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Chen J, Zhou Y, Wei X, Xu X, Qin Z, Ong CP, Ye ZW, Jin DY, Boitrel B, Yuan S, Chan JFW, Li H, Sun H. Development of Pan-Anti-SARS-CoV-2 Agents through Allosteric Inhibition of nsp14/nsp10 Complex. ACS Infect Dis 2024; 10:858-869. [PMID: 37897418 DOI: 10.1021/acsinfecdis.3c00356] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/30/2023]
Abstract
SARS-CoV-2 nsp14 functions both as an exoribonuclease (ExoN) together with its critical cofactor nsp10 and as an S-adenosyl methionine-dependent (guanine-N7) methyltransferase (MTase), which makes it an attractive target for the development of pan-anti-SARS-CoV-2 drugs. Herein, we screened a panel of compounds (and drugs) and found that certain compounds, especially Bi(III)-based compounds, could allosterically inhibit both MTase and ExoN activities of nsp14 potently. We further demonstrated that Bi(III) binds to both nsp14 and nsp10, resulting in the release of Zn(II) ions from the enzymes as well as alternation of protein quaternary structures. The in vitro activities of the compounds were also validated in SARS-CoV-2-infected mammalian cells. Importantly, we showed that nsp14 serves as an authentic target of Bi(III)-based antivirals in SARS-CoV-2-infected mammalian cells by quantification of both the protein and inhibitor. This study highlights the importance of nsp14/nsp10 as a potential target for the development of pan-antivirals against SARS-CoV-2 infection.
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Affiliation(s)
- Jingxin Chen
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry and CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Pokfulam Road, Pokfulam, Hong Kong 999077, P. R. China
| | - Ying Zhou
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry and CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Pokfulam Road, Pokfulam, Hong Kong 999077, P. R. China
| | - Xueying Wei
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry and CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Pokfulam Road, Pokfulam, Hong Kong 999077, P. R. China
- Department of Microbiology, The University of Hong Kong, Sassoon Road, Pokfulam, Hong Kong 999077, P. R. China
| | - Xiaohan Xu
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry and CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Pokfulam Road, Pokfulam, Hong Kong 999077, P. R. China
| | - Zhenzhi Qin
- Department of Microbiology, The University of Hong Kong, Sassoon Road, Pokfulam, Hong Kong 999077, P. R. China
| | - Chon Phin Ong
- School of Biomedical Sciences, The University of Hong Kong, Sassoon Road, Pokfulam, Hong Kong 999077, P. R. China
| | - Zi-Wei Ye
- School of Biomedical Sciences, The University of Hong Kong, Sassoon Road, Pokfulam, Hong Kong 999077, P. R. China
| | - Dong-Yan Jin
- School of Biomedical Sciences, The University of Hong Kong, Sassoon Road, Pokfulam, Hong Kong 999077, P. R. China
| | - Bernard Boitrel
- University of Rennes, CNRS, ISCR (Institut des Sciences Chimiques de Rennes)-UMR 6226, Rennes 35000, France
| | - Shuofeng Yuan
- Department of Microbiology, The University of Hong Kong, Sassoon Road, Pokfulam, Hong Kong 999077, P. R. China
| | - Jasper F-W Chan
- Department of Microbiology, The University of Hong Kong, Sassoon Road, Pokfulam, Hong Kong 999077, P. R. China
| | - Hongyan Li
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry and CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Pokfulam Road, Pokfulam, Hong Kong 999077, P. R. China
| | - Hongzhe Sun
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry and CAS-HKU Joint Laboratory of Metallomics on Health and Environment, The University of Hong Kong, Pokfulam Road, Pokfulam, Hong Kong 999077, P. R. China
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2
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Fibriani A, Taharuddin AAP, Yamahoki N, Stephanie R, Laurelia J, Agustiyanti DF, Wisnuwardhani PH, Angelina M, Rubiyana Y, Ningrum RA, Wardiana A, Desriani D, Iskandar F, Permatasari FA, Giri-Rachman EA. Porphyrin-derived carbon dots for an enhanced antiviral activity targeting the CTD of SARS-CoV-2 nucleocapsid. J Genet Eng Biotechnol 2023; 21:93. [PMID: 37801271 PMCID: PMC10558421 DOI: 10.1186/s43141-023-00548-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 09/20/2023] [Indexed: 10/07/2023]
Abstract
BACKGROUND Since effective antiviral drugs for COVID-19 are still limited in number, the exploration of compounds that have antiviral activity against SARS-CoV-2 is in high demand. Porphyrin is potentially developed as a COVID-19 antiviral drug. However, its low solubility in water restricts its clinical application. Reconstruction of porphyrin into carbon dots is expected to possess better solubility and bioavailability as well as lower biotoxicity. METHODS AND RESULTS In this study, we investigated the antiviral activity of porphyrin and porphyrin-derived carbon dots against SARS-CoV-2. Through the in silico analysis and assessment using a novel drug screening platform, namely dimer-based screening system, we demonstrated the capability of the antivirus candidates in inhibiting the dimerization of the C-terminal domain of SARS-CoV-2 Nucleocapsid. It was shown that porphyrin-derived carbon dots possessed lower cytotoxicity on Vero E6 cells than porphyrin. Furthermore, we also assessed their antiviral activity on the SARS-CoV-2-infected Vero E6 cells. The transformation of porphyrin into carbon dots substantially augmented its performance in disrupting SARS-CoV-2 propagation in vitro. CONCLUSIONS Therefore, this study comprehensively demonstrated the potential of porphyrin-derived carbon dots to be developed further as a promisingly safe and effective COVID-19 antiviral drug.
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Affiliation(s)
- Azzania Fibriani
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, 40132, Indonesia.
- Research Center for Nanoscience and Nanotechnology, Institut Teknologi Bandung, Bandung, 40132, Indonesia.
| | | | - Nicholas Yamahoki
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, 40132, Indonesia
| | - Rebecca Stephanie
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, 40132, Indonesia
| | - Jessica Laurelia
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, 40132, Indonesia
| | - Dian Fitria Agustiyanti
- Research Center for Genetic Engineering, Indonesian National Research and Innovation Agency (BRIN), Cibinong, 16911, Indonesia
| | - Popi Hadi Wisnuwardhani
- Research Center for Genetic Engineering, Indonesian National Research and Innovation Agency (BRIN), Cibinong, 16911, Indonesia
| | - Marissa Angelina
- Research Center for Pharmaceutical Ingredients and Traditional Medicine, Indonesian National Research and Innovation Agency (BRIN), Serpong, 15314, Indonesia
| | - Yana Rubiyana
- Research Center for Genetic Engineering, Indonesian National Research and Innovation Agency (BRIN), Cibinong, 16911, Indonesia
| | - Ratih Asmana Ningrum
- Research Center for Genetic Engineering, Indonesian National Research and Innovation Agency (BRIN), Cibinong, 16911, Indonesia
| | - Andri Wardiana
- Research Center for Genetic Engineering, Indonesian National Research and Innovation Agency (BRIN), Cibinong, 16911, Indonesia
| | - Desriani Desriani
- Research Center for Genetic Engineering, Indonesian National Research and Innovation Agency (BRIN), Cibinong, 16911, Indonesia
| | - Ferry Iskandar
- Research Center for Nanoscience and Nanotechnology, Institut Teknologi Bandung, Bandung, 40132, Indonesia
- Department of Physics, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Bandung, 40132, Indonesia
- Collaboration Research Center for Advanced Energy Materials, National Research and Innovation Agency-Institut Teknologi, Bandung, Bandung, 40132, Indonesia
| | - Fitri Aulia Permatasari
- Department of Physics, Faculty of Mathematics and Natural Sciences, Institut Teknologi Bandung, Bandung, 40132, Indonesia
- Collaboration Research Center for Advanced Energy Materials, National Research and Innovation Agency-Institut Teknologi, Bandung, Bandung, 40132, Indonesia
- Research Center for Chemistry, National Research and Innovation Agency (BRIN), Serpong, 15314, Indonesia
| | - Ernawati Arifin Giri-Rachman
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, 40132, Indonesia
- Research Center for Nanoscience and Nanotechnology, Institut Teknologi Bandung, Bandung, 40132, Indonesia
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3
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Asthana A, Corona A, Shin WJ, Kwak MJ, Gaughan C, Tramontano E, Jung JU, Schobert R, Jha BK, Silverman RH, Biersack B. Analogs of the Catechol Derivative Dynasore Inhibit HIV-1 Ribonuclease H, SARS-CoV-2 nsp14 Exoribonuclease, and Virus Replication. Viruses 2023; 15:1539. [PMID: 37515225 PMCID: PMC10385162 DOI: 10.3390/v15071539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 07/08/2023] [Accepted: 07/10/2023] [Indexed: 07/30/2023] Open
Abstract
Viral replication often depends on RNA maturation and degradation processes catalyzed by viral ribonucleases, which are therefore candidate targets for antiviral drugs. Here, we synthesized and studied the antiviral properties of a novel nitrocatechol compound (1c) and other analogs that are structurally related to the catechol derivative dynasore. Interestingly, compound 1c strongly inhibited two DEDD box viral ribonucleases, HIV-1 RNase H and SARS-CoV-2 nsp14 3'-to-5' exoribonuclease (ExoN). While 1c inhibited SARS-CoV-2 ExoN activity, it did not interfere with the mRNA methyltransferase activity of nsp14. In silico molecular docking placed compound 1c in the catalytic pocket of the ExoN domain of nsp14. Finally, 1c inhibited SARS-CoV-2 replication but had no toxicity to human lung adenocarcinoma cells. Given its simple chemical synthesis from easily available starting materials, these results suggest that 1c might be a lead compound for the design of new antiviral compounds that target coronavirus nsp14 ExoN and other viral ribonucleases.
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Affiliation(s)
- Abhishek Asthana
- Cancer Biology, Lerner Research Institute, Cleveland Clinic, 2111 East 96th St, Cleveland, OH 44106, USA
| | - Angela Corona
- Laboratorio di Virologia Molecolare, Dipartimento di Scienze della Vita e Dell'Ambiente, Universitá degli Studi di Cagliari, Cittadella Universitaria di Monserrato SS554, 09042 Monserrato, Italy
| | - Woo-Jin Shin
- Cancer Biology, Lerner Research Institute, Cleveland Clinic, 2111 East 96th St, Cleveland, OH 44106, USA
| | - Mi-Jeong Kwak
- Cancer Biology, Lerner Research Institute, Cleveland Clinic, 2111 East 96th St, Cleveland, OH 44106, USA
| | - Christina Gaughan
- Cancer Biology, Lerner Research Institute, Cleveland Clinic, 2111 East 96th St, Cleveland, OH 44106, USA
| | - Enzo Tramontano
- Laboratorio di Virologia Molecolare, Dipartimento di Scienze della Vita e Dell'Ambiente, Universitá degli Studi di Cagliari, Cittadella Universitaria di Monserrato SS554, 09042 Monserrato, Italy
| | - Jae U Jung
- Cancer Biology, Lerner Research Institute, Cleveland Clinic, 2111 East 96th St, Cleveland, OH 44106, USA
| | - Rainer Schobert
- Organic Chemistry 1, University of Bayreuth, Universitätsstrasse 30, 95440 Bayreuth, Germany
| | - Babal Kant Jha
- Center for Immunotherapy and Precision Immuno-Oncology, Lerner Research Institute and Department of Translational Hematology and Oncology Research, Taussig Cancer Institute, Cleveland Clinic, 2111 East 96th St, Cleveland, OH 44195, USA
| | - Robert H Silverman
- Cancer Biology, Lerner Research Institute, Cleveland Clinic, 2111 East 96th St, Cleveland, OH 44106, USA
| | - Bernhard Biersack
- Organic Chemistry 1, University of Bayreuth, Universitätsstrasse 30, 95440 Bayreuth, Germany
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4
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In Silico Binding of 2-Aminocyclobutanones to SARS-CoV-2 Nsp13 Helicase and Demonstration of Antiviral Activity. Int J Mol Sci 2023; 24:ijms24065120. [PMID: 36982188 PMCID: PMC10049026 DOI: 10.3390/ijms24065120] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 02/22/2023] [Accepted: 03/02/2023] [Indexed: 03/10/2023] Open
Abstract
The landscape of viral strains and lineages of SARS-CoV-2 keeps changing and is currently dominated by Delta and Omicron variants. Members of the latest Omicron variants, including BA.1, are showing a high level of immune evasion, and Omicron has become a prominent variant circulating globally. In our search for versatile medicinal chemistry scaffolds, we prepared a library of substituted ɑ-aminocyclobutanones from an ɑ-aminocyclobutanone synthon (11). We performed an in silico screen of this actual chemical library as well as other virtual 2-aminocyclobutanone analogs against seven SARS-CoV-2 nonstructural proteins to identify potential drug leads against SARS-CoV-2, and more broadly against coronavirus antiviral targets. Several of these analogs were initially identified as in silico hits against SARS-CoV-2 nonstructural protein 13 (Nsp13) helicase through molecular docking and dynamics simulations. Antiviral activity of the original hits as well as ɑ-aminocyclobutanone analogs that were predicted to bind more tightly to SARS-CoV-2 Nsp13 helicase are reported. We now report cyclobutanone derivatives that exhibit anti-SARS-CoV-2 activity. Furthermore, the Nsp13 helicase enzyme has been the target of relatively few target-based drug discovery efforts, in part due to a very late release of a high-resolution structure accompanied by a limited understanding of its protein biochemistry. In general, antiviral agents initially efficacious against wild-type SARS-CoV-2 strains have lower activities against variants due to heavy viral loads and greater turnover rates, but the inhibitors we are reporting have higher activities against the later variants than the wild-type (10–20X). We speculate this could be due to Nsp13 helicase being a critical bottleneck in faster replication rates of the new variants, so targeting this enzyme affects these variants to an even greater extent. This work calls attention to cyclobutanones as a useful medicinal chemistry scaffold, and the need for additional focus on the discovery of Nsp13 helicase inhibitors to combat the aggressive and immune-evading variants of concern (VOCs).
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5
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Arya R, Prashar V, Kumar M. Identification and characterization of aurintricarboxylic acid as a potential inhibitor of SARS-CoV-2 PLpro. Int J Biol Macromol 2023; 230:123347. [PMID: 36682650 PMCID: PMC9851725 DOI: 10.1016/j.ijbiomac.2023.123347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 12/20/2022] [Accepted: 01/16/2023] [Indexed: 01/21/2023]
Abstract
As the global health crisis due to evolution of mutations in SARS-CoV-2 continues, it is important to develop several effective antivirals to control the disease. Targeting papain-like protease (PLpro) of SARS-CoV-2 for drug development is a promising strategy due to its dual role in promoting viral replication and dysregulating host immune responses. Here, we screened a library of compounds to find potential inhibitors of PLpro. We find aurintricarboxylic acid (ATA) inhibits PLpro with Ki and IC50 values of 16 μM and 30 μM, respectively. The binding of ATA to PLpro was further characterized using isothermal titration calorimetry, differential scanning fluorimetry, dynamic light scattering and circular dichroism spectrometry. In vitro assays showed the antiviral potential of ATA with IC50 of 50 μM. In vivo efficacy was studied in Syrian hamsters and the results are being discussed.
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Affiliation(s)
- Rimanshee Arya
- Protein Crystallography Section, Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai 400094, India
| | - Vishal Prashar
- Protein Crystallography Section, Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai 400094, India
| | - Mukesh Kumar
- Protein Crystallography Section, Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai 400094, India.
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6
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Chinthapatla R, Sotoudegan M, Srivastava P, Anderson TK, Moustafa I, Passow K, Kennelly S, Moorthy R, Dulin D, Feng J, Harki D, Kirchdoerfer R, Cameron C, Arnold J. Interfering with nucleotide excision by the coronavirus 3'-to-5' exoribonuclease. Nucleic Acids Res 2023; 51:315-336. [PMID: 36546762 PMCID: PMC9841423 DOI: 10.1093/nar/gkac1177] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 11/11/2022] [Accepted: 11/27/2022] [Indexed: 12/24/2022] Open
Abstract
Some of the most efficacious antiviral therapeutics are ribonucleos(t)ide analogs. The presence of a 3'-to-5' proofreading exoribonuclease (ExoN) in coronaviruses diminishes the potency of many ribonucleotide analogs. The ability to interfere with ExoN activity will create new possibilities for control of SARS-CoV-2 infection. ExoN is formed by a 1:1 complex of nsp14 and nsp10 proteins. We have purified and characterized ExoN using a robust, quantitative system that reveals determinants of specificity and efficiency of hydrolysis. Double-stranded RNA is preferred over single-stranded RNA. Nucleotide excision is distributive, with only one or two nucleotides hydrolyzed in a single binding event. The composition of the terminal basepair modulates excision. A stalled SARS-CoV-2 replicase in complex with either correctly or incorrectly terminated products prevents excision, suggesting that a mispaired end is insufficient to displace the replicase. Finally, we have discovered several modifications to the 3'-RNA terminus that interfere with or block ExoN-catalyzed excision. While a 3'-OH facilitates hydrolysis of a nucleotide with a normal ribose configuration, this substituent is not required for a nucleotide with a planar ribose configuration such as that present in the antiviral nucleotide produced by viperin. Design of ExoN-resistant, antiviral ribonucleotides should be feasible.
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Affiliation(s)
- Rukesh Chinthapatla
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Mohamad Sotoudegan
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Pankaj Srivastava
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Thomas K Anderson
- Department of Biochemistry and Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ibrahim M Moustafa
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Kellan T Passow
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Samantha A Kennelly
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ramkumar Moorthy
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - David Dulin
- Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Junior Research Group 2, Interdisciplinary Center for Clinical Research, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Cauerstr. 3, 91058 Erlangen, Germany
| | - Joy Y Feng
- Gilead Sciences, Inc, Foster City, CA 94404, USA
| | - Daniel A Harki
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Robert N Kirchdoerfer
- Department of Biochemistry and Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Craig E Cameron
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Jamie J Arnold
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
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7
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Yang Z, Cai X, Ye Q, Zhao Y, Li X, Zhang S, Zhang L. High-Throughput Screening for the Potential Inhibitors of SARS-CoV-2 with Essential Dynamic Behavior. Curr Drug Targets 2023; 24:532-545. [PMID: 36876836 DOI: 10.2174/1389450124666230306141725] [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: 06/18/2022] [Revised: 11/09/2022] [Accepted: 01/11/2023] [Indexed: 03/07/2023]
Abstract
Global health security has been challenged by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) pandemic. Due to the lengthy process of generating vaccinations, it is vital to reposition currently available drugs in order to relieve anti-epidemic tensions and accelerate the development of therapies for Coronavirus Disease 2019 (COVID-19), the public threat caused by SARS-CoV-2. High throughput screening techniques have established their roles in the evaluation of already available medications and the search for novel potential agents with desirable chemical space and more cost-effectiveness. Here, we present the architectural aspects of highthroughput screening for SARS-CoV-2 inhibitors, especially three generations of virtual screening methodologies with structural dynamics: ligand-based screening, receptor-based screening, and machine learning (ML)-based scoring functions (SFs). By outlining the benefits and drawbacks, we hope that researchers will be motivated to adopt these methods in the development of novel anti- SARS-CoV-2 agents.
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Affiliation(s)
- Zhiwei Yang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Xinhui Cai
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Qiushi Ye
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Yizhen Zhao
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Xuhua Li
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Shengli Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
| | - Lei Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an710049, China
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8
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Developing New Tools to Fight Human Pathogens: A Journey through the Advances in RNA Technologies. Microorganisms 2022; 10:microorganisms10112303. [DOI: 10.3390/microorganisms10112303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 11/12/2022] [Accepted: 11/15/2022] [Indexed: 11/22/2022] Open
Abstract
A long scientific journey has led to prominent technological advances in the RNA field, and several new types of molecules have been discovered, from non-coding RNAs (ncRNAs) to riboswitches, small interfering RNAs (siRNAs) and CRISPR systems. Such findings, together with the recognition of the advantages of RNA in terms of its functional performance, have attracted the attention of synthetic biologists to create potent RNA-based tools for biotechnological and medical applications. In this review, we have gathered the knowledge on the connection between RNA metabolism and pathogenesis in Gram-positive and Gram-negative bacteria. We further discuss how RNA techniques have contributed to the building of this knowledge and the development of new tools in synthetic biology for the diagnosis and treatment of diseases caused by pathogenic microorganisms. Infectious diseases are still a world-leading cause of death and morbidity, and RNA-based therapeutics have arisen as an alternative way to achieve success. There are still obstacles to overcome in its application, but much progress has been made in a fast and effective manner, paving the way for the solid establishment of RNA-based therapies in the future.
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9
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Yuyukina SK, Zharkov DO. Mechanisms of Coronavirus Genome Stability As Potential Targets for Antiviral Drugs. HERALD OF THE RUSSIAN ACADEMY OF SCIENCES 2022; 92:470-478. [PMID: 36091852 PMCID: PMC9447942 DOI: 10.1134/s1019331622040256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 02/25/2022] [Accepted: 03/14/2022] [Indexed: 06/15/2023]
Abstract
The COVID-19 pandemic has made it necessary to create antivirals active against the SARS-CoV-2 coronavirus. One of the widely used strategies to fight off viral infections is the use of modified nucleoside analogues that inhibit viral replication by incorporating DNA or RNA into the growing chain, thus stopping its synthesis. The difficulty of using this method of treatment in the case of SARS-CoV-2 is that coronaviruses have an effective mechanism for maintaining genome stability. Its central element is the nsp14 protein, which is characterized by exonuclease activity, due to which incorrectly included and noncanonical nucleotides are removed from the 3' end of the growing RNA chain. Inhibitors of nsp14 exonuclease and nucleoside analogues resistant to its action are viewed as potential targets for anticoronavirus therapy.
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Affiliation(s)
- S. K. Yuyukina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - D. O. Zharkov
- Institute of Chemical Biology and Fundamental Medicine, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
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10
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Chinthapatla R, Sotoudegan M, Anderson T, Moustafa IM, Passow KT, Kennelly SA, Moorthy R, Dulin D, Feng JY, Harki DA, Kirchdoerfer R, Cameron CE, Arnold JJ. Interfering with nucleotide excision by the coronavirus 3'-to-5' exoribonuclease. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.08.11.503614. [PMID: 35982684 PMCID: PMC9387131 DOI: 10.1101/2022.08.11.503614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Some of the most efficacious antiviral therapeutics are ribonucleos(t)ide analogs. The presence of a 3'-to-5' proofreading exoribonuclease (ExoN) in coronaviruses diminishes the potency of many ribonucleotide analogs. The ability to interfere with ExoN activity will create new possibilities for control of SARS-CoV-2 infection. ExoN is formed by a 1:1 complex of nsp14 and nsp10 proteins. We have purified and characterized ExoN using a robust, quantitative system that reveals determinants of specificity and efficiency of hydrolysis. Double-stranded RNA is preferred over single-stranded RNA. Nucleotide excision is distributive, with only one or two nucleotides hydrolyzed in a single binding event. The composition of the terminal basepair modulates excision. A stalled SARS-CoV-2 replicase in complex with either correctly or incorrectly terminated products prevents excision, suggesting that a mispaired end is insufficient to displace the replicase. Finally, we have discovered several modifications to the 3'-RNA terminus that interfere with or block ExoN-catalyzed excision. While a 3'-OH facilitates hydrolysis of a nucleotide with a normal ribose configuration, this substituent is not required for a nucleotide with a planar ribose configuration such as that present in the antiviral nucleotide produced by viperin. Design of ExoN-resistant, antiviral ribonucleotides should be feasible.
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Affiliation(s)
- Rukesh Chinthapatla
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Mohamad Sotoudegan
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Thomas Anderson
- Department of Biochemistry and Institute of Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ibrahim M. Moustafa
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Kellan T. Passow
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Samantha A. Kennelly
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Ramkumar Moorthy
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - David Dulin
- Department of Physics and Astronomy, and LaserLaB Amsterdam, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
- Junior Research Group 2, Interdisciplinary Center for Clinical Research, Friedrich-Alexander-University Erlangen-Nürnberg (FAU), Cauerstr. 3, 91058 Erlangen, Germany
| | - Joy Y. Feng
- Gilead Sciences, Inc, Foster City, CA 94404, USA
| | - Daniel A. Harki
- Department of Medicinal Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
| | - Robert Kirchdoerfer
- Department of Biochemistry and Institute of Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Craig E. Cameron
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Jamie J. Arnold
- Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
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11
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Hernández S, Feracci M, De Jesus CT, El Kazzi P, Kaci R, Garlatti L, Mondielli C, Bailly F, Cotelle P, Touret F, de Lamballerie X, Coutard B, Decroly E, Canard B, Ferron F, Alvarez K. Identification of potent inhibitors of arenavirus and SARS-CoV-2 exoribonucleases by fluorescence polarization assay. Antiviral Res 2022; 204:105364. [PMID: 35716929 PMCID: PMC9212739 DOI: 10.1016/j.antiviral.2022.105364] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/08/2022] [Accepted: 06/13/2022] [Indexed: 01/17/2023]
Abstract
Viral exoribonucleases are uncommon in the world of RNA viruses. To date, they have only been identified in the Arenaviridae and the Coronaviridae families. The exoribonucleases of these viruses play a crucial role in the pathogenicity and interplay with host innate immune response. Moreover, coronaviruses exoribonuclease is also involved in a proofreading mechanism ensuring the genetic stability of the viral genome. Because of their key roles in virus life cycle, they constitute attractive target for drug design. Here we developed a sensitive, robust and reliable fluorescence polarization assay to measure the exoribonuclease activity and its inhibition in vitro. The effectiveness of the method was validated on three different viral exoribonucleases, including SARS-CoV-2, Lymphocytic Choriomeningitis and Machupo viruses. We performed a screening of a focused library consisting of 113 metal chelators. Hit compounds were recovered with an IC50 at micromolar level. We confirmed 3 hits in SARS-CoV-2 infected Vero-E6 cells.
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Affiliation(s)
- Sergio Hernández
- Université Aix-Marseille, Architecture et Fonction des Macromolécules Biologiques (AFMB) – UMR7257 CNRS – Case 932, 163 avenue de Luminy, Marseille CEDEX 09, 13288, France
| | - Mikael Feracci
- Université Aix-Marseille, Architecture et Fonction des Macromolécules Biologiques (AFMB) – UMR7257 CNRS – Case 932, 163 avenue de Luminy, Marseille CEDEX 09, 13288, France
| | - Carolina Trajano De Jesus
- Université Aix-Marseille, Architecture et Fonction des Macromolécules Biologiques (AFMB) – UMR7257 CNRS – Case 932, 163 avenue de Luminy, Marseille CEDEX 09, 13288, France
| | - Priscila El Kazzi
- Université Aix-Marseille, Architecture et Fonction des Macromolécules Biologiques (AFMB) – UMR7257 CNRS – Case 932, 163 avenue de Luminy, Marseille CEDEX 09, 13288, France
| | - Rafik Kaci
- Université Aix-Marseille, Architecture et Fonction des Macromolécules Biologiques (AFMB) – UMR7257 CNRS – Case 932, 163 avenue de Luminy, Marseille CEDEX 09, 13288, France
| | - Laura Garlatti
- Université Aix-Marseille, Architecture et Fonction des Macromolécules Biologiques (AFMB) – UMR7257 CNRS – Case 932, 163 avenue de Luminy, Marseille CEDEX 09, 13288, France
| | - Clemence Mondielli
- Evotec (France) SAS, Campus Curie, 195 route d’Espagne, 31036, Toulouse CEDEX, France
| | - Fabrice Bailly
- Univ Lille, INSERM, CHU Lille, UMR-S 1172, Lille Neuroscience and Cognition Research Center, F-59000, Lille, France
| | - Philippe Cotelle
- Univ Lille, INSERM, CHU Lille, UMR-S 1172, Lille Neuroscience and Cognition Research Center, F-59000, Lille, France,ENSCL-Centrale Lille, CS 90108, F-59652, Villeneuve d’Ascq, France
| | - Franck Touret
- Unité des Virus Émergents (UVE: Aix-Marseille University -IRD 190-Inserm 1207-IHU Méditerranée Infection), Marseille, France
| | - Xavier de Lamballerie
- Unité des Virus Émergents (UVE: Aix-Marseille University -IRD 190-Inserm 1207-IHU Méditerranée Infection), Marseille, France
| | - Bruno Coutard
- Unité des Virus Émergents (UVE: Aix-Marseille University -IRD 190-Inserm 1207-IHU Méditerranée Infection), Marseille, France
| | - Etienne Decroly
- Université Aix-Marseille, Architecture et Fonction des Macromolécules Biologiques (AFMB) – UMR7257 CNRS – Case 932, 163 avenue de Luminy, Marseille CEDEX 09, 13288, France
| | - Bruno Canard
- Université Aix-Marseille, Architecture et Fonction des Macromolécules Biologiques (AFMB) – UMR7257 CNRS – Case 932, 163 avenue de Luminy, Marseille CEDEX 09, 13288, France
| | - François Ferron
- Université Aix-Marseille, Architecture et Fonction des Macromolécules Biologiques (AFMB) – UMR7257 CNRS – Case 932, 163 avenue de Luminy, Marseille CEDEX 09, 13288, France,Corresponding author. AFMB, Case 932, 163 avenue de Luminy, 13288, Marseille Cedex 9, France
| | - Karine Alvarez
- Université Aix-Marseille, Architecture et Fonction des Macromolécules Biologiques (AFMB) – UMR7257 CNRS – Case 932, 163 avenue de Luminy, Marseille CEDEX 09, 13288, France,Corresponding author. AFMB, Case 932, 163 avenue de Luminy, 13288, Marseille Cedex 9, France
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12
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SARS-CoV-2 virus NSP14 Impairs NRF2/HMOX1 activation by targeting Sirtuin 1. Cell Mol Immunol 2022; 19:872-882. [PMID: 35732914 PMCID: PMC9217730 DOI: 10.1038/s41423-022-00887-w] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 04/22/2022] [Accepted: 05/23/2022] [Indexed: 12/12/2022] Open
Abstract
Most deaths from the COVID-19 pandemic are due to acute respiratory distress syndrome (ARDS)-related respiratory failure. Cytokine storms and oxidative stress are the major players in ARDS development during respiratory virus infections. However, it is still unknown how oxidative stress is regulated by viral and host factors in response to SARS-CoV-2 infection. Here, we found that activation of NRF2/HMOX1 significantly suppressed SARS-CoV-2 replication in multiple cell types by producing the metabolite biliverdin, whereas SARS-CoV-2 impaired the NRF2/HMOX1 axis through the action of the nonstructural viral protein NSP14. Mechanistically, NSP14 interacts with the catalytic domain of the NAD-dependent deacetylase Sirtuin 1 (SIRT1) and inhibits its ability to activate the NRF2/HMOX1 pathway. Furthermore, both genetic and pharmaceutical evidence corroborated the novel antiviral activity of SIRT1 against SARS-CoV-2. Therefore, our findings reveal a novel mechanism by which SARS-CoV-2 dysregulates the host antioxidant defense system and emphasize the vital role played by the SIRT1/NRF2 axis in host defense against SARS-CoV-2.
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13
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Ma Y, Luo M, Deng Y, Yang X, Wang X, Chen G, Qin Z, Deng Y, Nan M, Chen Y, Wang P, Wei H, Han L, Fang X, Liu Z. Antibiotic-Induced Primary Biles Inhibit SARS-CoV-2 Endoribonuclease Nsp15 Activity in Mouse Gut. Front Cell Infect Microbiol 2022; 12:896504. [PMID: 35967852 PMCID: PMC9366059 DOI: 10.3389/fcimb.2022.896504] [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: 03/15/2022] [Accepted: 06/14/2022] [Indexed: 11/16/2022] Open
Abstract
The gut microbiome profile of COVID-19 patients was found to correlate with a viral load of SARS-CoV-2, COVID-19 severity, and dysfunctional immune responses, suggesting that gut microbiota may be involved in anti-infection. In order to investigate the role of gut microbiota in anti-infection against SARS-CoV-2, we established a high-throughput in vitro screening system for COVID-19 therapeutics by targeting the endoribonuclease (Nsp15). We also evaluated the activity inhibition of the target by substances of intestinal origin, using a mouse model in an attempt to explore the interactions between gut microbiota and SARS-CoV-2. The results unexpectedly revealed that antibiotic treatment induced the appearance of substances with Nsp15 activity inhibition in the intestine of mice. Comprehensive analysis based on functional profiling of the fecal metagenomes and endoribonuclease assay of antibiotic-enriched bacteria and metabolites demonstrated that the Nsp15 inhibitors were the primary bile acids that accumulated in the gut as a result of antibiotic-induced deficiency of bile acid metabolizing microbes. This study provides a new perspective on the development of COVID-19 therapeutics using primary bile acids.
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Affiliation(s)
- Yao Ma
- Department of Biotechnology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Mei Luo
- Department of Biotechnology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yusheng Deng
- Department of Scientific Research, KMHD, Shenzhen, China
| | - Xiaoman Yang
- Department of Biotechnology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Xionglue Wang
- Department of Biotechnology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Guozhong Chen
- Department of Biotechnology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Zixin Qin
- Department of Biotechnology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Yun Deng
- Department of Biotechnology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Meiling Nan
- Key Laboratory for Experimental Teratology of Ministry of Education and Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yang Chen
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Peihui Wang
- Key Laboratory for Experimental Teratology of Ministry of Education and Advanced Medical Research Institute, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Hong Wei
- State Key Laboratory of Agricultural Microbiology, College of Animal Sciences and Technology, Huazhong Agricultural University, Wuhan, China
| | - Lijuan Han
- Department of Scientific Research, KMHD, Shenzhen, China
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- *Correspondence: Zhi Liu, ; Xiaodong Fang, ; Lijuan Han,
| | - Xiaodong Fang
- State Key Laboratory of Dampness Syndrome of Chinese Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
- *Correspondence: Zhi Liu, ; Xiaodong Fang, ; Lijuan Han,
| | - Zhi Liu
- Department of Biotechnology, Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
- *Correspondence: Zhi Liu, ; Xiaodong Fang, ; Lijuan Han,
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14
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Azali MA, Mohamed S, Harun A, Hussain FA, Shamsuddin S, Johan MF. Application of Baculovirus Expression Vector system (BEV) for COVID-19 diagnostics and therapeutics: a review. J Genet Eng Biotechnol 2022; 20:98. [PMID: 35792966 PMCID: PMC9259773 DOI: 10.1186/s43141-022-00368-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Accepted: 05/20/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND The baculovirus expression vector system has been developed for expressing a wide range of proteins, including enzymes, glycoproteins, recombinant viruses, and vaccines. The availability of the SARS-CoV-2 genome sequence has enabled the synthesis of SARS-CoV2 proteins in a baculovirus-insect cell platform for various applications. The most cloned SARS-CoV-2 protein is the spike protein, which plays a critical role in SARS-CoV-2 infection. It is available in its whole length or as subunits like S1 or the receptor-binding domain (RBD). Non-structural proteins (Nsps), another recombinant SARS-CoV-2 protein generated by the baculovirus expression vector system (BEV), are used in the identification of new medications or the repurposing of existing therapies for the treatment of COVID-19. Non-SARS-CoV-2 proteins generated by BEV for SARS-CoV-2 diagnosis or treatment include moloney murine leukemia virus reverse transcriptase (MMLVRT), angiotensin converting enzyme 2 (ACE2), therapeutic proteins, and recombinant antibodies. The recombinant proteins were modified to boost the yield or to stabilize the protein. CONCLUSION This review covers the wide application of the recombinant protein produced using the baculovirus expression technology for COVID-19 research. A lot of improvements have been made to produce functional proteins with high yields. However, there is still room for improvement and there are parts of this field of research that have not been investigated yet.
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Affiliation(s)
- Muhammad Azharuddin Azali
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia.,School of Agriculture Science and Biotechnology, Faculty of Bioresources and Food Industry, Universiti Sultan Zainal Abidin, 22200, Besut, Terengganu, Malaysia
| | - Salmah Mohamed
- School of Agriculture Science and Biotechnology, Faculty of Bioresources and Food Industry, Universiti Sultan Zainal Abidin, 22200, Besut, Terengganu, Malaysia
| | - Azian Harun
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia
| | - Faezahtul Arbaeyah Hussain
- Department of Pathology, School of Medical Sciences, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia
| | - Shaharum Shamsuddin
- School of Health Sciences, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia
| | - Muhammad Farid Johan
- Department of Haematology, School of Medical Sciences, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia.
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15
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Wang X, Tao C, Morozova I, Kalachikov S, Li X, Kumar S, Russo JJ, Ju J. Identifying Structural Features of Nucleotide Analogues to Overcome SARS-CoV-2 Exonuclease Activity. Viruses 2022; 14:v14071413. [PMID: 35891393 PMCID: PMC9324094 DOI: 10.3390/v14071413] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 06/24/2022] [Accepted: 06/25/2022] [Indexed: 01/27/2023] Open
Abstract
With the recent global spread of new SARS-CoV-2 variants, there remains an urgent need to develop effective and variant-resistant oral drugs. Recently, we reported in vitro results validating the use of combination drugs targeting both the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) and proofreading exonuclease (ExoN) as potential COVID-19 therapeutics. For the nucleotide analogues to be efficient SARS-CoV-2 inhibitors, two properties are required: efficient incorporation by RdRp and substantial resistance to excision by ExoN. Here, we have selected and evaluated nucleotide analogues with a variety of structural features for resistance to ExoN removal when they are attached at the 3′ RNA terminus. We found that dideoxynucleotides and other nucleotides lacking both 2′- and 3′-OH groups were most resistant to ExoN excision, whereas those possessing both 2′- and 3′-OH groups were efficiently removed. We also found that the 3′-OH group in the nucleotide analogues was more critical than the 2′-OH for excision by ExoN. Since the functionally important sequences in Nsp14/10 are highly conserved among all SARS-CoV-2 variants, these identified structural features of nucleotide analogues offer invaluable insights for designing effective RdRp inhibitors that can be simultaneously efficiently incorporated by the RdRp and substantially resist ExoN excision. Such newly developed RdRp terminators would be good candidates to evaluate their ability to inhibit SARS-CoV-2 in cell culture and animal models, perhaps combined with additional exonuclease inhibitors to increase their overall effectiveness.
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Affiliation(s)
- Xuanting Wang
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY 10027, USA; (X.W.); (C.T.); (I.M.); (S.K.); (X.L.); (S.K.); (J.J.R.)
- Department of Chemical Engineering, Columbia University, New York, NY 10027, USA
| | - Chuanjuan Tao
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY 10027, USA; (X.W.); (C.T.); (I.M.); (S.K.); (X.L.); (S.K.); (J.J.R.)
- Department of Chemical Engineering, Columbia University, New York, NY 10027, USA
| | - Irina Morozova
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY 10027, USA; (X.W.); (C.T.); (I.M.); (S.K.); (X.L.); (S.K.); (J.J.R.)
- Department of Chemical Engineering, Columbia University, New York, NY 10027, USA
| | - Sergey Kalachikov
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY 10027, USA; (X.W.); (C.T.); (I.M.); (S.K.); (X.L.); (S.K.); (J.J.R.)
- Department of Chemical Engineering, Columbia University, New York, NY 10027, USA
| | - Xiaoxu Li
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY 10027, USA; (X.W.); (C.T.); (I.M.); (S.K.); (X.L.); (S.K.); (J.J.R.)
- Department of Chemical Engineering, Columbia University, New York, NY 10027, USA
| | - Shiv Kumar
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY 10027, USA; (X.W.); (C.T.); (I.M.); (S.K.); (X.L.); (S.K.); (J.J.R.)
- Department of Chemical Engineering, Columbia University, New York, NY 10027, USA
| | - James J. Russo
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY 10027, USA; (X.W.); (C.T.); (I.M.); (S.K.); (X.L.); (S.K.); (J.J.R.)
- Department of Chemical Engineering, Columbia University, New York, NY 10027, USA
| | - Jingyue Ju
- Center for Genome Technology and Biomolecular Engineering, Columbia University, New York, NY 10027, USA; (X.W.); (C.T.); (I.M.); (S.K.); (X.L.); (S.K.); (J.J.R.)
- Department of Chemical Engineering, Columbia University, New York, NY 10027, USA
- Department of Molecular Pharmacology and Therapeutics, Columbia University, New York, NY 10032, USA
- Correspondence:
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16
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Ferrari D, Rubini M, Burns JS. The Potential of Purinergic Signaling to Thwart Viruses Including SARS-CoV-2. Front Immunol 2022; 13:904419. [PMID: 35784277 PMCID: PMC9248768 DOI: 10.3389/fimmu.2022.904419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 05/05/2022] [Indexed: 01/18/2023] Open
Abstract
A long-shared evolutionary history is congruent with the multiple roles played by purinergic signaling in viral infection, replication and host responses that can assist or hinder viral functions. An overview of the involvement of purinergic signaling among a range of viruses is compared and contrasted with what is currently understood for SARS-CoV-2. In particular, we focus on the inflammatory and antiviral responses of infected cells mediated by purinergic receptor activation. Although there is considerable variation in a patient's response to SARS-CoV-2 infection, a principle immediate concern in Coronavirus disease (COVID-19) is the possibility of an aberrant inflammatory activation causing diffuse lung oedema and respiratory failure. We discuss the most promising potential interventions modulating purinergic signaling that may attenuate the more serious repercussions of SARS-CoV-2 infection and aspects of their implementation.
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Affiliation(s)
- Davide Ferrari
- Section of Microbiology and Applied Pathology, University of Ferrara, Ferrara, Italy
- Department of Life Science and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Michele Rubini
- Department of Neuroscience and Rehabilitation, University of Ferrara, Ferrara, Italy
| | - Jorge S. Burns
- Department of Life Science and Biotechnology, University of Ferrara, Ferrara, Italy
- Department of Environmental and Prevention Sciences, University of Ferrara, Ferrara, Italy
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17
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Characterization of Aurintricarboxylic Acid (ATA) Interactions with Plasma Transporter Protein and SARS-CoV-2 Viral Targets: Correlation of Functional Activity and Binding Energetics. LIFE (BASEL, SWITZERLAND) 2022; 12:life12060872. [PMID: 35743905 PMCID: PMC9227171 DOI: 10.3390/life12060872] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/31/2022] [Accepted: 06/02/2022] [Indexed: 02/08/2023]
Abstract
In an effort to identify functional-energetic correlations leading to the development of efficient anti-SARS-CoV-2 therapeutic agents, we have designed synthetic analogs of aurintricarboxylic acid (ATA), a heterogeneous polymeric mixture of structurally related linear homologs known to exhibit a host of biological properties, including antiviral activity. These derivatives are evaluated for their ability to interact with a plasma transporter protein (human serum albumin), eukaryotic (yeast) ribosomes, and a SARS-CoV-2 target, the RNA-dependent RNA polymerase (RdRp). The resultant data are critical for characterizing drug distribution, bioavailability, and effective inhibition of host and viral targets. Promising lead compounds are selected on the basis of their binding energetics which have been characterized and correlated with functional activities as assessed by inhibition of RNA replication and protein synthesis. Our results reveal that the activity of heterogeneous ATA is mimicked by linear compounds of defined molecular weight, with a dichlorohexamer salicylic-acid derivative exhibiting the highest potency. These findings are instrumental for optimizing the design of structurally defined ATA analogs that fulfill the requirements of an antiviral drug with respect to bioavailability, homogeneity, and potency, thereby expanding the arsenal of therapeutic regimens that are currently available to address the urgent need for effective SARS-CoV-2 treatment strategies.
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18
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Deval J, Gurard-Levin ZA. Opportunities and Challenges in Targeting the Proofreading Activity of SARS-CoV-2 Polymerase Complex. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27092918. [PMID: 35566268 PMCID: PMC9103157 DOI: 10.3390/molecules27092918] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 04/29/2022] [Accepted: 04/30/2022] [Indexed: 01/01/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the COVID-19 pandemic. While the development of vaccines and the emergence of antiviral therapeutics is promising, alternative strategies to combat COVID-19 (and potential future pandemics) remain an unmet need. Coronaviruses feature a unique mechanism that may present opportunities for therapeutic intervention: the RNA polymerase complex of coronaviruses is distinct in its ability to proofread and remove mismatched nucleotides during genome replication and transcription. The proofreading activity has been linked to the exonuclease (ExoN) activity of non-structural protein 14 (NSP14). Here, we review the role of NSP14, and other NSPs, in SARS-CoV-2 replication and describe the assays that have been developed to assess the ExoN function. We also review the nucleoside analogs and non-nucleoside inhibitors known to interfere with the proofreading activity of NSP14. Although not yet validated, the potential use of non-nucleoside proofreading inhibitors in combination with chain-terminating nucleosides may be a promising avenue for the development of anti-CoV agents.
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Affiliation(s)
- Jerome Deval
- Aligos Therapeutics, Inc., San Francisco, CA 94080, USA
- Correspondence:
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19
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Caldera-Crespo LA, Paidas MJ, Roy S, Schulman CI, Kenyon NS, Daunert S, Jayakumar AR. Experimental Models of COVID-19. Front Cell Infect Microbiol 2022; 11:792584. [PMID: 35096645 PMCID: PMC8791197 DOI: 10.3389/fcimb.2021.792584] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 11/26/2021] [Indexed: 12/20/2022] Open
Abstract
COVID-19 is the most consequential pandemic of the 21st century. Since the earliest stage of the 2019-2020 epidemic, animal models have been useful in understanding the etiopathogenesis of SARS-CoV-2 infection and rapid development of vaccines/drugs to prevent, treat or eradicate SARS-CoV-2 infection. Early SARS-CoV-1 research using immortalized in-vitro cell lines have aided in understanding different cells and receptors needed for SARS-CoV-2 infection and, due to their ability to be easily manipulated, continue to broaden our understanding of COVID-19 disease in in-vivo models. The scientific community determined animal models as the most useful models which could demonstrate viral infection, replication, transmission, and spectrum of illness as seen in human populations. Until now, there have not been well-described animal models of SARS-CoV-2 infection although transgenic mouse models (i.e. mice with humanized ACE2 receptors with humanized receptors) have been proposed. Additionally, there are only limited facilities (Biosafety level 3 laboratories) available to contribute research to aid in eventually exterminating SARS-CoV-2 infection around the world. This review summarizes the most successful animal models of SARS-CoV-2 infection including studies in Non-Human Primates (NHPs) which were found to be susceptible to infection and transmitted the virus similarly to humans (e.g., Rhesus macaques, Cynomolgus, and African Green Monkeys), and animal models that do not require Biosafety level 3 laboratories (e.g., Mouse Hepatitis Virus models of COVID-19, Ferret model, Syrian Hamster model). Balancing safety, mimicking human COVID-19 and robustness of the animal model, the Murine Hepatitis Virus-1 Murine model currently represents the most optimal model for SARS-CoV-2/COVID19 research. Exploring future animal models will aid researchers/scientists in discovering the mechanisms of SARS-CoV-2 infection and in identifying therapies to prevent or treat COVID-19.
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Affiliation(s)
- Luis A Caldera-Crespo
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Miami Miller School of Medicine, Miami, FL, United States
- St. George's University Graduate Medical Education Program, University Centre Grenada, West Indies, Grenada
| | - Michael J Paidas
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Sabita Roy
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Carl I Schulman
- Department of Surgery, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Norma Sue Kenyon
- Department of Microbiology & Immunology, University of Miami Miller School of Medicine, Miami, FL, United States
- Department of Biomedical Engineering, University of Miami Miller School of Medicine, Miami, FL, United States
- Diabetes Research Institute, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Sylvia Daunert
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, United States
- Dr. JT Macdonald Foundation Biomedical Nanotechnology Institute, University of Miami Miller School of Medicine, Miami, FL, United States
- University of Miami Clinical and Translational Science Institute, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Arumugam R Jayakumar
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Miami Miller School of Medicine, Miami, FL, United States
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20
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Genomic, proteomic and metabolomic profiling of severe acute respiratory syndrome-Coronavirus-2. COMPUTATIONAL APPROACHES FOR NOVEL THERAPEUTIC AND DIAGNOSTIC DESIGNING TO MITIGATE SARS-COV-2 INFECTION 2022. [PMCID: PMC9300679 DOI: 10.1016/b978-0-323-91172-6.00019-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome-Coronavirus-2 (SARS-CoV-2) is one of the worst human health problems faced by humanity in recent centuries. An end to this health crisis relies on our ability to monitor viral transmission dynamics to check spread, develop therapeutics and preventatives for treatment of SARS-CoV-2 infection and understand the pathophysiology of the disease for better management of the patients. Omics technologies have played a crucial part in understanding the different aspects of COVID-19 disease. While whole-genome sequencing of SARS-CoV-2 isolates from across the globe has aided in the development of molecular diagnostic assays and informed about the viral evolution, knowledge of structure and function of viral proteome fueled the development of small molecule and biologicals therapeutics as well as vaccines. Concurrently, metabolomic profiling of samples from COVID-19 patients experiencing a varying level of disease severity has provided a snapshot of the pathophysiology of the disease helping device effective treatment regimen. This chapter deals with genomic, proteomic, and metabolomic profiling of SRAS-CoV-2.
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21
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Riccio AA, Sullivan ED, Copeland WC. Activation of the SARS-CoV-2 NSP14 3'-5' exoribonuclease by NSP10 and response to antiviral inhibitors. J Biol Chem 2021; 298:101518. [PMID: 34942146 PMCID: PMC8685350 DOI: 10.1016/j.jbc.2021.101518] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 12/15/2021] [Accepted: 12/17/2021] [Indexed: 12/22/2022] Open
Abstract
Understanding the core replication complex of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is essential to the development of novel coronavirus-specific antiviral therapeutics. Among the proteins required for faithful replication of the SARS-CoV-2 genome are nonstructural protein 14 (NSP14), a bifunctional enzyme with an N-terminal 3′-to-5′ exoribonuclease (ExoN) and a C-terminal N7-methyltransferase, and its accessory protein, NSP10. The difficulty in producing pure and high quantities of the NSP10/14 complex has hampered the biochemical and structural study of these important proteins. We developed a straightforward protocol for the expression and purification of both NSP10 and NSP14 from Escherichia coli and for the in vitro assembly and purification of a stoichiometric NSP10/14 complex with high yields. Using these methods, we observe that NSP10 provides a 260-fold increase in kcat/Km in the exoribonucleolytic activity of NSP14 and enhances protein stability. We also probed the effect of two small molecules on NSP10/14 activity, remdesivir monophosphate and the methyltransferase inhibitor S-adenosylhomocysteine. Our analysis highlights two important factors for drug development: first, unlike other exonucleases, the monophosphate nucleoside analog intermediate of remdesivir does not inhibit NSP14 activity; and second, S-adenosylhomocysteine modestly activates NSP14 exonuclease activity. In total, our analysis provides insights for future structure–function studies of SARS-CoV-2 replication fidelity for the treatment of coronavirus disease 2019.
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Affiliation(s)
- Amanda A Riccio
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709
| | - Eric D Sullivan
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709
| | - William C Copeland
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709.
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22
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Discovery of SARS-CoV-2 Nsp14 and Nsp16 Methyltransferase Inhibitors by High-Throughput Virtual Screening. Pharmaceuticals (Basel) 2021; 14:ph14121243. [PMID: 34959647 PMCID: PMC8705538 DOI: 10.3390/ph14121243] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 12/17/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) uses mRNA capping to evade the human immune system. The cap formation is performed by the SARS-CoV-2 mRNA cap methyltransferases (MTases) nsp14 and nsp16, which are emerging targets for the development of broad-spectrum antiviral agents. Here, we report results from high-throughput virtual screening against these two enzymes. The docking of seven million commercially available drug-like compounds and S-adenosylmethionine (SAM) co-substrate analogues against both MTases resulted in 80 virtual screening hits (39 against nsp14 and 41 against nsp16), which were purchased and tested using an enzymatic homogeneous time-resolved fluorescent energy transfer (HTRF) assay. Nine compounds showed micromolar inhibition activity (IC50 < 200 μM). The selectivity of the identified inhibitors was evaluated by cross-checking their activity against human glycine N-methyltransferase. The majority of the compounds showed poor selectivity for a specific MTase, no cytotoxic effects, and rather poor cell permeability. Nevertheless, the identified compounds represent good starting points that have the potential to be developed into efficient viral MTase inhibitors.
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23
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Hijikata A, Shionyu C, Nakae S, Shionyu M, Ota M, Kanaya S, Shirai T. Current status of structure-based drug repurposing against COVID-19 by targeting SARS-CoV-2 proteins. Biophys Physicobiol 2021; 18:226-240. [PMID: 34745807 PMCID: PMC8550875 DOI: 10.2142/biophysico.bppb-v18.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 09/30/2021] [Indexed: 01/31/2023] Open
Abstract
More than one and half years have passed, as of August 2021, since the COVID-19 caused by the novel coronavirus named SARS-CoV-2 emerged in 2019. While the recent success of vaccine developments likely reduces the severe cases, there is still a strong requirement of safety and effective therapeutic drugs for overcoming the unprecedented situation. Here we review the recent progress and the status of the drug discovery against COVID-19 with emphasizing a structure-based perspective. Structural data regarding the SARS-CoV-2 proteome has been rapidly accumulated in the Protein Data Bank, and up to 68% of the total amino acid residues encoded in the genome were covered by the structural data. Despite a global effort of in silico and in vitro screenings for drug repurposing, there is only a limited number of drugs had been successfully authorized by drug regulation organizations. Although many approved drugs and natural compounds, which exhibited antiviral activity in vitro, were considered potential drugs against COVID-19, a further multidisciplinary investigation is required for understanding the mechanisms underlying the antiviral effects of the drugs.
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Affiliation(s)
- Atsushi Hijikata
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan
| | - Clara Shionyu
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan
| | - Setsu Nakae
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan
| | - Masafumi Shionyu
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan
| | - Motonori Ota
- Department of Complex Systems Science, Graduate School of Informatics, Nagoya University, Nagoya, Aichi 464-8601, Japan
| | - Shigehiko Kanaya
- Computational Biology Lab. Division of Information Science, Graduate School of Science and Technology, Nara Institute of Science and Technology (NAIST), Ikoma, Nara 630-0192, Japan
| | - Tsuyoshi Shirai
- Faculty of Bioscience, Nagahama Institute of Bio-Science and Technology, Nagahama, Shiga 526-0829, Japan
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24
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KOCABAŞ F, USLU M. The current state of validated small molecules inhibiting SARS-CoV-2 nonstructural proteins. Turk J Biol 2021; 45:469-483. [PMID: 34803448 PMCID: PMC8573838 DOI: 10.3906/biy-2106-42] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 08/06/2021] [Indexed: 11/03/2022] Open
Abstract
The current COVID-19 outbreak has had a profound influence on public health and daily life. Despite all restrictions and vaccination programs, COVID-19 still can lead to fatality due to a lack of COVID-19-specific treatments. A number of studies have demonstrated the feasibility to develop therapeutics by targeting underlying components of the viral proteome. Here we reviewed recently developed and validated small molecule inhibitors of SARS-CoV-2's nonstructural proteins. We described the validation level of identified compounds specific for SARS-CoV-2 in the presence of in vitro and in vivo supporting data. The mechanisms of pharmacological activity, as well as approaches for developing improved SARS-CoV-2 NSP inhibitors have been emphasized.
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Affiliation(s)
- Fatih KOCABAŞ
- Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, İstanbulTurkey
| | - Merve USLU
- Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, İstanbulTurkey
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25
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Canal B, Fujisawa R, McClure AW, Deegan TD, Wu M, Ulferts R, Weissmann F, Drury LS, Bertolin AP, Zeng J, Beale R, Howell M, Labib K, Diffley JF. Identifying SARS-CoV-2 antiviral compounds by screening for small molecule inhibitors of nsp15 endoribonuclease. Biochem J 2021; 478:2465-2479. [PMID: 34198324 PMCID: PMC8286823 DOI: 10.1042/bcj20210199] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/05/2021] [Accepted: 05/07/2021] [Indexed: 02/07/2023]
Abstract
SARS-CoV-2 is responsible for COVID-19, a human disease that has caused over 2 million deaths, stretched health systems to near-breaking point and endangered economies of countries and families around the world. Antiviral treatments to combat COVID-19 are currently lacking. Remdesivir, the only antiviral drug approved for the treatment of COVID-19, can affect disease severity, but better treatments are needed. SARS-CoV-2 encodes 16 non-structural proteins (nsp) that possess different enzymatic activities with important roles in viral genome replication, transcription and host immune evasion. One key aspect of host immune evasion is performed by the uridine-directed endoribonuclease activity of nsp15. Here we describe the expression and purification of nsp15 recombinant protein. We have developed biochemical assays to follow its activity, and we have found evidence for allosteric behaviour. We screened a custom chemical library of over 5000 compounds to identify nsp15 endoribonuclease inhibitors, and we identified and validated NSC95397 as an inhibitor of nsp15 endoribonuclease in vitro. Although NSC95397 did not inhibit SARS-CoV-2 growth in VERO E6 cells, further studies will be required to determine the effect of nsp15 inhibition on host immune evasion.
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Affiliation(s)
- Berta Canal
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Ryo Fujisawa
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Allison W. McClure
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Tom D. Deegan
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - Mary Wu
- High Throughput Screening, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Rachel Ulferts
- Cell Biology of Infection Laboratory, the Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Florian Weissmann
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Lucy S. Drury
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Agustina P. Bertolin
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Jingkun Zeng
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Rupert Beale
- Cell Biology of Infection Laboratory, the Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Michael Howell
- High Throughput Screening, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
| | - Karim Labib
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, U.K
| | - John F.X. Diffley
- Chromosome Replication Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, U.K
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26
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Hay RT. An all-out assault on SARS-CoV-2 replication. Biochem J 2021; 478:2399-2403. [PMID: 34198321 PMCID: PMC8286832 DOI: 10.1042/bcj20210256] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/10/2021] [Accepted: 06/10/2021] [Indexed: 01/18/2023]
Abstract
The coronavirus pandemic has had a huge impact on public health with over 165 million people infected, 3.4 million deaths and a hugely deleterious effect on most economies. While vaccination effectively protects against the disease it is likely that viruses will evolve that can replicate in hosts immunised with the present vaccines. Thus, there is a great unmet need for effective antivirals that can block the development of serious disease in infected patients. The seven papers published in this issue of the Biochemical Journal address this need by expressing and purifying components required for viral replication, developing biochemical assays for these components and using the assays to screen a library of pre-existing pharmaceuticals for drugs that inhibited the target in vitro and inhibited viral replication in cell culture. The candidate drugs obtained are potential antivirals that may protect against SARS-CoV-2 infection. While not all the antiviral candidates will make it through to the clinic, they will be useful tool compounds and can act as the starting point for further drug discovery programmes.
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Affiliation(s)
- Ronald T. Hay
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, U.K
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27
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Identifying SARS-CoV-2 antiviral compounds by screening for small molecule inhibitors of nsp12/7/8 RNA-dependent RNA polymerase. Biochem J 2021; 478:2425-2443. [PMID: 34198323 PMCID: PMC8286815 DOI: 10.1042/bcj20210200] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 05/05/2021] [Accepted: 05/07/2021] [Indexed: 02/07/2023]
Abstract
The coronavirus disease 2019 (COVID-19) global pandemic has turned into the largest public health and economic crisis in recent history impacting virtually all sectors of society. There is a need for effective therapeutics to battle the ongoing pandemic. Repurposing existing drugs with known pharmacological safety profiles is a fast and cost-effective approach to identify novel treatments. The COVID-19 etiologic agent is the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a single-stranded positive-sense RNA virus. Coronaviruses rely on the enzymatic activity of the replication–transcription complex (RTC) to multiply inside host cells. The RTC core catalytic component is the RNA-dependent RNA polymerase (RdRp) holoenzyme. The RdRp is one of the key druggable targets for CoVs due to its essential role in viral replication, high degree of sequence and structural conservation and the lack of homologues in human cells. Here, we have expressed, purified and biochemically characterised active SARS-CoV-2 RdRp complexes. We developed a novel fluorescence resonance energy transfer-based strand displacement assay for monitoring SARS-CoV-2 RdRp activity suitable for a high-throughput format. As part of a larger research project to identify inhibitors for all the enzymatic activities encoded by SARS-CoV-2, we used this assay to screen a custom chemical library of over 5000 approved and investigational compounds for novel SARS-CoV-2 RdRp inhibitors. We identified three novel compounds (GSK-650394, C646 and BH3I-1) and confirmed suramin and suramin-like compounds as in vitro SARS-CoV-2 RdRp activity inhibitors. We also characterised the antiviral efficacy of these drugs in cell-based assays that we developed to monitor SARS-CoV-2 growth.
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28
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Identifying SARS-CoV-2 antiviral compounds by screening for small molecule inhibitors of nsp13 helicase. Biochem J 2021; 478:2405-2423. [PMID: 34198322 PMCID: PMC8286831 DOI: 10.1042/bcj20210201] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/05/2021] [Accepted: 05/10/2021] [Indexed: 12/16/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic, which is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a global public health challenge. While the efficacy of vaccines against emerging and future virus variants remains unclear, there is a need for therapeutics. Repurposing existing drugs represents a promising and potentially rapid opportunity to find novel antivirals against SARS-CoV-2. The virus encodes at least nine enzymatic activities that are potential drug targets. Here, we have expressed, purified and developed enzymatic assays for SARS-CoV-2 nsp13 helicase, a viral replication protein that is essential for the coronavirus life cycle. We screened a custom chemical library of over 5000 previously characterized pharmaceuticals for nsp13 inhibitors using a fluorescence resonance energy transfer-based high-throughput screening approach. From this, we have identified FPA-124 and several suramin-related compounds as novel inhibitors of nsp13 helicase activity in vitro. We describe the efficacy of these drugs using assays we developed to monitor SARS-CoV-2 growth in Vero E6 cells.
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