001 Donald J. Abraham (Hrsg.): Burger s Medicinal Chemistry & Drug Discovery, Vol. 1: Drug Discovery, 6th ed., Wiley,