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Ramphan S, Yimpring N, Tangsongcharoen C, Sornprasert S, Hitakarun A, Sornjai W, Roytrakul S, Panya A, Smith DR. Expression of dengue virus and Zika virus NS2B-NS3pro constructs alter cellular fatty acids, but co-expression with a Zika virus virus-like particle is detrimental to virus-like particle expression. BMC Res Notes 2023; 16:296. [PMID: 37891687 PMCID: PMC10605870 DOI: 10.1186/s13104-023-06572-z] [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: 11/07/2022] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
OBJECTIVE Studies have shown that Flavivirus infection remodels the host cell to favour viral replication. In particular, the host cell lipid profile is altered, and it has been proposed that this process alters membrane fluidity to allow wrapping of the outer structural proteins around the viral nucleocapsid. We investigated whether expression of the Zika virus (ZIKV) and dengue virus (DENV) protease induced alterations in the cellular lipid profile, and subsequently whether co-expression of these proteases with VLP constructs was able to improve VLP yield. RESULTS Our results showed that both ZIKV and DENV proteases induced alterations in the lipid profile, but that both active and inactive proteases induced many of the same changes. Neither co-transfection of protease and VLP constructs nor bicistronic vectors allowing expression of both protease and VLP separated by a cell cleavable linker improved VLP yield, and indeed many of the constructs showed significantly reduced VLP production. Further work in developing improved VLP expression platforms is required.
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Affiliation(s)
- Suwipa Ramphan
- Institute of Molecular Biosciences, Mahidol University, Salaya, 73170, Thailand
| | - Nathamon Yimpring
- Institute of Molecular Biosciences, Mahidol University, Salaya, 73170, Thailand
| | - Chontida Tangsongcharoen
- Department of Medical Technology, Faculty of Allied Health Sciences, Burapha University, Chonburi, 20130, Thailand
| | | | - Atitaya Hitakarun
- Institute of Molecular Biosciences, Mahidol University, Salaya, 73170, Thailand
| | - Wannapa Sornjai
- Institute of Molecular Biosciences, Mahidol University, Salaya, 73170, Thailand
| | - Sittiruk Roytrakul
- Functional Proteomics Technology, National Center for Genetic Engineering and Biotechnology (BIOTECH), Thailand Science Park, Pathumthani, 12120, Thailand
| | - Atikorn Panya
- Food Biotechnology Research Team, Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology (BIOTEC), Science Park, Pathumthani, 12120, Thailand
| | - Duncan R Smith
- Institute of Molecular Biosciences, Mahidol University, Salaya, 73170, Thailand.
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2
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Del Rosario García-Lozano M, Dragoni F, Gallego P, Mazzotta S, López-Gómez A, Boccuto A, Martínez-Cortés C, Rodríguez-Martínez A, Pérez-Sánchez H, Manuel Vega-Pérez J, Antonio Del Campo J, Vicenti I, Vega-Holm M, Iglesias-Guerra F. Piperazine-derived small molecules as potential Flaviviridae NS3 protease inhibitors. In vitro antiviral activity evaluation against Zika and Dengue viruses. Bioorg Chem 2023; 133:106408. [PMID: 36801791 DOI: 10.1016/j.bioorg.2023.106408] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 01/23/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023]
Abstract
Since 2011 Direct Acting antivirals (DAAs) drugs targeting different non-structural (NS) viral proteins (NS3, NS5A or NS5B inhibitors) have been approved for clinical use in HCV therapies. However, currently there are not licensed therapeutics to treat Flavivirus infections and the only licensed DENV vaccine, Dengvaxia, is restricted to patients with preexisting DENV immunity. Similarly to NS5 polymerase, the NS3 catalytic region is evolutionarily conserved among the Flaviviridae family sharing strong structural similarity with other proteases belonging to this family and therefore is an attractive target for the development of pan-flavivirus therapeutics. In this work we present a library of 34 piperazine-derived small molecules as potential Flaviviridae NS3 protease inhibitors. The library was developed through a privileged structures-based design and then biologically screened using a live virus phenotypic assay to determine the half-maximal inhibitor concentration (IC50) of each compound against ZIKV and DENV. Two lead compounds, 42 and 44, with promising broad-spectrum activity against ZIKV (IC50 6.6 µM and 1.9 µM respectively) and DENV (IC50 6.7 µM and 1.4 µM respectively) and a good security profile were identified. Besides, molecular docking calculations were performed to provide insights about key interactions with residues in NS3 proteases' active sites.
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Affiliation(s)
- María Del Rosario García-Lozano
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Seville, E-41071 Seville, Spain; SeLiver Group at the Institute of Biomedicine of Seville (IBIS), Virgen del Rocío University Hospital CSIC University of Seville, Seville, Spain
| | - Filippo Dragoni
- Department of Medical Biotechnologies, Siena University Hospital, Policlinico Le Scotte, Viale Bracci 16, 53100 Siena, Italy
| | - Paloma Gallego
- Unit for Clinical Management of Digestive Diseases and CIBERehd, Valme University Hospital, 41014 Seville, Spain
| | - Sarah Mazzotta
- Department of Chemistry, University of Milan, 20133 Milan, Italy
| | - Alejandro López-Gómez
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Seville, E-41071 Seville, Spain
| | - Adele Boccuto
- Department of Medical Biotechnologies, Siena University Hospital, Policlinico Le Scotte, Viale Bracci 16, 53100 Siena, Italy; VisMederi Research srl, Siena, Italy
| | - Carlos Martínez-Cortés
- Structural Bioinformatics and High Performance Computing (BIO-HPC) Research Group, UCAM Universidad Católica de Murcia, 30107 Murcia, Spain
| | - Alejandro Rodríguez-Martínez
- Department of Physical Chemistry and Institute of Biotechnology, University of Granada, Campus Fuentenueva sn, 18071 Granada, Spain
| | - Horacio Pérez-Sánchez
- Structural Bioinformatics and High Performance Computing (BIO-HPC) Research Group, UCAM Universidad Católica de Murcia, 30107 Murcia, Spain
| | - José Manuel Vega-Pérez
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Seville, E-41071 Seville, Spain
| | | | - Ilaria Vicenti
- Department of Medical Biotechnologies, Siena University Hospital, Policlinico Le Scotte, Viale Bracci 16, 53100 Siena, Italy.
| | - Margarita Vega-Holm
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Seville, E-41071 Seville, Spain.
| | - Fernando Iglesias-Guerra
- Department of Organic and Medicinal Chemistry, Faculty of Pharmacy, University of Seville, E-41071 Seville, Spain
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3
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Bhattacharya M, Bhowmik D, Tian Y, He H, Zhu F, Yin Q. The Dengue virus protease NS2B3 cleaves cyclic GMP-AMP synthase to suppress cGAS activation. J Biol Chem 2023; 299:102986. [PMID: 36754281 PMCID: PMC10011430 DOI: 10.1016/j.jbc.2023.102986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 01/27/2023] [Accepted: 01/29/2023] [Indexed: 02/10/2023] Open
Abstract
Dengue virus (DENV) is one of the most prevalent mosquito-transmitted human viruses that causes significant morbidity and mortality worldwide. To persist in the cell and consequently cause disease, DENV is evolved with mechanisms to suppress the induction of type I interferons by antagonizing cGAS-STING signaling. Using recombinant proteins and in vitro cleavage assays, we have shown that the DENV protease NS2B3 is capable of cleaving cGAS in the N-terminal region without disrupting the C-terminal catalytic center. This generates two major cleavage products: cleavage product N-terminal (CP-N) and cleavage product C-terminal (CP-C). We observed reduction in DNA-binding affinity of CP-C as compared to full-length cGAS. Reduction in DNA-binding affinity is also correlated with the decrease in enzymatic activity of CP-C. CP-N, on the other hand, has almost comparable DNA-binding ability as that of the full-length cGAS. In fact, CP-N competitively inhibits cyclic GMP-AMP production by both full-length cGAS and CP-C. We hypothesize that high DNA-binding affinity of CP-N enables it to sequester the DNA from CP-C and noncleaved full-length cGAS and thus reduces the rate of enzyme activation and cyclic GMP-AMP synthesis. Furthermore, we found that NS2B3 physically interacts with full-length cGAS and CP-C, laying the basis for their shuttling to and eventual degradation in the autophagosome. Overall, our study highlights a multifaceted and effective strategy by which an RNA virus antagonizes cGAS-STING signaling which may be useful for the design of antivirals targeting viral proteases.
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Affiliation(s)
| | - Debipreeta Bhowmik
- Department of Biological Science, Florida State University, Tallahassee, Florida, USA
| | - Yuan Tian
- Department of Biological Science, Florida State University, Tallahassee, Florida, USA
| | - Huan He
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, USA
| | - Fanxiu Zhu
- Department of Biological Science, Florida State University, Tallahassee, Florida, USA
| | - Qian Yin
- Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, USA; Department of Biological Science, Florida State University, Tallahassee, Florida, USA.
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Agback P, Lesovoy DM, Han X, Sun R, Sandalova T, Agback T, Achour A, Orekhov VY. 1H, 13C and 15N resonance assignment of backbone and IVL-methyl side chain of the S135A mutant NS3pro/NS2B protein of Dengue II virus reveals unique secondary structure features in solution. Biomol NMR Assign 2022; 16:135-145. [PMID: 35149939 PMCID: PMC9068680 DOI: 10.1007/s12104-022-10071-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
The serotype II Dengue (DENV 2) virus is the most prevalent of all four known serotypes. Herein, we present nearly complete 1H, 15N, and 13C backbone and 1H, 13C isoleucine, valine, and leucine methyl resonance assignment of the apo S135A catalytically inactive variant of the DENV 2 protease enzyme folded as a tandem formed between the serine protease domain NS3pro and the cofactor NS2B, as well as the secondary structure prediction of this complex based on the assigned chemical shifts using the TALOS-N software. Our results provide a solid ground for future elucidation of the structure and dynamic of the apo NS3pro/NS2B complex, key for adequate development of inhibitors, and a thorough molecular understanding of their function(s).
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Affiliation(s)
- Peter Agback
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, 750 07, Uppsala, Sweden.
| | - Dmitry M Lesovoy
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RA, 117997, Moscow, Russia
| | - Xiao Han
- Science for Life Laboratory, Department of Medicine, Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, SE‑171 76, Stockholm, Sweden
| | - Renhua Sun
- Science for Life Laboratory, Department of Medicine, Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, SE‑171 76, Stockholm, Sweden
| | - Tatyana Sandalova
- Science for Life Laboratory, Department of Medicine, Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, SE‑171 76, Stockholm, Sweden
| | - Tatiana Agback
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, 750 07, Uppsala, Sweden
| | - Adnane Achour
- Science for Life Laboratory, Department of Medicine, Solna, Karolinska Institute, and Division of Infectious Diseases, Karolinska University Hospital, SE‑171 76, Stockholm, Sweden
| | - Vladislav Yu Orekhov
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 465, 40530, Gothenburg, Sweden
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5
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Bhosale S, Kumar A. Screening of phytoconstituents of Andrographis paniculata against various targets of Japanese encephalitis virus: An in-silico and in-vitro target-based approach. Curr Res Pharmacol Drug Discov 2021; 2:100043. [PMID: 34909671 PMCID: PMC8663989 DOI: 10.1016/j.crphar.2021.100043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/25/2021] [Accepted: 07/29/2021] [Indexed: 01/02/2023] Open
Abstract
Japanese encephalitis (JE) is one of the viral diseases affecting millions of peoples across the globe specifically developing countries. There is no specific treatment available, however, vaccines are available for its prevention. Unfortunately, available vaccines are not effective against all clinical isolates and are also associated with neurological complications in some individuals. We have screened the selected phytoconstituents of Andrographis paniculata against various targets of Japanese encephalitis virus (JEV) using Schrodinger suite 2019-3. Among all selected phytoconstituents, andrographolide has shown a good binding affinity towards NS3 protease as compared to NS3 helicase and NS5 Rdrp (RNA dependent RNA polymerase) of JEV. The molecular dynamics (MD) results have also shown good stability of andrographolide in the active site of NS3 protease. The absorption, distribution, metabolism, excretion, and toxicity (ADMET) analysis has also indicated a good pharmacokinetic and safety profile of andrographolide. Finally, the in-vitro target-based assay have confirmed the inhibitory potential of andrographolide against the NS3 protease of JEV. In conclusion, andrographolide could have the potential to develop as an antiviral agent against JEV through inhibition of protease, however, further investigations are required. Andrographolide has shown stable binding conformation in the active site of protease of JEV. The protease of JEV was inhibited in a concentration dependent manner.
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Affiliation(s)
- Shailesh Bhosale
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Raebareli, Lucknow, UP, India
| | - Anoop Kumar
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER), Raebareli, Lucknow, UP, India
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6
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Rahman MM, Biswas S, Islam KJ, Paul AS, Mahato SK, Ali MA, Halim MA. Antiviral phytochemicals as potent inhibitors against NS3 protease of dengue virus. Comput Biol Med 2021; 134:104492. [PMID: 34022487 DOI: 10.1016/j.compbiomed.2021.104492] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 05/10/2021] [Accepted: 05/10/2021] [Indexed: 10/21/2022]
Abstract
Dengue, a mosquito-borne disease, has appeared as a major infectious disease globally. The virus requires its proteins to replicate and reproduce in the host cell. The NS3 protease converts the polyprotein to functional proteins with the help of the NS2B cofactor. Thus, NS3 protease is a promising target to develop antiviral inhibitors against the dengue virus. A systematic screening including ADMET properties, molecular docking, molecular dynamics (MD) simulation, binding free energy calculation, and QSAR studies is carried out to predict potent inhibitors against the NS3 protease. From the screening of 40 antiviral phytochemicals, ADMET properties analysis was used to screen out ligands that violate ADME rules and have probable toxicity. Cyanidin 3-Glucoside, Dithymoquinone, and Glabridin were predicted to be potent inhibitors against the NS3 protease according to their binding affinity. These ligands showed several noncovalent interactions, including hydrogen bond, hydrophobic interaction, electrostatic interaction, pi-sulfur interactions. The ligand-protein complexes were further scrutinized using 250 ns molecular dynamics simulation. The MM-PBSA binding free energy calculation was conducted to investigate their binding stability in dynamic conditions. The calculated pIC50(mM) value was predicted using the QSAR model with 89.91% goodness of fit. The predicted biologocal activity value for the ligands indicates they might have good potency.
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Affiliation(s)
- Md Mahbubur Rahman
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Sourav Biswas
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Kazi Jahidul Islam
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Archi Sundar Paul
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Shiplob Kumar Mahato
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Md Ackas Ali
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Mohammad A Halim
- Department of Physical Sciences, University of Arkansas-Fort Smith, Fort Smith, AR, USA.
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7
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Kai Y, Lilan X, Yaoming L. Monoclonal Antibody That Inhibits Cleavage Activity of Japanese Encephalitis Virus NS3. Monoclon Antib Immunodiagn Immunother 2021; 40:28-32. [PMID: 33625288 DOI: 10.1089/mab.2020.0038] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Flavivirus protease has been deemed a potential target for drug and therapeutics development due to its crucial role in viral replication. In this study we prepared a monoclonal antibody (mAb) against nonstructural protein 3 (NS3) protease portion of Japanese encephalitis virus (JEV), and evaluated its inhibitory effect for NS3 protease activity. First, a JEV NS3 protease-specific mAb (designated 2C2) was generated by the traditional cell fusion technique. Second, the binding specificity of 2C2 for NS3 protease was determined by indirect fluorescent assay and Western blotting. Finally, inhibitory effect of 2C2 for NS3 protease cleaving human stimulator of interferon gene was evaluated. Therefore, mAb 2C2 provides a potential diagnostic tool for differential diagnosis for patients who have been vaccinated with inactivated vaccine or naturally infected, and might be genetically reconstructed and optimized for new therapeutics development.
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Affiliation(s)
- Yi Kai
- Hubei Engineering Research Center of Viral Vector, Applied Biotechnology Research Center, Wuhan University of Bioengineering, Wuhan, China.,College of Life Science and Technology, Wuhan University of Bioengineering, Wuhan, China
| | - Xie Lilan
- Hubei Engineering Research Center of Viral Vector, Applied Biotechnology Research Center, Wuhan University of Bioengineering, Wuhan, China.,College of Life Science and Technology, Wuhan University of Bioengineering, Wuhan, China
| | - Li Yaoming
- Hubei Engineering Research Center of Viral Vector, Applied Biotechnology Research Center, Wuhan University of Bioengineering, Wuhan, China.,College of Life Science and Technology, Wuhan University of Bioengineering, Wuhan, China
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Chen TI, Hsu YK, Chou CY, Chen YH, Hsu ST, Liou YS, Dai YC, Chang MF, Chang SC. Hepatitis C Virus NS3 Protein Plays a Dual Role in WRN-Mediated Repair of Nonhomologous End Joining. J Virol 2019; 93:e01273-19. [PMID: 31462559 DOI: 10.1128/JVI.01273-19] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 08/16/2019] [Indexed: 12/18/2022] Open
Abstract
Hepatitis C virus (HCV) NS3 protein possesses protease and helicase activities and is considered an oncoprotein in virus-derived hepatocellular carcinoma. The NS3-associated oncogenesis has been studied but not fully understood. In this study, we have identified novel interactions of the NS3 protein with DNA repair factors, Werner syndrome protein (WRN) and Ku70, in both an HCV subgenomic replicon system and Huh7 cells expressing NS3. HCV NS3 protein inhibits WRN-mediated DNA repair and reduces the repair efficiency of nonhomologous end joining. It interferes with Ku70 recruitment to the double-strand break sites and alters the nuclear distribution of WRN-Ku repair complex. In addition, WRN is a substrate of the NS3/4A protease; the level of WRN protein is regulated by both the proteasome degradation pathway and HCV NS3/4A protease activity. The dual role of HCV NS3 and NS3/4A proteins in regulating the function and expression level of the WRN protein intensifies the effect of impairment on DNA repair. This may lead to an accumulation of DNA mutations and genome instability and, eventually, tumor development.IMPORTANCE HCV infection is a worldwide problem of public health and a major contributor to hepatocellular carcinoma. The single-stranded RNA virus with RNA-dependent RNA polymerase experiences a high error rate and develops strategies to escape the immune system and hepatocarcinogenesis. Studies have revealed the involvement of HCV proteins in the impairment of DNA repair. The present study aimed to further elucidate mechanisms by which the viral NS3 protein impairs the repair of DNA damage. Our results clearly indicate that HCV NS3/4A protease targets WRN for degradation, and, at the same time, diminishes the repair efficiency of nonhomologous end joining by interfering with the recruitment of Ku protein to the DNA double-strand break sites. The study describes a novel mechanism by which the NS3 protein influences DNA repair and provides new insight into the molecular mechanism of HCV pathogenesis.
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Xing H, Xu S, Jia F, Yang Y, Xu C, Qin C, Shi L. Zika NS2B is a crucial factor recruiting NS3 to the ER and activating its protease activity. Virus Res 2019; 275:197793. [PMID: 31676367 DOI: 10.1016/j.virusres.2019.197793] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 10/18/2019] [Accepted: 10/22/2019] [Indexed: 01/10/2023]
Abstract
Zika virus (ZIKV) is an emergent flavivirus associated with severe neurological disorders. ZIKV NS3 protein is a viral protease that cleaves the ZIKV polyprotein precursor into individual viral proteins. In this study, we found that ZIKV NS3 by itself exhibited mitochondrial localization, which was quite different from its endoplasmic reticulum (ER) localization in ZIKV-infected cells. We screened viral proteins and identified NS2B as the bona fide recruiter of NS3 to the ER. The NS2B C-terminal tail interacted with NS3 protease domain to retain NS3 on the ER. β-Sheet motifs that formed between NS2B and the NS3 protease domain played important roles in their interaction, while mutation in the β-strand of NS2B attenuated NS2B-NS3 interaction and impaired the ability of NS3 protease to cleave the polyprotein precursor into multiple viral proteins. Consequently, NS2B mutations led to severe inhibition of ZIKV replication and production due to insufficient NS3 protease activity. In summary, our study reveals the critical role of NS2B in NS3 recruitment and protease function and provides mechanistic insight into ZIKV replication.
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Affiliation(s)
- Huaipeng Xing
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China; Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Shan Xu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China; Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Fangfei Jia
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China; Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Yang Yang
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China; Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Caimin Xu
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China; Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China
| | - Chengfeng Qin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100005, China.
| | - Lei Shi
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China; Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, Beijing, 100005, China.
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10
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Peres-da-Silva A, Antunes D, Quintanilha Torres AL, Caffarena ER, Lampe E. Effects of the Q80K Polymorphism on the Physicochemical Properties of Hepatitis C Virus Subtype 1a NS3 Protease. Viruses 2019; 11:v11080691. [PMID: 31366046 PMCID: PMC6723822 DOI: 10.3390/v11080691] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 03/29/2019] [Revised: 06/04/2019] [Accepted: 06/13/2019] [Indexed: 02/07/2023] Open
Abstract
Hepatitis C virus genotype 1a (HCV-1a) comprises clades I and II. The Q80K polymorphism is found predominantly in clade I but rarely in clade II. Here, we investigated whether natural polymorphisms in HCV-1a clade II entailed structural protein changes when occurrence of the Q80K variant was simulated. Based on HCV-1a clade I and II protein sequences, the structure of the HCV-1a Q80K mutant NS3-4A was obtained by comparative modeling. Its physicochemical properties were studied by molecular dynamics simulations and network analysis. Results demonstrate that, in the presence of the K80 variant, clade II protease polymorphisms A91 and S/G174 led to variations in hydrogen bond occupancies. Structural analyses revealed differences in (i) flexibility of the H57 catalytic residue on the NS3 protease and (ii) correlations between amino acids on the NS3 protease and the NS4A cofactor. The latter indicated possible destabilization of interactions, resulting in increased separation of these proteins. The present findings describe how the relationships between different HCV-1a NS3 protease amino acid residues could affect the appearance of viral variants and the existence of distinct genetic barriers to HCV-1a isolates.
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Affiliation(s)
- Allan Peres-da-Silva
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz/FIOCRUZ, Rio de Janeiro, RJ 21040-900, Brazil.
| | - Deborah Antunes
- Programa de Computação Científica, Instituto Oswaldo Cruz/FIOCRUZ, Rio de Janeiro, RJ 21040-900, Brazil
| | - André Luiz Quintanilha Torres
- Laboratório de Biologia Computacional e Sistemas, Instituto Oswaldo Cruz/FIOCRUZ, Rio de Janeiro, RJ 21040-900, Brazil
- Laboratório de Bioinformática, Departamento de Bioquímica, Instituto de Química, Universidade Federal do Rio de Janeiro/UFRJ, Rio de Janeiro, RJ 21941-909, Brazil
| | - Ernesto Raul Caffarena
- Programa de Computação Científica, Instituto Oswaldo Cruz/FIOCRUZ, Rio de Janeiro, RJ 21040-900, Brazil
| | - Elisabeth Lampe
- Laboratório de Hepatites Virais, Instituto Oswaldo Cruz/FIOCRUZ, Rio de Janeiro, RJ 21040-900, Brazil
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Phoo WW, Zhang Z, Wirawan M, Chew EJC, Chew ABL, Kouretova J, Steinmetzer T, Luo D. Structures of Zika virus NS2B- NS3 protease in complex with peptidomimetic inhibitors. Antiviral Res 2018; 160:17-24. [PMID: 30315877 DOI: 10.1016/j.antiviral.2018.10.006] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Revised: 10/02/2018] [Accepted: 10/07/2018] [Indexed: 01/01/2023]
Abstract
Zika virus NS2B-NS3 protease plays an essential role in viral replication by processing the viral polyprotein into individual proteins. The viral protease is therefore considered as an ideal antiviral drug target. To facilitate the development of protease inhibitors, we report three high-resolution co-crystal structures of bZiPro with peptidomimetic inhibitors composed of a P1-P4 segment and different P1' residues. Compounds 1 and 2 possess small P1' groups that are split off by bZiPro, which could be detected by mass spectrometry. On the other hand, the more potent compound 3 contains a bulky P1' benzylamide structure that is resistant to cleavage by bZiPro, demonstrating that presence of an uncleavable C-terminal cap contributes to a slightly improved inhibitory potency. The N-terminal phenylacetyl residue occupies a position above the P1 side chain and therefore stabilizes a horseshoe-like backbone conformation of the bound inhibitors. The P4 moieties show unique intra- and intermolecular interactions. Our work reports the detailed binding mode interactions of substrate-analogue inhibitors within the S4-S1' pockets and explains the preference of bZiPro for basic P1-P3 residues. These new structures of protease-inhibitor complexes will guide the design of more effective NS2B-NS3 protease inhibitors with improved potency and bioavailability.
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Affiliation(s)
- Wint Wint Phoo
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore; School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Zhenzhen Zhang
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Melissa Wirawan
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Edwin Jun Chen Chew
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore
| | - Alvin Bing Liang Chew
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore; NTU Institute of Health Technologies, Interdisciplinary Graduate School, Nanyang Technological University, RTP 02-07, 50 Nanyang Drive, Singapore 637553, Singapore
| | - Jenny Kouretova
- Institute of Pharmaceutical Chemistry, Philipps University, Marbacher Weg 6, Marburg 35032, Germany
| | - Torsten Steinmetzer
- Institute of Pharmaceutical Chemistry, Philipps University, Marbacher Weg 6, Marburg 35032, Germany.
| | - Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, EMB 03-07, 59 Nanyang Drive, Singapore 636921, Singapore; NTU Institute of Structural Biology, Nanyang Technological University, EMB 06-01, 59 Nanyang Drive, Singapore 636921, Singapore.
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12
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O'Rourke A, Kremb S, Duggan BM, Sioud S, Kharbatia N, Raji M, Emwas AH, Gerwick WH, Voolstra CR. Identification of a 3-Alkylpyridinium Compound from the Red Sea Sponge Amphimedon chloros with In Vitro Inhibitory Activity against the West Nile Virus NS3 Protease. Molecules 2018; 23:E1472. [PMID: 29912151 PMCID: PMC6099703 DOI: 10.3390/molecules23061472] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [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: 05/21/2018] [Revised: 06/12/2018] [Accepted: 06/15/2018] [Indexed: 12/19/2022] Open
Abstract
Viruses are underrepresented as targets in pharmacological screening efforts, given the difficulties of devising suitable cell-based and biochemical assays. In this study we found that a pre-fractionated organic extract of the Red Sea sponge Amphimedon chloros was able to inhibit the West Nile Virus NS3 protease (WNV NS3). Using liquid chromatography⁻mass spectrometry (LC-MS) and nuclear magnetic resonance (NMR) spectroscopy, the identity of the bioactive compound was determined as a 3-alkylpyridinium with m/z = 190.16. Diffusion Ordered Spectroscopy (DOSY) NMR and NMR relaxation rate analysis suggest that the bioactive compound forms oligomers of up to 35 kDa. We observed that at 9.4 μg/mL there was up to 40⁻70% inhibitory activity on WNV NS3 protease in orthogonal biochemical assays for solid phase extracts (SPE) of A. chloros. However, the LC-MS purified fragment was effective at inhibiting the protease up to 95% at an approximate amount of 2 µg/mL with negligible cytotoxicity to HeLa cells based on a High-Content Screening (HCS) cytological profiling strategy. To date, 3-alkylpyridinium type natural products have not been reported to show antiviral activity since the first characterization of halitoxin, or 3-alkylpyridinium, in 1978. This study provides the first account of a 3-alkylpyridinium complex that exhibits a proposed antiviral activity by inhibiting the NS3 protease. We suggest that the here-described compound can be further modified to increase its stability and tested in a cell-based assay to explore its full potential as a potential novel antiviral capable of inhibiting WNV replication.
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Affiliation(s)
- Aubrie O'Rourke
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
| | - Stephan Kremb
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
| | - Brendan M Duggan
- Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
| | - Salim Sioud
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal 23955-6900, Saudi Arabia.
| | - Najeh Kharbatia
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal 23955-6900, Saudi Arabia.
| | - Misjudeen Raji
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal 23955-6900, Saudi Arabia.
| | - Abdul-Hamid Emwas
- King Abdullah University of Science and Technology (KAUST), Core Labs, Thuwal 23955-6900, Saudi Arabia.
| | - William H Gerwick
- Scripps Institution of Oceanography and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.
| | - Christian R Voolstra
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
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13
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Rehman S, Ashfaq UA, Ijaz B, Riazuddin S. Anti-hepatitis C virus activity and synergistic effect of Nymphaea alba extracts and bioactive constituents in liver infected cells. Microb Pathog 2018; 121:198-209. [PMID: 29775725 DOI: 10.1016/j.micpath.2018.05.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/14/2018] [Accepted: 05/14/2018] [Indexed: 10/21/2022]
Abstract
BACKGROUND Without an effective vaccine, hepatitis C virus (HCV) remains a global threat, inflicting 170-300 million carriers worldwide at risk of cirrhosis and hepatocellular carcinoma (HCC). Though various direct acting antivirals have been redeemed the hepatitis C treatment, a few restraints persist including possible side effects, viral resistance emergence, excessive cost which restricts its availability to a common person. HYPOTHESIS There is no preventive HCV vaccine available today so the discovery of potent antiviral natural flora and their bioactive constituents may help to develop preventive cures against HCV infection. STUDY DESIGN In current study, we aim to clarify anti-HCV activity of methanol and acetone extracts along with the purified fractions of Pakistani local plant, Nymphaea alba L (N. alba) using Huh-7 cell line as transfection model. Synergistic study of purified fractions with interferon was performed using MDBK cell line (expressing interferon receptors) as transfection model. MATERIALS AND METHODS Recent study by our research group has observed potent anti-HCV NS3 protease activity of methanol and acetone extracts of N. alba. Effect of N. alba extracts, its fractions precisely, the N1 and N8 fractions on HCV replication was demonstrated by analyzing viral gene expression using in vitro transfection model. Considering NS3 protease as a dynamic drug target, fourteen phytochemicals of N. alba were selected as ligands for interaction with NS3 protein using Molecular Operating Environment (MOE) software. Boceprevir, FDA approved NS3 protease inhibitor, was used as standard for comparative study in docking screening. RESULTS Herein we report 84% and 94% reduction of 3a genotype of HCV NS3/4A gene expression at mRNA level at non-toxic concentration. Specifically, two fractions 'N1' & 'N8' isolated from acetone extract suppressed HCV NS3 gene expression in transfected target cells with an EC50 value of 37 ± 0.03 μg/ml and 20 ± 0.02 μg/ml respectively. Similarly, viral genotype 1a replication is strongly suppressed in target cells by N. alba flower extracts and purified fractions. Moreover, combination of fractions with standard antiviral drug displayed synergistic effects for inhibition of HCV replication. Phytochemicals including Isoquercetin, Hyperoside, Quercetin, Reynoutrin, Apigenin and Isokaempferide displayed minimum binding energies as compared to standard protease inhibitor. CONCLUSION N. alba and its purified phytochemicals with new scaffolds might significantly serve as valuable and alternative regimen against HCV either alone or in combination with other potential anti-HCV agents.
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Affiliation(s)
- Sidra Rehman
- Translational Genomics Lab, Department of Biosciences, COMSATS Institute of Information Technology, Islamabad, Pakistan; Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan.
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan.
| | - Bushra Ijaz
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan.
| | - Sheikh Riazuddin
- Dean Post Graduate Study, Allama Iqbal Medical College, Lahore, Pakistan.
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14
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Pelliccia S, Wu YH, Coluccia A, La Regina G, Tseng CK, Famiglini V, Masci D, Hiscott J, Lee JC, Silvestri R. Inhibition of dengue virus replication by novel inhibitors of RNA-dependent RNA polymerase and protease activities. J Enzyme Inhib Med Chem 2017; 32:1091-1101. [PMID: 28776445 PMCID: PMC6010079 DOI: 10.1080/14756366.2017.1355791] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [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: 04/30/2017] [Revised: 07/01/2017] [Accepted: 07/12/2017] [Indexed: 11/26/2022] Open
Abstract
Dengue virus (DENV) is the leading mosquito-transmitted viral infection in the world. With more than 390 million new infections annually, and up to 1 million clinical cases with severe disease manifestations, there continues to be a need to develop new antiviral agents against dengue infection. In addition, there is no approved anti-DENV agents for treating DENV-infected patients. In the present study, we identified new compounds with anti-DENV replication activity by targeting viral replication enzymes - NS5, RNA-dependent RNA polymerase (RdRp) and NS3 protease, using cell-based reporter assay. Subsequently, we performed an enzyme-based assay to clarify the action of these compounds against DENV RdRp or NS3 protease activity. Moreover, these compounds exhibited anti-DENV activity in vivo in the ICR-suckling DENV-infected mouse model. Combination drug treatment exhibited a synergistic inhibition of DENV replication. These results describe novel prototypical small anti-DENV molecules for further development through compound modification and provide potential antivirals for treating DENV infection and DENV-related diseases.
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Affiliation(s)
- Sveva Pelliccia
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia – Fondazione Cenci Bolognetti, Roma, Italy
| | - Yu-Hsuan Wu
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Center of Infectious Disease and Signaling Research, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Antonio Coluccia
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia – Fondazione Cenci Bolognetti, Roma, Italy
| | - Giuseppe La Regina
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia – Fondazione Cenci Bolognetti, Roma, Italy
| | - Chin-Kai Tseng
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Center of Infectious Disease and Signaling Research, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Valeria Famiglini
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia – Fondazione Cenci Bolognetti, Roma, Italy
| | - Domiziana Masci
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia – Fondazione Cenci Bolognetti, Roma, Italy
| | - John Hiscott
- Istituto Pasteur Italia – Fondazione Cenci Bolognetti, Roma, Italy
| | - Jin-Ching Lee
- Department of Biotechnology, College of Life Science, Kaohsiung Medical University, Kaohsiung, Taiwan
- Graduate Institute of Natural Products, College of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan
- Research Center for Natural Products and Drug Development, Kaohsiung Medical University, Kaohsiung, Taiwan
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Romano Silvestri
- Department of Drug Chemistry and Technologies, Sapienza University of Rome, Laboratory affiliated to Istituto Pasteur Italia – Fondazione Cenci Bolognetti, Roma, Italy
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15
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Saleh NA, Elshemey WM. Structure-based drug design of novel peptidomimetic cellulose derivatives as HCV- NS3 protease inhibitors. Life Sci 2017; 187:58-63. [PMID: 28842311 DOI: 10.1016/j.lfs.2017.08.021] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Revised: 08/15/2017] [Accepted: 08/21/2017] [Indexed: 12/28/2022]
Abstract
Hepatitis C Virus (HCV) represents a global health threat not only due to the large number of reported worldwide HCV infections, but also due to the absence of a reliable vaccine for its prevention. HCV NS3 protease is one of the most important targets for drug design aiming at the deactivation of HCV. In the present work, molecular docking simulations are carried out for suggested novel NS3 protease inhibitors applied to the Egyptian genotype 4. These inhibitors are modifications of dimer cellulose by adding a hexa-peptide to the cellulose at one of the positions 2, 3, 6, 2', 3' or 6'. Results show that the inhibitor compound with the hexa-peptide at position 6 shows significantly higher simulation docking score with HCV NS3 protease active site. This is supported by low total energy value of docking system, formation of two H-bonds with HCV NS3 protease active site residues, high binding affinity and increased stability in the interaction system.
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Affiliation(s)
- Noha A Saleh
- Biophysic Department, Faculty of Science, Cairo University, Giza 12613, Egypt
| | - Wael M Elshemey
- Biophysic Department, Faculty of Science, Cairo University, Giza 12613, Egypt,.
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16
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Woestenenk E, Agback P, Unnerståle S, Henderson I, Agback T. Co-refolding of a functional complex of Dengue NS3 protease and NS2B co-factor domain and backbone resonance assignment by solution NMR. Protein Expr Purif 2017; 140:16-27. [PMID: 28751017 DOI: 10.1016/j.pep.2017.07.002] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 06/30/2017] [Accepted: 07/06/2017] [Indexed: 02/03/2023]
Abstract
A novel approach for separate expression of dengue virus NS3 protease and its NS2B cofactor domain is described in this paper. The two proteins are expressed in E.coli and purified separately and subsequently efficiently co-refolded to form a stable complex. This straightforward and robust method allows for separate isotope labeling of the two proteins, facilitating analysis by nuclear magnetic resonance (NMR) spectroscopy. Unlinked NS2B-NS3pro behaves better in NMR spectroscopy than linked NS2B-NS3pro, which has resulted in the backbone resonance assignment of the unlinked NS2B-NS3 complex bound to a peptidic boronic acid inhibitor.
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Affiliation(s)
| | - Peter Agback
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, PO Box 7015, SE-750 07, Uppsala, Sweden
| | | | - Ian Henderson
- Medivir AB, PO Box 1086, SE-141 22, Huddinge, Sweden
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17
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Ang MJY, Lim HA, Poulsen A, Wee JLK, Ng FM, Joy J, Hill J, Chia CSB. Miniature bovine pancreatic trypsin inhibitors (m-BPTIs) of the West Nile virus NS2B- NS3 protease. J Enzyme Inhib Med Chem 2016; 31:194-200. [PMID: 27241372 DOI: 10.1080/14756366.2016.1190713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
The mosquito-borne West Nile virus (WNV) causes a wide range of symptoms ranging from fever to the often fatal viral encephalitis. To date, no vaccine or drug therapy is available. The trypsin-like WNV NS2B-NS3 protease is deemed a plausible drug target and was shown to be inhibited by bovine pancreatic trypsin inhibitor (BPTI), a 58-residue protein isolated from bovine lung. Herein, we report a protein truncation study that resulted in a novel 14-residue cyclic peptide with equipotent inhibitory activity to native BPTI. We believe our truncation strategy can be further applied in the development of peptide-based inhibitors targeting trypsin-like proteases.
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Affiliation(s)
- Melgious J Y Ang
- a Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR) , Singapore , Singapore
| | - Huichang A Lim
- a Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR) , Singapore , Singapore
| | - Anders Poulsen
- a Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR) , Singapore , Singapore
| | - John Liang Kuan Wee
- a Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR) , Singapore , Singapore
| | - Fui Mee Ng
- a Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR) , Singapore , Singapore
| | - Joma Joy
- a Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR) , Singapore , Singapore
| | - Jeffrey Hill
- a Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR) , Singapore , Singapore
| | - C S Brian Chia
- a Experimental Therapeutics Centre, Agency for Science, Technology and Research (A*STAR) , Singapore , Singapore
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18
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Wang H, Guo C, Chen BZ, Ji M. Computational study on the drug resistance mechanism of HCV NS3 protease to BMS-605339. Biotechnol Appl Biochem 2016; 64:153-164. [PMID: 26790544 DOI: 10.1002/bab.1479] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 01/16/2016] [Indexed: 12/11/2022]
Abstract
NS3 protease plays a vital role in the replication of the hepatitis C virus (HCV). BMS-605339 is a novel linear tetra-peptide α-ketoamide inhibitor of NS3 protease and shows specificity for HCV NS3 protease genotype 1a and genotype 1b. Mutation at the key site 168 of the HCV NS3 protease can induce resistance to BMS-605339, which greatly affects the antiviral therapy efficacy to hepatitis C. In the present study, we employed molecular dynamics simulations, free energy calculations, and free energy decomposition to explore the drug resistance mechanism of BMS-605339 due to the three representative mutations D168C/Y/V. The free energy decomposition analysis indicates that the decrease in the binding affinity is mainly attributed to the decrease in both van der Waals and electrostatic interactions. After detailed analysis of our calculated results, we observed that the break of the salt bridge between residues 155 and 168 caused by the mutations D168C/Y/V is the original reason for the decrease in the binding ability between BMS-605339 and the mutant NS3 proteases. The obtained results will reveal the drug resistance mechanism between BMS-605339 and the mutant NS3 proteases, and provide valuable clue for designing novel and more potent drugs to HCV NS3 protease.
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Affiliation(s)
- Huiqun Wang
- School of Chemistry and Chemical Engineering, UCA S, Beijing, People's Republic of China
| | - Chenchen Guo
- School of Chemistry and Chemical Engineering, UCA S, Beijing, People's Republic of China
| | - Bo-Zhen Chen
- School of Chemistry and Chemical Engineering, UCA S, Beijing, People's Republic of China
| | - Mingjuan Ji
- School of Chemistry and Chemical Engineering, UCA S, Beijing, People's Republic of China
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19
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Abstract
INTRODUCTION The introduction of direct-acting antiviral (DAA) agents has revolutionized the treatment of hepatitis C virus (HCV) chronic infection. Non-structural 3 protease inhibitors are currently the most numerous class of DAAs on the market. AREAS COVERED This review mainly focuses on the tolerability and safety profile of asunaprevir (ASV)-containing DAA regimens. ASV is a second-wave protease inhibitor currently in Phase III clinical development in most countries and already available in Japan. EXPERT OPINION ASV shows potent antiviral effect and clinical efficacy on HCV genotypes 1 and 4. The all-oral combination daclatasvir/ASV reached high eradication rates in HCV genotype 1b and 4 infection, and a lower efficacy in genotype 1a infection. ASV presents a low potential for drug-drug interaction and a good tolerability as part of multiple, including all-oral, regimens. ASV is associated with a transient and usually mild increase in aminotransferase levels in a low percentage of cases. Due to the impaired pharmacokinetic profile observed in advanced liver disease, ASV use in patients with moderate or severe hepatic impairment is not allowed. In conclusion, ASV represents a powerful weapon against HCV infection and has to be considered an optimal option as a component of genotype tailored interferon-free combinations.
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Affiliation(s)
- Ivan Gentile
- a University of Naples "Federico II", Department of Clinical Medicine and Surgery , via S. Pansini 5, I-80131 Naples, Italy +39 081 746 3178 ; +39 081 746 3190 ;
| | - Emanuela Zappulo
- a University of Naples "Federico II", Department of Clinical Medicine and Surgery , via S. Pansini 5, I-80131 Naples, Italy +39 081 746 3178 ; +39 081 746 3190 ;
| | - Antonio Riccardo Buonomo
- a University of Naples "Federico II", Department of Clinical Medicine and Surgery , via S. Pansini 5, I-80131 Naples, Italy +39 081 746 3178 ; +39 081 746 3190 ;
| | - Riccardo Scotto
- a University of Naples "Federico II", Department of Clinical Medicine and Surgery , via S. Pansini 5, I-80131 Naples, Italy +39 081 746 3178 ; +39 081 746 3190 ;
| | - Guglielmo Borgia
- a University of Naples "Federico II", Department of Clinical Medicine and Surgery , via S. Pansini 5, I-80131 Naples, Italy +39 081 746 3178 ; +39 081 746 3190 ;
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20
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Dietz J, Lutz T, Knecht G, Gute P, Berkowski C, Lange CM, Khaykin P, Stephan C, Brodt HR, Herrmann E, Zeuzem S, Sarrazin C. Evolution and function of the HCV NS3 protease in patients with acute hepatitis C and HIV coinfection. Virology 2015; 485:213-22. [PMID: 26295281 DOI: 10.1016/j.virol.2015.06.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Revised: 06/12/2015] [Accepted: 06/26/2015] [Indexed: 01/03/2023]
Abstract
Little is known about the importance of the hepatitis C virus (HCV) NS3 protease in acute hepatitis C. In this prospective study, 82 consecutive patients with acute hepatitis C and human immunodeficiency virus (HIV) coinfection were enrolled. Individuals were infected with highly related HCV strains and the baseline NS3 quasispecies diversity and complexity was higher compared to a chronic hepatitis C control group (P<0.0001). Both parameters were comparable in patients with spontaneous clearance (n=6) versus treatment-induced SVR (n=5) or development of chronic hepatitis C (n=9). Longitudinal NS3 quasispecies kinetics showed a trend to a decreasing diversity and complexity (P<0.05) within 4 weeks in patients with spontaneous clearance compared to the other groups. The innate immune signalling protein CARDIF was cleaved to a similar extent independent of the outcome. Together with a more pronounced viral load decline (P<0.05), an early decreasing NS3 quasispecies evolution indicates spontaneous clearance of acute hepatitis C.
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Affiliation(s)
- Julia Dietz
- Department of Internal Medicine 1, J.W. Goethe University Hospital, Frankfurt, Germany
| | | | | | | | - Caterina Berkowski
- Department of Internal Medicine 1, J.W. Goethe University Hospital, Frankfurt, Germany
| | | | - Pavel Khaykin
- Department of Internal Medicine 2, J.W. Goethe University Hospital, Frankfurt, Germany
| | - Christoph Stephan
- Department of Internal Medicine 2, J.W. Goethe University Hospital, Frankfurt, Germany
| | - Hans-Reinhard Brodt
- Department of Internal Medicine 2, J.W. Goethe University Hospital, Frankfurt, Germany
| | - Eva Herrmann
- Institute of Biostatistics and Mathematical Modeling, J.W. Goethe University, Frankfurt, Germany
| | - Stefan Zeuzem
- Department of Internal Medicine 1, J.W. Goethe University Hospital, Frankfurt, Germany
| | - Christoph Sarrazin
- Department of Internal Medicine 1, J.W. Goethe University Hospital, Frankfurt, Germany.
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21
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Hajji H, Aherfi S, Motte A, Ravaux I, Mokhtari S, Ruiz JM, Poizot-Martin I, Tourres C, Tivoli N, Gérolami R, Tamalet C, Colson P. Diversity of 1,213 hepatitis C virus NS3 protease sequences from a clinical virology laboratory database in Marseille university hospitals, southeastern France. J Med Virol 2015; 87:1921-33. [PMID: 25959702 DOI: 10.1002/jmv.24261] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/06/2015] [Indexed: 12/21/2022]
Abstract
Infection with hepatitis C virus (HCV) represents a major public health concern worldwide. Recent therapeutic advances have been considerable, HCV genotype continuing to guide therapeutic management. Since 2008, HCV genotyping in our clinical microbiology laboratory at university hospitals of Marseille, Southeastern France, has been based on NS3 protease gene population sequencing, to allow concurrent HCV genotype and protease inhibitor (PI) genotypic resistance determinations. We aimed, first, to analyze the genetic diversity of HCV NS3 protease obtained from blood samples collected between 2003 and 2013 from patients monitored at university hospitals of Marseille and detect possible atypical sequences; and, second, to identify NS3 protease amino acid patterns associated with decreased susceptibility to HCV PIs. A total of 1,213 HCV NS3 protease sequences were available in our laboratory sequence database. We implemented a strategy based on bioinformatic tools to determine whether HCV sequences are representative of our local HCV genetic diversity, or divergent. In our 2003-2012 HCV NS3 protease sequence database, we delineated 32 clusters representative of the majority HCV genetic diversity, and 61 divergent sequences. Five of these divergent sequences showed less than 85% nucleotide identity with their top GenBank hit. In addition, among the 294 sequences obtained in 2013, three were divergent relative to these 32 previously delineated clusters. Finally, we detected both natural and on-treatment genotypic resistance to HCV NS3 PIs, including a substantial prevalence of Q80K substitutions associated with decreased susceptibility to simeprevir, a second generation PI.
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Affiliation(s)
- Hind Hajji
- Institut Hospitalo-Universitaire (IHU), Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Marseille, France
| | - Sarah Aherfi
- Institut Hospitalo-Universitaire (IHU), Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Marseille, France.,Aix-Marseille University, URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, Facultés de Médecine et de Pharmacie, Marseille, France
| | - Anne Motte
- Institut Hospitalo-Universitaire (IHU), Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Marseille, France
| | - Isabelle Ravaux
- IHU Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Service de Maladies Infectieuses, Centre Hospitalo-Universitaire Conception, Assistance Publique-Hôpitaux de Marseille, Marseille, France
| | - Saadia Mokhtari
- IHU Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Service de Maladies Infectieuses, Centre Hospitalo-Universitaire Nord, Marseille, France
| | - Jean-Marie Ruiz
- Assistance Publique-Hôpitaux de Marseille, Hôpitaux Sud, Service de Médecine en milieu pénitentiaire, Centre pénitentiaire de Marseille, Marseille, France
| | - Isabelle Poizot-Martin
- AP-HM Sainte-Marguerite, Service d'Immuno-hématologie clinique, Marseille, France.,Aix-Marseille University, INSERM, UMR 912 (SESSTIM), Marseille, France
| | - Christian Tourres
- Institut Hospitalo-Universitaire (IHU), Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Marseille, France
| | - Natacha Tivoli
- Institut Hospitalo-Universitaire (IHU), Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Marseille, France
| | - René Gérolami
- Service d'Hépato-Gastro-Entérologie, Centre Hospitalo-Universitaire Conception, Marseille, France
| | - Catherine Tamalet
- Institut Hospitalo-Universitaire (IHU), Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Marseille, France.,Aix-Marseille University, URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, Facultés de Médecine et de Pharmacie, Marseille, France
| | - Philippe Colson
- Institut Hospitalo-Universitaire (IHU), Méditerranée Infection, Pôle des Maladies Infectieuses et Tropicales Clinique et Biologique, Fédération de Bactériologie-Hygiène-Virologie, Centre Hospitalo-Universitaire Timone, Marseille, France.,Aix-Marseille University, URMITE UM 63 CNRS 7278 IRD 198 INSERM U1905, Facultés de Médecine et de Pharmacie, Marseille, France
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22
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Claveria-Gimeno R, Vega S, Grazu V, de la Fuente JM, Lanas A, Velazquez-Campoy A, Abian O. Rescuing compound bioactivity in a secondary cell-based screening by using γ-cyclodextrin as a molecular carrier. Int J Nanomedicine 2015; 10:2249-59. [PMID: 25834436 PMCID: PMC4371900 DOI: 10.2147/ijn.s79480] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [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] [Indexed: 12/13/2022] Open
Abstract
In vitro primary screening for identifying bioactive compounds (inhibitors, activators or pharmacological chaperones) against a protein target results in the discovery of lead compounds that must be tested in cell-based efficacy secondary screenings. Very often lead compounds do not succeed because of an apparent low potency in cell assays, despite an excellent performance in primary screening. Primary and secondary screenings differ significantly according to the conditions and challenges the compounds must overcome in order to interact with their intended target. Cellular internalization and intracellular metabolism are some of the difficulties the compounds must confront and different strategies can be envisaged for minimizing that problem. Using a novel screening procedure we have identified 15 compounds inhibiting the hepatitis C NS3 protease in an allosteric fashion. After characterizing biophysically the interaction with the target, some of the compounds were not able to inhibit viral replication in cell assays. In order to overcome this obstacle and potentially improve cellular internalization three of these compounds were complexed with γ-cyclodextrin. Two of them showed a five- and 16-fold activity increase, compared to their activity when delivered as free compounds in solution (while γ-cyclodextrin did not show antiviral activity by itself). The most remarkable result came from a third compound that showed no antiviral activity in cell assays when delivered free in solution, but its γ-cyclodextrin complex exhibited a 50% effective concentration of 5 μM. Thus, the antiviral activity of these compounds can be significantly improved, even completely rescued, using γ-cyclodextrin as carrier molecule.
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Affiliation(s)
- Rafael Claveria-Gimeno
- Instituto Aragonés de Ciencias de la Salud (IACS), Zaragoza, Spain
- IIS Aragón, Zaragoza, Spain
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit IQFR-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, Spain
| | - Sonia Vega
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit IQFR-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, Spain
| | - Valeria Grazu
- Instituto de Nanociencia de Aragon (INA), Universidad de Zaragoza, Zaragoza, Spain
| | - Jesús M de la Fuente
- Instituto de Nanociencia de Aragon (INA), Universidad de Zaragoza, Zaragoza, Spain
- Instituto de Ciencia de Materiales de Aragón (ICMA), CSIC-Universidad de Zaragoza, Zaragoza, Spain
- Institute NanoBiomedicine and Engineering, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Angel Lanas
- IIS Aragón, Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
- Servicio de Aparato Digestivo, Hospital Clínico Universitario Lozano Blesa, Zaragoza, Spain
- Department of Medicine, University of Zaragoza, Zaragoza, Spain
| | - Adrian Velazquez-Campoy
- IIS Aragón, Zaragoza, Spain
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit IQFR-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, Spain
- Fundacion ARAID, Government of Aragon, Spain
| | - Olga Abian
- Instituto Aragonés de Ciencias de la Salud (IACS), Zaragoza, Spain
- IIS Aragón, Zaragoza, Spain
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Joint Unit IQFR-CSIC-BIFI, Universidad de Zaragoza, Zaragoza, Spain
- Centro de Investigación Biomédica en Red en el Área Temática de Enfermedades Hepáticas y Digestivas (CIBERehd), Barcelona, Spain
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23
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Hoffmann L, Faffe DS, Lima JF, Capitanio TA, Cabral BC, Ürményi TP, Coelho HS, Rondinelli E, Villela-Nogueira CA, Silva R. No correspondence between resistance mutations in the HCV- NS3 protease at baseline and early telaprevir-based triple therapy. BBA Clin 2015; 3:146-51. [PMID: 26674563 DOI: 10.1016/j.bbacli.2015.01.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 01/23/2015] [Accepted: 01/26/2015] [Indexed: 02/06/2023]
Abstract
Direct-acting antiviral (DAA)-based therapy is the new standard treatment for chronic hepatitis C virus (HCV) infection. However, protease inhibitor (PI)-resistant viral variants have been often described. This study aimed to examine HCV-NS3 protease variants at baseline and at 4 weeks under triple therapy. To this end, we analyzed the presence of variants in HCV-NS3 protease region from peripheral blood samples of 16 patients infected with HCV-1 at baseline and at 4 weeks of combined therapy with telaprevir, pegylated interferon, and ribavirin, using next-generation sequencing. Several variants with synonymous and non-synonymous amino acid substitutions were detected at both time points. Variants detected at low frequency corresponded to 74% (HCV-1a) and 35% (HCV-1b) of non-synonymous substitutions. We found nine PI-resistance-associated variants (V36A, T54S, V55I, Q80K, Q80R, V107I, I132V, D168E, M175L) in HCV-NS3 of 10 patients. There was no correspondence of resistance-associated variant profile between baseline and at 4 weeks. Moreover, these resistance variants at baseline and short-term treatment are not good predictors of outcome under triple therapy. Our study also shows a large number of others minor and major non-synonymous variants in HCV-NS3 early in telaprevir-based therapy that can be important for further drug resistance association studies with newly developed PI agents. HCV-NS3 protease variants were analyzed at baseline and 4 weeks of triple therapy. Synonymous and non-synonymous variants, even at low frequency, were detected. Nine PI resistance mutations were identified in 10/16 patients in both time points. There was no correspondence between resistance mutation at baseline and 4 weeks. We provide a comprehensive databank of non-synonymous variants in HCV-NS3.
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de Bruijne J, Thomas XV, Rebers SP, Weegink CJ, Treitel MA, Hughes E, Bergmann JF, de Knegt RJ, Janssen HLA, Reesink HW, Molenkamp R, Schinkel J. Evolutionary dynamics of hepatitis C virus NS3 protease domain during and following treatment with narlaprevir, a potent NS3 protease inhibitor. J Viral Hepat 2013; 20:779-89. [PMID: 24168257 DOI: 10.1111/jvh.12104] [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] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/25/2012] [Accepted: 02/03/2013] [Indexed: 12/09/2022]
Abstract
Narlaprevir, a hepatitis C virus (HCV) NS3/4A serine protease inhibitor, has demonstrated robust antiviral activity in a placebo-controlled phase 1 study. To study evolutionary dynamics of resistant variants, the NS3 protease sequence was clonally analysed in thirty-two HCV genotype 1-infected patients following treatment with narlaprevir. Narlaprevir monotherapy was administered for one week (period 1) followed by narlaprevir/pegylated interferon-alpha-2b combination therapy with or without ritonavir (period 2) during two weeks, interrupted by a washout period of one month. Thereafter, all patients initiated pegylated interferon-alpha-2b/ribavirin combination therapy. Longitudinal clonal analysis was performed in those patients with NS3 mutations. After narlaprevir re-exposure, resistance-associated mutations at position V36, T54, R155 and A156 were detected in five patients in >95% of the clones. Narlaprevir retreatment resulted in a 2.58 and 5.06 log10 IU/mL viral load decline in patients with and without mutations, respectively (P=<0.01). After treatment, resistant variants were replaced with wild-type virus within 2-24 weeks in three patients. However, the R155K mutation was still observed 3.1 years after narlaprevir dosing in two patients in 5% and 45% of the viral population. Resistant variants could be detected early during treatment with narlaprevir. A slower viral load decline was observed in those patients with resistance-associated mutations detectable by direct population sequencing. These mutations disappeared within six months following treatment with the exception of R155K mutation, which persisted in two patients.
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Affiliation(s)
- J de Bruijne
- Department of Gastroenterology and Hepatology, Academic Medical Center, Amsterdam, The Netherlands
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25
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Bartolini B, Giombini E, Zaccaro P, Selleri M, Rozera G, Abbate I, Comandini UV, Ippolito G, Solmone M, Capobianchi MR. Extent of HCV NS3 protease variability and resistance-associated mutations assessed by next generation sequencing in HCV monoinfected and HIV/HCV coinfected patients. Virus Res 2013; 177:205-8. [PMID: 23954579 DOI: 10.1016/j.virusres.2013.08.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [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: 05/22/2013] [Revised: 08/01/2013] [Accepted: 08/02/2013] [Indexed: 02/07/2023]
Abstract
HCV quasispecies variability represents the background for the selection of mutations and for the development of drug resistance. Natural aminoacid changes in NS3, associated with reduced protease inhibitor susceptibility, have been observed in treatment-naïve patients. Massively parallel sequencing has been used to analyze NS3 quasispecies in patients infected with HCV genotype 1, naive to anti-HCV treatment, with/without HIV-coinfection, to establish the genetic heterogeneity and the presence of amino acid substitutions at positions responsible for drug resistance. Genomes carrying substitutions represented either predominant or minority components of viral quasispecies, and were observed in 85.7% of patients. Multiple substitutions, frequently associated on the same haplotype, were observed in 46.4% of patients. High resistance combinations were not detected, neither on the same genome, nor in the whole quasispecies. Heterogeneity of HCV NS3 was lower in HIV-coinfected as compared to HCV-monoinfected patients, but factors underlying this difference remain to be established. Although the relevance of naturally occurring mutations with respect of resistance development and probability of success of direct acting antivirals is questioned, UDPS may be beneficial to help understanding viral dynamics, providing high resolution view of viral diversity.
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Affiliation(s)
- Barbara Bartolini
- "L. Spallanzani" National Institute for Infectious Diseases, Via Portuense 292, 00149 Rome, Italy
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26
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Alaee M, Rajabi P, Sharifi Z, Farajollahi MM. Immunoreactivity assessment of hepatitis C virus NS3 protease and NS5A proteins expressed in TOPO cloning system. J Microbiol Immunol Infect 2012; 47:282-91. [PMID: 23040046 DOI: 10.1016/j.jmii.2012.08.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Revised: 06/30/2012] [Accepted: 08/09/2012] [Indexed: 01/29/2023]
Abstract
BACKGROUND Hepatitis C virus (HCV) is a major cause of acute and chronic liver disease. Numerous screening assays based on the detection of immunoresponses to HCV structural and nonstructural proteins have been designed. Various studies have demonstrated genotype-specific differences in anti-HCV antibody responses to different HCV proteins. METHODS Full-length NS3 protease and N-terminally truncated NS5A were expressed using pET TOPO 102/D system. Antigenicity of the purified recombinant proteins was assessed by immunoblotting and indirect enzyme-linked immunosorbent assay (ELISA). Furthermore, anti-HCV antibody responses to the recombinant proteins were evaluated in three prevalent genotypes in Iran. RESULTS We were able to express and purify NS5A and NS3 protease using TOPO cloning system. The HCV NS3 protease and NS5A produced in BL21 Star (DE3) was immunoreactive. Our results demonstrate that NS3 protease and NS5A have good immunoreactivity, but they are not sufficient for detecting all HCV-positive sera. No significant genotype-specific differences were detected in immunoresponses to the recombinant proteins. CONCLUSION In conclusion, we successfully isolated, expressed, and purified substantial amount of HCV NS3 protease and N-terminally truncated NS5A, and used them as capturing antigens in a screening ELISA assay with high sensitivity, reproducibility, and specificity. Accordingly, it is well confirmed that TOPO cloning system can be used as a dynamic system in order to express higher amount of immunoreactive viral proteins.
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Affiliation(s)
- Mahsa Alaee
- Department of Medical Biotechnology, Faculty of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran, Iran
| | - Peyman Rajabi
- Department of Medical Biotechnology, Faculty of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran, Iran
| | - Zohreh Sharifi
- Blood Transfusion Research Center, High Institute for Research and Education in Transfusion Medicine, Tehran, Iran
| | - Mohammad Morad Farajollahi
- Department of Medical Biotechnology, Faculty of Allied Medical Sciences, Tehran University of Medical Sciences, Tehran, Iran.
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27
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Chatel-Chaix L, Baril M, Lamarre D. Hepatitis C Virus NS3/4A Protease Inhibitors: A Light at the End of the Tunnel. Viruses 2010; 2:1752-1765. [PMID: 21994705 PMCID: PMC3185733 DOI: 10.3390/v2081752] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Revised: 08/12/2010] [Accepted: 08/18/2010] [Indexed: 12/28/2022] Open
Abstract
Hepatitis C virus (HCV) infection is a serious and growing threat to human health. The current treatment provides limited efficacy and is poorly tolerated, highlighting the urgent medical need for novel therapeutics. The membrane-targeted NS3 protein in complex with the NS4A comprises a serine protease domain (NS3/4A protease) that is essential for viral polyprotein maturation and contributes to the evasion of the host innate antiviral immunity by HCV. Therefore, the NS3/4A protease represents an attractive target for drug discovery, which is tied in with the challenge to develop selective small-molecule inhibitors. A rational drug design approach, based on the discovery of N-terminus product inhibition, led to the identification of potent and orally bioavailable NS3 inhibitors that target the highly conserved protease active site. This review summarizes the NS3 protease inhibitors currently challenged in clinical trials as one of the most promising antiviral drug class, and possibly among the first anti-HCV agents to be approved for the treatment of HCV infection.
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Affiliation(s)
| | | | - Daniel Lamarre
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +1-514-343-7127; Fax: +1-514-343-2165
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