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

  • A. Acharya
    A. Acharya
    School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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  • R. Agarwal
    R. Agarwal
    UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
    Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee 37996, United States
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  • M. B. Baker
    M. B. Baker
    Computer Science and Mathematics Division, Oak Ridge National Lab, Oak Ridge, Tennessee 37830, United States
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  • J. Baudry
    J. Baudry
    The University of Alabama in Huntsville, Department of Biological Sciences. 301 Sparkman Drive, Huntsville, Alabama 35899, United States
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  • D. Bhowmik
    D. Bhowmik
    Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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  • S. Boehm
    S. Boehm
    Computer Science and Mathematics Division, Oak Ridge National Lab, Oak Ridge, Tennessee 37830, United States
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  • K. G. Byler
    K. G. Byler
    The University of Alabama in Huntsville, Department of Biological Sciences. 301 Sparkman Drive, Huntsville, Alabama 35899, United States
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    S. Y. Chen
    Computational Science Initiative, Brookhaven National Laboratory, Upton, New York 11973, United States
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    L. Coates
    Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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  • C. J. Cooper
    C. J. Cooper
    UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
    Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee 37996, United States
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  • O. Demerdash
    O. Demerdash
    Biosciences Division, Oak Ridge National Lab, Oak Ridge, Tennessee 37830, United States
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  • I. Daidone
    I. Daidone
    Department of Physical and Chemical Sciences, University of L’Aquila, I-67010 L’Aquila, Italy
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  • J. D. Eblen
    J. D. Eblen
    UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
    The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue, Knoxville, Tennessee 37996, United States
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    S. Ellingson
    University of Kentucky, Division of Biomedical Informatics, College of Medicine, UK Medical Center MN 150, Lexington Kentucky 40536, United States
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    S. Forli
    Scripps Research, La Jolla, California 92037, United States
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    J. Glaser
    National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
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    J. C. Gumbart
    School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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    J. Gunnels
    HPC Engineering, Amazon Web Services, Seattle, Washington 98121, United States
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    O. Hernandez
    Computer Science and Mathematics Division, Oak Ridge National Lab, Oak Ridge, Tennessee 37830, United States
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    S. Irle
    Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
    Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
    Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee 37996, United States
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  • D. W. Kneller
    D. W. Kneller
    Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
  • A. Kovalevsky
    A. Kovalevsky
    Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
  • J. Larkin
    J. Larkin
    NVIDIA Corporation, Santa Clara, California 95051, United States
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  • T. J. Lawrence
    T. J. Lawrence
    Biosciences Division, Oak Ridge National Lab, Oak Ridge, Tennessee 37830, United States
  • S. LeGrand
    S. LeGrand
    NVIDIA Corporation, Santa Clara, California 95051, United States
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  • S.-H. Liu
    S.-H. Liu
    UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
    The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue, Knoxville, Tennessee 37996, United States
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  • J.C. Mitchell
    J.C. Mitchell
    Biosciences Division, Oak Ridge National Lab, Oak Ridge, Tennessee 37830, United States
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    G. Park
    Computational Science Initiative, Brookhaven National Laboratory, Upton, New York 11973, United States
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  • J.M. Parks
    J.M. Parks
    UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
    Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee 37996, United States
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  • A. Pavlova
    A. Pavlova
    School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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  • L. Petridis
    L. Petridis
    UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
    The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue, Knoxville, Tennessee 37996, United States
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  • D. Poole
    D. Poole
    NVIDIA Corporation, Santa Clara, California 95051, United States
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    L. Pouchard
    Computational Science Initiative, Brookhaven National Laboratory, Upton, New York 11973, United States
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    A. Ramanathan
    Data Science and Learning Division, Argonne National Lab, Lemont, Illinois 60439, United States
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    D. M. Rogers
    National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
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    D. Santos-Martins
    Scripps Research, La Jolla, California 92037, United States
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    Jubilee Development, Cambridge Massachusetts 02139, United States
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    A. Sedova
    Biosciences Division, Oak Ridge National Lab, Oak Ridge, Tennessee 37830, United States
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    Y. Shen
    UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
    Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee 37996, United States
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  • J. C. Smith*
    J. C. Smith
    UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
    The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue, Knoxville, Tennessee 37996, United States
    *Email: [email protected] (J.C.S.)
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  • M. D. Smith
    M. D. Smith
    UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
    The University of Tennessee, Knoxville. Department of Biochemistry & Cellular and Molecular Biology, 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue, Knoxville, Tennessee 37996, United States
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    C. Soto
    Computational Science Initiative, Brookhaven National Laboratory, Upton, New York 11973, United States
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    A. Tsaris
    National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
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    M. Thavappiragasam
    Biosciences Division, Oak Ridge National Lab, Oak Ridge, Tennessee 37830, United States
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    A. F. Tillack
    Scripps Research, La Jolla, California 92037, United States
  • J. V. Vermaas
    J. V. Vermaas
    National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
  • V. Q. Vuong
    V. Q. Vuong
    Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
    Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
    Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee 37996, United States
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    J. Yin
    National Center for Computational Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830, United States
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    S. Yoo
    Computational Science Initiative, Brookhaven National Laboratory, Upton, New York 11973, United States
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    M. Zahran
    Department of Biological Sciences, New York City College of Technology, The City University of New York (CUNY), Brooklyn, New York 11201, United States
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  • , and 
  • L. Zanetti-Polzi
    L. Zanetti-Polzi
    CNR Institute of Nanoscience, I-41125 Modena, Italy
Cite this: J. Chem. Inf. Model. 2020, 60, 12, 5832–5852
Publication Date (Web):December 16, 2020
https://doi.org/10.1021/acs.jcim.0c01010
Copyright © 2020 American Chemical Society

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    Abstract

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    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.

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    • Additional tables describing the simulations systems are provided; additionally, descriptive figures showing cluster diversity for each protein system are also provided (PDF)

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