Structure-Guided Design of Conformationally Constrained Cyclohexane Inhibitors of Severe Acute Respiratory Syndrome Coronavirus-2 3CL Protease

Dampalla, C; Kim, Y.; Bickmeier, N.; Rathnayake, A.; Nguyen, H.; Zheng, J.; Kashipathy, M.; Baird, M.; Battaile, K.; Lovell, S.; Perlman, S.; Chang, K.; Groutas, W.

doi:10.1021/acs.jmedchem.1c00319

Structure-Guided Design of Conformationally Constrained Cyclohexane Inhibitors of Severe Acute Respiratory Syndrome Coronavirus-2 3CL Protease

Journal Article · 31 December 2021 · Journal of Medicinal Chemistry

DOI:https://doi.org/10.1021/acs.jmedchem.1c00319· OSTI ID:1814884

Dampalla, C; Kim, Y.; Bickmeier, N.; Rathnayake, A.; Nguyen, H.; Zheng, J.; Kashipathy, M.; Baird, M.; Battaile, K.; Lovell, S.; Perlman, S.; Chang, K.; Groutas, W.

Research Organization:: Brookhaven National Laboratory (BNL), Upton, NY (United States)

Sponsoring Organization:: ~OTHER

DOE Contract Number:: SC0012704

OSTI ID:: 1814884

Report Number(s):: BNL-222040-2021-JACI

Journal Information:: Journal of Medicinal Chemistry, Journal Name: Journal of Medicinal Chemistry Journal Issue: 14 Vol. 64; ISSN 0022-2623

Country of Publication:: United States

Language:: English

References (41)

An introduction to data reduction: space-group determination, scaling and intensity statistics Evans, Philip R. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/s090744491003982x	journal	March 2011
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
A new coronavirus associated with human respiratory disease in China Wu, Fan; Zhao, Su; Yu, Bin Nature, Vol. 579, Issue 7798 https://doi.org/10.1038/s41586-020-2008-3	journal	February 2020
XDS Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2 https://doi.org/10.1107/s0907444909047337	journal	January 2010
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
Developments in the CCP 4 molecular-graphics project Potterton, Liz; McNicholas, Stuart; Krissinel, Eugene Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12 https://doi.org/10.1107/s0907444904023716	journal	November 2004
Targeting SARS-CoV-2 Proteases and Polymerase for COVID-19 Treatment: State of the Art and Future Opportunities Cannalire, Rolando; Cerchia, Carmen; Beccari, Andrea R. Journal of Medicinal Chemistry https://doi.org/10.1021/acs.jmedchem.0c01140	journal	November 2020
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2): a global pandemic and treatment strategies Sharma, Atul; Tiwari, Swapnil; Deb, Manas Kanti International Journal of Antimicrobial Agents, Vol. 56, Issue 2 https://doi.org/10.1016/j.ijantimicag.2020.106054	journal	August 2020
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
Linking Crystallographic Model and Data Quality Karplus, P. A.; Diederichs, K. Science, Vol. 336, Issue 6084 https://doi.org/10.1126/science.1218231	journal	May 2012
Structure-Based Design of Potent and Orally Active Isoindolinone Inhibitors of MDM2-p53 Protein–Protein Interaction Chessari, Gianni; Hardcastle, Ian R.; Ahn, Jong Sook Journal of Medicinal Chemistry, Vol. 64, Issue 7 https://doi.org/10.1021/acs.jmedchem.0c02188	journal	March 2021
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
Data processing and analysis with the autoPROC toolbox Vonrhein, Clemens; Flensburg, Claus; Keller, Peter Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/s0907444911007773	journal	March 2011
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/s0907444909052925	journal	January 2010
Reprint of “On the Size of the Active Site in Proteases. I. Papain” Schechter, Israel Biochemical and Biophysical Research Communications, Vol. 425, Issue 3 https://doi.org/10.1016/j.bbrc.2012.08.015	journal	August 2012
Activity profiling and crystal structures of inhibitor-bound SARS-CoV-2 papain-like protease: A framework for anti–COVID-19 drug design Rut, Wioletta; Lv, Zongyang; Zmudzinski, Mikolaj Science Advances, Vol. 6, Issue 42 https://doi.org/10.1126/sciadv.abd4596	journal	October 2020
A primer of deuterium in drug design Cargnin, Sarah; Serafini, Marta; Pirali, Tracey Future Medicinal Chemistry, Vol. 11, Issue 16 https://doi.org/10.4155/fmc-2019-0183	journal	August 2019
Deuterated drugs; updates and obviousness analysis Timmins, Graham S. Expert Opinion on Therapeutic Patents, Vol. 27, Issue 12 https://doi.org/10.1080/13543776.2017.1378350	journal	September 2017
A Novel, Nonaqueous Method for Regeneration of Aldehydes from Bisulfite Adducts Kjell, Douglas P.; Slattery, Brian J.; Semo, Michael J. The Journal of Organic Chemistry, Vol. 64, Issue 15 https://doi.org/10.1021/jo990543v	journal	July 1999
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
Broad-Spectrum Antivirals against 3C or 3C-Like Proteases of Picornaviruses, Noroviruses, and Coronaviruses Kim, Y.; Lovell, S.; Tiew, K. -C. Journal of Virology, Vol. 86, Issue 21 https://doi.org/10.1128/jvi.01348-12	journal	August 2012
Applications of Deuterium in Medicinal Chemistry Pirali, Tracey; Serafini, Marta; Cargnin, Sarah Journal of Medicinal Chemistry, Vol. 62, Issue 11 https://doi.org/10.1021/acs.jmedchem.8b01808	journal	January 2019
Resolving Some Old Problems in Protein Crystallography Evans, P. Science, Vol. 336, Issue 6084 https://doi.org/10.1126/science.1222162	journal	May 2012
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/s0907444910007493	journal	March 2010
Synopsis of Some Recent Tactical Application of Bioisosteres in Drug Design Meanwell, Nicholas A. Journal of Medicinal Chemistry, Vol. 54, Issue 8 https://doi.org/10.1021/jm1013693	journal	April 2011
Automatic indexing of rotation diffraction patterns Kabsch, W. Journal of Applied Crystallography, Vol. 21, Issue 1 https://doi.org/10.1107/s0021889887009737	journal	February 1988
N,N`-dissuccinimidyl carbonate: a useful reagent for alkoxycarbonylation of amines Ghosh, Arun K.; Doung, Tien T.; McKee, Sean P. Tetrahedron Letters, Vol. 33, Issue 20 https://doi.org/10.1016/s0040-4039(00)78856-3	journal	May 1992
Improved R-factors for diffraction data analysis in macromolecular crystallography Diederichs, Kay; Karplus, P. Andrew Nature Structural Biology, Vol. 4, Issue 4 https://doi.org/10.1038/nsb0497-269	journal	April 1997
MolProbity : all-atom structure validation for macromolecular crystallography Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1 https://doi.org/10.1107/s0907444909042073	journal	December 2009
An interactive web-based dashboard to track COVID-19 in real time Dong, Ensheng; Du, Hongru; Gardner, Lauren The Lancet Infectious Diseases, Vol. 20, Issue 5 https://doi.org/10.1016/s1473-3099(20)30120-1	journal	May 2020
A comparison of COVID-19, SARS and MERS Hu, Tingting; Liu, Ying; Zhao, Mingyi PeerJ, Vol. 8 https://doi.org/10.7717/peerj.9725	journal	January 2020
Global indicators of X-ray data quality Weiss, Manfred S. Journal of Applied Crystallography, Vol. 34, Issue 2 https://doi.org/10.1107/s0021889800018227	journal	April 2001
Curse or Cure? A Perspective on the Developability of Aldehydes as Active Pharmaceutical Ingredients Gampe, Christian; Verma, Vishal A. Journal of Medicinal Chemistry, Vol. 63, Issue 23 https://doi.org/10.1021/acs.jmedchem.0c01177	journal	September 2020
Phaser crystallographic software McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D. Journal of Applied Crystallography, Vol. 40, Issue 4 https://doi.org/10.1107/s0021889807021206	journal	July 2007
Structure-based design of antiviral drug candidates targeting the SARS-CoV-2 main protease Dai, Wenhao; Zhang, Bing; Jiang, Xia-Ming Science, Vol. 368, Issue 6497 https://doi.org/10.1126/science.abb4489	journal	April 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
Scaling and assessment of data quality Evans, Philip Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 1, p. 72-82 https://doi.org/10.1107/s0907444905036693	journal	December 2005
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
Discovery of Ketone-Based Covalent Inhibitors of Coronavirus 3CL Proteases for the Potential Therapeutic Treatment of COVID-19 Hoffman, Robert L.; Kania, Robert S.; Brothers, Mary A. Journal of Medicinal Chemistry, Vol. 63, Issue 21 https://doi.org/10.1021/acs.jmedchem.0c01063	journal	October 2020

Similar Records

Structure-Guided Design of Conformationally Constrained Cyclohexane Inhibitors of Severe Acute Respi

Journal Article · 2021 · J. Med. Chem. · OSTI ID:1815019

Exploring Noncovalent Protease Inhibitors for the Treatment of Severe Acute Respiratory Syndrome and Severe Acute Respiratory Syndrome-Like Coronaviruses

Journal Article · 2022 · ACS Infectious Diseases · OSTI ID:1885445

Related Subjects

99 GENERAL AND MISCELLANEOUS

Structure-Guided Design of Conformationally Constrained Cyclohexane Inhibitors of Severe Acute Respiratory Syndrome Coronavirus-2 3CL Protease

Citation Formats

References (41)

Similar Records

Related Subjects