1
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Feng Y, Nie J, Xie S, He Z, Hong H, Li J, Huang Y, Chen L, Li Y. Potassium xanthate-promoted reductive sulfuration reaction: from aldehydes to thiol, disulfide, and thioester derivatives. Chem Commun (Camb) 2024; 60:1140-1143. [PMID: 38189083 DOI: 10.1039/d3cc05637f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Herein, we developed a synthetic strategy for the direct construction of C-S bonds to obtain biologically active sulfur-containing compounds and a methodology involving the reductive sulfuration of aldehydes or ketones to obtain diverse substituted thiol, disulfide, and thioester derivatives. EtOCS2K is demonstrated as a potential substitute for the Berzelius reagent or Lawesson's reagent for the construction of C-S bonds.
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Affiliation(s)
- Yingqi Feng
- Jiangmen Key Laboratory of Synthetic Chemistry and Cleaner Production, School of Environmental & Chemical Engineering, Wuyi University, Jiangmen 529020, China.
| | - Jinli Nie
- Jiangmen Key Laboratory of Synthetic Chemistry and Cleaner Production, School of Environmental & Chemical Engineering, Wuyi University, Jiangmen 529020, China.
| | - Sijie Xie
- Jiangmen Key Laboratory of Synthetic Chemistry and Cleaner Production, School of Environmental & Chemical Engineering, Wuyi University, Jiangmen 529020, China.
| | - Ziqing He
- Jiangmen Key Laboratory of Synthetic Chemistry and Cleaner Production, School of Environmental & Chemical Engineering, Wuyi University, Jiangmen 529020, China.
| | - Huanliang Hong
- Jiangmen Key Laboratory of Synthetic Chemistry and Cleaner Production, School of Environmental & Chemical Engineering, Wuyi University, Jiangmen 529020, China.
| | - Jian Li
- Jiangmen Key Laboratory of Synthetic Chemistry and Cleaner Production, School of Environmental & Chemical Engineering, Wuyi University, Jiangmen 529020, China.
| | - Yubing Huang
- Jiangmen Key Laboratory of Synthetic Chemistry and Cleaner Production, School of Environmental & Chemical Engineering, Wuyi University, Jiangmen 529020, China.
| | - Lu Chen
- Jiangmen Key Laboratory of Synthetic Chemistry and Cleaner Production, School of Environmental & Chemical Engineering, Wuyi University, Jiangmen 529020, China.
| | - Yibiao Li
- Jiangmen Key Laboratory of Synthetic Chemistry and Cleaner Production, School of Environmental & Chemical Engineering, Wuyi University, Jiangmen 529020, China.
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2
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Bregnard TA, Fairchild D, Erlandsen H, Semenova IV, Szczepaniak R, Ahmed A, Weller SK, Korzhnev DM, Bezsonova I. Conformational exchange at a C 2H 2 zinc-binding site facilitates redox sensing by the PML protein. Structure 2023; 31:1086-1099.e6. [PMID: 37473756 PMCID: PMC10528520 DOI: 10.1016/j.str.2023.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 05/12/2023] [Accepted: 06/23/2023] [Indexed: 07/22/2023]
Abstract
The promyelocytic leukemia protein, PML, plays a vital role in the cellular response to oxidative stress; however, the molecular mechanism of its action remains poorly understood. Here, we identify redox-sensitive sites of PML. A molecule of PML is cysteine-rich and contains three zinc-binding domains including RING, B-box1, and B-box2. Using in vitro assays, we have compared the sensitivity of the isolated RING and B-box1 domains and shown that B-box1 is more sensitive to oxidation. NMR studies of PML dynamics showed that one of the Zn-coordination sites within the B-box1 undergoes significant conformational exchange, revealing a hotspot for exposure of reactive cysteines. In agreement with the in vitro data, enhancement of the B-box1 Zn-coordination dynamics led to more efficient recruitment of PML into PML nuclear bodies in cells. Overall, our results suggest that the increased sensitivity of B-box1 to oxidative stress makes this domain an important redox-sensing component of PML.
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Affiliation(s)
- Thomas A Bregnard
- Department of Molecular Biology and Biophysics, UCONN Health, Farmington, CT 06032, USA
| | - Daniel Fairchild
- Department of Molecular Biology and Biophysics, UCONN Health, Farmington, CT 06032, USA
| | - Heidi Erlandsen
- Center for Open Research Resources & Equipment, UCONN, Storrs, CT 06269, USA
| | - Irina V Semenova
- Department of Molecular Biology and Biophysics, UCONN Health, Farmington, CT 06032, USA
| | - Renata Szczepaniak
- Department of Molecular Biology and Biophysics, UCONN Health, Farmington, CT 06032, USA
| | - Affrin Ahmed
- Department of Molecular Biology and Biophysics, UCONN Health, Farmington, CT 06032, USA
| | - Sandra K Weller
- Department of Molecular Biology and Biophysics, UCONN Health, Farmington, CT 06032, USA
| | - Dmitry M Korzhnev
- Department of Molecular Biology and Biophysics, UCONN Health, Farmington, CT 06032, USA
| | - Irina Bezsonova
- Department of Molecular Biology and Biophysics, UCONN Health, Farmington, CT 06032, USA.
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3
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Rahman MA, Bissa M, Silva de Castro I, Helmold Hait S, Stamos JD, Bhuyan F, Hunegnaw R, Sarkis S, Gutowska A, Doster MN, Moles R, Hoang T, Miller Jenkins LM, Appella E, Venzon DJ, Choo-Wosoba H, Cardozo T, Baum MM, Appella DH, Robert-Guroff M, Franchini G. Vaccine plus microbicide effective in preventing vaginal SIV transmission in macaques. Nat Microbiol 2023; 8:905-918. [PMID: 37024617 PMCID: PMC10159859 DOI: 10.1038/s41564-023-01353-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 03/02/2023] [Indexed: 04/08/2023]
Abstract
The human immunodeficiency virus epidemic continues in sub-Saharan Africa, and particularly affects adolescent girls and women who have limited access to antiretroviral therapy. Here we report that the risk of vaginal simian immunodeficiency virus (SIV)mac251 acquisition is reduced by more than 90% using a combination of a vaccine comprising V1-deleted (V2 enhanced) SIV envelope immunogens with topical treatment of the zinc-finger inhibitor SAMT-247. Following 14 weekly intravaginal exposures to the highly pathogenic SIVmac251, 80% of a cohort of 20 macaques vaccinated and treated with SAMT-247 remained uninfected. In an arm of 18 vaccinated-only animals without microbicide, 40% of macaques remained uninfected. The combined SAMT-247/vaccine regimen was significantly more effective than vaccination alone. By analysing immune correlates of protection, we show that, by increasing zinc availability, SAMT-247 increases natural killer cytotoxicity and monocyte efferocytosis, and decreases T-cell activation to augment vaccine-induced protection.
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Affiliation(s)
- Mohammad Arif Rahman
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD, USA
| | - Massimiliano Bissa
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD, USA
| | | | - Sabrina Helmold Hait
- Section on Immune Biology of Retroviral Infection, National Cancer Institute, Bethesda, MD, USA
| | - James D Stamos
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD, USA
| | - Farzana Bhuyan
- Translational Autoinflammatory Diseases Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ruth Hunegnaw
- Section on Immune Biology of Retroviral Infection, National Cancer Institute, Bethesda, MD, USA
| | - Sarkis Sarkis
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD, USA
| | - Anna Gutowska
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD, USA
| | - Melvin N Doster
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD, USA
| | - Ramona Moles
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD, USA
| | - Tanya Hoang
- Section on Immune Biology of Retroviral Infection, National Cancer Institute, Bethesda, MD, USA
| | - Lisa M Miller Jenkins
- Collaborative Protein Technology Resource, Laboratory of Cell Biology, National Cancer Institute, Bethesda, MD, USA
| | - Ettore Appella
- Chemical Immunology Section, National Cancer Institute, Bethesda, MD, USA
| | - David J Venzon
- Biostatistics and Data Management Section, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Hyoyoung Choo-Wosoba
- Biostatistics and Data Management Section, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Timothy Cardozo
- New York University School of Medicine, NYU Langone Health, New York, NY, USA
| | - Marc M Baum
- Oak Crest Institute of Science, Monrovia, CA, USA
| | - Daniel H Appella
- Synthetic Bioactive Molecules Section, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Marjorie Robert-Guroff
- Section on Immune Biology of Retroviral Infection, National Cancer Institute, Bethesda, MD, USA
| | - Genoveffa Franchini
- Animal Models and Retroviral Vaccines Section, National Cancer Institute, Bethesda, MD, USA.
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4
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Investigation of the Low-Populated Excited States of the HIV-1 Nucleocapsid Domain. Viruses 2022; 14:v14030632. [PMID: 35337039 PMCID: PMC8950434 DOI: 10.3390/v14030632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/07/2022] [Accepted: 03/16/2022] [Indexed: 12/10/2022] Open
Abstract
The nucleocapsid domain (NCd), located at the C-terminus of the HIV-1 Gag protein, is involved in numerous stages of the replication cycle, such as the packaging of the viral genome and reverse transcription. It exists under different forms through the viral life cycle, depending on the processing of Gag by the HIV-1 protease. NCd is constituted of two adjacent zinc knuckles (ZK1 and ZK2), separated by a flexible linker and flanked by disordered regions. Here, conformational equilibria between a major and two minor states were highlighted exclusively in ZK2, by using CPMG and CEST NMR experiments. These minor states appear to be temperature dependent, and their populations are highest at physiological temperature. These minor states are present both in NCp7, the mature form of NCd, and in NCp9 and NCp15, the precursor forms of NCd, with increased populations. The role of these minor states in the targeting of NCd by drugs and its binding properties is discussed.
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5
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Mirzaie S, Abdi F, GhavamiNejad A, Lu B, Wu XY. Covalent Antiviral Agents. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1322:285-312. [PMID: 34258745 DOI: 10.1007/978-981-16-0267-2_11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Nowadays, many viral infections have emerged and are taking a huge toll on human lives globally. Meanwhile, viral resistance to current drugs has drastically increased. Hence, there is a pressing need to design potent broad-spectrum antiviral agents to treat a variety of viral infections and overcome viral resistance. Covalent inhibitors have the potential to achieve both goals owing to their biochemical efficiency, prolonged duration of action, and the capability to inhibit shallow, solvent-exposed substrate-binding domains. In this chapter, we review the structures, activities, and inhibition mechanisms of covalent inhibitors against severe acute respiratory syndrome coronavirus 2, dengue virus, enterovirus, hepatitis C virus, human immunodeficiency virus, and influenza viruses. We also discuss the application of in silico study in covalent inhibitor design.
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Affiliation(s)
- Sako Mirzaie
- Advanced Pharmaceutics and Drug Delivery Laboratory, Leslie L. Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada.
| | - Fatemeh Abdi
- Advanced Pharmaceutics and Drug Delivery Laboratory, Leslie L. Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Amin GhavamiNejad
- Advanced Pharmaceutics and Drug Delivery Laboratory, Leslie L. Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Brian Lu
- Advanced Pharmaceutics and Drug Delivery Laboratory, Leslie L. Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
| | - Xiao Yu Wu
- Advanced Pharmaceutics and Drug Delivery Laboratory, Leslie L. Dan Faculty of Pharmacy, University of Toronto, Toronto, ON, Canada
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6
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Dick A, Cocklin S. Recent Advances in HIV-1 Gag Inhibitor Design and Development. Molecules 2020; 25:molecules25071687. [PMID: 32272714 PMCID: PMC7181048 DOI: 10.3390/molecules25071687] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 03/31/2020] [Accepted: 04/05/2020] [Indexed: 02/06/2023] Open
Abstract
Acquired Immune Deficiency Syndrome (AIDS) treatment with combination antiretroviral therapy (cART) has improved the life quality of many patients since its implementation. However, resistance mutations and the accumulation of severe side effects associated with cART remain enormous challenges that need to be addressed with the continual design and redesign of anti-HIV drugs. In this review, we focus on the importance of the HIV-1 Gag polyprotein as the master coordinator of HIV-1 assembly and maturation and as an emerging drug target. Due to its multiple roles in the HIV-1 life cycle, the individual Gag domains are attractive but also challenging targets for inhibitor design. However, recent encouraging developments in targeting the Gag domains such as the capsid protein with highly potent and potentially long-acting inhibitors, as well as the exploration and successful targeting of challenging HIV-1 proteins such as the matrix protein, have demonstrated the therapeutic viability of this important protein. Such Gag-directed inhibitors have great potential for combating the AIDS pandemic and to be useful tools to dissect HIV-1 biology.
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7
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Miller Jenkins LM, Paine EL, Deshmukh L, Nikolayevskiy H, Lyons GC, Scerba MT, Rosenker KG, Luecke HF, Louis JM, Chertova E, Gorelick RJ, Ott DE, Clore GM, Appella DH. Inhibition of HIV Maturation via Selective Unfolding and Cross-Linking of Gag Polyprotein by a Mercaptobenzamide Acetylator. J Am Chem Soc 2019; 141:8327-8338. [PMID: 31042030 PMCID: PMC8496520 DOI: 10.1021/jacs.9b02743] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
For HIV to become infectious, any new virion produced from an infected cell must undergo a maturation process that involves the assembly of viral polyproteins Gag and Gag-Pol at the membrane surface. The self-assembly of these viral proteins drives formation of a new viral particle as well as the activation of HIV protease, which is needed to cleave the polyproteins so that the final core structure of the virus will properly form. Molecules that interfere with HIV maturation will prevent any new virions from infecting additional cells. In this manuscript, we characterize the unique mechanism by which a mercaptobenzamide thioester small molecule (SAMT-247) interferes with HIV maturation via a series of selective acetylations at highly conserved cysteine and lysine residues in Gag and Gag-Pol polyproteins. The results provide the first insights into how acetylation can be utilized to perturb the process of HIV maturation and reveal a new strategy to limit the infectivity of HIV.
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Affiliation(s)
- Lisa M. Miller Jenkins
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Elliott L. Paine
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Lalit Deshmukh
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, United States
| | - Herman Nikolayevskiy
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, United States
| | - Gaelyn C. Lyons
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Michael T. Scerba
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, United States
| | - Kara George Rosenker
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, United States
| | - Hans F. Luecke
- Advanced Mass Spectrometry Core, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, United States
| | - John M. Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, United States
| | - Elena Chertova
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - Robert J. Gorelick
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - David E. Ott
- AIDS and Cancer Virus Program, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland 21701, United States
| | - G. Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, United States
| | - Daniel H. Appella
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, Maryland 20892, United States
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8
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René B, Mauffret O, Fossé P. Retroviral nucleocapsid proteins and DNA strand transfers. BIOCHIMIE OPEN 2018; 7:10-25. [PMID: 30109196 PMCID: PMC6088434 DOI: 10.1016/j.biopen.2018.07.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 07/08/2018] [Indexed: 12/12/2022]
Abstract
An infectious retroviral particle contains 1000-1500 molecules of the nucleocapsid protein (NC) that cover the diploid RNA genome. NC is a small zinc finger protein that possesses nucleic acid chaperone activity that enables NC to rearrange DNA and RNA molecules into the most thermodynamically stable structures usually those containing the maximum number of base pairs. Thanks to the chaperone activity, NC plays an essential role in reverse transcription of the retroviral genome by facilitating the strand transfer reactions of this process. In addition, these reactions are involved in recombination events that can generate multiple drug resistance mutations in the presence of anti-HIV-1 drugs. The strand transfer reactions rely on base pairing of folded DNA/RNA structures. The molecular mechanisms responsible for NC-mediated strand transfer reactions are presented and discussed in this review. Antiretroviral strategies targeting the NC-mediated strand transfer events are also discussed.
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Affiliation(s)
- Brigitte René
- LBPA, ENS Paris-Saclay, UMR 8113, CNRS, Université Paris-Saclay, 61 Avenue du Président Wilson, 94235, Cachan, France
| | - Olivier Mauffret
- LBPA, ENS Paris-Saclay, UMR 8113, CNRS, Université Paris-Saclay, 61 Avenue du Président Wilson, 94235, Cachan, France
| | - Philippe Fossé
- LBPA, ENS Paris-Saclay, UMR 8113, CNRS, Université Paris-Saclay, 61 Avenue du Président Wilson, 94235, Cachan, France
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9
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de Paiva REF, Du Z, Nakahata DH, Lima FA, Corbi PP, Farrell NP. Gold‐Catalyzed C–S Aryl‐Group Transfer in Zinc Finger Proteins. Angew Chem Int Ed Engl 2018; 57:9305-9309. [DOI: 10.1002/anie.201803082] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 05/02/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Raphael E. F. de Paiva
- Department of Chemistry Virginia Commonwealth University 1001 W. Main Street Richmond VA 23284-2006 USA
- Institute of Chemistry University of Campinas—UNICAMP P.O. Box 6154, CEP 13083-970 Campinas, São Paulo Brazil
| | - Zhifeng Du
- Department of Chemistry Virginia Commonwealth University 1001 W. Main Street Richmond VA 23284-2006 USA
| | - Douglas H. Nakahata
- Institute of Chemistry University of Campinas—UNICAMP P.O. Box 6154, CEP 13083-970 Campinas, São Paulo Brazil
| | - Frederico A. Lima
- Centro Nacional de Pesquisa em Energia e Materiais Brazilian Synchrotron Light Laboratory—LNLS, 13084-971 Campinas SP Brazil
- European XFEL GmbH Holzkoppel 4 22869 Schenefeld Germany
| | - Pedro P. Corbi
- Institute of Chemistry University of Campinas—UNICAMP P.O. Box 6154, CEP 13083-970 Campinas, São Paulo Brazil
| | - Nicholas P. Farrell
- Department of Chemistry Virginia Commonwealth University 1001 W. Main Street Richmond VA 23284-2006 USA
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10
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de Paiva REF, Du Z, Nakahata DH, Lima FA, Corbi PP, Farrell NP. Gold‐Catalyzed C–S Aryl‐Group Transfer in Zinc Finger Proteins. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201803082] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Raphael E. F. de Paiva
- Department of Chemistry Virginia Commonwealth University 1001 W. Main Street Richmond VA 23284-2006 USA
- Institute of Chemistry University of Campinas—UNICAMP P.O. Box 6154, CEP 13083-970 Campinas, São Paulo Brazil
| | - Zhifeng Du
- Department of Chemistry Virginia Commonwealth University 1001 W. Main Street Richmond VA 23284-2006 USA
| | - Douglas H. Nakahata
- Institute of Chemistry University of Campinas—UNICAMP P.O. Box 6154, CEP 13083-970 Campinas, São Paulo Brazil
| | - Frederico A. Lima
- Centro Nacional de Pesquisa em Energia e Materiais Brazilian Synchrotron Light Laboratory—LNLS, 13084-971 Campinas SP Brazil
- European XFEL GmbH Holzkoppel 4 22869 Schenefeld Germany
| | - Pedro P. Corbi
- Institute of Chemistry University of Campinas—UNICAMP P.O. Box 6154, CEP 13083-970 Campinas, São Paulo Brazil
| | - Nicholas P. Farrell
- Department of Chemistry Virginia Commonwealth University 1001 W. Main Street Richmond VA 23284-2006 USA
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11
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Nikolayevskiy H, Scerba MT, Deschamps JR, Appella DH. Reaction Kinetics Direct a Rational Synthesis of an HIV-1 Inactivator of Nucleocapsid Protein 7 and Provide Mechanistic Insight into Cellular Metabolism and Antiviral Activity. Chemistry 2018; 24:9485-9489. [PMID: 29653024 DOI: 10.1002/chem.201801253] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Indexed: 12/14/2022]
Abstract
Mercaptobenzamide thioester SAMT-247 is a non-toxic, mutation-resistant HIV-1 maturation inhibitor with a unique mechanism of antiviral activity. NMR spectroscopic analyses of model reactions that mimic the cellular environment answered fundamental questions about the antiviral mechanism and inspired a high-yielding (64 % overall), scalable (75 mmol), and cost-effective ($4 mmol-1 ) three-step synthesis that will enable additional preclinical evaluation.
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Affiliation(s)
- Herman Nikolayevskiy
- Synthetic Bioactive Molecules Section, Laboratory of, Bioorganic Chemistry (LBC), National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of, Health (NIH), 8 Center Drive, Room 404, Bethesda, MD, 20892, USA
| | - Michael T Scerba
- Synthetic Bioactive Molecules Section, Laboratory of, Bioorganic Chemistry (LBC), National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of, Health (NIH), 8 Center Drive, Room 404, Bethesda, MD, 20892, USA
| | - Jeffrey R Deschamps
- Naval Research Laboratory, Code 6910, 4555 Overlook Ave. SW, Washington D.C., 20375, USA
| | - Daniel H Appella
- Synthetic Bioactive Molecules Section, Laboratory of, Bioorganic Chemistry (LBC), National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of, Health (NIH), 8 Center Drive, Room 404, Bethesda, MD, 20892, USA
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12
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Ren W, Ji D, Xu X. Metal cofactor modulated folding and target recognition of HIV-1 NCp7. PLoS One 2018; 13:e0196662. [PMID: 29715277 PMCID: PMC5929515 DOI: 10.1371/journal.pone.0196662] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 04/17/2018] [Indexed: 01/01/2023] Open
Abstract
The HIV-1 nucleocapsid 7 (NCp7) plays crucial roles in multiple stages of HIV-1 life cycle, and its biological functions rely on the binding of zinc ions. Understanding the molecular mechanism of how the zinc ions modulate the conformational dynamics and functions of the NCp7 is essential for the drug development and HIV-1 treatment. In this work, using a structure-based coarse-grained model, we studied the effects of zinc cofactors on the folding and target RNA(SL3) recognition of the NCp7 by molecular dynamics simulations. After reproducing some key properties of the zinc binding and folding of the NCp7 observed in previous experiments, our simulations revealed several interesting features in the metal ion modulated folding and target recognition. Firstly, we showed that the zinc binding makes the folding transition states of the two zinc fingers less structured, which is in line with the Hammond effect observed typically in mutation, temperature or denaturant induced perturbations to protein structure and stability. Secondly, We showed that there exists mutual interplay between the zinc ion binding and NCp7-target recognition. Binding of zinc ions enhances the affinity between the NCp7 and the target RNA, whereas the formation of the NCp7-RNA complex reshapes the intrinsic energy landscape of the NCp7 and increases the stability and zinc affinity of the two zinc fingers. Thirdly, by characterizing the effects of salt concentrations on the target RNA recognition, we showed that the NCp7 achieves optimal balance between the affinity and binding kinetics near the physiologically relevant salt concentrations. In addition, the effects of zinc binding on the inter-domain conformational flexibility and folding cooperativity of the NCp7 were also discussed.
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Affiliation(s)
- Weitong Ren
- School of Physics, Nanjing University, Nanjing 210093, China
| | - Dongqing Ji
- School of Physics, Nanjing University, Nanjing 210093, China
| | - Xiulian Xu
- School of Physical Science and Technology, Yangzhou University, Yangzhou 225002, China
- * E-mail:
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13
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Deshmukh L, Tugarinov V, Appella DH, Clore GM. Targeting a Dark Excited State of HIV-1 Nucleocapsid by Antiretroviral Thioesters Revealed by NMR Spectroscopy. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201713172] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Lalit Deshmukh
- Laboratory of Chemical Physics; National Institute of Diabetes and Digestive and Kidney Diseases; Bethesda MD 20892-0520 USA
- Present address: Department of Chemistry and Biochemistry; University of California, San Diego; La Jolla CA 92093 USA
| | - Vitali Tugarinov
- Laboratory of Chemical Physics; National Institute of Diabetes and Digestive and Kidney Diseases; Bethesda MD 20892-0520 USA
| | - Daniel H. Appella
- Laboratory of Bioorganic Chemistry; National Institute of Diabetes and Digestive and Kidney Diseases; Bethesda MD 20892-0830 USA
| | - G. Marius Clore
- Laboratory of Chemical Physics; National Institute of Diabetes and Digestive and Kidney Diseases; Bethesda MD 20892-0520 USA
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14
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Deshmukh L, Tugarinov V, Appella DH, Clore GM. Targeting a Dark Excited State of HIV-1 Nucleocapsid by Antiretroviral Thioesters Revealed by NMR Spectroscopy. Angew Chem Int Ed Engl 2018; 57:2687-2691. [PMID: 29345807 DOI: 10.1002/anie.201713172] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Indexed: 12/22/2022]
Abstract
HIV-1 nucleocapsid (NCp7) is a two Cys2 HisCys zinc knuckle (N-Zn and C-Zn) protein that plays a key role in viral replication. NCp7 conformational dynamics is characterized by NMR relaxation dispersion and chemical exchange saturation transfer measurements. While the N-Zn knuckle is conformationally stable, the C-Zn knuckle interconverts on the millisecond timescale between the major state, in which the zinc is coordinated by three cysteines and a histidine, and two folded minor species (with populations around 1 %) in which one of the coordination bonds (Cys413-Sγ-Zn or His421-Nϵ2-Zn) is hydrolyzed. These findings explain why antiretroviral thioesters specifically disrupt the C-Zn knuckle by initial acylation of Cys413, and show that transient, sparsely-populated ("dark"), excited states of proteins can present effective targets for rational drug design.
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Affiliation(s)
- Lalit Deshmukh
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, 20892-0520, USA.,Present address: Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Vitali Tugarinov
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, 20892-0520, USA
| | - Daniel H Appella
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, 20892-0830, USA
| | - G Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, 20892-0520, USA
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15
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Sancineto L, Iraci N, Tabarrini O, Santi C. NCp7: targeting a multitasking protein for next-generation anti-HIV drug development part 1: covalent inhibitors. Drug Discov Today 2017; 23:260-271. [PMID: 29107765 DOI: 10.1016/j.drudis.2017.10.017] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2017] [Revised: 10/02/2017] [Accepted: 10/17/2017] [Indexed: 11/16/2022]
Abstract
The major internal component of the HIV virion core is the nucleocapsid protein 7 (NCp7), a small, highly basic protein that is essential for multiple stages of the viral replicative cycle, and whose structure is preserved in all viral strains, including clinical isolates from therapy-experienced patients. This key protein is recognised as a potential target for an effective next-generation antiretroviral therapy, because it could offer the possibility to develop broad-spectrum agents that are less prone to select for resistant strains. Here, we provide a comprehensive overview of the covalent NCp7 inhibitors that have emerged over the past 25 years of drug discovery campaigns, emphasising, where possible, their structure-activity relationships (SARs) and pharmacophoric features.
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Affiliation(s)
- Luca Sancineto
- Department of Heterorganic Chemistry, Centre of Molecular and Macromolecular Studies, Lodz, Poland.
| | - Nunzio Iraci
- Department of Pharmacy, University of Salerno, Fisciano, Salerno, Italy
| | - Oriana Tabarrini
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
| | - Claudio Santi
- Department of Pharmaceutical Sciences, University of Perugia, Perugia, Italy
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16
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Zhang Y, Mantravadi PK, Jobbagy S, Bao W, Koh JT. Antagonizing the Androgen Receptor with a Biomimetic Acyltransferase. ACS Chem Biol 2016; 11:2797-2802. [PMID: 27548116 DOI: 10.1021/acschembio.6b00659] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The Androgen Receptor (AR) remains the leading target of advanced prostate cancer therapies. Thiosalicylamide analogs have previously been shown to act in cells as acyltransfer catalysts that are capable of transferring cellular acetate, presumably from acetyl-CoA, to HIV NCp7. Here we explore if the cellular acetyl-transfer activity of thiosalicylamides can be redirected to other cellular targets guided by ligands for AR. We constructed conjugates of thiosalicylamides and the AR-binding small molecule tolfenamic acid, which binds the BF-3 site of AR, proximal to the coactivator "FXXLF" binding surface. The thiosalicylamide-tolfenamic acid conjugate, YZ03, but not the separate thiosalicylamide plus tolfenamic acid, significantly enhanced acetylation of endogenous AR in CWR22Rv1 cells. Further analysis confirms that Lys720, a residue critical to FXXLF coactivator peptide binding, is a site of acyl-YZ03 acetylation. Under acyl-transfer conditions, YZ03 significantly enhances the ability of BF-3 site binding ligands to inhibit AR-coactivator peptide association. These data suggest that biomimetic acyltransferases can enhance protein-protein interaction inhibitors through covalent modification of critical interfacial residues.
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Affiliation(s)
- Yuchen Zhang
- Department of Chemistry and Biochemsitry, University of Delaware, Newark, Delaware 19716, United States
| | - Pavan K. Mantravadi
- Department of Chemistry and Biochemsitry, University of Delaware, Newark, Delaware 19716, United States
| | - Soma Jobbagy
- Department of Chemistry and Biochemsitry, University of Delaware, Newark, Delaware 19716, United States
| | - Wei Bao
- Department of Chemistry and Biochemsitry, University of Delaware, Newark, Delaware 19716, United States
| | - John T. Koh
- Department of Chemistry and Biochemsitry, University of Delaware, Newark, Delaware 19716, United States
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17
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Hartman TL, Yang L, Helfrick AN, Hassink M, Shank NI, George Rosenker K, Scerba MT, Saha M, Hughes E, Wang AQ, Xu X, Gupta P, Buckheit RW, Appella DH. Preclinical evaluation of a mercaptobenzamide and its prodrug for NCp7-targeted inhibition of human immunodeficiency virus. Antiviral Res 2016; 134:216-225. [PMID: 27568924 PMCID: PMC7113734 DOI: 10.1016/j.antiviral.2016.08.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 08/23/2016] [Accepted: 08/24/2016] [Indexed: 01/01/2023]
Abstract
Although the effective use of highly active antiretroviral therapy results in the suppression of virus production in infected individuals, it does not eliminate the infection and low level virus production in cells harboring virus in sanctuary sites. Thus, the continued search for new antiretroviral agents with unique and different mechanisms of HIV inhibition remains critical, and compounds that can reduce the level of virus production from cells already infected with HIV, as opposed to preventing de novo infection, would be of great benefit. A mercaptobenzamide (MDH-1-38) and its prodrug (NS1040) are being developed as potential therapeutic compounds targeting the zinc finger of HIV nucleocapsid. In the presence of esterase enzymes, NS1040 is designed to be converted to MDH-1-38 which has antiviral activity. While we presume that NS1040 is rapidly converted to MDH-1-38 in all experiments, the two compounds were tested side-by-side to determine whether the presence of a prodrug affects the antiviral activity or mechanism of action. The two compounds were evaluated against a panel of HIV-1 clinical isolates in human PBMCs and monocyte-macrophages and yielded EC50 values ranging from 0.7 to 13 μM with no toxicity up to 100 μM. MDH-1-38 and NS1040 remained equally active in human PBMCs in the presence of added serum proteins as well as against HIV-1 isolates resistant to reverse transcriptase, integrase or protease inhibitors. Cell-based and biochemical mechanism of antiviral action assays demonstrated MDH-1-38 and NS1040 were virucidal at concentrations of 15 and 50 μM, respectively. Cell to cell transmission of HIV in multiple passages was significantly reduced in CEM-SS and human PBMCs by reducing progeny virus infectivity at compound concentrations greater than 2 μM. The combination of either MDH-1-38 or NS1040 with other FDA-approved HIV drugs yielded additive to synergistic antiviral interactions with no evidence of antiviral antagonism or synergistic toxicity. Serial dose escalation was used in attempts to select for HIV strains resistant to MDH-1-38 and NS1040. Virus at several passages failed to replicate in cells treated at increased compound concentrations, which is consistent with the proposed mechanism of action of the virus inactivating compounds. Through 14 passages, resistance to the compounds has not been achieved. Most HIV inhibitors with mechanism of antiviral action targeting a viral protein would have selected for a drug resistant virus within 14 passages. These studies indicate that these NCp7-targeted compounds represent new potent anti-HIV drug candidates which could be effectively used in combination with all approved anti-HIV drugs.
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Affiliation(s)
| | - L Yang
- ImQuest Biosciences, Frederick, MD, USA
| | | | - M Hassink
- Laboratory of Bioorganic Chemistry, NIDDK, NIH, Bethesda, MD, USA
| | - N I Shank
- Laboratory of Bioorganic Chemistry, NIDDK, NIH, Bethesda, MD, USA
| | | | - M T Scerba
- Laboratory of Bioorganic Chemistry, NIDDK, NIH, Bethesda, MD, USA
| | - M Saha
- Laboratory of Bioorganic Chemistry, NIDDK, NIH, Bethesda, MD, USA
| | | | | | - X Xu
- NCATS, NIH, Bethesda, MD, USA
| | - P Gupta
- Laboratory of Bioorganic Chemistry, NIDDK, NIH, Bethesda, MD, USA
| | | | - D H Appella
- Laboratory of Bioorganic Chemistry, NIDDK, NIH, Bethesda, MD, USA.
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18
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Mori M, Kovalenko L, Lyonnais S, Antaki D, Torbett BE, Botta M, Mirambeau G, Mély Y. Nucleocapsid Protein: A Desirable Target for Future Therapies Against HIV-1. Curr Top Microbiol Immunol 2015; 389:53-92. [PMID: 25749978 PMCID: PMC7122173 DOI: 10.1007/82_2015_433] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
The currently available anti-HIV-1 therapeutics is highly beneficial to infected patients. However, clinical failures occur as a result of the ability of HIV-1 to rapidly mutate. One approach to overcome drug resistance is to target HIV-1 proteins that are highly conserved among phylogenetically distant viral strains and currently not targeted by available therapies. In this respect, the nucleocapsid (NC) protein, a zinc finger protein, is particularly attractive, as it is highly conserved and plays a central role in virus replication, mainly by interacting with nucleic acids. The compelling rationale for considering NC as a viable drug target is illustrated by the fact that point mutants of this protein lead to noninfectious viruses and by the inability to select viruses resistant to a first generation of anti-NC drugs. In our review, we discuss the most relevant properties and functions of NC, as well as recent developments of small molecules targeting NC. Zinc ejectors show strong antiviral activity, but are endowed with a low therapeutic index due to their lack of specificity, which has resulted in toxicity. Currently, they are mainly being investigated for use as topical microbicides. Greater specificity may be achieved by using non-covalent NC inhibitors (NCIs) targeting the hydrophobic platform at the top of the zinc fingers or key nucleic acid partners of NC. Within the last few years, innovative methodologies have been developed to identify NCIs. Though the antiviral activity of the identified NCIs needs still to be improved, these compounds strongly support the druggability of NC and pave the way for future structure-based design and optimization of efficient NCIs.
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Affiliation(s)
- Mattia Mori
- Dipartimento di Biotecnologie Chimica e Farmacia, Università degli Studi di Siena, via A. Moro 2, 53100, Siena, Italy
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19
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Asquith CRM, Meli ML, Konstantinova LS, Laitinen T, Poso A, Rakitin OA, Hofmann-Lehmann R, Allenspach K, Hilton ST. Novel fused tetrathiocines as antivirals that target the nucleocapsid zinc finger containing protein of the feline immunodeficiency virus (FIV) as a model of HIV infection. Bioorg Med Chem Lett 2014; 25:1352-5. [PMID: 25702849 DOI: 10.1016/j.bmcl.2014.12.047] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 12/12/2014] [Accepted: 12/13/2014] [Indexed: 01/06/2023]
Abstract
A novel series of fused tetrathiocines were prepared for evaluation of activity against the nucleocapsid protein of the feline immunodeficiency virus (FIV) in an in vitro cell culture approach. The results demonstrated that the compounds display potent nanomolar activity and low toxicity against this key model of HIV infection.
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Affiliation(s)
- Christopher R M Asquith
- UCL School of Pharmacy, Faculty of Life Sciences, University College London, London WC1N 1AX, United Kingdom
| | - Marina L Meli
- Clinical Laboratory and Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Zurich 8057, Switzerland
| | - Lidia S Konstantinova
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow 119991, Russian Federation
| | - Tuomo Laitinen
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Antti Poso
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, 70211 Kuopio, Finland
| | - Oleg A Rakitin
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow 119991, Russian Federation
| | - Regina Hofmann-Lehmann
- Clinical Laboratory and Center for Clinical Studies, Vetsuisse Faculty, University of Zurich, Zurich 8057, Switzerland
| | - Karin Allenspach
- Veterinary Clinical Sciences, Royal Veterinary College, Hatfield AL9 7TA, United Kingdom
| | - Stephen T Hilton
- UCL School of Pharmacy, Faculty of Life Sciences, University College London, London WC1N 1AX, United Kingdom.
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20
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Retrospective on the all-in-one retroviral nucleocapsid protein. Virus Res 2014; 193:2-15. [PMID: 24907482 PMCID: PMC7114435 DOI: 10.1016/j.virusres.2014.05.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 05/11/2014] [Accepted: 05/11/2014] [Indexed: 01/08/2023]
Abstract
This retrospective reviews 30 years of research on the retroviral nucleocapsid protein (NC) focusing on HIV-1 NC. Originally considered as a non-specific nucleic-acid binding protein, NC has seminal functions in virus replication. Indeed NC turns out to be a all-in-one viral protein that chaperones viral DNA synthesis and integration, and virus formation. As a chaperone NC provides assistance to genetic recombination thus allowing the virus to escape the immune response and antiretroviral therapies against HIV-1.
This review aims at briefly presenting a retrospect on the retroviral nucleocapsid protein (NC), from an unspecific nucleic acid binding protein (NABP) to an all-in-one viral protein with multiple key functions in the early and late phases of the retrovirus replication cycle, notably reverse transcription of the genomic RNA and viral DNA integration into the host genome, and selection of the genomic RNA together with the initial steps of virus morphogenesis. In this context we will discuss the notion that NC protein has a flexible conformation and is thus a member of the growing family of intrinsically disordered proteins (IDPs) where disorder may account, at least in part, for its function as a nucleic acid (NA) chaperone and possibly as a protein chaperone vis-à-vis the viral DNA polymerase during reverse transcription. Lastly, we will briefly review the development of new anti-retroviral/AIDS compounds targeting HIV-1 NC because it represents an ideal target due to its multiple roles in the early and late phases of virus replication and its high degree of conservation.
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21
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Niedzwiecki’ DJ, Iyer R, Borer PN, Movileanu L. Sampling a biomarker of the human immunodeficiency virus across a synthetic nanopore. ACS NANO 2013; 7:3341-50. [PMID: 23445080 PMCID: PMC3634884 DOI: 10.1021/nn400125c] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
One primary goal in nanobiotechnology is designing new methodologies for molecular biomedical diagnosis at stages much earlier than currently possible and without use of expensive reagents and sophisticated equipment. In this work, we show the proof of principle for single-molecule detection of the nucleocapsid protein 7 (NCp7), a protein biomarker of the HIV-1 virus, using synthetic nanopores and the resistive-pulse technique. The biosensing mechanism relied upon specific interactions between NCp7 and aptamers of stem-loop 3 (SL3) in the packaging domain of the retroviral RNA genome. One critical step of this study was the choice of the optimal size of the nanopores for accurate, label-free determinations of the dissociation constant of the NCp7 protein-SL3 RNA aptamer complex. Therefore, we systematically investigated the NCp7 protein-SL3 RNA aptamer complex employing two categories of nanopores in a silicon nitride membrane: (i) small, whose internal diameter was smaller than 6 nm, and (ii) large, whose internal diameter was in the range of 7 to 15 nm. Here, we demonstrate that only the use of nanopores with an internal diameter that is smaller than or comparable with the largest cross-sectional size of the NCp7-SL3 aptamer complex enables accurate measurement of the dissociation constant between the two interacting partners. Notably, this determination can be accomplished without the need for prior nanopore functionalization. Moreover, using small solid-state nanopores, we demonstrate the ability to detect drug candidates that inhibit the binding interactions between NCp7 and SL3 RNA by using a test case of N-ethylmaleimide.
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Affiliation(s)
| | - Raghuvaran Iyer
- Department of Chemistry, Syracuse University, 1-014 Center for Science and Technology, Syracuse, New York 13244-4100, USA
| | - Philip N. Borer
- Department of Chemistry, Syracuse University, 1-014 Center for Science and Technology, Syracuse, New York 13244-4100, USA
- Structural Biology, Biochemistry, and Biophysics Program, Syracuse University, 111 College Place, Syracuse, New York 13244-4100, USA
| | - Liviu Movileanu
- Department of Physics, Syracuse University, 201 Physics Building, Syracuse, New York 13244-1130, USA
- Structural Biology, Biochemistry, and Biophysics Program, Syracuse University, 111 College Place, Syracuse, New York 13244-4100, USA
- Syracuse Biomaterials Institute, Syracuse University, 121 Link Hall, Syracuse, New York 13244, USA
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22
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Goudreau N, Hucke O, Faucher AM, Grand-Maître C, Lepage O, Bonneau PR, Mason SW, Titolo S. Discovery and structural characterization of a new inhibitor series of HIV-1 nucleocapsid function: NMR solution structure determination of a ternary complex involving a 2:1 inhibitor/NC stoichiometry. J Mol Biol 2013; 425:1982-1998. [PMID: 23485336 DOI: 10.1016/j.jmb.2013.02.022] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 02/14/2013] [Accepted: 02/15/2013] [Indexed: 11/30/2022]
Abstract
The nucleocapsid (NC) protein is an essential factor with multiple functions within the human immunodeficiency virus type 1 (HIV-1) replication cycle. In this study, we describe the discovery of a novel series of inhibitors that targets HIV-1 NC protein by blocking its interaction with nucleic acids. This series was identified using a previously described capsid (CA) assembly assay, employing a recombinant HIV-1 CA-NC protein and immobilized TG-rich deoxyoligonucleotides. Using visible absorption spectroscopy, we were able to demonstrate that this new inhibitor series binds specifically and reversibly to the NC with a peculiar 2:1 stoichiometry. A fluorescence-polarization-based binding assay was also developed in order to monitor the inhibitory activities of this series of inhibitors. To better characterize the structural aspect of inhibitor binding onto NC, we performed NMR studies using unlabeled and (13)C,(15)N-double-labeled NC(1-55) protein constructs. This allowed the determination of the solution structure of a ternary complex characterized by two inhibitor molecules binding to the two zinc knuckles of the NC protein. To the best of our knowledge, this represents the first report of a high-resolution structure of a small-molecule inhibitor bound to NC, demonstrating sub-micromolar potency and moderate antiviral potency with one analogue of the series. This structure was compared with available NC/oligonucleotide complex structures and further underlined the high flexibility of the NC protein, allowing it to adopt many conformations in order to bind its different oligonucleotide/nucleomimetic targets. In addition, analysis of the interaction details between the inhibitor molecules and NC demonstrated how this novel inhibitor series is mimicking the guanosine nucleobases found in many reported complex structures.
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Affiliation(s)
- Nathalie Goudreau
- Department of Chemistry, Boehringer Ingelheim (Canada) Ltd., Research & Development, 2100 Cunard Street, Laval, QC, Canada H7S 2G5.
| | - Oliver Hucke
- Department of Chemistry, Boehringer Ingelheim (Canada) Ltd., Research & Development, 2100 Cunard Street, Laval, QC, Canada H7S 2G5.
| | - Anne-Marie Faucher
- Department of Chemistry, Boehringer Ingelheim (Canada) Ltd., Research & Development, 2100 Cunard Street, Laval, QC, Canada H7S 2G5
| | - Chantal Grand-Maître
- Department of Chemistry, Boehringer Ingelheim (Canada) Ltd., Research & Development, 2100 Cunard Street, Laval, QC, Canada H7S 2G5
| | - Olivier Lepage
- Department of Chemistry, Boehringer Ingelheim (Canada) Ltd., Research & Development, 2100 Cunard Street, Laval, QC, Canada H7S 2G5
| | - Pierre R Bonneau
- Department of Chemistry, Boehringer Ingelheim (Canada) Ltd., Research & Development, 2100 Cunard Street, Laval, QC, Canada H7S 2G5
| | - Stephen W Mason
- Department of Biological Sciences, Boehringer Ingelheim (Canada) Ltd., Research & Development, 2100 Cunard Street, Laval, QC, Canada H7S 2G5
| | - Steve Titolo
- Department of Biological Sciences, Boehringer Ingelheim (Canada) Ltd., Research & Development, 2100 Cunard Street, Laval, QC, Canada H7S 2G5
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23
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Vercruysse T, Basta B, Dehaen W, Humbert N, Balzarini J, Debaene F, Sanglier-Cianférani S, Pannecouque C, Mély Y, Daelemans D. A phenyl-thiadiazolylidene-amine derivative ejects zinc from retroviral nucleocapsid zinc fingers and inactivates HIV virions. Retrovirology 2012; 9:95. [PMID: 23146561 PMCID: PMC3542062 DOI: 10.1186/1742-4690-9-95] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Accepted: 10/24/2012] [Indexed: 11/25/2022] Open
Abstract
Background Sexual acquisition of the human immunodeficiency virus (HIV) through mucosal transmission may be prevented by using topically applied agents that block HIV transmission from one individual to another. Therefore, virucidal agents that inactivate HIV virions may be used as a component in topical microbicides. Results Here, we have identified 2-methyl-3-phenyl-2H-[1,2,4]thiadiazol-5-ylideneamine (WDO-217) as a low-molecular-weight molecule that inactivates HIV particles. Both HIV-1 and HIV-2 virions pretreated with this compound were unable to infect permissive cells. Moreover, WDO-217 was able to inhibit infections of a wide spectrum of wild-type and drug-resistant HIV-1, including clinical isolates, HIV-2 and SIV strains. Whereas the capture of virus by DC-SIGN was unaffected by the compound, it efficiently prevented the transmission of DC-SIGN-captured virus to CD4+ T-lymphocytes. Interestingly, exposure of virions to WDO-217 reduced the amount of virion-associated genomic RNA as measured by real-time RT-qPCR. Further mechanism-of-action studies demonstrated that WDO-217 efficiently ejects zinc from the zinc fingers of the retroviral nucleocapsid protein NCp7 and inhibits the cTAR destabilization properties of this protein. Importantly, WDO-217 was able to eject zinc from both zinc fingers, even when NCp7 was bound to oligonucleotides, while no covalent interaction between NCp7 and WDO-217 could be observed. Conclusion This compound is a new lead structure that can be used for the development of a new series of NCp7 zinc ejectors as candidate topical microbicide agents.
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Affiliation(s)
- Thomas Vercruysse
- Rega Institute for Medical Research, Laboratory for Virology and Chemotherapy, KU Leuven, Minderbroedersstraat 10, Leuven, B-3000, Belgium
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24
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Hung HC, Liu CL, Hsu JTA, Horng JT, Fang MY, Wu SY, Ueng SH, Wang MY, Yaw CW, Hou MH. Development of an anti-influenza drug screening assay targeting nucleoproteins with tryptophan fluorescence quenching. Anal Chem 2012; 84:6391-9. [PMID: 22712523 DOI: 10.1021/ac2022426] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recent studies have shown that NP (nucleoprotein), which possesses multiple functions in the viral life cycle, is a new potential anti-influenza drug target. NP inhibitors reliably induce conformational changes in NPs, and these changes may confer inhibition of the influenza virus. The six conserved tryptophan residues in NP can be used as an intrinsic probe to monitor the change in fluorescence of the tryptophan residues in the protein upon binding to an NP inhibitor. In the present study, we found that the fluorescence of recombinant NP proteins was quenched following the binding of available NP inhibitors (such as nucleozin) in a concentration- and time-dependent manner, which suggests that the inhibitor induced conformational changes in the NPs. The minimal fluorescence-quenching effect and weak binding constant of nucleozin to the swine-origin influenza virus H1N1pdm09 (SOIV) NP revealed that the SOIV is resistant to nucleozin. We have used the fluorescence-quenching property of tryptophans in NPs that were bound to ligands in a 96-well-plate-based drug screen to assess the ability of promising small molecules to interact with NPs and have identified one new anti-influenza drug, CSV0C001018, with a high SI value. This convenient method for drug screening may facilitate the development of antiviral drugs that target viruses other than the influenza virus, such as HIV and HBV.
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Affiliation(s)
- Hui-Chen Hung
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli, Taiwan
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25
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Breuer S, Chang MW, Yuan J, Torbett BE. Identification of HIV-1 inhibitors targeting the nucleocapsid protein. J Med Chem 2012; 55:4968-77. [PMID: 22587465 DOI: 10.1021/jm201442t] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The HIV-1 nucleocapsid (NC) is a RNA/DNA binding protein encoded within the Gag polyprotein, which is critical for the selection and chaperoning of viral genomic RNA during virion assembly. RNA/DNA binding occurs through a highly conserved zinc-knuckle motif present in NC. Given the necessity of NC-viral RNA/DNA interaction for viral replication, identification of compounds that disrupt the NC-RNA/DNA interaction may have value as an antiviral strategy. To identify small molecules that disrupt NC-viral RNA/DNA binding, a high-throughput fluorescence polarization assay was developed and a library of 14,400 diverse, druglike compounds was screened. Compounds that disrupted NC binding to a fluorescence-labeled DNA tracer were next evaluated by differential scanning fluorimetry to identify compounds that must bind to NC or Gag to impart their effects. Two compounds were identified that inhibited NC-DNA interaction, specifically bound NC with nanomolar affinity, and showed modest anti-HIV-1 activity in ex vivo cell assays.
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Affiliation(s)
- Sebastian Breuer
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
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26
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Mori M, Schult-Dietrich P, Szafarowicz B, Humbert N, Debaene F, Sanglier-Cianferani S, Dietrich U, Mély Y, Botta M. Use of virtual screening for discovering antiretroviral compounds interacting with the HIV-1 nucleocapsid protein. Virus Res 2012; 169:377-87. [PMID: 22634301 DOI: 10.1016/j.virusres.2012.05.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Revised: 05/14/2012] [Accepted: 05/16/2012] [Indexed: 12/16/2022]
Abstract
The HIV-1 nucleocapsid protein (NC) is considered as an emerging drug target for the therapy of AIDS. Several studies have highlighted the crucial role of NC within the viral replication cycle. However, although NC inhibition has provided in vitro and in vivo antiretroviral activity, drug-candidates which interfere with NC functions are still missing in the therapeutic arsenal against HIV. Based on previous studies, where the dynamic behavior of NC and its ligand binding properties have been investigated by means of computational methods, here we used a virtual screening protocol for discovering novel antiretroviral compounds which interact with NC. The antiretroviral activity of virtual hits was tested in vitro, whereas biophysical studies elucidated the direct interaction of most active compounds with NC(11-55), a peptide corresponding to the zinc finger domain of NC. Two novel antiretroviral small molecules capable of interacting with NC are presented here.
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Affiliation(s)
- Mattia Mori
- Università di Roma La Sapienza, Dipartimento di Chimica e Tecnologie del Farmaco, piazzale A. Moro 5, I-00185 Roma, Italy
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27
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Warui DM, Baranger AM. Identification of small molecule inhibitors of the HIV-1 nucleocapsid-stem-loop 3 RNA complex. J Med Chem 2012; 55:4132-41. [PMID: 22480197 DOI: 10.1021/jm2007694] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Stem-loop 3 RNA (SL3) in ψ-RNA is a highly conserved motif in different strains of HIV-1 and serves as a principle determinant for viral packaging. Viral encapsulation is critical for viral replication, and disruption of the nucleocapsid-ψ-RNA complex interferes with viral replication. We have used SL3 RNA as a target for identification of small molecule inhibitors of the interactions of nucleocapsid protein (NCp7) and ψ-RNA. We report the use of computational and high-throughput screening approaches to identify 16 compounds that bind SL3 RNA with micromolar affinities. Among the identified ligands, two molecules, compounds 7 and 17, bind with higher affinity to SL3 RNA than to double- and single-stranded RNAs. Four of the 16 SL3 RNA ligands inhibit interactions between SL3 RNA and NCp7 with micromolar inhibition constants. In general, the identified SL3 ligands have simple molecular structures and low molecular weights and are, therefore, possible lead compounds for the development of ligands that target the elements of ψ-RNA of HIV-1 with high affinity and specificity.
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Affiliation(s)
- Douglas M Warui
- Department of Chemistry, 361 Roger Adams Laboratory, University of Illinois, 600 South Mathews Avenue, Urbana, Illinois 61801, USA
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Waheed AA, Freed EO. HIV type 1 Gag as a target for antiviral therapy. AIDS Res Hum Retroviruses 2012; 28:54-75. [PMID: 21848364 DOI: 10.1089/aid.2011.0230] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Gag proteins of HIV-1 are central players in virus particle assembly, release, and maturation, and also function in the establishment of a productive infection. Despite their importance throughout the replication cycle, there are currently no approved antiretroviral therapies that target the Gag precursor protein or any of the mature Gag proteins. Recent progress in understanding the structural and cell biology of HIV-1 Gag function has revealed a number of potential Gag-related targets for possible therapeutic intervention. In this review, we summarize our current understanding of HIV-1 Gag and suggest some approaches for the development of novel antiretroviral agents that target Gag.
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Affiliation(s)
- Abdul A. Waheed
- Virus-Cell Interaction Section, HIV Drug Resistance Program, National Cancer Institute, Frederick, Maryland
| | - Eric O. Freed
- Virus-Cell Interaction Section, HIV Drug Resistance Program, National Cancer Institute, Frederick, Maryland
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Desjardins A, Yang A, Bouvette J, Omichinski JG, Legault P. Importance of the NCp7-like domain in the recognition of pre-let-7g by the pluripotency factor Lin28. Nucleic Acids Res 2011; 40:1767-77. [PMID: 22013165 PMCID: PMC3287177 DOI: 10.1093/nar/gkr808] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The pluripotency factor Lin28 is a highly conserved protein comprising a unique combination of RNA-binding motifs, an N-terminal cold-shock domain and a C-terminal region containing two retroviral-type CCHC zinc-binding domains. An important function of Lin28 is to inhibit the biogenesis of the let-7 family of microRNAs through a direct interaction with let-7 precursors. Here, we systematically characterize the determinants of the interaction between Lin28 and pre-let-7g by investigating the effect of protein and RNA mutations on in vitro binding. We determine that Lin28 binds with high affinity to the extended loop of pre-let-7g and that its C-terminal domain contributes predominantly to the affinity of this interaction. We uncover remarkable similarities between this C-terminal domain and the NCp7 protein of HIV-1, not only in terms of primary structure but also in their modes of RNA binding. This NCp7-like domain of Lin28 recognizes a G-rich bulge within pre-let-7g, which is adjacent to one of the Dicer cleavage sites. We hypothesize that the NCp7-like domain initiates RNA binding and partially unfolds the RNA. This partial unfolding would then enable multiple copies of Lin28 to bind the extended loop of pre-let-7g and protect the RNA from cleavage by the pre-microRNA processing enzyme Dicer.
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Affiliation(s)
- Alexandre Desjardins
- Département de Biochimie, Université de Montréal, CP 6128, Succursale Centre-Ville, Montréal, QC, Canada H3C 3J7
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30
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Delay of simian human immunodeficiency virus infection and control of viral replication in vaccinated macaques challenged in the presence of a topical microbicide. AIDS 2011; 25:1833-41. [PMID: 21750420 DOI: 10.1097/qad.0b013e32834a1d94] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE Development of an effective vaccine or topical compound to prevent HIV transmission remains a major goal for control of the AIDS pandemic. Using a nonhuman primate model of heterosexual HIV-1 transmission, we tested whether a topical microbicide that reduces viral infectivity can potentiate the efficacy of a T-cell-based HIV vaccine. DESIGN A DNA prime and rAd5 virus boost vaccination strategy was employed, and a topical microbicide against the HIV nucleocapsid protein was used. To rigorously test the combination hypothesis, the vaccine constructs contained only two transgenes and the topical microbicide inhibitor was used at a suboptimal dose. Vaccinees were exposed in the absence and presence of the topical microbicide to repeated vaginal R5 simian human immunodeficiency virus (SHIV)(SF162P3) challenge at an escalating dose to more closely mimic high-risk exposure of women to HIV. METHODS Infection status was determined by PCR. Antiviral immune responses were evaluated by gp120 ELISA and intracellular cytokine staining. RESULTS A significant delay in SHIV acquisition (log-rank test; P = 0.0416) was seen only in vaccinated macaques that were repeatedly challenged in the presence of the topical microbicide. Peak acute viremia was lower (Mann-Whitney test; P = 0.0387) and viral burden was also reduced (Mann-Whitney test; P = 0.0252) in the combination-treated animals. CONCLUSION The combined use of a topical microbicide to lower the initial viral seeding/spread and a T-cell-based vaccine to immunologically contain the early virological events of mucosal transmission holds promise as a preventive approach to control the spread of the AIDS epidemic.
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31
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Miller Jenkins LM, Ott DE, Hayashi R, Coren LV, Wang D, Xu Q, Schito ML, Inman JK, Appella DH, Appella E. Small-molecule inactivation of HIV-1 NCp7 by repetitive intracellular acyl transfer. Nat Chem Biol 2010; 6:887-9. [PMID: 20953192 PMCID: PMC2997617 DOI: 10.1038/nchembio.456] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Accepted: 09/15/2010] [Indexed: 11/09/2022]
Abstract
The zinc fingers of the HIV-1 nucleocapsid protein, NCp7, are prime targets for antiretroviral therapeutics. Here we show that S-acyl-2-mercaptobenzamide thioester (SAMT) chemotypes inhibit HIV by modifying the NCp7 region of Gag in infected cells, thereby blocking Gag processing and reducing infectivity. The thiol produced by SAMT reaction with NCp7 is acetylated by cellular enzymes to regenerate active SAMTs via a recycling mechanism unique among small-molecule inhibitors of HIV.
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Affiliation(s)
- Lisa M Miller Jenkins
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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32
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Goldschmidt V, Miller Jenkins LM, de Rocquigny H, Darlix JL, Mély Y. The nucleocapsid protein of HIV-1 as a promising therapeutic target for antiviral drugs. ACTA ACUST UNITED AC 2010. [DOI: 10.2217/hiv.10.3] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The nucleocapsid protein (NCp7) is a major HIV-1 structural protein that plays key roles in viral replication, mainly through its conserved zinc fingers that direct specific interactions with the viral nucleic acids. Owing to its high degree of conservation and critical functions, NCp7 represents a target of choice for drugs that can potentially complement HAART, thus possibly impairing the circulation of drug-resistant HIV-1 strains. Zinc ejectors showing potent antiretroviral activity were developed, but early generations suffered from limited selectively and significant toxicity. Compounds with improved selectivity have been developed and are being explored as topical microbicide candidates. Several classes of molecules inhibiting the interaction of NCp7 with the viral nucleic acids have also been developed. Although small molecules would be more suited for drug development, most molecules selected by screening showed limited antiretroviral activity. Peptides and RNA aptamers appear to be more promising, but the mechanism of their antiretroviral activity remains elusive. Substantial and more concerted efforts are needed to further develop anti-HIV drugs targeting NCp7 and bring them to the clinic.
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Affiliation(s)
- Valérie Goldschmidt
- Laboratoire de Biophotonique et Pharmacologie, UMR-CNRS 7213, Faculté de Pharmacie, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch-Cedex, France
| | - Lisa M Miller Jenkins
- Laboratory of Cell Biology, NCI, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hugues de Rocquigny
- Laboratoire de Biophotonique et Pharmacologie, UMR-CNRS 7213, Faculté de Pharmacie, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch-Cedex, France
| | - Jean-Luc Darlix
- LaboRetro, Unité de Virologie Humaine INSERM 758, Ecole Normale Supérieure de Lyon, 46 allée d’Italie, 69364 Lyon, France
| | - Yves Mély
- Laboratoire de Biophotonique et Pharmacologie, UMR-CNRS 7213, Faculté de Pharmacie, Université de Strasbourg, 74 route du Rhin, 67401 Illkirch-Cedex, France
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Inhibition of HIV-1 replication by a bis-thiadiazolbenzene-1,2-diamine that chelates zinc ions from retroviral nucleocapsid zinc fingers. Antimicrob Agents Chemother 2010; 54:1461-8. [PMID: 20124006 DOI: 10.1128/aac.01671-09] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The human immunodeficiency virus type 1 (HIV-1) nucleocapsid p7 (NCp7) protein holds two highly conserved "CCHC" zinc finger domains that are required for several phases of viral replication. Basic residues flank the zinc fingers, and both determinants are required for high-affinity binding to RNA. Several compounds were previously found to target NCp7 by reacting with the sulfhydryl group of cysteine residues from the zinc fingers. Here, we have identified an N,N'-bis(1,2,3-thiadiazol-5-yl)benzene-1,2-diamine (NV038) that efficiently blocks the replication of a wide spectrum of HIV-1, HIV-2, and simian immunodeficiency virus (SIV) strains. Time-of-addition experiments indicate that NV038 interferes with a step of the viral replication cycle following the viral entry but preceding or coinciding with the early reverse transcription reaction, pointing toward an interaction with the nucleocapsid protein p7. In fact, in vitro, NV038 efficiently depletes zinc from NCp7, which is paralleled by the inhibition of the NCp7-induced destabilization of cTAR (complementary DNA sequence of TAR). A chemical model suggests that the two carbonyl oxygens of the esters in this compound are involved in the chelation of the Zn(2+) ion. This compound thus acts via a different mechanism than the previously reported zinc ejectors, as its structural features do not allow an acyl transfer to Cys or a thiol-disulfide interchange. This new lead and the mechanistic study presented provide insight into the design of a future generation of anti-NCp7 compounds.
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34
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Lee SJ, Michel SLJ. Cysteine Oxidation Enhanced by Iron in Tristetraprolin, A Zinc Finger Peptide. Inorg Chem 2010; 49:1211-9. [DOI: 10.1021/ic9024298] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Seung Jae Lee
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201-1180
| | - Sarah L. J. Michel
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201-1180
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Identification by high throughput screening of small compounds inhibiting the nucleic acid destabilization activity of the HIV-1 nucleocapsid protein. Biochimie 2009; 91:916-23. [PMID: 19401213 DOI: 10.1016/j.biochi.2009.04.014] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2009] [Accepted: 04/15/2009] [Indexed: 11/22/2022]
Abstract
Due to its highly conserved zinc fingers and its nucleic acid chaperone properties which are critical for HIV-1 replication, the nucleocapsid protein (NC) constitutes a major target in AIDS therapy. Different families of molecules targeting NC zinc fingers and/or inhibiting the binding of NC with its target nucleic acids have been developed. However, their limited specificity and their cellular toxicity prompted us to develop a screening assay to target molecules able to inhibit NC chaperone properties, and more specifically the initial NC-promoted destabilization of the nucleic acid secondary structure. Since this destabilization is critically dependent on the properly folded fingers, the developed assay is thought to be highly specific. The assay was based on the use of cTAR DNA, a stem-loop sequence complementary to the transactivation response element, doubly labelled at its 5' and 3' ends by a rhodamine 6G fluorophore and a fluorescence quencher, respectively. Addition of NC(12-55), a peptide corresponding to the zinc finger domain of NC, to this doubly-labelled cTAR, led to a partial melting of the cTAR stem, which increases the distance between the two labels and thus, restores the rhodamine 6G fluorescence. Thus, positive hits were detected through the decrease of rhodamine 6G fluorescence. An "in-house" chemical library of 4800 molecules was screened and five compounds with IC(50) values in the micromolar range have been selected. The hits were shown by mass spectrometry and fluorescence anisotropy titration to prevent binding of NC(12-55) to cTAR through direct interaction with the NC folded fingers, but without promoting zinc ejection. These non-zinc ejecting NC binders are a new series of anti-NC molecules that could be used to rationally design molecules with potential anti-viral activities.
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Dietz J, Koch J, Kaur A, Raja C, Stein S, Grez M, Pustowka A, Mensch S, Ferner J, Möller L, Bannert N, Tampé R, Divita G, Mély Y, Schwalbe H, Dietrich U. Inhibition of HIV-1 by a peptide ligand of the genomic RNA packaging signal Psi. ChemMedChem 2008; 3:749-55. [PMID: 18205165 DOI: 10.1002/cmdc.200700194] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The interaction of the nucleocapsid NCp7 of the human immunodeficiency virus type 1 (HIV-1) Gag polyprotein with the RNA packaging signal Psi ensures specific encapsidation of the dimeric full length viral genome into nascent virus particles. Being an essential step in the HIV-1 replication cycle, specific genome encapsidation represents a promising target for therapeutic intervention. We previously selected peptides binding to HIV-1 Psi-RNA or stem loops (SL) thereof by phage display. Herein, we describe synthesis of peptide variants of the consensus HWWPWW motif on membrane supports to optimize Psi-RNA binding. The optimized peptide, psi-pepB, was characterized in detail with respect to its conformation and binding properties for the SL3 of the Psi packaging signal by NMR and tryptophan fluorescence quenching. Functional analysis revealed that psi-pepB caused a strong reduction of virus release by infected cells as monitored by reduced transduction efficiencies, capsid p24 antigen levels, and electron microscopy. Thus, this peptide shows antiviral activity and could serve as a lead compound to develop new drugs targeting HIV-1.
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Affiliation(s)
- Julia Dietz
- Georg-Speyer-Haus, Institute for Biomedical Research, Paul-Ehrlich-Str. 42-44, 60596 Frankfurt, Germany
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37
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Turpin JA, Schito ML, Jenkins LMM, Inman JK, Appella E. Topical microbicides: a promising approach for controlling the AIDS pandemic via retroviral zinc finger inhibitors. ADVANCES IN PHARMACOLOGY (SAN DIEGO, CALIF.) 2008; 56:229-56. [PMID: 18086414 DOI: 10.1016/s1054-3589(07)56008-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Affiliation(s)
- Jim A Turpin
- Preventions Sciences Program, Division of AIDS, NIAID, National Institutes of Health, Bethesda, Maryland 20892, USA
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38
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Jenkins LMM, Durell SR, Maynard AT, Stahl SJ, Inman JK, Appella E, Legault P, Omichinski JG. Comparison of the Specificity of Interaction of Cellular and Viral Zinc-Binding Domains with 2-Mercaptobenzamide Thioesters. J Am Chem Soc 2006; 128:11964-76. [PMID: 16953638 DOI: 10.1021/ja063329e] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The interactions of two 2-mercaptobenzamide thioester compounds with six diverse zinc-binding domains (ZBDs) have been analyzed by UV/visible spectroscopy, NMR spectroscopy, and nucleic acid binding assays. These thioester compounds serve as useful tools for probing the intrinsic chemical stability of ZBDs that exist within a variety of cellular and viral proteins. In our studies, the classical (Cys(2)His(2)) zinc finger ZBDs, the interleaved RING like ZBDs of protein kinase C delta (Cys(2)HisCys and HisCys(3)), and the carboxyl-terminal (Cys(2)HisCys) ZBD of Mouse Mammary Tumor Virus nucleocapsid protein (MMTV NCp10) were resistant to reaction with the thioester compounds. In contrast, the thioester compounds were able to efficiently eject zinc from the amino-terminal (Cys(2)HisCys) ZBD of MMTV NCp10, a Cys(2)HisCys ZBD from Friend of GATA-1 (FOG-1), and from both Cys(4) ZBDs of GATA-1. In all cases, zinc ejection led to a loss of protein structure. Interestingly, GATA-1 was resistant to reaction with the thioester compounds when bound to its target DNA sequence. The electronic and steric screening was calculated for select ZBDs to further explore their reactivity. Based on these results, it appears that both first and second zinc-coordination shell interactions within ZBDs, as well as nucleic acid binding, play important roles in determining the chemical stability and reactivity of ZBDs. These studies not only provide information regarding the relative reactivity of cysteine residues within structural ZBDs but also are crucial for the design of future therapeutic agents that selectively target ZBDs, such as those that occur in the HIV-1 nucleocapsid protein.
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Affiliation(s)
- Lisa M Miller Jenkins
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, 30602, USA
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García CC, Djavani M, Topisirovic I, Borden KLB, Salvato MS, Damonte EB. Arenavirus Z protein as an antiviral target: virus inactivation and protein oligomerization by zinc finger-reactive compounds. J Gen Virol 2006; 87:1217-1228. [PMID: 16603524 PMCID: PMC2423342 DOI: 10.1099/vir.0.81667-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Several disulfide-based and azoic compounds have shown antiviral and virucidal properties against arenaviruses in virus yield-inhibition and inactivation assays, respectively. The most effective virucidal agent, the aromatic disulfide NSC20625, was able to inactivate two strains of the prototype arenavirus species Lymphocytic choriomeningitis virus (LCMV). Inactivated viral particles retained the biological functions of the virion envelope glycoproteins in virus binding and uptake, but were unable to perform viral RNA replication. Furthermore, in inactivated virions, the electrophoretic profile of the Z protein was altered when analysed under non-reducing conditions, whereas the patterns of the proteins NP and GP1 remained unaffected. Treatment of a recombinant LCMV Z protein with the virucidal agents induced unfolding and oligomerization of Z to high-molecular-mass aggregates, probably due to metal-ion ejection and the formation of intermolecular disulfide bonds through the cysteine residues of the Z RING finger. NSC20625 also exhibited antiviral properties in LCMV-infected cells without affecting other cellular RING-motif proteins, such as the promyelocytic leukaemia protein PML. Altogether, the investigations described here illustrate the potential of the Z protein as a promising target for therapy and the prospects of the Z-reactive compounds to prevent arenavirus dissemination.
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Affiliation(s)
- Cybele C. García
- Laboratory of Virology, Department of Biological Chemistry, School of Sciences, University of Buenos Aires, Ciudad Universitaria, Pabellón 2, Piso 4, 1428 Buenos Aires, Argentina
| | - Mahmoud Djavani
- Institute of Human Virology, University of Maryland Biotechnology Center, Baltimore, MD 21201, USA
| | - Ivan Topisirovic
- Institute de Recherche en Immunologie et en Cancerologie, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Katherine L. B. Borden
- Institute de Recherche en Immunologie et en Cancerologie, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - María S. Salvato
- Institute of Human Virology, University of Maryland Biotechnology Center, Baltimore, MD 21201, USA
| | - Elsa B. Damonte
- Laboratory of Virology, Department of Biological Chemistry, School of Sciences, University of Buenos Aires, Ciudad Universitaria, Pabellón 2, Piso 4, 1428 Buenos Aires, Argentina
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Turner KB, Hagan NA, Fabris D. Inhibitory effects of archetypical nucleic acid ligands on the interactions of HIV-1 nucleocapsid protein with elements of Psi-RNA. Nucleic Acids Res 2006; 34:1305-16. [PMID: 16522643 PMCID: PMC1390681 DOI: 10.1093/nar/gkl004] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2006] [Revised: 02/10/2006] [Accepted: 02/10/2006] [Indexed: 11/14/2022] Open
Abstract
Disrupting the interactions between human immunodeficiency virus type 1 (HIV-1) nucleocapsid (NC) protein and structural elements of the packaging signal (Psi-RNA) could constitute an ideal strategy to inhibit the functions of this region of the genome leader in the virus life cycle. We have employed electrospray ionization (ESI) Fourier transform mass spectrometry (FTMS) to assess the ability of a series of nucleic acid ligands to bind selected structures of Psi-RNA and inhibit their specific interactions with NC in vitro. We found that the majority of the ligands included in the study were able to form stable non-covalent complexes with stem-loop 2, 3 and 4 (SL2-4), consistent with their characteristic nucleic acid binding modes. However, only aminoglycosidic antibiotics were capable of dissociating preformed NC*SL3 and NC*SL4 complexes, but not NC*SL2. The apparent specificity of these inhibitory effects is closely dependent on distinctive structural features of the different NC*RNA complexes. The trends observed for the IC50 values correlate very well with those provided by the ligand binding affinities and the dissociation constants of target NC*RNA complexes. This systematic investigation of archetypical nucleic acid ligands provides a valid framework to support the design of novel ligand inhibitors for HIV-1 treatment.
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Affiliation(s)
- Kevin B. Turner
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County1000 Hilltop Circle, Baltimore, MD 21228 USA
| | - Nathan A. Hagan
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County1000 Hilltop Circle, Baltimore, MD 21228 USA
| | - Daniele Fabris
- Department of Chemistry and Biochemistry, University of Maryland Baltimore County1000 Hilltop Circle, Baltimore, MD 21228 USA
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