Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19.

Abstract

We present a supercomputer-driven pipeline for in silico drug discovery using enhanced sampling molecular dynamics (MD) and ensemble docking. Ensemble docking makes use of MD results by docking compound databases into representative protein binding-site conformations, thus taking into account the dynamic properties of the binding sites. We also describe preliminary results obtained for 24 systems involving eight proteins of the proteome of SARS-CoV-2. The MD involves temperature replica exchange enhanced sampling, making use of massively parallel supercomputing to quickly sample the configurational space of protein drug targets. Using the Summit supercomputer at the Oak Ridge National Laboratory, more than 1 ms of enhanced sampling MD can be generated per day. We have ensemble docked repurposing databases to 10 configurations of each of the 24 SARS-CoV-2 systems using AutoDock Vina. Comparison to experiment demonstrates remarkably high hit rates for the top scoring tranches of compounds identified by our ensemble approach. We also demonstrate that, using Autodock-GPU on Summit, it is possible to perform exhaustive docking of one billion compounds in under 24 h. Finally, we discuss preliminary results and planned improvements to the pipeline, including the use of quantum mechanical (QM), machine learning, and artificial intelligence (AI) methods to cluster MD trajectories and rescore docking poses.

• Authors: A Acharya, R Agarwal, M B Baker, J Baudry, D Bhowmik, S Boehm, K G Byler, S Y Chen, L Coates, C J Cooper, O Demerdash, I Daidone, J D Eblen, S Ellingson, S Forli, J Glaser, J C Gumbart, J Gunnels, O Hernandez, S Irle, D W Kneller, A Kovalevsky, J Larkin, T J Lawrence, S LeGrand, S-H Liu, J C Mitchell, G Park, J M Parks, A Pavlova, L Petridis, D Poole, L Pouchard, A Ramanathan, D M Rogers, D Santos-Martins, A Scheinberg, A Sedova, Y Shen, J C Smith, M D Smith, C Soto, A Tsaris, M Thavappiragasam, A F Tillack, J V Vermaas, V Q Vuong, J Yin, S Yoo, M Zahran, L Zanetti-Polzi
• Journal: Journal of chemical information and modeling (J Chem Inf Model) Vol. 60 Issue 12 Pg. 5832-5852 (Dec 28 2020) ISSN: 1549-960X [Electronic] United States
• PMID: 33326239 (Publication Type: Journal Article, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't, Research Support, U.S. Gov't, Non-P.H.S.)

Chemical References

• Antiviral Agents
• Spike Glycoprotein, Coronavirus
• Viral Nonstructural Proteins
• spike protein, SARS-CoV-2

Topics

• Antiviral Agents (chemistry)
• Artificial Intelligence
• Binding Sites
• Computer Simulation
• Databases, Chemical
• Drug Design
• Drug Evaluation, Preclinical
• Humans
• Molecular Docking Simulation
• Protein Conformation
• SARS-CoV-2 (drug effects)
• Spike Glycoprotein, Coronavirus (chemistry)
• Structure-Activity Relationship
• Viral Nonstructural Proteins (chemistry)
• COVID-19 Drug Treatment