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1.
Cell Chem Biol ; 31(4): 623-624, 2024 Apr 18.
Article in English | MEDLINE | ID: mdl-38640898

ABSTRACT

In an interview with Samantha Nelson, a scientific editor of Cell Chemical Biology, the first and corresponding authors of the research article entitled "PROTAC-mediated degradation of HIV-1 Nef efficiently restores cell-surface CD4 and MHC-I expression and blocks HIV-1 replication" share insights on their paper and life as scientists.


Subject(s)
HIV-1 , nef Gene Products, Human Immunodeficiency Virus/metabolism , Down-Regulation , Cell Membrane/metabolism
2.
Cell Chem Biol ; 31(4): 658-668.e14, 2024 Apr 18.
Article in English | MEDLINE | ID: mdl-38508197

ABSTRACT

The HIV-1 Nef accessory factor enhances the viral life cycle in vivo, promotes immune escape of HIV-infected cells, and represents an attractive antiretroviral drug target. However, Nef lacks enzymatic activity and an active site, complicating traditional occupancy-based drug development. Here we describe the development of proteolysis targeting chimeras (PROTACs) for the targeted degradation of Nef. Nef-binding compounds, based on an existing hydroxypyrazole core, were coupled to ligands for ubiquitin E3 ligases via flexible linkers. The resulting bivalent PROTACs induced formation of a ternary complex between Nef and the cereblon E3 ubiquitin ligase thalidomide-binding domain in vitro and triggered Nef degradation in a T cell expression system. Nef-directed PROTACs efficiently rescued Nef-mediated MHC-I and CD4 downregulation in T cells and suppressed HIV-1 replication in donor PBMCs. Targeted degradation is anticipated to reverse all HIV-1 Nef functions and may help restore adaptive immune responses against HIV-1 reservoir cells in vivo.


Subject(s)
HIV-1 , T-Lymphocytes , Down-Regulation , Cell Membrane , Virus Replication , Proteolysis , Ubiquitin-Protein Ligases
3.
bioRxiv ; 2023 Sep 05.
Article in English | MEDLINE | ID: mdl-37645900

ABSTRACT

The HIV-1 Nef accessory factor is critical to the viral life cycle in vivo where it promotes immune escape of HIV-infected cells and viral persistence. While these features identify Nef as an attractive antiretroviral drug target, Nef lacks enzymatic activity and an active site, complicating development of occupancy-based drugs. Here we describe the development of proteolysis targeting chimeras (PROTACs) for the targeted degradation of Nef. Nef-binding compounds, based on a previously reported hydroxypyrazole core, were coupled to ligands for ubiquitin E3 ligases via flexible linkers. The resulting bivalent PROTACs induced formation of a ternary complex between Nef and the Cereblon E3 ubiquitin ligase, resulting in ubiquitylation of Nef and proteolytic degradation. Nef-directed PROTACs efficiently rescued Nef-mediated MHC-I and CD4 downregulation in T cells and suppressed HIV-1 replication in donor PBMCs. Targeted degradation of Nef is anticipated to reverse all HIV-1 Nef functions and may help restore adaptive immune responses against HIV-1 reservoir cells in vivo .

4.
Viruses ; 14(9)2022 09 13.
Article in English | MEDLINE | ID: mdl-36146831

ABSTRACT

While antiretroviral drugs have transformed the lives of HIV-infected individuals, chronic treatment is required to prevent rebound from viral reservoir cells. People living with HIV also are at higher risk for cardiovascular and neurocognitive complications, as well as cancer. Finding a cure for HIV-1 infection is therefore an essential goal of current AIDS research. This review is focused on the discovery of pharmacological inhibitors of the HIV-1 Nef accessory protein. Nef is well known to enhance HIV-1 infectivity and replication, and to promote immune escape of HIV-infected cells by preventing cell surface MHC-I display of HIV-1 antigens. Recent progress shows that Nef inhibitors not only suppress HIV-1 replication, but also restore sufficient MHC-I to the surface of infected cells to trigger a cytotoxic T lymphocyte response. Combining Nef inhibitors with latency reversal agents and therapeutic vaccines may provide a path to clearance of viral reservoirs.


Subject(s)
HIV Infections , HIV Seropositivity , HIV-1 , Anti-Retroviral Agents/therapeutic use , Drug Discovery , HIV Infections/drug therapy , HIV-1/physiology , Humans , Virulence Factors , nef Gene Products, Human Immunodeficiency Virus
5.
ACS Infect Dis ; 8(1): 91-105, 2022 01 14.
Article in English | MEDLINE | ID: mdl-34985256

ABSTRACT

HIV-1 Nef is an attractive target for antiretroviral drug discovery because of its role in promoting HIV-1 infectivity, replication, and host immune system avoidance. Here, we applied a screening strategy in which recombinant HIV-1 Nef protein was coupled to activation of the Src-family tyrosine kinase Hck, which enhances the HIV-1 life cycle in macrophages. Nef stimulates recombinant Hck activity in vitro, providing a robust assay for chemical library screening. High-throughput screening of more than 730 000 compounds using the Nef·Hck assay identified six unique hit compounds that bound directly to recombinant Nef by surface plasmon resonance (SPR) in vitro and inhibited HIV-1 replication in primary macrophages in the 0.04 to 5 µM range without cytotoxicity. Eighty-four analogs were synthesized around an isothiazolone scaffold from this series, many of which bound to recombinant Nef and inhibited HIV-1 infectivity in the low to submicromolar range. Compounds in this series restored MHC-I to the surface of HIV-infected primary cells and disrupted a recombinant protein complex of Nef with the C-terminal tail of MHC-I and the µ1 subunit of the AP-1 endocytic trafficking protein. Nef inhibitors in this class have the potential to block HIV-1 replication in myeloid cells and trigger recognition of HIV-infected cells by the adaptive immune system in vivo.


Subject(s)
HIV-1 , Down-Regulation , HIV-1/metabolism , Macrophages/metabolism , Virus Replication , src-Family Kinases/metabolism
6.
J Biol Chem ; 295(44): 15158-15171, 2020 10 30.
Article in English | MEDLINE | ID: mdl-32862141

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 down-regulation 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.


Subject(s)
Anti-HIV Agents/pharmacology , HIV-1/enzymology , Protein Kinase Inhibitors/pharmacology , Protein Kinases/metabolism , nef Gene Products, Human Immunodeficiency Virus/metabolism , CD4 Antigens/metabolism , Crystallography, X-Ray , Down-Regulation , HIV-1/pathogenicity , Immune Evasion , Major Histocompatibility Complex , Membrane Proteins/metabolism , Protein Kinases/drug effects , Protein Transport , Structure-Activity Relationship , nef Gene Products, Human Immunodeficiency Virus/chemistry
7.
ACS Infect Dis ; 6(2): 302-312, 2020 02 14.
Article in English | MEDLINE | ID: mdl-31775511

ABSTRACT

The HIV-1 Nef accessory factor is critical to the viral life cycle in vivo and promotes immune escape of infected cells via downregulation of cell-surface MHC-I. Previously, we discovered small molecules that bind directly to Nef and block many of its functions, including enhancement of viral infectivity and replication in T cell lines. These compounds also restore cell-surface MHC-I expression in HIV-infected CD4 T cells from AIDS patients, enabling recognition and killing by autologous cytotoxic T lymphocytes (CTLs). In this study, we describe the synthesis and evaluation of a diverse set of analogs based on the original hydroxypyrazole Nef inhibitor core. All analogs were screened for the interaction with recombinant HIV-1 Nef by surface plasmon resonance (SPR) and for antiretroviral activity in TZM-bl reporter cells infected with HIV-1. Active analogs were ranked on the basis of an activity score that integrates three aspects of the SPR data (affinity, residence time, and extent of binding) with antiretroviral activity. The top scoring compounds bound tightly to Nef by SPR, with KD values in the low nM to pM range, and displayed very slow dissociation from their Nef target. These analogs also suppressed HIV-1 replication in donor peripheral blood mononuclear cells (PBMCs) with IC50 values in the 1-10 nM range without cytotoxicity, inhibited Nef-mediated IL-2-inducible tyrosine kinase (Itk) and hematopoietic cell kinase (Hck) activation, and rescued MHC-I downregulation in a Nef-transfected T cell line. The development of Nef inhibitors based on the structure-activity relationships defined here has promise as a new approach to antiretroviral therapy that includes a path to eradication of HIV-infected cells via the adaptive immune response.


Subject(s)
Anti-Retroviral Agents/pharmacology , Histocompatibility Antigens Class I/genetics , Pyrazoles/pharmacology , Virus Replication/drug effects , nef Gene Products, Human Immunodeficiency Virus/antagonists & inhibitors , Cell Line , Down-Regulation , Drug Development , HIV-1/drug effects , HIV-1/physiology , Humans , Inhibitory Concentration 50 , Leukocytes, Mononuclear/virology , Tissue Donors
8.
JCI Insight ; 2(17)2017 09 07.
Article in English | MEDLINE | ID: mdl-28878119

ABSTRACT

Eradication of the HIV-1 latent reservoir represents the current paradigm to developing a cure for AIDS. HIV-1 has evolved multiple mechanisms to evade CD8 T cell responses, including HIV-1 Nef-mediated downregulation of MHC-I from the surface of infected cells. Nef transcripts and protein are detectable in samples from aviremic donors, suggesting that Nef expression in latently HIV-1-infected CD4 T cells protects them from immune-mediated clearance. Here, we tested 4 small molecule inhibitors of HIV-1 Nef in an in vitro primary CD4 T cell latency model and measured the ability of autologous ex vivo or HIV-1 peptide-expanded CD8 T cells to recognize and kill latently infected cells as a function of inhibitor treatment. Nef inhibition enhanced cytokine secretion by autologous CD8 T cells against latently HIV-1-infected targets in an IFN-γ release assay. Additionally, CD8 T cell-mediated elimination of latently HIV-1-infected cells was significantly enhanced following Nef blockade, measured as a reduction in the frequency of infected cells and Gag protein in cultures following viral outgrowth assays. We demonstrate for the first time to our knowledge that Nef blockade, in combination with HIV-specific CD8 T cell expansion, might be a feasible strategy to target the HIV-1 latent reservoir that should be tested further in vivo.


Subject(s)
Anti-HIV Agents/pharmacology , Gene Products, nef/antagonists & inhibitors , HIV-1/metabolism , Virus Latency , CD4-Positive T-Lymphocytes/immunology , CD4-Positive T-Lymphocytes/virology , CD8-Positive T-Lymphocytes/immunology , CD8-Positive T-Lymphocytes/virology , Cells, Cultured , Down-Regulation , Gene Products, nef/genetics , Gene Products, nef/metabolism , HIV-1/drug effects , Humans , Major Histocompatibility Complex/immunology
9.
J Biol Chem ; 292(7): 2670-2678, 2017 02 17.
Article in English | MEDLINE | ID: mdl-28031466

ABSTRACT

The HIV-1 Nef accessory factor enhances viral infectivity, immune evasion, and AIDS progression. Nef triggers rapid down-regulation of CD4 via the endocytic adaptor protein 2 (AP-2) complex, a process linked to enhanced viral infectivity and immune escape. Here, we describe a bimolecular fluorescence complementation (BiFC) assay to visualize the interaction of Nef with AP-2 and CD4 in living cells. Interacting protein pairs were fused to complementary non-fluorescent fragments of YFP and co-expressed in 293T cells. Nef interactions with both CD4 and AP-2 resulted in complementation of YFP and a bright fluorescent signal by confocal microcopy that localized to the cell periphery. Co-expression of the AP-2 α subunit enhanced the Nef·AP-2 σ2 subunit BiFC signal and vice versa, suggesting that the AP-2 α-σ2 hemicomplex interacts cooperatively with Nef. Mutagenesis of Nef amino acids Arg-134, Glu-174, and Asp-175, which stabilize Nef for AP-2 α-σ2 binding in a recent co-crystal structure, substantially reduced AP-2 interaction without affecting CD4 binding. A dimerization-defective mutant of Nef failed to interact with either CD4 or AP-2 in the BiFC assay, indicating that Nef quaternary structure is required for CD4 and AP-2 recruitment as well as CD4 down-regulation. A small molecule previously shown to bind the Nef dimerization interface also reduced Nef interactions with AP-2 and CD4 and restored CD4 expression to the surface of HIV-infected cells. Our findings provide a mechanistic explanation for previous observations that dimerization-defective Nef mutants fail to down-regulate CD4 and validate the Nef dimerization interface as a target site for antiretroviral drug development.


Subject(s)
CD4 Antigens/metabolism , Down-Regulation , HIV-1/metabolism , Transcription Factor AP-2/metabolism , nef Gene Products, Human Immunodeficiency Virus/metabolism , Cell Line , Dimerization , Fluorescence , Humans , Models, Molecular , Protein Binding , Subcellular Fractions/metabolism
10.
J Am Soc Mass Spectrom ; 27(6): 1048-61, 2016 06.
Article in English | MEDLINE | ID: mdl-27032648

ABSTRACT

Hydrogen exchange mass spectrometry can be used to compare the conformation and dynamics of proteins that are similar in tertiary structure. If relative deuterium levels are measured, differences in sequence, deuterium forward- and back-exchange, peptide retention time, and protease digestion patterns all complicate the data analysis. We illustrate what can be learned from such data sets by analyzing five variants (Consensus G2E, SF2, NL4-3, ELI, and LTNP4) of the HIV-1 Nef protein, both alone and when bound to the human Hck SH3 domain. Regions with similar sequence could be compared between variants. Although much of the hydrogen exchange features were preserved across the five proteins, the kinetics of Nef binding to Hck SH3 were not the same. These observations may be related to biological function, particularly for ELI Nef where we also observed an impaired ability to downregulate CD4 surface presentation. The data illustrate some of the caveats that must be considered for comparison experiments and provide a framework for investigations of other protein relatives, families, and superfamilies with HX MS. Graphical Abstract ᅟ.


Subject(s)
HIV-1/genetics , Mass Spectrometry , nef Gene Products, Human Immunodeficiency Virus/genetics , Amino Acid Sequence , Humans , Hydrogen , Proto-Oncogene Proteins c-hck , src Homology Domains
11.
Bioorg Med Chem Lett ; 26(5): 1480-1484, 2016 Mar 01.
Article in English | MEDLINE | ID: mdl-26852364

ABSTRACT

The HIV-1 Nef accessory factor enhances viral replication and promotes immune system evasion of HIV-infected cells, making it an attractive target for drug discovery. Recently we described a novel class of diphenylpyrazolodiazene compounds that bind directly to Nef in vitro and inhibit Nef-dependent HIV-1 infectivity and replication in cell culture. However, these first-generation Nef antagonists have several structural liabilities, including an azo linkage that led to poor oral bioavailability. The azo group was therefore replaced with either a one- or two-carbon linker. The resulting set of non-azo analogs retained nanomolar binding affinity for Nef by surface plasmon resonance, while inhibiting HIV-1 replication with micromolar potency in cell-based assays without cytotoxicity. Computational docking studies show that these non-azo analogs occupy the same predicted binding site within the HIV-1 Nef dimer interface as the original azo compound. Computational methods also identified a hot spot for inhibitor binding within this site that is defined by conserved HIV-1 Nef residues Asp108, Leu112, and Pro122. Pharmacokinetic evaluation of the non-azo B9 analogs in mice showed that replacement of the azo linkage dramatically enhanced oral bioavailability without substantially affecting plasma half-life or clearance. The improved oral bioavailability of non-azo diphenylpyrazolo Nef antagonists provides a starting point for further drug lead optimization in support of future efficacy testing in animal models of HIV/AIDS.


Subject(s)
Anti-HIV Agents/chemical synthesis , Anti-HIV Agents/pharmacology , Small Molecule Libraries/pharmacology , nef Gene Products, Human Immunodeficiency Virus/antagonists & inhibitors , Administration, Oral , Animals , Anti-HIV Agents/administration & dosage , Binding Sites/drug effects , Dose-Response Relationship, Drug , HIV-1/drug effects , Mice , Microbial Sensitivity Tests , Models, Molecular , Molecular Conformation , Molecular Docking Simulation , Small Molecule Libraries/administration & dosage , Small Molecule Libraries/chemical synthesis , Structure-Activity Relationship , Tumor Cells, Cultured , Virus Replication/drug effects
12.
Biochemistry ; 54(41): 6382-91, 2015 Oct 20.
Article in English | MEDLINE | ID: mdl-26440750

ABSTRACT

The HIV-1 virulence factor Nef interacts with the macrophage Src-family kinase Hck, resulting in constitutive kinase activation that contributes to viral replication and immune escape. Previous chemical library screens identified the diphenylfuranopyrimdine kinase inhibitor DFP-4AB, which selectively inhibits Nef-dependent Hck activity in biochemical assays and potently blocks HIV replication in vitro. In the present study, hydrogen exchange mass spectrometry (HX MS) was used to study conformational changes in downregulated Hck that result from Nef binding, as well as the impact of DFP-4AB on these changes. Remarkably, interaction with Nef induced only subtle changes in deuterium uptake by Hck, with the most significant changes in the N-lobe of the kinase domain adjacent to the docking site for Nef on the SH3 domain. No changes in hydrogen exchange were observed in the Hck SH2 domain or C-terminal tail, indicating that this regulatory interaction is unaffected by Nef binding. When HX MS was performed in the presence of DFP-4AB, the effect of Nef on Hck N-lobe dynamics was completely reversed. These results show that constitutive activation of Hck by HIV-1 Nef requires only modest changes to the conformational dynamics of the overall kinase structure. DFP-4AB reverses these effects, consistent with its activity against this Nef-induced signaling event in HIV-infected cells.


Subject(s)
HIV Infections/drug therapy , HIV Infections/metabolism , HIV-1/drug effects , Protein Kinase Inhibitors/pharmacology , Proto-Oncogene Proteins c-hck/antagonists & inhibitors , Proto-Oncogene Proteins c-hck/metabolism , nef Gene Products, Human Immunodeficiency Virus/metabolism , Enzyme Activation/drug effects , HIV-1/metabolism , Humans , Molecular Docking Simulation , Molecular Dynamics Simulation , Protein Conformation/drug effects , Protein Interaction Maps/drug effects , Protein Kinase Inhibitors/chemistry , Proto-Oncogene Proteins c-hck/chemistry , Virus Replication/drug effects , nef Gene Products, Human Immunodeficiency Virus/antagonists & inhibitors , src Homology Domains
13.
Anal Chem ; 87(14): 7030-5, 2015 Jul 21.
Article in English | MEDLINE | ID: mdl-26133569

ABSTRACT

In the companion paper to this work, we described development of a new type of hydrogen exchange (HX) mass spectrometry (MS) measurement that integrates Langmuir monolayers. With Langmuir monolayers, the lipid packing density can be reproducibly controlled and changed as desired. Analysis of HX in proteins that may undergo conformational changes as a function of lipid packing (for example, conformational rearrangements after insertion into a lipid layer) are then possible. We previously used neutron reflection to characterize just such a conformational change in the myristoylated HIV-1 Nef protein (myrNef): at high lipid packing density, myrNef could not insert into the lipids and maintained a compact conformation adjacent to the monolayer, whereas at lower lipid packing density, myrNef was able to insert N-terminal arm residues, causing displacement of the core domain away from the monolayer. In order to locate where conformation may have been altered by lipid association, we applied the HX MS Langmuir monolayer method to myrNef associated with monolayers of packing densities identical to those used for the prior neutron reflection measurements. The results show that the N-terminal region and the C-terminal unstructured loop undergo conformational changes when associated with a low density lipid monolayer. The results are not consistent with the hypothesis of myrNef dimerization upon membrane association in the absence of other myrNef binding partners. The HX MS Langmuir monolayer method provides new and meaningful information for myrNef that helps explain necessary conformational changes required for function at the membrane.


Subject(s)
HIV-1/metabolism , Hydrogen/chemistry , Mass Spectrometry , nef Gene Products, Human Immunodeficiency Virus/chemistry , Deuterium Exchange Measurement , Fatty Acids, Monounsaturated/chemistry , Humans , Membranes/metabolism , Recombinant Proteins/biosynthesis , Recombinant Proteins/chemistry , Recombinant Proteins/isolation & purification , nef Gene Products, Human Immunodeficiency Virus/genetics , nef Gene Products, Human Immunodeficiency Virus/metabolism
14.
Am J Obstet Gynecol ; 212(1): 71.e1-71.e8, 2015 Jan.
Article in English | MEDLINE | ID: mdl-25108145

ABSTRACT

OBJECTIVE: Primary human trophoblasts were previously shown to be resistant to viral infection, and able to confer this resistance to nontrophoblast cells. Can trophoblasts protect nontrophoblastic cells from infection by viruses or other intracellular pathogens that are implicated in perinatal infection? STUDY DESIGN: Isolated primary term human trophoblasts were cultured for 48-72 hours. Diverse nonplacental human cell lines (U2OS, human foreskin fibroblast, TZM-bl, MeWo, and Caco-2) were preexposed to either trophoblast conditioned medium, nonconditioned medium, or miR-517-3p for 24 hours. Cells were infected with several viral and nonviral pathogens known to be associated with perinatal infections. Cellular infection was defined and quantified by plaque assays, luciferase assays, microscopy, and/or colonization assays. Differences in infection were assessed by Student t test or analysis of variance with Bonferroni correction. RESULTS: Infection by rubella and other togaviruses, human immunodeficiency virus-1, and varicella zoster was attenuated in cells preexposed to trophoblast-conditioned medium (P < .05), and a partial effect by the chromosome 19 microRNA miR-517-3p on specific pathogens. The conditioned medium had no effect on infection by Toxoplasma gondii or Listeria monocytogenes. CONCLUSION: Our findings indicate that medium conditioned by primary human trophoblasts attenuates viral infection in nontrophoblastic cells. Our data point to a trophoblast-specific antiviral effect that may be exploited therapeutically.


Subject(s)
Disease Resistance , Fetal Diseases/virology , Trophoblasts/physiology , Virus Diseases/immunology , Cells, Cultured , Culture Media, Conditioned , Humans , Infant, Newborn
15.
Bioorg Med Chem Lett ; 24(7): 1702-6, 2014 Apr 01.
Article in English | MEDLINE | ID: mdl-24650642

ABSTRACT

HIV-1 Nef is a critical AIDS progression factor yet underexplored target for antiretroviral drug discovery. A recent high-throughput screen for pharmacological inhibitors of Nef-dependent Src-family kinase activation identified a diphenylpyrazolodiazene hit compound with submicromolar potency in HIV-1 replication assays against a broad range of primary Nef variants. This compound, known as 'B9', binds directly to Nef and inhibits its dimerization in cells as a possible mechanism of action. Here were synthesized a diverse set of B9 analogs and identified structural features essential to antiretroviral activity. Chemical modifications to each of the three rings present in the parent compound were identified that did not compromise antiviral action. These analogs will guide the development of next-generation compounds with appropriate pharmacological profiles for assessment of antiretroviral activity in vivo.


Subject(s)
Anti-HIV Agents/pharmacology , Azo Compounds/pharmacology , HIV Infections/drug therapy , HIV-1/drug effects , Pyrazoles/pharmacology , nef Gene Products, Human Immunodeficiency Virus/drug effects , Anti-HIV Agents/chemical synthesis , Anti-HIV Agents/chemistry , Azo Compounds/chemical synthesis , Azo Compounds/chemistry , Cell Line , Dose-Response Relationship, Drug , HIV Infections/virology , HIV-1/genetics , Humans , Microbial Sensitivity Tests , Molecular Structure , Pyrazoles/chemical synthesis , Pyrazoles/chemistry , Structure-Activity Relationship , nef Gene Products, Human Immunodeficiency Virus/genetics
16.
Retrovirology ; 10: 135, 2013 Nov 14.
Article in English | MEDLINE | ID: mdl-24229420

ABSTRACT

BACKGROUND: HIV-1 Nef is a viral accessory protein critical for AIDS progression. Nef lacks intrinsic catalytic activity and binds multiple host cell signaling proteins, including Hck and other Src-family tyrosine kinases. Nef binding induces constitutive Hck activation that may contribute to HIV pathogenesis by promoting viral infectivity, replication and downregulation of cell-surface MHC-I molecules. In this study, we developed a yeast-based phenotypic screen to identify small molecules that inhibit the Nef-Hck complex. RESULTS: Nef-Hck interaction was faithfully reconstituted in yeast cells, resulting in kinase activation and growth arrest. Yeast cells expressing the Nef-Hck complex were used to screen a library of small heterocyclic compounds for their ability to rescue growth inhibition. The screen identified a dihydrobenzo-1,4-dioxin-substituted analog of 2-quinoxalinyl-3-aminobenzene-sulfonamide (DQBS) as a potent inhibitor of Nef-dependent HIV-1 replication and MHC-I downregulation in T-cells. Docking studies predicted direct binding of DQBS to Nef which was confirmed in differential scanning fluorimetry assays with recombinant purified Nef protein. DQBS also potently inhibited the replication of HIV-1 NL4-3 chimeras expressing Nef alleles representative of all M-group HIV-1 clades. CONCLUSIONS: Our findings demonstrate the utility of a yeast-based growth reversion assay for the identification of small molecule Nef antagonists. Inhibitors of Nef function discovered with this assay, such as DQBS, may complement the activity of current antiretroviral therapies by enabling immune recognition of HIV-infected cells through the rescue of cell surface MHC-I.


Subject(s)
Anti-HIV Agents/pharmacology , Drug Evaluation, Preclinical/methods , Proto-Oncogene Proteins c-hck/antagonists & inhibitors , Quinoxalines/pharmacology , Saccharomyces cerevisiae/drug effects , Sulfonamides/pharmacology , nef Gene Products, Human Immunodeficiency Virus/antagonists & inhibitors , Anti-HIV Agents/isolation & purification , Humans , Molecular Docking Simulation , Protein Binding/drug effects , Proto-Oncogene Proteins c-hck/genetics , Quinoxalines/isolation & purification , Saccharomyces cerevisiae/genetics , Saccharomyces cerevisiae/growth & development , Sulfonamides/isolation & purification , nef Gene Products, Human Immunodeficiency Virus/genetics , Benzenesulfonamides
17.
Chem Biol ; 20(1): 82-91, 2013 Jan 24.
Article in English | MEDLINE | ID: mdl-23352142

ABSTRACT

HIV-1 Nef, a critical AIDS progression factor, represents an important target protein for antiretroviral drug discovery. Because Nef lacks intrinsic enzymatic activity, we developed an assay that couples Nef to the activation of Hck, a Src family member and Nef effector protein. Using this assay, we screened a large, diverse chemical library and identified small molecules that block Nef-dependent Hck activity with low micromolar potency. Of these, a diphenylpyrazolo compound demonstrated submicromolar potency in HIV-1 replication assays against a broad range of primary Nef variants. This compound binds directly to Nef via a pocket formed by the Nef dimerization interface and disrupts Nef dimerization in cells. Coupling of nonenzymatic viral accessory factors to host cell effector proteins amenable to high-throughput screening may represent a general strategy for the discovery of new antimicrobial agents.


Subject(s)
Anti-Retroviral Agents/chemistry , Anti-Retroviral Agents/pharmacology , HIV-1/drug effects , Small Molecule Libraries/chemistry , Small Molecule Libraries/pharmacology , nef Gene Products, Human Immunodeficiency Virus/antagonists & inhibitors , Cell Line , HIV Infections/drug therapy , HIV-1/physiology , Humans , Molecular Docking Simulation , Protein Multimerization/drug effects , Proto-Oncogene Proteins c-hck/metabolism , Pyrazoles/chemistry , Pyrazoles/pharmacology , Virus Replication/drug effects , nef Gene Products, Human Immunodeficiency Virus/metabolism
18.
J Mol Biol ; 410(5): 1008-22, 2011 Jul 29.
Article in English | MEDLINE | ID: mdl-21763503

ABSTRACT

Human immunodeficiency virus-1 (HIV-1) has evolved a cunning mechanism to circumvent the antiviral activity of the APOBEC3 family of host cell enzymes. HIV-1 Vif [viral (also called virion) infectivity factor], one of several HIV accessory proteins, targets APOBEC3 proteins for proteasomal degradation and downregulates their expression at the mRNA level. Despite the importance of Vif for HIV-1 infection, there is little conformational data on Vif alone or in complex with other cellular factors due to incompatibilities with many structural techniques and difficulties in producing suitable quantities of the protein for biophysical analysis. As an alternative, we have turned to hydrogen exchange mass spectrometry (HX MS), a conformational analysis method that is well suited for proteins that are difficult to study using X-ray crystallography and/or NMR. HX MS was used to probe the solution conformation of recombinant full-length HIV-1 Vif. Vif specifically interacted with the previously identified binding partner Hck and was able to cause kinase activation, suggesting that the Vif studied by HX MS retained a biochemically competent conformation relevant to Hck interaction. HX MS analysis of Vif alone revealed low deuteration levels in the N-terminal portion, indicating that this region contained structured or otherwise protected elements. In contrast, high deuteration levels in the C-terminal portion of Vif indicated that this region was likely unstructured in the absence of cellular interacting proteins. Several regions within Vif displayed conformational heterogeneity in solution, including the APOBEC3G/F binding site and the HCCH zinc finger. Taken together, these HX MS results provide new insights into the solution conformation of Vif.


Subject(s)
HIV-1/chemistry , vif Gene Products, Human Immunodeficiency Virus/chemistry , Amino Acid Motifs , Amino Acid Sequence , Biophysical Phenomena/drug effects , Deuterium Exchange Measurement , Enzyme Activation/drug effects , HIV-1/drug effects , Humans , Mass Spectrometry , Models, Biological , Molecular Sequence Data , Peptides/chemistry , Peptides/metabolism , Protein Binding/drug effects , Proto-Oncogene Proteins c-hck/metabolism , Recombinant Proteins/chemistry , Recombinant Proteins/metabolism , Solutions , Zinc/pharmacology , vif Gene Products, Human Immunodeficiency Virus/metabolism
19.
Mol Biol Cell ; 21(19): 3279-92, 2010 Oct 01.
Article in English | MEDLINE | ID: mdl-20702582

ABSTRACT

HIV-1 Nef triggers down-regulation of cell-surface MHC-I by assembling a Src family kinase (SFK)-ZAP-70/Syk-PI3K cascade. Here, we report that chemical disruption of the Nef-SFK interaction with the small molecule inhibitor 2c blocks assembly of the multi-kinase complex and represses HIV-1-mediated MHC-I down-regulation in primary CD4(+) T-cells. 2c did not interfere with the PACS-2-dependent trafficking of Nef required for the Nef-SFK interaction or the AP-1 and PACS-1-dependent sequestering of internalized MHC-I, suggesting the inhibitor specifically interfered with the Nef-SFK interaction required for triggering MHC-I down-regulation. Transport studies revealed Nef directs a highly regulated program to down-regulate MHC-I in primary CD4(+) T-cells. During the first two days after infection, Nef assembles the 2c-sensitive multi-kinase complex to trigger down-regulation of cell-surface MHC-I. By three days postinfection Nef switches to a stoichiometric mode that prevents surface delivery of newly synthesized MHC-I. Pharmacologic inhibition of the multi-kinase cascade prevents the Nef-dependent block in MHC-I transport, suggesting the signaling and stoichiometric modes are causally linked. Together, these studies resolve the seemingly controversial models that describe Nef-induced MHC-I down-regulation and provide new insights into the mechanism of Nef action.


Subject(s)
Down-Regulation/drug effects , HIV-1/drug effects , Histocompatibility Antigens Class I/metabolism , Small Molecule Libraries/pharmacology , nef Gene Products, Human Immunodeficiency Virus/metabolism , CD4-Positive T-Lymphocytes/drug effects , CD4-Positive T-Lymphocytes/enzymology , CD4-Positive T-Lymphocytes/virology , Cell Line , Endocytosis/drug effects , Humans , Multienzyme Complexes/metabolism , PTEN Phosphohydrolase/metabolism , Phosphatidylinositol 3-Kinases/metabolism , Protein Binding/drug effects , Protein Transport/drug effects , Signal Transduction/drug effects , Time Factors , Transcription Factor AP-1/metabolism , Vesicular Transport Proteins/metabolism , src-Family Kinases/metabolism
20.
Proc Natl Acad Sci U S A ; 106(50): 21167-72, 2009 Dec 15.
Article in English | MEDLINE | ID: mdl-19940238

ABSTRACT

The immune receptor signaling pathway is used by nonimmune cells, but the molecular adaptations that underlie its functional diversification are not known. Circulating platelets use the immune receptor homologue glycoprotein VI (GPVI) to respond to collagen exposed at sites of vessel injury. In contrast to immune cell responses, platelet activation must take place within seconds to successfully form thrombi in flowing blood. Here, we show that the GPVI receptor utilizes a unique intracellular proline-rich domain (PRD) to accelerate platelet activation, a requirement for efficient platelet adhesion to collagen under flow. The GPVI PRD specifically binds the Src-family kinase Lyn and directly activates it, presumably through SH3 displacement. In resting platelets, Lyn is constitutively bound to GPVI in an activated state and platelets lacking Lyn exhibit defective collagen adhesion like that of platelets with GPVI receptors lacking the PRD. These findings define a molecular priming mechanism that enables an immune-type receptor to adopt a hemostatic function. These studies also demonstrate that active kinases can constitutively associate with immune-type receptors without initiating signal transduction before receptor ligation, consistent with a recent molecular model of immune receptor signaling in which receptor ligation is required to bring active kinases to their receptor substrates.


Subject(s)
Hemostasis , Platelet Membrane Glycoproteins/physiology , src-Family Kinases/metabolism , Animals , Blood Platelets/metabolism , Collagen/metabolism , Mice , Platelet Activation/immunology , Platelet Adhesiveness , Platelet Membrane Glycoproteins/metabolism , Proline
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