Structure, function, and inhibitor targeting of HIV-1 Nef-effector kinase complexes

Abstract

Antiretroviral therapy has revolutionized the treatment of AIDS, turning a deadly disease into a manageable chronic condition. Life-long treatment is required because existing drugs do not eradicate HIV-infected cells. The emergence of drug-resistant viral strains and uncertain vaccine prospects highlight the pressing need for new therapeutic approaches with the potential to clear the virus. The HIV-1 accessory protein Nef is essential for viral pathogenesis, making it a promising target for antiretroviral drug discovery. Nef enhances viral replication and promotes immune escape of HIV-infected cells but lacks intrinsic enzymatic activity. Instead, Nef works through diverse interactions with host cell proteins primarily related to kinase signaling pathways and endosomal trafficking. This review emphasizes the structure, function, and biological relevance of Nef interactions with host cell protein-tyrosine kinases in the broader context of Nef functions related to enhancement of the viral life cycle and immune escape. Drug discovery targeting Nef-mediated kinase activation has allowed identification of promising inhibitors of multiple Nef functions. Pharmacological inhibitors of Nef-induced MHC-I downregulation restore the adaptive immune response to HIV-infected cells in vitro and have the potential to enhance immune recognition of latent viral reservoirs as part of a strategy for HIV clearance.

Nef dimerization defect abrogates HIV viremia and associated immune dysregulation in the Bone Marrow-Liver-Thymus-Spleen (BLTS) humanized mouse model

“…Then, using a series of dimerization-defective Nef mutants based on previous X-ray crystal structures (reviewed by Staudt, et al .) (Staudt et al, 2020), we demonstrate that Nef dimerization is essential for high-titer HIV replication in vivo . Furthermore, we show that Nef dimers are required for enhanced T cell-mediated immune activation, checkpoint inhibitor expression and dysregulation of many other immune signaling pathways in vivo .…”

“…Previous X-ray crystallography studies of HIV-1 Nef proteins either alone or in complexes with host cell kinase regulatory domains revealed that Nef forms homodimers (reviewed in Staudt et al, 2020). Comparison of these structures identified several residues common to these Nef dimer interfaces, including L112, Y115, and F121.…”

Nef Dimerization Defect Abrogates HIV Viremia and Associated Immune Dysregulation in the Bone Marrow-Liver-Thymus-Spleen (BLTS) Humanized Mouse Model.

“…First, we show that deletion of Nef allows complete control of HIV infection in BLTS mice. Then, using a series of dimerization-defective Nef mutants based on previous X-ray crystal structures (reviewed by Staudt, et al) [38], we demonstrate that Nef dimerization is essential for high-titer HIV replication in vivo. Furthermore, we show that Nef dimers are required for enhanced T cell-mediated immune activation, checkpoint inhibitor expression and dysregulation of many other immune signaling pathways in vivo.…”

Immune subversion by HIV: part B

“…The results of this study emphasize the importance of NEF in HIV‐1 pathogenesis. Initially labeled as a negative factor, this accessary protein was soon established rather as a positive factor for the virus as ΔNEF HIV‐1 exhibits low pathogenicity (reviewed in Staudt et al , 2020). NEF hijacks signaling pathways and contributes to T‐cell activation, thus increasing the number of HIV‐1 cell targets (Schrager & Marsh, 1999); it downregulates CD4 expression on infected T cells, thereby enhancing virion release (Guy et al , 1987); NEF downregulates MHC‐I, thus protecting infected cells from the cytotoxic T cells (Schwartz et al , 1996); NEF antagonizes cellular restriction factors SERINC3/5, which in the absence of NEF are incorporated into virions blocking viral infectivity (Fackler, 2015); NEF contributes to establishment of HIV‐1 latency (Kmiec et al , 2019).…”