Biopolym. Cell. 2026; 42(2):129-138.
https://doi.org/10.7124/bc.000B3F
Molecular and Cell Biotechnologies
Effect of antivirals and a peptidomimetic inhibitor on furin conformational stability: Molecular docking and molecular dynamics simulations
1, 2Khmil N. V., 1Shestopalova A. V.
  1. O. Ya. Usikov Institute for Radiophysics and Electronics, NAS of Ukraine
    12, Acad. Proskura Str., Kharkiv, Ukraine 61085
  2. Kharkiv National University of Radio Electronics
    14, Nauky Ave., Kharkiv, Ukraine 61166

Abstract

Aim. To evaluate the conformational stability and binding behavior of furin in complex with nelfinavir, remdesivir, and the macrocyclic peptidomimetic inhibitor 8 (PI8) using computational approaches. Methods. Molecular docking and 100-ns molecular dynamics (MD) simulations were used to characterize ligand-binding modes and assess the structural stability of furin–ligand complexes. Results. Docking analysis identified PI8 as the energetically most favorable compound (–9.1 kcal/mol) that forms stable interactions within the catalytic site, while nelfinavir and remdesivir showed slightly lower affinities (–8.7 and –8.9 kcal/mol, respectively). MD simulations confirmed the structural stability of all complexes over the 100-ns trajectory, supporting the reliability of the predicted binding modes. Conclusions. Molecular docking and MD approach provide a robust framework for identifying and characterizing potential furin inhibitors.
Keywords: furin, antivirals, macrocyclic peptidomimetic inhibitor 8, SARS-CoV-2 S protein, molecular docking, molecular dynamics simulation
Full text: (PDF, in English)

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