Dissociation of an antiviral compound from the internal pocket of human rhinovirus 14 capsid.
WIN antiviral compounds bind human rhinovirus, as well as enterovirus and parechovirus, in an internal cavity located within the viral protein capsid. Access to the buried pocket necessitates deviation from the average viral protein structure identified by crystallography. We investigated the dissociation of WIN 52084 from the pocket in human rhinovirus 14 by using an adiabatic, biased molecular dynamics simulation method. Multiple dissociation trajectories are used to characterize the pathway. WIN 52084 exits between the polypeptide chain near the ends of betaC and betaH in a series of steps. Small, transient packing defects in the protein are sufficient for dissociation. A number of torsion-angle transitions of the antiviral compound are involved, which suggests that flexibility in antiviral compounds is important for binding. It is interesting to note that dissociation is associated with an increase in the conformational fluctuations of residues never in direct contact with WIN 52084 over the course of dissociation. These residues are N-terminal residues in the viral proteins VP3 and VP4 and are located in the interior of the capsid near the icosahedral 5-fold axis. The observed changes in dynamics may be relevant to structural changes associated with virion uncoating and its inhibition by antiviral compounds.
Li
Yumin
Y
Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, IN 47907-2091, USA.
Zhou
Zhigang
Z
Post
Carol Beth
CB
D000998:Antiviral Agents / Q000378:metabolism*; D036022:Capsid Proteins / Q000737:chemistry / Q000378:metabolism*; D019295:Computational Biology; D003198:Computer Simulation; D006801:Humans; D007555:Isoxazoles / Q000378:metabolism*; D008958:Models, Molecular; D025341:Principal Component Analysis; D011487:Protein Conformation; D021122:Protein Subunits / Q000378:metabolism; D012229:Rhinovirus / Q000378:metabolism*
D000998:Antiviral Agents; D036022:Capsid Proteins; D007555:Isoxazoles; D021122:Protein Subunits; C049869:Win 52084