期刊
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
卷 24, 期 37, 页码 22898-22904出版社
ROYAL SOC CHEMISTRY
DOI: 10.1039/d2cp02882d
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资金
- Kaohsiung Medical University [KMU-DK(B)110004-1, KMU-DK(B)111001-1, KMU-TC111A03-4, NSTC-111-2113-M-037-008-]
- National Science and Technology Council of the Republic of China [KMU-DK(B)110004-1, KMU-DK(B)111001-1, KMU-TC111A03-4, NSTC-111-2113-M-037-008-]
This study investigates the binding mechanisms between Nirmatrelvir and 3CLpro protein and provides valuable insights for designing antiviral drugs.
Coronavirus 3C-like protease (3CLpro) is found in SARS-CoV-2 virus, which causes COVID-19. 3CLpro controls virus replication and is a major target for target-based antiviral discovery. As reported by Pfizer, Nirmatrelvir (PF-07321332) is a competitive protein inhibitor and a clinical candidate for orally delivered medication. However, the binding mechanisms between Nirmatrelvir and 3CLpro complex structures remain unknown. This study incorporated ligand Gaussian accelerated molecular dynamics, the one-dimensional and two-dimensional potential of mean force, normal molecular dynamics, and Kramers' rate theory to determine the binding and dissociation rate constants (k(off) and k(on)) associated with the binding of the 3CLpro protein to the Nirmatrelvir inhibitor. The proposed approach addresses the challenges in designing small-molecule antiviral drugs.
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