Increased HIV-1 sensitivity to neutralizing antibodies by mutations in the Env V3-coding region for resistance to CXCR4 antagonists

Abstract

HIV-1 passage in cell culture in the presence of chemokine receptor antagonists can result in selection of viruses with env mutations that confer resistance to these inhibitors. In the present study, we examined the effect of HIV-1 env mutations that confer resistance to CXCR4 antagonists on envelope (Env) sensitivity to neutralizing antibodies (NAbs). Serial passage of CXCR4-tropic HIV-1 NL4-3 in PM1/CCR5 cells under CXCR4 antagonists KRH-3955, AMD3100 and AMD070 yielded two KRH-3955-resistant, one AMD3100-resistant and one AMD070-resistant viruses. These viruses had multiple env mutations including the Env gp120 V3 region. The majority of viruses having these CXCR4 antagonist-resistant Envs showed higher sensitivity to NAbs 447-52D, b12 and 2F5 targeting the V3 region, the gp120 CD4-binding site and the gp41 membrane proximal region, respectively, compared to NL4-3 WT virus. Recombinant NL4-3 viruses with the V3-coding region replaced with those derived from the CXCR4 antagonist-resistant viruses showed increased sensitivity to NAbs b12, 2F5 and 447-52D. Molecular dynamics simulations of Env gp120 outer domains predicted that the V3 mutations increased levels of fluctuations at the tip and stem of the V3 loop. These results indicate that mutations in the V3-coding region that result in loss of viral sensitivity to CXCR4 antagonists increase viral sensitivity to NAbs, providing insights into our understanding of the interplay of viral Env accessibility to chemokine receptors and sensitivity to NAbs.

Allosteric Regulation of HIV-1 Capsid Structure for Gag Assembly, Virion Production, and Viral Infectivity by a Disordered Interdomain Linker

“…MD simulation of HIV-1 capsid monomer. HIV-1 capsid models were subjected to MD simulations essentially as described previously for viral structural proteins and enzymes (36,(74)(75)(76). Briefly, the simulations were done by the pmemd module in the Amber 16 program package (54) with the ff14SB force field (77) and the TIP3P water model for simulations of aqueous solutions (78).…”

“…Calculation of RMSF. RMSFs were calculated as described previously (74)(75)(76) to quantify structural dynamics of molecules in the MD simulations. RMSFs of the C␣ atoms were calculated to obtain information on atomic fluctuations of individual amino acid residues during MD simulations.…”

A Proposal for a Structural Model of the Feline Calicivirus Protease Bound to the Substrate Peptide under Physiological Conditions

“…The molecular model of the FCV F4 strain protease-substrate complex was subjected to MD simulation using modules in the AMBER program package (Case et al, 2014) as described for MD simulations of the HIV-1/SIV envelope gp120 subunit (Naganawa et al, 2008; Yokoyama et al, 2012a, 2016; Kuwata et al, 2013; Hikichi et al, 2016). After heating calculations for 20 ps until 310 K using the NVT ensemble for the constant volume, temperature, and numbers of particles in the system, simulation was executed using the NPT ensemble for the constant pressure, temperature, and numbers of particles in the system at 1 atm, at 310 K, and in 150 mM NaCl for 30 ns.…”

“…The molecular model of the FCV F4 strain protease-substrate complex was subjected to MD simulation essentially as described for simulations of the HIV-1/SIV envelope gp120 subunit (Naganawa et al, 2008; Yokoyama et al, 2012a, 2016; Kuwata et al, 2013; Hikichi et al, 2016). Briefly, the MD simulation was performed by the Particle Mesh Ewald Molecular Dynamics (PMEMD) module in the AMBER program package (Case et al, 2014), employing the Amber ff99SB-ILDN force field, a protein force field with improved side-chain torsion potentials (Lindorff-Larsen et al, 2010), and the TIP3P water model for simulation of aqueous solutions (Jorgensen et al, 1983).…”

Molecular Dynamics Simulation of the Influenza A(H3N2) Hemagglutinin Trimer Reveals the Structural Basis for Adaptive Evolution of the Recent Epidemic Clade 3C.2a

“…The MD simulations have been used to disclose the structural basis of the adaptation and evolution of the highly mutable human immunodeficiency virus (HIV). This includes elucidation of the HIV structural changes associated with the phenotypic changes in viral neutralization sensitivity and receptor tropism (Naganawa et al, 2008; Yokoyama et al, 2012, 2016; Kuwata et al, 2013), viral sensitivity to antiviral protein (Miyamoto et al, 2012), viral drug sensitivity (Yuan et al, 2013), viral growth in non-natural host cells (Yokoyama et al, 2016), and viral sensitivities to antibodies by drug-resistance mutations (Alam et al, 2016; Hikichi et al, 2016). …”