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High-Throughput Virtual Screening and Validation of a SARS-CoV-2 Main Protease Noncovalent Inhibitor

Journal Article · · Journal of Chemical Information and Modeling
 [1];  [2];  [3];  [4];  [5];  [4];  [1];  [6];  [5];  [1];  [3];  [1];  [7];  [2];  [7];  [8];  [1];  [8];  [9];  [8] more »;  [8];  [10];  [11];  [12];  [13];  [11];  [14];  [4];  [15];  [16] « less
  1. Data Science and Learning Division, Argonne National Laboratory, Lemont, Illinois 60439, United States, Department of Computer Science, University of Chicago, Chicago, Illinois 60615, United States, National Virtual Biotechnology Laboratory, Washington, District of Columbia 20585, United States
  2. Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States, National Virtual Biotechnology Laboratory, Washington, District of Columbia 20585, United States
  3. Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States, National Virtual Biotechnology Laboratory, Washington, District of Columbia 20585, United States
  4. Data Science and Learning Division, Argonne National Laboratory, Lemont, Illinois 60439, United States, National Virtual Biotechnology Laboratory, Washington, District of Columbia 20585, United States
  5. Department of Computer Science, University of Chicago, Chicago, Illinois 60615, United States, National Virtual Biotechnology Laboratory, Washington, District of Columbia 20585, United States
  6. Computing Environment and Life Sciences Directorate, Argonne National Laboratory, Lemont, Illinois 60439, United States, National Virtual Biotechnology Laboratory, Washington, District of Columbia 20585, United States
  7. Computational Biology Group, Biological Science Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States, National Virtual Biotechnology Laboratory, Washington, District of Columbia 20585, United States
  8. Department of Electrical and Computer Engineering, Rutgers University, Piscataway, New Jersey 08854, United States, National Virtual Biotechnology Laboratory, Washington, District of Columbia 20585, United States
  9. Bioscience Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States, National Virtual Biotechnology Laboratory, Washington, District of Columbia 20585, United States
  10. University of Illinois at Urbana-Champaign, Champaign, Illinois 61820, United States, National Virtual Biotechnology Laboratory, Washington, District of Columbia 20585, United States
  11. Department of Electrical and Computer Engineering, Rutgers University, Piscataway, New Jersey 08854, United States, Computational Science Initiative, Brookhaven National Laboratory, Upton, New York 11973, United States, National Virtual Biotechnology Laboratory, Washington, District of Columbia 20585, United States
  12. Computational Science Initiative, Brookhaven National Laboratory, Upton, New York 11973, United States, National Virtual Biotechnology Laboratory, Washington, District of Columbia 20585, United States
  13. Department of Computational and Systems Biology, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States, National Virtual Biotechnology Laboratory, Washington, District of Columbia 20585, United States
  14. Second Target Station, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States, National Virtual Biotechnology Laboratory, Washington, District of Columbia 20585, United States
  15. Joint Institute for Biological Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States, National Virtual Biotechnology Laboratory, Washington, District of Columbia 20585, United States
  16. Department of Computer Science, University of Chicago, Chicago, Illinois 60615, United States, Computing Environment and Life Sciences Directorate, Argonne National Laboratory, Lemont, Illinois 60439, United States, National Virtual Biotechnology Laboratory, Washington, District of Columbia 20585, United States
Not Available
Sponsoring Organization:
USDOE
OSTI ID:
1831317
Alternate ID(s):
OSTI ID: 1839395
OSTI ID: 1840207
OSTI ID: 1841104
OSTI ID: 1842310
OSTI ID: 1902336
Journal Information:
Journal of Chemical Information and Modeling, Journal Name: Journal of Chemical Information and Modeling Journal Issue: 1 Vol. 62; ISSN 1549-9596
Publisher:
American Chemical SocietyCopyright Statement
Country of Publication:
United States
Language:
English

References (60)

Stereoselective synthesis of stable isotope-labeled L-α-amino acids: Electrophilic amination of Oppolzer's acyl sultams in the synthesis of L-[15N]alanine, L-[15N]valine, L-[15N]leucine, L-[15N]phenylalanine and L-[1-13C, 15N]valine journal March 1996
Development and testing of a general amber force field journal January 2004
AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading journal January 2009
An open port sampling interface for liquid introduction atmospheric pressure ionization mass spectrometry: Open port sampling interface journal August 2015
FRED and HYBRID docking performance on standardized datasets journal June 2012
An Update on Current Therapeutic Drugs Treating COVID-19 journal May 2020
Characterization of SARS main protease and inhibitor assay using a fluorogenic substrate journal June 2004
ANCA: Anharmonic Conformational Analysis of Biomolecular Simulations journal May 2018
NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations journal September 2010
A molecular docking study repurposes FDA approved iron oxide nanoparticles to treat and control COVID-19 infection journal October 2020
A multi-pronged approach targeting SARS-CoV-2 proteins using ultra-large virtual screening journal February 2021
Virtual screening based on molecular docking of possible inhibitors of Covid-19 main protease journal November 2020
Artificial intelligence techniques for integrative structural biology of intrinsically disordered proteins journal February 2021
Malleability of the SARS-CoV-2 3CL Mpro Active-Site Cavity Facilitates Binding of Clinical Antivirals journal December 2020
Structure-guided design of a perampanel-derived pharmacophore targeting the SARS-CoV-2 main protease journal August 2021
Oxford–AstraZeneca COVID-19 vaccine efficacy journal January 2021
A deliberate approach to screening for initial crystallization conditions of biological macromolecules journal April 2003
Quantum chemical modeling of CoC bond activation in B12-dependent enzymes journal December 2001
Supercomputer-Based Ensemble Docking Drug Discovery Pipeline with Application to Covid-19 journal December 2020
ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB journal July 2015
Discovery of Ketone-Based Covalent Inhibitors of Coronavirus 3CL Proteases for the Potential Therapeutic Treatment of COVID-19 journal October 2020
An Overview of Severe Acute Respiratory Syndrome–Coronavirus (SARS-CoV) 3CL Protease Inhibitors: Peptidomimetics and Small Molecule Chemotherapy journal February 2016
Potent Noncovalent Inhibitors of the Main Protease of SARS-CoV-2 from Molecular Sculpting of the Drug Perampanel Guided by Free Energy Perturbation Calculations journal February 2021
Optimization of Triarylpyridinone Inhibitors of the Main Protease of SARS-CoV-2 to Low-Nanomolar Antiviral Potency journal July 2021
ZINC − A Free Database of Commercially Available Compounds for Virtual Screening journal December 2004
Conformer Generation with OMEGA: Algorithm and Validation Using High Quality Structures from the Protein Databank and Cambridge Structural Database journal March 2010
Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born journal April 2012
New Substructure Filters for Removal of Pan Assay Interference Compounds (PAINS) from Screening Libraries and for Their Exclusion in Bioassays journal April 2010
Evolution of the COVID-19 vaccine development landscape journal September 2020
Author Correction: VAMPnets for deep learning of molecular kinetics journal October 2018
Structural plasticity of SARS-CoV-2 3CL Mpro active site cavity revealed by room temperature X-ray crystallography journal June 2020
Feline coronavirus drug inhibits the main protease of SARS-CoV-2 and blocks virus replication journal August 2020
COVID-19: immunopathology and its implications for therapy journal April 2020
Ultra-large library docking for discovering new chemotypes journal February 2019
Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors journal April 2020
Protein-Ligand Blind Docking Using QuickVina-W With Inter-Process Spatio-Temporal Integration journal November 2017
Discovery of SARS-CoV-2 main protease inhibitors using a synthesis-directed de novo design model journal January 2021
Unusual zwitterionic catalytic site of SARS–CoV-2 main protease revealed by neutron crystallography journal October 2020
Conservation of substrate specificities among coronavirus main proteases journal March 2002
Coot model-building tools for molecular graphics journal November 2004
MolProbity : all-atom structure validation for macromolecular crystallography journal December 2009
PHENIX: a comprehensive Python-based system for macromolecular structure solution journal January 2010
Overview of the CCP 4 suite and current developments journal March 2011
Room-temperature X-ray crystallography reveals the oxidation and reactivity of cysteine residues in SARS-CoV-2 3CL M pro : insights into enzyme mechanism and drug design journal September 2020
Room-temperature neutron and X-ray data collection of 3CL M pro from SARS-CoV-2 journal September 2020
Design and Performance Characterization of RADICAL-Pilot on Leadership-Class Platforms journal April 2022
Drug Discovery Strategies for SARS-CoV-2 journal July 2020
Structure and inhibition of the SARS-CoV-2 main protease reveal strategy for developing dual inhibitors against M pro and cathepsin L journal November 2020
Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors journal March 2020
Masitinib is a broad coronavirus 3CL inhibitor that blocks replication of SARS-CoV-2 journal August 2021
High-resolution structures of the SARS-CoV-2 2′- O -methyltransferase reveal strategies for structure-based inhibitor design journal September 2020
3C-like protease inhibitors block coronavirus replication in vitro and improve survival in MERS-CoV–infected mice journal August 2020
Structures of Two Coronavirus Main Proteases: Implications for Substrate Binding and Antiviral Drug Design journal December 2007
DOVIS: an implementation for high-throughput virtual screening using AutoDock journal February 2008
http://Mcule.com: a public web service for drug discovery journal May 2012
OpenMM 7: Rapid development of high performance algorithms for molecular dynamics journal July 2017
Discovering Conformational Sub-States Relevant to Protein Function journal January 2011
Drug Design Targeting the Main Protease, the Achilles Heel of Coronaviruses journal December 2006
Transient Unfolding and Long-Range Interactions in Viral BCL2 M11 Enable Binding to the BECN1 BH3 Domain journal September 2020
Sub-Micromolar Inhibition of SARS-CoV-2 3CLpro by Natural Compounds journal September 2021

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