1
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Samrat SK, Bashir Q, Zhang R, Huang Y, Liu Y, Wu X, Brown T, Wang W, Zheng YG, Zhang QY, Chen Y, Li Z, Li H. A universal fluorescence polarization high throughput screening assay to target the SAM-binding sites of SARS-CoV-2 and other viral methyltransferases. Emerg Microbes Infect 2023; 12:2204164. [PMID: 37060263 PMCID: PMC10165934 DOI: 10.1080/22221751.2023.2204164] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 04/16/2023]
Abstract
SARS-CoV-2 has caused a global pandemic with significant humanity and economic loss since 2020. Currently, only limited options are available to treat SARS-CoV-2 infections for vulnerable populations. In this study, we report a universal fluorescence polarization (FP)-based high throughput screening (HTS) assay for SAM-dependent viral methyltransferases (MTases), using a fluorescent SAM-analogue, FL-NAH. We performed the assay against a reference MTase, NSP14, an essential enzyme for SARS-CoV-2 to methylate the N7 position of viral 5'-RNA guanine cap. The assay is universal and suitable for any SAM-dependent viral MTases such as the SARS-CoV-2 NSP16/NSP10 MTase complex and the NS5 MTase of Zika virus (ZIKV). Pilot screening demonstrated that the HTS assay was very robust and identified two candidate inhibitors, NSC 111552 and 288387. The two compounds inhibited the FL-NAH binding to the NSP14 MTase with low micromolar IC50. We used three functional MTase assays to unambiguously verified the inhibitory potency of these molecules for the NSP14 N7-MTase function. Binding studies indicated that these molecules are bound directly to the NSP14 MTase with similar low micromolar affinity. Moreover, we further demonstrated that these molecules significantly inhibited the SARS-CoV-2 replication in cell-based assays at concentrations not causing cytotoxicity. Furthermore, NSC111552 significantly synergized with known SARS-CoV-2 drugs including nirmatrelvir and remdesivir. Finally, docking suggested that these molecules bind specifically to the SAM-binding site on the NSP14 MTase. Overall, these molecules represent novel and promising candidates to further develop broad-spectrum inhibitors for the management of viral infections.
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Affiliation(s)
- Subodh Kumar Samrat
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Qamar Bashir
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Ran Zhang
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Yiding Huang
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Yuchen Liu
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Xiangmeng Wu
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Tyler Brown
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA, USA
| | - Wei Wang
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Y. George Zheng
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA, USA
| | - Qing-Yu Zhang
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Yin Chen
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Zhong Li
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
| | - Hongmin Li
- Department of Pharmacology and Toxicology, R. Ken Coit College of Pharmacy, The University of Arizona, Tucson, AZ, USA
- Department of Chemistry and Biochemistry, College of Science & College of Medicine, The University of Arizona, Tucson, AZ, USA
- The BIO5 Institute, The University of Arizona, Tucson, AZ, USA
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2
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Kamzeeva PN, Aralov AV, Alferova VA, Korshun VA. Recent Advances in Molecular Mechanisms of Nucleoside Antivirals. Curr Issues Mol Biol 2023; 45:6851-6879. [PMID: 37623252 PMCID: PMC10453654 DOI: 10.3390/cimb45080433] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/12/2023] [Accepted: 08/14/2023] [Indexed: 08/26/2023] Open
Abstract
The search for new drugs has been greatly accelerated by the emergence of new viruses and drug-resistant strains of known pathogens. Nucleoside analogues (NAs) are a prospective class of antivirals due to known safety profiles, which are important for rapid repurposing in the fight against emerging pathogens. Recent improvements in research methods have revealed new unexpected details in the mechanisms of action of NAs that can pave the way for new approaches for the further development of effective drugs. This review accounts advanced techniques in viral polymerase targeting, new viral and host enzyme targeting approaches, and prodrug-based strategies for the development of antiviral NAs.
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Affiliation(s)
| | | | | | - Vladimir A. Korshun
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (P.N.K.); (A.V.A.); (V.A.A.)
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3
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Samrat SK, Bashir Q, Huang Y, Trieshmann CW, Tharappel AM, Zhang R, Chen K, Geoge Zheng Y, Li Z, Li H. Broad-Spectrum Small-Molecule Inhibitors Targeting the SAM-Binding Site of Flavivirus NS5 Methyltransferase. ACS Infect Dis 2023; 9:1319-1333. [PMID: 37348028 PMCID: PMC10436986 DOI: 10.1021/acsinfecdis.2c00571] [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] [Indexed: 06/24/2023]
Abstract
Flavivirus infections, such as those caused by dengue virus (DENV), West Nile virus (WNV), yellow fever virus (YFV), and Zika virus (ZIKV), pose a rising threat to global health. There are no FDA-approved drugs for flaviviruses, although a small number of flaviviruses have vaccines. For flaviviruses or unknown viruses that may appear in the future, it is particularly desirable to identify broad-spectrum inhibitors. The NS5 protein is regarded as one of the most promising flavivirus drug targets because it is conserved across flaviviruses. In this study, we used FL-NAH, a fluorescent analog of the methyl donor S-adenosyl methionine (SAM), to develop a fluorescence polarization (FP)-based high throughput screening (HTS) assay to specifically target methyltransferase (MTase), a vital enzyme for flaviviruses that methylates the N7 and 2'-O positions of the viral 5'-RNA cap. Pilot screening identified two candidate MTase inhibitors, NSC 111552 and 288387. The two compounds inhibited the FL-NAH binding to the DENV3 MTase with low micromolar IC50. Functional assays verified the inhibitory potency of these molecules for the flavivirus MTase activity. Binding studies indicated that these molecules are bound directly to the DENV3 MTase with similar low micromolar affinity. Furthermore, we showed that these compounds greatly reduced ZIKV replication in cell-based experiments at dosages that did not cause cytotoxicity. Finally, docking studies revealed that these molecules bind to the SAM-binding region on the DENV3 MTase, and further mutagenesis studies verified residues important for the binding of these compounds. Overall, these compounds are innovative and attractive candidates for the development of broad-spectrum inhibitors for the treatment of flavivirus infections.
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Affiliation(s)
- Subodh Kumar Samrat
- Department of Pharmacology and Toxicology, R Ken Coit College of Pharmacy, The University of Arizona, 1703 E Mabel St, Tucson AZ, 85721-0207, USA
| | - Qamar Bashir
- Department of Pharmacology and Toxicology, R Ken Coit College of Pharmacy, The University of Arizona, 1703 E Mabel St, Tucson AZ, 85721-0207, USA
| | - Yiding Huang
- Department of Pharmacology and Toxicology, R Ken Coit College of Pharmacy, The University of Arizona, 1703 E Mabel St, Tucson AZ, 85721-0207, USA
| | - Carl William Trieshmann
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia, 30602, USA
| | - Anil Mathew Tharappel
- Department of Pharmacology and Toxicology, R Ken Coit College of Pharmacy, The University of Arizona, 1703 E Mabel St, Tucson AZ, 85721-0207, USA
| | - Ran Zhang
- Department of Pharmacology and Toxicology, R Ken Coit College of Pharmacy, The University of Arizona, 1703 E Mabel St, Tucson AZ, 85721-0207, USA
| | - Ke Chen
- Department of Pharmacology and Toxicology, R Ken Coit College of Pharmacy, The University of Arizona, 1703 E Mabel St, Tucson AZ, 85721-0207, USA
| | - Y. Geoge Zheng
- Department of Pharmacology and Toxicology, R Ken Coit College of Pharmacy, The University of Arizona, 1703 E Mabel St, Tucson AZ, 85721-0207, USA
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, Georgia, 30602, USA
| | - Zhong Li
- Department of Pharmacology and Toxicology, R Ken Coit College of Pharmacy, The University of Arizona, 1703 E Mabel St, Tucson AZ, 85721-0207, USA
| | - Hongmin Li
- Department of Pharmacology and Toxicology, R Ken Coit College of Pharmacy, The University of Arizona, 1703 E Mabel St, Tucson AZ, 85721-0207, USA
- Department of Chemistry and Biochemistry, College of Science & College of Medicine, The University of Arizona, Tucson AZ, 85721, USA
- The BIO5 Institute, The University of Arizona, Tucson, AZ 85721, USA
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4
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Fischer TR, Meidner L, Schwickert M, Weber M, Zimmermann RA, Kersten C, Schirmeister T, Helm M. Chemical biology and medicinal chemistry of RNA methyltransferases. Nucleic Acids Res 2022; 50:4216-4245. [PMID: 35412633 PMCID: PMC9071492 DOI: 10.1093/nar/gkac224] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 03/17/2022] [Accepted: 04/08/2022] [Indexed: 12/24/2022] Open
Abstract
RNA methyltransferases (MTases) are ubiquitous enzymes whose hitherto low profile in medicinal chemistry, contrasts with the surging interest in RNA methylation, the arguably most important aspect of the new field of epitranscriptomics. As MTases become validated as drug targets in all major fields of biomedicine, the development of small molecule compounds as tools and inhibitors is picking up considerable momentum, in academia as well as in biotech. Here we discuss the development of small molecules for two related aspects of chemical biology. Firstly, derivates of the ubiquitous cofactor S-adenosyl-l-methionine (SAM) are being developed as bioconjugation tools for targeted transfer of functional groups and labels to increasingly visible targets. Secondly, SAM-derived compounds are being investigated for their ability to act as inhibitors of RNA MTases. Drug development is moving from derivatives of cosubstrates towards higher generation compounds that may address allosteric sites in addition to the catalytic centre. Progress in assay development and screening techniques from medicinal chemistry have led to recent breakthroughs, e.g. in addressing human enzymes targeted for their role in cancer. Spurred by the current pandemic, new inhibitors against coronaviral MTases have emerged at a spectacular rate, including a repurposed drug which is now in clinical trial.
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Affiliation(s)
- Tim R Fischer
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Laurenz Meidner
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Marvin Schwickert
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Marlies Weber
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Robert A Zimmermann
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Christian Kersten
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Tanja Schirmeister
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Staudingerweg 5, 55128Mainz, Germany
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5
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Mahalapbutr P, Kongtaworn N, Rungrotmongkol T. Structural insight into the recognition of S-adenosyl-L-homocysteine and sinefungin in SARS-CoV-2 Nsp16/Nsp10 RNA cap 2'-O-Methyltransferase. Comput Struct Biotechnol J 2020; 18:2757-2765. [PMID: 33020707 PMCID: PMC7527316 DOI: 10.1016/j.csbj.2020.09.032] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 09/21/2020] [Accepted: 09/23/2020] [Indexed: 01/07/2023] Open
Abstract
The binding affinity towards SARS-CoV-2 nsp16 of SFG is higher than that of SAH. Asp99 is a key binding residue for SAH and SFG via charge-charge attraction. SFG could electrostatically interact with the 2′-OH and N3 groups of adenosine moiety of RNA substrate. The distance between 2′-OH of RNA and –NH3+ (at 6′ position) of SFG mimics the methyl transfer reaction.
The recent ongoing coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to rapidly spread across the world. To date, neither a specific antiviral drug nor a clinically effective vaccine is available. Among the 15 viral non-structural proteins (nsps), nsp16 methyltransferase has been considered as a potential target due to its crucial role in RNA cap 2′-O-methylation process, preventing the virus detection by cell innate immunity mechanisms. In the present study, molecular recognition between the two natural nucleoside analogs (S-adenosyl-l-homocysteine (SAH) and sinefungin (SFG)) and the SARS-CoV-2 nsp16/nsp10/m7GpppAC5 was studied using all-atom molecular dynamics simulations and free energy calculations based on MM/GBSA and WaterSwap approaches. The binding affinity and the number of hot-spot residues, atomic contacts, and H-bond formations of SFG/nsp16 complex were distinctly higher than those of SAH/nsp16 system, consistent with the lower water accessibility at the enzyme active site. Notably, only SFG could electrostatically interact with the 2′-OH and N3 of RNA’s adenosine moiety, mimicking the methyl transfer reaction of S-adenosyl-l-methionine substrate. The atomistic binding mechanism obtained from this work paves the way for further optimizations and designs of more specific SARS-CoV-2 nsp16 inhibitors in the fight against COVID-19.
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Affiliation(s)
- Panupong Mahalapbutr
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Napat Kongtaworn
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
| | - Thanyada Rungrotmongkol
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand
- Biocatalyst and Environmental Biotechnology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
- Corresponding author at: Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok 10330, Thailand.
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6
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Li Z, Sakamuru S, Huang R, Brecher M, Koetzner CA, Zhang J, Chen H, Qin CF, Zhang QY, Zhou J, Kramer LD, Xia M, Li H. Erythrosin B is a potent and broad-spectrum orthosteric inhibitor of the flavivirus NS2B-NS3 protease. Antiviral Res 2017; 150:217-225. [PMID: 29288700 DOI: 10.1016/j.antiviral.2017.12.018] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [Revised: 12/12/2017] [Accepted: 12/22/2017] [Indexed: 01/04/2023]
Abstract
Many flaviviruses, such as Zika virus (ZIKV), Dengue virus (DENV1-4) and yellow fever virus (YFV), are significant human pathogens. Infection with ZIKV, an emerging mosquito-borne flavivirus, is associated with increased risk of microcephaly in newborns and Guillain-Barré syndrome and other complications in adults. Currently, specific therapy does not exist for any flavivirus infections. In this study, we found that erythrosin B, an FDA-approved food additive, is a potent inhibitor for flaviviruses, including ZIKV and DENV2. Erythrosin B was found to inhibit the DENV2 and ZIKV NS2B-NS3 proteases with IC50 in low micromolar range, via a non-competitive mechanism. Erythrosin B can significantly reduce titers of representative flaviviruses, DENV2, ZIKV, YFV, JEV, and WNV, with micromolar potency and with excellent cytotoxicity profile. Erythrosin B can also inhibit ZIKV replication in ZIKV-relevant human placental and neural progenitor cells. As a pregnancy category B food additive, erythrosin B may represent a promising and easily developed therapy for management of infections by ZIKV and other flaviviruses.
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Affiliation(s)
- Zhong Li
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY 12208, USA
| | - Srilatha Sakamuru
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ruili Huang
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthew Brecher
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY 12208, USA
| | - Cheri A Koetzner
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY 12208, USA
| | - Jing Zhang
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY 12208, USA
| | - Haiying Chen
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Cheng-Feng Qin
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, People's Republic of China
| | - Qing-Yu Zhang
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY 12208, USA; Department of Biomedical Sciences, School of Public Health, University at Albany, PO Box 509, Empire State Plaza, Albany NY 12201, USA
| | - Jia Zhou
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Laura D Kramer
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY 12208, USA; Department of Biomedical Sciences, School of Public Health, University at Albany, PO Box 509, Empire State Plaza, Albany NY 12201, USA
| | - Menghang Xia
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hongmin Li
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY 12208, USA; Department of Biomedical Sciences, School of Public Health, University at Albany, PO Box 509, Empire State Plaza, Albany NY 12201, USA.
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7
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Li Z, Brecher M, Deng YQ, Zhang J, Sakamuru S, Liu B, Huang R, Koetzner CA, Allen CA, Jones SA, Chen H, Zhang NN, Tian M, Gao F, Lin Q, Banavali N, Zhou J, Boles N, Xia M, Kramer LD, Qin CF, Li H. Existing drugs as broad-spectrum and potent inhibitors for Zika virus by targeting NS2B-NS3 interaction. Cell Res 2017; 27:1046-1064. [PMID: 28685770 DOI: 10.1038/cr.2017.88] [Citation(s) in RCA: 135] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2017] [Revised: 05/19/2017] [Accepted: 06/05/2017] [Indexed: 02/07/2023] Open
Abstract
Recent outbreaks of Zika virus (ZIKV) highlight an urgent need for therapeutics. The protease complex NS2B-NS3 plays essential roles during flaviviral polyprotein processing, and thus represents an attractive drug target. Here, we developed a split luciferase complementation-based high-throughput screening assay to identify orthosteric inhibitors that directly target flavivirus NS2B-NS3 interactions. By screening a total of 2 816 approved and investigational drugs, we identified three potent candidates, temoporfin, niclosamide, and nitazoxanide, as flavivirus NS2B-NS3 interaction inhibitors with nanomolar potencies. Significantly, the most potent compound, temoporfin, not only inhibited ZIKV replication in human placental and neural progenitor cells, but also prevented ZIKV-induced viremia and mortality in mouse models. Structural docking suggests that temoporfin potentially binds NS3 pockets that hold critical NS2B residues, thus inhibiting flaviviral polyprotein processing in a non-competitive manner. As these drugs have already been approved for clinical use in other indications either in the USA or other countries, they represent promising and easily developed therapies for the management of infections by ZIKV and other flaviviruses.
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Affiliation(s)
- Zhong Li
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY 12208, USA
| | - Matthew Brecher
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY 12208, USA
| | - Yong-Qiang Deng
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Jing Zhang
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY 12208, USA
| | - Srilatha Sakamuru
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Binbin Liu
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY 12208, USA.,Department of Food Science, College of Food Science and Technology, Guangdong Ocean University, Zhanjiang, Guangdong 524000, China
| | - Ruili Huang
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cheri A Koetzner
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY 12208, USA
| | - Christina A Allen
- The Neural Stem Cell Institute, 1 Discovery Drive, Rensselaer, NY 12144, USA
| | - Susan A Jones
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY 12208, USA
| | - Haiying Chen
- Department of Pharmacology and Toxicology, Chemical Biology Program, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Na-Na Zhang
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Min Tian
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China
| | - Fengshan Gao
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY 12208, USA.,Department of Biochemistry and Molecular Biology, College of Life Science and Technology, Dalian University, Dalian, Liaoning 116622, China
| | - Qishan Lin
- Center for Functional Genomics, University at Albany, Rensselaer, NY 12144, USA
| | - Nilesh Banavali
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY 12208, USA.,Department of Biomedical Sciences, School of Public Health, University at Albany, PO Box 509, Empire State Plaza, Albany, NY 12201, USA
| | - Jia Zhou
- Department of Pharmacology and Toxicology, Chemical Biology Program, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Nathan Boles
- The Neural Stem Cell Institute, 1 Discovery Drive, Rensselaer, NY 12144, USA
| | - Menghang Xia
- National Center for Advancing Translational Sciences, National Institutes of Health, Bethesda, MD 20892, USA
| | - Laura D Kramer
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY 12208, USA.,Department of Biomedical Sciences, School of Public Health, University at Albany, PO Box 509, Empire State Plaza, Albany, NY 12201, USA
| | - Cheng-Feng Qin
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, China.,Guangzhou Eighth People's Hospital, Guangzhou Medical University, Guangzhou, Guangdong 510060, China
| | - Hongmin Li
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY 12208, USA.,Department of Biomedical Sciences, School of Public Health, University at Albany, PO Box 509, Empire State Plaza, Albany, NY 12201, USA
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8
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A conformational switch high-throughput screening assay and allosteric inhibition of the flavivirus NS2B-NS3 protease. PLoS Pathog 2017; 13:e1006411. [PMID: 28542603 PMCID: PMC5462475 DOI: 10.1371/journal.ppat.1006411] [Citation(s) in RCA: 109] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Revised: 06/07/2017] [Accepted: 05/15/2017] [Indexed: 12/02/2022] Open
Abstract
The flavivirus genome encodes a single polyprotein precursor requiring multiple cleavages by host and viral proteases in order to produce the individual proteins that constitute an infectious virion. Previous studies have revealed that the NS2B cofactor of the viral NS2B-NS3 heterocomplex protease displays a conformational dynamic between active and inactive states. Here, we developed a conformational switch assay based on split luciferase complementation (SLC) to monitor the conformational change of NS2B and to characterize candidate allosteric inhibitors. Binding of an active-site inhibitor to the protease resulted in a conformational change of NS2B and led to significant SLC enhancement. Mutagenesis of key residues at an allosteric site abolished this induced conformational change and SLC enhancement. We also performed a virtual screen of NCI library compounds to identify allosteric inhibitors, followed by in vitro biochemical screening of the resultant candidates. Only three of these compounds, NSC135618, 260594, and 146771, significantly inhibited the protease of Dengue virus 2 (DENV2) in vitro, with IC50 values of 1.8 μM, 11.4 μM, and 4.8 μM, respectively. Among the three compounds, only NSC135618 significantly suppressed the SLC enhancement triggered by binding of active-site inhibitor in a dose-dependent manner, indicating that it inhibits the conformational change of NS2B. Results from virus titer reduction assays revealed that NSC135618 is a broad spectrum flavivirus protease inhibitor, and can significantly reduce titers of DENV2, Zika virus (ZIKV), West Nile virus (WNV), and Yellow fever virus (YFV) on A549 cells in vivo, with EC50 values in low micromolar range. In contrast, the cytotoxicity of NSC135618 is only moderate with CC50 of 48.8 μM on A549 cells. Moreover, NSC135618 inhibited ZIKV in human placental and neural progenitor cells relevant to ZIKV pathogenesis. Results from binding, kinetics, Western blot, mass spectrometry and mutagenesis experiments unambiguously demonstrated an allosteric mechanism for inhibition of the viral protease by NSC135618.
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9
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Brecher M, Chen H, Li Z, Banavali NK, Jones SA, Zhang J, Kramer LD, Li H. Identification and Characterization of Novel Broad-Spectrum Inhibitors of the Flavivirus Methyltransferase. ACS Infect Dis 2015; 1:340-9. [PMID: 26726314 DOI: 10.1021/acsinfecdis.5b00070] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Flavivirus methyltransferase (MTase) is essential for viral replication. Here we report the identification of small molecules through virtual screening that putatively bind to the SAM-binding site of flavivirus MTase and inhibit its function. Six of these computationally predicted binders were identified to show significant MTase inhibition with low micromolar inhibitory activity. The most active compounds showed broad-spectrum activity against the MTase proteins of other flaviviruses. Two of these compounds also showed low cytotoxicity and high antiviral efficacy in cell-based assays. Competitive binding analyses indicated that the inhibitors performed their inhibitory function through competitive binding to the SAM cofactor binding site of the MTase. The crystal structure of the MTase-inhibitor complex further supports the mode of action and provides routes for their further optimization as flavivirus MTase inhibitors.
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Affiliation(s)
- Matthew Brecher
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, New York 12208, United States
| | - Hui Chen
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, New York 12208, United States
| | - Zhong Li
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, New York 12208, United States
| | - Nilesh K. Banavali
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, New York 12208, United States
- Department of Biomedical Sciences, School of Public Health, State University of New York, P.O. Box 509, Albany, New York 12201 United States
| | - Susan A. Jones
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, New York 12208, United States
| | - Jing Zhang
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, New York 12208, United States
| | - Laura D. Kramer
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, New York 12208, United States
- Department of Biomedical Sciences, School of Public Health, State University of New York, P.O. Box 509, Albany, New York 12201 United States
| | - Hongmin Li
- Wadsworth Center, New York State Department of Health, 120 New Scotland Avenue, Albany, New York 12208, United States
- Department of Biomedical Sciences, School of Public Health, State University of New York, P.O. Box 509, Albany, New York 12201 United States
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10
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Brecher M, Chen H, Liu B, Banavali NK, Jones SA, Zhang J, Li Z, Kramer LD, Li H. Novel Broad Spectrum Inhibitors Targeting the Flavivirus Methyltransferase. PLoS One 2015; 10:e0130062. [PMID: 26098995 PMCID: PMC4476580 DOI: 10.1371/journal.pone.0130062] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 05/15/2015] [Indexed: 01/17/2023] Open
Abstract
The flavivirus methyltransferase (MTase) is an essential enzyme that sequentially methylates the N7 and 2’-O positions of the viral RNA cap, using S-adenosyl-L-methionine (SAM) as a methyl donor. We report here that small molecule compounds, which putatively bind to the SAM-binding site of flavivirus MTase and inhibit its function, were identified by using virtual screening. In vitro methylation experiments demonstrated significant MTase inhibition by 13 of these compounds, with the most potent compound displaying sub-micromolar inhibitory activity. The most active compounds showed broad spectrum activity against the MTase proteins of multiple flaviviruses. Two of these compounds also exhibited low cytotoxicity and effectively inhibited viral replication in cell-based assays, providing further structural insight into flavivirus MTase inhibition.
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Affiliation(s)
- Matthew Brecher
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY, 12208 United States of America
| | - Hui Chen
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY, 12208 United States of America
| | - Binbin Liu
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY, 12208 United States of America
| | - Nilesh K. Banavali
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY, 12208 United States of America
- Department of Biomedical Sciences, School of Public Health, State University of New York, Albany, PO Box 509, New York, 12201, United States of America
| | - Susan A. Jones
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY, 12208 United States of America
| | - Jing Zhang
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY, 12208 United States of America
| | - Zhong Li
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY, 12208 United States of America
| | - Laura D. Kramer
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY, 12208 United States of America
- Department of Biomedical Sciences, School of Public Health, State University of New York, Albany, PO Box 509, New York, 12201, United States of America
| | - Hongmin Li
- Wadsworth Center, New York State Department of Health, 120 New Scotland Ave, Albany, NY, 12208 United States of America
- Department of Biomedical Sciences, School of Public Health, State University of New York, Albany, PO Box 509, New York, 12201, United States of America
- * E-mail:
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11
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Vernekar SKV, Qiu L, Zhang J, Kankanala J, Li H, Geraghty RJ, Wang Z. 5'-Silylated 3'-1,2,3-triazolyl Thymidine Analogues as Inhibitors of West Nile Virus and Dengue Virus. J Med Chem 2015; 58:4016-28. [PMID: 25909386 DOI: 10.1021/acs.jmedchem.5b00327] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
West Nile virus (WNV) and Dengue virus (DENV) are important human pathogens for which there are presently no vaccine or specific antivirals. We report herein a 5'-silylated nucleoside scaffold derived from 3'-azidothymidine (AZT) consistently and selectively inhibiting WNV and DENV at low micromolar concentrations. Further synthesis of various triazole bioisosteres demonstrated clear structure-activity relationships (SARs) in which the antiviral activity against WNV and DENV hinges largely on both the 5'-silyl group and the substituent of 3'-triazole or its bioisosteres. Particularly interesting is the 5' silyl group which turns on the antiviral activity against WNV and DENV while abrogating the previously reported antiviral potency against human immunodeficiency virus (HIV-1). The antiviral activity was confirmed through a plaque assay where viral titer reduction was observed in the presence of selected compounds. Molecular modeling and competitive S-adenosyl-l-methionine (SAM) binding assay suggest that these compounds likely confer antiviral activity via binding to methyltransferase (MTase).
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Affiliation(s)
- Sanjeev Kumar V Vernekar
- †Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Li Qiu
- †Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Jing Zhang
- ‡Wadsworth Center, New York State Department of Health, 120 New Scotland Ave., Albany, New York 12208, United States
| | - Jayakanth Kankanala
- †Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Hongmin Li
- ‡Wadsworth Center, New York State Department of Health, 120 New Scotland Ave., Albany, New York 12208, United States.,§Department of Biomedical Sciences, School of Public Health, University at Albany, Albany, New York 12201, United States
| | - Robert J Geraghty
- †Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Zhengqiang Wang
- †Center for Drug Design, Academic Health Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
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12
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Brecher MB, Li Z, Zhang J, Chen H, Lin Q, Liu B, Li H. Refolding of a fully functional flavivirus methyltransferase revealed that S-adenosyl methionine but not S-adenosyl homocysteine is copurified with flavivirus methyltransferase. Protein Sci 2014; 24:117-28. [PMID: 25352331 DOI: 10.1002/pro.2594] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2014] [Revised: 10/22/2014] [Accepted: 10/23/2014] [Indexed: 01/09/2023]
Abstract
Methylation of flavivirus RNA is vital for its stability and translation in the infected host cell. This methylation is mediated by the flavivirus methyltransferase (MTase), which methylates the N7 and 2'-O positions of the viral RNA cap by using S-adenosyl-l-methionine (SAM) as a methyl donor. In this report, we demonstrate that SAM, in contrast to the reaction by-product S-adenosyl-l-homocysteine, which was assumed previously, is copurified with the Dengue (DNV) and West Nile virus MTases produced in Escherichia coli (E. coli). This endogenous SAM can be removed by denaturation and refolding of the MTase protein. The refolded MTase of DNV serotype 3 (DNV3) displays methylation activity comparable to native enzyme, and its crystal structure at 2.1 Å is almost identical to that of native MTase. We characterized the binding of Sinefungin (SIN), a previously described SAM-analog inhibitor of MTase function, to the native and refolded DNV3 MTase by isothermal titration calorimetry, and found that SIN binds to refolded MTase with more than 16 times the affinity of SIN binding to the MTase purified natively. Moreover, we show that SAM is also copurified with other flavivirus MTases, indicating that purification by refolding may be a generally applicable tool for studying flavivirus MTase inhibition.
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Affiliation(s)
- Matthew B Brecher
- Wadsworth Center, New York State Department of Health, Albany, New York, 12208
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13
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Ghosh AK, Lv K. A convergent synthesis of carbocyclic sinefungin and its C5 epimer. European J Org Chem 2014; 2014:6761-6768. [PMID: 25530707 PMCID: PMC4267295 DOI: 10.1002/ejoc.201402812] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Indexed: 11/11/2022]
Abstract
A convergent synthesis of carbocyclic sinefungin 2 and its C5 epimer 3 is described. The key features in our synthesis include the use of commercial available L-methionine and readily available (1R, 4S)-4-hydroxy-2-cyclopentenyl acetate as starting materials, cross-metathesis coupling, enzymatic kinetic resolution and Staudinger reduction. The current synthesis is flexible and therefore provides convenient access to the synthesis of various carbocyclic SIN analogues for biological evaluation.
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Affiliation(s)
- Arun K. Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, Indiana, 47906 (USA)
| | - Kai Lv
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, Indiana, 47906 (USA)
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