1
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Biradar S, Agarwal Y, Das A, Shu ST, Samal J, Ho S, Kelly N, Mahesh D, Teredesai S, Castronova I, Mussina L, Mailliard RB, Smithgall TE, Bility MT. Nef defect attenuates HIV viremia and immune dysregulation in the bone marrow-liver-thymus-spleen (BLTS) humanized mouse model. Virology 2024; 598:110192. [PMID: 39106585 PMCID: PMC11458258 DOI: 10.1016/j.virol.2024.110192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 07/21/2024] [Accepted: 07/24/2024] [Indexed: 08/09/2024]
Abstract
In vitro studies have shown that deletion of nef and deleterious mutation in the Nef dimerization interface attenuates HIV replication and associated pathogenesis. Humanized rodents with human immune cells and lymphoid tissues are robust in vivo models for investigating the interactions between HIV and the human immune system. Here, we demonstrate that nef deletion impairs HIV replication and HIV-induced immune dysregulation in the blood and human secondary lymphoid tissue (human spleen) in bone marrow-liver-thymus-spleen (BLTS) humanized mice. Furthermore, we also show that nef defects (via deleterious mutations in the dimerization interface) impair HIV replication and HIV-induced immune dysregulation in the blood and human spleen in BLTS-humanized mice. We demonstrate that the reduced replication of nef-deleted and nef-defective HIV is associated with robust antiviral innate immune response, and T helper 1 response. Our results support the proposition that Nef may be a therapeutic target for adjuvants in HIV cure strategies.
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Affiliation(s)
- Shivkumar Biradar
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, School of Public Health, Pittsburgh, PA, USA
| | - Yash Agarwal
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, School of Public Health, Pittsburgh, PA, USA
| | - Antu Das
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, School of Public Health, Pittsburgh, PA, USA
| | - Sherry T Shu
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jasmine Samal
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, School of Public Health, Pittsburgh, PA, USA
| | - Sara Ho
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, School of Public Health, Pittsburgh, PA, USA
| | - Nickolas Kelly
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, School of Public Health, Pittsburgh, PA, USA
| | - Deepika Mahesh
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, School of Public Health, Pittsburgh, PA, USA
| | - Shreya Teredesai
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, School of Public Health, Pittsburgh, PA, USA
| | - Isabella Castronova
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, School of Public Health, Pittsburgh, PA, USA
| | - London Mussina
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, School of Public Health, Pittsburgh, PA, USA
| | - Robbie B Mailliard
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, School of Public Health, Pittsburgh, PA, USA
| | - Thomas E Smithgall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Moses T Bility
- Department of Infectious Diseases and Microbiology, University of Pittsburgh, School of Public Health, Pittsburgh, PA, USA; Department of Microbiology, Howard University, Washington, DC, USA.
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2
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Emert-Sedlak LA, Tice CM, Shi H, Alvarado JJ, Shu ST, Reitz AB, Smithgall TE. PROTAC-mediated degradation of HIV-1 Nef efficiently restores cell-surface CD4 and MHC-I expression and blocks HIV-1 replication. Cell Chem Biol 2024; 31:658-668.e14. [PMID: 38508197 PMCID: PMC11031313 DOI: 10.1016/j.chembiol.2024.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 12/20/2023] [Accepted: 02/20/2024] [Indexed: 03/22/2024]
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.
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Affiliation(s)
- Lori A Emert-Sedlak
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Colin M Tice
- Fox Chase Therapeutics Discovery, Inc., Pennsylvania Biotechnology Center, Doylestown, PA 18902, USA
| | - Haibin Shi
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - John J Alvarado
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Sherry T Shu
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Allen B Reitz
- Fox Chase Therapeutics Discovery, Inc., Pennsylvania Biotechnology Center, Doylestown, PA 18902, USA
| | - Thomas E Smithgall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA.
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3
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McCauley M, Huston M, Condren AR, Pereira F, Cline J, Yaple-Maresh M, Painter MM, Zimmerman GE, Robertson AW, Carney N, Goodall C, Terry V, Müller R, Sherman DH, Collins KL. Structure-Activity Relationships of Natural and Semisynthetic Plecomacrolides Suggest Distinct Pathways for HIV-1 Immune Evasion and Vacuolar ATPase-Dependent Lysosomal Acidification. J Med Chem 2024. [PMID: 38452116 DOI: 10.1021/acs.jmedchem.3c01574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/09/2024]
Abstract
The human immunodeficiency virus (HIV)-encoded accessory protein Nef enhances pathogenicity by reducing major histocompatibility complex I (MHC-I) cell surface expression, protecting HIV-infected cells from immune recognition. Nef-dependent downmodulation of MHC-I can be reversed by subnanomolar concentrations of concanamycin A (1), a well-known inhibitor of vacuolar ATPase, at concentrations below those that interfere with lysosomal acidification or degradation. We conducted a structure-activity relationship study that assessed 76 compounds for Nef inhibition, 24 and 72 h viability, and lysosomal neutralization in Nef-expressing primary T cells. This analysis demonstrated that the most potent compounds were natural concanamycins and their derivatives. Comparison against a set of new, semisynthetic concanamycins revealed that substituents at C-8 and acylation of C-9 significantly affected Nef potency, target cell viability, and lysosomal neutralization. These findings provide important progress toward understanding the mechanism of action of these compounds and the identification of an advanced lead anti-HIV Nef inhibitory compound.
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Affiliation(s)
- Morgan McCauley
- University of Michigan, Life Sciences Institute, Ann Arbor, Michigan 48109, United States
| | - Matthew Huston
- University of Michigan, Department of Internal Medicine, Ann Arbor, Michigan 48109, United States
| | - Alanna R Condren
- University of Michigan, Life Sciences Institute, Ann Arbor, Michigan 48109, United States
| | - Filipa Pereira
- University of Michigan, Life Sciences Institute, Ann Arbor, Michigan 48109, United States
| | - Joel Cline
- University of Michigan, Department of Internal Medicine, Ann Arbor, Michigan 48109, United States
| | - Marianne Yaple-Maresh
- University of Michigan, Department of Internal Medicine, Ann Arbor, Michigan 48109, United States
| | - Mark M Painter
- University of Michigan, Graduate Program in Immunology, Ann Arbor, Michigan 48109, United States
| | - Gretchen E Zimmerman
- University of Michigan, Department of Internal Medicine, Ann Arbor, Michigan 48109, United States
| | - Andrew W Robertson
- University of Michigan, Life Sciences Institute, Ann Arbor, Michigan 48109, United States
- University of Michigan Natural Products Discovery Core, Life Sciences Institute, Ann Arbor, Michigan 48109, United States
| | - Nolan Carney
- University of Michigan, Department of Chemistry, Ann Arbor, Michigan 48109, United States
| | - Christopher Goodall
- University of Michigan, Department of Internal Medicine, Ann Arbor, Michigan 48109, United States
| | - Valeri Terry
- University of Michigan, Department of Internal Medicine, Ann Arbor, Michigan 48109, United States
| | - Rolf Müller
- Helmholtz Institute for Pharmaceutical Research Saarland, Saarbrücken 66123, Germany
| | - David H Sherman
- University of Michigan, Department of Microbiology & Immunology, Ann Arbor, Michigan 48109, United States
- University of Michigan, Life Sciences Institute, Ann Arbor, Michigan 48109, United States
- University of Michigan, Department of Medicinal Chemistry, Ann Arbor, Michigan 48109, United States
- University of Michigan, Department of Chemistry, Ann Arbor, Michigan 48109, United States
| | - Kathleen L Collins
- University of Michigan, Graduate Program in Immunology, Ann Arbor, Michigan 48109, United States
- University of Michigan, Department of Internal Medicine, Ann Arbor, Michigan 48109, United States
- University of Michigan, Department of Microbiology & Immunology, Ann Arbor, Michigan 48109, United States
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4
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Emert-Sedlak LA, Tice CM, Shi H, Alvarado JJ, Shu ST, Reitz AB, Smithgall TE. PROTAC-mediated Degradation of HIV-1 Nef Efficiently Restores Cell-surface CD4 and MHC-I Expression and Blocks HIV-1 Replication. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.14.553289. [PMID: 37645900 PMCID: PMC10462000 DOI: 10.1101/2023.08.14.553289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
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 .
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5
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Heinrich F, Thomas CE, Alvarado JJ, Eells R, Thomas A, Doucet M, Whitlatch KN, Aryal M, Lösche M, Smithgall TE. Neutron Reflectometry and Molecular Simulations Demonstrate HIV-1 Nef Homodimer Formation on Model Lipid Bilayers. J Mol Biol 2023; 435:168009. [PMID: 36773691 PMCID: PMC10079580 DOI: 10.1016/j.jmb.2023.168009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/16/2023] [Accepted: 02/03/2023] [Indexed: 02/12/2023]
Abstract
The HIV-1 Nef protein plays a critical role in viral infectivity, high-titer replication in vivo, and immune escape of HIV-infected cells. Nef lacks intrinsic biochemical activity, functioning instead through interactions with diverse host cell signaling proteins and intracellular trafficking pathways. Previous studies have established an essential role for Nef homodimer formation at the plasma membrane for most if not all its functions. Here we combined neutron reflectometry of full-length myristoylated Nef bound to model lipid bilayers with molecular simulations based on previous X-ray crystal structures of Nef homodimers. This integrated approach provides direct evidence that Nef associates with the membrane as a homodimer with its structured core region displaced from the membrane for partner protein engagement. Parallel studies of a dimerization-defective mutant, Nef-L112D, demonstrate that the helical dimerization interface present in previous crystal structures stabilizes the membrane-bound dimer. X-ray crystallography of the Nef-L112D mutant in complex with the SH3 domain of the Nef-associated host cell kinase Hck revealed a monomeric 1:1 complex instead of the 2:2 dimer complex formed with wild-type Nef. Importantly, the crystal structure of the Nef-L112D core and SH3 interface are virtually identical to the wild-type complex, indicating that this mutation does not affect the overall Nef fold. These findings support the intrinsic capacity of Nef to homodimerize at lipid bilayers using structural features present in X-ray crystal structures of dimeric complexes.
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Affiliation(s)
- Frank Heinrich
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA; NIST Center for Neutron Research, Gaithersburg, MD 20899, USA
| | - Catherine E Thomas
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - John J Alvarado
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Rebecca Eells
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Alyssa Thomas
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA
| | - Mathieu Doucet
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Kindra N Whitlatch
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Manish Aryal
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Mathias Lösche
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA 15213, USA; NIST Center for Neutron Research, Gaithersburg, MD 20899, USA
| | - Thomas E Smithgall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA.
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6
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Majumder S, Deganutti G, Pipitò L, Chaudhuri D, Datta J, Giri K. Computer-aided de novo design and optimization of novel potential inhibitors of HIV-1 Nef protein. Comput Biol Chem 2023; 104:107871. [PMID: 37084691 DOI: 10.1016/j.compbiolchem.2023.107871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 04/07/2023] [Accepted: 04/14/2023] [Indexed: 04/23/2023]
Abstract
Nef is a small accessory protein pivotal in the HIV-1 viral replication cycle. It is a multifunctional protein and its interactions with kinases in host cells have been well characterized through many in vitro and structural studies. Nef forms a homodimer to activate the kinases and subsequently the phosphorylation pathways. The disruption of its homodimerization represents a valuable approach in the search for novel classes of antiretroviral. However, this research avenue is still underdeveloped as just a few Nef inhibitors have been reported so far, with very limited structural information about their mechanism of action. To address this issue, we have employed an in silico structure-based drug design strategy that combines de novo ligand design with molecular docking and extensive molecular dynamics simulations. Since the Nef pocket involved in homodimerization has high lipophilicity, the initial de novo-designed structures displayed poor drug-likeness and solubility. Taking information from the hydration sites within the homodimerization pocket, structural modifications in the initial lead compound have been introduced to improve the solubility and drug-likeness, without affecting the binding profile. We propose lead compounds that can be the starting point for further optimizations to deliver long-awaited, rationally designed Nef inhibitors.
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Affiliation(s)
| | - Giuseppe Deganutti
- Centre for Sport, Exercise, and Life Sciences, Coventry University, Coventry CV1 5FB, UK
| | - Ludovico Pipitò
- Centre for Sport, Exercise, and Life Sciences, Coventry University, Coventry CV1 5FB, UK
| | | | - Joyeeta Datta
- Department of Life Sciences, Presidency University, Kolkata, India
| | - Kalyan Giri
- Department of Life Sciences, Presidency University, Kolkata, India.
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7
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Chakravarty A, Yang PL. Targeted protein degradation as an antiviral approach. Antiviral Res 2023; 210:105480. [PMID: 36567024 PMCID: PMC10178900 DOI: 10.1016/j.antiviral.2022.105480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 12/01/2022] [Indexed: 12/24/2022]
Abstract
Targeted protein degradation (TPD) has emerged as a new modality in drug discovery. In this approach, small molecules are used to drive degradation of the target protein of interest. Whereas most direct-acting antivirals (DAAs) inhibit or derange the activity of their viral protein targets and have occupancy-driven pharmacology, small molecules with a TPD-based mechanism have event-driven pharmacology exerted through their ability to induce target degradation. These contrasting mechanisms can result in significant differences in drug efficacy and pharmacodynamics that may be useful in the development of new classes of antivirals. While now being widely pursued in cancer biology and autoimmune disease, TPD has not yet been widely applied as an antiviral strategy. Here, we briefly review TPD pharmacology along with the current status of tools available for developing small molecules that achieve antiviral activity through a TPD mechanism. We also highlight aspects of TPD that may be especially useful in the development of antivirals and that we hope will motivate pursuit of TPD-based antivirals by the antivirals research community.
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Affiliation(s)
- Antara Chakravarty
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Priscilla L Yang
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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8
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Aryal M, Lin D, Regan K, Du S, Shi H, Alvarado JJ, Ilina TV, Andreotti AH, Smithgall TE. The HIV-1 protein Nef activates the Tec family kinase Btk by stabilizing an intermolecular SH3-SH2 domain interaction. Sci Signal 2022; 15:eabn8359. [PMID: 36126115 PMCID: PMC9830684 DOI: 10.1126/scisignal.abn8359] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The Nef protein produced by the viruses HIV-1 and SIV drives efficient viral replication partially by inducing constitutive activation of host cell tyrosine kinases, including members of the Src and Tec families. Here, we uncovered the mechanism by which both HIV-1 and SIV Nef enhanced the activity of the Tec family kinase Btk in vitro and in cells. A Nef mutant that could not bind to the SH3 domain of Src family kinases activated Btk to the same extent as did wild-type Nef, demonstrating that Nef activated Src and Tec family kinases by distinct mechanisms. The Btk SH3-SH2 region formed a homodimer requiring the CD loop in the SH2 domain, which was stabilized by the binding of Nef homodimers. Alanine substitution of Pro327 in the CD loop of the Btk SH2 domain destabilized SH3-SH2 dimers, abolished the interaction with Nef, and prevented activation by Nef in vitro. In cells, Nef stabilized and activated wild-type but not P327A Btk homodimers at the plasma membrane. These data reveal that the interaction with Nef stabilizes Btk dimers through the SH3-SH2 interface to promote kinase activity and show that the HIV-1 Nef protein evolved distinct mechanisms to activate Src and Tec family tyrosine kinases to enhance viral replication.
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Affiliation(s)
- Manish Aryal
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh PA, 15219 USA
| | - David Lin
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011 USA
| | - Kiera Regan
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh PA, 15219 USA
| | - Shoucheng Du
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh PA, 15219 USA
| | - Haibin Shi
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh PA, 15219 USA
| | - John J. Alvarado
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh PA, 15219 USA
| | - Tatiana V. Ilina
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh PA, 15260 USA
| | - Amy H. Andreotti
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, 50011 USA
| | - Thomas E. Smithgall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh PA, 15219 USA
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9
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Emert-Sedlak LA, Shi H, Tice CM, Chen L, Alvarado JJ, Shu ST, Du S, Thomas CE, Wrobel JE, Reitz AB, Smithgall TE. Antiretroviral Drug Discovery Targeting the HIV-1 Nef Virulence Factor. Viruses 2022; 14:v14092025. [PMID: 36146831 PMCID: PMC9503669 DOI: 10.3390/v14092025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/06/2022] [Accepted: 09/08/2022] [Indexed: 11/16/2022] Open
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.
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Affiliation(s)
- Lori A. Emert-Sedlak
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Haibin Shi
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Colin M. Tice
- Fox Chase Chemical Diversity Center, Inc., Pennsylvania Biotechnology Center, Doylestown, PA 18902, USA
| | - Li Chen
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - John J. Alvarado
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Sherry T. Shu
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Shoucheng Du
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Catherine E. Thomas
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Jay E. Wrobel
- Fox Chase Chemical Diversity Center, Inc., Pennsylvania Biotechnology Center, Doylestown, PA 18902, USA
| | - Allen B. Reitz
- Fox Chase Chemical Diversity Center, Inc., Pennsylvania Biotechnology Center, Doylestown, PA 18902, USA
| | - Thomas E. Smithgall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
- Correspondence:
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10
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Duette G, Hiener B, Morgan H, Mazur FG, Mathivanan V, Horsburgh BA, Fisher K, Tong O, Lee E, Ahn H, Shaik A, Fromentin R, Hoh R, Bacchus-Souffan C, Nasr N, Cunningham AL, Hunt PW, Chomont N, Turville SG, Deeks SG, Kelleher AD, Schlub TE, Palmer S. The HIV-1 proviral landscape reveals that Nef contributes to HIV-1 persistence in effector memory CD4+ T cells. J Clin Invest 2022; 132:154422. [PMID: 35133986 PMCID: PMC8970682 DOI: 10.1172/jci154422] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 02/02/2022] [Indexed: 11/17/2022] Open
Abstract
Despite long-term antiretroviral therapy (ART), HIV-1 persists within a reservoir of CD4+ T cells that contribute to viral rebound if treatment is interrupted. Identifying the cellular populations that contribute to the HIV-1 reservoir and understanding the mechanisms of viral persistence are necessary to achieve an effective cure. In this regard, through Full-Length Individual Proviral Sequencing, we observed that the HIV-1 proviral landscape was different and changed with time on ART across naive and memory CD4+ T cell subsets isolated from 24 participants. We found that the proportion of genetically intact HIV-1 proviruses was higher and persisted over time in effector memory CD4+ T cells when compared with naive, central, and transitional memory CD4+ T cells. Interestingly, we found that escape mutations remained stable over time within effector memory T cells during therapy. Finally, we provided evidence that Nef plays a role in the persistence of genetically intact HIV-1. These findings posit effector memory T cells as a key component of the HIV-1 reservoir and suggest Nef as an attractive therapeutic target.
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Affiliation(s)
- Gabriel Duette
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Bonnie Hiener
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Hannah Morgan
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Fernando G. Mazur
- Post-graduation Program of Evolutionary Genetics and Molecular Biology, Federal University of São Carlos, São Carlos, Brazil
| | - Vennila Mathivanan
- The Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Bethany A. Horsburgh
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia
| | - Katie Fisher
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Orion Tong
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia
| | - Eunok Lee
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Haelee Ahn
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Ansari Shaik
- The Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Rémi Fromentin
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montreal, Quebec, Canada
| | - Rebecca Hoh
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Charline Bacchus-Souffan
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Najla Nasr
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Anthony L. Cunningham
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Peter W. Hunt
- Division of Experimental Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Nicolas Chomont
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal, Montreal, Quebec, Canada.,Department of Microbiology, Infectiology and Immunology, Université de Montréal, Montreal, Quebec, Canada
| | - Stuart G. Turville
- The Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Steven G. Deeks
- Department of Medicine, University of California, San Francisco, San Francisco, California, USA
| | - Anthony D. Kelleher
- The Kirby Institute, University of New South Wales, Sydney, New South Wales, Australia
| | - Timothy E. Schlub
- Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
| | - Sarah Palmer
- Centre for Virus Research, The Westmead Institute for Medical Research, Westmead, New South Wales, Australia.,Faculty of Medicine and Health, The University of Sydney, Sydney, New South Wales, Australia
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11
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Emert-Sedlak LA, Moukha-Chafiq O, Shi H, Du S, Alvarado JJ, Pathak V, Tanner SG, Hunter RN, Nebane M, Chen L, Ilina TV, Ishima R, Zhang S, Kuzmichev YV, Wonderlich ER, Schader SM, Augelli-Szafran CE, Ptak RG, Smithgall TE. Inhibitors of HIV-1 Nef-Mediated Activation of the Myeloid Src-Family Kinase Hck Block HIV-1 Replication in Macrophages and Disrupt MHC-I Downregulation. ACS Infect Dis 2022; 8:91-105. [PMID: 34985256 PMCID: PMC9274903 DOI: 10.1021/acsinfecdis.1c00288] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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.
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Affiliation(s)
- Lori A. Emert-Sedlak
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA 15219
| | - Omar Moukha-Chafiq
- Department of Chemistry, Southern Research Institute, 2000 Ninth Avenue South, Birmingham, AL 35205
| | - Haibin Shi
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA 15219
| | - Shoucheng Du
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA 15219
| | - John J. Alvarado
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA 15219
| | - Vibha Pathak
- Department of Chemistry, Southern Research Institute, 2000 Ninth Avenue South, Birmingham, AL 35205
| | - Samuel G. Tanner
- Department of Chemistry, Southern Research Institute, 2000 Ninth Avenue South, Birmingham, AL 35205
| | - Robert N. Hunter
- Department of Chemistry, Southern Research Institute, 2000 Ninth Avenue South, Birmingham, AL 35205
| | - Miranda Nebane
- Department of High-throughput Screening, Drug Discovery Division, Southern Research Institute, 2000 Ninth Avenue South, Birmingham, AL 35205
| | - Li Chen
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA 15219
| | - Tatiana V. Ilina
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260
| | - Rieko Ishima
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA 15260
| | - Sixue Zhang
- Department of High-throughput Screening, Drug Discovery Division, Southern Research Institute, 2000 Ninth Avenue South, Birmingham, AL 35205
| | - Yury V. Kuzmichev
- Department of Infectious Disease Research, Drug Development Division, Southern Research Institute, 431 Aviation Way, Frederick, MD 21701
| | - Elizabeth R. Wonderlich
- Department of Infectious Disease Research, Drug Development Division, Southern Research Institute, 431 Aviation Way, Frederick, MD 21701
| | - Susan M. Schader
- Department of Infectious Disease Research, Drug Development Division, Southern Research Institute, 431 Aviation Way, Frederick, MD 21701
| | | | - Roger G. Ptak
- Department of Infectious Disease Research, Drug Development Division, Southern Research Institute, 431 Aviation Way, Frederick, MD 21701
| | - Thomas E. Smithgall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA 15219
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12
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Shu ST, Li WF, Smithgall TE. Visualization of Host Cell Kinase Activation by Viral Proteins Using GFP Fluorescence Complementation and Immunofluorescence Microscopy. Bio Protoc 2021; 11:e4068. [PMID: 34327265 DOI: 10.21769/bioprotoc.4068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 03/29/2021] [Accepted: 04/01/2021] [Indexed: 11/02/2022] Open
Abstract
Non-receptor protein-tyrosine kinases regulate cellular responses to many external signals and are important drug discovery targets for cancer and infectious diseases. While many assays exist for the assessment of kinase activity in vitro, methods that report changes in tyrosine kinase activity in single cells have the potential to provide information about kinase responses at the cell population level. In this protocol, we combined bimolecular fluorescence complementation (BiFC), an established method for the assessment of protein-protein interactions, and immunofluorescence staining with phosphospecific antibodies to characterize changes in host cell tyrosine kinase activity in the presence of an HIV-1 virulence factor, Nef. Specifically, two Tec family kinases (Itk and Btk) as well as Nef were fused to complementary, non-fluorescent fragments of the Venus variant of YFP. Each kinase was expressed in 293T cells in the presence or absence of Nef and immunostained for protein expression and activity with anti-phosphotyrosine (pTyr) antibodies. Multi-color confocal microscopy revealed the interaction of Nef with each kinase (BiFC), kinase activity, and kinase protein expression. Strong BiFC signals were observed when Nef was co-expressed with both Itk and Btk, indicative of interaction, and a strong anti-pTyr immunoreactivity was also seen. The BiFC, pTyr, and kinase expression signals co-localized to the plasma membrane, consistent with Nef-mediated kinase activation in this subcellular compartment. Image analysis allowed calculation of pTyr-to-kinase protein ratios, which showed a range of responses in individual cells across the population that shifted upward in the presence of Nef and back down in the presence of a kinase inhibitor. This method has the potential to reveal changes in steady-state non-receptor tyrosine kinase activity and subcellular localization in a cell population in response to other protein-kinase interactions, information that is not attainable from immunoblotting or other in vitro methods.
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Affiliation(s)
- Sherry T Shu
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Wing Fai Li
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Thomas E Smithgall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
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13
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Synergy and allostery in ligand binding by HIV-1 Nef. Biochem J 2021; 478:1525-1545. [PMID: 33787846 PMCID: PMC8079166 DOI: 10.1042/bcj20201002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 03/29/2021] [Accepted: 03/31/2021] [Indexed: 11/27/2022]
Abstract
The Nef protein of human and simian immunodeficiency viruses boosts viral pathogenicity through its interactions with host cell proteins. By combining the polyvalency of its large unstructured regions with the binding selectivity and strength of its folded core domain, Nef can associate with many different host cell proteins, thereby disrupting their functions. For example, the combination of a linear proline-rich motif and hydrophobic core domain surface allows Nef to bind tightly and specifically to SH3 domains of Src family kinases. We investigated whether the interplay between Nef's flexible regions and its core domain could allosterically influence ligand selection. We found that the flexible regions can associate with the core domain in different ways, producing distinct conformational states that alter the way in which Nef selects for SH3 domains and exposes some of its binding motifs. The ensuing crosstalk between ligands might promote functionally coherent Nef-bound protein ensembles by synergizing certain subsets of ligands while excluding others. We also combined proteomic and bioinformatics analyses to identify human proteins that select SH3 domains in the same way as Nef. We found that only 3% of clones from a whole-human fetal library displayed Nef-like SH3 selectivity. However, in most cases, this selectivity appears to be achieved by a canonical linear interaction rather than by a Nef-like ‘tertiary' interaction. Our analysis supports the contention that Nef's mode of hijacking SH3 domains is a virus-specific adaptation with no or very few cellular counterparts. Thus, the Nef tertiary binding surface is a promising virus-specific drug target.
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14
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Raghuvanshi R, Bharate SB. Recent Developments in the Use of Kinase Inhibitors for Management of Viral Infections. J Med Chem 2021; 65:893-921. [PMID: 33539089 DOI: 10.1021/acs.jmedchem.0c01467] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Kinases are a group of therapeutic targets involved in the progression of numerous diseases, including cancer, rheumatoid arthritis, Alzheimer's disease, and viral infections. The majority of approved antiviral agents are inhibitors of virus-specific targets that are encoded by individual viruses. These inhibitors are narrow-spectrum agents that can cause resistance development. Viruses are dependent on host cellular proteins, including kinases, for progression of their life-cycle. Thus, targeting kinases is an important therapeutic approach to discovering broad-spectrum antiviral agents. As there are a large number of FDA approved kinase inhibitors for various indications, their repurposing for viral infections is an attractive and time-sparing strategy. Many kinase inhibitors, including baricitinib, ruxolitinib, imatinib, tofacitinib, pacritinib, zanubrutinib, and ibrutinib, are under clinical investigation for COVID-19. Herein, we discuss FDA approved kinase inhibitors, along with a repertoire of clinical/preclinical stage kinase inhibitors that possess antiviral activity or are useful in the management of viral infections.
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Affiliation(s)
- Rinky Raghuvanshi
- Medicinal Chemistry Division,CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India.,Academy of Scientific & Innovative Research, Ghaziabad 201002, India
| | - Sandip B Bharate
- Medicinal Chemistry Division,CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India.,Academy of Scientific & Innovative Research, Ghaziabad 201002, India
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15
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Painter MM, Zimmerman GE, Merlino MS, Robertson AW, Terry VH, Ren X, McLeod MR, Gomez-Rodriguez L, Garcia KA, Leonard JA, Leopold KE, Neevel AJ, Lubow J, Olson E, Piechocka-Trocha A, Collins DR, Tripathi A, Raghavan M, Walker BD, Hurley JH, Sherman DH, Collins KL. Concanamycin A counteracts HIV-1 Nef to enhance immune clearance of infected primary cells by cytotoxic T lymphocytes. Proc Natl Acad Sci U S A 2020; 117:23835-23846. [PMID: 32900948 PMCID: PMC7519347 DOI: 10.1073/pnas.2008615117] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Nef is an HIV-encoded accessory protein that enhances pathogenicity by down-regulating major histocompatibility class I (MHC-I) expression to evade killing by cytotoxic T lymphocytes (CTLs). A potent Nef inhibitor that restores MHC-I is needed to promote immune-mediated clearance of HIV-infected cells. We discovered that the plecomacrolide family of natural products restored MHC-I to the surface of Nef-expressing primary cells with variable potency. Concanamycin A (CMA) counteracted Nef at subnanomolar concentrations that did not interfere with lysosomal acidification or degradation and were nontoxic in primary cell cultures. CMA specifically reversed Nef-mediated down-regulation of MHC-I, but not CD4, and cells treated with CMA showed reduced formation of the Nef:MHC-I:AP-1 complex required for MHC-I down-regulation. CMA restored expression of diverse allotypes of MHC-I in Nef-expressing cells and inhibited Nef alleles from divergent clades of HIV and simian immunodeficiency virus, including from primary patient isolates. Lastly, we found that restoration of MHC-I in HIV-infected cells was accompanied by enhanced CTL-mediated clearance of infected cells comparable to genetic deletion of Nef. Thus, we propose CMA as a lead compound for therapeutic inhibition of Nef to enhance immune-mediated clearance of HIV-infected cells.
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Affiliation(s)
- Mark M Painter
- Graduate Program in Immunology, University of Michigan, Ann Arbor, MI 48109
| | | | - Madeline S Merlino
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
| | - Andrew W Robertson
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
- Natural Products Discovery Core, Life Sciences Institute, University of Michigan Ann Arbor, MI 48109
| | - Valeri H Terry
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
| | - Xuefeng Ren
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
| | - Megan R McLeod
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
| | - Lyanne Gomez-Rodriguez
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
- Graduate Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109
| | - Kirsten A Garcia
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
| | - Jolie A Leonard
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
| | - Kay E Leopold
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
| | - Andrew J Neevel
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
| | - Jay Lubow
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109
| | - Eli Olson
- Graduate Program in Immunology, University of Michigan, Ann Arbor, MI 48109
| | - Alicja Piechocka-Trocha
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139
- Howard Hughes Medical Institute, Chevy Chase, MD 20815
| | - David R Collins
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139
- Howard Hughes Medical Institute, Chevy Chase, MD 20815
| | - Ashootosh Tripathi
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
- Natural Products Discovery Core, Life Sciences Institute, University of Michigan Ann Arbor, MI 48109
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Malini Raghavan
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109
| | - Bruce D Walker
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139
- Howard Hughes Medical Institute, Chevy Chase, MD 20815
| | - James H Hurley
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720
| | - David H Sherman
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109
| | - Kathleen L Collins
- Graduate Program in Immunology, University of Michigan, Ann Arbor, MI 48109;
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI 48109
- Cellular and Molecular Biology Graduate Program, University of Michigan, Ann Arbor, MI 48109
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16
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Staudt RP, Smithgall TE. Nef homodimers down-regulate SERINC5 by AP-2-mediated endocytosis to promote HIV-1 infectivity. J Biol Chem 2020; 295:15540-15552. [PMID: 32873704 DOI: 10.1074/jbc.ra120.014668] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 08/24/2020] [Indexed: 12/13/2022] Open
Abstract
SERINC5 is a multipass intrinsic membrane protein that suppresses HIV-1 infectivity when incorporated into budding virions. The HIV-1 Nef virulence factor prevents viral incorporation of SERINC5 by triggering its down-regulation from the producer cell membrane through an AP-2-dependent endolysosomal pathway. However, the mechanistic basis for SERINC5 down-regulation by Nef remains elusive. Here we demonstrate that Nef homodimers are important for SERINC5 down-regulation, trafficking to late endosomes, and exclusion from newly synthesized viral particles. Based on previous X-ray crystal structures, we mutated three conserved residues in the Nef dimer interface (Leu112, Tyr115, and Phe121) and demonstrated attenuated homodimer formation in a cell-based fluorescence complementation assay. Point mutations at each position reduced the infectivity of HIV-1 produced from transfected 293T cells, the Jurkat TAg T-cell line, and donor mononuclear cells in a SERINC5-dependent manner. In SERINC5-transfected 293T cells, virion incorporation of SERINC5 was increased by dimerization-defective Nef mutants, whereas down-regulation of SERINC5 from the membrane of transfected Jurkat cells by these mutants was significantly reduced. Nef dimer interface mutants also failed to trigger internalization of SERINC5 and localization to Rab7+ late endosomes in T cells. Importantly, fluorescence complementation assays demonstrated that dimerization-defective Nef mutants retained interaction with both SERINC5 and AP-2. These results show that down-regulation of SERINC5 and subsequent enhancement of viral infectivity require Nef homodimers and support a mechanism by which the Nef dimer bridges SERINC5 to AP-2 for endocytosis. Pharmacological disruption of Nef homodimers may control HIV-1 infectivity and viral spread by enhancing virion incorporation of SERINC5.
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Affiliation(s)
- Ryan P Staudt
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Thomas E Smithgall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, School of Medicine, Pittsburgh, Pennsylvania, USA.
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17
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Staudt RP, Alvarado JJ, Emert-Sedlak LA, Shi H, Shu ST, Wales TE, Engen JR, Smithgall TE. Structure, function, and inhibitor targeting of HIV-1 Nef-effector kinase complexes. J Biol Chem 2020; 295:15158-15171. [PMID: 32862141 DOI: 10.1074/jbc.rev120.012317] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/28/2020] [Indexed: 11/06/2022] Open
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.
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Affiliation(s)
- Ryan P Staudt
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - John J Alvarado
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Lori A Emert-Sedlak
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Haibin Shi
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Sherry T Shu
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, USA
| | - John R Engen
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, USA
| | - Thomas E Smithgall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.
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18
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Li WF, Aryal M, Shu ST, Smithgall TE. HIV-1 Nef dimers short-circuit immune receptor signaling by activating Tec-family kinases at the host cell membrane. J Biol Chem 2020; 295:5163-5174. [PMID: 32144207 DOI: 10.1074/jbc.ra120.012536] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 03/04/2020] [Indexed: 01/08/2023] Open
Abstract
The HIV-1 virulence factor Nef promotes high-titer viral replication, immune escape, and pathogenicity. Nef interacts with interleukin-2-inducible T-cell kinase (Itk) and Bruton's tyrosine kinase (Btk), two Tec-family kinases expressed in HIV-1 target cells (CD4 T cells and macrophages, respectively). Using a cell-based bimolecular fluorescence complementation assay, here we demonstrate that Nef recruits both Itk and Btk to the cell membrane and induces constitutive kinase activation in transfected 293T cells. Nef homodimerization-defective mutants retained their interaction with both kinases but failed to induce activation, supporting a role for Nef homodimer formation in the activation mechanism. HIV-1 infection up-regulates endogenous Itk activity in SupT1 T cells and donor-derived peripheral blood mononuclear cells. However, HIV-1 strains expressing Nef variants with mutations in the dimerization interface replicated poorly and were significantly attenuated in Itk activation. We conclude that direct activation of Itk and Btk by Nef at the membrane in HIV-infected cells may override normal immune receptor control of Tec-family kinase activity to enhance the viral life cycle.
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Affiliation(s)
- Wing Fai Li
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, Pennsylvania 15219
| | - Manish Aryal
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, Pennsylvania 15219
| | - Sherry T Shu
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, Pennsylvania 15219
| | - Thomas E Smithgall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, Pennsylvania 15219
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19
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Shi H, Tice CM, Emert-Sedlak L, Chen L, Li WF, Carlsen M, Wrobel JE, Reitz AB, Smithgall TE. Tight-Binding Hydroxypyrazole HIV-1 Nef Inhibitors Suppress Viral Replication in Donor Mononuclear Cells and Reverse Nef-Mediated MHC-I Downregulation. ACS Infect Dis 2020; 6:302-312. [PMID: 31775511 DOI: 10.1021/acsinfecdis.9b00382] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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.
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Affiliation(s)
- Haibin Shi
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Suite 523 Bridgeside Point II, 450 Technology Drive, Pittsburgh, Pennsylvania 15219, United States
| | - Colin M. Tice
- Fox Chase Chemical Diversity Center, Inc., Pennsylvania Biotechnology Center, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
| | - Lori Emert-Sedlak
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Suite 523 Bridgeside Point II, 450 Technology Drive, Pittsburgh, Pennsylvania 15219, United States
| | - Li Chen
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Suite 523 Bridgeside Point II, 450 Technology Drive, Pittsburgh, Pennsylvania 15219, United States
| | - Wing Fai Li
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Suite 523 Bridgeside Point II, 450 Technology Drive, Pittsburgh, Pennsylvania 15219, United States
| | - Marianne Carlsen
- Fox Chase Chemical Diversity Center, Inc., Pennsylvania Biotechnology Center, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
| | - Jay E. Wrobel
- Fox Chase Chemical Diversity Center, Inc., Pennsylvania Biotechnology Center, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
| | - Allen B. Reitz
- Fox Chase Chemical Diversity Center, Inc., Pennsylvania Biotechnology Center, 3805 Old Easton Road, Doylestown, Pennsylvania 18902, United States
| | - Thomas E. Smithgall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Suite 523 Bridgeside Point II, 450 Technology Drive, Pittsburgh, Pennsylvania 15219, United States
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20
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Liu B, Zhang X, Zhang W, Wu L, Jing S, Liu W, Xia B, Zou F, Lu L, Ma X, He D, Hu Q, Zhang Y, Deng K, Cai W, Tang X, Peng T, Zhang H, Li L. Lovastatin Inhibits HIV-1-Induced MHC-I Downregulation by Targeting Nef-AP-1 Complex Formation: A New Strategy to Boost Immune Eradication of HIV-1 Infected Cells. Front Immunol 2019; 10:2151. [PMID: 31572371 PMCID: PMC6749138 DOI: 10.3389/fimmu.2019.02151] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 08/27/2019] [Indexed: 01/05/2023] Open
Abstract
Current combined antiretroviral therapy (cART) mainly targets 3 of the 15 HIV proteins leaving many potential viral vulnerabilities unexploited. To purge the HIV-1 latent reservoir, various strategies including “shock and kill” have been developed. A key question is how to restore impaired immune surveillance. HIV-1 protein Nef has long been known to mediate the downregulation of cell-surface MHC-I and assist HIV-1 to evade the immune system. Through high throughput screening of Food and Drug Administration (FDA) approved drugs, we identified lovastatin, a statin drug, to significantly antagonize Nef to downregulate MHC-I, CD4, and SERINC5, and inhibit the intrinsic infectivity of virions. In addition, lovastatin boosted autologous CTLs to eradicate the infected cells and effectively inhibit the subsequent viral rebound in CD4+ T-lymphocytes isolated from HIV-1-infected individuals receiving suppressive cART. Furthermore, we found that lovastatin inhibits Nef-induced MHC-I downregulation by directly binding with Nef and disrupting the Nef–AP-1 complex. These results demonstrate that lovastatin is a promising agent for counteracting Nef-mediated downregulation of MHC-I, CD4, and SERINC5. Lovastatin could potentially be used in the clinic to enhance anti-HIV-1 immune surveillance.
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Affiliation(s)
- Bingfeng Liu
- Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Institute of Human Virology, Sun Yat-sen University, Guangzhou, China.,Department of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Xu Zhang
- Sino-French Hoffmann Institute, Guangzhou Medical University, Guangzhou, China
| | - Wanying Zhang
- Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Institute of Human Virology, Sun Yat-sen University, Guangzhou, China
| | - Liyang Wu
- Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Institute of Human Virology, Sun Yat-sen University, Guangzhou, China
| | - Shuliang Jing
- Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Institute of Human Virology, Sun Yat-sen University, Guangzhou, China
| | - Weiwei Liu
- Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Institute of Human Virology, Sun Yat-sen University, Guangzhou, China
| | - Baijin Xia
- Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Institute of Human Virology, Sun Yat-sen University, Guangzhou, China
| | - Fan Zou
- Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Institute of Human Virology, Sun Yat-sen University, Guangzhou, China.,Department of Molecular Therapy, Qianyang Biomedical Research Institute, Guangzhou, China.,Guangzhou Women and Children Hospital, Institute of Pediatrics, Guangzhou Medical University, Guangzhou, China
| | - Lijuan Lu
- Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Institute of Human Virology, Sun Yat-sen University, Guangzhou, China
| | - Xiancai Ma
- Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Institute of Human Virology, Sun Yat-sen University, Guangzhou, China
| | - Dalian He
- Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Institute of Human Virology, Sun Yat-sen University, Guangzhou, China
| | - Qifei Hu
- Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Institute of Human Virology, Sun Yat-sen University, Guangzhou, China.,Department of Molecular Therapy, Qianyang Biomedical Research Institute, Guangzhou, China
| | - Yiwen Zhang
- Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Institute of Human Virology, Sun Yat-sen University, Guangzhou, China
| | - Kai Deng
- Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Institute of Human Virology, Sun Yat-sen University, Guangzhou, China
| | - Weiping Cai
- Department of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Xiaoping Tang
- Department of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
| | - Tao Peng
- Sino-French Hoffmann Institute, Guangzhou Medical University, Guangzhou, China
| | - Hui Zhang
- Key Laboratory of Tropical Disease Control of Ministry of Education, Guangdong Engineering Research Center for Antimicrobial Agent and Immunotechnology, Zhongshan School of Medicine, Institute of Human Virology, Sun Yat-sen University, Guangzhou, China.,Department of Molecular Therapy, Qianyang Biomedical Research Institute, Guangzhou, China
| | - Linghua Li
- Department of Infectious Diseases, Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, China
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21
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Abstract
Latent viral reservoirs in long-living cell populations are the main obstacle to a cure of HIV/AIDS. HIV-1 latency is controlled by the activation status of infected cells and their ability to return to a resting phenotype associated with silencing of viral gene expression. These cellular features are not just determined by the host since HIV-1 has evolved sophisticated mechanisms to alter cellular activation and survival to its advantage. Especially the HIV-1 accessory proteins Nef and Vpu exert numerous activities to promote viral replication and immune evasion affecting the size and preservation of the viral reservoir. Here, we review how antagonistic and synergistic functions of Nef and Vpu might affect HIV-1 latency. We also discuss whether these two accessory factors represent suitable targets to improve the ‘shock and kill’ cure strategy.
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Affiliation(s)
- Dorota Kmiec
- Institute of Molecular Virology, ULM University Medical Center, Meyerhofstr 1, Ulm 89081, Germany
| | - Smitha Srinivasachar
- Institute of Molecular Virology, ULM University Medical Center, Meyerhofstr 1, Ulm 89081, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, ULM University Medical Center, Meyerhofstr 1, Ulm 89081, Germany
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22
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Wu M, Alvarado JJ, Augelli-Szafran CE, Ptak RG, Smithgall TE. A single β-octyl glucoside molecule induces HIV-1 Nef dimer formation in the absence of partner protein binding. PLoS One 2018; 13:e0192512. [PMID: 29415006 PMCID: PMC5802939 DOI: 10.1371/journal.pone.0192512] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 01/24/2018] [Indexed: 01/05/2023] Open
Abstract
The HIV-1 Nef accessory protein is essential for viral pathogenicity and AIDS progression. Nef forms complexes with multiple host cell factors to facilitate viral replication and promote immune escape of HIV-infected cells. Previous X-ray crystal structures demonstrate that Nef forms homodimers, the orientation of which are influenced by host cell binding partners. In cell-based fluorescence complementation assays, Nef forms homodimers at the plasma membrane. However, recombinant Nef proteins often exist as monomers in solution, suggesting that membrane interaction may also trigger monomer to dimer transitions. In this study, we show that monomeric Nef core proteins can be induced to form dimers in the presence of low concentrations of the non-ionic surfactant, β-octyl glucoside (βOG). X-ray crystallography revealed that a single βOG molecule is present in the Nef dimer, with the 8-carbon acyl chain of the ligand binding to a hydrophobic pocket formed by the dimer interface. This Nef-βOG dimer interface involves helix αB, as observed in previous dimer structures, as well as a helix formed by N-terminal residues 54-66. Nef dimer formation is stabilized in solution by the addition of βOG, providing biochemical validation for the crystal structure. These observations together suggest that the interaction with host cell lipid mediators or other hydrophobic ligands may play a role in Nef dimerization, which has been previously linked to multiple Nef functions including host cell protein kinase activation, CD4 downregulation, and enhancement of HIV-1 replication.
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Affiliation(s)
- Mousheng Wu
- Department of Chemistry, Drug Discovery Division, Southern Research Institute, Birmingham, AL, United States of America
| | - John J. Alvarado
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
| | - Corinne E. Augelli-Szafran
- Department of Chemistry, Drug Discovery Division, Southern Research Institute, Birmingham, AL, United States of America
| | - Roger G. Ptak
- Department of Infectious Disease Research, Southern Research Institute, Frederick, MD, United States of America
| | - Thomas E. Smithgall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States of America
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23
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Che Nordin MA, Teow SY. Review of Current Cell-Penetrating Antibody Developments for HIV-1 Therapy. Molecules 2018; 23:molecules23020335. [PMID: 29415435 PMCID: PMC6017373 DOI: 10.3390/molecules23020335] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 01/06/2018] [Accepted: 01/08/2018] [Indexed: 12/22/2022] Open
Abstract
The discovery of highly active antiretroviral therapy (HAART) in 1996 has significantly reduced the global mortality and morbidity caused by the acquired immunodeficiency syndrome (AIDS). However, the therapeutic strategy of HAART that targets multiple viral proteins may render off-target toxicity and more importantly results in drug-resistant escape mutants. These have been the main challenges for HAART and refinement of this therapeutic strategy is urgently needed. Antibody-mediated treatments are emerging therapeutic modalities for various diseases. Most therapeutic antibodies have been approved by Food and Drug Administration (FDA) mainly for targeting cancers. Previous studies have also demonstrated the promising effect of therapeutic antibodies against HIV-1, but there are several limitations in this therapy, particularly when the viral targets are intracellular proteins. The conventional antibodies do not cross the cell membrane, hence, the pathogenic intracellular proteins cannot be targeted with this classical therapeutic approach. Over the years, the advancement of antibody engineering has permitted the therapeutic antibodies to comprehensively target both extra- and intra-cellular proteins in various infections and diseases. This review aims to update on the current progress in the development of antibody-based treatment against intracellular targets in HIV-1 infection. We also attempt to highlight the challenges and limitations in the development of antibody-based therapeutic modalities against HIV-1.
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Affiliation(s)
- Muhamad Alif Che Nordin
- Kulliyyah of Medicine and Health Sciences (KMHS), Kolej Universiti INSANIAH, 09300 Kuala Ketil, Kedah, Malaysia.
| | - Sin-Yeang Teow
- Sunway Institute for Healthcare Development (SIHD), School of Healthcare and Medical Sciences (SHMS), Sunway University, Jalan Universiti, Bandar Sunway, 47500 Subang Jaya, Selangor Darul Ehsan, Malaysia.
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24
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Moroco JA, Alvarado JJ, Staudt RP, Shi H, Wales TE, Smithgall TE, Engen JR. Remodeling of HIV-1 Nef Structure by Src-Family Kinase Binding. J Mol Biol 2018; 430:310-321. [PMID: 29258818 PMCID: PMC5801098 DOI: 10.1016/j.jmb.2017.12.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 12/07/2017] [Accepted: 12/10/2017] [Indexed: 11/25/2022]
Abstract
The HIV-1 accessory protein Nef controls multiple aspects of the viral life cycle and host immune response, making it an attractive therapeutic target. Previous X-ray crystal structures of Nef in complex with key host cell binding partners have shed light on protein-protein interactions critical to Nef function. Crystal structures of Nef in complex with either the SH3 or tandem SH3-SH2 domains of Src-family kinases reveal distinct dimer conformations of Nef. However, the existence of these Nef dimer complexes in solution has not been established. Here we used hydrogen exchange mass spectrometry (HX MS) to compare the solution conformation of Nef alone and in complexes with the SH3 or the SH3-SH2 domains of the Src-family kinase Hck. HX MS revealed that interaction with the Hck SH3 or tandem SH3-SH2 domains induces protection of the Nef αB-helix from deuterium uptake, consistent with a role for αB in dimer formation. HX MS analysis of a Nef mutant (position Asp123, a site buried in the Nef:SH3 dimer but surface exposed in the Nef:SH3-SH2 complex), showed a Hck-induced conformational change in Nef relative to wild-type Nef. These results support a model in which Src-family kinase binding induces conformational changes in Nef to expose residues critical for interaction with the μ1 subunit of adaptor protein 1 and the major histocompatibility complex-1 tail, and subsequent major histocompatibility complex-1 downregulation and immune escape of HIV-infected cells required for functional interactions with downstream binding partners.
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Affiliation(s)
- Jamie A Moroco
- Department of Chemistry and Chemical Biology, Maildrop 412TF, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA.
| | - John Jeff Alvarado
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Bridgeside Point II, Suite 523, 450 Technology Drive, Pittsburgh, PA 15219, USA.
| | - Ryan P Staudt
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Bridgeside Point II, Suite 523, 450 Technology Drive, Pittsburgh, PA 15219, USA.
| | - Haibin Shi
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Bridgeside Point II, Suite 523, 450 Technology Drive, Pittsburgh, PA 15219, USA.
| | - Thomas E Wales
- Department of Chemistry and Chemical Biology, Maildrop 412TF, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA.
| | - Thomas E Smithgall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Bridgeside Point II, Suite 523, 450 Technology Drive, Pittsburgh, PA 15219, USA.
| | - John R Engen
- Department of Chemistry and Chemical Biology, Maildrop 412TF, Northeastern University, 360 Huntington Avenue, Boston, MA 02115, USA.
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25
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Mujib S, Saiyed A, Fadel S, Bozorgzad A, Aidarus N, Yue FY, Benko E, Kovacs C, Emert-Sedlak LA, Smithgall TE, Ostrowski MA. Pharmacologic HIV-1 Nef blockade promotes CD8 T cell-mediated elimination of latently HIV-1-infected cells in vitro. JCI Insight 2017; 2:93684. [PMID: 28878119 PMCID: PMC5621880 DOI: 10.1172/jci.insight.93684] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 07/25/2017] [Indexed: 12/16/2022] Open
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.
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Affiliation(s)
- Shariq Mujib
- Institute of Medical Science (IMS), Department of Medicine, and
| | - Aamir Saiyed
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Saleh Fadel
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Ardalan Bozorgzad
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Nasra Aidarus
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Feng Yun Yue
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Erika Benko
- Maple Leaf Medical Clinic, Toronto, Ontario, Canada
| | - Colin Kovacs
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
- Maple Leaf Medical Clinic, Toronto, Ontario, Canada
| | - Lori A. Emert-Sedlak
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Thomas E. Smithgall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Mario A. Ostrowski
- Institute of Medical Science (IMS), Department of Medicine, and
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
- Keenan Research Centre for Biomedical Science of St. Michael’s Hospital, Toronto, Ontario, Canada
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26
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Shu ST, Emert-Sedlak LA, Smithgall TE. Cell-based Fluorescence Complementation Reveals a Role for HIV-1 Nef Protein Dimerization in AP-2 Adaptor Recruitment and CD4 Co-receptor Down-regulation. J Biol Chem 2016; 292:2670-2678. [PMID: 28031466 DOI: 10.1074/jbc.m116.770016] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 12/21/2016] [Indexed: 02/03/2023] Open
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.
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Affiliation(s)
- Sherry T Shu
- From the Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15219
| | - Lori A Emert-Sedlak
- From the Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15219
| | - Thomas E Smithgall
- From the Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15219
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27
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Identification of Binding Mode and Prospective Structural Features of Novel Nef Protein Inhibitors as Potential Anti-HIV Drugs. Cell Biochem Biophys 2016; 75:49-64. [DOI: 10.1007/s12013-016-0774-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 11/28/2016] [Indexed: 12/16/2022]
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28
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Liang H, Ruan H, Ouyang Q, Lai L. Herb-target interaction network analysis helps to disclose molecular mechanism of traditional Chinese medicine. Sci Rep 2016; 6:36767. [PMID: 27833111 PMCID: PMC5105066 DOI: 10.1038/srep36767] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 10/20/2016] [Indexed: 12/15/2022] Open
Abstract
Though many studies have been performed to elucidate molecular mechanism of traditional Chinese medicines (TCMs) by identifying protein-compound interactions, no systematic analysis at herb level was reported. TCMs are prescribed by herbs and all compounds from a certain herb should be considered as a whole, thus studies at herb level may provide comprehensive understanding of TCMs. Here, we proposed a computational strategy to study molecular mechanism of TCM at herb level and used it to analyze a TCM anti-HIV formula. Herb-target network analysis was carried out between 17 HIV-related proteins and SH formula as well as three control groups based on systematic docking. Inhibitory herbs were identified and active compounds enrichment was found to contribute to the therapeutic effectiveness of herbs. Our study demonstrates that computational analysis of TCMs at herb level can catch the rationale of TCM formulation and serve as guidance for novel TCM formula design.
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Affiliation(s)
- Hao Liang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Hao Ruan
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Qi Ouyang
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China.,State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, China.,Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Luhua Lai
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China.,Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China.,State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, School of Physics, Peking University, Beijing 100871, China.,Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
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29
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Roberts JM, Tarafdar S, Joseph RE, Andreotti AH, Smithgall TE, Engen JR, Wales TE. Dynamics of the Tec-family tyrosine kinase SH3 domains. Protein Sci 2016; 25:852-64. [PMID: 26808198 DOI: 10.1002/pro.2887] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Revised: 01/13/2016] [Accepted: 01/19/2016] [Indexed: 11/10/2022]
Abstract
The Src Homology 3 (SH3) domain is an important regulatory domain found in many signaling proteins. X-ray crystallography and NMR structures of SH3 domains are generally conserved but other studies indicate that protein flexibility and dynamics are not. We previously reported that based on hydrogen exchange mass spectrometry (HX MS) studies, there is variable flexibility and dynamics among the SH3 domains of the Src-family tyrosine kinases and related proteins. Here we have extended our studies to the SH3 domains of the Tec family tyrosine kinases (Itk, Btk, Tec, Txk, Bmx). The SH3 domains of members of this family augment the variety in dynamics observed in previous SH3 domains. Txk and Bmx SH3 were found to be highly dynamic in solution by HX MS and Bmx was unstructured by NMR. Itk and Btk SH3 underwent a clear EX1 cooperative unfolding event, which was localized using pepsin digestion and mass spectrometry after hydrogen exchange labeling. The unfolding was localized to peptide regions that had been previously identified in the Src-family and related protein SH3 domains, yet the kinetics of unfolding were not. Sequence alignment does not provide an easy explanation for the observed dynamics behavior, yet the similarity of location of EX1 unfolding suggests that higher-order structural properties may play a role. While the exact reason for such dynamics is not clear, such motions can be exploited in intra- and intermolecular binding assays of proteins containing the domains.
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Affiliation(s)
- Justin M Roberts
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, Massachusetts, 02115
| | - Sreya Tarafdar
- Department of Microbiology & Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, 15219
| | - Raji E Joseph
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, Iowa, 50011
| | - Amy H Andreotti
- Roy J. Carver Department of Biochemistry, Biophysics & Molecular Biology, Iowa State University, Ames, Iowa, 50011
| | - Thomas E Smithgall
- Department of Microbiology & Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, 15219
| | - John R Engen
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, Massachusetts, 02115
| | - Thomas E Wales
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, Massachusetts, 02115
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30
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Synthesis and evaluation of orally active small molecule HIV-1 Nef antagonists. Bioorg Med Chem Lett 2016; 26:1480-1484. [PMID: 26852364 DOI: 10.1016/j.bmcl.2016.01.043] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 01/13/2016] [Accepted: 01/15/2016] [Indexed: 01/31/2023]
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.
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31
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Kidd BA, Wroblewska A, Boland MR, Agudo J, Merad M, Tatonetti NP, Brown BD, Dudley JT. Mapping the effects of drugs on the immune system. Nat Biotechnol 2015; 34:47-54. [PMID: 26619012 PMCID: PMC4706827 DOI: 10.1038/nbt.3367] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2015] [Accepted: 08/11/2015] [Indexed: 11/18/2022]
Abstract
Understanding how drugs affect the immune system has consequences for treating disease and minimizing unwanted side effects. Here we present an integrative computational approach for predicting interactions between drugs and immune cells in a system-wide manner. The approach matches gene sets between transcriptional signatures to determine their similarity. We apply the method to model the interactions between 1,309 drugs and 221 immune cell types and predict 69,995 known and novel interactions. The resulting immune-cell pharmacology map is used to predict how 5 drugs influence 4 immune cell types in humans and mice. To validate the predictions, we analyzed patient records and examined cell population changes from in vivo experiments. Our method offers a tool for screening thousands of interactions to identify relationships between drugs and the immune system.
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Affiliation(s)
- Brian A Kidd
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Aleksandra Wroblewska
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Mary R Boland
- Department of Biomedical Informatics, Systems Biology and Medicine, Columbia University Medical Center, New York, New York, USA
| | - Judith Agudo
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Miriam Merad
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Nicholas P Tatonetti
- Department of Biomedical Informatics, Systems Biology and Medicine, Columbia University Medical Center, New York, New York, USA
| | - Brian D Brown
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Joel T Dudley
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.,Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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32
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Wales TE, Hochrein JM, Morgan CR, Emert-Sedlak LA, Smithgall TE, Engen JR. Subtle Dynamic Changes Accompany Hck Activation by HIV-1 Nef and are Reversed by an Antiretroviral Kinase Inhibitor. Biochemistry 2015; 54:6382-91. [PMID: 26440750 PMCID: PMC4615603 DOI: 10.1021/acs.biochem.5b00875] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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.
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Affiliation(s)
- Thomas E. Wales
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA 02115
| | - James M. Hochrein
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA 02115
| | - Christopher R. Morgan
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA 02115
| | - Lori A. Emert-Sedlak
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219
| | - Thomas E. Smithgall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219
| | - John R. Engen
- Department of Chemistry & Chemical Biology, Northeastern University, Boston, MA 02115
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Vérollet C, Le Cabec V, Maridonneau-Parini I. HIV-1 Infection of T Lymphocytes and Macrophages Affects Their Migration via Nef. Front Immunol 2015; 6:514. [PMID: 26500651 PMCID: PMC4594015 DOI: 10.3389/fimmu.2015.00514] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 09/22/2015] [Indexed: 12/17/2022] Open
Abstract
The human immunodeficiency virus (HIV-1) disseminates in the body and is found in several organs and tissues. Although HIV-1 mainly targets both CD4+ T lymphocytes and macrophages, it has contrasting effects between these cell populations. HIV-1 infection namely reduces the viability of CD4+ T cells, whereas infected macrophages are long-lived. In addition, the migration of T cells is reduced by the infection, whereas HIV-1 differentially modulates the migration modes of macrophages. In 2-dimensions (2D) assays, infected macrophages are less motile compared to the control counterparts. In 3D environments, macrophages use two migration modes that are dependent on the matrix architecture: amoeboid and mesenchymal migration. HIV-1-infected macrophages exhibit a reduced amoeboid migration but an enhanced mesenchymal migration, via the viral protein Nef. Indeed, the mesenchymal migration involves podosomes, and Nef stabilizes these cell structures through the activation of the tyrosine kinase Hck, which in turn phosphorylates the Wiskott–Aldrich syndrome protein (WASP). WASP is a key player in actin remodeling and cell migration. The reprogramed motility of infected macrophages observed in vitro correlates in vivo with enhanced macrophage infiltration in experimental tumors in Nef-transgenic mice compared to control mice. In conclusion, HIV infection of host target cells modifies their migration capacity; we infer that HIV-1 enhances virus spreading in confined environments by reducing T cells migration, and facilitates virus dissemination into different organs and tissues of the human body by enhancing macrophage mesenchymal migration.
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Affiliation(s)
- Christel Vérollet
- CNRS UMR 5089, Institut de Pharmacologie et de Biologie Structurale (IPBS) , Toulouse , France ; Institut de Pharmacologie et de Biologie Structurale (IPBS), Université Toulouse III - Paul Sabatier , Toulouse , France
| | - Véronique Le Cabec
- CNRS UMR 5089, Institut de Pharmacologie et de Biologie Structurale (IPBS) , Toulouse , France ; Institut de Pharmacologie et de Biologie Structurale (IPBS), Université Toulouse III - Paul Sabatier , Toulouse , France
| | - Isabelle Maridonneau-Parini
- CNRS UMR 5089, Institut de Pharmacologie et de Biologie Structurale (IPBS) , Toulouse , France ; Institut de Pharmacologie et de Biologie Structurale (IPBS), Université Toulouse III - Paul Sabatier , Toulouse , France
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Engineering and Validation of a Vector for Concomitant Expression of Rare Transfer RNA (tRNA) and HIV-1 nef Genes in Escherichia coli. PLoS One 2015; 10:e0130446. [PMID: 26147991 PMCID: PMC4492947 DOI: 10.1371/journal.pone.0130446] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Accepted: 05/20/2015] [Indexed: 11/19/2022] Open
Abstract
Relative ease in handling and manipulation of Escherichia coli strains make them primary candidate to express proteins heterologously. Overexpression of heterologous genes that contain codons infrequently used by E. coli is related with difficulties such as mRNA instability, early termination of transcription and/or translation, deletions and/or misincorporation, and cell growth inhibition. These codon bias -associated problems are addressed by co-expressing ColE1-compatible, rare tRNA expressing helper plasmids. However, this approach has inadequacies, which we have addressed by engineering an expression vector that concomitantly expresses the heterologous protein of interest, and rare tRNA genes in E. coli. The expression vector contains three (argU, ileY, leuW) rare tRNA genes and a useful multiple cloning site for easy in-frame cloning. To maintain the overall size of the parental plasmid vector, the rare tRNA genes replaced the non-essential DNA segments in the vector. The cloned gene is expressed under the control of T7 promoter and resulting recombinant protein has a C-terminal 6His tag for IMAC-mediated purification. We have evaluated the usefulness of this expression vector by expressing three HIV-1 genes namely HIV-1 p27 (nef), HIV-1 p24 (ca), and HIV-1 vif in NiCo21(DE3) E.coli and demonstrated the advantages of using expression vector that concomitantly expresses rare tRNA and heterologous genes.
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Pawlak EN, Dikeakos JD. HIV-1 Nef: a master manipulator of the membrane trafficking machinery mediating immune evasion. Biochim Biophys Acta Gen Subj 2015; 1850:733-41. [PMID: 25585010 DOI: 10.1016/j.bbagen.2015.01.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 12/09/2014] [Accepted: 01/06/2015] [Indexed: 11/25/2022]
Abstract
BACKGROUND Many viral genomes encode a limited number of proteins, illustrating their innate efficiency in bypassing host immune surveillance. This concept of genomic efficiency is exemplified by the 9 kb RNA genome of human immunodeficiency virus 1 (HIV-1), encoding 15 proteins sub-divided according to function. The enzymatic group includes proteins such as the drug targets reverse transcriptase and protease. In contrast, the accessory proteins lack any known enzymatic or structural function, yet are essential for viral fitness and HIV-1 pathogenesis. Of these, the HIV-1 accessory protein Nef is a master manipulator of host cellular processes, ensuring efficient counterattack against the host immune response, as well as long-term evasion of immune surveillance. In particular, the ability of Nef to downmodulate major histocompatibility complex class I (MHC-I) is a key cellular event that enables HIV-1 to bypass the host's defenses by evading the adaptive immune response. SCOPE OF REVIEW In this article, we briefly review how various pathogenic viruses control cell-surface MHC-I, and then focus on the mechanisms and implications of HIV-1 Nef-mediated MHC-I downregulation via modulation of the host membrane trafficking machinery. CONCLUSION The extensive interaction network formed between Nef and numerous membrane trafficking regulators suggests that Nef's role in evading the immune surveillance system intersects multiple host membrane trafficking pathways. SIGNIFICANCE Nef's ability to evade the immune surveillance system is linked to AIDS pathogenesis. Thus, a complete understanding of the molecular pathways that are subverted by Nef in order to downregulate MHC-I will enhance our understanding of HIV-1's progression to AIDS.
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Affiliation(s)
- Emily N Pawlak
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, Ontario, Canada, N6A 5C1
| | - Jimmy D Dikeakos
- Department of Microbiology and Immunology, Schulich School of Medicine and Dentistry, The University of Western Ontario, London, Ontario, Canada, N6A 5C1.
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Moroco JA, Baumgartner MP, Rust HL, Choi HG, Hur W, Gray NS, Camacho CJ, Smithgall TE. A Discovery Strategy for Selective Inhibitors of c-Src in Complex with the Focal Adhesion Kinase SH3/SH2-binding Region. Chem Biol Drug Des 2014; 86:144-55. [PMID: 25376742 DOI: 10.1111/cbdd.12473] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Revised: 09/29/2014] [Accepted: 10/29/2014] [Indexed: 11/30/2022]
Abstract
The c-Src tyrosine kinase co-operates with the focal adhesion kinase to regulate cell adhesion and motility. Focal adhesion kinase engages the regulatory SH3 and SH2 domains of c-Src, resulting in localized kinase activation that contributes to tumor cell metastasis. Using assay conditions where c-Src kinase activity required binding to a tyrosine phosphopeptide based on the focal adhesion kinase SH3-SH2 docking sequence, we screened a kinase-biased library for selective inhibitors of the Src/focal adhesion kinase peptide complex versus c-Src alone. This approach identified an aminopyrimidinyl carbamate compound, WH-4-124-2, with nanomolar inhibitory potency and fivefold selectivity for c-Src when bound to the phospho-focal adhesion kinase peptide. Molecular docking studies indicate that WH-4-124-2 may preferentially inhibit the 'DFG-out' conformation of the kinase active site. These findings suggest that interaction of c-Src with focal adhesion kinase induces a unique kinase domain conformation amenable to selective inhibition.
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Affiliation(s)
- Jamie A Moroco
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA, 15219, USA
| | - Matthew P Baumgartner
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA, 15260, USA
| | - Heather L Rust
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA, 15219, USA
| | - Hwan Geun Choi
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School , 250 Longwood Avenue, Boston, MA, 02115, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, 250 Longwood Avenue, Boston, MA, 02115, USA
| | - Wooyoung Hur
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School , 250 Longwood Avenue, Boston, MA, 02115, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, 250 Longwood Avenue, Boston, MA, 02115, USA
| | - Nathanael S Gray
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School , 250 Longwood Avenue, Boston, MA, 02115, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, 250 Longwood Avenue, Boston, MA, 02115, USA
| | - Carlos J Camacho
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, PA, 15260, USA
| | - Thomas E Smithgall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 450 Technology Drive, Pittsburgh, PA, 15219, USA
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Moonsamy S, Bhakat S, Soliman MES. Dynamic features of apo and bound HIV-Nef protein reveal the anti-HIV dimerization inhibition mechanism. J Recept Signal Transduct Res 2014; 35:346-56. [DOI: 10.3109/10799893.2014.984310] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Smithgall TE, Thomas G. Small molecule inhibitors of the HIV-1 virulence factor, Nef. DRUG DISCOVERY TODAY. TECHNOLOGIES 2014; 10:e523-9. [PMID: 24451644 DOI: 10.1016/j.ddtec.2013.07.002] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Although antiretroviral therapy has revolutionized the clinical management of AIDS, life-long treatment is required because these drugs do not eradicate HIV- infected cells. Chronic antiretroviral therapy may not protect AIDS patients from cognitive impairment, raising important quality of life issues. Because of the rise of HIV strains resistant to current drugs and uncertain vaccine prospects, an urgent need exists for the discovery and development of new therapeutic approaches. This review is focused on one such approach, which involves targeting HIV-1 Nef, a viral accessory protein essential for AIDS pathogenesis.
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Alvarado JJ, Tarafdar S, Yeh JI, Smithgall TE. Interaction with the Src homology (SH3-SH2) region of the Src-family kinase Hck structures the HIV-1 Nef dimer for kinase activation and effector recruitment. J Biol Chem 2014; 289:28539-53. [PMID: 25122770 DOI: 10.1074/jbc.m114.600031] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
HIV-1 Nef supports high titer viral replication in vivo and is essential for AIDS progression. Nef function depends on interactions with multiple host cell effectors, including Hck and other Src-family kinases. Here we describe the x-ray crystal structure of Nef in complex with the Hck SH3-SH2 regulatory region to a resolution of 1.86 Å. The complex crystallized as a dimer of complexes, with the conserved Nef PXXPXR motif engaging the Hck SH3 domain. A new intercomplex contact was found between SH3 Glu-93, and Nef Arg-105. Mutagenesis of Hck SH3 Glu-93 interfered with Nef·Hck complex formation and kinase activation in cells. The Hck SH2 domains impinge on the N-terminal region of Nef to stabilize a dimer conformation that exposes Asp-123, a residue critical for Nef function. Our results suggest that in addition to serving as a kinase effector for Nef, Hck binding may reorganize the Nef dimer for functional interaction with other signaling partners.
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Affiliation(s)
- John Jeff Alvarado
- From the Departments of Microbiology and Molecular Genetics and Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15219 and
| | - Sreya Tarafdar
- From the Departments of Microbiology and Molecular Genetics and Department of Infectious Diseases and Microbiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania 15261
| | - Joanne I Yeh
- Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15219 and
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Rathinam NK, Saravanan C, Parimal P, Perumal V, Perumal M. Molecular interactions of graphene with HIV-Vpr, Nef and Gag proteins: A new approach for treating HIV infections. KOREAN J CHEM ENG 2014. [DOI: 10.1007/s11814-014-0049-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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41
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Tarafdar S, Poe JA, Smithgall TE. The accessory factor Nef links HIV-1 to Tec/Btk kinases in an Src homology 3 domain-dependent manner. J Biol Chem 2014; 289:15718-28. [PMID: 24722985 DOI: 10.1074/jbc.m114.572099] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The HIV-1 Nef virulence factor interacts with multiple host cell-signaling proteins. Nef binds to the Src homology 3 domains of Src family kinases, resulting in kinase activation important for viral infectivity, replication, and MHC-I down-regulation. Itk and other Tec family kinases are also present in HIV target cells, and Itk has been linked to HIV-1 infectivity and replication. However, the molecular mechanism linking Itk to HIV-1 is unknown. In this study, we explored the interaction of Nef with Tec family kinases using a cell-based bimolecular fluorescence complementation assay. In this approach, interaction of Nef with a partner kinase juxtaposes nonfluorescent YFP fragments fused to the C terminus of each protein, resulting in YFP complementation and a bright fluorescent signal. Using bimolecular fluorescence complementation, we observed that Nef interacts with the Tec family members Bmx, Btk, and Itk but not Tec or Txk. Interaction with Nef occurs through the kinase Src homology 3 domains and localizes to the plasma membrane. Allelic variants of Nef from all major HIV-1 subtypes interacted strongly with Itk in this assay, demonstrating the highly conserved nature of this interaction. A selective small molecule inhibitor of Itk kinase activity (BMS-509744) potently blocked wild-type HIV-1 infectivity and replication, but not that of a Nef-defective mutant. Nef induced constitutive Itk activation in transfected cells that was sensitive to inhibitor treatment. Taken together, these results provide the first evidence that Nef interacts with cytoplasmic tyrosine kinases of the Tec family and suggest that Nef provides a mechanistic link between HIV-1 and Itk signaling in the viral life cycle.
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Affiliation(s)
- Sreya Tarafdar
- From the Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15219 and the Department of Infectious Diseases and Microbiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pennsylvania 15261
| | - Jerrod A Poe
- From the Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15219 and
| | - Thomas E Smithgall
- From the Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15219 and
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42
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Iyer PC, Zhao J, Emert-Sedlak LA, Moore KK, Smithgall TE, Day BW. Synthesis and structure-activity analysis of diphenylpyrazolodiazene inhibitors of the HIV-1 Nef virulence factor. Bioorg Med Chem Lett 2014; 24:1702-6. [PMID: 24650642 DOI: 10.1016/j.bmcl.2014.02.045] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Revised: 02/12/2014] [Accepted: 02/18/2014] [Indexed: 10/25/2022]
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.
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Affiliation(s)
- Prema C Iyer
- Department of Pharmaceutical Sciences, University of Pittsburgh School of Pharmacy, Pittsburgh, PA 15261, USA; University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA 15261, USA
| | - Jielu Zhao
- Department of Pharmaceutical Sciences, University of Pittsburgh School of Pharmacy, Pittsburgh, PA 15261, USA; University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA 15261, USA
| | - Lori A Emert-Sedlak
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Bridgeside Point II, Suite 523, 450 Technology Drive, Pittsburgh, PA 15219, USA
| | - Kerry K Moore
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Thomas E Smithgall
- University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA 15261, USA; Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Bridgeside Point II, Suite 523, 450 Technology Drive, Pittsburgh, PA 15219, USA.
| | - Billy W Day
- Department of Pharmaceutical Sciences, University of Pittsburgh School of Pharmacy, Pittsburgh, PA 15261, USA; University of Pittsburgh Drug Discovery Institute, Pittsburgh, PA 15261, USA; Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, USA
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Poe JA, Vollmer L, Vogt A, Smithgall TE. Development and validation of a high-content bimolecular fluorescence complementation assay for small-molecule inhibitors of HIV-1 Nef dimerization. ACTA ACUST UNITED AC 2013; 19:556-65. [PMID: 24282155 DOI: 10.1177/1087057113513640] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Nef is a human immunodeficiency virus 1 (HIV-1) accessory factor essential for viral pathogenesis and AIDS progression. Many Nef functions require dimerization, and small molecules that block Nef dimerization may represent antiretroviral drug leads. Here we describe a cell-based assay for Nef dimerization inhibitors based on bimolecular fluorescence complementation (BiFC). Nef was fused to nonfluorescent, complementary fragments of yellow fluorescent protein (YFP) and coexpressed in the same cell population. Dimerization of Nef resulted in juxtaposition of the YFP fragments and reconstitution of the fluorophore. For automation, the Nef-YFP fusion proteins plus a monomeric red fluorescent protein (mRFP) reporter were expressed from a single vector, separated by picornavirus "2A" linker peptides to permit equivalent translation of all three proteins. Validation studies revealed a critical role for gating on the mRFP-positive subpopulation of transfected cells, as well as use of the mRFP signal to normalize the Nef-BiFC signal. Nef-BiFC/mRFP ratios resulting from cells expressing wild-type versus dimerization-defective Nef were very clearly separated, with Z factors consistently in the 0.6 to 0.7 range. A fully automated pilot screen of the National Cancer Institute Diversity Set III identified several hit compounds that reproducibly blocked Nef dimerization in the low micromolar range. This BiFC-based assay has the potential to identify cell-active small molecules that directly interfere with Nef dimerization and function.
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Affiliation(s)
- Jerrod A Poe
- 1Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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44
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Trible RP, Narute P, Emert-Sedlak LA, Alvarado JJ, Atkins K, Thomas L, Kodama T, Yanamala N, Korotchenko V, Day BW, Thomas G, Smithgall TE. Discovery of a diaminoquinoxaline benzenesulfonamide antagonist of HIV-1 Nef function using a yeast-based phenotypic screen. Retrovirology 2013; 10:135. [PMID: 24229420 PMCID: PMC3874621 DOI: 10.1186/1742-4690-10-135] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Accepted: 10/31/2013] [Indexed: 11/10/2022] Open
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.
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Affiliation(s)
- Ronald P Trible
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Bridgeside Point II, Suite 523, 15219, Pittsburgh, PA USA
| | - Purushottam Narute
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Bridgeside Point II, Suite 523, 15219, Pittsburgh, PA USA
| | - Lori A Emert-Sedlak
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Bridgeside Point II, Suite 523, 15219, Pittsburgh, PA USA
| | - John Jeff Alvarado
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Bridgeside Point II, Suite 523, 15219, Pittsburgh, PA USA
| | - Katelyn Atkins
- School of Medicine, Oregon Health and Science University, 97239, Portland, OR, USA
| | - Laurel Thomas
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Bridgeside Point II, Suite 523, 15219, Pittsburgh, PA USA
| | - Toshiaki Kodama
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Bridgeside Point II, Suite 523, 15219, Pittsburgh, PA USA
| | - Naveena Yanamala
- Department of Structural Biology, University of Pittsburgh School of Medicine, 15261, Pittsburgh, PA USA
| | - Vasiliy Korotchenko
- Department of Pharmaceutical Sciences, University of Pittsburgh School of Pharmacy, 15261, Pittsburgh, PA USA
| | - Billy W Day
- Department of Pharmaceutical Sciences, University of Pittsburgh School of Pharmacy, 15261, Pittsburgh, PA USA
| | - Gary Thomas
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Bridgeside Point II, Suite 523, 15219, Pittsburgh, PA USA
| | - Thomas E Smithgall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Bridgeside Point II, Suite 523, 15219, Pittsburgh, PA USA
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Perrone R, Nadai M, Poe JA, Frasson I, Palumbo M, Palù G, Smithgall TE, Richter SN. Formation of a unique cluster of G-quadruplex structures in the HIV-1 Nef coding region: implications for antiviral activity. PLoS One 2013; 8:e73121. [PMID: 24015290 PMCID: PMC3754912 DOI: 10.1371/journal.pone.0073121] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 07/24/2013] [Indexed: 01/10/2023] Open
Abstract
G-quadruplexes are tetraplex structures of nucleic acids that can form in G-rich sequences. Their presence and functional role have been established in telomeres, oncogene promoters and coding regions of the human chromosome. In particular, they have been proposed to be directly involved in gene regulation at the level of transcription. Because the HIV-1 Nef protein is a fundamental factor for efficient viral replication, infectivity and pathogenesis in vitro and in vivo, we investigated G-quadruplex formation in the HIV-1 nef gene to assess the potential for viral inhibition through G-quadruplex stabilization. A comprehensive computational analysis of the nef coding region of available strains showed the presence of three conserved sequences that were uniquely clustered. Biophysical testing proved that G-quadruplex conformations were efficiently stabilized or induced by G-quadruplex ligands in all three sequences. Upon incubation with a G-quadruplex ligand, Nef expression was reduced in a reporter gene assay and Nef-dependent enhancement of HIV-1 infectivity was significantly repressed in an antiviral assay. These data constitute the first evidence of the possibility to regulate HIV-1 gene expression and infectivity through G-quadruplex targeting and therefore open a new avenue for viral treatment.
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Affiliation(s)
- Rosalba Perrone
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Matteo Nadai
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Jerrod A. Poe
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Ilaria Frasson
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Manlio Palumbo
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Padua, Italy
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Thomas E. Smithgall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America
| | - Sara N. Richter
- Department of Molecular Medicine, University of Padua, Padua, Italy
- * E-mail:
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Witkowski W, Verhasselt B. Contributions of HIV-1 Nef to immune dysregulation in HIV-infected patients: a therapeutic target? Expert Opin Ther Targets 2013; 17:1345-56. [PMID: 23967871 DOI: 10.1517/14728222.2013.830712] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION HIV accessory protein Nef is a factor responsible for many of the viral pathogenic effects. Progression to AIDS is dramatically delayed and in some well-documented cases completely abolished on infection with naturally occurring HIV strains lacking intact nef sequences in their genomes. The topic of this review is the contribution of Nef to the immune pathology as a possible target in HIV-infected patients. AREAS COVERED An overview of known Nef functions accounting for its role in pathogenesis is presented, emphasizing interactions with dendritic cells and macrophages, and Nef-induced exosome secretion, all involved in immune dysregulation during the course of HIV infection. Current approaches to Nef inhibition by different classes of compounds are reviewed. EXPERT OPINION Blocking Nef for therapeutic purposes is a challenging endeavor mainly due to intrinsic properties of this HIV accessory protein. Nef has multiple interfaces to interact with host proteins and lacks a catalytic domain. Potential benefits arising from the development of successful inhibitors could however prove beneficial for reducing gradual deterioration of immune system in chronically infected patients in absence of functional cure.
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Affiliation(s)
- Wojciech Witkowski
- Department of Clinical Chemistry, Microbiology and Immunology of Ghent University , Gent , Belgium +32 93323658 ; +32 93323659 ;
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Perrone R, Nadai M, Frasson I, Poe JA, Butovskaya E, Smithgall TE, Palumbo M, Palù G, Richter SN. A dynamic G-quadruplex region regulates the HIV-1 long terminal repeat promoter. J Med Chem 2013; 56:6521-30. [PMID: 23865750 DOI: 10.1021/jm400914r] [Citation(s) in RCA: 140] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
G-Quadruplexes, noncanonical nucleic acid structures, act as silencers in the promoter regions of human genes; putative G-quadruplex forming sequences are also present in promoters of other mammals, yeasts, and prokaryotes. Here we show that also the HIV-1 LTR promoter exploits G-quadruplex-mediated transcriptional regulation with striking similarities to eukaryotic promoters and that treatment with a G-quadruplex ligand inhibits HIV-1 infectivity. Computational analysis on 953 HIV-1 strains substantiated a highly conserved G-rich sequence corresponding to Sp1 and NF-κB binding sites. Biophysical/biochemical analysis proved that two mutually exclusive parallel-like intramolecular G-quadruplexes, stabilized by small molecule ligands, primarily fold in this region. Mutations disrupting G-quadruplex formation enhanced HIV promoter activity in cells, whereas treatment with a G-quadruplex ligand impaired promoter activity and displayed antiviral effects. These findings disclose the possibility of inhibiting the HIV-1 LTR promoter by G-quadruplex-interacting small molecules, providing a new pathway to development of anti-HIV-1 drugs with unprecedented mechanism of action.
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Affiliation(s)
- Rosalba Perrone
- Department of Molecular Medicine, University of Padua, Italy
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