Date post: | 22-May-2018 |
Category: |
Documents |
Upload: | hoangquynh |
View: | 217 times |
Download: | 3 times |
Solving Structure Based Design Problems using Discovery Studio 1.7Building a Flexible Docking Protocol
C. M. (Venkat) VenkatachalamFellow, Life Sciences
Dipesh RisalMarketing, Life Sciences
Overview
• Flexible Docking – elements and challenges• Key Pipeline Pilot Components used in Flexible Docking• Validation of Components• Example workflow for Flexible Docking• Validation of workflow• Work in progress
Flexible Docking (aka ‘Induced Fit’)• Input
– Three dimensional structure of protein
– 2D structure of a ligand
• Output– Generate docked ligand poses
• Challenges– Forcefield, Scoring
– Ligand conformational sampling
– Ligand position and orientational sampling
– Flexibility of Protein• Side chain variations, local and global
• Large movements of protein chain
– Placement of water
• Many of these challenges are addressed in DS 1.7 with well-validated and published algorithms
• The well-validated CHARMm Forcefield and engine underlies all algorithms
Value of Flexible Docking• Experimental evidence shows
that there are variations in protein structure observed when different ligands are bound in it.
• Virtual high-throughput screening generally employs a single receptor structure with a wide variety of ligands. Ignoring protein flexibility can lead to erroneous docking results.
• Protein flexibility may play a vital role in the mechanism (pathway) of ligand docking.
Thymidine Kinase:1kim complex from xray
Variation in Side chains in Estrogen: 1err vs 3ert
residue Δchi1 Δchi2
LEU345 -8.6 19.4
LEU346 -3.1 13.6
THR347 -17.2 0
ARG352 -10.2 -12.07
LEU354 3.1 -12.48
GLU385 -15.6 -14.0
ILE389 -14.2 -11.2
TRP393 6.1 -18.2
ARG394 -15.0 -23.3
MET421 -107.7 47.3
HIS524 128.5 -31.3
LEU525 -69.3 44.5
LEU536 120.2 -94.4
TYR537 179.6 82.0
ASP538 -14.0 -55.0
LEU539 32.4 -10.6
1err
3ert
Δchi = chi(3ert) -chi(1err)
Discovery Studio and Pipeline Pilot
• The Flexible Docking protocol requires a Pipeline Pilot Client• Can be run in Pipeline Pilot or Discovery Studio 1.7
In this presentation…• We introduce 3 Pipeline Pilot components and a Flexible
Docking workflow• ChiRotor
– We show that ChiRotor correctly reconstructs selected side chains with/without ligand present
• ChiFlex– We show that this adequately identifies flexible residues in the
binding site and generates a representative set of protein structures with diverse side chain conformations for docking considerations
• CDOCKER– We show that this successfully docks ligands when correct side
chain conformations are present• Flexible Docking Workflow
– We show this workflow produces correct ligand poses in several protein systems using both native and cross docking.
Key Components used to build a Flexible Docking Workflow
Protein (ChiFlex) Side Chain Conformations
Set of protein structureswith diverse side chainconformations
Proteinw/woutligand
(ChiRotor)Side Chain Builder
Protein structurewith only side chainconformations refined
Protein Ligand+ CDOCKERA set of ligand posesdocked into the rigid protein
ChiRotorV. Z. Spassov, L. Yan, P. K. Flook, “The Dominant Role of Side-chain Backbone Interactions in Structural Realization of Amino-acid Code. ChiRotor: a Side-chain Prediction Algorithm Based on Side-chain Backbone Interactions”, Protein Science 16, 1-13 (2007).
CDOCKERG. Wu, D. H. Robertson, C. L. Brooks III and M. Veith, Detailed Analysis of Grid-Based Molecular Docking: A Case Study of CDOCKER- A CHARMm-Based MD Docking Algorithm, J. Comp. Chem. 24, 1549-1562, 2003.J. A. Erickson, M. Jalaie, D. H. Robertson, R. A. Lewis and M. Vieth, “Lessons in Molecular Recognition: The Effects of Ligand and Protein Flexibility on Molecular Docking Accuracy”, J. Med. Chem., 47 (1), 45 -55, 2004
ChiRotor & ChiFlex Schematic1 2
CDOCKER Schematic
Block Diagram of a Flexible Docking Protocol
3D Structure of Protein
ChiFlex: Side Chain Conformations
n Protein Structuresdiffering in side chainconformations
Start: Loop overn Protein Structures
Stage 1: Dock Ligand to Protein using CDOCKER
→ 1 ligand pose
ChiRotor:Rebuild Side chains
Stage 2: Dock Ligand to Proteinusing CDOCKER
Save Ligand Poses andProtein Structure
Flexible Docking Workflow in Pipeline Pilot
Validation
Questions that Validation should address
• ChiRotor– Does ChiRotor (‘Side Chain Builder’) find the experimentally known
side chain conformations? (It is critical that this produces the correct side chain conformations for the Flexible Docking workflow, since during the CDOCKER step the protein is held rigid with the side chain conformations assigned by ChiRotor.)
• ChiFlex– Does ChiFlex (‘Side Chain Conformations’) identify the flexible
residues in a protein and generate a set of low energy side chain conformations for further considerations?
• CDOCKER– Does CDocker give reasonable ligand dockings if the correct side
chain conformations are present in the receptor?
Does ChiRotor construct the correct side chain conformations if a correct ligand pose is given?
ChiRotor:
ChiRotor: Placement of Side Chains in Thymidine Kinase Structures
ComplexRMSD
(Å)Time
(secs)
1e2k 1.09 176
1e2m 1.85 216
1e2p 1.34 211
1ki2 1.9 215
1ki3 1.35 219
1ki4 1.16 322
1ki6 0.76 345
1ki7 0.79 379
1kim 0.74 270
1qhi 1.48 435
2ki5 -1 1.30 274
2ki5 -2 1.02 343
ChiRotor calculation with ligand present
RMSD to Crystal Structure side chain coordinates
Side chains within 4 angstroms from any ligand atom selected for placement
Computing time for Dell M 70 Pentium 2 GHz single processor
Side Chain Conformations in HUMAN CDK 2 COMPLEXED WITH THE INHIBITOR STAUROSPORINE -ChiRotor without the ligand
1aq1ILE10 0.0651
VAL18 0.2585
LYS33 0.519
VAL64 0.2018
PHE80 0.2069
GLU81 0.1778
PHE82 0.4024
LEU83 1.444
HIS84 0.0814
GLN85 0.4196
ASP86 0.8786
GLN131 2.6595
ASN132 1.9583
LEU134 0.4575
ASP145 1.0151 Protein shown with Ligand
Does ChiFlex (‘Side Chain Conformations’) identify the flexible residues in a protein
and generate a set of low energy side chain conformations for further
considerations?
ChiFlex:
Identification of Flexible Residues
Thymidine Kinase (1kim)His58 Glu83 Ile97 Ile100 Gln125 Tyr132 Arg163 Tyr172 Arg176 Arg222 Glu225Lowest RMSD to Crystal Side Chains ~1.0 angstroms
CDK2 (1aq1)Ile10 Lys33 Phe80 Glu81 Leu83 His84 Gln 85 Asp86 Gln131 Asn132 Leu134 Asp145Lowest RMSD to Crystal Side Chains ~1.8 angstroms
Residues identified by ChiFlex as highly flexible (>2 Å)
Does CDOCKER find the correct ligand pose if the correct protein structure is given?
CDOCKER:
CDOCKER Results: RMSD to 41 Crystal Structures
RMSD
0.00
2.00
4.00
6.00
8.00
10.00
12.00
0.00 5.00 10.00 15.00 20.00 25.00 30.00 35.00 40.00
RMSD
1apu (PENICILLOPEPSIN )
1uvs (Thrombin)
1htf (hiv protease)
1pgp (PhosphogluconateDehydrogenase )
Proteins
RM
SD
Same Dataset as Erickson et al. J Med Chem (2004) 47:45-55
Flexible Docking Workflow:Validation Results
Flexible Docking of 1kim ligand into 1kim receptor
Xray Ligand is shown in green.Ligand RMSD to xray = 0.8 angstrom
Flexible Docking of 1ki4 ligand into 1kim receptor
Xray Ligand is shown in green.Ligand RMSD to xray = 1.0 angstrom
Flexible Docking Summary
Ligand RMS to Xray(w/wout receptor flex)
System pdb codes (A, B) ResSel1 aA bB aB bA
Thymidine Kinase 1kim, 1ki4 α 1.2 1.1 1.3/1.1 0.9/3.7
Estrogen Receptor 1err, 3ert β 1.3 1.7 1.4/5.65 1.9/5.2
CDK2 1aq1, 1dm2 α 0.7 0.8 1.3/5.7 1.7/1.6
COX2 1cx2, 3pgh β 1.3 1.7 2.7/6.1 2.4/5.1
Neuraminidase 1nsc, 1a4q α 1.4 1.5 2.1/1.8 2.2/4.2
Thermolysin 1kr6, 1kjo β 1.8 4.4 4.2/4.9 1.6/1.9
HIV-RT 1rth, 1c1c α 2 1.8 2.1/8.8 1.7/3.1
Factor Xa 1ksn, 1xka β 1.9 2.4 1.9/7.0 2.1/8.6
Ligand RMS to XRAYw/wout Receptor Flex
nativedocking
crossdocking
1 ResSel – Residue Selection for ChiRotor and ChiFlexα Residues within 3.5Å from Xray Ligand in both ChiRotor and ChiFlexβ Residues within 3.5Å from Xray Ligand in ChiFlex and additional residues in ChiRotor
Strengths of the Approach
• ChiRotor – ability to reliably predict side chain conformations
• Very flexible interface• Power of modifying the workings by modifying
workflow• Extendable interface – adding LOOPER• Docking engine may be replaced• Consistent, validated force field – CHARMm• A rational approach to Ligand…Protein
interaction problem
Further Work in Progress• Improving Efficiency by
– Intelligent Ligand Placement – Protein structure refinement during docking
• More validation over larger dataset• Fine tuning parameters of the workflow
– Number of Protein side chain conformations– CDOCKER docking parameters
Concluding Remarks
• 3 Pipeline components (ChiFlex, ChiRotor, CDOCKER) have been constructed and validation results presented.
• A Flexible Docking protocol employing the 3 components shows promise in handling protein side chain flexibility in Ligand docking.
• This workflow demonstrates the power and flexibility of the DS platform.
Thanks to …• Accelrys
– R&D• Al Maynard (Structure Based Design) • Eric Yan (CHARMm)• Jürgen Koska (Flexible Docking Workflow)• Lisa Yan (Proteins)• Nan-Jie Deng (Simulation, CHARMm)• Velin Spassov (ChiRotor, ChiFlex)• Paul Flook (Direction)
– Marketing• Sylvia Tara
– Application Scientists• > 25 PhD Scientists world wide participating in validation
• External Collaboration– Charles E. Brooks (CHARMm, CDOCKER)