Damaging the conical morphology of HIV-1 capsid by targeting the FG-binding pocket and disfavoring pentameric subunits needed for core closure

  • bioRxiv. 2026 Mar 20:2026.03.19.712970. doi: 10.64898/2026.03.19.712970.
William M McFadden  1  2 ,  Karen A Kirby  1  2 ,  Zachary C Lorson  1  2 ,  Lei Wang  3 ,  Carolyn M Highland  4  5 ,  Sophie R Harvey  6  7 ,  Savannah Brancato  1  2 ,  Andres Emanuelli Castaner  1  2 ,  Haijuan Du  1  2 ,  Vicki H Wysocki  8  9 ,  Zhengqiang Wang  3 ,  Robert A Dick  1  2  4 ,  Stefan G Sarafianos  1  2
Affiliations
  • 1. Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA.
  • 2. Children's Healthcare of Atlanta, Atlanta, GA, USA.
  • 3. Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN, USA.
  • 4. Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
  • 5. Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, NY, USA.
  • 6. Campus Chemical Instrumentation Center Mass Spectrometry and Proteomics Facility, The Ohio State University, Columbus, OH, USA.
  • 7. Native Mass Spectrometry Guided Structural Biology Center, The Ohio State University, Columbus, OH, USA.
  • 8. School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA.
  • 9. Native MS Guided Structural Biology Center, Georgia Institute of Technology, Atlanta, GA, USA.
PMID: 41889801 DOI: 10.64898/2026.03.19.712970
Abstract

The HIV-1 capsid is an essential viral component, targeted by the long-acting antiretroviral Lenacapavir (LEN). LEN binds to the HIV-1 capsid protein (CA) at the phenylalanine-glycine (FG) binding pocket (FGBP), a site for multiple host-factor and Antiviral interactions in CA hexamers (CAHEX). Previously, we generated a chemical library to investigate the FGBP; ZW-1261, a lead compound, exhibits potent Antiviral activity and strong inter-subunit interactions within CAHEX. Here, we report the molecular mechanism by which ZW-1261 affects the morphology and integrity of capsid lattice. ZW-1261 alone rapidly induces tubular CA assemblies; simultaneous addition of ZW-1261 with the assembly cofactor inositol hexaphosphate (IP6) forms morphologically distinct tubes. In mature virions, IP6 is required for the assembly of both CAHEX and CA pentamers (CAPENT). Cryogenic-electron microscopy analysis of in vitro assembled capsid-like particles (CLPs) with IP6 suggests that ZW-1261 leads to the absence of CAPENT and damages the pre-formed conical lattice. To elucidate how this FGBP-targeting Antiviral impacts CAPENT, we further solved structures of CAPENT-only icosahedral assemblies (T = 1), formed by reported mutations, that were treated with ZW-1261. We find that ZW-1261 binding in these constrained T = 1 assemblies converts CAPENT to a CAHEX-like conformation. Collectively, this suggests a mechanism by which addition of FGBP-binding inhibitor to native cores leads to the absence of CAPENT, impacting capsid closure and core integrity.

Keywords
Capsid; Electron Microscopy; HIV-1; Lenacapavir; Structural biology.
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