MD Simulation in Pose Refinement and Scoring Using AMBER Workflows
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1 MD Simulation in Pose Refinement and Scoring Using AMBER Workflows Yuan Hu (On behalf of Merck D3R Team) D3R Grand Challenge 2 Webinar Department of Chemistry, Modeling & Informatics Merck Research Laboratories, Merck & Co., Inc. March 27, 2017
2 Outline Overview of the D3R Predictions from Merck Today just the Stage 1 results Merck Team & Result Ranking Overall Pose Prediction and Scoring Approach Structure Preparation & Docking AMBER Workflows for Pose Refinement & Ranking Case Study & Lessons Learned Ranking with Ensemble-based MD-MMGBSA Pose Exploration with MD 2
3 Acknowledgement Merck D3R Team Modeling Ying-Duo Gao Xavier Fradera Yuan Hu Andreas Verras Deping Wang Hongwu Wang James Fells Kira Armacost Alejandro Crespo Brad Sherborne Informatics Huijun Wang Zhengwei Peng Robert Sheridan Motivation To refine and share our best practices To be engaged in the scientific community To better understand the capability of sciences in industry & academia 3
4 Overall Approach for Stage 1 Step 1: preparation as a team 102 D3R dataset Literature search Data mining from PDB and CHEMBL Structure Preparation Schrodinger s ligprep/prepwizard (Protomer/Tautomer, fill missing loop) 4
5 Overall Approach for Stage 1 Step 1: preparation as a team 102 D3R dataset Literature search Data mining from PDB and CHEMBL Structure Preparation Schrodinger s ligprep/prepwizard (Protomer/Tautomer, fill missing loop) Step 2: docking experiments Glide Ensemble Docking Submission A Colony Entropy Docking Submission B Glide+Gold Docking Submission C Visual Inspection (A+C) Submission E 5
6 Overall Approach for Stage 1 Step 1: preparation as a team 102 D3R dataset Literature search Data mining from PDB and CHEMBL Structure Preparation Schrodinger s ligprep/prepwizard (Protomer/Tautomer, fill missing loop) Step 2: docking experiments Glide Ensemble Docking Submission A Colony Entropy Docking Submission B Glide+Gold Docking Submission C Visual Inspection (A+C) Submission E Step 3: MD-MMGBSA MD simulations using multiple replicates MD pose refinement Submission D Ensemble-based MMGBSA ranking 6
7 Overall Approach for Stage 1 Step 1: preparation as a team 102 D3R dataset Literature search Data mining from PDB and CHEMBL Structure Preparation Schrodinger s ligprep/prepwizard (Protomer/Tautomer, fill missing loop) Step 2: docking experiments Glide Ensemble Docking Submission A Colony Entropy Docking Submission B Glide+Gold Docking Submission C Visual Inspection (A+C) Submission E Step 3: MD-MMGBSA MD simulations using multiple replicates Can MD be used to refine docking pose? How does MD-MMGBSA perform in ranking? MD pose refinement Submission D Ensemble-based MMGBSA ranking 7
8 Overall conclusion: MD improves pose prediction and ranking Mean RMSD to Crystal (Å) Mean RMSD of Top Scoring Poses A: Ensemble Docking C: Glide+Gold E: Visual Selection B: Colony Entropy Docking D: MD refinement D: MD-MMGBSA Kendalls Tau (Stage 1-Ligand Scoring) A: Ensemble Docking * n=36 C: Glide+Gold 8
9 Overall conclusion: MD improves pose prediction and ranking Mean RMSD to Crystal (Å) Mean RMSD of Top Scoring Poses A: Ensemble Docking C: Glide+Gold E: Visual Selection B: Colony Entropy Docking D: MD refinement D: MD-MMGBSA Kendalls Tau (Stage 1-Ligand Scoring) A: Ensemble Docking * n=36 C: Glide+Gold 9
10 Glide Ensemble Docking & AMBER workflows Completely automated Ensemble Docking AMBER MD-MMGBSA workflows Ligand/Protein Structure Preparation Glide XP Ensemble Docking 36 ligands x40 templates =1,440 Pose selection Rank by score rmsd >= 1.0 A to previously selected pose to ensure diversity Top Scoring Pose *Workflow was validated before on 40 native ligands *Workflow was validated in large data sets. Y. Hu, B. Sherborne, Z. Guo, et al.. How to Obtain Reliable and Reproducible MMGBSA Results? manuscript in preparation. 10
11 Glide Ensemble Docking & AMBER workflows Completely automated Ensemble Docking AMBER MD-MMGBSA workflows Ligand/Protein Structure Preparation Glide XP Ensemble Docking 36 ligands x40 templates =1,440 Pose selection Rank by score rmsd >= 1.0 A to previously selected pose to ensure diversity CRAY: 7h GPU: 3h 10-15cmpds/day Top Scoring Pose *Workflow was validated before on 40 native ligands *Workflow was validated in large data sets. Y. Hu, B. Sherborne, Z. Guo. How to Obtain Reliable and Reproducible MMGBSA Results? manuscript in preparation. 11
12 Glide Ensemble Docking & AMBER workflows Completely automated Ensemble Docking AMBER MD-MMGBSA workflows Ligand/Protein Structure Preparation Pose Selection Glide XP Ensemble Docking 36 ligands x40 templates =1,440 Pose selection Rank by score rmsd >= 1.0 A to previously selected pose to ensure diversity CRAY: 7h GPU: 3h 10-15cmpds/day Top Scoring Pose *Workflow was validated before on 40 native ligands *Workflow was validated in large data sets. Y. Hu, B. Sherborne, Z. Guo. How to Obtain Reliable and Reproducible MMGBSA Results? manuscript in preparation. 12
13 Good template is important for docking Similarity matters Docking Pose RMSD to X-ray Crystal (Å) Similarity>0.5 More templates More active Size by activity Red: Activity > 1 μm Green: Activity <= 1 μm 2D Similarity of closest template ligand in ensemble of complexes (descriptor: ECFP6) 13
14 Good template is important for docking Similarity matters Docking Pose RMSD to X-ray Crystal (Å) Similarity<=0.5 More templates More active Similarity>0.5 More templates More active Size by activity Red: Activity > 1 μm Green: Activity <= 1 μm 2D Similarity of closest template ligand in ensemble of complexes (descriptor: ECFP6) 14
15 Good template is important for docking Similarity matters Docking Pose RMSD to X-ray Crystal (Å) Similarity<0.5 Less templates More inactive Similarity<=0.5 More templates More active Similarity>0.5 More templates More active Size by activity Red: Activity > 1 μm Green: Activity <= 1 μm 2D Similarity of closest template ligand in ensemble of complexes (descriptor: ECFP6) 15
16 Question 1 Can MD be used to refine docking pose? 16
17 Pose refinement with MD Pose from Docking Pose from MD Pose no help ΔRMSD > 0.5 Å ΔRMSD < Å -0.5 <ΔRMSD < 0.5 Å RMSD to X-ray Crystal (Å) Pose maintained 0 Pose improved Docking Pose RMSD to X-ray Crystal (Å) 17
18 Case Study-success: FXR_3 Ligand interactions optimized through MD Ligand moves to create stable H-bond Crystal Structure Docking Pose MD refinement RMSD 2.00 Å RMSD 0.92 Å 18
19 Case Study-success: FXR_3 Ligand interactions optimized through MD 19
20 Case Study-success: FXR_10 Protein optimized through MD MD reorients the Asn to make H-bond contact Crystal Structure Docking Pose MD refinement RMSD 2.26 Å RMSD 1.41 Å 20
21 Case Study-success: FXR_10 Protein optimized through MD MD reorients the Asn to make H-bond contact Crystal Structure Docking Pose MD refinement RMSD 2.26 Å RMSD 1.41 Å 21
22 Case Study-success: FXR_10 Protein optimized through MD 22
23 Case Study-failure: FXR_15 MD workflow can t rescue reversed pose The docked pose has a reverse direction comparing to x-ray Hard to refine the structure with MD Crystal Structure Docking Pose MD refinement RMSD 8.83 Å RMSD 9.37 Å 23
24 Case Study-failure: FXR_15 MD workflow can t rescue reversed pose 24
25 Case Study-failure: FXR_18 MD workflow can t address very large protein movements Protein conformation change Ligand RMSD to X-ray Docking: 9.36 Å MD: Å Chain opened up in template Crystal Structure Docking Template Protein RMSD 2.59 Å MD refinement 25
26 Case Study-failure: FXR_18 MD workflow can t address very large protein movements 26
27 Lesson learned from previous D3R challenge: Explicit solvent free energy methods have not yet outperformed faster scoring methods in blinded protein-ligand affinity predictions. -D3R website (Posted October 11, 2016) Question 2 How does MD-MMGBSA perform in ligand scoring? 27
28 MD-MMGBSA improves on docking scores D: MD-MMGBSA Docking Methods ΔG pred (kcal/mol) A:Glide Ensemble Docking C:Xscore Docking IC50 (um) Gold ChemScore Prime MMGBSA Score binding pocket is deep inside challenge data set for implicit model (MMGBSA) Stage1: 36cmpds 28
29 Summary Lessons o o o o Ensemble docking performs well in pose prediction & ranking, if there are suitably close protein complexes available MD maintains or refines docking poses (protein and ligand) and extends the limit of prediction MD can t refine challenging poses Ensemble-based MD-MMGBSA ranking improves on docking scores Teamwork broke the challenge down to manageable portions Next o o AMBER MD-MMGBSA to AMBER TI CPU to GPU Towards accurate binding affinity prediction with pmemdgt: an efficient implementation of GPU-accelerated Thermodynamics Integration. T. Lee, Y. Hu, B. Sherborne, Z. Guo, D.M. York. submitted. 29
30 Thank You! 30
31 Pose exploration with MD Multiple studies show that the low energy snapshots correlate with best pose prediction 650ps 10 frames Avg *average energy of the 10 lowest energy snapshots for each trajectory of 22 MD simulations differed by the initial position. Onufriev, A.; Bashford, D.; Case, D. Proteins, 2004, 55, Hou, et al. J Comput Chem Apr 15;32(5):
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