9BOB

Crystal Structure of A173V/L50F SARS-CoV-2 Main Protease in Complex with GC376

Summary for 9BOB

• Entry DOI: 10.2210/pdb9bob/pdb
• Related PRD ID: PRD_002495
• Descriptor: 3C-like proteinase nsp5, N~2~-[(benzyloxy)carbonyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide (3 entities in total)
• Functional Keywords: hydrolase, viral protein
• Biological source: Severe acute respiratory syndrome coronavirus 2
• Total number of polymer chains: 1
• Total formula weight: 34293.10

Authors

Papini, C.,Kenneson, J.,Anderson, K.S. (deposition date: 2024-05-03, release date: 2025-02-12, Last modification date: 2025-03-12)

Primary citation

Kenneson, J.R.,Papini, C.,Tang, S.,Huynh, K.,Zhang, C.H.,Jorgensen, W.L.,Anderson, K.S.
Exploring Possible Drug-Resistant Variants of SARS-CoV-2 Main Protease (M pro ) with Noncovalent Preclinical Candidate, Mpro61.
Acs Bio Med Chem Au, 5:215-226, 2025

PubMed Abstract: SARS-CoV-2 M inhibitors, such as nirmatrelvir, have proven efficacy in clinical use. Nirmatrelvir was developed in a target-based approach against wild-type M, with the anticipation that prolonged usage may cause enrichment of drug-resistant mutations and persistence of COVID infections. Although globally prevalent drug-resistant mutations have not yet been observed, individual cases have recently been reported among patients following treatment with Paxlovid-a formulation of nirmatrelvir. Mutations E166V and E166A have been detected in these drug-resistant clinical isolates, consistent with predictions from viral passage experiments and therefore necessitate ongoing drug development. In this study, we selected seven M variants (T21I, L50F, E166V, A173V, T190I, E166V/L50F, and A173V/L50F), which have been repeatedly found in viral passage experiments. We investigated their kinetic and structural properties, as well as resistance level to M inhibitors: nirmatrelvir, GC376-a similar peptidomimetic for feline COVID infections, and our in-house-developed nonpeptidomimetic inhibitor Mpro61. Mpro61 maintains potency against the single variants (except for E166V) and the A173/L50F double variant, with values similar to those of the wild type. In contrast, while nirmatrelvir and GC376 were still effective against the A173V/L50F double variant, their values significantly increased up to 10-fold. None of the inhibitors appeared to be potent against E166V-containing variants. Our structural analysis revealed a significant movement of Ser1 residue in all E166V-containing variants in the presence or absence of an inhibitor. The new orientation of the Ser1 suggested potential strategies for medicinal chemistry modifications of Mpro61 to enhance hydrogen-bonding interactions between these variants and Mpro61 derivatives. These studies provide critical insights into guiding the future design of additional Mpro61 derivatives that would potentially inhibit variants with the pan-drug-resistant E166V mutation.

PubMed: 39990941
DOI: 10.1021/acsbiomedchemau.4c00109

Experimental method

X-RAY DIFFRACTION (1.87 Å)