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McFadden WM, Casey-Moore MC, Bare GAL, Kirby KA, Wen X, Li G, Wang H, Slack RL, Snyder AA, Lorson ZC, Kaufman IL, Cilento ME, Tedbury PR, Gembicky M, Olson AJ, Torbett BE, Sharpless KB, Sarafianos SG. Identification of clickable HIV-1 capsid-targeting probes for viral replication inhibition. Cell Chem Biol 2024; 31:477-486.e7. [PMID: 38518746 DOI: 10.1016/j.chembiol.2024.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 12/15/2023] [Accepted: 02/27/2024] [Indexed: 03/24/2024]
Abstract
Of the targets for HIV-1 therapeutics, the capsid core is a relatively unexploited but alluring drug target due to its indispensable roles throughout virus replication. Because of this, we aimed to identify "clickable" covalent modifiers of the HIV-1 capsid protein (CA) for future functionalization. We screened a library of fluorosulfate compounds that can undergo sulfur(VI) fluoride exchange (SuFEx) reactions, and five compounds were identified as hits. These molecules were further characterized for antiviral effects. Several compounds impacted in vitro capsid assembly. One compound, BBS-103, covalently bound CA via a SuFEx reaction to Tyr145 and had antiviral activity in cell-based assays by perturbing virus production, but not uncoating. The covalent binding of compounds that target the HIV-1 capsid could aid in the future design of antiretroviral drugs or chemical probes that will help study aspects of HIV-1 replication.
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Affiliation(s)
- William M McFadden
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, 1760 Haygood Drive NE, Atlanta, GA 30322, USA; Children's Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Mary C Casey-Moore
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA; Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO 65212, USA
| | - Grant A L Bare
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Karen A Kirby
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, 1760 Haygood Drive NE, Atlanta, GA 30322, USA; Children's Healthcare of Atlanta, Atlanta, GA 30322, USA; Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA; Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO 65212, USA
| | - Xin Wen
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, 1760 Haygood Drive NE, Atlanta, GA 30322, USA; Children's Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Gencheng Li
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hua Wang
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Ryan L Slack
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, 1760 Haygood Drive NE, Atlanta, GA 30322, USA; Children's Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Alexa A Snyder
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, 1760 Haygood Drive NE, Atlanta, GA 30322, USA; Children's Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Zachary C Lorson
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, 1760 Haygood Drive NE, Atlanta, GA 30322, USA; Children's Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Isabella L Kaufman
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, 1760 Haygood Drive NE, Atlanta, GA 30322, USA; Children's Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Maria E Cilento
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, 1760 Haygood Drive NE, Atlanta, GA 30322, USA; Children's Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Philip R Tedbury
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, 1760 Haygood Drive NE, Atlanta, GA 30322, USA; Children's Healthcare of Atlanta, Atlanta, GA 30322, USA; Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA; Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO 65212, USA
| | - Milan Gembicky
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92521, United States
| | - Arthur J Olson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bruce E Torbett
- Center for Immunity and Immunotherapies, Seattle Children's Research Institute, Seattle, WA 98101, USA; Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98101, USA
| | - K Barry Sharpless
- Department of Chemistry and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Stefan G Sarafianos
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, 1760 Haygood Drive NE, Atlanta, GA 30322, USA; Children's Healthcare of Atlanta, Atlanta, GA 30322, USA; Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA; Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO 65212, USA.
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Yapo V, Majumder K, Tedbury PR, Wen X, Ong YT, Johnson MC, Sarafianos SG. HIV-2 inhibits HIV-1 gene expression via two independent mechanisms during cellular co-infection. J Virol 2023; 97:e0187022. [PMID: 37991365 PMCID: PMC10734542 DOI: 10.1128/jvi.01870-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 06/28/2023] [Indexed: 11/23/2023] Open
Abstract
IMPORTANCE Twenty-five years after the first report that HIV-2 infection can reduce HIV-1-associated pathogenesis in dual-infected patients, the mechanisms are still not well understood. We explored these mechanisms in cell culture and showed first that these viruses can co-infect individual cells. Under specific conditions, HIV-2 inhibits HIV-1 through two distinct mechanisms, a broad-spectrum interferon response and an HIV-1-specific inhibition conferred by the HIV-2 TAR. The former could play a prominent role in dually infected individuals, whereas the latter targets HIV-1 promoter activity through competition for HIV-1 Tat binding when the same target cell is dually infected. That mechanism suppresses HIV-1 transcription by stalling RNA polymerase II complexes at the promoter through a minimal inhibitory region within the HIV-2 TAR. This work delineates the sequence of appearance and the modus operandi of each mechanism.
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Affiliation(s)
- Vincent Yapo
- CS Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, Missouri, USA
| | - Kinjal Majumder
- CS Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, Missouri, USA
| | - Philip R. Tedbury
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Xin Wen
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Yee T. Ong
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
| | - Marc C. Johnson
- CS Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, Missouri, USA
| | - Stefan G. Sarafianos
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, School of Medicine, Emory University, Atlanta, Georgia, USA
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3
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Tedbury PR, Manfredi C, Degenhardt F, Conway J, Horwath MC, McCracken C, Sorscher AJ, Moreau S, Wright C, Edwards C, Brewer J, Guarner J, de Wit E, Williamson BN, Suthar MS, Ong YT, Roback JD, Alter DN, Holter JC, Karlsen TH, Sacchi N, Romero-Gómez M, Invernizzi P, Fernández J, Buti M, Albillos A, Julià A, Valenti L, Asselta R, Banales JM, Bujanda L, de Cid R, Sarafianos SG, Hong JS, Sorscher EJ, Ehrhardt A. Mechanisms by which the cystic fibrosis transmembrane conductance regulator may influence SARS-CoV-2 infection and COVID-19 disease severity. FASEB J 2023; 37:e23220. [PMID: 37801035 PMCID: PMC10760435 DOI: 10.1096/fj.202300077r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/31/2023] [Accepted: 09/12/2023] [Indexed: 10/07/2023]
Abstract
Patients with cystic fibrosis (CF) exhibit pronounced respiratory damage and were initially considered among those at highest risk for serious harm from SARS-CoV-2 infection. Numerous clinical studies have subsequently reported that individuals with CF in North America and Europe-while susceptible to severe COVID-19-are often spared from the highest levels of virus-associated mortality. To understand features that might influence COVID-19 among patients with cystic fibrosis, we studied relationships between SARS-CoV-2 and the gene responsible for CF (i.e., the cystic fibrosis transmembrane conductance regulator, CFTR). In contrast to previous reports, we found no association between CFTR carrier status (mutation heterozygosity) and more severe COVID-19 clinical outcomes. We did observe an unexpected trend toward higher mortality among control individuals compared with silent carriers of the common F508del CFTR variant-a finding that will require further study. We next performed experiments to test the influence of homozygous CFTR deficiency on viral propagation and showed that SARS-CoV-2 production in primary airway cells was not altered by the absence of functional CFTR using two independent protocols. On the contrary, experiments performed in vitro strongly indicated that virus proliferation depended on features of the mucosal fluid layer known to be disrupted by absent CFTR in patients with CF, including both low pH and increased viscosity. These results point to the acidic, viscous, and mucus-obstructed airways in patients with cystic fibrosis as unfavorable for the establishment of coronaviral infection. Our findings provide new and important information concerning relationships between the CF clinical phenotype and severity of COVID-19.
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Affiliation(s)
- Philip R. Tedbury
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, United States
- Children’s Healthcare of Atlanta, Atlanta, Georgia, United States
| | - Candela Manfredi
- Children’s Healthcare of Atlanta, Atlanta, Georgia, United States
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, United States
| | - Frauke Degenhardt
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Joseph Conway
- Northeast Georgia Medical Center, Gainesville, Georgia, United States
| | - Michael C. Horwath
- Department of Pathology, Emory University School of Medicine, Atlanta, Georgia, United States
| | - Courtney McCracken
- Children’s Healthcare of Atlanta, Atlanta, Georgia, United States
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, United States
| | - Adam J. Sorscher
- Dartmouth University School of Medicine, Hanover, New Hampshire, United States
| | - Sandy Moreau
- Elliot Hospital, Manchester, New Hampshire, United States
| | | | - Carolina Edwards
- Northeast Georgia Medical Center, Gainesville, Georgia, United States
| | - Jo Brewer
- Northeast Georgia Medical Center, Gainesville, Georgia, United States
| | | | - Emmie de Wit
- Laboratory of Virology, Division of Intramural Research, NIAID, National Institutes of Health, Hamilton, Montana, United States
| | - Brandi N. Williamson
- Laboratory of Virology, Division of Intramural Research, NIAID, National Institutes of Health, Hamilton, Montana, United States
| | - Mehul S. Suthar
- Children’s Healthcare of Atlanta, Atlanta, Georgia, United States
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, United States
| | - Yee T. Ong
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, United States
- Children’s Healthcare of Atlanta, Atlanta, Georgia, United States
| | - John D. Roback
- Department of Pathology, Emory University School of Medicine, Atlanta, Georgia, United States
| | - David N. Alter
- Department of Pathology, Emory University School of Medicine, Atlanta, Georgia, United States
| | - Jan C. Holter
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Tom H. Karlsen
- Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Research Institute for Internal Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet and University of Oslo, Oslo, Norway
- Norwegian PSC Research Center, Department of Transplantation Medicine, Division of Surgery, Inflammatory Diseases and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway
- Section for Gastroenterology, Department of Transplantation Medicine, Division for Cancer Medicine, Surgery and Transplantation, Oslo University Hospital Rikshospitalet, Oslo, Norway
| | | | - Manuel Romero-Gómez
- Hospital Universitario Virgen del Rocío de Sevilla, Sevilla, Spain
- Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Instituto de Biomedicina de Sevilla (IBIS), Sevilla, Spain
- University of Sevilla, Sevilla, Spain
- Digestive Diseases Unit, Virgen del Rocio University Hospital, Institute of Biomedicine of Seville, University of Seville, Seville, Spain
| | - Pietro Invernizzi
- European Reference Network on Hepatological Diseases (ERN RARE-LIVER), Fondazione IRCCS San Gerardo dei Tintori, Monza, Italy
- Division of Gastroenterology, Center for Autoimmune Liver Diseases, Department of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Javier Fernández
- Hospital Clinic, University of Barcelona, and IDIBAPS, Barcelona, Spain
- European Foundation for the Study of Chronic Liver Failure (EF-CLIF), Barcelona, Spain
| | - Maria Buti
- Liver Unit. Hospital Universitario Valle Hebron and CIBEREHD del Instituto Carlos III. Barcelona, Spain
| | - Agustin Albillos
- Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Department of Gastroenterology, Hospital Universitario Ramón y Cajal, University of Alcalá, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
| | - Antonio Julià
- Vall d’Hebron Institut de Recerca (VHIR), Vall d’Hebron Hospital Universitari, Barcelona, Spain
| | - Luca Valenti
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
- Biological Resorce Center, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico Milano, Milan Italy
| | - Rosanna Asselta
- Department of Biomedical Sciences, Humanitas University, Pieve Emanuele, Milan, Italy
- IRCCS Humanitas Research Hospital, Rozzano, Milan, Italy
| | - Jesus M. Banales
- Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute – Donostia University Hospital, University of the Basque Country (UPV/EHU), CIBERehd, Ikerbasque, San Sebastian, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
| | - Luis Bujanda
- Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
- Department of Liver and Gastrointestinal Diseases, Biodonostia Health Research Institute – Donostia University Hospital, University of the Basque Country (UPV/EHU), CIBERehd, Ikerbasque, San Sebastian, Spain
| | - Rafael de Cid
- Genomes for Life-GCAT lab. German Trias I Pujol Research Institute (IGTP), Badalona, Spain
| | | | - Stefan G. Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, United States
- Children’s Healthcare of Atlanta, Atlanta, Georgia, United States
| | - Jeong S. Hong
- Children’s Healthcare of Atlanta, Atlanta, Georgia, United States
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, United States
| | - Eric J. Sorscher
- Children’s Healthcare of Atlanta, Atlanta, Georgia, United States
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, United States
| | - Annette Ehrhardt
- Children’s Healthcare of Atlanta, Atlanta, Georgia, United States
- Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, United States
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4
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Cilento ME, Wen X, Reeve AB, Ukah OB, Snyder AA, Carrillo CM, Smith CP, Edwards K, Wahoski CC, Kitzler DR, Kodama EN, Mitsuya H, Parniak MA, Tedbury PR, Sarafianos SG. HIV-1 Resistance to Islatravir/Tenofovir Combination Therapy in Wild-Type or NRTI-Resistant Strains of Diverse HIV-1 Subtypes. Viruses 2023; 15:1990. [PMID: 37896768 PMCID: PMC10612037 DOI: 10.3390/v15101990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 09/15/2023] [Accepted: 09/18/2023] [Indexed: 10/29/2023] Open
Abstract
Tenofovir disoproxil fumarate (TDF) and islatravir (ISL, 4'-ethynyl-2-fluoro-2'-deoxyadensine, or MK-8591) are highly potent nucleoside reverse transcriptase inhibitors. Resistance to TDF and ISL is conferred by K65R and M184V, respectively. Furthermore, K65R and M184V increase sensitivity to ISL and TDF, respectively. Therefore, these two nucleoside analogs have opposing resistance profiles and could present a high genetic barrier to resistance. To explore resistance to TDF and ISL in combination, we performed passaging experiments with HIV-1 WT, K65R, or M184V in the presence of ISL and TDF. We identified K65R, M184V, and S68G/N mutations. The mutant most resistant to ISL was S68N/M184V, yet it remained susceptible to TDF. To further confirm our cellular findings, we implemented an endogenous reverse transcriptase assay to verify in vitro potency. To better understand the impact of these resistance mutations in the context of global infection, we determined potency of ISL and TDF against HIV subtypes A, B, C, D, and circulating recombinant forms (CRF) 01_AE and 02_AG with and without resistance mutations. In all isolates studied, we found K65R imparted hypersensitivity to ISL whereas M184V conferred resistance. We demonstrated that the S68G polymorphism can enhance fitness of drug-resistant mutants in some genetic backgrounds. Collectively, the data suggest that the opposing resistance profiles of ISL and TDF suggest that a combination of the two drugs could be a promising drug regimen for the treatment of patients infected with any HIV-1 subtype, including those who have failed 3TC/FTC-based therapies.
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Affiliation(s)
- Maria E. Cilento
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Xin Wen
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Aaron B. Reeve
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Obiaara B. Ukah
- CS Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Alexa A. Snyder
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Ciro M. Carrillo
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Cole P. Smith
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Kristin Edwards
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Claudia C. Wahoski
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Deborah R. Kitzler
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Eiichi N. Kodama
- Division of Infectious Disease, International Institute of Disaster Science, Tohoku University, Sendai 980-8572, Japan
| | - Hiroaki Mitsuya
- Department of Refractory Viral Infections, National Center for Global Health & Medicine Research Institute, Tokyo 162-8655, Japan
- Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
- Department of Clinical Sciences, Kumamoto University Hospital, Kumamoto 860-8556, Japan
| | - Michael A. Parniak
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Philip R. Tedbury
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Stefan G. Sarafianos
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
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5
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Liu D, Ndongwe TP, Ji J, Huber AD, Michailidis E, Rice CM, Ralston R, Tedbury PR, Sarafianos SG. Mechanisms of Action of the Host-Targeting Agent Cyclosporin A and Direct-Acting Antiviral Agents against Hepatitis C Virus. Viruses 2023; 15:v15040981. [PMID: 37112961 PMCID: PMC10143304 DOI: 10.3390/v15040981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/30/2023] [Accepted: 04/04/2023] [Indexed: 04/29/2023] Open
Abstract
Several direct-acting antivirals (DAAs) are available, providing interferon-free strategies for a hepatitis C cure. In contrast to DAAs, host-targeting agents (HTAs) interfere with host cellular factors that are essential in the viral replication cycle; as host genes, they are less likely to rapidly mutate under drug pressure, thus potentially exhibiting a high barrier to resistance, in addition to distinct mechanisms of action. We compared the effects of cyclosporin A (CsA), a HTA that targets cyclophilin A (CypA), to DAAs, including inhibitors of nonstructural protein 5A (NS5A), NS3/4A, and NS5B, in Huh7.5.1 cells. Our data show that CsA suppressed HCV infection as rapidly as the fastest-acting DAAs. CsA and inhibitors of NS5A and NS3/4A, but not of NS5B, suppressed the production and release of infectious HCV particles. Intriguingly, while CsA rapidly suppressed infectious extracellular virus levels, it had no significant effect on the intracellular infectious virus, suggesting that, unlike the DAAs tested here, it may block a post-assembly step in the viral replication cycle. Hence, our findings shed light on the biological processes involved in HCV replication and the role of CypA.
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Affiliation(s)
- Dandan Liu
- CS Bond Life Sciences Center, Department of Molecular Microbiology & Immunology, University of Missouri, Columbia, MO 65201, USA
| | - Tanya P Ndongwe
- CS Bond Life Sciences Center, Department of Molecular Microbiology & Immunology, University of Missouri, Columbia, MO 65201, USA
| | - Juan Ji
- CS Bond Life Sciences Center, Department of Molecular Microbiology & Immunology, University of Missouri, Columbia, MO 65201, USA
| | - Andrew D Huber
- CS Bond Life Sciences Center, Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65201, USA
| | - Eleftherios Michailidis
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
- Laboratory of Biochemical Pharmacology, Center for ViroScience and Cure, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Robert Ralston
- CS Bond Life Sciences Center, Department of Molecular Microbiology & Immunology, University of Missouri, Columbia, MO 65201, USA
| | - Philip R Tedbury
- CS Bond Life Sciences Center, Department of Molecular Microbiology & Immunology, University of Missouri, Columbia, MO 65201, USA
- Laboratory of Biochemical Pharmacology, Center for ViroScience and Cure, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Stefan G Sarafianos
- CS Bond Life Sciences Center, Department of Molecular Microbiology & Immunology, University of Missouri, Columbia, MO 65201, USA
- Laboratory of Biochemical Pharmacology, Center for ViroScience and Cure, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA 30322, USA
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6
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Balasubramaniam A, Tedbury PR, Mwangi SM, Liu Y, Li G, Merlin D, Gracz AD, He P, Sarafianos SG, Srinivasan S. SARS-CoV-2 Induces Epithelial-Enteric Neuronal Crosstalk Stimulating VIP Release. Biomolecules 2023; 13:207. [PMID: 36830577 PMCID: PMC9953368 DOI: 10.3390/biom13020207] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/06/2023] [Accepted: 01/13/2023] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Diarrhea is present in up to 30-50% of patients with COVID-19. The mechanism of SARS-CoV-2-induced diarrhea remains unclear. We hypothesized that enterocyte-enteric neuron interactions were important in SARS-CoV-2-induced diarrhea. SARS-CoV-2 induces endoplasmic reticulum (ER) stress in enterocytes causing the release of damage associated molecular patterns (DAMPs). The DAMPs then stimulate the release of enteric neurotransmitters that disrupt gut electrolyte homeostasis. METHODS Primary mouse enteric neurons (EN) were exposed to a conditioned medium from ACE2-expressing Caco-2 colonic epithelial cells infected with SARS-CoV-2 or treated with tunicamycin (ER stress inducer). Vasoactive intestinal peptides (VIP) expression and secretion by EN were assessed by RT-PCR and ELISA, respectively. Membrane expression of NHE3 was determined by surface biotinylation. RESULTS SARS-CoV-2 infection led to increased expression of BiP/GRP78, a marker and key regulator for ER stress in Caco-2 cells. Infected cells secreted the DAMP protein, heat shock protein 70 (HSP70), into the culture media, as revealed by proteomic and Western analyses. The expression of VIP mRNA in EN was up-regulated after treatment with a conditioned medium of SARS-CoV-2-infected Caco-2 cells. CD91, a receptor for HSP70, is abundantly expressed in the cultured mouse EN. Tunicamycin, an inducer of ER stress, also induced the release of HSP70 and Xbp1s, mimicking SARS-CoV-2 infection. Co-treatment of Caco-2 with tunicamycin (apical) and VIP (basolateral) induced a synergistic decrease in membrane expression of Na+/H+ exchanger (NHE3), an important transporter that mediates intestinal Na+/fluid absorption. CONCLUSIONS Our findings demonstrate that SARS-CoV-2 enterocyte infection leads to ER stress and the release of DAMPs that up-regulates the expression and release of VIP by EN. VIP in turn inhibits fluid absorption through the downregulation of brush-border membrane expression of NHE3 in enterocytes. These data highlight the role of epithelial-enteric neuronal crosstalk in COVID-19-related diarrhea.
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Affiliation(s)
- Arun Balasubramaniam
- Division of Digestive Diseases, Department of Medicine, Emory University, Atlanta, GA 30322, USA
- VA Medical Center Atlanta, Decatur, GA 30033, USA
| | | | - Simon M. Mwangi
- Division of Digestive Diseases, Department of Medicine, Emory University, Atlanta, GA 30322, USA
- VA Medical Center Atlanta, Decatur, GA 30033, USA
| | - Yunshan Liu
- Division of Digestive Diseases, Department of Medicine, Emory University, Atlanta, GA 30322, USA
- VA Medical Center Atlanta, Decatur, GA 30033, USA
| | - Ge Li
- Division of Digestive Diseases, Department of Medicine, Emory University, Atlanta, GA 30322, USA
- VA Medical Center Atlanta, Decatur, GA 30033, USA
| | - Didier Merlin
- VA Medical Center Atlanta, Decatur, GA 30033, USA
- Institute for Biomedical Sciences, Center for Inflammation, Immunity and Infection, Digestive Disease Research Group, Georgia State University, Atlanta, GA 30302, USA
| | - Adam D. Gracz
- Division of Digestive Diseases, Department of Medicine, Emory University, Atlanta, GA 30322, USA
| | - Peijian He
- Division of Digestive Diseases, Department of Medicine, Emory University, Atlanta, GA 30322, USA
| | | | - Shanthi Srinivasan
- Division of Digestive Diseases, Department of Medicine, Emory University, Atlanta, GA 30322, USA
- VA Medical Center Atlanta, Decatur, GA 30033, USA
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7
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Lan S, Neilsen G, Slack RL, Cantara WA, Castaner AE, Lorson ZC, Lulkin N, Zhang H, Lee J, Cilento ME, Tedbury PR, Sarafianos SG. Nirmatrelvir Resistance in SARS-CoV-2 Omicron_BA.1 and WA1 Replicons and Escape Strategies. bioRxiv 2023:2022.12.31.522389. [PMID: 36656782 PMCID: PMC9844013 DOI: 10.1101/2022.12.31.522389] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The antiviral component of Paxlovid, nirmatrelvir (NIR), forms a covalent bond with Cys145 of SARS-CoV-2 nsp5. To explore NIR resistance we designed mutations to impair binding of NIR over substrate. Using 12 Omicron (BA.1) and WA.1 SARS-CoV-2 replicons, cell-based complementation and enzymatic assays, we showed that in both strains, E166V imparted high NIR resistance (∼55-fold), with major decrease in WA1 replicon fitness (∼20-fold), but not BA.1 (∼2-fold). WA1 replicon fitness was restored by L50F. These differences may contribute to a potentially lower barrier to resistance in Omicron than WA1. E166V is rare in untreated patients, albeit more prevalent in paxlovid-treated EPIC-HR clinical trial patients. Importantly, NIR-resistant replicons with E166V or E166V/L50F remained susceptible to a) the flexible GC376, and b) PF-00835231, which forms additional interactions. Molecular dynamics simulations show steric clashes between the rigid and bulky NIR t-butyl and β-branched V166 distancing the NIR warhead from its Cys145 target. In contrast, GC376, through "wiggling and jiggling" accommodates V166 and still covalently binds Cys145. PF-00835231 uses its strategically positioned methoxy-indole to form a β-sheet and overcome E166V. Drug design based on strategic flexibility and main chain-targeting may help develop second-generation nsp5-targeting antivirals efficient against NIR-resistant viruses.
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8
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Shah R, Gallardo CM, Jung YH, Clock B, Dixon JR, McFadden WM, Majumder K, Pintel DJ, Corces VG, Torbett BE, Tedbury PR, Sarafianos SG. Activation of HIV-1 proviruses increases downstream chromatin accessibility. iScience 2022; 25:105490. [PMID: 36505924 PMCID: PMC9732416 DOI: 10.1016/j.isci.2022.105490] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 09/15/2022] [Accepted: 10/31/2022] [Indexed: 11/09/2022] Open
Abstract
It is unclear how the activation of HIV-1 transcription affects chromatin structure. We interrogated chromatin organization both genome-wide and nearby HIV-1 integration sites using Hi-C and ATAC-seq. In conjunction, we analyzed the transcription of the HIV-1 genome and neighboring genes. We found that long-range chromatin contacts did not differ significantly between uninfected cells and those harboring an integrated HIV-1 genome, whether the HIV-1 genome was actively transcribed or inactive. Instead, the activation of HIV-1 transcription changes chromatin accessibility immediately downstream of the provirus, demonstrating that HIV-1 can alter local cellular chromatin structure. Finally, we examined HIV-1 and neighboring host gene transcripts with long-read sequencing and found populations of chimeric RNAs both virus-to-host and host-to-virus. Thus, multiomics profiling revealed that the activation of HIV-1 transcription led to local changes in chromatin organization and altered the expression of neighboring host genes.
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Affiliation(s)
- Raven Shah
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30329, USA
- Children’s Healthcare of Atlanta, Atlanta, GA 30329, USA
| | - Christian M. Gallardo
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA 98101, USA
| | - Yoonhee H. Jung
- Department of Biology, Emory University, Atlanta, GA 30329, USA
| | - Ben Clock
- Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Jesse R. Dixon
- Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - William M. McFadden
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30329, USA
- Children’s Healthcare of Atlanta, Atlanta, GA 30329, USA
| | - Kinjal Majumder
- Institute for Molecular Virology and McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - David J. Pintel
- Department of Molecular Microbiology and Immunology, Christopher S. Bond Life Sciences Center, University of Missouri School of Medicine, Columbia, MO 65211, USA
| | | | - Bruce E. Torbett
- Center for Immunity and Immunotherapies, Seattle Children’s Research Institute, Seattle, WA 98101, USA
- Department of Pediatrics, University of Washington School of Medicine, Seattle, WA 98101, USA
| | - Philip R. Tedbury
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30329, USA
- Children’s Healthcare of Atlanta, Atlanta, GA 30329, USA
| | - Stefan G. Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30329, USA
- Children’s Healthcare of Atlanta, Atlanta, GA 30329, USA
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9
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Cilento ME, Ong YT, Tedbury PR, Sarafianos SG. Drug Interactions in Lenacapavir-Based Long-Acting Antiviral Combinations. Viruses 2022; 14:1202. [PMID: 35746673 PMCID: PMC9229705 DOI: 10.3390/v14061202] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 05/25/2022] [Accepted: 05/27/2022] [Indexed: 02/04/2023] Open
Abstract
Long-acting (LA) anti-HIV regimens show promise for increasing dosing intervals and consequently, improving the patients' quality of life. The first FDA-approved LA therapy is Cabenuva, which comprises rilpivirine (a non-nucleoside reverse transcriptase inhibitor) and cabotegravir (integrase strand transfer inhibitor). Novel promising LA anti-HIV agents such as lenacapavir (a capsid-targeting antiviral) and islatravir (EFdA, a nucleoside reverse transcriptase translocation inhibitor) need to be explored as combination therapies. Therefore, we sought to determine whether combination of lenacapavir with islatravir, rilpivirine, or cabotegravir displayed synergy, additivity, or antagonism. We performed dose-response matrices of these drug combinations in an HIV-1 reporter cell line and subsequently analyzed the data with SynergyFinder Plus, which employs four major drug interaction models: highest single agent, Bliss independence, Loewe additivity, and zero interaction potency. Most of these models predict additive inhibition by the studied drug combinations This work highlights the importance of effective drug combinations in LA-regimens.
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Affiliation(s)
| | | | | | - Stefan G. Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Children’s Healthcare of Atlanta, Atlanta, GA 30307, USA; (M.E.C.); (Y.T.O.); (P.R.T.)
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10
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Chhetri BK, Tedbury PR, Sweeney-Jones AM, Mani L, Soapi K, Manfredi C, Sorscher E, Sarafianos SG, Kubanek J. Marine Natural Products as Leads against SARS-CoV-2 Infection. J Nat Prod 2022; 85:657-665. [PMID: 35290044 PMCID: PMC8936055 DOI: 10.1021/acs.jnatprod.2c00015] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Indexed: 05/13/2023]
Abstract
Since early 2020, disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a global pandemic, causing millions of infections and deaths worldwide. Despite rapid deployment of effective vaccines, it is apparent that the global community lacks multipronged interventions to combat viral infection and disease. A major limitation is the paucity of antiviral drug options representing diverse molecular scaffolds and mechanisms of action. Here we report the antiviral activities of three distinct marine natural products─homofascaplysin A (1), (+)-aureol (2), and bromophycolide A (3)─evidenced by their ability to inhibit SARS-CoV-2 replication at concentrations that are nontoxic toward human airway epithelial cells. These compounds stand as promising candidates for further exploration toward the discovery of novel drug leads against SARS-CoV-2.
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Affiliation(s)
- Bhuwan Khatri Chhetri
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Philip R. Tedbury
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | | | - Luke Mani
- Institute of Applied Sciences, University of South Pacific, Suva, Fiji
| | - Katy Soapi
- Institute of Applied Sciences, University of South Pacific, Suva, Fiji
| | - Candela Manfredi
- Department of Pediatrics, Division of Pulmonary Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Eric Sorscher
- Department of Pediatrics, Division of Pulmonary Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Stefan G. Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Julia Kubanek
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA 30332, USA
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332, USA
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11
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McFadden WM, Snyder AA, Kirby KA, Tedbury PR, Raj M, Wang Z, Sarafianos SG. Rotten to the core: antivirals targeting the HIV-1 capsid core. Retrovirology 2021; 18:41. [PMID: 34937567 PMCID: PMC8693499 DOI: 10.1186/s12977-021-00583-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/09/2021] [Indexed: 12/20/2022] Open
Abstract
The capsid core of HIV-1 is a large macromolecular assembly that surrounds the viral genome and is an essential component of the infectious virus. In addition to its multiple roles throughout the viral life cycle, the capsid interacts with multiple host factors. Owing to its indispensable nature, the HIV-1 capsid has been the target of numerous antiretrovirals, though most capsid-targeting molecules have not had clinical success until recently. Lenacapavir, a long-acting drug that targets the HIV-1 capsid, is currently undergoing phase 2/3 clinical trials, making it the most successful capsid inhibitor to-date. In this review, we detail the role of the HIV-1 capsid protein in the virus life cycle, categorize antiviral compounds based on their targeting of five sites within the HIV-1 capsid, and discuss their molecular interactions and mechanisms of action. The diverse range of inhibition mechanisms provides insight into possible new strategies for designing novel HIV-1 drugs and furthers our understanding of HIV-1 biology. ![]()
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Affiliation(s)
- William M McFadden
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Alexa A Snyder
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Karen A Kirby
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA.,Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Philip R Tedbury
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA.,Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Monika Raj
- Department of Chemistry, Emory University, Atlanta, GA, 30322, USA
| | - Zhengqiang Wang
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Stefan G Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA. .,Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA.
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12
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Tao S, Zandi K, Bassit L, Ong YT, Verma K, Liu P, Downs-Bowen JA, McBrayer T, LeCher JC, Kohler JJ, Tedbury PR, Kim B, Amblard F, Sarafianos SG, Schinazi RF. Comparison of anti-SARS-CoV-2 activity and intracellular metabolism of remdesivir and its parent nucleoside. Curr Res Pharmacol Drug Discov 2021; 2:100045. [PMID: 34870151 PMCID: PMC8357487 DOI: 10.1016/j.crphar.2021.100045] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/05/2021] [Accepted: 08/08/2021] [Indexed: 02/07/2023] Open
Abstract
Remdesivir, a monophosphate prodrug of nucleoside analog GS-441524, is widely used for the treatment of moderate to severe COVID-19. It has been suggested to use GS-441524 instead of remdesivir in the clinic and in new inhalation formulations. Thus, we compared the anti-SARS-CoV-2 activity of remdesivir and GS-441524 in Vero E6, Vero CCL-81, Calu-3, Caco-2 cells, and anti-HCoV-OC43 activity in Huh-7 cells. We also compared the cellular pharmacology of these two compounds in Vero E6, Vero CCL-81, Calu-3, Caco-2, Huh-7, 293T, BHK-21, 3T3 and human airway epithelial (HAE) cells. Overall, remdesivir exhibited greater potency and superior intracellular metabolism than GS-441524 except in Vero E6 and Vero CCL-81 cells.
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Key Words
- ACE2, angiotensin-converting enzyme 2
- Anti-SARS-CoV-2
- Antiviral agents
- CES1, carboxylesterase 1
- COVID-19
- COVID-19, coronavirus disease 2019
- CatA, cathepsin A
- Coronavirus
- DP, diphosphate
- GS-441524
- HAE, human airway epithelial
- HCoV-OC43
- HINT1, histidine triad nucleotide-binding protein 1
- MP, monophosphate
- NTP, nucleoside triphosphate
- Pharmacology
- Remdesivir
- SARS-CoV-2, severe acute respiratory syndrome coronavirus 2
- TP, triphosphate
- WHO, World Health Organization
- icSARS-CoV-2-mNG, SARS-CoV-2 infectious clone virus containing mNeonGreen reporter
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Affiliation(s)
- Sijia Tao
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Keivan Zandi
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Leda Bassit
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Yee Tsuey Ong
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Kiran Verma
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Peng Liu
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Jessica A. Downs-Bowen
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Tamara McBrayer
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Julia C. LeCher
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - James J. Kohler
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Philip R. Tedbury
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Baek Kim
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Franck Amblard
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Stefan G. Sarafianos
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Raymond F. Schinazi
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA, USA
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13
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Sahani RL, Diana-Rivero R, Vernekar SKV, Wang L, Du H, Zhang H, Castaner AE, Casey MC, Kirby KA, Tedbury PR, Xie J, Sarafianos SG, Wang Z. Design, Synthesis and Characterization of HIV-1 CA-Targeting Small Molecules: Conformational Restriction of PF74. Viruses 2021; 13:v13030479. [PMID: 33804121 PMCID: PMC8000227 DOI: 10.3390/v13030479] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/10/2021] [Accepted: 03/10/2021] [Indexed: 12/30/2022] Open
Abstract
Small molecules targeting the PF74 binding site of the HIV-1 capsid protein (CA) confer potent and mechanistically unique antiviral activities. Structural modifications of PF74 could further the understanding of ligand binding modes, diversify ligand chemical classes, and allow identification of new variants with balanced antiviral activity and metabolic stability. In the current work, we designed and synthesized three series of PF74-like analogs featuring conformational constraints at the aniline terminus or the phenylalanine carboxamide moiety, and characterized them using a biophysical thermal shift assay (TSA), cell-based antiviral and cytotoxicity assays, and in vitro metabolic stability assays in human and mouse liver microsomes. These studies showed that the two series with the phenylalanine carboxamide moiety replaced by a pyridine or imidazole ring can provide viable hits. Subsequent SAR identified an improved analog 15 which effectively inhibited HIV-1 (EC50 = 0.31 μM), strongly stabilized CA hexamer (ΔTm = 8.7 °C), and exhibited substantially enhanced metabolic stability (t1/2 = 27 min for 15 vs. 0.7 min for PF74). Metabolic profiles from the microsomal stability assay also indicate that blocking the C5 position of the indole ring could lead to increased resistance to oxidative metabolism.
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Affiliation(s)
- Rajkumar Lalji Sahani
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA; (R.L.S.); (R.D.-R.); (S.K.V.V.); (L.W.); (J.X.)
| | - Raquel Diana-Rivero
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA; (R.L.S.); (R.D.-R.); (S.K.V.V.); (L.W.); (J.X.)
| | - Sanjeev Kumar V. Vernekar
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA; (R.L.S.); (R.D.-R.); (S.K.V.V.); (L.W.); (J.X.)
| | - Lei Wang
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA; (R.L.S.); (R.D.-R.); (S.K.V.V.); (L.W.); (J.X.)
| | - Haijuan Du
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; (H.D.); (H.Z.); (A.E.C.); (K.A.K.); (P.R.T.); (S.G.S.)
- Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Huanchun Zhang
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; (H.D.); (H.Z.); (A.E.C.); (K.A.K.); (P.R.T.); (S.G.S.)
- Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Andres Emanuelli Castaner
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; (H.D.); (H.Z.); (A.E.C.); (K.A.K.); (P.R.T.); (S.G.S.)
- Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Mary C. Casey
- Department of Molecular Microbiology and Immunology, School of Medicine, Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA;
| | - Karen A. Kirby
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; (H.D.); (H.Z.); (A.E.C.); (K.A.K.); (P.R.T.); (S.G.S.)
- Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Philip R. Tedbury
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; (H.D.); (H.Z.); (A.E.C.); (K.A.K.); (P.R.T.); (S.G.S.)
- Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Jiashu Xie
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA; (R.L.S.); (R.D.-R.); (S.K.V.V.); (L.W.); (J.X.)
| | - Stefan G. Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; (H.D.); (H.Z.); (A.E.C.); (K.A.K.); (P.R.T.); (S.G.S.)
- Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Zhengqiang Wang
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA; (R.L.S.); (R.D.-R.); (S.K.V.V.); (L.W.); (J.X.)
- Correspondence: ; Tel.: +1-612-626-7025
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14
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Francis AC, Marin M, Singh PK, Achuthan V, Prellberg MJ, Palermino-Rowland K, Lan S, Tedbury PR, Sarafianos SG, Engelman AN, Melikyan GB. Publisher Correction: HIV-1 replication complexes accumulate in nuclear speckles and integrate into speckle-associated genomic domains. Nat Commun 2020; 11:6165. [PMID: 33244008 PMCID: PMC7692523 DOI: 10.1038/s41467-020-20152-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Ashwanth C Francis
- Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA.
| | - Mariana Marin
- Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Parmit K Singh
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA.,Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Vasudevan Achuthan
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA.,Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Mathew J Prellberg
- Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Kristina Palermino-Rowland
- Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Shuiyun Lan
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Philip R Tedbury
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Stefan G Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Alan N Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA.,Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Gregory B Melikyan
- Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA. .,Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA.
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15
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Shah R, Lan S, Puray-Chavez MN, Liu D, Tedbury PR, Sarafianos SG. Single-cell Multiplexed Fluorescence Imaging to Visualize Viral Nucleic Acids and Proteins and Monitor HIV, HTLV, HBV, HCV, Zika Virus, and Influenza Infection. J Vis Exp 2020. [PMID: 33191939 DOI: 10.3791/61843] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Capturing the dynamic replication and assembly processes of viruses has been hindered by the lack of robust in situ hybridization (ISH) technologies that enable sensitive and simultaneous labeling of viral nucleic acid and protein. Conventional DNA fluorescence in situ hybridization (FISH) methods are often not compatible with immunostaining. We have therefore developed an imaging approach, MICDDRP (multiplex immunofluorescent cell-based detection of DNA, RNA and protein), which enables simultaneous single-cell visualization of DNA, RNA, and protein. Compared to conventional DNA FISH, MICDDRP utilizes branched DNA (bDNA) ISH technology, which dramatically improves oligonucleotide probe sensitivity and detection. Small modifications of MICDDRP enable imaging of viral proteins concomitantly with nucleic acids (RNA or DNA) of different strandedness. We have applied these protocols to study the life cycles of multiple viral pathogens, including human immunodeficiency virus (HIV)-1, human T-lymphotropic virus (HTLV)-1, hepatitis B virus (HBV), hepatitis C virus (HCV), Zika virus (ZKV), and influenza A virus (IAV). We demonstrated that we can efficiently label viral nucleic acids and proteins across a diverse range of viruses. These studies can provide us with improved mechanistic understanding of multiple viral systems, and in addition, serve as a template for application of multiplexed fluorescence imaging of DNA, RNA, and protein across a broad spectrum of cellular systems.
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Affiliation(s)
- Raven Shah
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine
| | - Shuiyun Lan
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine
| | - Maritza N Puray-Chavez
- Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine
| | - Dandan Liu
- Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine
| | - Philip R Tedbury
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine
| | - Stefan G Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine;
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16
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Wang L, Casey MC, Vernekar SKV, Sahani RL, Kankanala J, Kirby KA, Du H, Hachiya A, Zhang H, Tedbury PR, Xie J, Sarafianos SG, Wang Z. Novel HIV-1 capsid-targeting small molecules of the PF74 binding site. Eur J Med Chem 2020; 204:112626. [PMID: 32814250 DOI: 10.1016/j.ejmech.2020.112626] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/22/2020] [Accepted: 06/25/2020] [Indexed: 10/23/2022]
Abstract
The PF74 binding site in HIV-1 capsid protein (CA) is a compelling antiviral drug target. Although PF74 confers mechanistically distinct antiviral phenotypes by competing against host factors for CA binding, it suffers from prohibitively low metabolic stability. Therefore, there has been increasing interest in designing novel sub-chemotypes of PF74 with similar binding mode and improved metabolic stability. We report herein our efforts to explore the inter-domain interacting indole moiety for designing novel CA-targeting small molecules. Our design includes simple substitution on the indole ring, and more importantly, novel sub-chemotypes with the indole moiety replaced with a few less electron-rich rings. All 56 novel analogs were synthesized and evaluated for antiviral activity, cytotoxicity, and impact on CA hexamer stability. Selected analogs were tested for metabolic stability in liver microsomes. Molecular modeling was performed to verify compound binding to the PF74 site. In the end, 5-hydroxyindole analogs (8,9 and 12) showed improved potency (up to 20-fold) over PF74. Of the novel sub-chemotypes, α- and β-naphthyl analogs (33 and 27) exhibited sub micromolar antiviral potencies comparable to that of PF74. Interestingly, although only moderately inhibiting HIV-1 (single-digit micromolar EC50s), analogs of the 2-indolone sub-chemotype consistently lowered the melting point (Tm) of CA hexamers, some with improved metabolic stability over PF74.
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Affiliation(s)
- Lei Wang
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Mary C Casey
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Christopher S. Bond Life Sciences Center, Columbia, MO, 65211, USA
| | - Sanjeev Kumar V Vernekar
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Rajkumar Lalji Sahani
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Jayakanth Kankanala
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Karen A Kirby
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Haijuan Du
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Atsuko Hachiya
- Clinical Research Center, Nagoya Medical Center, National Hospital Organization, Nagoya, Aichi, 460-0001, Japan
| | - Huanchun Zhang
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Philip R Tedbury
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Jiashu Xie
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Stefan G Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Zhengqiang Wang
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN, 55455, USA.
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17
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Francis AC, Marin M, Singh PK, Achuthan V, Prellberg MJ, Palermino-Rowland K, Lan S, Tedbury PR, Sarafianos SG, Engelman AN, Melikyan GB. HIV-1 replication complexes accumulate in nuclear speckles and integrate into speckle-associated genomic domains. Nat Commun 2020; 11:3505. [PMID: 32665593 PMCID: PMC7360574 DOI: 10.1038/s41467-020-17256-8] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 06/19/2020] [Indexed: 12/12/2022] Open
Abstract
The early steps of HIV-1 infection, such as uncoating, reverse transcription, nuclear import, and transport to integration sites are incompletely understood. Here, we imaged nuclear entry and transport of HIV-1 replication complexes in cell lines, primary monocyte-derived macrophages (MDMs) and CD4+ T cells. We show that viral replication complexes traffic to and accumulate within nuclear speckles and that these steps precede the completion of viral DNA synthesis. HIV-1 transport to nuclear speckles is dependent on the interaction of the capsid proteins with host cleavage and polyadenylation specificity factor 6 (CPSF6), which is also required to stabilize the association of the viral replication complexes with nuclear speckles. Importantly, integration site analyses reveal a strong preference for HIV-1 to integrate into speckle-associated genomic domains. Collectively, our results demonstrate that nuclear speckles provide an architectural basis for nuclear homing of HIV-1 replication complexes and subsequent integration into associated genomic loci. Early steps of HIV infection of primary human cells remain poorly understood. Here, Francis et al. show that early viral replication complexes accumulate within nuclear speckles, in reliance on viral capsid/host CPSF6 interactions, and preferentially integrate in speckle-associated genomic domains.
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Affiliation(s)
- Ashwanth C Francis
- Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA.
| | - Mariana Marin
- Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Parmit K Singh
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA.,Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Vasudevan Achuthan
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA.,Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Mathew J Prellberg
- Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Kristina Palermino-Rowland
- Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Shuiyun Lan
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Philip R Tedbury
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Stefan G Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Alan N Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA.,Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Gregory B Melikyan
- Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA. .,Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA.
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18
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Liu D, Ndongwe TP, Puray-Chavez M, Casey MC, Izumi T, Pathak VK, Tedbury PR, Sarafianos SG. Effect of P-body component Mov10 on HCV virus production and infectivity. FASEB J 2020; 34:9433-9449. [PMID: 32496609 DOI: 10.1096/fj.201800641r] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Revised: 03/28/2020] [Accepted: 05/04/2020] [Indexed: 12/11/2022]
Abstract
Mov10 is a processing body (P-body) protein and an interferon-stimulated gene that can affect replication of retroviruses, hepatitis B virus, and hepatitis C virus (HCV). The mechanism of HCV inhibition by Mov10 is unknown. Here, we investigate the effect of Mov10 on HCV infection and determine the virus life cycle steps affected by changes in Mov10 overexpression. Mov10 overexpression suppresses HCV RNA in both infectious virus and subgenomic replicon systems. Additionally, Mov10 overexpression decreases the infectivity of released virus, unlike control P-body protein DCP1a that has no effect on HCV RNA production or infectivity of progeny virus. Confocal imaging of uninfected cells shows endogenous Mov10 localized at P-bodies. However, in HCV-infected cells, Mov10 localizes in circular structures surrounding cytoplasmic lipid droplets with NS5A and core protein. Mutagenesis experiments show that the RNA binding activity of Mov10 is required for HCV inhibition, while its P-body localization, helicase, and ATP-binding functions are not required. Unexpectedly, endogenous Mov10 promotes HCV replication, as CRISPR-Cas9-based Mov10 depletion decreases HCV replication and infection levels. Our data reveal an important and complex role for Mov10 in HCV replication, which can be perturbed by excess or insufficient Mov10.
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Affiliation(s)
- Dandan Liu
- Christopher Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, USA
| | - Tanyaradzwa P Ndongwe
- Christopher Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, USA
| | - Maritza Puray-Chavez
- Christopher Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, USA
| | - Mary C Casey
- Christopher Bond Life Sciences Center, Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, USA
| | - Taisuke Izumi
- Viral Mutation Section, HIV Dynamics and Replication Program, National Cancer Institute-Frederick, Frederick, MD, USA
| | - Vinay K Pathak
- Viral Mutation Section, HIV Dynamics and Replication Program, National Cancer Institute-Frederick, Frederick, MD, USA
| | - Philip R Tedbury
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Stefan G Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
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19
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Wang L, Casey MC, Vernekar SKV, Do HT, Sahani RL, Kirby KA, Du H, Hachiya A, Zhang H, Tedbury PR, Xie J, Sarafianos SG, Wang Z. Chemical profiling of HIV-1 capsid-targeting antiviral PF74. Eur J Med Chem 2020; 200:112427. [PMID: 32438252 DOI: 10.1016/j.ejmech.2020.112427] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 04/18/2020] [Accepted: 05/05/2020] [Indexed: 12/22/2022]
Abstract
The capsid protein (CA) of HIV-1 plays essential roles in multiple steps of the viral replication cycle by assembling into functional capsid core, controlling the kinetics of uncoating and nuclear entry, and interacting with various host factors. Targeting CA represents an attractive yet underexplored antiviral approach. Of all known CA-targeting small molecule chemotypes, the peptidomimetic PF74 is particularly interesting because it binds to the same pocket used by a few important host factors, resulting in highly desirable antiviral phenotypes. However, further development of PF74 entails understanding its pharmacophore and mitigating its poor metabolic stability. We report herein the design, synthesis, and evaluation of a large number of PF74 analogs aiming to provide a comprehensive chemical profiling of PF74 and advance the understanding on its detailed binding mechanism and pharmacophore. The analogs, containing structural variations mainly in the aniline domain and/or the indole domain, were assayed for their effect on stability of CA hexamers, antiviral activity, and cytotoxicity. Selected analogs were also tested for metabolic stability in liver microsomes, alone or in the presence of a CYP3A inhibitor. Collectively, our studies identified important pharmacophore elements and revealed additional binding features of PF74, which could aid in future design of improved ligands to better probe the molecular basis of CA-host factor interactions, design strategies to disrupt them, and ultimately identify viable CA-targeting antiviral leads.
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Affiliation(s)
- Lei Wang
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Mary C Casey
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Christopher S. Bond Life Sciences Center, Columbia, MO, 65211, USA
| | - Sanjeev Kumar V Vernekar
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Ha T Do
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Rajkumar Lalji Sahani
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Karen A Kirby
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Haijuan Du
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Atsuko Hachiya
- Clinical Research Center, Nagoya Medical Center, National Hospital Organization, Nagoya, Aichi, 460-0001, Japan
| | - Huanchun Zhang
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Philip R Tedbury
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Jiashu Xie
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Stefan G Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Zhengqiang Wang
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN, 55455, USA.
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20
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Alfadhli A, Staubus AO, Tedbury PR, Novikova M, Freed EO, Barklis E. Analysis of HIV-1 Matrix-Envelope Cytoplasmic Tail Interactions. J Virol 2019; 93:e01079-19. [PMID: 31375589 PMCID: PMC6803273 DOI: 10.1128/jvi.01079-19] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 07/30/2019] [Indexed: 01/08/2023] Open
Abstract
The matrix (MA) domains of HIV-1 precursor Gag (PrGag) proteins direct PrGag proteins to plasma membrane (PM) assembly sites where envelope (Env) protein trimers are incorporated into virus particles. MA targeting to PM sites is facilitated by its binding to phosphatidylinositol-(4,5)-bisphosphate [PI(4,5)P2], and MA binding to cellular RNAs appears to serve a chaperone function that prevents MA from associating with intracellular membranes prior to arrival at the PI(4,5)P2-rich PM. Investigations have shown genetic evidence of an interaction between MA and the cytoplasmic tails (CTs) of Env trimers that contributes to Env incorporation into virions, but demonstrations of direct MA-CT interactions have proven more difficult. In direct binding assays, we show here that MA binds to Env CTs. Using MA mutants, matrix-capsid (MACA) proteins, and MA proteins incubated in the presence of inositol polyphosphate, we show a correlation between MA trimerization and CT binding. RNA ligands with high affinities for MA reduced MA-CT binding levels, suggesting that MA-RNA binding interferes with trimerization and/or directly or indirectly blocks MA-CT binding. Rough-mapping studies indicate that C-terminal CT helices are involved in MA binding and are in agreement with cell culture studies with replication-competent viruses. Our results support a model in which full-length HIV-1 Env trimers are captured in assembling PrGag lattices by virtue of their binding to MA trimers.IMPORTANCE The mechanism by which HIV-1 envelope (Env) protein trimers assemble into virus particles is poorly understood but involves an interaction between Env cytoplasmic tails (CTs) and the matrix (MA) domain of the structural precursor Gag (PrGag) proteins. We show here that direct binding of MA to Env CTs correlates with MA trimerization, suggesting models where MA lattices regulate CT interactions and/or MA-CT trimer-trimer associations increase the avidity of MA-CT binding. We also show that MA binding to RNA ligands impairs MA-CT binding, potentially by interfering with MA trimerization and/or directly or allosterically blocking MA-CT binding sites. Rough mapping implicated CT C-terminal helices in MA binding, in agreement with cell culture studies on MA-CT interactions. Our results indicate that targeting HIV-1 MA-CT interactions may be a promising avenue for antiviral therapy.
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Affiliation(s)
- Ayna Alfadhli
- Department of Molecular Microbiology and Immunology, Oregon Health & Sciences University, Portland, Oregon, USA
| | - August O Staubus
- Department of Molecular Microbiology and Immunology, Oregon Health & Sciences University, Portland, Oregon, USA
| | - Philip R Tedbury
- Virus-Cell Interaction Section, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Mariia Novikova
- Virus-Cell Interaction Section, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Eric O Freed
- Virus-Cell Interaction Section, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Eric Barklis
- Department of Molecular Microbiology and Immunology, Oregon Health & Sciences University, Portland, Oregon, USA
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21
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Puray-Chavez MN, Farghali MH, Yapo V, Huber AD, Liu D, Ndongwe TP, Casey MC, Laughlin TG, Hannink M, Tedbury PR, Sarafianos SG. Effects of Moloney Leukemia Virus 10 Protein on Hepatitis B Virus Infection and Viral Replication. Viruses 2019; 11:v11070651. [PMID: 31319455 PMCID: PMC6669478 DOI: 10.3390/v11070651] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 07/09/2019] [Accepted: 07/11/2019] [Indexed: 12/16/2022] Open
Abstract
Moloney leukemia virus 10 (MOV10) is an RNA helicase that has been shown to affect the replication of several viruses. The effect of MOV10 on Hepatitis B virus (HBV) infection is not known and its role on the replication of this virus is poorly understood. We investigated the effect of MOV10 down-regulation and MOV10 over-expression on HBV in a variety of cell lines, as well as in an infection system using a replication competent virus. We report that MOV10 down-regulation, using siRNA, shRNA, and CRISPR/Cas9 gene editing technology, resulted in increased levels of HBV DNA, HBV pre-genomic RNA, and HBV core protein. In contrast, MOV10 over-expression reduced HBV DNA, HBV pre-genomic RNA, and HBV core protein. These effects were consistent in all tested cell lines, providing strong evidence for the involvement of MOV10 in the HBV life cycle. We demonstrated that MOV10 does not interact with HBV-core. However, MOV10 binds HBV pgRNA and this interaction does not affect HBV pgRNA decay rate. We conclude that the restriction of HBV by MOV10 is mediated through effects at the level of viral RNA.
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Affiliation(s)
- Maritza N Puray-Chavez
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO 65212, USA
| | - Mahmoud H Farghali
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO 65212, USA
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Tanta University, Tanta QXXV+C5, Egypt
| | - Vincent Yapo
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO 65212, USA
| | - Andrew D Huber
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Columbia, MO 65211, USA
| | - Dandan Liu
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO 65212, USA
| | - Tanyaradzwa P Ndongwe
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO 65212, USA
| | - Mary C Casey
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO 65212, USA
| | - Thomas G Laughlin
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Mark Hannink
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA
| | - Philip R Tedbury
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO 65212, USA.
| | - Stefan G Sarafianos
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
- Department of Molecular Microbiology and Immunology, School of Medicine, University of Missouri, Columbia, MO 65212, USA.
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.
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22
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Puray-Chavez M, Tedbury PR, Huber AD, Ukah OB, Yapo V, Liu D, Ji J, Wolf JJ, Engelman AN, Sarafianos SG. Multiplex single-cell visualization of nucleic acids and protein during HIV infection. Nat Commun 2017; 8:1882. [PMID: 29192235 PMCID: PMC5709414 DOI: 10.1038/s41467-017-01693-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 10/05/2017] [Indexed: 01/09/2023] Open
Abstract
Technical limitations in simultaneous microscopic visualization of RNA, DNA, and proteins of HIV have curtailed progress in this field. To address this need we develop a microscopy approach, multiplex immunofluorescent cell-based detection of DNA, RNA and Protein (MICDDRP), which is based on branched DNA in situ hybridization technology. MICDDRP enables simultaneous single-cell visualization of HIV (a) spliced and unspliced RNA, (b) cytoplasmic and nuclear DNA, and (c) Gag. We use MICDDRP to visualize incoming capsid cores containing RNA and/or nascent DNA and follow reverse transcription kinetics. We also report transcriptional “bursts” of nascent RNA from integrated proviral DNA, and concomitant HIV-1, HIV-2 transcription in co-infected cells. MICDDRP can be used to simultaneously detect multiple viral nucleic acid intermediates, characterize the effects of host factors or drugs on steps of the HIV life cycle, or its reactivation from the latent state, thus facilitating the development of antivirals and latency reactivating agents. Technical limitations in simultaneous microscopic visualization of HIV transcription from individual integration sites have curtailed progress in the field. Here the authors report a branched DNA in situ hybridization method for direct single-cell visualization of HIV DNA, RNA, and protein.
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Affiliation(s)
- Maritza Puray-Chavez
- CS Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.,Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA
| | - Philip R Tedbury
- CS Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.,Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA.,Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30332, USA
| | - Andrew D Huber
- CS Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.,Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, 65211, USA
| | - Obiaara B Ukah
- CS Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.,Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA
| | - Vincent Yapo
- CS Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.,Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA
| | - Dandan Liu
- CS Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.,Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA
| | - Juan Ji
- CS Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA
| | - Jennifer J Wolf
- CS Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA.,Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA
| | - Alan N Engelman
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.,Department of Medicine, Harvard Medical School, Boston, MA, 02115, USA
| | - Stefan G Sarafianos
- CS Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA. .,Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine, Columbia, MO, 65212, USA. .,Department of Veterinary Pathobiology, University of Missouri, Columbia, MO, 65211, USA. .,Department of Biochemistry, University of Missouri, Columbia, MO, 65201, USA. .,Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30332, USA.
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23
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Abstract
The viral restriction factor SERINC5 inhibits HIV-1 infection via unknown mechanisms. Sood and co-workers now show that SERINC5 suppresses HIV-1 fusogenicity and increases sensitivity to neutralizing antibodies by perturbing the folding of the fusion machinery. This work advances our understanding of host-virus interactions and provides a compelling case for considering the host immune system in studies of restriction factor mechanisms.
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Affiliation(s)
- Philip R Tedbury
- From the Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, .,Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, Missouri, and
| | - Stefan G Sarafianos
- From the Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, .,Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, Missouri, and.,the Department of Biochemistry, University of Missouri, Columbia, Missouri 65212
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Mercredi PY, Bucca N, Loeliger B, Gaines CR, Mehta M, Bhargava P, Tedbury PR, Charlier L, Floquet N, Muriaux D, Favard C, Sanders CR, Freed EO, Marchant J, Summers MF. Structural and Molecular Determinants of Membrane Binding by the HIV-1 Matrix Protein. J Mol Biol 2016; 428:1637-55. [PMID: 26992353 DOI: 10.1016/j.jmb.2016.03.005] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 03/09/2016] [Accepted: 03/10/2016] [Indexed: 10/22/2022]
Abstract
Assembly of HIV-1 particles is initiated by the trafficking of viral Gag polyproteins from the cytoplasm to the plasma membrane, where they co-localize and bud to form immature particles. Membrane targeting is mediated by the N-terminally myristoylated matrix (MA) domain of Gag and is dependent on the plasma membrane marker phosphatidylinositol-4,5-bisphosphate [PI(4,5)P2]. Recent studies revealed that PI(4,5)P2 molecules containing truncated acyl chains [tr-PI(4,5)P2] are capable of binding MA in an "extended lipid" conformation and promoting myristoyl exposure. Here we report that tr-PI(4,5)P2 molecules also readily bind to non-membrane proteins, including HIV-1 capsid, which prompted us to re-examine MA-PI(4,5)P2 interactions using native lipids and membrane mimetic liposomes and bicelles. Liposome binding trends observed using a recently developed NMR approach paralleled results of flotation assays, although the affinities measured under the equilibrium conditions of NMR experiments were significantly higher. Native PI(4,5)P2 enhanced MA binding to liposomes designed to mimic non-raft-like regions of the membrane, suggesting the possibility that binding of the protein to disordered domains may precede Gag association with, or nucleation of, rafts. Studies with bicelles revealed a subset of surface and myr-associated MA residues that are sensitive to native PI(4,5)P2, but cleft residues that interact with the 2'-acyl chains of tr-PI(4,5)P2 molecules in aqueous solution were insensitive to native PI(4,5)P2 in bicelles. Our findings call to question extended-lipid MA:membrane binding models, and instead support a model put forward from coarse-grained simulations indicating that binding is mediated predominantly by dynamic, electrostatic interactions between conserved basic residues of MA and multiple PI(4,5)P2 and phosphatidylserine molecules.
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Affiliation(s)
- Peter Y Mercredi
- Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Nadine Bucca
- Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Burk Loeliger
- Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Christy R Gaines
- Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Mansi Mehta
- Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Pallavi Bhargava
- Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Maryland, Baltimore County, Baltimore, MD 21250, USA
| | - Philip R Tedbury
- Virus-Cell Interaction Section, HIV Dynamics and Replication Program, National Cancer Institute at Fredrick, Fredrick, MD 21702-1201, USA
| | - Landry Charlier
- Institut des Biomolécules Max Mousseron, CNRS UMR5247, Université Montpellier, Faculté de Pharmacie, Montpellier Cedex 05, France
| | - Nicolas Floquet
- Institut des Biomolécules Max Mousseron, CNRS UMR5247, Université Montpellier, Faculté de Pharmacie, Montpellier Cedex 05, France
| | - Delphine Muriaux
- Centre d'études d'agents Pathogénes et Biotechnologies pour la Santé CNRS-UMR 5236, Université Montpellier, Montpellier Cedex 5, France
| | - Cyril Favard
- Centre d'études d'agents Pathogénes et Biotechnologies pour la Santé CNRS-UMR 5236, Université Montpellier, Montpellier Cedex 5, France
| | - Charles R Sanders
- Department of Biochemistry, Center for Structural Biology, and Institute of Chemical Biology, Vanderbilt University School of Medicine, Nashville, TN 37240-7917, USA
| | - Eric O Freed
- Virus-Cell Interaction Section, HIV Dynamics and Replication Program, National Cancer Institute at Fredrick, Fredrick, MD 21702-1201, USA.
| | - Jan Marchant
- Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Maryland, Baltimore County, Baltimore, MD 21250, USA.
| | - Michael F Summers
- Department of Chemistry and Biochemistry, Howard Hughes Medical Institute, University of Maryland, Baltimore County, Baltimore, MD 21250, USA.
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Tedbury PR, Mercredi PY, Gaines CR, Summers MF, Freed EO. Elucidating the mechanism by which compensatory mutations rescue an HIV-1 matrix mutant defective for gag membrane targeting and envelope glycoprotein incorporation. J Mol Biol 2015; 427:1413-1427. [PMID: 25659909 PMCID: PMC4844178 DOI: 10.1016/j.jmb.2015.01.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 01/20/2015] [Accepted: 01/27/2015] [Indexed: 01/08/2023]
Abstract
The matrix (MA) domain of the human immunodeficiency virus (HIV) 1 Gag is responsible for Gag targeting to the plasma membrane where virions assemble. MA also plays a role in the incorporation of the viral envelope (Env) glycoproteins and can influence particle infectivity post-maturation and post-entry. A highly basic region of MA targets Gag to the plasma membrane via specific binding to phosphatidylinositol-4,5-bisphosphate [PI(4,5)P2]. This binding also triggers exposure of an amino-terminal myristate moiety, which anchors Gag to the membrane. An MA mutant deficient for PI(4,5)P2 binding, 29KE/31KE, has been shown to mislocalize within the cell, leading to particle assembly in a multivesicular body compartment and defective release of cell-free particles in HeLa and 293T cells. Despite the defect in virus production in these cells, release of the 29KE/31KE mutant is not significantly reduced in primary T cells, macrophages and Jurkat T cells. 29KE/31KE virions also display an infectivity defect associated with impaired Env incorporation, irrespective of the producer cell line. Here we examine the properties of 29KE/31KE by analyzing compensatory mutations obtained by a viral adaptation strategy. The MA mutant 16EK restores virus release through enhanced membrane binding. 16EK also influences the infectivity defect, in combination with an additional MA mutant, 62QR. Additionally, the 29KE/31KE MA mutant displays a defect in proteolytic cleavage of the murine leukemia virus Env cytoplasmic tail in pseudotyped virions. Our findings elucidate the mechanism whereby an MA mutant defective in PI(4,5)P2 binding can be rescued and highlight the ability of MA to influence Env glycoprotein function.
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Affiliation(s)
- Philip R Tedbury
- Virus-Cell Interaction Section, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA
| | - Peter Y Mercredi
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Christy R Gaines
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Michael F Summers
- Howard Hughes Medical Institute and Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA
| | - Eric O Freed
- Virus-Cell Interaction Section, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA.
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Abstract
The advances made in the treatment of HIV-1 infection represent a major success of modern biomedical research, prolonging healthy life and reducing virus transmission. There remain, however, many challenges relating primarily to side effects of long-term therapy and the ever-present danger of the emergence of drug-resistant strains. To counter these threats, there is a continuing need for new and better drugs, ideally targeting multiple independent steps in the HIV-1 replication cycle. The most successful current drugs target the viral enzymes: protease (PR), reverse transcriptase (RT), and integrase (IN). In this review, we outline the advances made in targeting the Gag protein and its mature products, particularly capsid and nucleocapsid, and highlight possible targets for future pharmacological intervention.
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Affiliation(s)
- Philip R Tedbury
- Virus-Cell Interaction Section, HIV Drug Resistance Program, National Cancer Institute, Center for Cancer Research, Frederick, MD, 21702-1201, USA
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Abstract
Retroviruses comprise a large, diverse group that infects a broad range of host organisms. Pathogenicity varies widely; the human immunodeficiency virus is the causative agent of acquired immunodeficiency syndrome, one of the world's leading infectious causes of death, while many nonhuman retroviruses cause cancer in the host. Retroviruses have been studied intensively, and great strides have been made in understanding aspects of retroviral biology. While the principal functions of the viral structural proteins are well understood, there remain many incompletely characterized domains. One of these is the cytoplasmic tail (CT) of the envelope glycoprotein. Several functions of the CT are highly conserved, whereas other properties are unique to a specific retrovirus. For example, the lentiviruses encode envelope glycoproteins with particularly large cytoplasmic domains. The functions of the long lentiviral envelope CT are still being deciphered. The reported functions of retroviral envelope CTs are discussed in this chapter.
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Affiliation(s)
- Philip R Tedbury
- Virus-Cell Interaction Section, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA
| | - Eric O Freed
- Virus-Cell Interaction Section, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, USA.
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Abstract
Incorporation of the viral envelope (Env) glycoprotein is a critical requirement for the production of infectious HIV-1 particles. It has long been appreciated that the matrix (MA) domain of the Gag polyprotein and the cytoplasmic tail of Env are central players in the process of Env incorporation, but the precise mechanisms have been elusive. Several recent developments have thrown light on the contributions of both proteins, prompting a re-evaluation of the role of MA during Env incorporation. The two domains appear to play distinct but complementary roles, with the cytoplasmic tail of Env responsible for directing Env to the site of assembly and the matrix domain accommodating the cytoplasmic tail of Env in the Gag lattice.
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Affiliation(s)
- Philip R Tedbury
- Virus-Cell Interaction Section, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA.
| | - Eric O Freed
- Virus-Cell Interaction Section, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, Frederick, MD 21702-1201, USA.
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Tedbury PR, Ablan SD, Freed EO. Global rescue of defects in HIV-1 envelope glycoprotein incorporation: implications for matrix structure. PLoS Pathog 2013; 9:e1003739. [PMID: 24244165 PMCID: PMC3828165 DOI: 10.1371/journal.ppat.1003739] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 09/05/2013] [Indexed: 02/01/2023] Open
Abstract
The matrix (MA) domain of HIV-1 Gag plays key roles in membrane targeting of Gag, and envelope (Env) glycoprotein incorporation into virions. Although a trimeric MA structure has been available since 1996, evidence for functional MA trimers has been elusive. The mechanism of HIV-1 Env recruitment into virions likewise remains unclear. Here, we identify a point mutation in MA that rescues the Env incorporation defects imposed by an extensive panel of MA and Env mutations. Mapping the mutations onto the putative MA trimer reveals that the incorporation-defective mutations cluster at the tips of the trimer, around the perimeter of a putative gap in the MA lattice into which the cytoplasmic tail of gp41 could insert. By contrast, the rescue mutation is located at the trimer interface, suggesting that it may confer rescue of Env incorporation via modification of MA trimer interactions, a hypothesis consistent with additional mutational analysis. These data strongly support the existence of MA trimers in the immature Gag lattice and demonstrate that rescue of Env incorporation defects is mediated by modified interactions at the MA trimer interface. The data support the hypothesis that mutations in MA that block Env incorporation do so by imposing a steric clash with the gp41 cytoplasmic tail, rather than by disrupting a specific MA-gp41 interaction. The importance of the trimer interface in rescuing Env incorporation suggests that the trimeric arrangement of MA may be a critical factor in permitting incorporation of Env into the Gag lattice. One of the enduring problems in HIV-1 research is the mechanism of incorporation of the viral envelope (Env) glycoprotein into viral particles. Several models have been proposed ranging from an entirely passive process to a requirement for binding of Env by the matrix (MA) domain of the Gag precursor polyprotein. It is clear that specific regions within MA and Env play important roles, as mutations in these domains can prevent Env incorporation. We have identified a point mutation in MA that rescues a broad range of Env-incorporation defective mutations, located both in MA and in Env. Our investigations into the mechanism of rescue have revealed the importance of interactions between MA monomers at a trimeric interface. Our results are consistent with previously published crystallographic models and now provide functional support for the existence of MA trimers in the immature Gag lattice. Furthermore, as the modification of trimer interactions plays a role in the rescue of Env incorporation, we propose that MA trimerization and the organization of the MA lattice may be critical factors in Env incorporation.
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Affiliation(s)
- Philip R. Tedbury
- Virus-Cell Interaction Section, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
| | - Sherimay D. Ablan
- Virus-Cell Interaction Section, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
| | - Eric O. Freed
- Virus-Cell Interaction Section, HIV Drug Resistance Program, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
- * E-mail:
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30
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Tedbury PR, Harris M. Characterisation of the role of zinc in the hepatitis C virus NS2/3 auto-cleavage and NS3 protease activities. J Mol Biol 2006; 366:1652-60. [PMID: 17239391 DOI: 10.1016/j.jmb.2006.12.062] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2006] [Revised: 12/14/2006] [Accepted: 12/19/2006] [Indexed: 11/20/2022]
Abstract
Cleavage of the hepatitis C virus polyprotein between the non-structural NS2 and NS3 proteins is mediated by a poorly characterised auto-proteolytic activity that maps to the C terminus of NS2 and the N terminus of NS3, but is distinct from the NS3 protease activity responsible for downstream cleavages in the polyprotein. We have exploited the fact that the minimal precursor (residues 904-1206 of the HCV polyprotein) can be expressed as an insoluble protein in Escherichia coli and subsequently refolded into a form active for both auto-cleavage and NS3 protease activity, to further characterise the NS2/3 auto-cleavage activity. We show that both activities are zinc-dependent and show an absolute requirement for cysteine residues 1123, 1125 and 1171 within NS3. In contrast cysteine 922 (within NS2) is only required for NS2/3 auto-cleavage activity and histidine 1175 is only required for NS3 activity. Although the complete NS3 protease domain (including the C-terminal alpha-helix) is required for NS2/3 auto-cleavage, the activity of the NS3 protease is not essential. Lastly we show that the NS2/3 auto-cleavage activity is more sensitive to zinc chelation by 1,10-phenanthroline than the NS3 protease activity. This observation is consistent with different conformations of the precursor competent for either NS2/3 auto-cleavage or NS3 protease activity; these two conformations can be distinguished by their relative strength and geometry of zinc coordination.
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Affiliation(s)
- Philip R Tedbury
- Institute of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
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31
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Murphy JE, Tedbury PR, Homer-Vanniasinkam S, Walker JH, Ponnambalam S. Biochemistry and cell biology of mammalian scavenger receptors. Atherosclerosis 2006; 182:1-15. [PMID: 15904923 DOI: 10.1016/j.atherosclerosis.2005.03.036] [Citation(s) in RCA: 247] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2004] [Revised: 03/10/2005] [Accepted: 03/24/2005] [Indexed: 01/14/2023]
Abstract
Scavenger receptors are integral membrane proteins that bind a wide variety of ligands including modified or oxidised low-density lipoproteins, apoptotic cells and pathogens. Modified low-density lipoprotein accumulation is thought to be an early event in vascular disease and thus scavenger receptor function is critical in this context. The scavenger receptor family has at least eight different subclasses (A-H) which bear little sequence homology to each other but recognize common ligands. Here we review our current understanding of the scavenger receptor subclasses with emphasis on their genetics, protein structure, biochemical properties, membrane trafficking, intracellular signalling and links to disease states. We also highlight emerging areas where scavenger receptors play roles in cell and animal physiology.
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Affiliation(s)
- Jane E Murphy
- School of Biochemistry and Microbiology, University of Leeds, Leeds LS2 9JT, UK
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