8HQJ

Crystal structure of SARS-Cov-2 main protease Y54C mutant in complex with inhibitor YH-53

Summary for 8HQJ

• Entry DOI: 10.2210/pdb8hqj/pdb
• Descriptor: 3C-like proteinase nsp5, N-[(2S)-1-[[(2S)-1-(1,3-benzothiazol-2-yl)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]-4-methoxy-1H-indole-2-carboxamide (3 entities in total)
• Functional Keywords: viral protein-inhibitor complex, viral protein/inhibitor
• Biological source: Severe acute respiratory syndrome coronavirus 2
• Total number of polymer chains: 2
• Total formula weight: 67328.96

Authors

Zhou, X.L.,Zhang, J.,Li, J. (deposition date: 2022-12-13, release date: 2023-12-20, Last modification date: 2025-01-01)

Primary citation

Luo, J.,Wang, W.,Jiang, H.,Li, W.,Zeng, P.,Wang, J.,Zhou, X.,Zou, X.,Chen, S.,Wang, Q.,Zhang, J.,Li, J.
Crystal structures of main proteases of SARS-CoV-2 variants bound to a benzothiazole-based inhibitor.
Acta Biochim.Biophys.Sin., 55:1257-1264, 2023

PubMed Abstract: Main protease (M ) serves as an indispensable factor in the life cycle of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) as well as its constantly emerging variants and is therefore considered an attractive target for antiviral drug development. Benzothiazole-based inhibitors targeting M have recently been investigated by several groups and proven to be promising leads for coronaviral drug development. In the present study, we determine the crystal structures of a benzothiazole-based inhibitor, YH-53, bound to M mutants from SARS-CoV-2 variants of concern (VOCs) or variants of interest (VOIs), including K90R (Beta, B.1.351), G15S (Lambda, C.37), Y54C (Delta, AY.4), M49I (Omicron, BA.5) and P132H (Omicron, B.1.1.529). The structures show that the benzothiazole group in YH-53 forms a C-S covalent bond with the sulfur atom of catalytic residue Cys145 in SARS-CoV-2 M mutants. Structural analysis reveals the key molecular determinants necessary for interaction and illustrates the binding mode of YH-53 to these mutant M s. In conclusion, structural insights from this study offer more information to develop benzothiazole-based drugs that are broader spectrum, more effective and safer.

PubMed: 37357528
DOI: 10.3724/abbs.2023053

Experimental method

X-RAY DIFFRACTION (1.74 Å)