1
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Akther T, McFadden WM, Zhang H, Kirby KA, Sarafianos SG, Wang Z. Design and Synthesis of New GS-6207 Subtypes for Targeting HIV-1 Capsid Protein. Int J Mol Sci 2024; 25:3734. [PMID: 38612545 PMCID: PMC11012105 DOI: 10.3390/ijms25073734] [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: 02/06/2024] [Revised: 03/08/2024] [Accepted: 03/22/2024] [Indexed: 04/14/2024] Open
Abstract
HIV-1 capsid protein (CA) is the molecular target of the recently FDA-approved long acting injectable (LAI) drug lenacapavir (GS-6207). The quick emergence of CA mutations resistant to GS-6207 necessitates the design and synthesis of novel sub-chemotypes. We have conducted the structure-based design of two new sub-chemotypes combining the scaffold of GS-6207 and the N-terminal cap of PF74 analogs, the other important CA-targeting chemotype. The design was validated via induced-fit molecular docking. More importantly, we have worked out a general synthetic route to allow the modular synthesis of novel GS-6207 subtypes. Significantly, the desired stereochemistry of the skeleton C2 was confirmed via an X-ray crystal structure of the key synthetic intermediate 22a. Although the newly synthesized analogs did not show significant potency, our efforts herein will facilitate the future design and synthesis of novel subtypes with improved potency.
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Affiliation(s)
- Thamina Akther
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA;
| | - William M. McFadden
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; (W.M.M.); (H.Z.)
| | - Huanchun Zhang
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; (W.M.M.); (H.Z.)
| | - Karen A. Kirby
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; (W.M.M.); (H.Z.)
| | - Stefan G. Sarafianos
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; (W.M.M.); (H.Z.)
| | - Zhengqiang Wang
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN 55455, USA;
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2
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Bruce A, Adebomi V, Czabala P, Palmer J, McFadden WM, Lorson ZC, Slack RL, Bhardwaj G, Sarafianos SG, Raj M. A Tag-Free Platform for Synthesis and Screening of Cyclic Peptide Libraries. Angew Chem Int Ed Engl 2024:e202320045. [PMID: 38529717 DOI: 10.1002/anie.202320045] [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: 12/26/2023] [Revised: 03/06/2024] [Accepted: 03/25/2024] [Indexed: 03/27/2024]
Abstract
In the realm of high-throughput screening (HTS), macrocyclic peptide libraries traditionally necessitate decoding tags, essential for both library synthesis and identifying hit peptide sequences post-screening. Our innovation introduces a tag-free technology platform for synthesizing cyclic peptide libraries in solution and facilitates screening against biological targets to identify peptide binders through unconventional intramolecular CyClick and DeClick chemistries (CCDC) discovered through our research. This combination allows for the synthesis of diverse cyclic peptide libraries, the incorporation of various amino acids, and facile linearization and decoding of cyclic peptide binder sequences. Our sensitivity-enhancing derivatization method, utilized in tandem with nano LC-MS/MS, enables the sequencing of peptides even at exceedingly low picomolar concentrations. Employing our technology platform, we have successfully unearthed novel cyclic peptide binders against a monoclonal antibody and the first cyclic peptide binder of HIV capsid protein responsible for viral infections as validated by microscale thermal shift assays (TSA), biolayer interferometry (BLI) and functional assays.
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Affiliation(s)
- Angele Bruce
- Department of Chemistry, Emory University, Atlanta, Georgia, 30322, United States
| | - Victor Adebomi
- Department of Chemistry, Emory University, Atlanta, Georgia, 30322, United States
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, United States, 98195
| | - Patrick Czabala
- Department of Chemistry, Emory University, Atlanta, Georgia, 30322, United States
| | - Jonathan Palmer
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, United States, 98195
| | - 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, United States
- Children's Healthcare of Atlanta, Atlanta, GA, 30322, United States
| | - 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, United States
- Children's Healthcare of Atlanta, Atlanta, GA, 30322, United States
| | - 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, United States
- Children's Healthcare of Atlanta, Atlanta, GA, 30322, United States
| | - Gaurav Bhardwaj
- Department of Medicinal Chemistry, University of Washington, Seattle, WA, United States, 98195
| | - 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, United States
- Children's Healthcare of Atlanta, Atlanta, GA, 30322, United States
| | - Monika Raj
- Department of Chemistry, Emory University, Atlanta, Georgia, 30322, United States
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3
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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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4
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Amblard F, LeCher JC, De R, Zhou S, Liu P, Goh SL, Tao S, Patel D, Downs-Bowen J, Zandi K, Zhang H, Chaudhry G, McBrayer T, Muczynski M, Al-Homoudi A, Engel J, Lan S, Sarafianos SG, Kovari LC, Schinazi RF. Synthesis and biological evaluation of novel peptidomimetic inhibitors of the coronavirus 3C-like protease. Eur J Med Chem 2024; 268:116263. [PMID: 38432056 DOI: 10.1016/j.ejmech.2024.116263] [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: 12/13/2023] [Revised: 02/13/2024] [Accepted: 02/17/2024] [Indexed: 03/05/2024]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and related variants, are responsible for the devastating coronavirus disease 2019 (COVID-19) pandemic. The SARS-CoV-2 main protease (Mpro) plays a central role in the replication of the virus and represents an attractive drug target. Herein, we report the discovery of novel SARS-CoV-2 Mpro covalent inhibitors, including highly effective compound NIP-22c which displays high potency against several key variants and clinically relevant nirmatrelvir Mpro E166V mutants.
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Affiliation(s)
- Franck Amblard
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA.
| | - Julia C LeCher
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Ramyani De
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Shaoman Zhou
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Peng Liu
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Shu Ling Goh
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Sijia Tao
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Dharmeshkumar Patel
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Jessica Downs-Bowen
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Keivan Zandi
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Huanchun Zhang
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Gitika Chaudhry
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Tamara McBrayer
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Michael Muczynski
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Abdullah Al-Homoudi
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Joseph Engel
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Shuiyun Lan
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Stefan G Sarafianos
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA
| | - Ladislau C Kovari
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit, MI, 48201, USA
| | - Raymond F Schinazi
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, and Children's Healthcare of Atlanta, Atlanta, GA, 30322, USA.
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5
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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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6
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Havranek B, Demissie R, Lee H, Lan S, Zhang H, Sarafianos SG, Jean-Luc Ayitou A, Islam SM. Discovery of Nirmatrelvir Resistance Mutations in SARS-CoV-2 3CLpro: A Computational-Experimental Approach. J Chem Inf Model 2023; 63:7180-7188. [PMID: 37947496 PMCID: PMC10976418 DOI: 10.1021/acs.jcim.3c01269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2023]
Abstract
The COVID-19 pandemic has emphasized the urgency for effective antiviral therapies against SARS-CoV-2. Targeting the main protease (3CLpro) of the virus has emerged as a promising approach, and nirmatrelvir (PF-07321332), the active component of Pfizer's oral drug Paxlovid, has demonstrated remarkable clinical efficacy. However, the emergence of resistance mutations poses a challenge to its continued success. In this study, we employed alchemical free energy perturbation (FEP) alanine scanning to identify nirmatrelvir-resistance mutations within SARS-CoV-2 3CLpro. FEP identified several mutations, which were validated through in vitro IC50 experiments and found to result in 8- and 72-fold increases in nirmatrelvir IC50 values. Additionally, we constructed SARS-CoV-2 omicron replicons containing these mutations, and one of the mutants (S144A/E166A) displayed a 20-fold increase in EC50, confirming the role of FEP in identifying drug-resistance mutations. Our findings suggest that FEP can be a valuable tool in proactively monitoring the emergence of resistant strains and guiding the design of future inhibitors with reduced susceptibility to drug resistance. As nirmatrelvir is currently widely used for treating COVID-19, this research has important implications for surveillance efforts and antiviral development.
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Affiliation(s)
- Brandon Havranek
- Sidney Kimmel Medical College at Thomas Jefferson University, Philadelphia, PA 19107, USA
- ComputePharma, LLC., Chicago, IL, USA, 60607
| | - Robel Demissie
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
- Biophysics Core at Research Resource Center, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Hyun Lee
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL 60607, USA
- Biophysics Core at Research Resource Center, University of Illinois at Chicago, Chicago, IL 60607, USA
| | - Shuiyun Lan
- Center for ViroScience and Cure, 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
| | - Huanchun Zhang
- Center for ViroScience and Cure, 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
| | - Stefan G. Sarafianos
- Center for ViroScience and Cure, 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
| | | | - Shahidul M. Islam
- ComputePharma, LLC., Chicago, IL, USA, 60607
- Department of Chemistry, Delaware State University, Dover, DE, 19901, USA
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7
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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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8
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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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9
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Gres AT, Kirby KA, McFadden WM, Du H, Liu D, Xu C, Bryer AJ, Perilla JR, Shi J, Aiken C, Fu X, Zhang P, Francis AC, Melikyan GB, Sarafianos SG. Multidisciplinary studies with mutated HIV-1 capsid proteins reveal structural mechanisms of lattice stabilization. Nat Commun 2023; 14:5614. [PMID: 37699872 PMCID: PMC10497533 DOI: 10.1038/s41467-023-41197-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [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: 11/25/2020] [Accepted: 08/25/2023] [Indexed: 09/14/2023] Open
Abstract
HIV-1 capsid (CA) stability is important for viral replication. E45A and P38A mutations enhance and reduce core stability, thus impairing infectivity. Second-site mutations R132T and T216I rescue infectivity. Capsid lattice stability was studied by solving seven crystal structures (in native background), including P38A, P38A/T216I, E45A, E45A/R132T CA, using molecular dynamics simulations of lattices, cryo-electron microscopy of assemblies, time-resolved imaging of uncoating, biophysical and biochemical characterization of assembly and stability. We report pronounced and subtle, short- and long-range rearrangements: (1) A38 destabilized hexamers by loosening interactions between flanking CA protomers in P38A but not P38A/T216I structures. (2) Two E45A structures showed unexpected stabilizing CANTD-CANTD inter-hexamer interactions, variable R18-ring pore sizes, and flipped N-terminal β-hairpin. (3) Altered conformations of E45Aa α9-helices compared to WT, E45A/R132T, WTPF74, WTNup153, and WTCPSF6 decreased PF74, CPSF6, and Nup153 binding, and was reversed in E45A/R132T. (4) An environmentally sensitive electrostatic repulsion between E45 and D51 affected lattice stability, flexibility, ion and water permeabilities, electrostatics, and recognition of host factors.
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Affiliation(s)
- Anna T Gres
- C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Department of Chemistry, University of Missouri, Columbia, MO, USA
| | - Karen A Kirby
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - William M McFadden
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Haijuan Du
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Dandan Liu
- C.S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine, Columbia, MO, USA
| | - Chaoyi Xu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
| | - Alexander J Bryer
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
| | - Juan R Perilla
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
- Department of Physics & Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jiong Shi
- Department of Pathology, Immunology & Microbiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Christopher Aiken
- Department of Pathology, Immunology & Microbiology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Xiaofeng Fu
- Department of Structural Biology, University of Pittsburgh, School of Medicine, Pittsburgh, PA, USA
| | - Peijun Zhang
- Department of Structural Biology, University of Pittsburgh, School of Medicine, Pittsburgh, PA, USA
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, UK
- Electron Bio-Imaging Centre, Diamond Light Sources, Harwell Science and Innovation Campus, Didcot, UK
| | - Ashwanth C Francis
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
- Division of Pediatric Infectious Diseases, Emory University School of Medicine, Atlanta, GA, USA
| | - Gregory B Melikyan
- Children's Healthcare of Atlanta, Atlanta, GA, USA
- Division of Pediatric Infectious Diseases, Emory University School of Medicine, Atlanta, GA, USA
| | - Stefan G Sarafianos
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA.
- Children's Healthcare of Atlanta, Atlanta, GA, USA.
- Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine, Columbia, MO, USA.
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10
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McFadden WM, Sarafianos SG. Biology of the hepatitis B virus (HBV) core and capsid assembly modulators (CAMs) for chronic hepatitis B (CHB) cure. Glob Health Med 2023; 5:199-207. [PMID: 37655181 PMCID: PMC10461335 DOI: 10.35772/ghm.2023.01065] [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: 05/22/2023] [Revised: 06/03/2023] [Accepted: 06/30/2023] [Indexed: 09/02/2023]
Abstract
Hepatitis B virus (HBV) is a hepadnavirus, a small DNA virus that infects liver tissue, with some unusual replication steps that share similarities to retroviruses. HBV infection can lead to chronic hepatitis B (CHB), a life-long infection associated with significant risks of liver disease, especially if untreated. HBV is a significant global health problem, with hundreds of millions currently living with CHB. Currently approved strategies to prevent or inhibit HBV are highly effective, however, a cure for CHB has remained elusive. To achieve a cure, elimination of the functionally integrated HBV covalently closed chromosomal DNA (cccDNA) genome is required. The capsid core is an essential component of HBV replication, serving roles when establishing infection and in creating new virions. Over the last two and a half decades, significant efforts have been made to find and characterize antivirals that target the capsid, specifically the HBV core protein (Cp). The antivirals that interfere with the kinetics and morphology of the capsid, termed capsid assembly modulators (CAMs), are extremely potent, and clinical investigations indicate they are well tolerated and highly effective. Several CAMs offer the potential to cure CHB by decreasing the cccDNA pools. Here, we review the biology of the HBV capsid, focused on Cp, and the development of inhibitors that target it.
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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, Atlanta, GA, USA
- Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Stefan G. Sarafianos
- Center for ViroScience and Cure, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Children's Healthcare of Atlanta, Atlanta, GA, USA
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11
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Cicka D, Niu Q, Qui M, Qian K, Miller E, Fan D, Mo X, Ivanov AA, Sarafianos SG, Du Y, Fu H. TMPRSS2 and SARS-CoV-2 SPIKE interaction assay for uHTS. J Mol Cell Biol 2023; 15:mjad017. [PMID: 36921991 PMCID: PMC10399917 DOI: 10.1093/jmcb/mjad017] [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: 04/28/2022] [Revised: 11/21/2022] [Accepted: 03/13/2023] [Indexed: 03/17/2023] Open
Abstract
SARS-CoV-2, the coronavirus that causes the disease COVID-19, has claimed millions of lives over the past 2 years. This demands rapid development of effective therapeutic agents that target various phases of the viral replication cycle. The interaction between host transmembrane serine protease 2 (TMPRSS2) and viral SPIKE protein is an important initial step in SARS-CoV-2 infection, offering an opportunity for therapeutic development of viral entry inhibitors. Here, we report the development of a time-resolved fluorescence/Förster resonance energy transfer (TR-FRET) assay for monitoring the TMPRSS2-SPIKE interaction in lysate from cells co-expressing these proteins. The assay was configured in a 384-well-plate format for high-throughput screening with robust assay performance. To enable large-scale compound screening, we further miniaturized the assay into 1536-well ultrahigh-throughput screening (uHTS) format. A pilot screen demonstrated the utilization of the assay for uHTS. Our optimized TR-FRET uHTS assay provides an enabling platform for expanded screening campaigns to discover new classes of small-molecule inhibitors that target the SPIKE and TMPRSS2 protein-protein interaction.
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Affiliation(s)
- Danielle Cicka
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
- Graduate Program in Molecular and Systems Pharmacology, Laney Graduate School of Emory University, Atlanta, GA 30322, USA
| | - Qiankun Niu
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Min Qui
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
- Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Kun Qian
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Eric Miller
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
- Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
| | - Dacheng Fan
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Xiulei Mo
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
- Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
| | - Andrey A Ivanov
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
- Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA 30322, USA
- Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
| | - Stefan G Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Yuhong Du
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
- Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA 30322, USA
- Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
| | - Haian Fu
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, GA 30322, USA
- Emory Chemical Biology Discovery Center, Emory University School of Medicine, Atlanta, GA 30322, USA
- Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
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12
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Xue G, Yu HJ, Buffone C, Huang SW, Lee K, Goh SL, Gres AT, Guney MH, Sarafianos SG, Luban J, Diaz-Griffero F, KewalRamani VN. The HIV-1 capsid core is an opportunistic nuclear import receptor. Nat Commun 2023; 14:3782. [PMID: 37355754 PMCID: PMC10290713 DOI: 10.1038/s41467-023-39146-5] [Citation(s) in RCA: 6] [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: 02/16/2018] [Accepted: 06/01/2023] [Indexed: 06/26/2023] Open
Abstract
The movement of viruses and other large macromolecular cargo through nuclear pore complexes (NPCs) is poorly understood. The human immunodeficiency virus type 1 (HIV-1) provides an attractive model to interrogate this process. HIV-1 capsid (CA), the chief structural component of the viral core, is a critical determinant in nuclear transport of the virus. HIV-1 interactions with NPCs are dependent on CA, which makes direct contact with nucleoporins (Nups). Here we identify Nup35, Nup153, and POM121 to coordinately support HIV-1 nuclear entry. For Nup35 and POM121, this dependence was dependent cyclophilin A (CypA) interaction with CA. Mutation of CA or removal of soluble host factors changed the interaction with the NPC. Nup35 and POM121 make direct interactions with HIV-1 CA via regions containing phenylalanine glycine motifs (FG-motifs). Collectively, these findings provide additional evidence that the HIV-1 CA core functions as a macromolecular nuclear transport receptor (NTR) that exploits soluble host factors to modulate NPC requirements during nuclear invasion.
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Affiliation(s)
- Guangai Xue
- Model Development Section, Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD, 21702, USA
| | - Hyun Jae Yu
- Basic Science Program, Leidos Biomedical Research, Frederick National Laboratory, Frederick, MD, 21702, USA
| | - Cindy Buffone
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Szu-Wei Huang
- Model Development Section, Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD, 21702, USA
| | - KyeongEun Lee
- Model Development Section, Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD, 21702, USA
| | - Shih Lin Goh
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Anna T Gres
- Bond Life Sciences Center, Chemistry, University of Missouri, Columbia, MO, 65201, USA
| | - Mehmet Hakan Guney
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Stefan G Sarafianos
- Bond Life Sciences Center, Chemistry, University of Missouri, Columbia, MO, 65201, USA
- Bond Life Sciences Center, MMI, Biochemistry, University of Missouri, Columbia, MO, 65201, USA
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Jeremy Luban
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Felipe Diaz-Griffero
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Vineet N KewalRamani
- Model Development Section, Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD, 21702, USA.
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13
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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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14
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Abstract
Not many structures are common among all viruses: only nucleic acid and a protein coat [...].
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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, Atlanta, GA 30322, USA
- Children’s Healthcare of Atlanta, 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
- Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
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15
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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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16
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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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17
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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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18
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Yadav R, Courouble VV, Dey SK, Harrison JJE, Timm J, Hopkins JB, Slack RL, Sarafianos SG, Ruiz FX, Griffin PR, Arnold E. Biochemical and structural insights into SARS-CoV-2 polyprotein processing by Mpro. Sci Adv 2022; 8:eadd2191. [PMID: 36490335 PMCID: PMC9733933 DOI: 10.1126/sciadv.add2191] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 11/02/2022] [Indexed: 06/17/2023]
Abstract
SARS-CoV-2, a human coronavirus, is the causative agent of the COVID-19 pandemic. Its genome is translated into two large polyproteins subsequently cleaved by viral papain-like protease and main protease (Mpro). Polyprotein processing is essential yet incompletely understood. We studied Mpro-mediated processing of the nsp7-11 polyprotein, whose mature products include cofactors of the viral replicase, and identified the order of cleavages. Integrative modeling based on mass spectrometry (including hydrogen-deuterium exchange and cross-linking) and x-ray scattering yielded a nsp7-11 structural ensemble, demonstrating shared secondary structural elements with individual nsps. The pattern of cross-links and HDX footprint of the C145A Mpro and nsp7-11 complex demonstrate preferential binding of the enzyme active site to the polyprotein junction sites and additional transient contacts to help orient the enzyme on its substrate for cleavage. Last, proteolysis assays were used to characterize the effect of inhibitors/binders on Mpro processing/inhibition using the nsp7-11 polyprotein as substrate.
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Affiliation(s)
- Ruchi Yadav
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA
| | - Valentine V. Courouble
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA
- Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, FL, USA
| | - Sanjay K. Dey
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA
| | | | - Jennifer Timm
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ, USA
| | - Jesse B. Hopkins
- BioCAT, Department of Physics, Illinois Institute of Technology, Chicago, IL, USA
| | - Ryan L. Slack
- Division of Laboratory of Biochemical Pharmacology and Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Stefan G. Sarafianos
- Division of Laboratory of Biochemical Pharmacology and Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
- Children’s Healthcare of Atlanta, Atlanta, GA, USA
| | - Francesc X. Ruiz
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA
| | - Patrick R. Griffin
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA
- Skaggs Graduate School of Chemical and Biological Sciences, The Scripps Research Institute, Jupiter, FL, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, FL, USA
- Department of Molecular Medicine, UF Scripps Biomedical Research, University of Florida, Jupiter, FL, USA
| | - Eddy Arnold
- Center for Advanced Biotechnology and Medicine (CABM), Rutgers University, Piscataway, NJ, USA
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ, USA
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19
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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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20
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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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21
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Sun Q, Biswas A, Vijayan RSK, Craveur P, Forli S, Olson AJ, Castaner AE, Kirby KA, Sarafianos SG, Deng N, Levy R. Structure-based virtual screening workflow to identify antivirals targeting HIV-1 capsid. J Comput Aided Mol Des 2022; 36:193-203. [PMID: 35262811 PMCID: PMC8904208 DOI: 10.1007/s10822-022-00446-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/24/2022] [Indexed: 02/07/2023]
Abstract
We have identified novel HIV-1 capsid inhibitors targeting the PF74 binding site. Acting as the building block of the HIV-1 capsid core, the HIV-1 capsid protein plays an important role in the viral life cycle and is an attractive target for antiviral development. A structure-based virtual screening workflow for hit identification was employed, which includes docking 1.6 million commercially-available drug-like compounds from the ZINC database to the capsid dimer, followed by applying two absolute binding free energy (ABFE) filters on the 500 top-ranked molecules from docking. The first employs the Binding Energy Distribution Analysis Method (BEDAM) in implicit solvent. The top-ranked compounds are then refined using the Double Decoupling method in explicit solvent. Both docking and BEDAM refinement were carried out on the IBM World Community Grid as part of the FightAIDS@Home project. Using this virtual screening workflow, we identified 24 molecules with calculated binding free energies between − 6 and − 12 kcal/mol. We performed thermal shift assays on these molecules to examine their potential effects on the stability of HIV-1 capsid hexamer and found that two compounds, ZINC520357473 and ZINC4119064 increased the melting point of the latter by 14.8 °C and 33 °C, respectively. These results support the conclusion that the two ZINC compounds are primary hits targeting the capsid dimer interface. Our simulations also suggest that the two hit molecules may bind at the capsid dimer interface by occupying a new sub-pocket that has not been exploited by existing CA inhibitors. The possible causes for why other top-scored compounds suggested by ABFE filters failed to show measurable activity are discussed.
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Affiliation(s)
- Qinfang Sun
- Center for Biophysics and Computational Biology and Department of Chemistry, Temple University, Philadelphia, PA, 19122, USA
| | - Avik Biswas
- Center for Biophysics and Computational Biology and Department of Chemistry, Temple University, Philadelphia, PA, 19122, USA
| | - R S K Vijayan
- Institute for Applied Cancer Science, MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - Pierrick Craveur
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Stefano Forli
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Arthur J Olson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Andres Emanuelli Castaner
- 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
| | - 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
| | - 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
| | - Nanjie Deng
- Department of Chemistry and Physical Sciences, Pace University, New York, NY, 10038, USA.
| | - Ronald Levy
- Center for Biophysics and Computational Biology and Department of Chemistry, Temple University, Philadelphia, PA, 19122, USA
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22
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Gruenke PR, Aneja R, Welbourn S, Ukah OB, Sarafianos SG, Burke DH, Lange MJ. Selection and identification of an RNA aptamer that specifically binds the HIV-1 capsid lattice and inhibits viral replication. Nucleic Acids Res 2022; 50:1701-1717. [PMID: 35018437 PMCID: PMC8860611 DOI: 10.1093/nar/gkab1293] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [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: 09/20/2021] [Revised: 11/23/2021] [Accepted: 12/16/2021] [Indexed: 01/25/2023] Open
Abstract
The HIV-1 capsid core participates in several replication processes. The mature capsid core is a lattice composed of capsid (CA) monomers thought to assemble first into CA dimers, then into ∼250 CA hexamers and 12 CA pentamers. CA assembly requires conformational flexibility of each unit, resulting in the presence of unique, solvent-accessible surfaces. Significant advances have improved our understanding of the roles of the capsid core in replication; however, the contributions of individual CA assembly forms remain unclear and there are limited tools available to evaluate these forms in vivo. Here, we have selected aptamers that bind CA lattice tubes. We describe aptamer CA15-2, which selectively binds CA lattice, but not CA monomer or CA hexamer, suggesting that it targets an interface present and accessible only on CA lattice. CA15-2 does not compete with PF74 for binding, indicating that it likely binds a non-overlapping site. Furthermore, CA15-2 inhibits HIV-1 replication when expressed in virus producer cells, but not target cells, suggesting that it binds a biologically-relevant site during virus production that is either not accessible during post-entry replication steps or is accessible but unaltered by aptamer binding. Importantly, CA15-2 represents the first aptamer that specifically recognizes the HIV-1 CA lattice.
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Affiliation(s)
- Paige R Gruenke
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.,Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Rachna Aneja
- Department of Molecular Microbiology & Immunology, School of Medicine, University of Missouri, Columbia, MO 65211, USA
| | - Sarah Welbourn
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Obiaara B Ukah
- Department of Molecular Microbiology & Immunology, School of Medicine, University of Missouri, Columbia, MO 65211, USA
| | - Stefan G Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Donald H Burke
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.,Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.,Department of Molecular Microbiology & Immunology, School of Medicine, University of Missouri, Columbia, MO 65211, USA
| | - Margaret J Lange
- Department of Molecular Microbiology & Immunology, School of Medicine, University of Missouri, Columbia, MO 65211, USA
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23
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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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24
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Sahani RL, Akther T, Cilento ME, Castaner AE, Zhang H, Kirby KA, Xie J, Sarafianos SG, Wang Z. Potency and metabolic stability: a molecular hybrid case in the design of novel PF74-like small molecules targeting HIV-1 capsid protein. RSC Med Chem 2021; 12:2031-2044. [PMID: 35028563 DOI: 10.1039/d1md00292a] [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] [Received: 08/31/2021] [Accepted: 09/27/2021] [Indexed: 12/27/2022] Open
Abstract
PF74 (1) is a potent and well-characterized prototypical small molecule targeting human immunodeficiency virus type 1 (HIV-1) capsid protein (CA), but not a viable antiviral lead due to the lack of metabolic stability. We report herein our molecular hybridization-based medicinal chemistry efforts toward potent and metabolically stable PF74-like small molecules. The design of the new sub-chemotype 4 rationally combines binding features of two recently reported PF74-like compounds 2 and 3. The subsequent confirmation and structure-activity relationship (SAR) of hit 4a entailed the chemical synthesis of 37 novel analogs, most of which showed modest but meaningful thermal shift, and low μM antiviral activity. The most potent analogs (4a, 4d, 4o, and 4r) all exhibited noticeably improved metabolic stability over PF74. Molecular modeling suggests that these new analogs bind to the PF74 binding site. Overall, our work demonstrated that the molecular hybridization approach is suitable for designing compounds with balanced potency and metabolic stability.
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Affiliation(s)
- Rajkumar Lalji Sahani
- Center for Drug Design, College of Pharmacy, University of Minnesota Minneapolis MN 55455 USA
| | - Thamina Akther
- Center for Drug Design, College of Pharmacy, University of Minnesota Minneapolis MN 55455 USA
| | - Maria E Cilento
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine Atlanta GA 30322 USA
| | - Andres Emanuelli Castaner
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine Atlanta GA 30322 USA
| | - Huanchun Zhang
- 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
| | - 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.,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
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Hachiya A, Kubota M, Shigemi U, Ode H, Yokomaku Y, Kirby KA, Sarafianos SG, Iwatani Y. Specific mutations in the HIV-1 G-tract of the 3'-polypurine tract cause resistance to integrase strand transfer inhibitors. J Antimicrob Chemother 2021; 77:574-577. [PMID: 34894227 PMCID: PMC8865006 DOI: 10.1093/jac/dkab448] [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] [Received: 08/03/2021] [Accepted: 11/08/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND In vitro selection experiments identified viruses resistant to integrase strand transfer inhibitors (INSTIs) carrying mutations in the G-tract (six guanosines) of the 3'-polypurine tract (3'-PPT). A clinical study also reported that mutations in the 3'-PPT were observed in a patient receiving dolutegravir monotherapy. However, recombinant viruses with the 3'-PPT mutations that were found in the clinical study were recently shown to be susceptible to INSTIs. OBJECTIVES To identify the specific mutation(s) in the G-tract of the 3'-PPT for acquiring INSTI resistance, we constructed infectious clones bearing single or multiple mutations and systematically characterized the susceptibility of these clones to both first- and second-generation INSTIs. METHODS The infectious clones were tested for their infectivity and susceptibility to INSTIs in a single-cycle assay using TZM-bl cells. RESULTS A single mutation of thymidine (T) at the fifth position (GGG GTG) in the G-tract of the 3'-PPT had no effect on INSTI resistance. A double mutation, cytidine (C) or 'T' at the second position and 'T' at the fifth position (GCG GTG and GTG GTG), increased resistance to INSTIs, with the appearance of a plateau in the maximal percentage inhibition (MPI) of the dose-response curves, consistent with a non-competitive mechanism of inhibition. CONCLUSIONS Mutations at the second and fifth positions in the G-tract of the 3'-PPT may result in complex resistance mechanism(s), rather than simply affecting INSTI binding at the IN active site.
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Affiliation(s)
- Atsuko Hachiya
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Aichi, Japan,Corresponding author. Present address: Tokyo Medical University, Department of Laboratory Medicine, 6-7-1, Nishishinjuku, Shinjuku-ku, Tokyo 160-0023, Japan and Nitobe Bunka College, Department of Infectious Diseases and Immunology, 3-43-16, Nakano, Nakano-ku, Tokyo 164-0001, Japan. E-mail:
| | - Mai Kubota
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Aichi, Japan
| | - Urara Shigemi
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Aichi, Japan
| | - Hirotaka Ode
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Aichi, Japan
| | - Yoshiyuki Yokomaku
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Aichi, Japan
| | - Karen A Kirby
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA,Children’s Healthcare of Atlanta, Atlanta, GA, USA
| | - Stefan G Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA,Children’s Healthcare of Atlanta, Atlanta, GA, USA
| | - Yasumasa Iwatani
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Aichi, Japan,Department of AIDS Research, Nagoya University Graduate School of Medicine, Aichi, Japan
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26
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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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27
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Sun Q, Levy RM, Kirby KA, Wang Z, Sarafianos SG, Deng N. Molecular Dynamics Free Energy Simulations Reveal the Mechanism for the Antiviral Resistance of the M66I HIV-1 Capsid Mutation. Viruses 2021; 13:v13050920. [PMID: 34063519 PMCID: PMC8156065 DOI: 10.3390/v13050920] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [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: 04/01/2021] [Revised: 04/30/2021] [Accepted: 05/11/2021] [Indexed: 12/26/2022] Open
Abstract
While drug resistance mutations can often be attributed to the loss of direct or solvent-mediated protein−ligand interactions in the drug-mutant complex, in this study we show that a resistance mutation for the picomolar HIV-1 capsid (CA)-targeting antiviral (GS-6207) is mainly due to the free energy cost of the drug-induced protein side chain reorganization in the mutant protein. Among several mutations, M66I causes the most suppression of the GS-6207 antiviral activity (up to ~84,000-fold), and only 83- and 68-fold reductions for PF74 and ZW-1261, respectively. To understand the molecular basis of this drug resistance, we conducted molecular dynamics free energy simulations to study the structures, energetics, and conformational free energy landscapes involved in the inhibitors binding at the interface of two CA monomers. To minimize the protein−ligand steric clash, the I66 side chain in the M66I−GS-6207 complex switches to a higher free energy conformation from the one adopted in the apo M66I. In contrast, the binding of GS-6207 to the wild-type CA does not lead to any significant M66 conformational change. Based on an analysis that decomposes the absolute binding free energy into contributions from two receptor conformational states, it appears that it is the free energy cost of side chain reorganization rather than the reduced protein−ligand interaction that is largely responsible for the drug resistance against GS-6207.
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Affiliation(s)
- Qinfang Sun
- Center for Biophysics and Computational Biology and Department of Chemistry, Temple University, Philadelphia, PA 19122, USA;
| | - Ronald M. Levy
- Center for Biophysics and Computational Biology and Department of Chemistry, Temple University, Philadelphia, PA 19122, USA;
- Correspondence: (R.M.L.); (N.D.)
| | - Karen A. Kirby
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; (K.A.K.); (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;
| | - Stefan G. Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA; (K.A.K.); (S.G.S.)
- Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Nanjie Deng
- Department of Chemistry and Physical Sciences, Pace University, New York, NY 10038, USA
- Correspondence: (R.M.L.); (N.D.)
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28
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Dupont L, Bloor S, Williamson JC, Cuesta SM, Shah R, Teixeira-Silva A, Naamati A, Greenwood EJD, Sarafianos SG, Matheson NJ, Lehner PJ. The SMC5/6 complex compacts and silences unintegrated HIV-1 DNA and is antagonized by Vpr. Cell Host Microbe 2021; 29:792-805.e6. [PMID: 33811831 PMCID: PMC8118623 DOI: 10.1016/j.chom.2021.03.001] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [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: 10/02/2020] [Revised: 12/31/2020] [Accepted: 02/26/2021] [Indexed: 12/16/2022]
Abstract
Silencing of nuclear DNA is an essential feature of innate immune responses to invading pathogens. Early in infection, unintegrated lentiviral cDNA accumulates in the nucleus yet remains poorly expressed. In HIV-1-like lentiviruses, the Vpr accessory protein enhances unintegrated viral DNA expression, suggesting Vpr antagonizes cellular restriction. We previously showed how Vpr remodels the host proteome, identifying multiple cellular targets. We now screen these using a targeted CRISPR-Cas9 library and identify SMC5-SMC6 complex localization factor 2 (SLF2) as the Vpr target responsible for silencing unintegrated HIV-1. SLF2 recruits the SMC5/6 complex to unintegrated lentiviruses, and depletion of SLF2, or the SMC5/6 complex, increases viral expression. ATAC-seq demonstrates that Vpr-mediated SLF2 depletion increases chromatin accessibility of unintegrated virus, suggesting that the SMC5/6 complex compacts viral chromatin to silence gene expression. This work implicates the SMC5/6 complex in nuclear immunosurveillance of extrachromosomal DNA and defines its targeting by Vpr as an evolutionarily conserved antagonism.
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Affiliation(s)
- Liane Dupont
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, UK
| | - Stuart Bloor
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, UK
| | - James C Williamson
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, UK
| | | | - Raven Shah
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Ana Teixeira-Silva
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, UK
| | - Adi Naamati
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, UK
| | - Edward J D Greenwood
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, UK
| | - Stefan G Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children's Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Nicholas J Matheson
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, UK
| | - Paul J Lehner
- Cambridge Institute for Therapeutic Immunology & Infectious Disease, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0AW, UK.
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Zandi K, Musall K, Oo A, Cao D, Liang B, Hassandarvish P, Lan S, Slack RL, Kirby KA, Bassit L, Amblard F, Kim B, AbuBakar S, Sarafianos SG, Schinazi RF. Baicalein and Baicalin Inhibit SARS-CoV-2 RNA-Dependent-RNA Polymerase. Microorganisms 2021; 9:microorganisms9050893. [PMID: 33921971 PMCID: PMC8143456 DOI: 10.3390/microorganisms9050893] [Citation(s) in RCA: 71] [Impact Index Per Article: 23.7] [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: 03/30/2021] [Revised: 04/16/2021] [Accepted: 04/20/2021] [Indexed: 01/18/2023] Open
Abstract
Coronavirus Disease 2019 (COVID-19) is a deadly emerging infectious disease caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Because SARS-CoV-2 is easily transmitted through the air and has a relatively long incubation time, COVID-19 has rapidly developed into a global pandemic. As there are no antiviral agents for the prevention and treatment of this severe pathogen except for remdesivir, development of antiviral therapies to treat infected individuals remains highly urgent. Here, we showed that baicalein and baicalin exhibited significant antiviral activity against SARS-CoV-2, the causative agent of COVID-19 through in vitro studies. Our data through cell-based and biochemical studies showed that both compounds act as SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) inhibitors directly and inhibit the activity of the SARS-CoV-2 RdRp, but baicalein was more potent. We also showed specific binding of baicalein to the SARS-CoV-2 RdRp, making it a potential candidate for further studies towards therapeutic development for COVID-19 as a selective non-nucleoside polymerase inhibitor.
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Affiliation(s)
- 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 30322, USA; (K.M.); (A.O.); (S.L.); (R.L.S.); (K.A.K.); (L.B.); (F.A.); (B.K.); (S.G.S.); (R.F.S.)
- Correspondence: ; Tel.: +1-404-727-1575
| | - Katie Musall
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA; (K.M.); (A.O.); (S.L.); (R.L.S.); (K.A.K.); (L.B.); (F.A.); (B.K.); (S.G.S.); (R.F.S.)
| | - Adrian Oo
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA; (K.M.); (A.O.); (S.L.); (R.L.S.); (K.A.K.); (L.B.); (F.A.); (B.K.); (S.G.S.); (R.F.S.)
| | - Dongdong Cao
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA; (D.C.); (B.L.)
| | - Bo Liang
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA; (D.C.); (B.L.)
| | - Pouya Hassandarvish
- Tropical Infectious Diseases Research and Education Center, Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia; (P.H.); (S.A.)
| | - Shuiyun Lan
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA; (K.M.); (A.O.); (S.L.); (R.L.S.); (K.A.K.); (L.B.); (F.A.); (B.K.); (S.G.S.); (R.F.S.)
| | - Ryan L. Slack
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA; (K.M.); (A.O.); (S.L.); (R.L.S.); (K.A.K.); (L.B.); (F.A.); (B.K.); (S.G.S.); (R.F.S.)
| | - Karen A. Kirby
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine and Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA; (K.M.); (A.O.); (S.L.); (R.L.S.); (K.A.K.); (L.B.); (F.A.); (B.K.); (S.G.S.); (R.F.S.)
| | - 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 30322, USA; (K.M.); (A.O.); (S.L.); (R.L.S.); (K.A.K.); (L.B.); (F.A.); (B.K.); (S.G.S.); (R.F.S.)
| | - 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 30322, USA; (K.M.); (A.O.); (S.L.); (R.L.S.); (K.A.K.); (L.B.); (F.A.); (B.K.); (S.G.S.); (R.F.S.)
| | - 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 30322, USA; (K.M.); (A.O.); (S.L.); (R.L.S.); (K.A.K.); (L.B.); (F.A.); (B.K.); (S.G.S.); (R.F.S.)
- Center for Drug Discovery, Children’s Healthcare of Atlanta, Atlanta, GA 30322, USA
| | - Sazaly AbuBakar
- Tropical Infectious Diseases Research and Education Center, Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur 50603, Malaysia; (P.H.); (S.A.)
| | - 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 30322, USA; (K.M.); (A.O.); (S.L.); (R.L.S.); (K.A.K.); (L.B.); (F.A.); (B.K.); (S.G.S.); (R.F.S.)
| | - 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 30322, USA; (K.M.); (A.O.); (S.L.); (R.L.S.); (K.A.K.); (L.B.); (F.A.); (B.K.); (S.G.S.); (R.F.S.)
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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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Abstract
HIV reverse transcriptase (RT) is an enzyme that plays a major role in the replication cycle of HIV and has been a key target of anti-HIV drug development efforts. Because of the high genetic diversity of the virus, mutations in RT can impart resistance to various RT inhibitors. As the prevalence of drug resistance mutations is on the rise, it is necessary to design strategies that will lead to drugs less susceptible to resistance. Here we provide an in-depth review of HIV reverse transcriptase, current RT inhibitors, novel RT inhibitors, and mechanisms of drug resistance. We also present novel strategies that can be useful to overcome RT's ability to escape therapies through drug resistance. While resistance may not be completely avoidable, designing drugs based on the strategies and principles discussed in this review could decrease the prevalence of drug resistance.
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Affiliation(s)
- Maria E Cilento
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States.,Children's Healthcare of Atlanta, Atlanta, Georgia 30307, United States
| | - Karen A Kirby
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States.,Children's Healthcare of Atlanta, Atlanta, Georgia 30307, United States
| | - Stefan G Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States.,Children's Healthcare of Atlanta, Atlanta, Georgia 30307, United States
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32
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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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33
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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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34
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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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35
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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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36
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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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37
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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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38
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Hayashi S, Higashi-Kuwata N, Das D, Tomaya K, Yamada K, Murakami S, Venzon DJ, Hattori SI, Isogawa M, Sarafianos SG, Mitsuya H, Tanaka Y. 7-Deaza-7-fluoro modification confers on 4'-cyano-nucleosides potent activity against entecavir/adefovir-resistant HBV variants and favorable safety. Antiviral Res 2020; 176:104744. [PMID: 32084506 PMCID: PMC7164687 DOI: 10.1016/j.antiviral.2020.104744] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 10/26/2019] [Revised: 01/20/2020] [Accepted: 02/10/2020] [Indexed: 12/15/2022]
Abstract
We designed, synthesized and identified a novel nucleoside derivative, 4'-C-cyano-7-deaza-7-fluoro-2'-deoxyadenosine (CdFA), which exerts potent anti-HBV activity (IC50 ~26 nM) with favorable hepatocytotoxicity (CC50 ~56 μM). Southern blot analysis using wild-type HBV (HBVWT)-encoding-plasmid-transfected HepG2 cells revealed that CdFA efficiently suppresses the production of HBVWT (IC50 = 153.7 nM), entecavir (ETV)-resistant HBV carrying L180M/S202G/M204V substitutions (HBVETVR; IC50 = 373.2 nM), and adefovir dipivoxil (ADV)-resistant HBV carrying A181T/N236T substitutions (HBVADVR; IC50=192.6 nM), whereas ETV and ADV were less potent against HBVETVR and HBVADVR (IC50: >1,000 and 4,022.5 nM, respectively). Once-daily peroral administration of CdFA to human-liver-chimeric mice over 14 days (1 mg/kg/day) comparably blocked HBVWT and HBVETVR viremia by 0.7 and 1.2 logs, respectively, without significant changes in body-weight or serum human-albumin levels, although ETV only slightly suppressed HBVETVR viremia (CdFA vs ETV; p = 0.032). Molecular modeling suggested that ETV-TP has good nonpolar interactions with HBVWT reverse transcriptase (RTWT)'s Met204 and Asp205, while CdFA-TP fails to interact with Met204, in line with the relatively inferior activity against HBVWT of CdFA compared to ETV (IC50: 0.026 versus 0.003 nM). In contrast, the 4'-cyano of CdFA-TP forms good nonpolar contacts with RTWT's Leu180 and RTETVR's Met180, while ETV-TP loses interactions with RTETVR's Met180, explaining in part why ETV is less potent against HBVETVR than CdFA. The present results show that CdFA exerts potent activity against HBVWT, HBVETVR and HBVADVR with enhanced safety and that 7-deaza-7-fluoro modification confers potent activity against drug-resistant HBV variants and favorable safety, shedding light to further design more potent and safer anti-HBV nucleoside analogs.
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Affiliation(s)
- Sanae Hayashi
- Department of Virology & Liver Unit, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Nobuyo Higashi-Kuwata
- Department of Refractory Viral Infections, National Center for Global Health & Medicine Research Institute, Tokyo, Japan
| | - Debananda Das
- Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kota Tomaya
- Biochemicals Division, Yamasa Corporation, Choshi, Chiba, Japan
| | - Kohei Yamada
- Biochemicals Division, Yamasa Corporation, Choshi, Chiba, Japan
| | - Shuko Murakami
- Department of Virology & Liver Unit, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - David J Venzon
- Biostatistics and Data Management Section, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Shin-Ichiro Hattori
- Department of Refractory Viral Infections, National Center for Global Health & Medicine Research Institute, Tokyo, Japan
| | - Masanori Isogawa
- Department of Virology & Liver Unit, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Stefan G Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia
| | - Hiroaki Mitsuya
- Department of Refractory Viral Infections, National Center for Global Health & Medicine Research Institute, Tokyo, Japan; Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA; Department of Clinical Sciences, Kumamoto University Hospital, Kumamoto, Japan.
| | - Yasuhito Tanaka
- Department of Virology & Liver Unit, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan.
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Wang L, Sarafianos SG, Wang Z. Cutting into the Substrate Dominance: Pharmacophore and Structure-Based Approaches toward Inhibiting Human Immunodeficiency Virus Reverse Transcriptase-Associated Ribonuclease H. Acc Chem Res 2020; 53:218-230. [PMID: 31880912 DOI: 10.1021/acs.accounts.9b00450] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Human immunodeficiency virus (HIV) reverse transcriptase (RT) contains two distinct functional domains: a DNA polymerase (pol) domain and a ribonuclease H (RNase H) domain, both of which are required for viral genome replication. Over the last 3 decades, RT has been at the forefront of HIV drug discovery efforts with numerous nucleoside reverse transcriptase inhibitors (NRTIs) and non-nucleoside reverse transcriptase inhibitors (NNRTIs) approved by the FDA. However, all these RT inhibitors target only the pol function, and inhibitors of RT-associated RNase H have yet to enter the development pipeline, which in itself manifests both the opportunity and challenges of targeting RNase H: if developed, RT RNase H inhibitors would represent a mechanistically novel class of HIV drugs that can be particularly valuable in treating HIV strains resistant to current drugs. The challenges include (1) the difficulty in selectively targeting RT RNase H over RT pol due to their close interplay both spatially and temporally and over HIV-1 integrase strand transfer (INST) activity because of their active site similarities; (2) to a larger extent, the inability of active site inhibitors to confer significant antiviral effect, presumably due to a steep substrate barrier by which the pre-existing substrate prevents access of small molecules to the active site. As a result, previously reported RT RNase H inhibitors typically lacked target specificity and significant antiviral potency. Achieving meaningful antiviral activity via active site targeting likely entails selective and ultrapotent RNase H inhibition to allow small molecules to cut into the dominance of substrates. Based on a pharmacophore model informed by prior work, we designed and redesigned a few metal-chelating chemotypes, such as 2-hydroxyisoquinolinedione (HID), hydroxypyridonecarboxylic acid (HPCA), 3-hydroxypyrimidine-2,4-dione (HPD), and N-hydroxythienopyrimidine-2,4-dione (HTPD). Analogues of these chemotypes generally exhibited improved potency and selectivity inhibiting RT RNase H over the best previous compounds and further validated the pharmacophore model. Extended structure-activity relationship (SAR) on the HPD inhibitor type by mainly altering the linkage generated a few subtypes showing exceptional potency (single-digit nanomolar) and excellent selectivity over the inhibition of RT pol and INST. In parallel, a structure-based approach also allowed us to design a unique double-winged HPD subtype to potently and selectively inhibit RT RNase H and effectively compete against the RNA/DNA substrate. Significantly, all potent HPD subtypes consistently inhibited HIV-1 in the cell culture, suggesting that carefully designed active site RNase H inhibitors with ultrapotency could partially overcome the barrier to antiviral phenotype. Overall, in addition to identifying our own inhibitor types, our medicinal chemistry efforts demonstrated the value of pharmacophore and structure-based approaches in designing active side-directed RNase H inhibitors and could provide a viable path to validating RNase H as a novel antiviral target.
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Affiliation(s)
- Lei Wang
- State Key Laboratory of Fine Chemicals, Department of Pharmacy, School of Chemical Engineering, Dalian University of Technology, Dalian 116024, China
| | - Stefan G. Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Zhengqiang Wang
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, Minnesota 55455, United States
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40
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Abstract
The ribonuclease H (RNH) activity of HIV-1 reverse transcriptase (RT) is essential for viral replication and can be a target for drug development. Yet, no RNH inhibitor to date has substantial antiviral activity to allow advancement into clinical development. Herein, we describe our characterization of the detailed binding mechanisms of RNH active-site inhibitors, YLC2-155 and ZW566, that bind to the RNH domain through divalent metal ions, using NMR, molecular docking, and quantum mechanical calculations. In the presence of Mg2+, NMR spectra of RNH exhibited split (two) resonances for some residues upon inhibitor binding, suggesting two binding modes, an observation consistent with the docking results. The relative populations of the two binding conformers were independent of inhibitor or Mg2+ concentration, with one conformation consistently more favored. In our docking study, one distinctive pose of ZW566 showed more interactions with surrounding residues of RNH compared to the analogous binding pose of YLC2-155. Inhibitor titration experiments revealed a lower dissociation constant for ZW566 compared to YLC2-155, in agreement with its higher inhibitory activity. Mg2+ titration data also indicated a stronger dependence on Mg2+ for the RNH interaction with ZW566 compared to YLC2-155. Combined docking and quantum mechanical calculation results suggest that stronger metal coordination as well as more protein-inhibitor interactions may account for the higher binding affinity of ZW566. These findings support the idea that strategies for the development of potent competitive active site RNH inhibitors should take into account not only metal-inhibitor coordination but also protein-inhibitor interaction and conformational selectivity.
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Affiliation(s)
- Zhaoyong Xi
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15260, United States
| | - Zhengqiang Wang
- Center for Drug Design, College of Pharmacy, University of Minnesota, 516 Delaware Street SE, PWB 7-215,
MMC 204, Minneapolis, Minnesota 55455, United States
| | - Stefan G. Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States
| | - Nataliya S. Myshakina
- Department of Natural Science, Chatham University, Woodland Road, Pittsburgh, Pennsylvania 15232, United States
| | - Rieko Ishima
- Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Avenue, Pittsburgh, Pennsylvania 15260, United States
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Njenda DT, Aralaguppe SG, Singh K, Rao R, Sönnerborg A, Sarafianos SG, Neogi U. Antiretroviral potency of 4'-ethnyl-2'-fluoro-2'-deoxyadenosine, tenofovir alafenamide and second-generation NNRTIs across diverse HIV-1 subtypes. J Antimicrob Chemother 2019; 73:2721-2728. [PMID: 30053052 DOI: 10.1093/jac/dky256] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 06/04/2018] [Indexed: 01/21/2023] Open
Abstract
Objectives 4'-Ethnyl-2'-fluoro-2'-deoxyadenosine (EFdA) is a novel translocation-defective reverse transcriptase inhibitor. We investigated the virological and biochemical inhibitory potentials of EFdA against a broad spectrum of subtype-specific chimeric viruses and compared it with tenofovir alafenamide, nevirapine, efavirenz, rilpivirine and etravirine. Methods pNL4.3 chimeric viruses encoding gag-pol from treatment-naive patients (n = 24) and therapy-failure patients (n = 3) and a panel of reverse transcriptase inhibitor-resistant strains (n = 7) were used to compare the potency of reverse transcriptase inhibitor drugs. The phenotypic drug susceptibility assay was performed using TZM-bl cells. In vitro inhibition assays were done using patient-derived reverse transcriptase. IC50 values of NNRTIs were calculated using a PicoGreen-based spectrophotometric assay. Steady-state kinetics were used to determine the apparent binding affinity (Km.dNTP) of triphosphate form of EFdA (EFdA-TP) and dATP. Results Among the chimeric treatment-naive viruses, EFdA had an ex vivo antiretroviral activity [median (IQR) EC50 = 1.4 nM (0.6-2.1 nM)] comparable to that of tenofovir alafenamide [1.6 nM (0.5-3.6 nM)]. Subtype-specific differences were found for etravirine (P = 0.004) and rilpivirine (P = 0.017), where HIV-1C had the highest EC50 values. EFdA had a greater comparative efficiency [calculated by dividing the efficiency of monophosphate form of EFdA (EFdA-MP) incorporation (kcat.EFdA-TP/Km.EFdA-TP) over the efficiency of dATP incorporation (kcat.dATP/Km.dATP)] compared with the natural substrate dATP, with a fold change of between 1.6 and 3.2. Ex vivo analysis on reverse transcriptase inhibitor-resistant strains showed EFdA to have a higher potency. Despite the presence of rilpivirine DRMs, some non-B strains showed hypersusceptibility to rilpivirine. Conclusions Our combined virological and biochemical data suggest that EFdA inhibits both WT and reverse transcriptase inhibitor-resistant viruses efficiently in a subtype-independent manner. In contrast, HIV-1C is least susceptible to etravirine and rilpivirine.
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Affiliation(s)
- Duncan T Njenda
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Stockholm, Sweden.,Division of Medical Virology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Shambhu G Aralaguppe
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Kamalendra Singh
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Stockholm, Sweden.,Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, USA.,Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Rohit Rao
- Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
| | - Anders Sönnerborg
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Stockholm, Sweden.,Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden
| | - Stefan G Sarafianos
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO, USA.,Bond Life Sciences Center, University of Missouri, Columbia, MO, USA.,Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, USA
| | - Ujjwal Neogi
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Huddinge, Stockholm, Sweden
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Martinez-Lopez A, Persaud M, Chavez MP, Zhang H, Rong L, Liu S, Wang TT, Sarafianos SG, Diaz-Griffero F. Glycosylated diphyllin as a broad-spectrum antiviral agent against Zika virus. EBioMedicine 2019; 47:269-283. [PMID: 31501074 PMCID: PMC6796538 DOI: 10.1016/j.ebiom.2019.08.060] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 08/24/2019] [Accepted: 08/24/2019] [Indexed: 11/27/2022] Open
Abstract
Background Flaviviruses such as Zika cause sporadic pandemic outbreaks worldwide. There is an urgent need for anti-Zika virus (ZIKV) drugs to prevent mother-to-child transmission of ZIKV, new infections in high-risk populations, and the infection of medical personnel in ZIKV-affected areas. Methods Here, we showed that the small molecule 6-deoxyglucose-diphyllin (DGP) exhibited anti-ZIKV activity both in vitro and in vivo. DGP potently blocked ZIKV infection across all human and monkey cell lines tested. DGP also displayed broad-spectrum antiviral activity against other flaviviruses. Remarkably, DGP prevented ZIKV-induced mortality in mice lacking the type I interferon receptor (Ifnar1−/−). Cellular and virological experiments showed that DGP blocked ZIKV at a pre-fusion step or during fusion, which prevented the delivery of viral contents into the cytosol of the target cell. Mechanistic studies revealed that DGP prevented the acidification of endosomal/lysosomal compartments in target cells, thus inhibiting ZIKV fusion with cellular membranes and infection. Findings These investigations revealed that DGP inhibits ZIKV infection in vitro and in vivo. Interpretation The small molecule DGP has great potential for preclinical studies and the ability to inhibit ZIKV infection in humans.
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Affiliation(s)
- Alicia Martinez-Lopez
- Department of Microbiology and Immunology, Albert Einstein College of Medicine Bronx, NY 10461, USA
| | - Mirjana Persaud
- Department of Microbiology and Immunology, Albert Einstein College of Medicine Bronx, NY 10461, USA
| | - Maritza Puray Chavez
- Laboratory of Biochemical Pharmacology Emory University, Emory University, Atlanta, GA 30322, USA
| | - Hongjie Zhang
- School of Chinese Medicine, Hong Kong Baptist University, 7 Baptist University Road, Kowloon Tong, Hong Kong SAR, People's Republic of China
| | - Lijun Rong
- Microbiology and Immunology College of Medicine, University of Illinois at Chicago, IL 60612, USA
| | - Shufeng Liu
- Laboratory of Vector-borne Viral Diseases, Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20903, USA
| | - Tony T Wang
- Laboratory of Vector-borne Viral Diseases, Division of Viral Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20903, USA
| | - Stefan G Sarafianos
- Laboratory of Biochemical Pharmacology Emory University, Emory University, Atlanta, GA 30322, USA
| | - Felipe Diaz-Griffero
- Department of Microbiology and Immunology, Albert Einstein College of Medicine Bronx, NY 10461, USA.
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Slack RL, Ilina TV, Xi Z, Giacobbi NS, Kawai G, Parniak MA, Sarafianos SG, Sluis Cremer N, Ishima R. Conformational Changes in HIV-1 Reverse Transcriptase that Facilitate Its Maturation. Structure 2019; 27:1581-1593.e3. [PMID: 31471129 DOI: 10.1016/j.str.2019.08.004] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 07/10/2019] [Accepted: 08/09/2019] [Indexed: 01/18/2023]
Abstract
HIV-1 reverse transcriptase (RT) is translated as part of the Gag-Pol polyprotein that is proteolytically processed by HIV-1 protease (PR) to finally become a mature heterodimer, composed of a p66 and a p66-derived 51-kDa subunit, p51. Our previous work suggested that tRNALys3 binding to p66/p66 introduces conformational changes in the ribonuclease (RNH) domain of RT that facilitate efficient cleavage of p66 to p51 by PR. In this study, we characterized the conformational changes in the RNH domain of p66/p66 imparted by tRNALys3 using NMR. Moreover, the importance of tRNALys3 in RT maturation was confirmed in cellulo by modulating the levels of Lys-tRNA synthetase, which affects recruitment of tRNALys3 to the virus. We also employed nonnucleoside RT inhibitors, to modulate the p66 dimer-monomer equilibrium and monitor the resulting structural changes. Taken together, our data provide unique insights into the conformational changes in p66/p66 that drive PR cleavage.
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Affiliation(s)
- Ryan L Slack
- Department of Structural Biology, University of Pittsburgh School of Medicine, Room 1037, Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Tatiana V Ilina
- Department of Structural Biology, University of Pittsburgh School of Medicine, Room 1037, Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Zhaoyong Xi
- Department of Structural Biology, University of Pittsburgh School of Medicine, Room 1037, Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA
| | - Nicholas S Giacobbi
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Gota Kawai
- Department of Life and Environmental Sciences, Chiba Institute of Technology, Chiba, Japan
| | - Michael A Parniak
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
| | - Stefan G Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Nicolas Sluis Cremer
- Department of Medicine, Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA.
| | - Rieko Ishima
- Department of Structural Biology, University of Pittsburgh School of Medicine, Room 1037, Biomedical Science Tower 3, 3501 Fifth Avenue, Pittsburgh, PA 15260, USA.
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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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Huber AD, Pineda DL, Liu D, Boschert KN, Gres AT, Wolf JJ, Coonrod EM, Tang J, Laughlin TG, Yang Q, Puray-Chavez MN, Ji J, Singh K, Kirby KA, Wang Z, Sarafianos SG. Novel Hepatitis B Virus Capsid-Targeting Antiviral That Aggregates Core Particles and Inhibits Nuclear Entry of Viral Cores. ACS Infect Dis 2019; 5:750-758. [PMID: 30582687 DOI: 10.1021/acsinfecdis.8b00235] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
An estimated 240 million are chronically infected with hepatitis B virus (HBV), which can lead to liver disease, cirrhosis, and hepatocellular carcinoma. Currently, HBV treatment options include only nucleoside reverse transcriptase inhibitors and the immunomodulatory agent interferon alpha, and these treatments are generally not curative. New treatments with novel mechanisms of action, therefore, are highly desired for HBV therapy. The viral core protein (Cp) has gained attention as a possible therapeutic target because of its vital roles in the HBV life cycle. Several classes of capsid assembly effectors (CAEs) have been described in detail, and these compounds all increase capsid assembly rate but inhibit HBV replication by different mechanisms. In this study, we have developed a thermal shift-based screening method for CAE discovery and characterization, filling a much-needed gap in high-throughput screening methods for capsid-targeting molecules. Using this approach followed by cell-based screening, we identified the compound HF9C6 as a CAE with low micromolar potency against HBV replication. HF9C6 caused large multicapsid aggregates when capsids were assembled in vitro and analyzed by transmission electron microscopy. Interestingly, when HBV-expressing cells were treated with HF9C6, Cp was excluded from cell nuclei, suggesting that this compound may inhibit nuclear entry of Cp and capsids. Furthermore, mutational scanning of Cp suggested that HF9C6 binds the known CAE binding pocket, indicating that key Cp-compound interactions within this pocket have a role in determining the CAE mechanism of action.
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Affiliation(s)
- Andrew D. Huber
- Christopher S. Bond Life Sciences Center, University of Missouri, 1201 E. Rollins St., Columbia, Missouri 65211, United States
| | - Dallas L. Pineda
- Christopher S. Bond Life Sciences Center, University of Missouri, 1201 E. Rollins St., Columbia, Missouri 65211, United States
- Department of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, Missouri 65211, United States
| | - Dandan Liu
- Christopher S. Bond Life Sciences Center, University of Missouri, 1201 E. Rollins St., Columbia, Missouri 65211, United States
- Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine, M616 Medical Sciences Building, Columbia, Missouri 65211, United States
| | - Kelsey N. Boschert
- Christopher S. Bond Life Sciences Center, University of Missouri, 1201 E. Rollins St., Columbia, Missouri 65211, United States
- Department of Nutrition and Exercise Physiology, University of Missouri, 204 Gwynn Hall, Columbia, Missouri 65211, United States
| | - Anna T. Gres
- Christopher S. Bond Life Sciences Center, University of Missouri, 1201 E. Rollins St., Columbia, Missouri 65211, United States
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| | - Jennifer J. Wolf
- Christopher S. Bond Life Sciences Center, University of Missouri, 1201 E. Rollins St., Columbia, Missouri 65211, United States
- Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine, M616 Medical Sciences Building, Columbia, Missouri 65211, United States
| | - Emily M. Coonrod
- Christopher S. Bond Life Sciences Center, University of Missouri, 1201 E. Rollins St., Columbia, Missouri 65211, United States
- Division of Biological Sciences, University of Missouri, 105 Tucker Hall, Columbia, Missouri 65211, United States
| | - Jing Tang
- Center for Drug Design, Academic Health Center, University of Minnesota, 312 Church St. SE, Minneapolis, Minnesota 55455, United States
| | - Thomas G. Laughlin
- Christopher S. Bond Life Sciences Center, University of Missouri, 1201 E. Rollins St., Columbia, Missouri 65211, United States
- Department of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, Missouri 65211, United States
| | - Qiongying Yang
- Christopher S. Bond Life Sciences Center, University of Missouri, 1201 E. Rollins St., Columbia, Missouri 65211, United States
- Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine, M616 Medical Sciences Building, Columbia, Missouri 65211, United States
| | - Maritza N. Puray-Chavez
- Christopher S. Bond Life Sciences Center, University of Missouri, 1201 E. Rollins St., Columbia, Missouri 65211, United States
- Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine, M616 Medical Sciences Building, Columbia, Missouri 65211, United States
| | - Juan Ji
- Christopher S. Bond Life Sciences Center, University of Missouri, 1201 E. Rollins St., Columbia, Missouri 65211, United States
- Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine, M616 Medical Sciences Building, Columbia, Missouri 65211, United States
| | - Kamalendra Singh
- Christopher S. Bond Life Sciences Center, University of Missouri, 1201 E. Rollins St., Columbia, Missouri 65211, United States
- Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine, M616 Medical Sciences Building, Columbia, Missouri 65211, United States
| | - Karen A. Kirby
- Christopher S. Bond Life Sciences Center, University of Missouri, 1201 E. Rollins St., Columbia, Missouri 65211, United States
- Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine, M616 Medical Sciences Building, Columbia, Missouri 65211, United States
| | - Zhengqiang Wang
- Center for Drug Design, Academic Health Center, University of Minnesota, 312 Church St. SE, Minneapolis, Minnesota 55455, United States
| | - Stefan G. Sarafianos
- Christopher S. Bond Life Sciences Center, University of Missouri, 1201 E. Rollins St., Columbia, Missouri 65211, United States
- Department of Biochemistry, University of Missouri, 117 Schweitzer Hall, Columbia, Missouri 65211, United States
- Department of Molecular Microbiology & Immunology, University of Missouri School of Medicine, M616 Medical Sciences Building, Columbia, Missouri 65211, United States
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Singh K, Sarafianos SG, Sönnerborg A. Long-Acting Anti-HIV Drugs Targeting HIV-1 Reverse Transcriptase and Integrase. Pharmaceuticals (Basel) 2019; 12:E62. [PMID: 31010004 PMCID: PMC6631967 DOI: 10.3390/ph12020062] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [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: 03/17/2019] [Revised: 04/16/2019] [Accepted: 04/18/2019] [Indexed: 12/20/2022] Open
Abstract
One of the major factors contributing to HIV-1 drug resistance is suboptimal adherence to combination antiretroviral therapy (cART). Currently, recommended cART for HIV-1 treatment is a three-drug combination, whereas the pre-exposure prophylaxis (PrEP) regimens consist of one or two antivirals. Treatment regimens require adherence to a once or twice (in a subset of patients) daily dose. Long-acting formulations such as injections administered monthly could improve adherence and convenience, and thereby have potential to enhance the chances of expected outcomes, although long-lasting drug concentrations can also contribute to clinical issues like adverse events and development of drug resistance. Globally, two long-acting antivirals have been approved, and fifteen are in clinical trials. More than half of investigational long-acting antivirals target HIV-1 reverse transcriptase (HIV-1 RT) and/or integrase (HIV-1 IN). Here, we discuss the status and potential of long-acting inhibitors, including rilpivirine (RPV), dapivirine (DPV), and 4-ethynyl-2-fluoro-2-deoxyadenosine (EFdA; also known as MK-8591), which target RT, and cabotegravir (CAB), which targets IN. The outcomes of various clinical trials appear quite satisfactory, and the future of long-acting HIV-1 regimens appears bright.
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Affiliation(s)
- Kamal Singh
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO 65211, USA.
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Huddinge 14186, Stockholm, Sweden.
| | - Stefan G Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA.
| | - Anders Sönnerborg
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia, MO 65211, USA.
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Huddinge 14186, Stockholm, Sweden.
- Division of Infectious Diseases, Department of Medicine Huddinge, Karolinska Institute, Huddinge 14186, Stockholm, Sweden.
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Tang J, Do HT, Huber AD, Casey MC, Kirby KA, Wilson DJ, Kankanala J, Parniak MA, Sarafianos SG, Wang Z. Pharmacophore-based design of novel 3-hydroxypyrimidine-2,4-dione subtypes as inhibitors of HIV reverse transcriptase-associated RNase H: Tolerance of a nonflexible linker. Eur J Med Chem 2019; 166:390-399. [PMID: 30739822 PMCID: PMC6459026 DOI: 10.1016/j.ejmech.2019.01.081] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [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: 12/19/2018] [Revised: 01/17/2019] [Accepted: 01/30/2019] [Indexed: 11/29/2022]
Abstract
The pharmacophore of active site inhibitors of human immunodeficiency virus (HIV) reverse transcriptase (RT)-associated RNase H typically entails a flexible linker connecting the chelating core and the hydrophobic aromatics. We report herein that novel 3-hydroxypyrimidine-2,4-dione (HPD) subtypes with a nonflexible C-6 carbonyl linkage exhibited potent and selective biochemical inhibitory profiles with strong RNase H inhibition at low nM, weak to moderate integrase strand transfer (INST) inhibition at low μM, and no to marginal RT polymerase (pol) inhibition up to 10 μM. A few analogues also demonstrated significant antiviral activity without cytotoxicity. The overall inhibitory profile is comparable to or better than that of previous HPD subtypes with a flexible C-6 linker, suggesting that the nonflexible carbonyl linker can be tolerated in the design of novel HIV RNase H active site inhibitors.
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Affiliation(s)
- Jing Tang
- 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
| | - Andrew D Huber
- Department of Veterinary Pathobiology, College of Veterinary Medicine, University of Missouri, Christopher S. Bond Life Sciences Center, Columbia, MO, 65211, 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
| | - Karen A Kirby
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Christopher S. Bond Life Sciences Center, Columbia, MO, 65211, USA; Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Daniel J Wilson
- 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
| | - Michael A Parniak
- Department of Microbiology & Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, 15219, USA
| | - Stefan G Sarafianos
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Christopher S. Bond Life Sciences Center, Columbia, MO, 65211, USA; Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA; Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Zhengqiang Wang
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN, 55455, USA.
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Tang J, Huber AD, Pineda DL, Boschert KN, Wolf JJ, Kankanala J, Xie J, Sarafianos SG, Wang Z. 5-Aminothiophene-2,4-dicarboxamide analogues as hepatitis B virus capsid assembly effectors. Eur J Med Chem 2019; 164:179-192. [PMID: 30594676 PMCID: PMC6362850 DOI: 10.1016/j.ejmech.2018.12.047] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 12/06/2018] [Accepted: 12/19/2018] [Indexed: 02/08/2023]
Abstract
Chronic hepatitis B virus (HBV) infection represents a major health threat. Current FDA-approved drugs do not cure HBV. Targeting HBV core protein (Cp) provides an attractive approach toward HBV inhibition and possibly infection cure. We have previously identified and characterized a 5-amino-3-methylthiophene-2,4-dicarboxamide (ATDC) compound as a structurally novel hit for capsid assembly effectors (CAEs). We report herein hit validation through studies on absorption, distribution, metabolism and excretion (ADME) properties and pharmacokinetics (PK), and hit optimization via analogue synthesis aiming to probe the structure-activity relationship (SAR) and structure-property relationship (SPR). In the end, these medicinal chemistry efforts led to the identification of multiple analogues strongly binding to Cp, potently inhibiting HBV replication in nanomolar range without cytotoxicity, and exhibiting good oral bioavailability (F). Two of our analogues, 19o (EC50 = 0.11 μM, CC50 > 100 μM, F = 25%) and 19k (EC50 = 0.31 μM, CC50 > 100 μM, F = 46%), displayed overall lead profiles superior to reported CAEs 7-10 used in our studies.
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Affiliation(s)
- Jing Tang
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN, 55455, 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
| | - Dallas L Pineda
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA; Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA
| | - Kelsey N Boschert
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA; Department of Nutrition and Exercise Physiology, University of Missouri, Columbia, MO, 65211, USA
| | - Jennifer J Wolf
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA; Department of Molecular Microbiology & Immunology, School of Medicine, University of Missouri, Columbia, MO, 65211, USA
| | - Jayakanth Kankanala
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Jiashu Xie
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Stefan G Sarafianos
- Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, 65211, USA; Department of Biochemistry, University of Missouri, Columbia, MO, 65211, USA; Department of Molecular Microbiology & Immunology, School of Medicine, University of Missouri, Columbia, MO, 65211, USA
| | - Zhengqiang Wang
- Center for Drug Design, College of Pharmacy, University of Minnesota, Minneapolis, MN, 55455, USA.
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Wu X, Xu G, Li X, Xu W, Li Q, Liu W, Kirby KA, Loh ML, Li J, Sarafianos SG, Qu CK. Small Molecule Inhibitor that Stabilizes the Autoinhibited Conformation of the Oncogenic Tyrosine Phosphatase SHP2. J Med Chem 2018; 62:1125-1137. [PMID: 30457860 DOI: 10.1021/acs.jmedchem.8b00513] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Genetic mutations in the phosphatase PTPN11 (SHP2) are associated with childhood leukemias. These mutations cause hyperactivation of SHP2 due to the disruption of the autoinhibitory conformation. By targeting the activation-associated protein conformational change, we have identified an SHP2 inhibitor ( E)-1-(1-(5-(3-(2,4-dichlorophenyl)acryloyl)-2-ethoxy-4-hydroxybenzyl)-1,2,5,6-tetrahydropyridin-3-yl)-1 H-benzo[ d]imidazol-2(3 H)-one (LY6, 1) using computer-aided drug design database screening combined with cell-based assays. This compound inhibited SHP2 with an IC50 value of 9.8 μM, 7-fold more selective for SHP2 than the highly related SHP1. Fluorescence titration, thermal shift, and microscale thermophoresis quantitative binding assays confirmed its direct binding to SHP2. This compound was further verified to effectively inhibit SHP2-mediated cell signaling and proliferation. Furthermore, mouse and patient leukemia cells with PTPN11 activating mutations were more sensitive to this inhibitor than wild-type cells. This small molecule SHP2 inhibitor has a potential to serve as a lead compound for further optimization studies to develop novel anti-SHP2 therapeutic agents.
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Affiliation(s)
- Xiaoqin Wu
- Department of Pediatrics, Division of Hematology/Oncology, Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta , Emory University School of Medicine , Atlanta , Georgia 30322 , United States
| | - Gang Xu
- Department of Medicine, Division of Hematology and Oncology, Case Comprehensive Cancer Center , Case Western Reserve University , Cleveland , Ohio 44106 , United States
| | - Xiaobo Li
- Department of Pediatrics, Division of Hematology/Oncology, Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta , Emory University School of Medicine , Atlanta , Georgia 30322 , United States.,Department of Medicine, Division of Hematology and Oncology, Case Comprehensive Cancer Center , Case Western Reserve University , Cleveland , Ohio 44106 , United States
| | - Weiren Xu
- Department of Medicine, Division of Hematology and Oncology, Case Comprehensive Cancer Center , Case Western Reserve University , Cleveland , Ohio 44106 , United States
| | - Qianjin Li
- Department of Pediatrics, Division of Hematology/Oncology, Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta , Emory University School of Medicine , Atlanta , Georgia 30322 , United States
| | - Wei Liu
- Department of Medicine, Division of Hematology and Oncology, Case Comprehensive Cancer Center , Case Western Reserve University , Cleveland , Ohio 44106 , United States
| | - Karen A Kirby
- Department of Pediatrics, Laboratory of Biochemical Pharmacology , Emory University School of Medicine , Atlanta , Georgia 30322 , United States
| | - Mignon L Loh
- Department of Pediatrics, Division of Pediatric Hematology-Oncology , University of California, San Francisco , San Francisco , California 94122 , United States
| | - Jun Li
- School of Pharmacy , Anhui Medical University , Hefei 230032 , China
| | - Stefan G Sarafianos
- Department of Pediatrics, Laboratory of Biochemical Pharmacology , Emory University School of Medicine , Atlanta , Georgia 30322 , United States
| | - Cheng-Kui Qu
- Department of Pediatrics, Division of Hematology/Oncology, Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta , Emory University School of Medicine , Atlanta , Georgia 30322 , United States.,Department of Medicine, Division of Hematology and Oncology, Case Comprehensive Cancer Center , Case Western Reserve University , Cleveland , Ohio 44106 , United States
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50
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de la Higuera I, Ferrer-Orta C, Moreno E, de Ávila AI, Soria ME, Singh K, Caridi F, Sobrino F, Sarafianos SG, Perales C, Verdaguer N, Domingo E. Contribution of a Multifunctional Polymerase Region of Foot-and-Mouth Disease Virus to Lethal Mutagenesis. J Virol 2018; 92:e01119-18. [PMID: 30068642 PMCID: PMC6158410 DOI: 10.1128/jvi.01119-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [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: 06/28/2018] [Accepted: 07/23/2018] [Indexed: 01/01/2023] Open
Abstract
Viral RNA-dependent RNA polymerases (RdRps) are major determinants of high mutation rates and generation of mutant spectra that mediate RNA virus adaptability. The RdRp of the picornavirus foot-and-mouth disease virus (FMDV), termed 3D, is a multifunctional protein that includes a nuclear localization signal (NLS) in its N-terminal region. Previous studies documented that some amino acid substitutions within the NLS altered nucleotide recognition and enhanced the incorporation of the mutagenic purine analogue ribavirin in viral RNA, but the mutants tested were not viable and their response to lethal mutagenesis could not be studied. Here we demonstrate that NLS amino acid substitution M16A of FMDV serotype C does not affect infectious virus production but accelerates ribavirin-mediated virus extinction. The mutant 3D displays polymerase activity, RNA binding, and copying processivity that are similar to those of the wild-type enzyme but shows increased ribavirin-triphosphate incorporation. Crystal structures of the mutant 3D in the apo and RNA-bound forms reveal an expansion of the template entry channel due to the replacement of the bulky Met by Ala. This is a major difference with other 3D mutants with altered nucleotide analogue recognition. Remarkably, two distinct loop β9-α11 conformations distinguish 3Ds that exhibit higher or lower ribavirin incorporation than the wild-type enzyme. This difference identifies a specific molecular determinant of ribavirin sensitivity of FMDV. Comparison of several polymerase mutants indicates that different domains of the molecule can modify nucleotide recognition and response to lethal mutagenesis. The connection of this observation with current views on quasispecies adaptability is discussed.IMPORTANCE The nuclear localization signal (NLS) of the foot-and-mouth disease virus (FMDV) polymerase includes residues that modulate the sensitivity to mutagenic agents. Here we have described a viable NLS mutant with an amino acid replacement that facilitates virus extinction by ribavirin. The corresponding polymerase shows increased incorporation of ribavirin triphosphate and local structural modifications that implicate the template entry channel. Specifically, comparison of the structures of ribavirin-sensitive and ribavirin-resistant FMDV polymerases has identified loop β9-α11 conformation as a determinant of sensitivity to ribavirin mutagenesis.
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Affiliation(s)
| | - Cristina Ferrer-Orta
- Structural Biology Unit, Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Barcelona, Spain
| | - Elena Moreno
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Cantoblanco, Madrid, Spain
| | - Ana Isabel de Ávila
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Cantoblanco, Madrid, Spain
| | - María Eugenia Soria
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Cantoblanco, Madrid, Spain
| | - Kamalendra Singh
- Christopher S. Bond Life Sciences Center and Department of Microbiology & Immunology, School of Medicine, University of Missouri, Columbia, Missouri, USA
| | - Flavia Caridi
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Cantoblanco, Madrid, Spain
| | - Francisco Sobrino
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Cantoblanco, Madrid, Spain
| | - Stefan G Sarafianos
- Christopher S. Bond Life Sciences Center and Department of Microbiology & Immunology, School of Medicine, University of Missouri, Columbia, Missouri, USA
| | - Celia Perales
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Cantoblanco, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
- Liver Unit, Internal Medicine, Laboratory of Malalties Hepàtiques, Vall d'Hebron Institut de Recerca-Hospital Universitari Vall d'Hebron (VHIR-HUVH), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Nuria Verdaguer
- Structural Biology Unit, Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Barcelona, Spain
| | - Esteban Domingo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Cantoblanco, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
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