Related Experiment Video
Updated: Aug 28, 2025

Engineering Antiviral Agents via Surface Plasmon Resonance
Published on: June 14, 2022
Structural insights into Nirmatrelvir (PF-07321332)-3C-like SARS-CoV-2 protease complexation: a ligand Gaussian
Yeng-Tseng Wang1,2,3, Jun-Min Liao2,3,4, Wen-Wei Lin1,2,3,4
1School of Post-Baccalaureate Medicine, College of Medicine, Kaohsiung Medical University, Taiwan. c00jsw00@kmu.edu.tw.
Abstract:
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 (koff and kon) associated with the binding of the 3CLpro protein to the Nirmatrelvir inhibitor. The proposed approach addresses the challenges in designing small-molecule antiviral drugs.
More Related Videos
Related Concept Videos
Protein Complex Assembly
Many viruses self-assemble into a fully functional unit using the infected host cell to...
Protein Organization
The primary structure of a protein is its amino acid sequence....
The Proteasome Structure
The proteasome is an...
Protein Complexes with Interchangeable Parts
The SCF ubiquitin ligase is a protein complex of five individual proteins. This complex attaches ubiquitin to other target proteins to mark them for degradation. In order...

