Structural Studies of a Rationally Selected Multi-Drug Resistant HIV-1 Protease Reveal Synergistic Effect of Distal Mutations on Flap Dynamics

Abstract

We report structural analysis of HIV protease variant PRS17 which was rationally selected by machine learning to represent wide classes of highly drug-resistant variants. Crystal structures were solved of PRS17 in the inhibitor-free form and in complex with antiviral inhibitor, darunavir. Despite its 17 mutations, PRS17 has only one mutation (V82S) in the inhibitor/substrate binding cavity, yet exhibits high resistance to all clinical inhibitors. PRS17 has none of the major mutations (I47V, I50V, I54ML, L76V and I84V) associated with darunavir resistance, but has 10,000-fold weaker binding affinity relative to the wild type PR. Comparable binding affinity of 8000-fold weaker than PR is seen for drug resistant mutant PR20, which bears 3 mutations associated with major resistance to darunavir (I47V, I54L and I84V). Inhibitor-free PRS17 shows an open flap conformation with a curled tip correlating with G48V flap mutation. NMR studies on inactive PRS17 D25N unambiguously confirm that the flaps adopt mainly an open conformation in solution very similar to that in the inhibitor-free crystal structure. In PRS17, the hinge loop cluster of mutations, E35D, M36I and S37D, contributes to the altered flap dynamics by a mechanism similar to that of PR20. An additional K20R mutation anchors an altered conformation of the hinge loop. Flap mutations M46L and G48V in PRS17/DRV complex alter the Phe53 conformation by steric hindrance between the side chains. Unlike the L10F mutation in PR20, L10I in PRS17 does not break the inter-subunit ion pair or diminish the dimer stability, consistent with a very low dimer dissociation constant comparable to that of wild type PR. Distal mutations A71V, L90M and I93L propagate alterations to the catalytic site of PRS17. PRS17 exhibits a molecular mechanism whereby mutations act synergistically to alter the flap dynamics resulting in significantly weaker binding yet maintaining active site contacts with darunavir.

Analysis of drug resistance in HIV protease

“…The inhibitors bind to an active site that is under selective pressure to still recognize its biological substrate. Many of the most highly resistant strains demonstrate multi-drug resistance [6, 13, 14, 24]. Therefore, we expect some level cross-prediction and this work quantifies it.…”

“…The existence of cross-resistance is well known and our lab has used similar approaches to identify interesting multi-drug resistant mutants for structural study [6, 13, 14]. …”

“…The validity of this approach was verified by experimental studies [13, 14]. Machine learning was used to rigorously select representative highly resistant PR sequences for biochemical and structural characterization.…”

Exploring the flap dynamics of the South African HIV subtype C protease in presence of FDA‐approved inhibitors: MD study

“…In order to determine the curling behaviour of the flap tip residues, the TriCα angle between Gly49–Ile50–Gly51 for each monomer is measured . The flaps of the HIV‐1 PR have been shown to be asymmetric in their dynamic motions and the tips of the flaps have been known to display twisting . As such, the dihedral angle ( Ф ) amongst residues Ile50–Asp25–Ile149–Asp124 was taken into account in understanding the flap twisting of HIV‐1 PR …”

“…[23,24] The flaps of the HIV-1 PR have been shown to be asymmetric in their dynamic motions [25] and the tips of the flaps have been known to display twisting. [26] As such, the dihedral angle (Ф) amongst residues Ile50-Asp25-Ile149-Asp124 was taken into account in understanding the flap twisting of HIV-1 PR. [27] 2 | COMPUTATIONAL METHODS…”