Ligand Versatility and Resistance Mechanism of Monotherapy-Grade HIV‑1 Protease Inhibitor GRL-142 Binding the Multidrug Resistant Variant p51: Insights from 1 μs MD Simulations

TL;DR

This study uses molecular simulations to understand how the HIV-1 protease inhibitor GRL-142 interacts with a drug-resistant HIV variant, revealing insights into resistance mechanisms and potential drug optimization.

Contribution

The study reveals a novel binding mode of GRL-142 to a multidrug-resistant HIV protease variant and highlights structural versatility and resistance mechanisms.

Findings

GRL-142 shows a novel binding mode in the resistant p51 variant with higher affinity than the wild-type complex.

The P2′ functional group detachment disrupts key interactions needed for inhibition in the resistant variant.

Fluorine-mediated interactions help stabilize both wild-type and resistant variant complexes with GRL-142.

Abstract

The emergence of
HIV-1 highly resistant strains and the prevalence
of HIV-associated neurocognitive disorders (HAND), are two of the
biggest challenges posed to combination antiretroviral therapy (cART),
despite promising advances in treatment. To address these issues,
the protease inhibitor GRL-142 (G), an extremely potent and central
nervous system (CNS)-penetrating antiretroviral, has recently been
experimentally proposed as monotherapy and enhanced cART efficacy
against HAND. Using all-atom molecular dynamics (MD) simulations of
up to 1 μs, this study elucidates the energetics, dynamics,
and bonding interactions that govern the inhibitory mechanism of G
against the highly resistant HIV-1 protease, p51, for which it exhibited
the lowest experimental potency. Our MD trajectories allow us to capture
the complex structural and dynamical interplay between this state-of-the-art
inhibitor and p51. The protein mechanism of resistance involves retention
or even improvement of structural stability at key active regions,
expansion of its active site cavity, and disruption of the HB network
with the inhibitor, compared to the wild-type (Wt) complex. As a consequence,
the inhibitory backbone binding mechanism of G is lost at the P2′
functional group moiety. Yet, G engages in direct drug–protein
interactions that compensate for the loss of the crystallographic
flap-water and undergoes a binding mode transition, preserving important
interactions to the inhibitory mechanism. Conserved fluorine-mediated
interactions help stabilize both Wt–G and p51–G complexes.
The calculated MMPBSA binding energy of Wt–G during the entire
trajectory is in close agreement with the experimental value (ΔG
MMPBSA = −16.1 kcal mol–1 vs ΔG
exp = −14.9 kcal mol–1). For the Mut–G system, there is slightly
less affinity with ΔG
MMPBSA = −15.5
kcal mol–1. The novel binding mode of G in p51–G
has a higher affinity of (ΔG = −18.4
kcal mol–1), which highlights its relevance from
a structure-based drug design perspective and the structural versatility
of inhibitor G. Despite this energetic favorability, the detachment
of P2′ from its canonical subsite, disrupts key pharmacophoric
interactions and the bioactive conformation required for inhibition,
indicating that optimization of P2′ is needed to preserve the
backbone binding mechanism against highly resistant strains.

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