Computer simulation study of the binding of an antiviral agent to a sensitive and a resistant human rhinovirus.
Molecular dynamics simulations have been used to study the free energy of binding of an antiviral agent to the human rhinovirus HRV-14 and to a mutant in which a valine residue in the antiviral binding pocket is replaced by leucine. The simulations predict that the antiviral should bind to the two viruses with similar affinity, in apparent disagreement with experimental results. Possible origins of this discrepancy are outlined. Of particular importance is the apparent need for methods to systematically sample all significant conformations of the leucine side chain.
Lybrand
T P
TP
Department of Medicinal Chemistry, University of Minnesota, Minneapolis 55455.
McCammon
J A
JA
D000998:Antiviral Agents / Q000378:metabolism*; D002213:Capsid / Q000235:genetics / Q000378:metabolism*; D003198:Computer Simulation; D007930:Leucine; D011485:Protein Binding; D011487:Protein Conformation; D012229:Rhinovirus / Q000187:drug effects* / Q000235:genetics / Q000378:metabolism; D012984:Software; D013329:Structure-Activity Relationship; D013816:Thermodynamics; D014633:Valine
D000998:Antiviral Agents; D007930:Leucine; D014633:Valine