Structural basis of HIV-1 capsid recognition by PF74 and CPSF6

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 111; no. 52; pp. 18625 - 18630
• Main Authors: Bhattacharya, Akash, Alam, Steven L., Fricke, Thomas, Zadrozny, Kaneil, Sedzicki, Jaroslaw, Taylor, Alexander B., Demeler, Borries, Pornillos, Owen, Ganser-Pornillos, Barbie K., Diaz-Griffero, Felipe, Ivanov, Dmitri N., Yeager, Mark
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 30.12.2014; National Acad Sciences; National Academy of Sciences, Washington, DC (United States)
• Subjects: BASIC BIOLOGICAL SCIENCES; Binding sites; Biochemistry; Biological Sciences; Capsid; Capsid - chemistry; Capsid - metabolism; Cells; Crystal lattices; Crystal structure; Crystallography, X-Ray; Crystals; Cytoplasm; drug discovery; fluorescence polarization; HIV; HIV 1; HIV Infections; HIV-1 - chemistry; HIV-1 - metabolism; HIV-1 CA protein; Human immunodeficiency virus; Human immunodeficiency virus 1; Indoles; Indoles - chemistry; Indoles - pharmacology; Infections; isothermal calorimetry; mRNA Cleavage and Polyadenylation Factors - chemistry; mRNA Cleavage and Polyadenylation Factors - metabolism; Nuclear Pore Complex Proteins - chemistry; Nuclear Pore Complex Proteins - metabolism; Phenylalanine - analogs & derivatives; Phenylalanine - chemistry; Phenylalanine - pharmacology; Protein Binding; Proteins; Viruses; X-ray crystallography; X-ray crystallography; fluorescence polarization; isothermal calorimetry; HIV-1 CA protein; drug discovery
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.1419945112

Significance Events that occur between entry of the HIV-1 capsid into the cytoplasm of the target cell and the delivery of the viral genetic material into the nucleus constitute some of the less well understood processes in the viral life cycle. We demonstrated that PF74, a small-molecule inhibitor of HIV-1, and the host proteins CPSF6 and NUP153 bind to a preformed pocket within the CA protein hexamers that exist within the assembled capsid. Our results suggest that key features of the CA hexameric lattice remain intact upon docking at the nuclear pore. In addition, low molecular weight ligands that better mimic virus–host, protein–protein interactions at the intersubunit interfaces within the assembled viral capsid may offer novel avenues for therapeutic intervention. Upon infection of susceptible cells by HIV-1, the conical capsid formed by ∼250 hexamers and 12 pentamers of the CA protein is delivered to the cytoplasm. The capsid shields the RNA genome and proteins required for reverse transcription. In addition, the surface of the capsid mediates numerous host–virus interactions, which either promote infection or enable viral restriction by innate immune responses. In the intact capsid, there is an intermolecular interface between the N-terminal domain (NTD) of one subunit and the C-terminal domain (CTD) of the adjacent subunit within the same hexameric ring. The NTD–CTD interface is critical for capsid assembly, both as an architectural element of the CA hexamer and pentamer and as a mechanistic element for generating lattice curvature. Here we report biochemical experiments showing that PF-3450074 (PF74), a drug that inhibits HIV-1 infection, as well as host proteins cleavage and polyadenylation specific factor 6 (CPSF6) and nucleoporin 153 kDa (NUP153), bind to the CA hexamer with at least 10-fold higher affinities compared with nonassembled CA or isolated CA domains. The crystal structure of PF74 in complex with the CA hexamer reveals that PF74 binds in a preformed pocket encompassing the NTD–CTD interface, suggesting that the principal inhibitory target of PF74 is the assembled capsid. Likewise, CPSF6 binds in the same pocket. Given that the NTD–CTD interface is a specific molecular signature of assembled hexamers in the capsid, binding of NUP153 at this site suggests that key features of capsid architecture remain intact upon delivery of the preintegration complex to the nucleus.