Expedited Approach toward the Rational Design of Noncovalent SARS-CoV-2 Main Protease Inhibitors

Kitamura, Naoya; Sacco, Michael Dominic; Ma, Chunlong; Hu, Yanmei; Townsend, Julia Alma; Meng, Xiangzhi; Zhang, Fushun; Zhang, Xiujun; Ba, Mandy; Szeto, Tommy; Kukuljac, Adis; Marty, Michael Thomas; Schultz, David; Cherry, Sara; Xiang, Yan; Chen, Yu; Wang, Jun

doi:10.1021/acs.jmedchem.1c00509

Expedited Approach toward the Rational Design of Noncovalent SARS-CoV-2 Main Protease Inhibitors

Journal Article · Tue Feb 01 04:00:00 EST 2022 · J. Med. Chem.

DOI:https://doi.org/10.1021/acs.jmedchem.1c00509· OSTI ID:1854215

Kitamura, Naoya; Sacco, Michael Dominic; Ma, Chunlong; Hu, Yanmei; Townsend, Julia Alma; Meng, Xiangzhi; Zhang, Fushun; Zhang, Xiujun; Ba, Mandy; Szeto, Tommy; Kukuljac, Adis; Marty, Michael Thomas; Schultz, David; Cherry, Sara; Xiang, Yan; Chen, Yu; Wang, Jun

Research Organization:: Advanced Photon Source (APS), Argonne National Laboratory (ANL), Argonne, IL (US)

Sponsoring Organization:: DOE - Office Of Science; NIH

OSTI ID:: 1854215

Journal Information:: J. Med. Chem., Journal Name: J. Med. Chem. Journal Issue: (4) Vol. 65

Country of Publication:: United States

Language:: ENGLISH

References (33)

Neutral red uptake assay for the estimation of cell viability/cytotoxicity Repetto, Guillermo; del Peso, Ana; Zurita, Jorge L. Nature Protocols, Vol. 3, Issue 7 https://doi.org/10.1038/nprot.2008.75	journal	June 2008
Baricitinib plus Remdesivir for Hospitalized Adults with Covid-19 Kalil, Andre C.; Patterson, Thomas F.; Mehta, Aneesh K. New England Journal of Medicine, Vol. 384, Issue 9 https://doi.org/10.1056/NEJMoa2031994	journal	March 2021
Crystal structure of SARS-CoV-2 main protease in complex with the natural product inhibitor shikonin illuminates a unique binding mode Li, Jian; Zhou, Xuelan; Zhang, Yan Science Bulletin, Vol. 66, Issue 7 https://doi.org/10.1016/j.scib.2020.10.018	journal	April 2021
3C-like protease inhibitors block coronavirus replication in vitro and improve survival in MERS-CoV–infected mice Rathnayake, Athri D.; Zheng, Jian; Kim, Yunjeong Science Translational Medicine, Vol. 12, Issue 557 https://doi.org/10.1126/scitranslmed.abc5332	journal	August 2020
REFMAC 5 for the refinement of macromolecular crystal structures Murshudov, Garib N.; Skubák, Pavol; Lebedev, Andrey A. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444911001314	journal	March 2011
The SARS-CoV-2 main protease as drug target Ullrich, Sven; Nitsche, Christoph Bioorganic & Medicinal Chemistry Letters, Vol. 30, Issue 17 https://doi.org/10.1016/j.bmcl.2020.127377	journal	September 2020
Drug Development and Medicinal Chemistry Efforts toward SARS‐Coronavirus and Covid‐19 Therapeutics Ghosh, Arun K.; Brindisi, Margherita; Shahabi, Dana ChemMedChem, Vol. 15, Issue 11 https://doi.org/10.1002/cmdc.202000223	journal	May 2020
Cysteine proteases as therapeutic targets: does selectivity matter? A systematic review of calpain and cathepsin inhibitors Siklos, Marton; BenAissa, Manel; Thatcher, Gregory R. J. Acta Pharmaceutica Sinica B, Vol. 5, Issue 6 https://doi.org/10.1016/j.apsb.2015.08.001	journal	November 2015
Efficacy of a 3C-like protease inhibitor in treating various forms of acquired feline infectious peritonitis Pedersen, Niels C.; Kim, Yunjeong; Liu, Hongwei Journal of Feline Medicine and Surgery, Vol. 20, Issue 4 https://doi.org/10.1177/1098612X17729626	journal	May 2017
Specific Binding of Adamantane Drugs and Direction of Their Polar Amines in the Pore of the Influenza M2 Transmembrane Domain in Lipid Bilayers and Dodecylphosphocholine Micelles Determined by NMR Spectroscopy Cady, Sarah D.; Wang, Jun; Wu, Yibing Journal of the American Chemical Society, Vol. 133, Issue 12 https://doi.org/10.1021/ja102581n	journal	March 2011
Ebselen, Disulfiram, Carmofur, PX-12, Tideglusib, and Shikonin Are Nonspecific Promiscuous SARS-CoV-2 Main Protease Inhibitors Ma, Chunlong; Hu, Yanmei; Townsend, Julia Alma ACS Pharmacology & Translational Science, Vol. 3, Issue 6 https://doi.org/10.1021/acsptsci.0c00130	journal	October 2020
Application of Dually Activated Michael Acceptor to the Rational Design of Reversible Covalent Inhibitor for Enterovirus 71 3C Protease Ma, Yuying; Li, Linfeng; He, Shuai Journal of Medicinal Chemistry, Vol. 62, Issue 13 https://doi.org/10.1021/acs.jmedchem.9b00387	journal	June 2019
Discovery, Synthesis, And Structure-Based Optimization of a Series of N -( tert -Butyl)-2-( N -arylamido)-2-(pyridin-3-yl) Acetamides (ML188) as Potent Noncovalent Small Molecule Inhibitors of the Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) 3CL Protease Jacobs, Jon; Grum-Tokars, Valerie; Zhou, Ya Journal of Medicinal Chemistry, Vol. 56, Issue 2 https://doi.org/10.1021/jm301580n	journal	January 2013
SARS-CoV-2 Mpro inhibitors and activity-based probes for patient-sample imaging Rut, Wioletta; Groborz, Katarzyna; Zhang, Linlin Nature Chemical Biology, Vol. 17, Issue 2 https://doi.org/10.1038/s41589-020-00689-z	journal	October 2020
MOLREP an Automated Program for Molecular Replacement Vagin, A.; Teplyakov, A. Journal of Applied Crystallography, Vol. 30, Issue 6, p. 1022-1025 https://doi.org/10.1107/S0021889897006766	journal	December 1997
Can Cysteine Protease Cross-Class Inhibitors Achieve Selectivity? Cianni, Lorenzo; Feldmann, Christian Wolfgang; Gilberg, Erik Journal of Medicinal Chemistry, Vol. 62, Issue 23 https://doi.org/10.1021/acs.jmedchem.9b00683	journal	July 2019
Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors Zhang, Linlin; Lin, Daizong; Sun, Xinyuanyuan Science https://doi.org/10.1126/science.abb3405	journal	March 2020
Bayesian Deconvolution of Mass and Ion Mobility Spectra: From Binary Interactions to Polydisperse Ensembles Marty, Michael T.; Baldwin, Andrew J.; Marklund, Erik G. Analytical Chemistry, Vol. 87, Issue 8 https://doi.org/10.1021/acs.analchem.5b00140	journal	April 2015
Discovery of a Novel Inhibitor of Coronavirus 3CL Protease for the Potential Treatment of COVID-19 Boras, Britton; Jones, Rhys M.; Anson, Brandon J. BioRxiv https://doi.org/10.1101/2020.09.12.293498	posted_content	January 2021
Evaluation of SARS-CoV-2 3C-like protease inhibitors using self-assembled monolayer desorption ionization mass spectrometry Gurard-Levin, Zachary A.; Liu, Cheng; Jekle, Andreas Antiviral Research, Vol. 182 https://doi.org/10.1016/j.antiviral.2020.104924	journal	October 2020
Coot model-building tools for molecular graphics Emsley, Paul; Cowtan, Kevin Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132 https://doi.org/10.1107/S0907444904019158	journal	November 2004
Reversal of the Progression of Fatal Coronavirus Infection in Cats by a Broad-Spectrum Coronavirus Protease Inhibitor Kim, Yunjeong; Liu, Hongwei; Galasiti Kankanamalage, Anushka C. PLOS Pathogens, Vol. 12, Issue 3 https://doi.org/10.1371/journal.ppat.1005531	journal	March 2016
The in vitro antiviral activity of lactoferrin against common human coronaviruses and SARS-CoV-2 is mediated by targeting the heparan sulfate co-receptor Hu, Yanmei; Meng, Xiangzhi; Zhang, Fushun Emerging Microbes & Infections, Vol. 10, Issue 1 https://doi.org/10.1080/22221751.2021.1888660	journal	January 2021
Discovery of N-(benzo[1,2,3]triazol-1-yl)-N-(benzyl)acetamido)phenyl) carboxamides as severe acute respiratory syndrome coronavirus (SARS-CoV) 3CLpro inhibitors: Identification of ML300 and noncovalent nanomolar inhibitors with an induced-fit binding Turlington, Mark; Chun, Aspen; Tomar, Sakshi Bioorganic & Medicinal Chemistry Letters, Vol. 23, Issue 22 https://doi.org/10.1016/j.bmcl.2013.08.112	journal	November 2013
Exploring Ugi-Azide Four-Component Reaction Products for Broad-Spectrum Influenza Antivirals with a High Genetic Barrier to Drug Resistance Zhang, Jiantao; Hu, Yanmei; Foley, Christopher Scientific Reports, Vol. 8, Issue 1 https://doi.org/10.1038/s41598-018-22875-9	journal	March 2018
Validating Enterovirus D68-2A ^pro as an Antiviral Drug Target and the Discovery of Telaprevir as a Potent D68-2A ^pro Inhibitor Musharrafieh, Rami; Ma, Chunlong; Zhang, Jiantao Journal of Virology, Vol. 93, Issue 7 https://doi.org/10.1128/JVI.02221-18	journal	January 2019
Challenges for Targeting SARS-CoV-2 Proteases as a Therapeutic Strategy for COVID-19 Steuten, Kas; Kim, Heeyoung; Widen, John C. ACS Infectious Diseases, Vol. 7, Issue 6 https://doi.org/10.1021/acsinfecdis.0c00815	journal	February 2021
Boceprevir, GC-376, and calpain inhibitors II, XII inhibit SARS-CoV-2 viral replication by targeting the viral main protease Ma, Chunlong; Sacco, Michael Dominic; Hurst, Brett Cell Research, Vol. 30, Issue 8 https://doi.org/10.1038/s41422-020-0356-z	journal	June 2020
Pharmacological Characterization of the Spectrum of Antiviral Activity and Genetic Barrier to Drug Resistance of M2-S31N Channel Blockers Ma, Chunlong; Zhang, Jiantao; Wang, Jun Molecular Pharmacology, Vol. 90, Issue 3 https://doi.org/10.1124/mol.116.105346	journal	July 2016
Structure and inhibition of the SARS-CoV-2 main protease reveal strategy for developing dual inhibitors against M ^pro and cathepsin L Sacco, Michael Dominic; Ma, Chunlong; Lagarias, Panagiotis Science Advances, Vol. 6, Issue 50 https://doi.org/10.1126/sciadv.abe0751	journal	November 2020
Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors Jin, Zhenming; Du, Xiaoyu; Xu, Yechun Nature, Vol. 582, Issue 7811 https://doi.org/10.1038/s41586-020-2223-y	journal	April 2020
SARS-CoV-2 M ^pro inhibitors with antiviral activity in a transgenic mouse model Qiao, Jingxin; Li, Yue-Shan; Zeng, Rui Science, Vol. 371, Issue 6536 https://doi.org/10.1126/science.abf1611	journal	February 2021
COVID-19: Drug Targets and Potential Treatments Gil, Carmen; Ginex, Tiziana; Maestro, Inés Journal of Medicinal Chemistry, Vol. 63, Issue 21 https://doi.org/10.1021/acs.jmedchem.0c00606	journal	June 2020

Similar Records

Hit Expansion of a Noncovalent SARS-CoV-2 Main Protease Inhibitor

Journal Article · Sun Apr 03 20:00:00 EDT 2022 · ACS Pharmacology & Translational Science · OSTI ID:1864414

Rational Design of Hybrid SARS-CoV-2 Main Protease Inhibitors Guided by the Superimposed Cocrystal S

Journal Article · Tue Jun 01 00:00:00 EDT 2021 · ACS Pharmacol. Transl. Sci. · OSTI ID:1818322

Contribution of the catalytic dyad of SARS-CoV-2 main protease to binding covalent and noncovalent inhibitors

Journal Article · Thu Jun 01 20:00:00 EDT 2023 · Journal of Biological Chemistry · OSTI ID:1987791

Expedited Approach toward the Rational Design of Noncovalent SARS-CoV-2 Main Protease Inhibitors

Citation Formats

References (33)

Similar Records

Related Subjects