7LMD

SARS-CoV-2 3CLPro in complex with 2-(benzotriazol-1-yl)-N-[4-(1H-pyrazol-4-yl)phenyl]-N-(3-thienylmethyl)acetamide

Summary for 7LMD

• Entry DOI: 10.2210/pdb7lmd/pdb
• Descriptor: 3C-like proteinase, 2-(benzotriazol-1-yl)-~{N}-[4-(1~{H}-pyrazol-4-yl)phenyl]-~{N}-(thiophen-3-ylmethyl)ethanamide (3 entities in total)
• Functional Keywords: 3clpro, sars-cov-2 main protease, sars-cov-2 3clpro, inhibitor complex, protease, viral protein, hydrolase-inhibitor complex, hydrolase/inhibitor
• Biological source: Severe acute respiratory syndrome coronavirus 2 (2019-nCoV,SARS-CoV-2)
• Total number of polymer chains: 1
• Total formula weight: 34240.03

Authors

Goins, C.M.,Arya, T.,Macdonald, J.D.,Stauffer, S.R. (deposition date: 2021-02-05, release date: 2021-08-11, Last modification date: 2023-10-18)

Primary citation

Han, S.H.,Goins, C.M.,Arya, T.,Shin, W.J.,Maw, J.,Hooper, A.,Sonawane, D.P.,Porter, M.R.,Bannister, B.E.,Crouch, R.D.,Lindsey, A.A.,Lakatos, G.,Martinez, S.R.,Alvarado, J.,Akers, W.S.,Wang, N.S.,Jung, J.U.,Macdonald, J.D.,Stauffer, S.R.
Structure-Based Optimization of ML300-Derived, Noncovalent Inhibitors Targeting the Severe Acute Respiratory Syndrome Coronavirus 3CL Protease (SARS-CoV-2 3CL pro ).
J.Med.Chem., 65:2880-2904, 2022

PubMed Abstract: Starting from the MLPCN probe compound ML300, a structure-based optimization campaign was initiated against the recent severe acute respiratory syndrome coronavirus (SARS-CoV-2) main protease (3CL). X-ray structures of SARS-CoV-1 and SARS-CoV-2 3CL enzymes in complex with multiple ML300-based inhibitors, including the original probe ML300, were obtained and proved instrumental in guiding chemistry toward probe compound (CCF0058981). The disclosed inhibitors utilize a noncovalent mode of action and complex in a noncanonical binding mode not observed by peptidic 3CL inhibitors. DMPK profiling highlights key areas where further optimization in the series is required to obtain useful probes. Antiviral activity was established using a SARS-CoV-2-infected Vero E6 cell viability assay and a plaque formation assay. Compound demonstrates nanomolar activity in these respective assays, comparable in potency to remdesivir. These findings have implications for antiviral development to combat current and future SARS-like zoonotic coronavirus outbreaks.

PubMed: 34347470
DOI: 10.1021/acs.jmedchem.1c00598

Experimental method

X-RAY DIFFRACTION (1.96 Å)