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

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 (ΔGMMPBSA = -16.1 kcal mol-1 vs ΔGexp = -14.9 kcal mol-1). For the Mut-G system, there is slightly less affinity with ΔGMMPBSA = -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.