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Di Paco G, Macchiagodena M, Procacci P. Identification of Potential Inhibitors of the SARS-CoV-2 NSP13 Helicase via Structure-Based Ligand Design, Molecular Docking and Nonequilibrium Alchemical Simulations. ChemMedChem 2024; 19:e202400095. [PMID: 38456332 DOI: 10.1002/cmdc.202400095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 03/06/2024] [Accepted: 03/06/2024] [Indexed: 03/09/2024]
Abstract
We have assembled a computational pipeline based on virtual screening, docking techniques, and nonequilibrium molecular dynamics simulations, with the goal of identifying possible inhibitors of the SARS-CoV-2 NSP13 helicase, catalyzing by ATP hydrolysis the unwinding of double or single-stranded RNA in the viral replication process inside the host cell. The druggable sites for broad-spectrum inhibitors are represented by the RNA binding sites at the 5' entrance and 3' exit of the central channel, a structural motif that is highly conserved across coronaviruses. Potential binders were first generated using structure-based ligand techniques. Their potency was estimated by using four popular docking scoring functions. Common docking hits for NSP13 were finally tested using advanced nonequilibrium alchemical techniques for binding free energy calculations on a high-performing parallel cluster. Four potential NSP13 inhibitors with potency from submicrimolar to nanomolar were finally identified.
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Affiliation(s)
- Giorgio Di Paco
- Dipartimento di Chimica "Ugo Schiff", Universit'a degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Marina Macchiagodena
- Dipartimento di Chimica "Ugo Schiff", Universit'a degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
| | - Piero Procacci
- Dipartimento di Chimica "Ugo Schiff", Universit'a degli Studi di Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, Italy
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2
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Zhang C, Yu J, Deng M, Zhang Q, Jin F, Chen L, Li Y, He B. Development of a Fluorescent Assay and Imidazole-Containing Inhibitors by Targeting SARS-CoV-2 Nsp13 Helicase. Molecules 2024; 29:2301. [PMID: 38792162 DOI: 10.3390/molecules29102301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Revised: 04/30/2024] [Accepted: 05/05/2024] [Indexed: 05/26/2024] Open
Abstract
Nsp13, a non-structural protein belonging to the coronavirus family 1B (SF1B) helicase, exhibits 5'-3' polarity-dependent DNA or RNA unwinding using NTPs. Crucially, it serves as a key component of the viral replication-transcription complex (RTC), playing an indispensable role in the coronavirus life cycle and thereby making it a promising target for broad-spectrum antiviral therapies. The imidazole scaffold, known for its antiviral potential, has been proposed as a potential scaffold. In this study, a fluorescence-based assay was designed by labeling dsDNA substrates with a commercial fluorophore and monitoring signal changes upon Nsp13 helicase activity. Optimization and high-throughput screening validated the feasibility of this approach. In accordance with the structural characteristics of ADP, we employed a structural-based design strategy to synthesize three classes of imidazole-based compounds through substitution reaction. Through in vitro activity research, pharmacokinetic parameter analysis, and molecular docking simulation, we identified compounds A16 (IC50 = 1.25 μM) and B3 (IC50 = 0.98 μM) as potential lead antiviral compounds for further targeted drug research.
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Affiliation(s)
- Chuang Zhang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, Guizhou Medical University, Guiyang 550004, China
| | - Junhui Yu
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, Guizhou Medical University, Guiyang 550004, China
| | - Mingzhenlong Deng
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, Guizhou Medical University, Guiyang 550004, China
| | - Qingqing Zhang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, Guizhou Medical University, Guiyang 550004, China
| | - Fei Jin
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, Guizhou Medical University, Guiyang 550004, China
| | - Lei Chen
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, Guizhou Medical University, Guiyang 550004, China
| | - Yan Li
- School of Basic Medical Science, Guizhou Medical University, Guiyang 550004, China
| | - Bin He
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, Guizhou Medical University, Guiyang 550004, China
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3
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Majrashi TA, El Hassab MA, Mahmoud SH, Mostafa A, Wahsh EA, Elkaeed EB, Hassan FE, Eldehna WM, Abdelgawad SM. In vitro biological evaluation and in silico insights into the antiviral activity of standardized olive leaves extract against SARS-CoV-2. PLoS One 2024; 19:e0301086. [PMID: 38662719 PMCID: PMC11045091 DOI: 10.1371/journal.pone.0301086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 03/08/2024] [Indexed: 04/28/2024] Open
Abstract
There is still a great global need for efficient treatments for the management of SARS-CoV-2 illness notwithstanding the availability and efficacy of COVID-19 vaccinations. Olive leaf is an herbal remedy with a potential antiviral activity that could improve the recovery of COVID-19 patients. In this work, the olive leaves major metabolites were screened in silico for their activity against SARS-CoV-2 by molecular docking on several viral targets such as methyl transferase, helicase, Plpro, Mpro, and RdRp. The results of in silico docking study showed that olive leaves phytoconstituents exhibited strong potential antiviral activity against SARS-CoV-2 selected targets. Verbacoside demonstrated a strong inhibition against methyl transferase, helicase, Plpro, Mpro, and RdRp (docking scores = -17.2, -20, -18.2, -19.8, and -21.7 kcal/mol.) respectively. Oleuropein inhibited 5rmm, Mpro, and RdRp (docking scores = -15, -16.6 and -18.6 kcal/mol., respectively) respectively. Apigenin-7-O-glucoside exhibited activity against methyl transferase and RdRp (docking score = -16.1 and -19.4 kcal/mol., respectively) while Luteolin-7-O-glucoside inhibited Plpro and RdRp (docking score = -15.2 and -20 kcal/mol., respectively). The in vitro antiviral assay was carried out on standardized olive leaf extract (SOLE) containing 20% oleuropein and IC50 was calculated. The results revealed that 20% SOLE demonstrated a moderate antiviral activity against SARS-CoV-2 with IC50 of 118.3 μg /mL. Accordingly, olive leaf could be a potential herbal therapy against SARS-CoV-2 but more in vivo and clinical investigations are recommended.
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Affiliation(s)
- Taghreed A. Majrashi
- Department of Pharmacognosy, College of Pharmacy, King Khalid University, Asir, Saudi Arabia
| | - Mahmoud A. El Hassab
- Department of Medicinal Chemistry, Faculty of Pharmacy, King Salman International University (KSIU), South Sinai, Egypt
| | - Sara H. Mahmoud
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza, Egypt
| | - Ahmed Mostafa
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza, Egypt
| | - Engy A. Wahsh
- Clinical Pharmacy Department, Faculty of Pharmacy, October 6 University, Giza Governorate, Egypt
| | - Eslam B. Elkaeed
- Department of Pharmaceutical Sciences, College of Pharmacy, AlMaarefa University, Riyadh, Saudi Arabia
| | - Fatma E. Hassan
- Department of Physiology, General Medicine Practice Program, Batterjee Medical College, Jeddah, Saudi Arabia
- Medical Physiology Department, Kasr Alainy, Faculty of Medicine, Cairo University, Giza, Egypt
| | - Wagdy M. Eldehna
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh, Egypt
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4
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Inniss NL, Rzhetskaya M, Ling-Hu T, Lorenzo-Redondo R, Bachta KE, Satchell KJF, Hultquist JF. Activity and inhibition of the SARS-CoV-2 Omicron nsp13 R392C variant using RNA duplex unwinding assays. SLAS Discov 2024; 29:100145. [PMID: 38301954 DOI: 10.1016/j.slasd.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 01/29/2024] [Indexed: 02/03/2024]
Abstract
SARS-CoV-2 nsp13 helicase is an essential enzyme for viral replication and a promising target for antiviral drug development. This study compares the double-stranded RNA (dsRNA) unwinding activity of nsp13 and the Omicron nsp13R392C variant, which is predominant in currently circulating lineages. Using in vitro gel- and fluorescence-based assays, we found that both nsp13 and nsp13R392C have dsRNA unwinding activity with equivalent kinetics. Furthermore, the R392C mutation had no effect on the efficiency of the nsp13-specific helicase inhibitor SSYA10-001. We additionally confirmed the activity of several other helicase inhibitors against nsp13, including punicalagin that inhibited dsRNA unwinding at nanomolar concentrations. Overall, this study reveals the utility of using dsRNA unwinding assays to screen small molecules for antiviral activity against nsp13 and the Omicron nsp13R392C variant. Continual monitoring of newly emergent variants will be essential for considering resistance profiles of lead compounds as they are advanced towards next-generation therapeutic development.
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Affiliation(s)
- Nicole L Inniss
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA; Center for Structural Biology of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Margarita Rzhetskaya
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA; Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA; Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Ted Ling-Hu
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA; Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA; Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Ramon Lorenzo-Redondo
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA; Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Kelly E Bachta
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA; Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Karla J F Satchell
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA; Center for Structural Biology of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA; Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA.
| | - Judd F Hultquist
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA; Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA; Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA.
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5
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Yazdi AK, Pakarian P, Perveen S, Hajian T, Santhakumar V, Bolotokova A, Li F, Vedadi M. Kinetic Characterization of SARS-CoV-2 nsp13 ATPase Activity and Discovery of Small-Molecule Inhibitors. ACS Infect Dis 2022; 8:1533-1542. [PMID: 35822715 PMCID: PMC9305828 DOI: 10.1021/acsinfecdis.2c00165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Indexed: 11/29/2022]
Abstract
SARS-CoV-2 non-structural protein 13 (nsp13) is a highly conserved helicase and RNA 5'-triphosphatase. It uses the energy derived from the hydrolysis of nucleoside triphosphates for directional movement along the nucleic acids and promotes the unwinding of double-stranded nucleic acids. Nsp13 is essential for replication and propagation of all human and non-human coronaviruses. Combined with its defined nucleotide binding site and druggability, nsp13 is one of the most promising candidates for the development of pan-coronavirus therapeutics. Here, we report the development and optimization of bioluminescence assays for kinetic characterization of nsp13 ATPase activity in the presence and absence of single-stranded DNA. Screening of a library of 5000 small molecules in the presence of single-stranded DNA resulted in the discovery of six nsp13 small-molecule inhibitors with IC50 values ranging from 6 ± 0.5 to 50 ± 6 μM. In addition to providing validated methods for high-throughput screening of nsp13 in drug discovery campaigns, the reproducible screening hits we present here could potentially be chemistry starting points toward the development of more potent and selective nsp13 inhibitors, enabling the discovery of antiviral therapeutics.
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Affiliation(s)
| | - Paknoosh Pakarian
- Structural Genomics Consortium,
University of Toronto, Toronto, Ontario M5G 1L7,
Canada
| | - Sumera Perveen
- Structural Genomics Consortium,
University of Toronto, Toronto, Ontario M5G 1L7,
Canada
| | - Taraneh Hajian
- Structural Genomics Consortium,
University of Toronto, Toronto, Ontario M5G 1L7,
Canada
| | | | - Albina Bolotokova
- Structural Genomics Consortium,
University of Toronto, Toronto, Ontario M5G 1L7,
Canada
| | - Fengling Li
- Structural Genomics Consortium,
University of Toronto, Toronto, Ontario M5G 1L7,
Canada
| | - Masoud Vedadi
- Structural Genomics Consortium,
University of Toronto, Toronto, Ontario M5G 1L7,
Canada
- Department of Pharmacology and Toxicology,
University of Toronto, Toronto, Ontario M5S 1A8,
Canada
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6
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da Costa RA, da Rocha JAP, Pinheiro AS, da Costa ADSS, da Rocha ECM, Silva RC, Gonçalves ADS, Santos CBR, Brasil DDSB. A Computational Approach Applied to the Study of Potential Allosteric Inhibitors Protease NS2B/NS3 from Dengue Virus. Molecules 2022; 27:molecules27134118. [PMID: 35807364 PMCID: PMC9268547 DOI: 10.3390/molecules27134118] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/01/2022] [Accepted: 06/02/2022] [Indexed: 12/10/2022] Open
Abstract
Dengue virus (DENV) is a danger to more than 400 million people in the world, and there is no specific treatment. Thus, there is an urgent need to develop an effective method to combat this pathology. NS2B/NS3 protease is an important biological target due it being necessary for viral replication and the fact that it promotes the spread of the infection. Thus, this study aimed to design DENV NS2B/NS3pro allosteric inhibitors from a matrix compound. The search was conducted using the Swiss Similarity tool. The compounds were subjected to molecular docking calculations, molecular dynamics simulations (MD) and free energy calculations. The molecular docking results showed that two compounds, ZINC000001680989 and ZINC000001679427, were promising and performed important hydrogen interactions with the Asn152, Leu149 and Ala164 residues, showing the same interactions obtained in the literature. In the MD, the results indicated that five residues, Lys74, Leu76, Asn152, Leu149 and Ala166, contribute to the stability of the ligand at the allosteric site for all of the simulated systems. Hydrophobic, electrostatic and van der Waals interactions had significant effects on binding affinity. Physicochemical properties, lipophilicity, water solubility, pharmacokinetics, druglikeness and medicinal chemistry were evaluated for four compounds that were more promising, showed negative indices for the potential penetration of the Blood Brain Barrier and expressed high human intestinal absorption, indicating a low risk of central nervous system depression or drowsiness as the the side effects. The compound ZINC000006694490 exhibited an alert with a plausible level of toxicity for the purine base chemical moiety, indicating hepatotoxicity and chromosome damage in vivo in mouse, rat and human organisms. All of the compounds selected in this study showed a synthetic accessibility (SA) score lower than 4, suggesting the ease of new syntheses. The results corroborate with other studies in the literature, and the computational approach used here can contribute to the discovery of new and potent anti-dengue agents.
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Affiliation(s)
- Renato A. da Costa
- Graduate Program in Science and Environment, Institute of Exact and Natural Sciences, Federal University of Pará (UFPA), Belém 66075-110, PA, Brazil; (A.S.P.); (A.d.S.S.d.C.); (D.d.S.B.B.)
- Federal Institute of Education, Science and Technology of Pará Campus Castanhal, Castanhal 68740-970, PA, Brazil
- Correspondence: ; Tel.: +55-91-985484622
| | - João A. P. da Rocha
- Federal Institute of Education, Science and Technology of Pará—Campus Bragança, Bragança 68600-000, PA, Brazil; (J.A.P.d.R.); (E.C.M.d.R.)
| | - Alan S. Pinheiro
- Graduate Program in Science and Environment, Institute of Exact and Natural Sciences, Federal University of Pará (UFPA), Belém 66075-110, PA, Brazil; (A.S.P.); (A.d.S.S.d.C.); (D.d.S.B.B.)
| | - Andréia do S. S. da Costa
- Graduate Program in Science and Environment, Institute of Exact and Natural Sciences, Federal University of Pará (UFPA), Belém 66075-110, PA, Brazil; (A.S.P.); (A.d.S.S.d.C.); (D.d.S.B.B.)
| | - Elaine C. M. da Rocha
- Federal Institute of Education, Science and Technology of Pará—Campus Bragança, Bragança 68600-000, PA, Brazil; (J.A.P.d.R.); (E.C.M.d.R.)
| | - Rai. C. Silva
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto 14040-901, SP, Brazil;
| | - Arlan da S. Gonçalves
- Federal Institute of Education, Science and Technology of Espírito Santo, Vila Velha 29106-010, ES, Brazil;
| | - Cleydson B. R. Santos
- Laboratory of Modeling and Computational Chemistry, Department of Biological and Health Sciences, Federal University of Amapá, Macapá 68902-280, AP, Brazil;
| | - Davi do S. B. Brasil
- Graduate Program in Science and Environment, Institute of Exact and Natural Sciences, Federal University of Pará (UFPA), Belém 66075-110, PA, Brazil; (A.S.P.); (A.d.S.S.d.C.); (D.d.S.B.B.)
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7
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Ricci F, Gitto R, Pitasi G, De Luca L. In Silico Insights towards the Identification of SARS-CoV-2 NSP13 Helicase Druggable Pockets. Biomolecules 2022; 12:biom12040482. [PMID: 35454070 PMCID: PMC9029846 DOI: 10.3390/biom12040482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 02/04/2023] Open
Abstract
The merging of distinct computational approaches has become a powerful strategy for discovering new biologically active compounds. By using molecular modeling, significant efforts have recently resulted in the development of new molecules, demonstrating high efficiency in reducing the replication of severe acute respiratory coronavirus 2 (SARS-CoV-2), the agent responsible for the COVID-19 pandemic. We have focused our interest on non-structural protein Nsp13 (NTPase/helicase), as a crucial protein, embedded in the replication–transcription complex (RTC), that controls the virus life cycle. To assist in the identification of the most druggable surfaces of Nsps13, we applied a combination of four computational tools: FTMap, SiteMap, Fpocket and LigandScout. These software packages explored the binding sites for different three-dimensional structures of RTC complexes (PDB codes: 6XEZ, 7CXM, 7CXN), thus, detecting several hot spots, that were clustered to obtain ensemble consensus sites, through a combination of four different approaches. The comparison of data provided new insights about putative druggable sites that might be employed for further docking simulations on druggable surfaces of Nsps13, in a scenario of repurposing drugs.
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8
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Abstract
R-loops are by-products of transcription that must be tightly regulated to maintain genomic stability and gene expression. Here, we describe a mechanism for the regulation of the R-loop-specific helicase, senataxin (SETX), and identify the ubiquitin specific peptidase 11 (USP11) as an R-loop regulator. USP11 de-ubiquitinates SETX and its depletion increases SETX K48-ubiquitination and protein turnover. Loss of USP11 decreases SETX steady-state levels and reduces R-loop dissolution. Ageing of USP11 knockout cells restores SETX levels via compensatory transcriptional downregulation of the E3 ubiquitin ligase, KEAP1. Loss of USP11 reduces SETX enrichment at KEAP1 promoter, leading to R-loop accumulation, enrichment of the endonuclease XPF and formation of double-strand breaks. Overexpression of KEAP1 increases SETX K48-ubiquitination, promotes its degradation and R-loop accumulation. These data define a ubiquitination-dependent mechanism for SETX regulation, which is controlled by the opposing activities of USP11 and KEAP1 with broad applications for cancer and neurological disease.
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Affiliation(s)
- Mateusz Jurga
- School of Bioscience, Department of Molecular Biology and Biotechnology, The Healthy Lifespan Institute and the Institute of Neuroscience, University of Sheffield, Sheffield, UK
- The Institute of Cancer Therapeutics, University of Bradford, Bradford, UK
| | - Arwa A Abugable
- School of Bioscience, Department of Molecular Biology and Biotechnology, The Healthy Lifespan Institute and the Institute of Neuroscience, University of Sheffield, Sheffield, UK
| | | | - Sherif F El-Khamisy
- School of Bioscience, Department of Molecular Biology and Biotechnology, The Healthy Lifespan Institute and the Institute of Neuroscience, University of Sheffield, Sheffield, UK.
- The Institute of Cancer Therapeutics, University of Bradford, Bradford, UK.
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9
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Kronenberger T, Sá Magalhães Serafim M, Kumar Tonduru A, Gonçalves Maltarollo V, Poso A. Ligand Accessibility Insights to the Dengue Virus NS3-NS2B Protease Assessed by Long-Timescale Molecular Dynamics Simulations. ChemMedChem 2021; 16:2524-2534. [PMID: 33899341 PMCID: PMC8453957 DOI: 10.1002/cmdc.202100246] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Indexed: 11/12/2022]
Abstract
Dengue is a tropical disease caused by the dengue virus (DENV), with an estimate of 300 million new cases every year. Due to the limited vaccine efficiency and absence of effective antiviral treatment, new drug candidates are urgently needed. DENV NS3-NS2B protease complex is essential for viral post-translational processing and maturation, and this enzyme has been extensively studied as a relevant drug target. Crystal structures often underestimate NS3-NS2B flexibility, whereas they can adopt different conformational states depending on the bound substrate. We conducted molecular dynamics simulations (∼30 μs) with a non- and covalently bound inhibitor to understand the conformational changes in the DENV-3 NS3-NS2B complex. Our results show that the open-closing movement of the protease exposes multiple druggable subpockets that can be investigated in later drug discovery efforts.
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Affiliation(s)
- Thales Kronenberger
- Department of Medical Oncology and PneumologyUniversity Hospital of TübingenOtfried-Müller-Strasse 1472076TübingenGermany
- School of PharmacyUniversity of Eastern FinlandKuopio70211Finland
| | - Mateus Sá Magalhães Serafim
- Departamento de MicrobiologiaUniversidade Federal de Minas Gerais (UFMG)Av. Antônio Carlos, 6627PampulhaCEP 31270-901Belo HorizonteBrazil
| | | | - Vinícius Gonçalves Maltarollo
- Departamento de Produtos FarmacêuticosUniversidade Federal de Minas Gerais (UFMG)Av. Antônio Carlos, 6627PampulhaCEP 31270-901Belo HorizonteBrazil
| | - Antti Poso
- Department of Medical Oncology and PneumologyUniversity Hospital of TübingenOtfried-Müller-Strasse 1472076TübingenGermany
- School of PharmacyUniversity of Eastern FinlandKuopio70211Finland
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10
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Newman JA, Douangamath A, Yadzani S, Yosaatmadja Y, Aimon A, Brandão-Neto J, Dunnett L, Gorrie-Stone T, Skyner R, Fearon D, Schapira M, von Delft F, Gileadi O. Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase. Nat Commun 2021; 12:4848. [PMID: 34381037 DOI: 10.1101/2021.03.15.435326] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 07/28/2021] [Indexed: 05/25/2023] Open
Abstract
There is currently a lack of effective drugs to treat people infected with SARS-CoV-2, the cause of the global COVID-19 pandemic. The SARS-CoV-2 Non-structural protein 13 (NSP13) has been identified as a target for anti-virals due to its high sequence conservation and essential role in viral replication. Structural analysis reveals two "druggable" pockets on NSP13 that are among the most conserved sites in the entire SARS-CoV-2 proteome. Here we present crystal structures of SARS-CoV-2 NSP13 solved in the APO form and in the presence of both phosphate and a non-hydrolysable ATP analog. Comparisons of these structures reveal details of conformational changes that provide insights into the helicase mechanism and possible modes of inhibition. To identify starting points for drug development we have performed a crystallographic fragment screen against NSP13. The screen reveals 65 fragment hits across 52 datasets opening the way to structure guided development of novel antiviral agents.
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Affiliation(s)
- Joseph A Newman
- Centre for Medicines Discovery, University of Oxford, Oxford, UK.
| | - Alice Douangamath
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - Setayesh Yadzani
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | | | - Antony Aimon
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - José Brandão-Neto
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - Louise Dunnett
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - Tyler Gorrie-Stone
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - Rachael Skyner
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - Daren Fearon
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - Matthieu Schapira
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Frank von Delft
- Centre for Medicines Discovery, University of Oxford, Oxford, UK
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
- Faculty of Science, University of Johannesburg, Johannesburg, South Africa
| | - Opher Gileadi
- Centre for Medicines Discovery, University of Oxford, Oxford, UK
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11
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Newman JA, Douangamath A, Yadzani S, Yosaatmadja Y, Aimon A, Brandão-Neto J, Dunnett L, Gorrie-Stone T, Skyner R, Fearon D, Schapira M, von Delft F, Gileadi O. Structure, mechanism and crystallographic fragment screening of the SARS-CoV-2 NSP13 helicase. Nat Commun 2021; 12:4848. [PMID: 34381037 PMCID: PMC8358061 DOI: 10.1038/s41467-021-25166-6] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 07/28/2021] [Indexed: 12/24/2022] Open
Abstract
There is currently a lack of effective drugs to treat people infected with SARS-CoV-2, the cause of the global COVID-19 pandemic. The SARS-CoV-2 Non-structural protein 13 (NSP13) has been identified as a target for anti-virals due to its high sequence conservation and essential role in viral replication. Structural analysis reveals two "druggable" pockets on NSP13 that are among the most conserved sites in the entire SARS-CoV-2 proteome. Here we present crystal structures of SARS-CoV-2 NSP13 solved in the APO form and in the presence of both phosphate and a non-hydrolysable ATP analog. Comparisons of these structures reveal details of conformational changes that provide insights into the helicase mechanism and possible modes of inhibition. To identify starting points for drug development we have performed a crystallographic fragment screen against NSP13. The screen reveals 65 fragment hits across 52 datasets opening the way to structure guided development of novel antiviral agents.
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Affiliation(s)
- Joseph A Newman
- Centre for Medicines Discovery, University of Oxford, Oxford, UK.
| | - Alice Douangamath
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - Setayesh Yadzani
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | | | - Antony Aimon
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - José Brandão-Neto
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - Louise Dunnett
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - Tyler Gorrie-Stone
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - Rachael Skyner
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - Daren Fearon
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
| | - Matthieu Schapira
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Frank von Delft
- Centre for Medicines Discovery, University of Oxford, Oxford, UK
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot, UK
- Faculty of Science, University of Johannesburg, Johannesburg, South Africa
| | - Opher Gileadi
- Centre for Medicines Discovery, University of Oxford, Oxford, UK
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12
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Kim J, Park SJ, Park J, Shin H, Jang YS, Woo JS, Min DH. Identification of a Direct-Acting Antiviral Agent Targeting RNA Helicase via a Graphene Oxide Nanobiosensor. ACS Appl Mater Interfaces 2021; 13:25715-25726. [PMID: 34036784 DOI: 10.1021/acsami.1c04641] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Dengue virus (DENV), an arbovirus transmitted by mosquitoes, causes infectious diseases such as dengue fever, dengue hemorrhagic fever, and dengue shock syndrome. Despite the dangers posed by DENV, there are no approved antiviral drugs for treatment of DENV infection. Considering the potential for a global dengue outbreak, rapid development of antiviral agents against DENV infections is crucial as a preemptive measure; thus, the selection of apparent drug targets, such as the viral enzymes involved in the viral life cycle, is recommended. Helicase, a potential drug target in DENV, is a crucial viral enzyme that unwinds double-stranded viral RNA, releasing single-stranded RNA genomes during viral replication. Therefore, an inhibitor of helicase activity could serve as a direct-acting antiviral agent. Here, we introduce an RNA helicase assay based on graphene oxide, which enables fluorescence-based analysis of RNA substrate-specific helicase enzyme activity. This assay demonstrated high reliability and ability for high-throughput screening, identifying a new helicase inhibitor candidate, micafungin (MCFG), from an FDA-approved drug library. As a direct-acting antiviral agent targeting RNA helicase, MCFG inhibits DENV proliferation in cells and an animal model. Notably, in vivo, MCFG treatment reduced viremia, inflammatory cytokine levels, and viral loads in several tissues and improved survival rates by up to 40% in a lethal mouse model. Therefore, we suggest MCFG as a potential direct-acting antiviral drug candidate.
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Affiliation(s)
- Jungho Kim
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Se-Jin Park
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Jisang Park
- Department of Bioactive Material Sciences and Institute of Bioactive Materials, Jeonbuk National University, Jeonju 54896, Republic of Korea
- Department of Molecular Biology and the Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Hojeong Shin
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
| | - Yong-Suk Jang
- Department of Bioactive Material Sciences and Institute of Bioactive Materials, Jeonbuk National University, Jeonju 54896, Republic of Korea
- Department of Molecular Biology and the Institute for Molecular Biology and Genetics, Jeonbuk National University, Jeonju 54896, Republic of Korea
| | - Jae-Sung Woo
- Center for RNA Research, Institute for Basic Science (IBS), Seoul National University, Seoul 08826, Republic of Korea
- Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Dal-Hee Min
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
- Institute of Biotherapeutics Convergence Technology, Lemonex Inc., Seoul 06683, Republic of Korea
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13
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Abidi SH, Almansour NM, Amerzhanov D, Allemailem KS, Rafaqat W, Ibrahim MAA, la Fleur P, Lukac M, Ali S. Repurposing potential of posaconazole and grazoprevir as inhibitors of SARS-CoV-2 helicase. Sci Rep 2021; 11:10290. [PMID: 33986405 PMCID: PMC8119689 DOI: 10.1038/s41598-021-89724-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 04/13/2021] [Indexed: 01/08/2023] Open
Abstract
As the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) pandemic engulfs millions worldwide, the quest for vaccines or drugs against the virus continues. The helicase protein of SARS-CoV-2 represents an attractive target for drug discovery since inhibition of helicase activity can suppress viral replication. Using in silico approaches, we have identified drugs that interact with SARS-CoV-2 helicase based on the presence of amino acid arrangements matching binding sites of drugs in previously annotated protein structures. The drugs exhibiting an RMSD of ≤ 3.0 Å were further analyzed using molecular docking, molecular dynamics (MD) simulation, and post-MD analyses. Using these approaches, we found 12 drugs that showed strong interactions with SARS-CoV-2 helicase amino acids. The analyses were performed using the recently available SARS-CoV-2 helicase structure (PDB ID: 5RL6). Based on the MM-GBSA approach, out of the 12 drugs, two drugs, namely posaconazole and grazoprevir, showed the most favorable binding energy, - 54.8 and - 49.1 kcal/mol, respectively. Furthermore, of the amino acids found conserved among all human coronaviruses, 10/11 and 10/12 were targeted by, respectively, grazoprevir and posaconazole. These residues are part of the crucial DEAD-like helicase C and DEXXQc_Upf1-like/ DEAD-like helicase domains. Strong interactions of posaconazole and grazoprevir with conserved amino acids indicate that the drugs can be potent against SARS-CoV-2. Since the amino acids are conserved among the human coronaviruses, the virus is unlikely to develop resistance mutations against these drugs. Since these drugs are already in use, they may be immediately repurposed for SARS-CoV-2 therapy.
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Affiliation(s)
- Syed Hani Abidi
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, Pakistan
| | - Nahlah Makki Almansour
- Department of Biology, College of Science, University of Hafr Al Batin, Hafr Al Batin, Saudi Arabia
| | - Daulet Amerzhanov
- Nazarbayev University School of Medicine, Nazarbayev University, Astana, Kazakhstan
| | - Khaled S Allemailem
- Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah, Saudi Arabia
| | | | - Mahmoud A A Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia, 61519, Egypt
| | - Philip la Fleur
- Nazarbayev University School of Medicine, Nazarbayev University, Astana, Kazakhstan
| | - Martin Lukac
- Department of Computer Science, School of Engineering and Digital Sciences, Nazarbayev University, Astana, Kazakhstan
| | - Syed Ali
- Nazarbayev University School of Medicine, Nazarbayev University, Astana, Kazakhstan.
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14
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Ahmad S, Waheed Y, Ismail S, Bhatti S, Abbasi SW, Muhammad K. Structure-Based Virtual Screening Identifies Multiple Stable Binding Sites at the RecA Domains of SARS-CoV-2 Helicase Enzyme. Molecules 2021; 26:1446. [PMID: 33800013 PMCID: PMC7962107 DOI: 10.3390/molecules26051446] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 03/04/2021] [Accepted: 03/04/2021] [Indexed: 02/07/2023] Open
Abstract
With the emergence and global spread of the COVID-19 pandemic, the scientific community worldwide has focused on search for new therapeutic strategies against this disease. One such critical approach is targeting proteins such as helicases that regulate most of the SARS-CoV-2 RNA metabolism. The purpose of the current study was to predict a library of phytochemicals derived from diverse plant families with high binding affinity to SARS-CoV-2 helicase (Nsp13) enzyme. High throughput virtual screening of the Medicinal Plant Database for Drug Design (MPD3) database was performed on SARS-CoV-2 helicase using AutoDock Vina. Nilotinib, with a docking value of -9.6 kcal/mol, was chosen as a reference molecule. A compound (PubChem CID: 110143421, ZINC database ID: ZINC257223845, eMolecules: 43290531) was screened as the best binder (binding energy of -10.2 kcal/mol on average) to the enzyme by using repeated docking runs in the screening process. On inspection, the compound was disclosed to show different binding sites of the triangular pockets collectively formed by Rec1A, Rec2A, and 1B domains and a stalk domain at the base. The molecule is often bound to the ATP binding site (referred to as binding site 2) of the helicase enzyme. The compound was further discovered to fulfill drug-likeness and lead-likeness criteria, have good physicochemical and pharmacokinetics properties, and to be non-toxic. Molecular dynamic simulation analysis of the control/lead compound complexes demonstrated the formation of stable complexes with good intermolecular binding affinity. Lastly, affirmation of the docking simulation studies was accomplished by estimating the binding free energy by MMPB/GBSA technique. Taken together, these findings present further in silco investigation of plant-derived lead compounds to effectively address COVID-19.
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Affiliation(s)
- Sajjad Ahmad
- Foundation University Medical College, Foundation University Islamabad, DHA-I, Islamabad 44000, Pakistan; (S.A.); (S.I.)
- Department of Health and Biological Sciences, Abasyn University, Peshawar 25000, Pakistan
| | - Yasir Waheed
- Foundation University Medical College, Foundation University Islamabad, DHA-I, Islamabad 44000, Pakistan; (S.A.); (S.I.)
| | - Saba Ismail
- Foundation University Medical College, Foundation University Islamabad, DHA-I, Islamabad 44000, Pakistan; (S.A.); (S.I.)
| | - Saadia Bhatti
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 44000, Pakistan;
| | - Sumra Wajid Abbasi
- NUMS Department of Biological Sciences, National University of Medical Sciences, Abid Majeed Rd, The Mall, Rawalpindi 46000, Pakistan;
| | - Khalid Muhammad
- Department of Biology, College of Science, United Arab Emirates University, Al Ain 15551, United Arab Emirates
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15
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Abstract
RNA helicases are responsible for virtually all of RNA metabolism. Viral and bacterial pathogens typically encode their own RNA helicases. Hence, this family of enzymes is increasingly recognized as potential targets for treatment of a variety of diseases. However, the conserved structural similarities among helicase families present an obstacle to the idea of developing specific inhibitors. In order to identify potential modulators of RNA helicase activity, rapid screening approaches are needed. This has been accomplished by optimizing and adapting standard helicase assays to function in high-throughput modalities. These optimized assays have enabled the application of rapid screening approaches to be applied toward discovering helicase inhibitors. This chapter provides detailed protocols for utilizing a medium to high-throughput approach for inhibitor discovery.
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Affiliation(s)
- John C Marecki
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Alicia K Byrd
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Kevin D Raney
- Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
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16
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Ugurel OM, Mutlu O, Sariyer E, Kocer S, Ugurel E, Inci TG, Ata O, Turgut-Balik D. Evaluation of the potency of FDA-approved drugs on wild type and mutant SARS-CoV-2 helicase (Nsp13). Int J Biol Macromol 2020; 163:1687-1696. [PMID: 32980406 PMCID: PMC7513821 DOI: 10.1016/j.ijbiomac.2020.09.138] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 09/15/2020] [Accepted: 09/19/2020] [Indexed: 02/07/2023]
Abstract
SARS-CoV-2 has caused COVID-19 outbreak with nearly 2 M infected people and over 100K death worldwide, until middle of April 2020. There is no confirmed drug for the treatment of COVID-19 yet. As the disease spread fast and threaten human life, repositioning of FDA approved drugs may provide fast options for treatment. In this aspect, structure-based drug design could be applied as a powerful approach in distinguishing the viral drug target regions from the host. Evaluation of variations in SARS-CoV-2 genome may ease finding specific drug targets in the viral genome. In this study, 3458 SARS-CoV-2 genome sequences isolated from all around the world were analyzed. Incidence of C17747T and A17858G mutations were observed to be much higher than others and they were on Nsp13, a vital enzyme of SARS-CoV-2. Effect of these mutations was evaluated on protein-drug interactions using in silico methods. The most potent drugs were found to interact with the key and neighbor residues of the active site responsible from ATP hydrolysis. As result, cangrelor, fludarabine, folic acid and polydatin were determined to be the most potent drugs which have potency to inhibit both the wild type and mutant SARS-CoV-2 helicase. Clinical data supporting these findings would be important towards overcoming COVID-19.
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Affiliation(s)
- Osman Mutluhan Ugurel
- Yildiz Technical University, Faculty of Chemical and Metallurgical Engineering, Department of Bioengineering, Davutpasa Campus, 34210 Esenler, Istanbul, Turkey; Altinbas University, School of Engineering and Natural Science, Department of Basic Science, 34217 Bagcilar, Istanbul, Turkey
| | - Ozal Mutlu
- Marmara University, Faculty of Arts and Sciences, Department of Biology, Goztepe Campus, 34722 Kadikoy, Istanbul, Turkey
| | - Emrah Sariyer
- Artvin Coruh University, Vocational School of Health Services, Medical Laboratory Techniques, Artvin, Turkey
| | - Sinem Kocer
- Istanbul Yeni Yuzyil University, Faculty of Pharmacy, Department of Pharmaceutical Biotechnology, 34010 Cevizlibag, Istanbul, Turkey
| | - Erennur Ugurel
- Yildiz Technical University, Faculty of Chemical and Metallurgical Engineering, Department of Bioengineering, Davutpasa Campus, 34210 Esenler, Istanbul, Turkey
| | - Tugba Gul Inci
- Yildiz Technical University, Faculty of Chemical and Metallurgical Engineering, Department of Bioengineering, Davutpasa Campus, 34210 Esenler, Istanbul, Turkey
| | - Oguz Ata
- Altinbas University, School of Engineering and Natural Science, Department of Software Engineering, 34217 Bagcilar, Istanbul, Turkey
| | - Dilek Turgut-Balik
- Yildiz Technical University, Faculty of Chemical and Metallurgical Engineering, Department of Bioengineering, Davutpasa Campus, 34210 Esenler, Istanbul, Turkey.
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17
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Abstract
The raging COVID-19 pandemic caused by SARS-CoV-2 has infected tens of millions of people and killed several hundred thousand patients worldwide. Currently, there are no effective drugs or vaccines available for treating coronavirus infections. In this study, we have focused on the SARS-CoV-2 helicase (Nsp13), which is critical for viral replication and the most conserved nonstructural protein within the coronavirus family. Using homology modeling that couples published electron-density with molecular dynamics (MD)-based structural refinements, we generated structural models of the SARS-CoV-2 helicase in its apo- and ATP/RNA-bound conformations. We performed virtual screening of ∼970 000 chemical compounds against the ATP-binding site to identify potential inhibitors. Herein, we report docking hits of approved human drugs targeting the ATP-binding site. Importantly, two of our top drug hits have significant activity in inhibiting purified recombinant SARS-CoV-2 helicase, providing hope that these drugs can be potentially repurposed for the treatment of COVID-19.
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Affiliation(s)
- Mark Andrew White
- Sealy Center for Structural Biology and Molecular Biophysics, The University of Texas Medical Branch, Galveston, TX 77555, USA
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Wei Lin
- Department of Integrative Biology & Pharmacology, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Texas Therapeutics Institute, Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Xiaodong Cheng
- Department of Integrative Biology & Pharmacology, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Texas Therapeutics Institute, Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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18
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Braun NJ, Quek JP, Huber S, Kouretova J, Rogge D, Lang‐Henkel H, Cheong EZK, Chew BLA, Heine A, Luo D, Steinmetzer T. Structure-Based Macrocyclization of Substrate Analogue NS2B-NS3 Protease Inhibitors of Zika, West Nile and Dengue viruses. ChemMedChem 2020; 15:1439-1452. [PMID: 32501637 PMCID: PMC7497253 DOI: 10.1002/cmdc.202000237] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Indexed: 11/06/2022]
Abstract
A series of cyclic active-site-directed inhibitors of the NS2B-NS3 proteases from Zika (ZIKV), West Nile (WNV), and dengue-4 (DENV4) viruses has been designed. The most potent compounds contain a reversely incorporated d-lysine residue in the P1 position. Its side chain is connected to the P2 backbone, its α-amino group is converted into a guanidine to interact with the conserved Asp129 side chain in the S1 pocket, and its C terminus is connected to the P3 residue via different linker segments. The most potent compounds inhibit the ZIKV protease with Ki values <5 nM. Crystal structures of seven ZIKV protease inhibitor complexes were determined to support the inhibitor design. All the cyclic compounds possess high selectivity against trypsin-like serine proteases and furin-like proprotein convertases. Both WNV and DENV4 proteases are inhibited less efficiently. Nonetheless, similar structure-activity relationships were observed for these enzymes, thus suggesting their potential application as pan-flaviviral protease inhibitors.
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Affiliation(s)
- Niklas J. Braun
- Institute of Pharmaceutical ChemistryPhilipps UniversityMarbacher Weg 635032MarburgGermany
| | - Jun P. Quek
- Lee Kong Chian School of MedicineNanyang Technological University, EMB 03–0759 Nanyang DriveSingapore636921Singapore
- Institute of Structural BiologyNanyang Technological University EMB 06–0159 Nanyang DriveSingapore636921Singapore
| | - Simon Huber
- Institute of Pharmaceutical ChemistryPhilipps UniversityMarbacher Weg 635032MarburgGermany
| | - Jenny Kouretova
- Institute of Pharmaceutical ChemistryPhilipps UniversityMarbacher Weg 635032MarburgGermany
| | - Dorothee Rogge
- Institute of Pharmaceutical ChemistryPhilipps UniversityMarbacher Weg 635032MarburgGermany
| | - Heike Lang‐Henkel
- Institute of Pharmaceutical ChemistryPhilipps UniversityMarbacher Weg 635032MarburgGermany
| | - Ezekiel Z. K. Cheong
- School of Biological SciencesNanyang Technological University60 Nanyang Dr.Singapore637551Singapore
| | - Bing L. A. Chew
- Lee Kong Chian School of MedicineNanyang Technological University, EMB 03–0759 Nanyang DriveSingapore636921Singapore
- Institute of Structural BiologyNanyang Technological University EMB 06–0159 Nanyang DriveSingapore636921Singapore
- Institute of Health TechnologiesInterdisciplinary Graduate ProgrammeNanyang Technological University61 Nanyang Dr.Singapore637335Singapore
| | - Andreas Heine
- Institute of Pharmaceutical ChemistryPhilipps UniversityMarbacher Weg 635032MarburgGermany
| | - Dahai Luo
- Lee Kong Chian School of MedicineNanyang Technological University, EMB 03–0759 Nanyang DriveSingapore636921Singapore
- Institute of Structural BiologyNanyang Technological University EMB 06–0159 Nanyang DriveSingapore636921Singapore
- School of Biological SciencesNanyang Technological University60 Nanyang Dr.Singapore637551Singapore
| | - Torsten Steinmetzer
- Institute of Pharmaceutical ChemistryPhilipps UniversityMarbacher Weg 635032MarburgGermany
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19
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Abstract
G-Quadruplexes (G4s) are non-canonical secondary structures formed within guanine-rich regions of DNA or RNA. G4 sequences/structures have been detected in human and in viral genomes, including Coronaviruses Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) and SARS-CoV-2. Here, we outline the existing evidence indicating that G4 ligands and inhibitors of SARS-CoV-2 helicase may exert some antiviral activity reducing viral replication and can represent a potential therapeutic approach to tackle the COVID-19 pandemic due to SARS-CoV-2 infection. We also discuss how repositioning of FDA-approved drugs against helicase activity of other viruses, could represent a rapid strategy to limit deaths associated with COVID-19 pandemic.
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Affiliation(s)
- Nadia Panera
- Research Unit of Molecular Genetics of Complex Phenotypes, Bambino Gesù Children's Hospital, IRCCS, 4, Piazza Sant'Onofrio, 00165, Rome, Italy
| | - Alberto Eugenio Tozzi
- Multifactorial Disease and Complex Phenotype Research Area, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Anna Alisi
- Research Unit of Molecular Genetics of Complex Phenotypes, Bambino Gesù Children's Hospital, IRCCS, 4, Piazza Sant'Onofrio, 00165, Rome, Italy.
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20
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Kurniawan I, Rosalinda M, Ikhsan N. Implementation of ensemble methods on QSAR Study of NS3 inhibitor activity as anti-dengue agent. SAR QSAR Environ Res 2020; 31:477-492. [PMID: 32546117 DOI: 10.1080/1062936x.2020.1773534] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 05/20/2020] [Indexed: 06/11/2023]
Abstract
Dengue fever is a disease transmitted by infected mosquitoes. This disease spreads in several countries, especially those with a tropical climate. To date, there is no specific drug that can be used to treat dengue. Use of clinically investigated drugs, such as Balapiravir, is still not effective in inhibiting the activity of virus replication. The design of a drug candidate can be performed by using the non-structural protein 3 (NS3) as target. This study aimed to develop QSAR models to predict the inhibitory activity class of NS3 inhibitors. The classification was performed by using feature importance analysis for selecting the descriptors and three ensemble methods, i.e. random forest (RF), adaptive boosting (AdaBoost), and extremely randomized trees (ERT), for model design and prediction. Hyperparameter tuning was performed to improve the performance of the models. Based on the results, we found that model 9, developed from ERT produced the best performance with values of accuracy and AUC equal to 0.73 and 0.82, respectively. Use of y-scrambling method allowed us to confirm that the model was not related to the chance correlation.
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Affiliation(s)
- I Kurniawan
- School of Computing, Telkom University , Bandung, Indonesia
- Research Center of Human Centric Engineering, Telkom University , Bandung, Indonesia
| | - M Rosalinda
- Research Center of Human Centric Engineering, Telkom University , Bandung, Indonesia
| | - N Ikhsan
- School of Computing, Telkom University , Bandung, Indonesia
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21
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Coronado MA, Eberle RJ, Bleffert N, Feuerstein S, Olivier DS, de Moraes FR, Willbold D, Arni RK. Zika virus NS2B/NS3 proteinase: A new target for an old drug - Suramin a lead compound for NS2B/NS3 proteinase inhibition. Antiviral Res 2018; 160:118-125. [PMID: 30393012 DOI: 10.1016/j.antiviral.2018.10.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 09/25/2018] [Accepted: 10/24/2018] [Indexed: 01/15/2023]
Abstract
Zika virus infection is the focus of much research due to the medical and social repercussions. Due the role of the viral NS2B/NS3 proteinase in maturation of the viral proteins, it had become an attractive antiviral target. Numerous investigations on viral epidemiology, structure and function analysis, vaccines, and therapeutic drugs have been conducted around the world. At present, no approved vaccine or even drugs have been reported. Thus, there is an urgent need to develop therapeutic agents to cure this epidemic disease. In the present study, we identified the polyanion suramin, an approved antiparasitic drug with antiviral properties, as a potential inhibitor of Zika virus complex NS2B/NS3 proteinase with IC50 of 47 μM. Using fluorescence spectroscopy results we could determine a kd value of 28 μM and had shown that the ligand does not affect the thermal stability of the protein. STD NMR spectroscopy experiments and molecular docking followed by molecular dynamics simulation identified the binding epitopes of the molecule and shows the mode of interaction, respectively. The computational analysis showed that suramin block the Ser135 residue and interact with the catalytically histidine residue.
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Affiliation(s)
- Monika Aparecida Coronado
- Multiuser Center for Biomolecular Innovation, Department of Physics, Universidade Estadual Paulista (UNESP), São José do Rio Preto SP, 15054-000, Brazil.
| | - Raphael Josef Eberle
- Multiuser Center for Biomolecular Innovation, Department of Physics, Universidade Estadual Paulista (UNESP), São José do Rio Preto SP, 15054-000, Brazil
| | - Nicole Bleffert
- Institute of Complex System, Structural Biochemistry (ICS-6), Forchungszentrum Jülich, Germany; Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße, Germany
| | - Sophie Feuerstein
- Institute of Complex System, Structural Biochemistry (ICS-6), Forchungszentrum Jülich, Germany; Institute of Complex System, Structural Biochemistry (ICS-6), Forchungszentrum Jülich, Germany
| | - Danilo Silva Olivier
- Multiuser Center for Biomolecular Innovation, Department of Physics, Universidade Estadual Paulista (UNESP), São José do Rio Preto SP, 15054-000, Brazil
| | - Fabio Rogerio de Moraes
- Multiuser Center for Biomolecular Innovation, Department of Physics, Universidade Estadual Paulista (UNESP), São José do Rio Preto SP, 15054-000, Brazil
| | - Dieter Willbold
- Institute of Complex System, Structural Biochemistry (ICS-6), Forchungszentrum Jülich, Germany; Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße, Germany
| | - Raghuvir Krishnaswamy Arni
- Multiuser Center for Biomolecular Innovation, Department of Physics, Universidade Estadual Paulista (UNESP), São José do Rio Preto SP, 15054-000, Brazil.
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22
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Davidson RB, Hendrix J, Geiss BJ, McCullagh M. Allostery in the dengue virus NS3 helicase: Insights into the NTPase cycle from molecular simulations. PLoS Comput Biol 2018; 14:e1006103. [PMID: 29659571 PMCID: PMC5919694 DOI: 10.1371/journal.pcbi.1006103] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 04/26/2018] [Accepted: 03/22/2018] [Indexed: 12/29/2022] Open
Abstract
The C-terminus domain of non-structural 3 (NS3) protein of the Flaviviridae viruses (e.g. HCV, dengue, West Nile, Zika) is a nucleotide triphosphatase (NTPase) -dependent superfamily 2 (SF2) helicase that unwinds double-stranded RNA while translocating along the nucleic polymer. Due to these functions, NS3 is an important target for antiviral development yet the biophysics of this enzyme are poorly understood. Microsecond-long molecular dynamic simulations of the dengue NS3 helicase domain are reported from which allosteric effects of RNA and NTPase substrates are observed. The presence of a bound single-stranded RNA catalytically enhances the phosphate hydrolysis reaction by affecting the dynamics and positioning of waters within the hydrolysis active site. Coupled with results from the simulations, electronic structure calculations of the reaction are used to quantify this enhancement to be a 150-fold increase, in qualitative agreement with the experimental enhancement factor of 10–100. Additionally, protein-RNA interactions exhibit NTPase substrate-induced allostery, where the presence of a nucleotide (e.g. ATP or ADP) structurally perturbs residues in direct contact with the phosphodiester backbone of the RNA. Residue-residue network analyses highlight pathways of short ranged interactions that connect the two active sites. These analyses identify motif V as a highly connected region of protein structure through which energy released from either active site is hypothesized to move, thereby inducing the observed allosteric effects. These results lay the foundation for the design of novel allosteric inhibitors of NS3. Non-structural protein 3 (NS3) is a Flaviviridae (e.g. Hepatitis C, dengue, and Zika viruses) helicase that unwinds double stranded RNA while translocating along the nucleic polymer during viral genome replication. As a member of superfamily 2 (SF2) helicases, NS3 utilizes the free energy of nucleotide triphosphate (NTP) binding, hydrolysis, and product unbinding to perform its functions. While much is known about SF2 helicases, the pathways and mechanisms through which free energy is transduced between the NTP hydrolysis active site and RNA binding cleft remains elusive. Here we present a multiscale computational study to characterize the allosteric effects induced by the RNA and NTPase substrates (ATP, ADP, and Pi) as well as the pathways of short-range, residue-residue interactions that connect the two active sites. Results from this body of molecular dynamics simulations and electronic structure calculations are highlighted in context to the NTPase enzymatic cycle, allowing for development of testable hypotheses for validation of these simulations. Our insights, therefore, provide novel details about the biophysics of NS3 and guide the next generation of experimental studies.
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Affiliation(s)
- Russell B. Davidson
- Department of Chemistry, Colorado State University, Fort Collins, Colorado, United States of America
| | - Josie Hendrix
- Department of Chemistry, Colorado State University, Fort Collins, Colorado, United States of America
| | - Brian J. Geiss
- Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, Colorado, United States of America
- School of Biomedical Engineering, Colorado State University, Fort Collins, Colorado, United States of America
| | - Martin McCullagh
- Department of Chemistry, Colorado State University, Fort Collins, Colorado, United States of America
- * E-mail:
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23
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2017] [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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24
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Qu YJ, Ge L, Bai JL, Cao YY, Jin YW, Wang H, Yang L, Song F. p.Val19Glyfs*21 and p.Leu228* variants in the survival of motor neuron 1 trigger nonsense-mediated mRNA decay causing the SMN1 PTC+ transcripts degradation. Mutat Res 2017; 806:31-38. [PMID: 28950212 DOI: 10.1016/j.mrfmmm.2017.09.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Revised: 08/24/2017] [Accepted: 09/12/2017] [Indexed: 06/07/2023]
Abstract
Spinal Muscular Atrophy (SMA) results from loss-of-function mutations in the survival of motor neuron 1 (SMN1) gene. Our previous research showed that 40% of variants were nonsense or frameshift variants and SMN1 mRNA levels in the patients carrying these variants were significantly decreased. Here we selected one rare variant (p.Val19Glyfs*21) and one common variant (p.Leu228*) to explore the degradation mechanism of mutant transcripts. The levels of full-length (FL)-SMN1 transcripts and SMN protein in the cell lines from the patients with these variants were both significantly reduced (p<0.01). Treatment with two translation inhibitors (puromycin and Cycloheximide (CHX)) markedly increased the levels of FL-SMN1 transcripts with premature translation termination codons (PTCs) (p<0.01) and showed time-dependent (10h>5.5h) but not dose-dependent effects. Moreover, the knockdown of UPF1, a key factor in nonsense-mediated mRNA decay (NMD) by lentivirus, led to a 3.1-fold increase (p<0.01) in FL-SMN1 transcript levels in patient fibroblasts. Our research provides evidence that these two PTC-generating variants (p.Val19Glyfs*21 and p.Leu228*) can trigger NMD, causing rapid degradation of SMN1 transcripts thereby resulting in SMN protein deficiency. These two variants are highly pathogenic and are associated with more severe SMA phenotypes. Varying NMD efficiency after treatment with puromycin and CHX in different cell types was also observed.
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Affiliation(s)
- Yu-Jin Qu
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing, 100020, China.
| | - Lin Ge
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing, 100020, China.
| | - Jin-Li Bai
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing, 100020, China.
| | - Yan-Yan Cao
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing, 100020, China.
| | - Yu-Wei Jin
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing, 100020, China.
| | - Hong Wang
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing, 100020, China.
| | - Lan Yang
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing, 100020, China.
| | - Fang Song
- Department of Medical Genetics, Capital Institute of Pediatrics, Beijing, 100020, China.
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25
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Roy A, Lim L, Srivastava S, Lu Y, Song J. Solution conformations of Zika NS2B-NS3pro and its inhibition by natural products from edible plants. PLoS One 2017; 12:e0180632. [PMID: 28700665 PMCID: PMC5503262 DOI: 10.1371/journal.pone.0180632] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 06/19/2017] [Indexed: 12/20/2022] Open
Abstract
The recent Zika viral (ZIKV) epidemic has been associated with severe neurological pathologies such as neonatal microcephaly and Guillain-Barre syndrome but unfortunately no vaccine or medication is effectively available yet. Zika NS2B-NS3pro is essential for the proteolysis of the viral polyprotein and thereby viral replication. Thus NS2B-NS3pro represents an attractive target for anti-Zika drug discovery/design. Here, we have characterized the solution conformations and catalytic parameters of both linked and unlinked Zika NS2B-NS3pro complexes and found that the unlinked complex manifested well-dispersed NMR spectra. Subsequently with selective isotope-labeling using NMR spectroscopy, we demonstrated that C-terminal residues (R73-K100) of NS2B is highly disordered without any stable tertiary and secondary structures in the Zika NS2B-NS3pro complex in the free state. Upon binding to the well-characterized serine protease inhibitor, bovine pancreatic trypsin inhibitor (BPTI), only the extreme C-terminal residues (L86-K100) remain disordered. Additionally, we have identified five flavonoids and one natural phenol rich in edible plants including fruits and vegetables, which inhibit Zika NS2B-NS3pro in a non-competitive mode, with Ki ranging from 770 nM for Myricetin to 34.02 μM for Apigenin. Molecular docking showed that they all bind to a pocket on the back of the active site and their structure-activity relationship was elucidated. Our study provides valuable insights into the solution conformation of Zika NS2B-NS3pro and further deciphers its susceptibility towards allosteric inhibition by natural products. As these natural product inhibitors fundamentally differ from the currently-known active site inhibitors in terms of both inhibitory mode and chemical scaffold, our finding might open a new avenue for development of better allosteric inhibitors to fight ZIKV infection.
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Affiliation(s)
- Amrita Roy
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Liangzhong Lim
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Shagun Srivastava
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Yimei Lu
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Jianxing Song
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
- * E-mail:
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26
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Hermawan I, Furuta A, Higashi M, Fujita Y, Akimitsu N, Yamashita A, Moriishi K, Tsuneda S, Tani H, Nakakoshi M, Tsubuki M, Sekiguchi Y, Noda N, Tanaka J. Four Aromatic Sulfates with an Inhibitory Effect against HCV NS3 Helicase from the Crinoid Alloeocomatella polycladia. Mar Drugs 2017; 15:md15040117. [PMID: 28398249 PMCID: PMC5408263 DOI: 10.3390/md15040117] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 04/04/2017] [Accepted: 04/06/2017] [Indexed: 01/14/2023] Open
Abstract
Bioassay-guided separation of a lipophilic extract of the crinoid Alloeocomatella polycladia, inhibiting the activity of HCV NS3 helicase, yielded two groups of molecules: cholesterol sulfate and four new aromatic sulfates 1–4. The structures of the aromatics were elucidated by spectroscopic analysis in addition to theoretical studies. The aromatic sulfates 1–4 showed moderate inhibition against NS3 helicase with IC50 values of 71, 95, 7, and 5 μM, respectively.
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Affiliation(s)
- Idam Hermawan
- Department of Chemistry, Biology and Marine Science, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan.
| | - Atsushi Furuta
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan.
| | - Masahiro Higashi
- Department of Chemistry, Biology and Marine Science, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan.
| | - Yoshihisa Fujita
- General Education Center, Okinawa Prefectural University of Arts, 1-4 Shuri Tounokura, Naha, Okinawa 903-8602, Japan.
| | - Nobuyoshi Akimitsu
- Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
| | - Atsuya Yamashita
- Department of Microbiology, Faculty of Medicine, Graduate School of Interdisciplinary Research, University of Yamanashi, 1110 Shimokato, Chuo-shi, Yamanashi 409-3898, Japan.
| | - Kohji Moriishi
- Department of Microbiology, Faculty of Medicine, Graduate School of Interdisciplinary Research, University of Yamanashi, 1110 Shimokato, Chuo-shi, Yamanashi 409-3898, Japan.
| | - Satoshi Tsuneda
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.
| | - Hidenori Tani
- Environmental Measurement Research Institute, National Institute of Advanced Industrial Science and Technology, 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan.
| | - Masamichi Nakakoshi
- Department of Pharmaceutical Sciences, Toho University, 2-2-1, Miyama, Funabashi-shi, Chiba 274-8510, Japan.
| | - Masayoshi Tsubuki
- Institute of Medical Chemistry, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan.
| | - Yuji Sekiguchi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan.
| | - Naohiro Noda
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan.
| | - Junichi Tanaka
- Department of Chemistry, Biology and Marine Science, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan.
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27
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Van den Bossche A, Hardwick SW, Ceyssens PJ, Hendrix H, Voet M, Dendooven T, Bandyra KJ, De Maeyer M, Aertsen A, Noben JP, Luisi BF, Lavigne R. Structural elucidation of a novel mechanism for the bacteriophage-based inhibition of the RNA degradosome. eLife 2016; 5:e16413. [PMID: 27447594 PMCID: PMC4980113 DOI: 10.7554/elife.16413] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 07/18/2016] [Indexed: 01/08/2023] Open
Abstract
In all domains of life, the catalysed degradation of RNA facilitates rapid adaptation to changing environmental conditions, while destruction of foreign RNA is an important mechanism to prevent host infection. We have identified a virus-encoded protein termed gp37/Dip, which directly binds and inhibits the RNA degradation machinery of its bacterial host. Encoded by giant phage фKZ, this protein associates with two RNA binding sites of the RNase E component of the Pseudomonas aeruginosa RNA degradosome, occluding them from substrates and resulting in effective inhibition of RNA degradation and processing. The 2.2 Å crystal structure reveals that this novel homo-dimeric protein has no identifiable structural homologues. Our biochemical data indicate that acidic patches on the convex outer surface bind RNase E. Through the activity of Dip, фKZ has evolved a unique mechanism to down regulate a key metabolic process of its host to allow accumulation of viral RNA in infected cells.
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Affiliation(s)
- An Van den Bossche
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
- Division of Bacterial diseases, Scientific Institute of Public Health, Brussels, Belgium
| | - Steven W Hardwick
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Pieter-Jan Ceyssens
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
- Division of Bacterial diseases, Scientific Institute of Public Health, Brussels, Belgium
| | - Hanne Hendrix
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Marleen Voet
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Tom Dendooven
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
| | - Katarzyna J Bandyra
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Marc De Maeyer
- Biochemistry, Molecular and Structural Biology Scetion, KU Leuven, Leuven, Belgium
| | - Abram Aertsen
- Laboratory of Food Microbiology, KU Leuven, Leuven, Belgium
| | - Jean-Paul Noben
- Biomedical Research Institute, University of Hasselt, Diepenbeek, Belgium
- Transnational University Limburg, University of Hasselt, Diepenbeek, Belgium
| | - Ben F Luisi
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
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28
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Dwivedi VD, Tripathi IP, Mishra SK. In silico evaluation of inhibitory potential of triterpenoids from Azadirachta indica against therapeutic target of dengue virus, NS2B-NS3 protease. J Vector Borne Dis 2016; 53:156-161. [PMID: 27353586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023] Open
Abstract
BACKGROUND & OBJECTIVES NS2B-NS3 protease (NS2B-NS3 pro ) of dengue virus (DENV) is the prime therapeutic target for the development of anti-dengue drug to combat the DENV infection, which is currently an increasing health problem in many countries. In the area of antiviral drug discovery, numerous reports on the antiviral activity of various medicinal plants against dengue viruses have been published. Neem plant (Azadirachta indica) is one among those medicinal plants which is reported to show potential antiviral activity against DENV. But active principle of neem plant extract which has inhibitory potential against DENV NS2B-NS3 pro is not yet reported. The aim of the present study was to explore the inhibitory potential of five triterpenoids from neem plant, viz. nimbin, desacetylnimbin, desacetylsalannin, azadirachtin and salannin, against DENV NS2B-NS3 pro. METHODS The molecular 3D structural data of DENV NS2B-NS3 pro and selected triterpenoids of neem plant were collected from protein databank (PDB ID: 2VBC) and PubChem database respectively. The molecular docking approach was employed to find out the in silico inhibitory potential of the five triterpenoids against DENV NS2B- NS3 pro. RESULTS The molecular docking results showed that nimbin, desacetylnimbin and desacetylsalannin have good binding affinity with DENV NS2B-NS3 pro , while azadirachtin and salannin did not show any interaction with the target protein. It was observed that the DENV NS2B-NS3 pro binding energy for nimbin, desacetylnimbin and desacetylsalannin were -5.56, -5.24 and -3.43 kcal/mol, respectively. INTERPRETATION & CONCLUSION The findings attained through this study on the molecular interaction mode of three neem triterpenoids and DENV NS2B-NS3 pro can be considered for further in vitro and in vivo validation for designing new potential drugs for DENV infection.
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Affiliation(s)
- Vivek Dhar Dwivedi
- Faculty of Science and Environment, Mahatma Gandhi Chitrakoot Gramodaya Vishwavidyalaya, Chitrakoot, Satna, Madhya Pradesh; Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh, India
| | - Indra Prasad Tripathi
- Faculty of Science and Environment, Mahatma Gandhi Chitrakoot Gramodaya Vishwavidyalaya, Chitrakoot, Satna, Madhya Pradesh, India
| | - Sarad Kumar Mishra
- Department of Biotechnology, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, Uttar Pradesh, India
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29
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Lee S, Yoon KD, Lee M, Cho Y, Choi G, Jang H, Kim B, Jung D, Oh J, Kim G, Oh J, Jeong Y, Kwon HJ, Bae SK, Min D, Windisch MP, Heo T, Lee C. Identification of a resveratrol tetramer as a potent inhibitor of hepatitis C virus helicase. Br J Pharmacol 2016; 173:191-211. [PMID: 26445091 PMCID: PMC4813382 DOI: 10.1111/bph.13358] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 09/16/2015] [Accepted: 10/02/2015] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND AND PURPOSE Hepatitis C virus (HCV) infection is responsible for various chronic inflammatory liver diseases. Here, we have identified a naturally occurring compound with anti-HCV activity and have elucidated its mode of antiviral action. EXPERIMENTAL APPROACH Luciferase reporter and real-time RT-PCR assays were used to measure HCV replication. Western blot, fluorescence-labelled HCV replicons and infectious clones were employed to quantitate expression levels of viral proteins. Resistant HCV mutant mapping, in vitro NS3 protease, helicase, NS5B polymerase and drug affinity responsive target stability assays were also used to study the antiviral mechanism. KEY RESULTS A resveratrol tetramer, vitisin B from grapevine root extract showed high potency against HCV replication (EC50 = 6 nM) with relatively low cytotoxicity (EC50 >10 μM). Combined treatment of vitisin B with an NS5B polymerase inhibitor (sofosbuvir) exhibited a synergistic or at least additive antiviral activity. Analysis of a number of vitisin B-resistant HCV variants suggested an NS3 helicase as its potential target. We confirmed a direct binding between vitisin B and a purified NS3 helicase in vitro. Vitisin B was a potent inhibitor of a HCV NS3 helicase (IC50 = 3 nM). In vivo, Finally, we observed a preferred tissue distribution of vitisin B in the liver after i.p. injection in rats, at clinically attainable concentrations. Conclusion and Implications Vitisin B is one of the most potent HCV helicase inhibitors identified so far. Vitisin B is thus a prime candidate to be developed as the first HCV drug derived from natural products.
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Affiliation(s)
- Sungjin Lee
- College of PharmacyDongguk UniversityGoyangKorea
| | - Kee Dong Yoon
- College of Pharmacy and Integrated Research Institute of Pharmaceutical SciencesThe Catholic University of KoreaBucheonKorea
| | - Myungeun Lee
- Hepatitis Research LaboratoryInstitut Pasteur KoreaSeongnamKorea
| | - Yoojin Cho
- Hepatitis Research LaboratoryInstitut Pasteur KoreaSeongnamKorea
| | - Gahee Choi
- Hepatitis Research LaboratoryInstitut Pasteur KoreaSeongnamKorea
| | - Hongje Jang
- Department of ChemistrySeoul National UniversitySeoulKorea
| | - BeomSeok Kim
- Translational Research Center for Protein Function Control, Department of Biotechnology, College of Life Science and BiotechnologyYonsei UniversitySeoulKorea
| | - Da‐Hee Jung
- Department of Bio and Nano ChemistryKookmin UniversitySeoulKorea
| | - Jin‐Gyo Oh
- College of Pharmacy and Integrated Research Institute of Pharmaceutical SciencesThe Catholic University of KoreaBucheonKorea
| | - Geon‐Woo Kim
- Department of BiotechnologyYonsei UniversitySeoulKorea
| | - Jong‐Won Oh
- Department of BiotechnologyYonsei UniversitySeoulKorea
| | - Yong‐Joo Jeong
- Department of Bio and Nano ChemistryKookmin UniversitySeoulKorea
| | - Ho Jeong Kwon
- Translational Research Center for Protein Function Control, Department of Biotechnology, College of Life Science and BiotechnologyYonsei UniversitySeoulKorea
| | - Soo Kyung Bae
- College of Pharmacy and Integrated Research Institute of Pharmaceutical SciencesThe Catholic University of KoreaBucheonKorea
| | - Dal‐Hee Min
- Department of ChemistrySeoul National UniversitySeoulKorea
| | - Marc P Windisch
- Hepatitis Research LaboratoryInstitut Pasteur KoreaSeongnamKorea
| | - Tae‐Hwe Heo
- College of Pharmacy and Integrated Research Institute of Pharmaceutical SciencesThe Catholic University of KoreaBucheonKorea
| | - Choongho Lee
- College of PharmacyDongguk UniversityGoyangKorea
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30
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Furuta A, Tsubuki M, Endoh M, Miyamoto T, Tanaka J, Salam KA, Akimitsu N, Tani H, Yamashita A, Moriishi K, Nakakoshi M, Sekiguchi Y, Tsuneda S, Noda N. Identification of Hydroxyanthraquinones as Novel Inhibitors of Hepatitis C Virus NS3 Helicase. Int J Mol Sci 2015; 16:18439-53. [PMID: 26262613 PMCID: PMC4581254 DOI: 10.3390/ijms160818439] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 07/14/2015] [Accepted: 07/31/2015] [Indexed: 01/27/2023] Open
Abstract
Hepatitis C virus (HCV) is an important etiological agent of severe liver diseases, including cirrhosis and hepatocellular carcinoma. The HCV genome encodes nonstructural protein 3 (NS3) helicase, which is a potential anti-HCV drug target because its enzymatic activity is essential for viral replication. Some anthracyclines are known to be NS3 helicase inhibitors and have a hydroxyanthraquinone moiety in their structures; mitoxantrone, a hydroxyanthraquinone analogue, is also known to inhibit NS3 helicase. Therefore, we hypothesized that the hydroxyanthraquinone moiety alone could also inhibit NS3 helicase. Here, we performed a structure-activity relationship study on a series of hydroxyanthraquinones by using a fluorescence-based helicase assay. Hydroxyanthraquinones inhibited NS3 helicase with IC50 values in the micromolar range. The inhibitory activity varied depending on the number and position of the phenolic hydroxyl groups, and among different hydroxyanthraquinones examined, 1,4,5,8-tetrahydroxyanthraquinone strongly inhibited NS3 helicase with an IC50 value of 6 µM. Furthermore, hypericin and sennidin A, which both have two hydroxyanthraquinone-like moieties, were found to exert even stronger inhibition with IC50 values of 3 and 0.8 µM, respectively. These results indicate that the hydroxyanthraquinone moiety can inhibit NS3 helicase and suggest that several key chemical structures are important for the inhibition.
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Affiliation(s)
- Atsushi Furuta
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan.
| | - Masayoshi Tsubuki
- Institute of Medical Chemistry, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan.
| | - Miduki Endoh
- Institute of Medical Chemistry, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan.
| | - Tatsuki Miyamoto
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan.
| | - Junichi Tanaka
- Department of Chemistry, Biology and Marine Science, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan.
| | - Kazi Abdus Salam
- Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
| | - Nobuyoshi Akimitsu
- Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
| | - Hidenori Tani
- Environmental Measurement Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 16-1 Onogawa, Tsukuba, Ibaraki 305-8569, Japan.
| | - Atsuya Yamashita
- Department of Microbiology, Division of Medicine, Graduate School of Medicine and Engineering, University of Yamanashi, 1110 Shimokato, Chuo-shi, Yamanashi 409-3898, Japan.
| | - Kohji Moriishi
- Department of Microbiology, Division of Medicine, Graduate School of Medicine and Engineering, University of Yamanashi, 1110 Shimokato, Chuo-shi, Yamanashi 409-3898, Japan.
| | - Masamichi Nakakoshi
- Department of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi-shi, Chiba 274-8510, Japan.
| | - Yuji Sekiguchi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan.
| | - Satoshi Tsuneda
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.
| | - Naohiro Noda
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan.
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Salam KA, Furuta A, Noda N, Tsuneda S, Sekiguchi Y, Yamashita A, Moriishi K, Nakakoshi M, Tani H, Roy SR, Tanaka J, Tsubuki M, Akimitsu N. PBDE: structure-activity studies for the inhibition of hepatitis C virus NS3 helicase. Molecules 2014; 19:4006-20. [PMID: 24699145 PMCID: PMC6271602 DOI: 10.3390/molecules19044006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2014] [Revised: 03/05/2014] [Accepted: 03/13/2014] [Indexed: 01/05/2023] Open
Abstract
The helicase portion of the hepatitis C virus nonstructural protein 3 (NS3) is considered one of the most validated targets for developing direct acting antiviral agents. We isolated polybrominated diphenyl ether (PBDE) 1 from a marine sponge as an NS3 helicase inhibitor. In this study, we evaluated the inhibitory effects of PBDE (1) on the essential activities of NS3 protein such as RNA helicase, ATPase, and RNA binding activities. The structure-activity relationship analysis of PBDE (1) against the HCV ATPase revealed that the biphenyl ring, bromine, and phenolic hydroxyl group on the benzene backbone might be a basic scaffold for the inhibitory potency.
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Affiliation(s)
- Kazi Abdus Salam
- Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
| | - Atsushi Furuta
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.
| | - Naohiro Noda
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.
| | - Satoshi Tsuneda
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.
| | - Yuji Sekiguchi
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan.
| | - Atsuya Yamashita
- Department of Microbiology, Graduate School of Medicine and Engineering, University of Yamanashi, 1110 Shimokato, Chuo-shi, Yamanashi 409-3898, Japan.
| | - Kohji Moriishi
- Department of Microbiology, Graduate School of Medicine and Engineering, University of Yamanashi, 1110 Shimokato, Chuo-shi, Yamanashi 409-3898, Japan.
| | - Masamichi Nakakoshi
- Faculty of Pharmaceutical Sciences, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan.
| | - Hidenori Tani
- Research Institute for Environmental Management Technology, National Institute of Advanced Industrial Science and Technology (AIST), 16-1, Onogawa, Tsukuba, Ibaraki 305-8569, Japan.
| | - Sona Rani Roy
- Department of Chemistry, Biology and Marine Science, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan.
| | - Junichi Tanaka
- Department of Chemistry, Biology and Marine Science, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan.
| | - Masayoshi Tsubuki
- Institute of Medical Chemistry, Hoshi University, Ebara 2-4-41, Shinagawa-ku, Tokyo 142-8501, Japan.
| | - Nobuyoshi Akimitsu
- Radioisotope Center, The University of Tokyo, 2-11-16 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.
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Ang MJY, Li Z, Lim HA, Ng FM, Then SW, Wee JLK, Joy J, Hill J, Chia CSB. A P2 and P3 substrate specificity comparison between the Murray Valley encephalitis and West Nile virus NS2B/NS3 protease using C-terminal agmatine dipeptides. Peptides 2014; 52:49-52. [PMID: 24333681 DOI: 10.1016/j.peptides.2013.12.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Revised: 12/02/2013] [Accepted: 12/02/2013] [Indexed: 12/26/2022]
Abstract
The Murray Valley encephalitis virus (MVEV) and the West Nile virus (WNV) are mosquito-borne single-stranded RNA Flaviviruses responsible for many cases of viral encephalitis and deaths worldwide. The former is endemic in north Australia and Papua New Guinea while the latter has spread to different parts of the world and was responsible for a recent North American outbreak in 2012, resulting in 243 fatalities. There is currently no approved vaccines or drugs against MVEV and WNV viral infections. A plausible drug target is the viral non-structural NS2B/NS3 protease due to its role in viral replication. This trypsin-like serine protease recognizes and cleaves viral polyproteins at the C-terminal end of an arginine residue, opening an avenue for the development of peptide-based antivirals. This communication compares the P2 and P3 residue preferences of the MVEV and WNV NS2B/NS3 proteases using a series of C-terminal agmatine dipeptides. Our results revealed that both viral enzymes were highly specific toward lysines at the P2 and P3 positions, suggesting that a peptidomimetic viral protease inhibitor developed against one virus should also be active against the other.
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Affiliation(s)
- Melgious Jin Yan Ang
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #03-01, Singapore 138669, Singapore
| | - Zhitao Li
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #03-01, Singapore 138669, Singapore
| | - Huichang Annie Lim
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #03-01, Singapore 138669, Singapore
| | - Fui Mee Ng
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #03-01, Singapore 138669, Singapore
| | - Siew Wen Then
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #03-01, Singapore 138669, Singapore
| | - John Liang Kuan Wee
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #03-01, Singapore 138669, Singapore
| | - Joma Joy
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #03-01, Singapore 138669, Singapore
| | - Jeffrey Hill
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #03-01, Singapore 138669, Singapore
| | - C S Brian Chia
- Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR), 31 Biopolis Way, Nanos #03-01, Singapore 138669, Singapore.
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Subissi L, Imbert I, Ferron F, Collet A, Coutard B, Decroly E, Canard B. SARS-CoV ORF1b-encoded nonstructural proteins 12-16: replicative enzymes as antiviral targets. Antiviral Res 2014; 101:122-30. [PMID: 24269475 PMCID: PMC7113864 DOI: 10.1016/j.antiviral.2013.11.006] [Citation(s) in RCA: 114] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Revised: 10/22/2013] [Accepted: 11/11/2013] [Indexed: 12/17/2022]
Abstract
The SARS (severe acute respiratory syndrome) pandemic caused ten years ago by the SARS-coronavirus (SARS-CoV) has stimulated a number of studies on the molecular biology of coronaviruses. This research has provided significant new insight into many mechanisms used by the coronavirus replication-transcription complex (RTC). The RTC directs and coordinates processes in order to replicate and transcribe the coronavirus genome, a single-stranded, positive-sense RNA of outstanding length (∼27-32kilobases). Here, we review the up-to-date knowledge on SARS-CoV replicative enzymes encoded in the ORF1b, i.e., the main RNA-dependent RNA polymerase (nsp12), the helicase/triphosphatase (nsp13), two unusual ribonucleases (nsp14, nsp15) and RNA-cap methyltransferases (nsp14, nsp16). We also review how these enzymes co-operate with other viral co-factors (nsp7, nsp8, and nsp10) to regulate their activity. These last ten years of research on SARS-CoV have considerably contributed to unravel structural and functional details of one of the most fascinating replication/transcription machineries of the RNA virus world. This paper forms part of a series of invited articles in Antiviral Research on "From SARS to MERS: 10years of research on highly pathogenic human coronaviruses".
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Affiliation(s)
- Lorenzo Subissi
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257 - CNRS et Aix-Marseille Université, ESIL Case 925, 13288 Marseille, France
| | - Isabelle Imbert
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257 - CNRS et Aix-Marseille Université, ESIL Case 925, 13288 Marseille, France
| | - François Ferron
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257 - CNRS et Aix-Marseille Université, ESIL Case 925, 13288 Marseille, France
| | - Axelle Collet
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257 - CNRS et Aix-Marseille Université, ESIL Case 925, 13288 Marseille, France
| | - Bruno Coutard
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257 - CNRS et Aix-Marseille Université, ESIL Case 925, 13288 Marseille, France
| | - Etienne Decroly
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257 - CNRS et Aix-Marseille Université, ESIL Case 925, 13288 Marseille, France
| | - Bruno Canard
- Laboratoire Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257 - CNRS et Aix-Marseille Université, ESIL Case 925, 13288 Marseille, France.
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Rothan HA, Buckle MJ, Ammar YA, Mohammadjavad P, Shatrah O, Noorsaadah AR, Rohana Y. Study the antiviral activity of some derivatives of tetracycline and non-steroid anti inflammatory drugs towards dengue virus. Trop Biomed 2013; 30:681-690. [PMID: 24522138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Various clinical symptoms are caused by dengue virus ranging from mild fever to severe hemorrhagic fever while there is no successful anti-dengue therapeutics available. Among different strategies towards identifying and developing anti-dengue therapeutics, testing anti-dengue properties of known drugs could represent an efficient strategy for which information of its medical approval, toxicity and side effects is readily available. In this study, we evaluated the antiviral activity of some medical compounds towards dengue NS2B-NS3 protease (DENV2 NS2B-NS3pro) as a target to inhibit dengue virus replication. Mefenamic acid, a non-steroid anti inflammatory drug and doxycycline, a derivative antibiotic of tetracycline both showed significant inhibition potential against DENV2 NS2B-NS3pro Ki values 32 ± 2 μM and 55 ± 5 μM respectively. The effective cytotoxic concentrations of 50% (CC50) against Vero cells were evaluated for mefenamic acid (150 ± 5 μM) and doxycycline (125 ± 4 μM). Concentrations lower than CC50 were used to test the inhibition potential of these compounds against DENV2 replication in Vero cells. The results showed significant reduction in viral load after applying mefenamic acid and doxycyline in concentration dependent manner. Mefenamic acid reduced viral RNA at EC50 of 32 ± 4 μM whilst doxycycline EC50 was 40 ± 3 μM. Mefenamic acid showed higher selectivity against dengue virus replication in vitro compared to doxycycline. These findings underline the need for further experimental and clinical studies on these drugs utilizing its anti-dengue and anti-inflammatory activities to attenuate the clinical symptoms of dengue infection.
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Affiliation(s)
- H A Rothan
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - M J Buckle
- Department of Pharmacy, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Y A Ammar
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - P Mohammadjavad
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - O Shatrah
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - A R Noorsaadah
- Department of Chemistry, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Y Rohana
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
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Liang XH, Crooke ST. RNA helicase A is not required for RISC activity. Biochim Biophys Acta 2013; 1829:1092-101. [PMID: 23895878 DOI: 10.1016/j.bbagrm.2013.07.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2013] [Revised: 06/29/2013] [Accepted: 07/22/2013] [Indexed: 01/13/2023]
Abstract
It has been shown that siRNAs can compete with each other or with endogenous miRNAs for RISC components. This competition may complicate the interpretations of phenotypes observed through siRNA-mediated knockdown of genes, especially those genes implicated in the RISC pathway. In this study, we re-examined the function of RNA helicase A (RHA), which has been previously proposed to function in RISC loading based on siRNA-mediated knockdown studies. Here we show that reduced RISC activity or loading of siRNAs was observed only in cells depleted of RHA using siRNA, but not using RNaseH-dependent antisense oligonucleotides (ASOs), suggesting that the impaired RISC function stems from the competition between pre-existing and newly transfected siRNAs, but not from reduction of the RHA protein. This view is further supported by the findings that cells depleted of a control protein, NCL1, using siRNA, but not ASO, exhibited similar defects on the loading and activity of a subsequently transfected siRNA. Transfection of RHA or NCL1 siRNAs, but not ASOs, reduced the levels of endogenous miRNAs, suggesting a competition mechanism. As a positive control, we showed that reduction of MOV10 by either siRNA or ASO decreased siRNA activity, confirming its role in RISC function. Together, our results indicate that RHA is not required for RISC activity or loading, and suggest that proper controls are required when using siRNAs to functionalize genes to avoid competition effects.
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Affiliation(s)
- Xue-Hai Liang
- Department of Core Antisense Research, ISIS Pharmaceuticals, Inc., 2855 Gazelle Court, Carlsbad, CA 92010, USA.
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Kołakowska A, Godzik P, Madaliński K. [Methods of testing potential inhibitors of hepatitis C in Huh-7.5 cell line]. Med Dosw Mikrobiol 2013; 65:275-283. [PMID: 24730216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
INTRODUCTION According to WHO reports, there are 130-170 million persons chronically infected with hepatitis C virus on a global scale. There is no effective vaccine against HCV, and the current standard of chronic hepatitis C therapy has limited efficiency and undesirable side effects. Current studies are focused on searching for a new therapeutic agents, which are specifically targeted against the virus. The aim of the study was to develop a methodology for testing the activity and cytotoxicity of potential helicase inhibitors (derivatives of anthracycline antibiotics) in Huh-7.5 cell line infected with HCV. METHODS The Huh-7.5 cell line was infected with the JFH1 (Japanese Fulminant Hepatitis) RNA by lipofection. The cytotoxicity of anthracycline antibiotics was measured by Cell Proliferation Kit II(XTT), after 1, 2, 3, 4 and 24 hours after incubation with tetrazolium salt XTT. The activity ofanthracycline antibiotics was examined by Real-Time PCR method. RESULTS The study allowed to optimize the conditions of cytotoxicity and activity studies of anthracycline antibiotics. CONCLUSIONS Huh-7.5 cell line infected with HCV is a robust cell culture model for screening new antivirals against HCV.
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Abstract
BACKGROUND Hepatitis C is a treatment-resistant disease affecting millions of people worldwide. The hepatitis C virus (HCV) genome is a single-stranded RNA molecule. After infection of the host cell, viral RNA is translated into a polyprotein that is cleaved by host and viral proteinases into functional, structural and non-structural, viral proteins. Cleavage of the polyprotein involves the viral NS3/4A proteinase, a proven drug target. HCV mutates as it replicates and, as a result, multiple emerging quasispecies become rapidly resistant to anti-virals, including NS3/4A inhibitors. METHODOLOGY/PRINCIPAL FINDINGS To circumvent drug resistance and complement the existing anti-virals, NS3/4A inhibitors, which are additional and distinct from the FDA-approved telaprevir and boceprevir α-ketoamide inhibitors, are required. To test potential new avenues for inhibitor development, we have probed several distinct exosites of NS3/4A which are either outside of or partially overlapping with the active site groove of the proteinase. For this purpose, we employed virtual ligand screening using the 275,000 compound library of the Developmental Therapeutics Program (NCI/NIH) and the X-ray crystal structure of NS3/4A as a ligand source and a target, respectively. As a result, we identified several novel, previously uncharacterized, nanomolar range inhibitory scaffolds, which suppressed of the NS3/4A activity in vitro and replication of a sub-genomic HCV RNA replicon with a luciferase reporter in human hepatocarcinoma cells. The binding sites of these novel inhibitors do not significantly overlap with those of α-ketoamides. As a result, the most common resistant mutations, including V36M, R155K, A156T, D168A and V170A, did not considerably diminish the inhibitory potency of certain novel inhibitor scaffolds we identified. CONCLUSIONS/SIGNIFICANCE Overall, the further optimization of both the in silico strategy and software platform we developed and lead compounds we identified may lead to advances in novel anti-virals.
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Affiliation(s)
- Sergey A. Shiryaev
- Inflammatory and Infectious Disease Center, Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
| | - Anton V. Cheltsov
- R&D Department, Q-MOL L.L.C., San Diego, California, United States of America
- * E-mail: (AVC) (AC); (AYS) (AS)
| | - Alex Y. Strongin
- Inflammatory and Infectious Disease Center, Sanford-Burnham Medical Research Institute, La Jolla, California, United States of America
- * E-mail: (AVC) (AC); (AYS) (AS)
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Shiryaev SA, Cheltsov AV, Gawlik K, Ratnikov BI, Strongin AY. Virtual ligand screening of the National Cancer Institute (NCI) compound library leads to the allosteric inhibitory scaffolds of the West Nile Virus NS3 proteinase. Assay Drug Dev Technol 2010; 9:69-78. [PMID: 21050032 DOI: 10.1089/adt.2010.0309] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Viruses of the genus Flavivirus are responsible for significant human disease and mortality. The N-terminal domain of the flaviviral nonstructural (NS)3 protein codes for the serine, chymotrypsin-fold proteinase (NS3pro). The presence of the nonstructural (NS)2B cofactor, which is encoded by the upstream gene in the flaviviral genome, is necessary for NS3pro to exhibit its proteolytic activity. The two-component NS2B-NS3pro functional activity is essential for the viral polyprotein processing and replication. Both the structure and the function of NS2B-NS3pro are conserved in the Flavivirus family. Because of its essential function in the posttranslational processing of the viral polyprotein precursor, NS2B-NS3pro is a promising target for anti-flavivirus drugs. To identify selective inhibitors with the reduced cross-reactivity and off-target effects, we focused our strategy on the allosteric inhibitors capable of targeting the NS2B-NS3pro interface rather than the NS3pro active site. Using virtual ligand screening of the diverse, ∼275,000-compound library and the catalytic domain of the two-component West Nile virus (WNV) NS2B-NS3pro as a receptor, we identified a limited subset of the novel inhibitory scaffolds. Several of the discovered compounds performed as allosteric inhibitors and exhibited a nanomolar range potency in the in vitro cleavage assays. The inhibitors were also potent in cell-based assays employing the sub-genomic, luciferase-tagged WNV and Dengue viral replicons. The selectivity of the inhibitors was confirmed using the in vitro cleavage assays with furin, a human serine proteinase, the substrate preferences of which are similar to those of WNV NS2B-NS3pro. Conceptually, the similar in silico drug discovery strategy may be readily employed for the identification of inhibitors of other flaviviruses.
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Affiliation(s)
- Sergey A Shiryaev
- Inflammatory and Infectious Disease Center, Sanford-Burnham Medical Research Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037, USA
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Mukovnia AV, Komissarov VV, Kritsyn AM, Mit'kevich VA, Tunitskaia VL, Kochetkov SN. [The interaction of NS3 protein of hepatitis C virus with polymethylen derivatives of nucleic bases]. Mol Biol (Mosk) 2010; 44:1045-1053. [PMID: 21290826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
NS3 protein of hepatitis C virus plays the key role in the virus functioning. It possesses three enzymatic activities, namely protease activity, associated with N-terminal domain of the protein, and helicase/NTPase activities specific for C-terminal domain. Here, the effect of some polimethylenic derivatives of the nucleic bases on helicase and ATPase enzyme activities has been studied. Several of compounds tested displayed inhibitory activity towards NS3 helicase. However, most compounds demonstrated strong activating effect on ATPase activity of the enzyme as well as several other ATPases. The ATPase activating mechanism was not described earlier. The activation potency of the compounds depended on substrate/activator concentration ratio, and was maximal at the 1000:1. The activation mechanism scheme that allows us to explain phenomena observed is proposed.
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Kandil S, Biondaro S, Vlachakis D, Cummins AC, Coluccia A, Berry C, Leyssen P, Neyts J, Brancale A. Discovery of a novel HCV helicase inhibitor by a de novo drug design approach. Bioorg Med Chem Lett 2009; 19:2935-7. [PMID: 19414257 DOI: 10.1016/j.bmcl.2009.04.074] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2009] [Revised: 04/14/2009] [Accepted: 04/17/2009] [Indexed: 01/22/2023]
Abstract
Herein we report a successful application of a computer-aided design approach to identify a novel HCV helicase inhibitor. A de novo drug design methodology was used to generate an initial set of structures that could potentially bind to a putative binding site. Further structure refinement was carried out through docking a series of focused virtual libraries. The most promising compound was synthesised and it exhibited a submicromolar inhibition of the HCV helicase.
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Affiliation(s)
- Sahar Kandil
- The Welsh School of Pharmacy, Cardiff University, Cardiff, United Kingdom
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Liu Z, Kenworthy R, Green C, Tang H. Molecular determinants of nucleolar translocation of RNA helicase A. Exp Cell Res 2007; 313:3743-54. [PMID: 17822697 DOI: 10.1016/j.yexcr.2007.07.037] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2007] [Revised: 07/11/2007] [Accepted: 07/27/2007] [Indexed: 11/30/2022]
Abstract
RNA helicase A (RHA) is a member of the DEAH-box family of DNA/RNA helicases involved in multiple cellular processes and the life cycles of many viruses. The subcellular localization of RHA is dynamic despite its steady-state concentration in the nucleoplasm. We have previously shown that it shuttles rapidly between the nucleus and the cytoplasm by virtue of a bidirectional nuclear transport domain (NTD) located in its carboxyl terminus. Here, we investigate the molecular determinants for its translocation within the nucleus and, more specifically, its redistribution from the nucleoplasm to nucleolus or the perinucleolar region. We found that low temperature treatment, transcription inhibition or replication of hepatitis C virus caused the intranuclear redistribution of the protein, suggesting that RHA shuttles between the nucleolus and nucleoplasm and becomes trapped in the nucleolus or the perinucleolar region upon blockade of transport to the nucleoplasm. Both the NTD and ATPase activity were essential for RHA's transport to the nucleolus or perinucleolar region. One of the double-stranded RNA binding domains (dsRBD II) was also required for this nucleolar translocation (NoT) phenotype. RNA interference studies revealed that RHA is essential for survival of cultured hepatoma cells and the ATPase activity appears to be important for this critical role.
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Affiliation(s)
- Zhe Liu
- Department of Biological Science, Florida State University, Tallahassee, FL 32306-4370, USA
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42
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Umehara T, Fukuda K, Nishikawa F, Sekiya S, Kohara M, Hasegawa T, Nishikawa S. Designing and analysis of a potent bi-functional aptamers that inhibit protease and helicase activities of HCV NS3. ACTA ACUST UNITED AC 2007:195-6. [PMID: 17150545 DOI: 10.1093/nass/48.1.195] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Nonstructural protein 3 (NS3) of hepatitis C virus (HCV) is a multi-functional enzyme having protease and helicase activities. NS3 is essential for HCV replication and proliferation. Previously, we obtained RNA aptamers against NS3 protease domain (Protease aptamer; deltaNEO-III and G9-II) and helicase domain (helicase aptamer; #5), and they inhibited the enzyme activities, respectively. We designed and constructed new bi-functional aptamers NEO-35-sX and G925-sX (X: 5-51 nts) by conjugating protease and helicase aptamers via oligo U spacer. Some of them showed 10-fold higher helicase inhibition than helicase aptamer #5 alone.
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Affiliation(s)
- Takuya Umehara
- Institute of Biological Resources and Functions, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki 305-8566, Japan
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Borowski P, Lang M, Haag A, Baier A. Tropolone and its derivatives as inhibitors of the helicase activity of hepatitis C virus nucleotide triphosphatase/helicase. Antivir Chem Chemother 2007; 18:103-9. [PMID: 17542155 DOI: 10.1177/095632020701800206] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
In this report, we demonstrate the interaction of the non-structural protein 3 (NS3) of hepatitis C virus (HCV) with alkaloide tropolone (2-hydroxy-2,4,6-heptatriene-1-one) and its derivatives. The compounds were biochemically screened separately against the ATPase and helicase activities of HCV NS3. In the investigations presented, alkaIoide tropolone and its derivatives significantly inhibited the helicase activity of the viral protein when using a DNA substrate, with 50% inhibitory concentration values within a low micromolar range. The results using the RNA substrate were unexpected--none of the tropolone derivatives excerted any modulating influence towards the unwinding activity. Surprisingly, no influence of the nucleoside triphosphatase (NTPase) turnover was observed. Evidence is presented confirming that these compounds do not act by blocking the NTP-binding site, but by occupying an additional allosteric regulatory site. Further mechanisms of action, particularly of some of the derivatives, are discussed.
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Affiliation(s)
- Peter Borowski
- Department of Molecular Biology, Institute of Environmental Protection, John Paul II Catholic University of Lublin, Lublin, Poland.
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44
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Ujjinamatada RK, Baier A, Borowski P, Hosmane RS. An analogue of AICAR with dual inhibitory activity against WNV and HCV NTPase/helicase: synthesis and in vitro screening of 4-carbamoyl-5-(4,6-diamino-2,5-dihydro-1,3,5-triazin-2-yl)imidazole-1-beta-D-ribofuranoside. Bioorg Med Chem Lett 2007; 17:2285-8. [PMID: 17289387 PMCID: PMC2674300 DOI: 10.1016/j.bmcl.2007.01.074] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2006] [Revised: 01/13/2007] [Accepted: 01/18/2007] [Indexed: 10/23/2022]
Abstract
The title compound (4) was synthesized by the reaction of ethyl 1-(2,3,5-tri-O-benzoyl-beta-d-ribofuranosyl)-5-formylimidazole-4-carboxylate with excess guanidine in ethanol at reflux. Compound 4 was evaluated in vitro against NTPases/helicases of four different viruses of the Flaviviridae family, including the West Nile virus (WNV), hepatitis C virus (HCV), dengue virus (DENV), and the Japanese encephalitis virus (JEV), employing both an RNA and a DNA substrate. The compound showed activity against NTPase/helicase of WNV and HCV with an IC(50) of 23 and 37 microM, respectively, when a DNA substrate was employed, while no activity was observed when an RNA substrate was used. There was no activity against the NTPase/helicase of either DENV or JEV irrespective of whether an RNA or a DNA substrate was employed. Considering that Flaviviridae are RNA viruses, the observed absence of activity against an RNA substrate, but the presence of activity against a DNA substrate is intriguing and somewhat surprising. The preliminary studies show that compound 4 does not form a tight complex with either an RNA or a DNA substrate, suggesting that its mechanism of action may involve direct interaction with the enzyme.
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Affiliation(s)
- Ravi K. Ujjinamatada
- Laboratory for Drug Design and Synthesis, Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, Maryland 21250, USA
| | - Andrea Baier
- The Faculty of Mathematics & Natural Sciences, The John Paul II Catholic University of Lublin, 20-718 Lublin, Poland
| | - Peter Borowski
- The Faculty of Mathematics & Natural Sciences, The John Paul II Catholic University of Lublin, 20-718 Lublin, Poland
| | - Ramachandra S. Hosmane
- Laboratory for Drug Design and Synthesis, Department of Chemistry and Biochemistry, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, Maryland 21250, USA
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45
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Carta A, Loriga G, Piras S, Paglietti G, Ferrone M, Fermeglia M, Pricl S, La Colla P, Secci B, Collu G, Loddo R. Synthesis and in vitro evaluation of the anti-viral activity of N-[4-(1H(2H)-benzotriazol-1(2)-yl)phenyl]alkylcarboxamides. Med Chem 2007; 2:577-89. [PMID: 17105439 DOI: 10.2174/1573406410602060577] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A series N-[4-(1H(2H)-benzotriazol-1(2)-yl)phenyl]alkylcarboxamides (8e-k, 9e-i, k, l) and their parent amines (5a-c and 6a-d) were prepared according to Schemes (1 and 2). Compounds were evaluated in vitro for cytotoxicity and antiviral activity against a wide spectrum of RNA (positive- and negative-sense) viruses, like [Bovine Viral Diarrhea Virus (BVDV), Yellow Fever Virus (YFV), Coxsackie Virus B (CVB-2), Polio Virus (Sb-1), Human Immunodeficiency Virus (HIV-1), Respiratory Syncytial Virus (RSV)] or double-stranded (dsRNA) virus, like Reoviridae (Reo-1). The Entero (CVB-2 and Sb-1) were the only viruses inhibited by title compounds. In particular, two of them emerged for their selective, although not very potent, antiviral activity: 8i, which was the most active against CVB-2 (CC50 >100 microM; EC50 = 10 microM) and 9l, which was the most active against Sb-1 (CC50 90 microM; EC50 = 30 microm). Title compounds were evaluated in silico against the Sb-1 helicase, as the crystal structure of this enzyme was not available, the corresponding 3D model was obtained by homology techniques (see Fig. 2).
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Affiliation(s)
- Antonio Carta
- Dipartimento Farmaco Chimico Tossicologico, Facoltà di Farmacia, Università di Sassari, via Muroni 23/a, 07100 Sassari, Italy.
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46
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Frick DN. The hepatitis C virus NS3 protein: a model RNA helicase and potential drug target. Curr Issues Mol Biol 2007; 9:1-20. [PMID: 17263143 PMCID: PMC3571657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2023] Open
Abstract
The C-terminal portion of hepatitis C virus (HCV) nonstructural protein 3 (NS3) forms a three domain polypeptide that possesses the ability to travel along RNA or single-stranded DNA (ssDNA) in a 3' to 5' direction. Fueled byATP hydrolysis, this movement allows the protein to displace complementary strands of DNA or RNA and proteins bound to the nucleic acid. HCV helicase shares two domains common to other motor proteins, one of which appears to rotate upon ATP binding. Several models have been proposed to explain how this conformational change leads to protein movement and RNA unwinding, but no model presently explains all existing experimental data. Compounds recently reported to inhibit HCV helicase, which include numerous small molecules, RNA aptamers and antibodies, will be useful for elucidating the role of a helicase in positive-sense single-stranded RNA virus replication and might serve as templates for the design of novel antiviral drugs.
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Affiliation(s)
- David N Frick
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY 10595, USA.
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47
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van Rij RP, Saleh MC, Berry B, Foo C, Houk A, Antoniewski C, Andino R. The RNA silencing endonuclease Argonaute 2 mediates specific antiviral immunity in Drosophila melanogaster. Genes Dev 2006; 20:2985-95. [PMID: 17079687 PMCID: PMC1620017 DOI: 10.1101/gad.1482006] [Citation(s) in RCA: 431] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Most organisms have evolved defense mechanisms to protect themselves from viruses and other pathogens. Arthropods lack the protein-based adaptive immune response found in vertebrates. Here we show that the central catalytic component of the RNA-induced silencing complex (RISC), the nuclease Argonaute 2 (Ago-2), is essential for antiviral defense in adult Drosophila melanogaster. Ago-2-defective flies are hypersensitive to infection with a major fruit fly pathogen, Drosophila C virus (DCV), and with Cricket Paralysis virus (CrPV). Increased mortality in ago-2 mutant flies was associated with a dramatic increase in viral RNA accumulation and virus titers. The physiological significance of this antiviral mechanism is underscored by our finding that DCV encodes a potent suppressor of RNA interference (RNAi). This suppressor binds long double-stranded RNA (dsRNA) and inhibits Dicer-2-mediated processing of dsRNA into short interfering RNA (siRNA), but does not bind short siRNAs or disrupt the microRNA (miRNA) pathway. Based on these results we propose that RNAi is a major antiviral immune defense mechanism in Drosophila.
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Affiliation(s)
- Ronald P van Rij
- Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, CA 94143, USA
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48
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Mueller NH, Yon C, Ganesh VK, Padmanabhan R. Characterization of the West Nile virus protease substrate specificity and inhibitors. Int J Biochem Cell Biol 2006; 39:606-14. [PMID: 17188926 DOI: 10.1016/j.biocel.2006.10.025] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2006] [Revised: 10/05/2006] [Accepted: 10/11/2006] [Indexed: 12/21/2022]
Abstract
West Nile virus (WNV), a mosquito-borne member of Flaviviridae, is a human pathogen causing widespread disease for which there is no vaccine or chemotherapy. The two-component viral serine protease consists of a heterodimeric complex between the hydrophilic domain of the cofactor, NS2B (NS2BH) and the protease domain (NS3-pro). The protease is essential for polyprotein processing followed by assembly of viral replicase and genome replication. Therefore, the protease is an excellent target for development of antiviral therapeutics. Here, we report the expression in Escherichia coli, purification, and characterization of biochemical and kinetic properties of the WNV protease. Furthermore, we show that the WNV and the dengue virus type 2 (DENV-2) proteases are inhibited by aprotinin with inhibitor constants of 0.16 and 0.026 microM, respectively. Molecular modeling of the WNV protease/aprotinin complex, based on the known crystal structures of the WNV NS2BH-N3pro and aprotinin, suggest a potentially strong interaction between the P2 Lys and the protease activator peptide, NS2BH. This conclusion based on molecular modeling is in agreement with our data of a higher k(cat)/Km value with the substrate, Boc-Gly-Lys-Arg-MCA than the Boc-Gly-Arg-Arg-MCA and is also consistent with the results of an earlier study that were based on substrate-based inhibitor peptides.
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Affiliation(s)
- Niklaus H Mueller
- Department of Microbiology and Immunology, Georgetown University School of Medicine, 3900 Reservoir Road NW, Med-Dent SW309, Washington, DC 20057, USA.
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49
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Abstract
Knockouts by homologous recombination are frequently used to investigate the function of genes in Dictyostelium and other organisms. Antisense-mediated gene silencing and RNA interference (RNAi) are convenient alternatives to reduce gene expression to different levels and to silence multigene families. We describe here the methods for efficient RNA interference in Dictyostelium and some useful mutant strains that enhance the success rate or may serve as convenient controls. We believe that it is helpful to also discuss failed attempts to optimize and expand the system because these are rarely discussed in the literature. In addition, a list of in silico and experimentally identified components in the RNAi and antisense pathway is presented.
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50
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Samanta M, Iwakiri D, Kanda T, Imaizumi T, Takada K. EB virus-encoded RNAs are recognized by RIG-I and activate signaling to induce type I IFN. EMBO J 2006; 25:4207-14. [PMID: 16946700 PMCID: PMC1570431 DOI: 10.1038/sj.emboj.7601314] [Citation(s) in RCA: 230] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2006] [Accepted: 08/02/2006] [Indexed: 11/08/2022] Open
Abstract
Epstein-Barr virus (EBV)-encoded small RNAs (EBERs) are nonpolyadenylated, untranslated RNAs, exist most abundantly in latently EBV-infected cells, and are expected to show secondary structures with many short stem-loops. Retinoic acid-inducible gene I (RIG-I) is a cytosolic protein that detects viral double-stranded RNA (dsRNA) inside the cell and initiates signaling pathways leading to the induction of protective cellular genes, including type I interferons (IFNs). We investigated whether EBERs were recognized by RIG-I as dsRNA. Transfection of RIG-I plasmid induced IFNs and IFN-stimulated genes (ISGs) in EBV-positive Burkitt's lymphoma (BL) cells, but not in their EBV-negative counterparts or EBER-knockout EBV-infected BL cells. Transfection of EBER plasmid or in vitro-synthesized EBERs induced expression of type I IFNs and ISGs in RIG-I-expressing, EBV-negative BL cells, but not in RIG-I-minus counterparts. EBERs activated RIG-I's substrates, NF-kappaB and IFN regulatory factor 3, which were necessary for type I IFN activation. It was also shown that EBERs co-precipitated with RIG-I. These results indicate that EBERs are recognized by RIG-I and activate signaling to induce type I IFN in EBV-infected cells.
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Affiliation(s)
- Mrinal Samanta
- Department of Tumor Virology, Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
| | - Dai Iwakiri
- Department of Tumor Virology, Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
| | - Teru Kanda
- Department of Tumor Virology, Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
| | - Tadaatsu Imaizumi
- Department of Vascular Biology, Institute of Brain Science, Hirosaki University School of Medicine, Hirosaki, Japan
| | - Kenzo Takada
- Department of Tumor Virology, Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
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