9NSK

Room-temperature X-ray structure of SARS-CoV-2 main protease in complex with inhibitor BBH-3

This is a non-PDB format compatible entry.

Summary for 9NSK

• Entry DOI: 10.2210/pdb9nsk/pdb
• Descriptor: 3C-like proteinase nsp5, N-(tert-butylcarbamoyl)-3-methyl-L-valyl-3,4-dichloro-N-{(1Z,2S)-1-imino-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-phenylalaninamide (3 entities in total)
• Functional Keywords: sars-cov-2, main protease, protease inhibitor, viral protein, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
• Biological source: Severe acute respiratory syndrome coronavirus 2
• Total number of polymer chains: 1
• Total formula weight: 34409.10

Authors

Bhandari, D.,Coates, L.,Kovalevsky, A. (deposition date: 2025-03-17, release date: 2025-07-30)

Primary citation

Bhandari, D.,Coates, L.,Aniana, A.,Louis, J.M.,Bonnesen, P.V.,Kovalevsky, A.
Influence of Steric and Electronic Properties of P2 Groups on Covalent Inhibitor Binding to SARS-CoV-2 Main Protease.
Acs Infect Dis., 11:1697-1706, 2025

PubMed Abstract: The main protease (MPro) of SARS-CoV-2 is a critical enzyme required for viral replication, making it a prime target for antiviral drug development. Covalent inhibitors, which form a stable interaction with the catalytic C145, have demonstrated strong inhibition of MPro, but the influence of steric and electronic properties of P2 substituents, designed to engage the S2 substrate-binding subsite within the MPro active site, on inhibitor binding affinity remains underexplored. In this study, we design and characterize two hybrid covalent inhibitors, BBH-3 and BBH-4, and present their X-ray crystallographic structures in complex with MPro, providing molecular insights into how their distinct P2 groups, a dichlorobenzyl moiety in BBH-3 and an adamantyl substituent in BBH-4, affect binding conformation and active site adaptability. Comparative structural analyses with previously characterized inhibitors, including BBH-2 and Mcule-5948770040, reveal how the P2 bulkiness and electronic properties influence active site dynamics, particularly through interactions with the S2 and S5 subsites. The P2 group of BBH-3 induces conformational shifts in the S2 helix and the S5 loop, while BBH-4 displaces M49, stabilizing its binding through hydrophobic interactions. Isothermal titration calorimetry further elucidates the impact of P2 modifications on inhibitor affinity, revealing a delicate balance between enthalpic and entropic contributions. The data demonstrate that BBH-3 exhibits less favorable binding, affirming that dichlorobenzyl substitution at the P2 position has a more negative impact on the affinity for MPro than bulky saturated cyclic groups. This underscores the feature that MPro active site malleability may be accompanied by a conformational strain.

PubMed: 40437897
DOI: 10.1021/acsinfecdis.5c00246

Experimental method

X-RAY DIFFRACTION (1.9 Å)