Biology subjects

Zadorozhnyi, R.

Publications and source records attributed to Zadorozhnyi, R..

4 recordsLinked to original sources

bioRxiv2026

Structural Basis of Second-Generation HIV-1 Maturation Inhibitor Activity by Magic Angle Spinning NMR

The CA-SP1 junction of HIV-1 Gag forms a six-helix bundle (6HB) within the immature Gag lattice, sequestering the CA-SP1 cleavage site. Maturation inhibitors (MIs), such as Bevirimat (BVM) and its analogs, are an emerging class of HIV-1 antiviral compounds that stabilize Gag maturation intermediates by interfering with CA-SP1 proteolytic processing. Here, we report the binding modes of a potent second-generation BVM analog with an extended scaffold, HRF-4467, in crystalline CACTD-SP1-NC11 assemblies with inositol hexakisphosphate (IP6), as determined by magic-angle-spinning solid-state NMR (MAS NMR) spectroscopy. The atomic-level structure reveals that HRF-4467 binds asymmetrically in the SP1-NC11 six-helix bundle and stabilizes its helical conformation in the immature lattice, in both the wild-type and the BVM-resistant SP1-V7A Gag variant. Additionally, in the presence of HRF-4467, IP6 adopts distinct conformations in the wild-type CACTD-SP1-NC11 and the SP1-V7A variant. Taken together, our results establish a molecular basis for HRF-4467's improved antiviral activity relative to BVM and suggest strategies for designing inhibitors with enhanced performance against MI-resistant HIV-1 variants for potential therapeutic use.

biophysics↗

bioRxiv2025

Structural Basis for HIV-1 Maturation Inhibition by PF-46396 Determined by MAS NMR

Among the different types of HIV-1 maturation inhibitors, those that stabilize the junction between the capsid protein C-terminal domain (CACTD) and the spacer peptide 1 (SP1) within the immature Gag lattice are promising candidates for antiretroviral therapies. Here, we report the atomic- resolution structure of CACTD-SP1 assemblies with the small-molecule maturation inhibitor PF- 46396 and the assembly cofactor inositol hexakisphosphate (IP6), determined by magic angle spinning (MAS) NMR spectroscopy. Our results reveal that although the two PF-46396 enantiomers exhibit distinct binding modes, they both possess similar anti-HIV potency. PF-46396 binding arrests IP6 dynamics in the six-helix bundle pore, and the two enantiomers induce unique IP6 orientations in the pore. Importantly, our data suggest the presence of monoanionic IP6 form IP6 in the complex. Our study establishes the structural basis for PF-46396 action and suggests a mechanistic model for drug resistance.

biophysics↗

bioRxiv2022

Structural Basis of HIV-1 Maturation Inhibitor Binding and Activity

HIV-1 maturation inhibitors (MIs) interfere with the final step in the viral lifecycle by disrupting the ordered proteolytic processing of the viral Gag polyprotein into its individual domains. Bevirimat (BVM) and its analogs interfere with the final catalytic cleavage of spacer peptide 1 (SP1) from the capsid protein (CA) C-terminal domain (CACTD), by binding to and stabilizing the CACTD-SP1 region. MIs are under development as alternative drugs to augment current antiretroviral therapies. Although promising, their mechanism of action and associated virus resistance pathways remain poorly understood at the molecular, biochemical, and structural levels. Here, we report atomic-resolution magic angle spinning (MAS) NMR structures of microcrystalline assemblies of CACTD-SP1 complexed with BVM and/or the assembly cofactor inositol hexakisphosphate (IP6). BVM and IP6 can bind simultaneously to SP1, with BVM positioned in the center of its 6-helix bundle in a unique conformation. Importantly, the NMR-observed structural effects of BVM on IP6 binding suggest that the inhibitor stabilizes the 6-helix bundle in multiple ways. In addition, BVM-resistant SP1-A1V and SP1-V7A variants exhibit distinct conformational and binding characteristics. Taken together, our results reveal a novel allosteric mechanism by which BVM disrupts maturation and provide a structural explanation for BVM resistance as well as important guidance for the design of new MIs.

biophysics↗

bioRxiv2020

Permeability of the HIV-1 capsid to metabolites modulates viral DNA synthesis

Reverse transcription, an essential event in the HIV-1 lifecycle, requires deoxynucleotide triphosphates (dNTPs) to fuel DNA synthesis, thus requiring penetration of dNTPs into the viral core. The central cavity of the capsid protein (CA) hexamer reveals itself as a plausible channel that allows the passage of dNTPs into assembled capsids. Nevertheless, the molecular mechanism of nucleotide import into the capsid remains unknown. Employing all-atom molecular dynamics simulations, we established that cooperative binding between nucleotides inside a CA hexamer cavity results in energetically-favorable conditions for passive translocation of dNTPs into the HIV-1 capsid. Furthermore, binding of the host cell metabolite inositol hexakisphosphate (IP6) enhances dNTP import, while binding of synthesized molecules like benzenehexacarboxylic acid (BHC) inhibits it. The enhancing effect on reverse transcription by IP6 and the consequences of interactions between CA and nucleotides were corroborated using atomic force microscopy, transmission electron microscopy, and virological assays. Collectively, our results provide an atomistic description of the permeability of the HIV-1 capsid to small molecules and reveal a novel mechanism for the involvement of metabolites in HIV-1 capsid stabilization, nucleotide import and reverse transcription.

biophysics↗