Cell Type-Dependent Escape of Capsid Inhibitors by Simian Immunodeficiency Virus SIVcpz

Abstract

Pandemic HIV-1 is the result of zoonotic transmission of Simian immunodeficiency virus (SIV) from chimpanzee species Pan troglodytes troglodytes (SIVcpzPtt). The related Pan troglodytes schweinfurthii is the host of a similar virus, SIVcpzPts, which did not spread to humans. We tested these viruses with small-molecule capsid inhibitors (PF57, PF74, and GS-CA1) that interact with a binding groove in the capsid that is also used by CPSF6. While HIV-1 was sensitive to capsid inhibitors in cell lines, human macrophages and PBMCs, SIVcpzPtt was resistant in rhesus FRhL-2 cells and human PBMCs but was sensitive to PF74 in human HOS and HeLa cells. SIVcpzPts was insensitive to PF74 in FRhL-2 cells, HeLa cells, PBMCs, and macrophages, but was inhibited by PF74 in HOS cells. The truncated version of CPSF6 (CPSF6-358) inhibited SIVcpzPtt and HIV-1 while, in contrast, SIVcpzPts was resistant to CPSF6-358. Homology modelling of HIV-1, SIVcpzPtt, and SIVcpzPts capsids and binding energy estimates suggest that these three viruses bind similarly with the host proteins cyclophilin A (CYPA) and CPSF6 as well as the capsid inhibitor PF74. Cyclosporin A treatment, mutating the CYPA-binding loop in the capsid or CYPA-knockout eliminated SIVcpzPts' resistance to PF74 in HeLa cells. These experiments revealed that the antiviral capacity of PF74 is controlled by CYPA in a virus- and cell type-specific manner. Our data indicate that SIVcpz viruses can use infection pathways that escape the antiviral activity of PF74. We further suggest that the antiviral activity of PF74 capsid inhibitors depends on cellular cofactors. IMPORTANCE HIV-1 originated from SIVcpzPtt, but not from the related SIVcpzPts, and thus it is important to describe the molecular infection of SIVcpzPts in human cells to understand zoonosis of SIVs. Pharmacological HIV-1 capsid inhibitors (e.g., PF74) bind a capsid groove that is also a binding site for the cellular protein CPSF6. SIVcpzPts was resistant to PF74 in HeLa cells but sensitive in HOS, thus indicating cell-line specific resistance. Both SIVcpz viruses showed a resistance to PF74 in human PBMCs. Modulating the presence of cyclophilin A or its binding to capsid in HeLa cells overcame SIVcpzPts resistance to PF74. These results indicate that early cytoplasmic infection events of SIVcpzPts may differ between cell types and affect, in an unknown manner, the antiviral activity of capsid inhibitors. Thus, capsid inhibitors depend on the activity or interaction of currently uncharacterized cellular factors.

Human immunodeficiency virus-1 core: The Trojan horse in virus–host interaction

“…GS-CA and GS-62072, developed from PF74, disrupt the CA interaction with CPSF6 and NUP153, enhancing innate immune responses and ultimately eliminating the HIV-1; additionally, the long-acting activity makes them suitable for clinical treatment ( Carnes et al, 2018 ). However, some epidemic variants breakthrough PF74 inhibition independent of reduction of PF74 binding, two SIVs that are not sensitive to PF74 and GS-CA have been recently identified ( Siddiqui et al, 2019 ; Twizerimana et al, 2020 ). The newly emerged immune evasion strategies of HIV-1 transmitted variant makes it difficult to develop broad-spectrum anti-HIV-1 medicine, but additional studies targeting diverse HIV-1variants may uncover distinct mechanisms to escape restriction by these CA inhibitors ( Twizerimana et al, 2020 ; Saito and Yamashita, 2021 ).…”

“…However, some epidemic variants breakthrough PF74 inhibition independent of reduction of PF74 binding, two SIVs that are not sensitive to PF74 and GS-CA have been recently identified ( Siddiqui et al, 2019 ; Twizerimana et al, 2020 ). The newly emerged immune evasion strategies of HIV-1 transmitted variant makes it difficult to develop broad-spectrum anti-HIV-1 medicine, but additional studies targeting diverse HIV-1variants may uncover distinct mechanisms to escape restriction by these CA inhibitors ( Twizerimana et al, 2020 ; Saito and Yamashita, 2021 ). Altough conformational changes induced by CA-mutant decrease the sensitivity to CA inhibitor ( Selyutina et al, 2022a ), and anti-HIV activity of CA inhibitor strictly dependent on cell types ( Twizerimana et al, 2020 ), it is promising that further study of CA-related immune evasion will clearly eluciated HIV-1’s pathogenic mechanism and provide a theoretical basis for antiviral therapeutics.…”

The cyclophilin A-binding loop of the capsid regulates the human TRIM5α sensitivity of nonpandemic HIV-1

“…The GST-CYPA-based pulldown experiments followed a protocol previously described ( 43 ). To confirm the expression of primate TRIM5 proteins, cells were lysed using RIPA lysis buffer [25 mM Tris-HCl (pH 8.0), 137 mM NaCl, 1% NP-40, 1% glycerol, 0.5% sodium deoxycholate, 0.1% sodium dodecyl sulfate (SDS), 2 mM ethylenediaminetetraacetic acid (EDTA), and protease inhibitor cocktail set III (Calbiochem, Darmstadt, Germany).…”

“…The structural models of the HIV-1 M capsid and CYPA generated by TopModel ( 44 , 45 ) were taken from ref. 43 . The capsid-CYPA complex was formed by superimposing the structures of the components onto the proteins of the cryo-EM structure PDB ID 5FJB.…”

TopSuite Web Server: A Meta-Suite for Deep-Learning-Based Protein Structure and Quality Prediction

“…Unlike traditional model averaging and/or energy minimization refinement protocols used in other meta-servers such as I-TASSER and MULTICOM, which also use majority-voting consensus in the form of clustering, this strategy optimizes the TopScore (a DNN-based score rather than an energy function) to overcome the problems of majority voting mentioned earlier. TopScore and TopModel have been used prospectively and successfully in several applications. ,− …”