Exploring the Molecular
Mechanism of Cross-Resistance
to HIV‑1 Integrase Strand Transfer Inhibitors by Molecular
Dynamics Simulation and Residue Interaction Network Analysis
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Abstract
The rapid emergence of cross-resistance to the integrase
strand
transfer inhibitors (INSTIs) has become a serious problem in the therapy
of human immunodeficiency virus type 1 (HIV-1) infection. Understanding
the detailed molecular mechanism of INSTIs cross-resistance is therefore
critical for the development of new effective therapy against cross-resistance.
On the basis of the homology modeling constructed structure of tetrameric
HIV-1 intasome, the detailed molecular mechanism of the cross-resistance
mutation E138K/Q148K to three important INSTIs (Raltegravir (RAL,
FDA approved in 2007), Elvitegravir (EVG, FDA approved in 2012), and
Dolutegravir (DTG, phase III clinical trials)) was investigated by
using molecular dynamics (MD) simulation and residue interaction network
(RIN) analysis. The results from conformation analysis and binding
free energy calculation can provide some useful information about
the detailed binding mode and cross-resistance mechanism for the three
INSTIs to HIV-1 intasome. Binding free energy decomposition analysis
revealed that Pro145 residue in the 140s 1oop (Gly140 to Gly149) of
the HIV-1 intasome had strong hydrophobic interactions with INSTIs
and played an important role in the binding of INSTIs to HIV-1 intasome
active site. A systematic comparison and analysis of the RIN proves
that the communications between the residues in the resistance mutant
is increased when compared with that of the wild-type HIV-1 intasome.
Further analysis indicates that residue Pro145 may play an important
role and is relevant to the structure rearrangement in HIV-1 intasome
active site. In addition, the chelating ability of the oxygen atoms
in INSTIs (e.g., RAL and EVG) to Mg<sup>2+</sup> in the active site
of the mutated intasome was reduced due to this conformational change
and is also responsible for the cross-resistance mechanism. Notably,
the cross-resistance mechanism we proposed could give some important
information for the future rational design of novel INSTIs overcoming
cross-resistance. Furthermore, the combination use of molecular dynamics
simulation and residue interaction network analysis can be generally
applicable to investigate drug resistance mechanism for other biomolecular
systems