Biology subjects

Snyder, A. A.

Publications and source records attributed to Snyder, A. A..

4 recordsLinked to original sources

bioRxiv2026

Structural and Mechanistic Basis of F227C-Mediated Hypersusceptibility to Islatravir in HIV-1 Reverse Transcriptase

Islatravir (ISL; 4'-ethynyl-2-fluoro-2'-deoxyadenosine (EFdA)), a first-in-class nucleoside reverse transcriptase (RT) translocation inhibitor (NRTTI), was recently approved by the FDA for the treatment of HIV-1 infection in combination with the non-nucleoside RT inhibitor (NNRTI), doravirine (DOR). Notably, the RT mutation F227C, which confers clinical resistance to multiple NNRTIs, including DOR, unexpectedly increases susceptibility to ISL. To elucidate the mechanistic basis of this hypersusceptibility, we determined a 1.8 angstrom crystal structure of F227C RT in complex with a ddGMP-terminated primer/template and ISL-triphosphate. The structure reveals conformational rearrangements that propagate into a cleft, thereby affecting ATP-mediated unblocking of chain-terminating antivirals. Complementary biochemical assays showed that although F227C does not significantly affect ISL incorporation, it alters RT translocation and impairs ATP-dependent phosphorolytic excision of ISL-terminated primers, thereby enhancing ISL susceptibility. These findings establish direct structural and mechanistic links between NNRTI resistance and ISL hypersusceptibility, providing a structural foundation for rationally designed, resistance-informed combination regimens that exploit this unique collateral sensitivity.

biochemistry↗

bioRxiv2026

Unraveling the Mechanism of HIV-1 Hypersusceptibility to Tenofovir Imparted by Islatravir Resistance Mutations

In response to the newly approved antiretroviral therapy (ART) islatravir (ISL), the M184V and A114S resistance mutations have emerged in the human immunodeficiency virus type 1 reverse transcriptase (HIV-1 RT). These mutations markedly hypersensitize RT to the globally administered ART tenofovir disoproxil fumarate (TDF). We have solved six structures - four by X-ray crystallography and two by cryo-EM - that capture the single- and double-mutant RTs during inhibitor incorporation and demonstrate the role of the mutations in altering protein-antiviral interactions. These snapshots reveal that the smaller, more flexible TDF diphosphate (TDF-DP) can better accommodate mutation-induced active site changes than ISL triphosphate (ISL-TP). Structural differences between the two inhibitors are consistent with biochemical determination of inhibitory constants (Kis), highlighting differences at the step of inhibitor incorporation. Virological evaluation of ISL and TDF combinations reveals additive inhibition of HIV-1. Given the converse ISL hypersusceptibility imparted by the TDF-resistant K65R mutation, we propose ISL and TDF as a combination that can inspire future therapeutic options.

biochemistry↗

bioRxiv2026

HIV-1 Reverse Transcriptase interactions with Long-acting NNRTI, Depulfavirine (VM1500A)

Non-nucleoside reverse transcriptase inhibitors (NNRTIs) are key components of combination antiretroviral therapy (ART) for the treatment of human immunodeficiency virus type 1 (HIV-1) infection, binding an allosteric pocket of reverse transcriptase (RT) and inhibiting viral replication. Although second-generation NNRTIs have improved potency and resistance profiles compared to first-generation NNRTIs, the continued emergence of resistant viral strains and the need for long-acting therapeutic options underscore the importance of developing next-generation compounds. Depulfavirine (VM1500A) is a potent NNRTI being developed as a long-acting formulation. Its prodrug, elsulfavirine (ESV), is approved for HIV-1 treatment in Eurasian countries as a once-daily oral regimen and has demonstrated favorable antiviral efficacy, pharmacokinetics, and tolerability in clinical studies. Here, we report the 2.4 [A] crystal structure of HIV-1 RT in complex with depulfavirine, revealing an extended binding conformation within the NNRTI pocket that reaches from the back of the binding pocket to the entrance. These interactions may shed light on mechanisms of resistance to the F227C mutation, with and without V106 substitution, and Y188L. Notably, depulfavirine maintains potent inhibition of common NNRTI-resistant RT variants, including K103N and Y181C. Combination studies of ESV with antivirals from diverse inhibitor categories demonstrated additive or near-synergistic activity with islatravir (ISL), cabotegravir (CAB), lenacapavir (LEN), and tenofovir (TDF). These findings highlight the broad resistance profile and potential of the depulfavirine combination.

biochemistry↗

bioRxiv2025

Structural, biophysical, and virological mechanistic characterization of HIV-1 capsid-targeting antivirals

Due to its significant role in virus replication, the HIV capsid is an attractive antiviral target. This is validated by the recent clinical approval of lenacapavir for both treatment and pre-exposure prophylaxis (PrEP). PF74 is a well-characterized capsid-targeting antiviral that was discontinued in further study due to potency and metabolic issues. We hypothesized that making chemical modifications at certain sites of PF74 could result in capsid-targeting antivirals with improved potency and bioavailability. Our cumulative studies show that making changes at the R1 and R3 positions of PF74 results in compounds with increased antiviral potency, increased stability of wild-type HIV capsid hexamers and virions, tighter binding to wild-type HIV capsid hexamer compared to PF74, and different interactions at the "FG" binding site of capsid compared to PF74. These data provide insights into the design of future capsid-targeting antivirals relevant for clinical use.

biochemistry↗