Methods: A sequence of homology modeling using Schrödinger PRIME software, docking experiments using PYMOL then repeated with the nine Gag and Gag-Pol cleavage peptides, and molecular dynamics (MD) simulations using the Wayne State University Grid Nano Molecular Dynamics (NAMD) v. 2.9 were carried out
Results: Genotypic results (ViroSeq test) indicate that the isolate is resistant to indinavir, lopinavir/r, nelfinavir, fosamprenavir and possibly resistant to tipranavir, darunavir, and atazanavir without evidence of resistance to saquinavir. The phenotypic test indicates resistance to atazanavir, atazanavir/r, fosamprenavir/r, and nelfinavir and partial sensitivity to darunavir/r, lopinavir/r, and tipranavir/r. The isolate is sensitive to saquinavir based on both the phenotypic and genotypic test results. Surprisingly, the virus replicative capacity for the codon 28 insertion mutant is only 28% relative to the wild-type (100% reference). To evaluate changes in molecular recognition of the protease inhibitors and the nine substrate peptides we performed a series of 40 ns MD simulations as described in the Methods section. These results indicate major changes in both inhibitor and substrate binding when compared to the wild-type HIV-1 protease.
Conclusion: The five residue insertion mutation exhibits altered binding properties of both the Gag and GagPol substrates and the nine protease inhibitors. MD experiments indicate that the active site cleft insertion mutation also reduces inhibitor binding as observed earlier based on genotypic and phenotypic tests.
E. A. Wong,
B. Keusch, None
B. Kuiper, None
I. Kovari, None
H. Salimnia, Nanosphere: Grant Investigator , Grant recipient and Research grant
BioFire: Grant Investigator , Grant recipient and Research grant
GenMark: Grant Investigator , Grant recipient and Research grant
Accelerate: Grant Investigator , Grant recipient and Research grant
AdvanDx: Grant Investigator , Grant recipient and Research grant
J. Veltman, None
L. Kovari, None