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Trivedi A, Kardam V, Inampudi KK, Vrati S, Gupta D, Singh A, Kayampeta SR, Appaiahgari MB, Sehgal D. Identification of a novel inhibitor of SARS-CoV-2 main protease: an in silico, biochemical, and cell-based approach. FEBS J 2023; 290:5496-5513. [PMID: 37657928 DOI: 10.1111/febs.16947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/06/2023] [Accepted: 08/31/2023] [Indexed: 09/03/2023]
Abstract
The recurrent nature of coronavirus outbreaks, severity of the COVID-19 pandemic, rapid emergence of novel variants, and concerns over the effectiveness of existing vaccines against novel variants have highlighted the need to develop therapeutic interventions. Targeted efforts to identify inhibitors of crucial viral proteins are the preferred strategy. In this study, we screened FDA-approved and natural product libraries using in silico approach for potential hits against the SARS-CoV-2 main protease (Mpro) and experimentally validated their potency using in vitro biochemical and cell-based assays. Seven potential hits were identified through in silico screening and were subsequently evaluated in SARS-CoV-2-based cell-free assays, followed by testing in the HCoV-229E-based culture system. Of the tested compounds, 4-(3,4-dihydroxyphenyl)-6,7-dihydroxy-1-isopropyl-1H-benzofuro[3,2-b]pyrazolo[4,3-e]pyridin-3(2H)-one (PubChem CID:71755304, hereafter referred to as STL522228) exhibited significant antiviral activity. Subsequently, its potential as a novel COVID therapeutic molecule was validated in the SARS-CoV-2-culture system, where STL522228 demonstrated superior antiviral activity (EC50 = 0.44 μm) compared to Remdesivir (EC50 = 0.62 μm). Based on these findings, we report the strong anti-coronavirus activity of STL522228, and propose that it as a promising pan-coronavirus Mpro inhibitor for further experimental and preclinical validation.
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Affiliation(s)
- Aditya Trivedi
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar Institution of Eminence, Greater Noida, Uttar Pradesh, India
| | - Vandana Kardam
- Department of Chemistry, School of Natural Sciences, Shiv Nadar Institution of Eminence, Greater Noida, Uttar Pradesh, India
| | | | - Sudhanshu Vrati
- Laboratory of Virology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Dharmender Gupta
- Laboratory of Virology, Regional Centre for Biotechnology, NCR Biotech Science Cluster, Faridabad, India
| | - Aekagra Singh
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar Institution of Eminence, Greater Noida, Uttar Pradesh, India
| | - Sarala Rani Kayampeta
- Research and Development Division, Srikara Biologicals Private Limited, Tirupati, India
| | | | - Deepak Sehgal
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar Institution of Eminence, Greater Noida, Uttar Pradesh, India
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Kumar A, Hooda P, Puri A, Khatter R, S. Al-Dosari M, Sinha N, Parvez MK, Sehgal D. Methotrexate, an anti-inflammatory drug, inhibits Hepatitis E viral replication. J Enzyme Inhib Med Chem 2023; 38:2280500. [PMID: 37975328 PMCID: PMC11003484 DOI: 10.1080/14756366.2023.2280500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 10/30/2023] [Indexed: 11/19/2023] Open
Abstract
Hepatitis E Virus (HEV) is a positively oriented RNA virus having a 7.2 kb genome. HEV consists of three open reading frames (ORF1-3). Of these, ORF1 codes for the enzymes Methyltransferase (Mtase), Papain-like cysteine protease (PCP), RNA helicase, and RNA-dependent RNA polymerase (RdRp). Unavailability of a vaccine or effective drug against HEV and considering the side effects associated with the off-label use of ribavirin (RBV) and pegylated interferons, an alternative approach is required by the modulation of specific enzymes to prevent the infection. HEV helicase is involved in unwinding the double-stranded RNA, RNA processing, transcriptional regulation, and pre-mRNA processing. Therefore, we screened FDA-approved compounds from the ZINC15 database against the modelled 3D structure of HEV helicase and found that methotrexate and compound A (Pubchem ID BTB07890) inhibit the NTPase and dsRNA unwinding activity leading to inhibition of HEV RNA replication. This may be further authenticated by in vivo study.
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Affiliation(s)
- Akash Kumar
- Department of Life Sciences, Virology lab, Shiv Nadar Institution of Eminence, Greater Noida, India
| | - Preeti Hooda
- Department of Life Sciences, Virology lab, Shiv Nadar Institution of Eminence, Greater Noida, India
| | - Anindita Puri
- Department of Life Sciences, Virology lab, Shiv Nadar Institution of Eminence, Greater Noida, India
| | - Radhika Khatter
- Department of Life Sciences, Virology lab, Shiv Nadar Institution of Eminence, Greater Noida, India
| | - Mohammed S. Al-Dosari
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Neha Sinha
- Department of Infectious Diseases and Microbiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Mohammad K. Parvez
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Deepak Sehgal
- Department of Life Sciences, Virology lab, Shiv Nadar Institution of Eminence, Greater Noida, India
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Hooda P, Al-Dosari M, Sinha N, Parvez MK, Sehgal D. Inhibition of HEV Replication by FDA-Approved RdRp Inhibitors. ACS OMEGA 2023; 8:41570-41578. [PMID: 37969986 PMCID: PMC10633873 DOI: 10.1021/acsomega.3c05637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/11/2023] [Accepted: 10/12/2023] [Indexed: 11/17/2023]
Abstract
Hepatitis E virus (HEV) is primarily a hepatotropic virus that is responsible for acute hepatitis E in the general population and for chronic hepatitis in immunocompromised individuals. In the absence of a globally accessible vaccine, pegylated interferon-α and ribavirin are the only antiviral agents available for the treatment of chronic patients. As viral RNA-dependent RNA polymerases (RdRps) are indispensable for RNA replication, they are considered potential drug targets. In this study, we screened some well-known RdRp inhibitor molecules, notably, favipiravir, sofosbuvir, remdesivir, filibuvir, and tegobuvir. Of these, monotherapy with favipiravir and sofosbuvir inhibited the RdRp activity with an IC50 value of 10.2 ± 4.9 and 5.2 ± 2.9 μM, respectively, compared to the reference drug ribavirin (3.5 ± 1.6 μM). Further investigation of the combination therapy showed a reduction in viral RNA copy numbers by approximately 90%. Therefore, favipiravir has an additive effect when used with sofosbuvir. Therefore, we propose that favipiravir is a promising anti-HEV drug that can be used in combination with sofosbuvir.
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Affiliation(s)
- Preeti Hooda
- Virology
Lab, Department of Life Sciences, Shiv Nadar
Institute of Eminence, Gautam Budh
Nagar 201314, India
| | - Mohammed Al-Dosari
- Department
of Pharmacognosy, College of Pharmacy, King
Saud University, Riyadh 11451, Saudi Arabia
| | - Neha Sinha
- Department
of Infectious Diseases and Microbiology, School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, United States
| | - Mohammad K. Parvez
- Department
of Pharmacognosy, College of Pharmacy, King
Saud University, Riyadh 11451, Saudi Arabia
| | - Deepak Sehgal
- Virology
Lab, Department of Life Sciences, Shiv Nadar
Institute of Eminence, Gautam Budh
Nagar 201314, India
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4
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Buchanan FJT, Chen S, Harris M, Herod MR. The hepatitis E virus ORF1 hypervariable region confers partial cyclophilin dependency. J Gen Virol 2023; 104:001919. [PMID: 37942835 PMCID: PMC10768694 DOI: 10.1099/jgv.0.001919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 10/27/2023] [Indexed: 11/10/2023] Open
Abstract
Hepatitis E virus (HEV) is an emerging pathogen responsible for more than 20 million cases of acute hepatitis globally per annum. Healthy individuals typically have a self-limiting infection, but mortality rates in some populations such as pregnant women can reach 30 %. A detailed understanding of the virus lifecycle is lacking, mainly due to limitations in experimental systems. In this regard, the cyclophilins are an important family of proteins that have peptidyl-prolyl isomerase activity and play roles in the replication of a number of positive-sense RNA viruses, including hepatotropic viruses such as hepatitis C virus (HCV). Cyclophilins A and B (CypA/B) are the two most abundant Cyps in hepatocytes and are therefore potential targets for pan-viral therapeutics. Here, we investigated the importance of CypA and CypB for HEV genome replication using sub-genomic replicons. Using a combination of pharmacological inhibition by cyclosporine A (CsA), and silencing by small hairpin RNA we find that CypA and CypB are not essential for HEV replication. However, we find that silencing of CypB reduces replication of some HEV isolates in some cells. Furthermore, sensitivity to Cyp silencing appears to be partly conferred by the sequence within the hypervariable region of the viral polyprotein. These data suggest HEV is atypical in its requirements for cyclophilin for viral genome replication and that this phenomenon could be genotype- and sequence-specific.
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Affiliation(s)
- Frazer J. T. Buchanan
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Shucheng Chen
- Department of Paediatrics, Harvard Medical School, Boston, Massachusetts, USA
| | - Mark Harris
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Morgan R. Herod
- School of Molecular and Cellular Biology, Faculty of Biological Sciences and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK
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Fieulaine S, Tubiana T, Bressanelli S. De novo modelling of HEV replication polyprotein: Five-domain breakdown and involvement of flexibility in functional regulation. Virology 2023; 578:128-140. [PMID: 36527931 DOI: 10.1016/j.virol.2022.12.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/14/2022]
Abstract
Hepatitis E virus (HEV), a major cause of acute viral hepatitis, is a single-stranded, positive-sense RNA virus. As such, it encodes a 1700-residue replication polyprotein pORF1 that directs synthesis of new viral RNA in infected cells. Here we report extensive modeling with AlphaFold2 of the full-length pORF1, and its production by in vitro translation. From this, we give a detailed update on the breakdown into domains of HEV pORF1. We also provide evidence that pORF1's N-terminal domain is likely to oligomerize to form a dodecameric pore, homologously to what has been described for Chikungunya virus. Beyond providing accurate folds for its five domains, our work highlights that there is no canonical protease encoded in pORF1 and that flexibility in several functionally important regions rather than proteolytic processing may serve to regulate HEV RNA synthesis.
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Affiliation(s)
- Sonia Fieulaine
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
| | - Thibault Tubiana
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
| | - Stéphane Bressanelli
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
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Wani TA, Zargar S, Hussain A. Spectroscopic, Thermodynamic and Molecular Docking Studies on Molecular Mechanisms of Drug Binding to Proteins. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238405. [PMID: 36500497 PMCID: PMC9738057 DOI: 10.3390/molecules27238405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 11/29/2022] [Indexed: 12/04/2022]
Abstract
Molecular recognition, which is the process of biological macromolecules interacting with each other or various small molecules with a high specificity and affinity to form a specific complex, constitutes the basis of all processes in living organisms [...].
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Affiliation(s)
- Tanveer A. Wani
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
- Correspondence:
| | - Seema Zargar
- Department of Biochemistry, College of Science, King Saud University, P.O. Box 22452, Riyadh 11451, Saudi Arabia
| | - Afzal Hussain
- Department of Pharmacognosy, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
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Hooda P, Chaudhary M, Parvez MK, Sinha N, Sehgal D. Inhibition of Hepatitis E Virus Replication by Novel Inhibitor Targeting Methyltransferase. Viruses 2022; 14:v14081778. [PMID: 36016400 PMCID: PMC9415367 DOI: 10.3390/v14081778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 08/07/2022] [Accepted: 08/11/2022] [Indexed: 11/17/2022] Open
Abstract
Hepatitis E Virus (HEV) is a quasi-enveloped virus having a single-stranded, positive-sense RNA genome (~7.2 kb), flanked with a 5′ methylated cap and a 3′ polyadenylated tail. The HEV open reading frame 1 (ORF1) encodes a 186-kDa polyprotein speculated to get processed and produce Methyltransferase (MTase), one of the four essential replication enzymes. In this study, we report the identification of the MTase inhibitor, which may potentially deplete its enzymatic activity, thus causing the cessation of viral replication. Using in silico screening through docking, we identified ten putative compounds, which were tested for their anti-MTase activity. This resulted in the identification of 3-(4-Hydroxyphenyl)propionic acid (HPPA), with an IC50 value of 0.932 ± 0.15 μM, which could be perceived as an effective HEV inhibitor. Furthermore, the compound was tested for inhibition of HEV replication in the HEV culture system. The viral RNA copies were markedly decreased from ~3.2 × 106 in untreated cells to ~4.3 × 102.8 copies in 800 μM HPPA treated cells. Therefore, we propose HPPA as a potential drug-like inhibitor against HEV-MTase, which would need further validation through in vivo analysis using animal models and the administration of Pharmacokinetic and Pharmacodynamic (PK/PD) studies.
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Affiliation(s)
- Preeti Hooda
- Virology Laboratory, Department of Life Sciences, Shiv Nadar University, Gautam Budh Nagar, Greater Noida 201314, India
| | - Meenakshi Chaudhary
- Virology Laboratory, Department of Life Sciences, Shiv Nadar University, Gautam Budh Nagar, Greater Noida 201314, India
| | - Mohammad K. Parvez
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
- Correspondence: (M.K.P.); (D.S.)
| | - Neha Sinha
- Department of Infectious Diseases and Microbiology, School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Deepak Sehgal
- Virology Laboratory, Department of Life Sciences, Shiv Nadar University, Gautam Budh Nagar, Greater Noida 201314, India
- Correspondence: (M.K.P.); (D.S.)
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