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Li A, Zhao K, Duan Y, Zhang B, Zheng Y, Zhu C, Chen Q, Liu WB, Hui L, Xia Y, Cheng X. SARS-CoV-2 nsp13 suppresses hepatitis B virus replication by targeting cccDNA transcription. J Virol 2024:e0104224. [PMID: 39373477 DOI: 10.1128/jvi.01042-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Accepted: 09/09/2024] [Indexed: 10/08/2024] Open
Abstract
SARS-CoV-2 nonstructural protein 13 (nsp13) has been shown to selectively suppress the transcription of episomal DNA while sparing chromosomal DNA. Hepatitis B Virus (HBV) harbors covalently closed circular DNA (cccDNA), a form of viral episomal DNA found within infected hepatocyte nuclei. The persistence of cccDNA is the major cause of chronic HBV infection. In this study, we investigated the impact of SARS-CoV-2 nsp13 on HBV replication, particularly in the context of cccDNA. Our findings demonstrate that nsp13 effectively hinders HBV replication by suppressing the transcription of HBV cccDNA, both in vitro and in vivo. Additionally, we observed that SARS-CoV-2 nsp13 binds to HBV cccDNA and its NTPase and helicase activities contribute significantly to inhibiting HBV replication. Furthermore, our screening identified the interaction between nsp13 and structural maintenance of chromosomes 4, opening new avenues for future mechanistic inquiries. This study presents the evidence suggesting the potential utilization of SARS-CoV-2 nsp13 as a strategy to impede HBV replication by specifically targeting cccDNA. These findings provide a proof of concept for exploring nsp13 as a prospective approach in combating HBV infection. IMPORTANCE To effectively combat hepatitis B virus (HBV), it is imperative to develop potent antiviral medications targeting covalently closed circular DNA (cccDNA). Our investigation aimed to assess the impact of SARS-CoV-2 nsp13 on HBV replication across diverse HBV models, confirming its ability to significantly reduce several HBV replication markers. Additionally, our identification of the interaction between nsp13 and SMC4 opens the door for further mechanistic exploration. This marks a paradigm shift in our approach to HBV antiviral therapy, introducing an entirely novel perspective. Our findings propose a novel strategy for developing anti-HBV drugs that specifically target HBV cccDNA.
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Affiliation(s)
- Aixin Li
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Medical School, Wuhan University, Wuhan, China
- School of Medical Laboratory, Shandong Second Medical University, Weifang, China
| | - Kaitao Zhao
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Yurong Duan
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Bei Zhang
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Medical School, Wuhan University, Wuhan, China
| | - Yingcheng Zheng
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Medical School, Wuhan University, Wuhan, China
- School of Life Sciences, Hubei University, Wuhan, China
| | - Chengliang Zhu
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, China
| | - Qiongrong Chen
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan, Chile
| | - Wen-Bo Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, Hubei, China
| | - Lixia Hui
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Medical School, Wuhan University, Wuhan, China
- School of Medical Laboratory, Shandong Second Medical University, Weifang, China
| | - Yuchen Xia
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Medical School, Wuhan University, Wuhan, China
- Hubei Jiangxia Laboratory, Wuhan, China
- Pingyuan Laboratory, Henan, China
| | - Xiaoming Cheng
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, TaiKang Medical School, Wuhan University, Wuhan, China
- Department of Pathology, Zhongnan Hospital of Wuhan University, Wuhan, Chile
- Hubei Jiangxia Laboratory, Wuhan, China
- Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Diseases, Wuhan, China
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2
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Cui W, Duan Y, Gao Y, Wang W, Yang H. Structural review of SARS-CoV-2 antiviral targets. Structure 2024; 32:1301-1321. [PMID: 39241763 DOI: 10.1016/j.str.2024.08.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 07/25/2024] [Accepted: 08/06/2024] [Indexed: 09/09/2024]
Abstract
The coronavirus disease 2019 (COVID-19), the disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), represents the most disastrous infectious disease pandemic of the past century. As a member of the Betacoronavirus genus, the SARS-CoV-2 genome encodes a total of 29 proteins. The spike protein, RNA-dependent RNA polymerase, and proteases play crucial roles in the virus replication process and are promising targets for drug development. In recent years, structural studies of these viral proteins and of their complexes with antibodies and inhibitors have provided valuable insights into their functions and laid a solid foundation for drug development. In this review, we summarize the structural features of these proteins and discuss recent progress in research regarding therapeutic development, highlighting mechanistically representative molecules and those that have already been approved or are under clinical investigation.
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Affiliation(s)
- Wen Cui
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, China
| | - Yinkai Duan
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Yan Gao
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Clinical Research and Trial Center, Shanghai 201203, China
| | - Wei Wang
- College of Pharmacy, Chongqing Medical University, Chongqing 400016, China.
| | - Haitao Yang
- Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China; Shanghai Clinical Research and Trial Center, Shanghai 201203, China.
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3
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Grimes SL, Denison MR. The Coronavirus helicase in replication. Virus Res 2024; 346:199401. [PMID: 38796132 PMCID: PMC11177069 DOI: 10.1016/j.virusres.2024.199401] [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: 11/30/2023] [Revised: 04/16/2024] [Accepted: 05/17/2024] [Indexed: 05/28/2024]
Abstract
The coronavirus nonstructural protein (nsp) 13 encodes an RNA helicase (nsp13-HEL) with multiple enzymatic functions, including unwinding and nucleoside phosphatase (NTPase) activities. Attempts for enzymatic inactivation have defined the nsp13-HEL as a critical enzyme for viral replication and a high-priority target for antiviral development. Helicases have been shown to play numerous roles beyond their canonical ATPase and unwinding activities, though these functions are just beginning to be explored in coronavirus biology. Recent genetic and biochemical studies, as well as work in structurally-related helicases, have provided evidence that supports new hypotheses for the helicase's potential role in coronavirus replication. Here, we review several aspects of the coronavirus nsp13-HEL, including its reported and proposed functions in viral replication and highlight fundamental areas of research that may aid the development of helicase inhibitors.
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Affiliation(s)
- Samantha L Grimes
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Mark R Denison
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA.
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4
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Caohuy H, Eidelman O, Chen T, Mungunsukh O, Yang Q, Walton NI, Pollard BS, Khanal S, Hentschel S, Florez C, Herbert AS, Pollard HB. Inflammation in the COVID-19 airway is due to inhibition of CFTR signaling by the SARS-CoV-2 spike protein. Sci Rep 2024; 14:16895. [PMID: 39043712 PMCID: PMC11266487 DOI: 10.1038/s41598-024-66473-4] [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: 12/15/2023] [Accepted: 07/01/2024] [Indexed: 07/25/2024] Open
Abstract
SARS-CoV-2-contributes to sickness and death in COVID-19 patients partly by inducing a hyper-proinflammatory immune response in the host airway. This hyper-proinflammatory state involves activation of signaling by NFκB, and unexpectedly, ENaC, the epithelial sodium channel. Post-infection inflammation may also contribute to "Long COVID"/PASC. Enhanced signaling by NFκB and ENaC also marks the airway of patients suffering from cystic fibrosis, a life-limiting proinflammatory genetic disease due to inactivating mutations in the CFTR gene. We therefore hypothesized that inflammation in the COVID-19 airway might similarly be due to inhibition of CFTR signaling by SARS-CoV-2 spike protein, and therefore activation of both NFκB and ENaC signaling. We used western blot and electrophysiological techniques, and an organoid model of normal airway epithelia, differentiated on an air-liquid-interface (ALI). We found that CFTR protein expression and CFTR cAMP-activated chloride channel activity were lost when the model epithelium was exposed to SARS-CoV-2 spike proteins. As hypothesized, the absence of CFTR led to activation of both TNFα/NFκB signaling and α and γ ENaC. We had previously shown that the cardiac glycoside drugs digoxin, digitoxin and ouabain blocked interaction of spike protein and ACE2. Consistently, addition of 30 nM concentrations of the cardiac glycoside drugs, prevented loss of both CFTR protein and CFTR channel activity. ACE2 and CFTR were found to co-immunoprecipitate in both basal cells and differentiated epithelia. Thus spike-dependent CFTR loss might involve ACE2 as a bridge between Spike and CFTR. In addition, spike exposure to the epithelia resulted in failure of endosomal recycling to return CFTR to the plasma membrane. Thus, failure of CFTR recovery from endosomal recycling might be a mechanism for spike-dependent loss of CFTR. Finally, we found that authentic SARS-CoV-2 virus infection induced loss of CFTR protein, which was rescued by the cardiac glycoside drugs digitoxin and ouabain. Based on experiments with this organoid model of small airway epithelia, and comparisons with 16HBE14o- and other cell types expressing normal CFTR, we predict that inflammation in the COVID-19 airway may be mediated by inhibition of CFTR signaling by the SARS-CoV-2 spike protein, thus inducing a cystic fibrosis-like clinical phenotype. To our knowledge this is the first time COVID-19 airway inflammation has been experimentally traced in normal subjects to a contribution from SARS-CoV-2 spike-dependent inhibition of CFTR signaling.
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Affiliation(s)
- Hung Caohuy
- Department of Anatomy, Physiology and Genetics, Uniformed Services University School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
- Collaborative Health Initiative Research Program (CHIRP), Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
- Consortium for Health and Military Performance (CHAMP), Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
| | - Ofer Eidelman
- Department of Anatomy, Physiology and Genetics, Uniformed Services University School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
- Collaborative Health Initiative Research Program (CHIRP), Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
| | - Tinghua Chen
- Department of Anatomy, Physiology and Genetics, Uniformed Services University School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
- Collaborative Health Initiative Research Program (CHIRP), Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
- Consortium for Health and Military Performance (CHAMP), Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
| | - Ognoon Mungunsukh
- Department of Anatomy, Physiology and Genetics, Uniformed Services University School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
- Consortium for Health and Military Performance (CHAMP), Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
- Center for Military Precision Health, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
| | - Qingfeng Yang
- Department of Anatomy, Physiology and Genetics, Uniformed Services University School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
- Center for the Study of Traumatic Stress (CSTS), and Department of Psychiatry, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
| | - Nathan I Walton
- Department of Anatomy, Physiology and Genetics, Uniformed Services University School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
- Collaborative Health Initiative Research Program (CHIRP), Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
- Consortium for Health and Military Performance (CHAMP), Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA
| | | | - Sara Khanal
- Virology Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD, 21702, USA
- The Geneva Foundation, Tacoma, WA, 98402, USA
| | - Shannon Hentschel
- Virology Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD, 21702, USA
- Cherokee Nation Assurance, Catoosa, OK, 74015, USA
| | - Catalina Florez
- Virology Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD, 21702, USA
- The Geneva Foundation, Tacoma, WA, 98402, USA
| | - Andrew S Herbert
- Virology Division, United States Army Medical Research Institute of Infectious Diseases (USAMRIID), Fort Detrick, Frederick, MD, 21702, USA
| | - Harvey B Pollard
- Department of Anatomy, Physiology and Genetics, Uniformed Services University School of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA.
- Collaborative Health Initiative Research Program (CHIRP), Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA.
- Consortium for Health and Military Performance (CHAMP), Uniformed Services University of the Health Sciences, Bethesda, MD, 20814, USA.
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5
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Sales AH, Fu I, Durandin A, Ciervo S, Lupoli TJ, Shafirovich V, Broyde S, Geacintov NE. Variable Inhibition of DNA Unwinding Rates Catalyzed by the SARS-CoV-2 Helicase Nsp13 by Structurally Distinct Single DNA Lesions. Int J Mol Sci 2024; 25:7930. [PMID: 39063172 PMCID: PMC11276626 DOI: 10.3390/ijms25147930] [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: 05/23/2024] [Revised: 07/09/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
The SARS-CoV-2 helicase, non-structural protein 13 (Nsp13), plays an essential role in viral replication, translocating in the 5' → 3' direction as it unwinds double-stranded RNA/DNA. We investigated the impact of structurally distinct DNA lesions on DNA unwinding catalyzed by Nsp13. The selected lesions include two benzo[a]pyrene (B[a]P)-derived dG adducts, the UV-induced cyclobutane pyrimidine dimer (CPD), and the pyrimidine (6-4) pyrimidone (6-4PP) photolesion. The experimentally observed unwinding rate constants (kobs) and processivities (P) were examined. Relative to undamaged DNA, the kobs values were diminished by factors of up to ~15 for B[a]P adducts but only by factors of ~2-5 for photolesions. A minor-groove-oriented B[a]P adduct showed the smallest impact on P, which decreased by ~11% compared to unmodified DNA, while an intercalated one reduced P by ~67%. However, the photolesions showed a greater impact on the processivities; notably, the CPD, with the highest kobs value, exhibited the lowest P, which was reduced by ~90%. Our findings thus show that DNA unwinding efficiencies are lesion-dependent and most strongly inhibited by the CPD, leading to the conclusion that processivity is a better measure of DNA lesions' inhibitory effects than unwinding rate constants.
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Affiliation(s)
- Ana H. Sales
- Chemistry Department, New York University, 31 Washington Place, New York, NY 10003, USA; (A.H.S.); (A.D.); (S.C.); (T.J.L.); (V.S.)
| | - Iwen Fu
- Biology Department, New York University, 24 Waverly Place, New York, NY 10003, USA; (I.F.); (S.B.)
| | - Alexander Durandin
- Chemistry Department, New York University, 31 Washington Place, New York, NY 10003, USA; (A.H.S.); (A.D.); (S.C.); (T.J.L.); (V.S.)
| | - Sam Ciervo
- Chemistry Department, New York University, 31 Washington Place, New York, NY 10003, USA; (A.H.S.); (A.D.); (S.C.); (T.J.L.); (V.S.)
| | - Tania J. Lupoli
- Chemistry Department, New York University, 31 Washington Place, New York, NY 10003, USA; (A.H.S.); (A.D.); (S.C.); (T.J.L.); (V.S.)
| | - Vladimir Shafirovich
- Chemistry Department, New York University, 31 Washington Place, New York, NY 10003, USA; (A.H.S.); (A.D.); (S.C.); (T.J.L.); (V.S.)
| | - Suse Broyde
- Biology Department, New York University, 24 Waverly Place, New York, NY 10003, USA; (I.F.); (S.B.)
| | - Nicholas E. Geacintov
- Chemistry Department, New York University, 31 Washington Place, New York, NY 10003, USA; (A.H.S.); (A.D.); (S.C.); (T.J.L.); (V.S.)
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6
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Abstract
Coronavirus Disease-19 (COVID-19) pandemic is caused by SARS-CoV-2 that has infected more than 600 million people and killed more than 6 million people worldwide. This infection affects mainly certain groups of people that have high susceptibility to present severe COVID-19 due to comorbidities. Moreover, the long-COVID-19 comprises a series of symptoms that may remain in some patients for months after infection that further compromises their health. Thus, since this pandemic is profoundly affecting health, economy, and social life of societies, a deeper understanding of viral replication cycle could help to envisage novel therapeutic alternatives that limit or stop COVID-19. Several findings have unexpectedly discovered that mitochondria play a critical role in SARS-CoV-2 cell infection. Indeed, it has been suggested that this organelle could be the origin of its replication niches, the double membrane vesicles (DMV). In this regard, mitochondria derived vesicles (MDV), involved in mitochondria quality control, discovered almost 15 years ago, comprise a subpopulation characterized by a double membrane. MDV shedding is induced by mitochondrial stress, and it has a fast assembly dynamic, reason that perhaps has precluded their identification in electron microscopy or tomography studies. These and other features of MDV together with recent SARS-CoV-2 protein interactome and other findings link SARS-CoV-2 to mitochondria and support that these vesicles are the precursors of SARS-CoV-2 induced DMV. In this work, the morphological, biochemical, molecular, and cellular evidence that supports this hypothesis is reviewed and integrated into the current model of SARS-CoV-2 cell infection. In this scheme, some relevant questions are raised as pending topics for research that would help in the near future to test this hypothesis. The intention of this work is to provide a novel framework that could open new possibilities to tackle SARS-CoV-2 pandemic through mitochondria and DMV targeted therapies.
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Affiliation(s)
- Pavel Montes de Oca-B
- Neurociencia Cognitiva, Instituto de Fisiologia-UNAM, CDMX, CDMX, 04510, Mexico
- Unidad de Neurobiologia Dinamica, Instituto Nacional de Neurologia y Neurocirugia, CDMX, CDMX, 14269, Mexico
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7
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Li CW, Chao TL, Lai CL, Lin CC, Pan MYC, Cheng CL, Kuo CJ, Wang LHC, Chang SY, Liang PH. Systematic Studies on the Anti-SARS-CoV-2 Mechanisms of Tea Polyphenol-Related Natural Products. ACS OMEGA 2024; 9:23984-23997. [PMID: 38854515 PMCID: PMC11154727 DOI: 10.1021/acsomega.4c02392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 04/22/2024] [Accepted: 05/09/2024] [Indexed: 06/11/2024]
Abstract
The causative pathogen of COVID-19, severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2), utilizes the receptor-binding domain (RBD) of the spike protein to bind to human receptor angiotensin-converting enzyme 2 (ACE2). Further cleavage of spike by human proteases furin, TMPRSS2, and/or cathepsin L facilitates viral entry into the host cells for replication, where the maturation of polyproteins by 3C-like protease (3CLpro) and papain-like protease (PLpro) yields functional nonstructural proteins (NSPs) such as RNA-dependent RNA polymerase (RdRp) to synthesize mRNA of structural proteins. By testing the tea polyphenol-related natural products through various assays, we found that the active antivirals prevented SARS-CoV-2 entry by blocking the RBD/ACE2 interaction and inhibiting the relevant human proteases, although some also inhibited the viral enzymes essential for replication. Due to their multitargeting properties, these compounds were often misinterpreted for their antiviral mechanisms. In this study, we provide a systematic protocol to check and clarify their anti-SARS-CoV-2 mechanisms, which should be applicable for all of the antivirals.
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Affiliation(s)
- Chen-Wei Li
- Institute
of Biochemical Sciences, National Taiwan
University, Taipei 10617, Taiwan
| | - Tai-Ling Chao
- Department
of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University, Taipei 10048, Taiwan
| | - Chin-Lan Lai
- Institute
of Biochemical Sciences, National Taiwan
University, Taipei 10617, Taiwan
| | - Cheng-Chin Lin
- Institute
of Biochemical Sciences, National Taiwan
University, Taipei 10617, Taiwan
| | - Max Yu-Chen Pan
- Institute
of Molecular and Cellular Biology, National
Tsing Hua University, Hsinchu 30013, Taiwan
| | - Chieh-Ling Cheng
- Institute
of Biochemical Sciences, National Taiwan
University, Taipei 10617, Taiwan
| | - Chih-Jung Kuo
- Department
of Veterinary Medicine, National Chung Hsing
University, Taichung 40227, Taiwan
| | - Lily Hui-Ching Wang
- Institute
of Molecular and Cellular Biology, National
Tsing Hua University, Hsinchu 30013, Taiwan
| | - Sui-Yuan Chang
- Department
of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University, Taipei 10048, Taiwan
- Department
of Laboratory Medicine, National Taiwan
University Hospital, Taipei 10002, Taiwan
| | - Po-Huang Liang
- Institute
of Biological Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Institute
of Biochemical Sciences, National Taiwan
University, Taipei 10617, Taiwan
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8
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Chen S, Jiang Z, Li Q, Pan W, Chen Y, Liu J. Viral RNA capping: Mechanisms and antiviral therapy. J Med Virol 2024; 96:e29622. [PMID: 38682614 DOI: 10.1002/jmv.29622] [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: 12/19/2023] [Revised: 03/25/2024] [Accepted: 04/11/2024] [Indexed: 05/01/2024]
Abstract
RNA capping is an essential trigger for protein translation in eukaryotic cells. Many viruses have evolved various strategies for initiating the translation of viral genes and generating progeny virions in infected cells via synthesizing cap structure or stealing the RNA cap from nascent host messenger ribonucleotide acid (mRNA). In addition to protein translation, a new understanding of the role of the RNA cap in antiviral innate immunity has advanced the field of mRNA synthesis in vitro and therapeutic applications. Recent studies on these viral RNA capping systems have revealed startlingly diverse ways and molecular machinery. A comprehensive understanding of how viruses accomplish the RNA capping in infected cells is pivotal for designing effective broad-spectrum antiviral therapies. Here we systematically review the contemporary insights into the RNA-capping mechanisms employed by viruses causing human and animal infectious diseases, while also highlighting its impact on host antiviral innate immune response. The therapeutic applications of targeting RNA capping against viral infections and the development of RNA-capping inhibitors are also summarized.
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Affiliation(s)
- Saini Chen
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Zhimin Jiang
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Qiuchen Li
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Wenliang Pan
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yu Chen
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jinhua Liu
- National Key Laboratory of Veterinary Public Health and Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Key Laboratory for Prevention and Control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, College of Veterinary Medicine, China Agricultural University, Beijing, China
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9
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Kuzikov M, Reinshagen J, Wycisk K, Corona A, Esposito F, Malune P, Manelfi C, Iaconis D, Beccari A, Tramontano E, Nowotny M, Windshügel B, Gribbon P, Zaliani A. Drug repurposing screen to identify inhibitors of the RNA polymerase (nsp12) and helicase (nsp13) from SARS-CoV-2 replication and transcription complex. Virus Res 2024; 343:199356. [PMID: 38490582 PMCID: PMC10958470 DOI: 10.1016/j.virusres.2024.199356] [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: 08/28/2023] [Revised: 02/26/2024] [Accepted: 03/13/2024] [Indexed: 03/17/2024]
Abstract
Coronaviruses contain one of the largest genomes among the RNA viruses, coding for 14-16 non-structural proteins (nsp) that are involved in proteolytic processing, genome replication and transcription, and four structural proteins that build the core of the mature virion. Due to conservation across coronaviruses, nsps form a group of promising drug targets as their inhibition directly affects viral replication and, therefore, progression of infection. A minimal but fully functional replication and transcription complex was shown to be formed by one RNA-dependent RNA polymerase (nsp12), one nsp7, two nsp8 accessory subunits, and two helicase (nsp13) enzymes. Our approach involved, targeting nsp12 and nsp13 to allow multiple starting point to interfere with virus infection progression. Here we report a combined in-vitro repurposing screening approach, identifying new and confirming reported SARS-CoV-2 nsp12 and nsp13 inhibitors.
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Affiliation(s)
- Maria Kuzikov
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP) and Fraunhofer Cluster of Excellence for Immune mediated diseases (CIMD), Schnackenburgallee 114, 22525 Hamburg, and Theodor Stern Kai 7, 60590 Frankfurt, Germany; Constructor University, School of Science, Campus Ring 1, 28759 Bremen, Germany.
| | - Jeanette Reinshagen
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP) and Fraunhofer Cluster of Excellence for Immune mediated diseases (CIMD), Schnackenburgallee 114, 22525 Hamburg, and Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Krzysztof Wycisk
- Laboratory of Protein Structure - International Institute of Molecular and Cell Biology, 4 Ks. Trojdena Street, 02-109 Warsaw, Poland
| | - Angela Corona
- Dipartimento di Scienze della vita e dell'ambiente, Cittadella Universitaria di Monserrato, SS-554, Monserrato, Cagliari, Italy
| | - Francesca Esposito
- Dipartimento di Scienze della vita e dell'ambiente, Cittadella Universitaria di Monserrato, SS-554, Monserrato, Cagliari, Italy
| | - Paolo Malune
- Dipartimento di Scienze della vita e dell'ambiente, Cittadella Universitaria di Monserrato, SS-554, Monserrato, Cagliari, Italy
| | - Candida Manelfi
- EXSCALATE, Dompé farmaceutici S.p.A., Via Tommaso De Amicis, 95, Napoli, 80131, Italy
| | - Daniela Iaconis
- EXSCALATE, Dompé farmaceutici S.p.A., Via Tommaso De Amicis, 95, Napoli, 80131, Italy
| | - Andrea Beccari
- EXSCALATE, Dompé farmaceutici S.p.A., Via Tommaso De Amicis, 95, Napoli, 80131, Italy
| | - Enzo Tramontano
- Dipartimento di Scienze della vita e dell'ambiente, Cittadella Universitaria di Monserrato, SS-554, Monserrato, Cagliari, Italy
| | - Marcin Nowotny
- Laboratory of Protein Structure - International Institute of Molecular and Cell Biology, 4 Ks. Trojdena Street, 02-109 Warsaw, Poland
| | - Björn Windshügel
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP) and Fraunhofer Cluster of Excellence for Immune mediated diseases (CIMD), Schnackenburgallee 114, 22525 Hamburg, and Theodor Stern Kai 7, 60590 Frankfurt, Germany; Constructor University, School of Science, Campus Ring 1, 28759 Bremen, Germany
| | - Philip Gribbon
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP) and Fraunhofer Cluster of Excellence for Immune mediated diseases (CIMD), Schnackenburgallee 114, 22525 Hamburg, and Theodor Stern Kai 7, 60590 Frankfurt, Germany
| | - Andrea Zaliani
- Fraunhofer Institute for Translational Medicine and Pharmacology (ITMP) and Fraunhofer Cluster of Excellence for Immune mediated diseases (CIMD), Schnackenburgallee 114, 22525 Hamburg, and Theodor Stern Kai 7, 60590 Frankfurt, Germany
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10
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Inniss NL, Rzhetskaya M, Ling-Hu T, Lorenzo-Redondo R, Bachta KE, Satchell KJF, Hultquist JF. Activity and inhibition of the SARS-CoV-2 Omicron nsp13 R392C variant using RNA duplex unwinding assays. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:100145. [PMID: 38301954 PMCID: PMC11160173 DOI: 10.1016/j.slasd.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Accepted: 01/29/2024] [Indexed: 02/03/2024]
Abstract
SARS-CoV-2 nsp13 helicase is an essential enzyme for viral replication and a promising target for antiviral drug development. This study compares the double-stranded RNA (dsRNA) unwinding activity of nsp13 and the Omicron nsp13R392C variant, which is predominant in currently circulating lineages. Using in vitro gel- and fluorescence-based assays, we found that both nsp13 and nsp13R392C have dsRNA unwinding activity with equivalent kinetics. Furthermore, the R392C mutation had no effect on the efficiency of the nsp13-specific helicase inhibitor SSYA10-001. We additionally confirmed the activity of several other helicase inhibitors against nsp13, including punicalagin that inhibited dsRNA unwinding at nanomolar concentrations. Overall, this study reveals the utility of using dsRNA unwinding assays to screen small molecules for antiviral activity against nsp13 and the Omicron nsp13R392C variant. Continual monitoring of newly emergent variants will be essential for considering resistance profiles of lead compounds as they are advanced towards next-generation therapeutic development.
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Affiliation(s)
- Nicole L Inniss
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA; Center for Structural Biology of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Margarita Rzhetskaya
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA; Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA; Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Ted Ling-Hu
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA; Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA; Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Ramon Lorenzo-Redondo
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA; Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Kelly E Bachta
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA; Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA
| | - Karla J F Satchell
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA; Center for Structural Biology of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA; Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA.
| | - Judd F Hultquist
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA; Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA; Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL 60611 USA.
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11
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Vijay A, Sreyas Adury VS, Mukherjee A. Targeting RdRp of SARS-CoV-2 with De Novo Molecule Generation. ACS APPLIED BIO MATERIALS 2024; 7:609-616. [PMID: 37566736 DOI: 10.1021/acsabm.3c00339] [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] [Indexed: 08/13/2023]
Abstract
Viruses are known for their extremely high mutation rates, allowing them to evade both the human immune system and many forms of standard medicine. Despite this, the RNA dependent RNA polymerase (RdRp) of the RNA viruses has been largely conserved, and any significant mutation of this protein is unlikely. The recent COVID-19 pandemic presents a need for therapeutics. We have designed a de novo drug design algorithm that generates strong binding ligands from scratch, based on only the structure of the target protein's receptor. In this paper, we applied our method to target SARS-CoV-2 RdRp and generated several de novo molecules. We then chose some drug molecules based on the structural similarity to some of our strongest binding de novo molecules. Subsequently, we showed, using rigorous all-atom explicit-water free energy calculations in near-microsecond time scales using state-of-the-art well-tempered metadynamics simulations, that some of our de novo generated ligands bind more strongly to RdRp than the recent FDA approved drug remdesivir in its active form, remdesivir triphosphate (RTP). We elucidated the binding mechanism for some of the top binders and compared it with RTP. We believe that this work will be useful both by presenting lead structures for RdRp inhibition and by delivering key insights into the residues of the protein potentially involved in the binding/unbinding of these small molecule drugs, leading to more targeted studies in the future.
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Affiliation(s)
- Amal Vijay
- Department of Chemistry, Indian Institute of Science Education and Research, Pune 411008, India
| | | | - Arnab Mukherjee
- Department of Chemistry, Indian Institute of Science Education and Research, Pune 411008, India
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12
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He M, Cao L, Liu L, Jin X, Zheng B, Liu X, Zhuang J, Zhang F, Yang Z, Ji Y, Xu T, Huang S, Chen J, Xie L, Li K, Hou P, Pan J, Guo D, Li C. Reconstitution of RNA cap methylation reveals different features of SARS-CoV-2 and SARS-CoV methyltransferases. J Med Virol 2024; 96:e29411. [PMID: 38285434 DOI: 10.1002/jmv.29411] [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: 10/09/2023] [Revised: 12/06/2023] [Accepted: 12/11/2023] [Indexed: 01/30/2024]
Abstract
Cap RNA methylations play important roles in the replication, evasion of host RNA sensor recognition, and pathogenesis. Coronaviruses possess both guanine N7- and 2'-O-ribose methyltransferases (N7-MTase and 2'-O-MTase) encoded by nonstructural protein (nsp) 14 and nsp16/10 complex, respectively. In this study, we reconstituted the two-step RNA methylations of N7-MTase and 2'-O-MTase of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in vitro and demonstrated its common and different features in comparison with that of SARS-CoV. We revealed that the nsp16/10 2'-O-MTase of SARS-CoV-2 has a broader substrate selectivity than the counterpart of SARS-CoV and can accommodate both unmethylated and uncapped RNA substrates in a sequence-independent manner. Most intriguingly, the substrate selectivity of nsp16/10 complex is not determined by the apoenzyme of nsp16 MTase but by its cofactor nsp10. These results provide insight into the unique features of SARS-CoV-2 MTases and may help develop strategies to precisely intervene in the methylation pathway and pathogenesis of SARS-CoV-2.
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Affiliation(s)
- Miao He
- MOE Key Laboratory of Tropical Disease Control, Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Liu Cao
- MOE Key Laboratory of Tropical Disease Control, Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Lihong Liu
- Guangzhou Laboratory, Guangzhou International Bio-Island, Guangzhou, Guangdong, China
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xu Jin
- MOE Key Laboratory of Tropical Disease Control, Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Birong Zheng
- MOE Key Laboratory of Tropical Disease Control, Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
- Guangzhou Laboratory, Guangzhou International Bio-Island, Guangzhou, Guangdong, China
| | - Xue Liu
- MOE Key Laboratory of Tropical Disease Control, Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Jiaxin Zhuang
- MOE Key Laboratory of Tropical Disease Control, Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Fushi Zhang
- MOE Key Laboratory of Tropical Disease Control, Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Zixiao Yang
- MOE Key Laboratory of Tropical Disease Control, Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
- Guangzhou Laboratory, Guangzhou International Bio-Island, Guangzhou, Guangdong, China
| | - Yanxi Ji
- MOE Key Laboratory of Tropical Disease Control, Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Tiefeng Xu
- MOE Key Laboratory of Tropical Disease Control, Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
- Guangzhou Laboratory, Guangzhou International Bio-Island, Guangzhou, Guangdong, China
| | - Siyao Huang
- MOE Key Laboratory of Tropical Disease Control, Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
- Guangzhou Laboratory, Guangzhou International Bio-Island, Guangzhou, Guangdong, China
| | - Junhai Chen
- MOE Key Laboratory of Tropical Disease Control, Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Luyang Xie
- MOE Key Laboratory of Tropical Disease Control, Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Kun Li
- MOE Key Laboratory of Tropical Disease Control, Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
- Guangzhou Laboratory, Guangzhou International Bio-Island, Guangzhou, Guangdong, China
| | - Panpan Hou
- MOE Key Laboratory of Tropical Disease Control, Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Jian Pan
- MOE Key Laboratory of Tropical Disease Control, Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
| | - Deyin Guo
- Guangzhou Laboratory, Guangzhou International Bio-Island, Guangzhou, Guangdong, China
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Chunmei Li
- MOE Key Laboratory of Tropical Disease Control, Centre for Infection and Immunity Studies, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, China
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13
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Sulimov AV, Ilin IS, Tashchilova AS, Kondakova OA, Kutov DC, Sulimov VB. Docking and other computing tools in drug design against SARS-CoV-2. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2024; 35:91-136. [PMID: 38353209 DOI: 10.1080/1062936x.2024.2306336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 01/10/2024] [Indexed: 02/16/2024]
Abstract
The use of computer simulation methods has become an indispensable component in identifying drugs against the SARS-CoV-2 coronavirus. There is a huge body of literature on application of molecular modelling to predict inhibitors against target proteins of SARS-CoV-2. To keep our review clear and readable, we limited ourselves primarily to works that use computational methods to find inhibitors and test the predicted compounds experimentally either in target protein assays or in cell culture with live SARS-CoV-2. Some works containing results of experimental discovery of corresponding inhibitors without using computer modelling are included as examples of a success. Also, some computational works without experimental confirmations are also included if they attract our attention either by simulation methods or by databases used. This review collects studies that use various molecular modelling methods: docking, molecular dynamics, quantum mechanics, machine learning, and others. Most of these studies are based on docking, and other methods are used mainly for post-processing to select the best compounds among those found through docking. Simulation methods are presented concisely, information is also provided on databases of organic compounds that can be useful for virtual screening, and the review itself is structured in accordance with coronavirus target proteins.
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Affiliation(s)
- A V Sulimov
- Dimonta Ltd., Moscow, Russia
- Research Computing Center, Lomonosov Moscow State University, Moscow, Russia
| | - I S Ilin
- Research Computing Center, Lomonosov Moscow State University, Moscow, Russia
| | - A S Tashchilova
- Dimonta Ltd., Moscow, Russia
- Research Computing Center, Lomonosov Moscow State University, Moscow, Russia
| | - O A Kondakova
- Research Computing Center, Lomonosov Moscow State University, Moscow, Russia
| | - D C Kutov
- Dimonta Ltd., Moscow, Russia
- Research Computing Center, Lomonosov Moscow State University, Moscow, Russia
| | - V B Sulimov
- Dimonta Ltd., Moscow, Russia
- Research Computing Center, Lomonosov Moscow State University, Moscow, Russia
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14
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Liao Y, Wang H, Liao H, Sun Y, Tan L, Song C, Qiu X, Ding C. Classification, replication, and transcription of Nidovirales. Front Microbiol 2024; 14:1291761. [PMID: 38328580 PMCID: PMC10847374 DOI: 10.3389/fmicb.2023.1291761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Accepted: 11/06/2023] [Indexed: 02/09/2024] Open
Abstract
Nidovirales is one order of RNA virus, with the largest single-stranded positive sense RNA genome enwrapped with membrane envelope. It comprises four families (Arterividae, Mesoniviridae, Roniviridae, and Coronaviridae) and has been circulating in humans and animals for almost one century, posing great threat to livestock and poultry,as well as to public health. Nidovirales shares similar life cycle: attachment to cell surface, entry, primary translation of replicases, viral RNA replication in cytoplasm, translation of viral proteins, virion assembly, budding, and release. The viral RNA synthesis is the critical step during infection, including genomic RNA (gRNA) replication and subgenomic mRNAs (sg mRNAs) transcription. gRNA replication requires the synthesis of a negative sense full-length RNA intermediate, while the sg mRNAs transcription involves the synthesis of a nested set of negative sense subgenomic intermediates by a discontinuous strategy. This RNA synthesis process is mediated by the viral replication/transcription complex (RTC), which consists of several enzymatic replicases derived from the polyprotein 1a and polyprotein 1ab and several cellular proteins. These replicases and host factors represent the optimal potential therapeutic targets. Hereby, we summarize the Nidovirales classification, associated diseases, "replication organelle," replication and transcription mechanisms, as well as related regulatory factors.
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Affiliation(s)
- Ying Liao
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Huan Wang
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Huiyu Liao
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Yingjie Sun
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Lei Tan
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Cuiping Song
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Xusheng Qiu
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Chan Ding
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, China
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15
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Dinata R, Nisa N, Arati C, Rasmita B, Uditraj C, Siddhartha R, Bhanushree B, Saeed-Ahmed L, Manikandan B, Bidanchi RM, Abinash G, Pori B, Khushboo M, Roy VK, Gurusubramanian G. Repurposing immune boosting and anti-viral efficacy of Parkia bioactive entities as multi-target directed therapeutic approach for SARS-CoV-2: exploration of lead drugs by drug likeness, molecular docking and molecular dynamics simulation methods. J Biomol Struct Dyn 2024; 42:43-81. [PMID: 37021347 DOI: 10.1080/07391102.2023.2192797] [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: 12/09/2022] [Accepted: 03/10/2023] [Indexed: 04/07/2023]
Abstract
The COVID-19 pandemic has caused adverse health (severe respiratory, enteric and systemic infections) and environmental impacts that have threatened public health and the economy worldwide. Drug repurposing and small molecule multi-target directed herbal medicine therapeutic approaches are the most appropriate exploration strategies for SARS-CoV-2 drug discovery. This study identified potential multi-target-directed Parkia bioactive entities against SARS-CoV-2 receptors (S-protein, ACE2, TMPRSS2, RBD/ACE2, RdRp, MPro, and PLPro) using ADMET, drug-likeness, molecular docking (AutoDock, FireDock and HDOCK), molecular dynamics simulation and MM-PBSA tools. One thousand Parkia bioactive entities were screened out by virtual screening and forty-five bioactive phytomolecules were selected based on favorable binding affinity and acceptable pharmacokinetic and pharmacodynamics properties. The binding affinity values of Parkia phyto-ligands (AutoDock: -6.00--10.40 kcal/mol; FireDock: -31.00--62.02 kcal/mol; and HDOCK: -150.0--294.93 kcal/mol) were observed to be higher than the reference antiviral drugs (AutoDock: -5.90--9.10 kcal/mol; FireDock: -35.64--59.35 kcal/mol; and HDOCK: -132.82--211.87 kcal/mol), suggesting a potent modulatory action of Parkia bioactive entities against the SARS-CoV-2. Didymin, rutin, epigallocatechin gallate, epicatechin-3-0-gallate, hyperin, ursolic acid, lupeol, stigmasta-5,24(28)-diene-3-ol, ellagic acid, apigenin, stigmasterol, and campesterol strongly bound with the multiple targets of the SARS-CoV-2 receptors, inhibiting viral entry, attachment, binding, replication, transcription, maturation, packaging and spread. Furthermore, ACE2, TMPRSS2, and MPro receptors possess significant molecular dynamic properties, including stability, compactness, flexibility and total binding energy. Residues GLU-589, and LEU-95 of ACE2, GLN-350, HIS-186, and ASP-257 of TMPRSS2, and GLU-14, MET-49, and GLN-189 of MPro receptors contributed to the formation of hydrogen bonds and binding interactions, playing vital roles in inhibiting the activity of the receptors. Promising results were achieved by developing multi-targeted antiviral Parkia bioactive entities as lead and prospective candidates under a small molecule strategy against SARS-CoV-2 pathogenesis. The antiviral activity of Parkia bioactive entities needs to be further validated by pre-clinical and clinical trials.
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Affiliation(s)
- Roy Dinata
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | - Nisekhoto Nisa
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | - Chettri Arati
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | | | - Chetia Uditraj
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | | | | | | | - Bose Manikandan
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | | | - Giri Abinash
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | - Buragohain Pori
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | - Maurya Khushboo
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
| | - Vikas Kumar Roy
- Department of Zoology, Mizoram University, Aizawl, Mizoram, India
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16
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Small GI, Fedorova O, Olinares PDB, Chandanani J, Banerjee A, Choi YJ, Molina H, Chait BT, Darst SA, Campbell EA. Structural and functional insights into the enzymatic plasticity of the SARS-CoV-2 NiRAN domain. Mol Cell 2023; 83:3921-3930.e7. [PMID: 37890482 PMCID: PMC10843261 DOI: 10.1016/j.molcel.2023.10.001] [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: 06/07/2023] [Revised: 08/28/2023] [Accepted: 10/03/2023] [Indexed: 10/29/2023]
Abstract
The enzymatic activity of the SARS-CoV-2 nidovirus RdRp-associated nucleotidyltransferase (NiRAN) domain is essential for viral propagation, with three distinct activities associated with modification of the nsp9 N terminus, NMPylation, RNAylation, and deRNAylation/capping via a GDP-polyribonucleotidyltransferase reaction. The latter two activities comprise an unconventional mechanism for initiating viral RNA 5' cap formation, while the role of NMPylation is unclear. The structural mechanisms for these diverse enzymatic activities have not been properly delineated. Here, we determine high-resolution cryoelectron microscopy (cryo-EM) structures of catalytic intermediates for the NMPylation and deRNAylation/capping reactions, revealing diverse nucleotide binding poses and divalent metal ion coordination sites to promote its repertoire of activities. The deRNAylation/capping structure explains why GDP is a preferred substrate for the capping reaction over GTP. Altogether, these findings enhance our understanding of the promiscuous coronaviral NiRAN domain, a therapeutic target, and provide an accurate structural platform for drug development.
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Affiliation(s)
- Gabriel I Small
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Olga Fedorova
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA
| | - Paul Dominic B Olinares
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Joshua Chandanani
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Anoosha Banerjee
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA; Tri-Institutional Program in Chemical Biology, The Rockefeller University, New York, New York, USA
| | - Young Joo Choi
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Seth A Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Elizabeth A Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
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17
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Inniss NL, Kozic J, Li F, Rosas-Lemus M, Minasov G, Rybáček J, Zhu Y, Pohl R, Shuvalova L, Rulíšek L, Brunzelle JS, Bednárová L, Štefek M, Kormaník JM, Andris E, Šebestík J, Li ASM, Brown PJ, Schmitz U, Saikatendu K, Chang E, Nencka R, Vedadi M, Satchell KJ. Discovery of a Druggable, Cryptic Pocket in SARS-CoV-2 nsp16 Using Allosteric Inhibitors. ACS Infect Dis 2023; 9:1918-1931. [PMID: 37728236 PMCID: PMC10961098 DOI: 10.1021/acsinfecdis.3c00203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023]
Abstract
A collaborative, open-science team undertook discovery of novel small molecule inhibitors of the SARS-CoV-2 nsp16-nsp10 2'-O-methyltransferase using a high throughput screening approach with the potential to reveal new inhibition strategies. This screen yielded compound 5a, a ligand possessing an electron-deficient double bond, as an inhibitor of SARS-CoV-2 nsp16 activity. Surprisingly, X-ray crystal structures revealed that 5a covalently binds within a previously unrecognized cryptic pocket near the S-adenosylmethionine binding cleft in a manner that prevents occupation by S-adenosylmethionine. Using a multidisciplinary approach, we examined the mechanism of binding of compound 5a to the nsp16 cryptic pocket and developed 5a derivatives that inhibited nsp16 activity and murine hepatitis virus replication in rat lung epithelial cells but proved cytotoxic to cell lines canonically used to examine SARS-CoV-2 infection. Our study reveals the druggability of this newly discovered SARS-CoV-2 nsp16 cryptic pocket, provides novel tool compounds to explore the site, and suggests a new approach for discovery of nsp16 inhibition-based pan-coronavirus therapeutics through structure-guided drug design.
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Affiliation(s)
- Nicole L. Inniss
- Department of Microbiology-Immunology and Center for Structural Biology of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, 60611, United States
| | - Ján Kozic
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Monica Rosas-Lemus
- Department of Microbiology-Immunology and Center for Structural Biology of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, 60611, United States
| | - George Minasov
- Department of Microbiology-Immunology and Center for Structural Biology of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, 60611, United States
| | - Jiří Rybáček
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Yingjie Zhu
- WuXi AppTec Co., Ltd, China (Shanghai) Pilot Free Trade Zone, Shanghai, 201308, China
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Ludmilla Shuvalova
- Department of Pharmacology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, 60611, United States
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Joseph S. Brunzelle
- Northwestern Synchrotron Research Center, Life Sciences Collaborative Access Team, Northwestern University, Argonne, IL, 60439, United States
| | - Lucie Bednárová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Milan Štefek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Ján Michael Kormaník
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Erik Andris
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Jaroslav Šebestík
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Alice Shi Ming Li
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada, and Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Peter J. Brown
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada
| | - Uli Schmitz
- Structural Chemistry, Gilead Pharmaceuticals, San Mateo, CA, 94404, United States
| | - Kumar Saikatendu
- Takeda Development Center Americas, Inc., San Diego, CA, 92121, United States
| | - Edcon Chang
- Takeda Development Center Americas, Inc., San Diego, CA, 92121, United States
| | - Radim Nencka
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 6, 160 00, Czech Republic
| | - Masoud Vedadi
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario M5S 1A8, Canada, and Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario M5G 0A3, Canada
| | - Karla J.F. Satchell
- Department of Microbiology-Immunology and Center for Structural Biology of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, 60611, United States
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18
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Häring C, Jungwirth J, Schroeder J, Löffler B, Engert B, Ehrhardt C. The Local Anaesthetic Procaine Prodrugs ProcCluster ® and Procaine Hydrochloride Impair SARS-CoV-2 Replication and Egress In Vitro. Int J Mol Sci 2023; 24:14584. [PMID: 37834031 PMCID: PMC10572566 DOI: 10.3390/ijms241914584] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/14/2023] [Accepted: 09/19/2023] [Indexed: 10/15/2023] Open
Abstract
As vaccination efforts against SARS-CoV-2 progress in many countries, there is still an urgent need for efficient antiviral treatment strategies for those with severer disease courses, and lately, considerable efforts have been undertaken to repurpose existing drugs as antivirals. The local anaesthetic procaine has been investigated for antiviral properties against several viruses over the past decades. Here, we present data on the inhibitory effect of the procaine prodrugs ProcCluster® and procaine hydrochloride on SARS-CoV-2 infection in vitro. Both procaine prodrugs limit SARS-CoV-2 progeny virus titres as well as reduce interferon and cytokine responses in a proportional manner to the virus load. The addition of procaine during the early stages of the SARS-CoV-2 replication cycle in a cell culture first limits the production of subgenomic RNA transcripts, and later affects the replication of the viral genomic RNA. Interestingly, procaine additionally exerts a prominent effect on SARS-CoV-2 progeny virus release when added late during the replication cycle, when viral RNA production and protein production are already largely completed.
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Affiliation(s)
- Clio Häring
- Section of Experimental Virology, Institute of Medical Microbiology, Center for Molecular Biomedicine (CMB), Jena University Hospital, 07745 Jena, Germany; (C.H.); (J.J.); (J.S.)
| | - Johannes Jungwirth
- Section of Experimental Virology, Institute of Medical Microbiology, Center for Molecular Biomedicine (CMB), Jena University Hospital, 07745 Jena, Germany; (C.H.); (J.J.); (J.S.)
| | - Josefine Schroeder
- Section of Experimental Virology, Institute of Medical Microbiology, Center for Molecular Biomedicine (CMB), Jena University Hospital, 07745 Jena, Germany; (C.H.); (J.J.); (J.S.)
| | - Bettina Löffler
- Institute of Medical Microbiology, Jena University Hospital, 07747 Jena, Germany;
| | | | - Christina Ehrhardt
- Section of Experimental Virology, Institute of Medical Microbiology, Center for Molecular Biomedicine (CMB), Jena University Hospital, 07745 Jena, Germany; (C.H.); (J.J.); (J.S.)
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19
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Small GI, Fedorova O, Olinares PDB, Chandanani J, Banerjee A, Choi YJ, Molina H, Chait B, Darst SA, Campbell EA. Structural and functional insights into the enzymatic plasticity of the SARS-CoV-2 NiRAN Domain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.25.558837. [PMID: 37808858 PMCID: PMC10557602 DOI: 10.1101/2023.09.25.558837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
The enzymatic activity of the SARS-CoV-2 nidovirus RdRp-associated nucleotidyltransferase (NiRAN) domain is essential for viral propagation, with three distinct activities associated with modification of the nsp9 N-terminus, NMPylation, RNAylation, and deRNAylation/capping via a GDP-polyribonucleotidyltransferase reaction. The latter two activities comprise an unconventional mechanism for initiating viral RNA 5'-cap formation, while the role of NMPylation is unclear. The structural mechanisms for these diverse enzymatic activities have not been properly delineated. Here we determine high-resolution cryo-electron microscopy structures of catalytic intermediates for the NMPylation and deRNAylation/capping reactions, revealing diverse nucleotide binding poses and divalent metal ion coordination sites to promote its repertoire of activities. The deRNAylation/capping structure explains why GDP is a preferred substrate for the capping reaction over GTP. Altogether, these findings enhance our understanding of the promiscuous coronaviral NiRAN domain, a therapeutic target, and provide an accurate structural platform for drug development.
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Affiliation(s)
- Gabriel I Small
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Olga Fedorova
- Department of Chemistry and Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
- Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA
| | - Paul Dominic B Olinares
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Joshua Chandanani
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Anoosha Banerjee
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Young Joo Choi
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
- Present address: University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27599, USA
| | - Henrik Molina
- Proteomics Resource Center, The Rockefeller University, New York, NY 10065, USA
| | - Brian Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, NY, USA
| | - Seth A Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
| | - Elizabeth A Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA
- Lead contact:
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20
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Marx SK, Mickolajczyk KJ, Craig J, Thomas C, Pfeffer A, Abell S, Carrasco J, Franzi M, Huang J, Kim H, Brinkerhoff H, Kapoor T, Gundlach J, Laszlo A. Observing inhibition of the SARS-CoV-2 helicase at single-nucleotide resolution. Nucleic Acids Res 2023; 51:9266-9278. [PMID: 37560916 PMCID: PMC10516658 DOI: 10.1093/nar/gkad660] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 07/13/2023] [Accepted: 07/31/2023] [Indexed: 08/11/2023] Open
Abstract
The genome of SARS-CoV-2 encodes for a helicase (nsp13) that is essential for viral replication and highly conserved across related viruses, making it an attractive antiviral target. Here we use nanopore tweezers, a high-resolution single-molecule technique, to gain detailed insight into how nsp13 turns ATP-hydrolysis into directed motion along nucleic acid strands. We measured nsp13 both as it translocates along single-stranded DNA or unwinds double-stranded DNA. Our data reveal nsp13's single-nucleotide steps, translocating at ∼1000 nt/s or unwinding at ∼100 bp/s. Nanopore tweezers' high spatiotemporal resolution enables detailed kinetic analysis of nsp13 motion. As a proof-of-principle for inhibition studies, we observed nsp13's motion in the presence of the ATPase inhibitor ATPγS. We construct a detailed picture of inhibition in which ATPγS has multiple mechanisms of inhibition. The dominant mechanism of inhibition depends on the application of assisting force. This lays the groundwork for future single-molecule inhibition studies with viral helicases.
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Affiliation(s)
- Sinduja K Marx
- Department of Physics, University of Washington, Seattle, WA 98195, USA
| | - Keith J Mickolajczyk
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY, USA
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, USA
| | - Jonathan M Craig
- Department of Physics, University of Washington, Seattle, WA 98195, USA
| | | | - Akira M Pfeffer
- Department of Physics, University of Washington, Seattle, WA 98195, USA
| | - Sarah J Abell
- Department of Physics, University of Washington, Seattle, WA 98195, USA
| | | | - Michaela C Franzi
- Department of Physics, University of Washington, Seattle, WA 98195, USA
| | - Jesse R Huang
- Department of Physics, University of Washington, Seattle, WA 98195, USA
| | - Hwanhee C Kim
- Department of Physics, University of Washington, Seattle, WA 98195, USA
| | - Henry Brinkerhoff
- Department of Physics, University of Washington, Seattle, WA 98195, USA
| | - Tarun M Kapoor
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY, USA
| | - Jens H Gundlach
- Department of Physics, University of Washington, Seattle, WA 98195, USA
| | - Andrew H Laszlo
- Department of Physics, University of Washington, Seattle, WA 98195, USA
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21
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Grimes SL, Choi YJ, Banerjee A, Small G, Anderson-Daniels J, Gribble J, Pruijssers AJ, Agostini ML, Abu-Shmais A, Lu X, Darst SA, Campbell E, Denison MR. A mutation in the coronavirus nsp13-helicase impairs enzymatic activity and confers partial remdesivir resistance. mBio 2023; 14:e0106023. [PMID: 37338298 PMCID: PMC10470589 DOI: 10.1128/mbio.01060-23] [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: 05/03/2023] [Accepted: 05/04/2023] [Indexed: 06/21/2023] Open
Abstract
Coronaviruses (CoVs) encode nonstructural proteins 1-16 (nsps 1-16) which form replicase complexes that mediate viral RNA synthesis. Remdesivir (RDV) is an adenosine nucleoside analog antiviral that inhibits CoV RNA synthesis. RDV resistance mutations have been reported only in the nonstructural protein 12 RNA-dependent RNA polymerase (nsp12-RdRp). We here show that a substitution mutation in the nsp13-helicase (nsp13-HEL A335V) of the betacoronavirus murine hepatitis virus (MHV) that was selected during passage with the RDV parent compound confers partial RDV resistance independently and additively when expressed with co-selected RDV resistance mutations in the nsp12-RdRp. The MHV A335V substitution did not enhance replication or competitive fitness compared to WT MHV and remained sensitive to the active form of the cytidine nucleoside analog antiviral molnupiravir (MOV). Biochemical analysis of the SARS-CoV-2 helicase encoding the homologous substitution (A336V) demonstrates that the mutant protein retained the ability to associate with the core replication proteins nsps 7, 8, and 12 but had impaired helicase unwinding and ATPase activity. Together, these data identify a novel determinant of nsp13-HEL enzymatic activity, define a new genetic pathway for RDV resistance, and demonstrate the importance of surveillance for and testing of helicase mutations that arise in SARS-CoV-2 genomes. IMPORTANCE Despite the development of effective vaccines against COVID-19, the continued circulation and emergence of new variants support the need for antivirals such as RDV. Understanding pathways of antiviral resistance is essential for surveillance of emerging variants, development of combination therapies, and for identifying potential new targets for viral inhibition. We here show a novel RDV resistance mutation in the CoV helicase also impairs helicase functions, supporting the importance of studying the individual and cooperative functions of the replicase nonstructural proteins 7-16 during CoV RNA synthesis. The homologous nsp13-HEL mutation (A336V) has been reported in the GISAID database of SARS-CoV-2 genomes, highlighting the importance of surveillance of and genetic testing for nucleoside analog resistance in the helicase.
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Affiliation(s)
- Samantha L. Grimes
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Young J. Choi
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, New York, USA
| | - Anoosha Banerjee
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, New York, USA
- Tri-Institutional Program in Chemical Biology, The Rockefeller University, New York, New York, USA
| | - Gabriel Small
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, New York, USA
| | - Jordan Anderson-Daniels
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jennifer Gribble
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Andrea J. Pruijssers
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology and Inflammation, Nashville, Tennessee, USA
| | - Maria L. Agostini
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Alexandra Abu-Shmais
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Xiaotao Lu
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Seth A. Darst
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, New York, USA
| | - Elizabeth Campbell
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, New York, USA
| | - Mark R. Denison
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
- Vanderbilt Institute for Infection, Immunology and Inflammation, Nashville, Tennessee, USA
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22
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Maio N, Raza MK, Li Y, Zhang DL, Bollinger JM, Krebs C, Rouault TA. An iron-sulfur cluster in the zinc-binding domain of the SARS-CoV-2 helicase modulates its RNA-binding and -unwinding activities. Proc Natl Acad Sci U S A 2023; 120:e2303860120. [PMID: 37552760 PMCID: PMC10438387 DOI: 10.1073/pnas.2303860120] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 06/26/2023] [Indexed: 08/10/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, uses an RNA-dependent RNA polymerase along with several accessory factors to replicate its genome and transcribe its genes. Nonstructural protein (nsp) 13 is a helicase required for viral replication. Here, we found that nsp13 ligates iron, in addition to zinc, when purified anoxically. Using inductively coupled plasma mass spectrometry, UV-visible absorption, EPR, and Mössbauer spectroscopies, we characterized nsp13 as an iron-sulfur (Fe-S) protein that ligates an Fe4S4 cluster in the treble-clef metal-binding site of its zinc-binding domain. The Fe-S cluster in nsp13 modulates both its binding to the template RNA and its unwinding activity. Exposure of the protein to the stable nitroxide TEMPOL oxidizes and degrades the cluster and drastically diminishes unwinding activity. Thus, optimal function of nsp13 depends on a labile Fe-S cluster that is potentially targetable for COVID-19 treatment.
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Affiliation(s)
- Nunziata Maio
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD20892
| | - Md Kausar Raza
- Department of Chemistry, The Pennsylvania State University, University Park, PA16802
| | - Yan Li
- National Institute of Neurological Disorders and Stroke, NIH, Proteomics Core Facility, Bethesda, MD20892
| | - De-Liang Zhang
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD20892
| | - J. Martin Bollinger
- Department of Chemistry, The Pennsylvania State University, University Park, PA16802
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA16802
| | - Carsten Krebs
- Department of Chemistry, The Pennsylvania State University, University Park, PA16802
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA16802
| | - Tracey A. Rouault
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD20892
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23
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Yu J, Im H, Lee G. Unwinding mechanism of SARS-CoV helicase (nsp13) in the presence of Ca 2+, elucidated by biochemical and single-molecular studies. Biochem Biophys Res Commun 2023; 668:35-41. [PMID: 37235917 PMCID: PMC10193821 DOI: 10.1016/j.bbrc.2023.05.062] [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: 05/07/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023]
Abstract
The recent outbreak of COVID-19 has created a serious health crisis with fatFal infectious viral diseases, such as Severe Acute Respiratory Syndrome (SARS). The nsp13, a helicase of coronaviruses is an essential element for viral replication that unwinds secondary structures of DNA and RNA, and is thus considered a major therapeutic target for treatment. The replication of coronaviruses and other retroviruses occurs in the cytoplasm of infected cells, in association with viral replication organelles, called virus-induced cytosolic double-membrane vesicles (DMVs). In addition, an increase in cytosolic Ca2+ concentration accelerates viral replication. However, the molecular mechanism of nsp13 in the presence of Ca2+ is not well understood. In this study, we applied biochemical methods and single-molecule techniques to demonstrate how nsp13 achieves its unwinding activity while performing ATP hydrolysis in the presence of Ca2+. Our study found that nsp13 could efficiently unwind double stranded (ds) DNA under physiological concentration of Ca2+ of cytosolic DMVs. These findings provide new insights into the properties of nsp13 in the range of calcium in cytosolic DMVs.
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Affiliation(s)
- Jeongmin Yu
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 61005, South Korea
| | - Hyeryeon Im
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 61005, South Korea
| | - Gwangrog Lee
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju, 61005, South Korea.
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24
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Alam MM, Hannan SB, Saikat TA, Limon MBH, Topu MR, Rana MJ, Salauddin A, Bosu S, Rahman MZ. Beta, Delta, and Omicron, Deadliest Among SARS-CoV-2 Variants: A Computational Repurposing Approach. Evol Bioinform Online 2023; 19:11769343231182258. [PMID: 37457042 PMCID: PMC10338667 DOI: 10.1177/11769343231182258] [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: 10/12/2022] [Accepted: 05/25/2023] [Indexed: 07/18/2023] Open
Abstract
SARS-CoV-2 has been highly susceptible to mutations since its emergence in Wuhan, China, and its subsequent propagation due to containing an RNA as its genome. The emergence of variants with improved transmissibility still poses a grave threat to global health. The spike protein mutation is mainly responsible for higher transmissibility and risk severity. This study retrieved SARS-CoV-2 variants structural and nonstructural proteins (NSPs) sequences from several geographic locations, including Africa, Asia, Europe, Oceania, and North and South America. First, multiple sequence alignments with BioEdit and protein homology modeling were performed using the SWISS Model. Then the structure visualization and structural analysis were performed by superimposing against the Wuhan sequence by Pymol to retrieve the RMSD values. Sequence alignment revealed familiar, uncommon regional among variants and, interestingly, a few unique mutations in Beta, Delta, and Omicron. Structural analysis of such unique mutations revealed that they caused structural deviations in Beta, Delta, and Omicron spike proteins. In addition, these variants were more severe in terms of hospitalization, sickness, and higher mortality, which have a substantial relationship with the structural deviations because of those unique mutations. Such evidence provides insight into the SARS-CoV-2 spike protein vulnerability toward mutation and their structural and functional deviations, particularly in Beta, Delta, and Omicron, which might be the cause of their broader coverage. This knowledge can help us with regional vaccine strain selection, virus pathogenicity testing, diagnosis, and treatment with more specific vaccines.
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Affiliation(s)
- Mohammad Mamun Alam
- Mohammad Mamun Alam, International Centre for Diarrhoeal Disease Research, 68, Shaheed Tajuddin Ahmed Sarani, Mohakhali, Dhaka 1212, Bangladesh.
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25
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Slanina H, Madhugiri R, Wenk K, Reinke T, Schultheiß K, Schultheis J, Karl N, Linne U, Ziebuhr J. Conserved Characteristics of NMPylation Activities of Alpha- and Betacoronavirus NiRAN Domains. J Virol 2023; 97:e0046523. [PMID: 37199624 PMCID: PMC10308930 DOI: 10.1128/jvi.00465-23] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 04/28/2023] [Indexed: 05/19/2023] Open
Abstract
Coronavirus genome replication and expression are mediated by the viral replication-transcription complex (RTC) which is assembled from multiple nonstructural proteins (nsp). Among these, nsp12 represents the central functional subunit. It harbors the RNA-directed RNA polymerase (RdRp) domain and contains, at its N terminus, an additional domain called NiRAN which is widely conserved in coronaviruses and other nidoviruses. In this study, we produced bacterially expressed coronavirus nsp12s to investigate and compare NiRAN-mediated NMPylation activities from representative alpha- and betacoronaviruses. We found that the four coronavirus NiRAN domains characterized to date have a number of conserved properties, including (i) robust nsp9-specific NMPylation activities that appear to operate largely independently of the C-terminal RdRp domain, (ii) nucleotide substrate preference for UTP followed by ATP and other nucleotides, (iii) dependence on divalent metal ions, with Mn2+ being preferred over Mg2+, and (iv) a key role of N-terminal residues (particularly Asn2) of nsp9 for efficient formation of a covalent phosphoramidate bond between NMP and the N-terminal amino group of nsp9. In this context, a mutational analysis confirmed the conservation and critical role of Asn2 across different subfamilies of the family Coronaviridae, as shown by studies using chimeric coronavirus nsp9 variants in which six N-terminal residues were replaced with those from other corona-, pito- and letovirus nsp9 homologs. The combined data of this and previous studies reveal a remarkable degree of conservation among coronavirus NiRAN-mediated NMPylation activities, supporting a key role of this enzymatic activity in viral RNA synthesis and processing. IMPORTANCE There is strong evidence that coronaviruses and other large nidoviruses evolved a number of unique enzymatic activities, including an additional RdRp-associated NiRAN domain, that are conserved in nidoviruses but not in most other RNA viruses. Previous studies of the NiRAN domain mainly focused on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and suggested different functions for this domain, such as NMPylation/RNAylation of nsp9, RNA guanylyltransferase activities involved in canonical and/or unconventional RNA capping pathways, and other functions. To help resolve partly conflicting information on substrate specificities and metal ion requirements reported previously for the SARS-CoV-2 NiRAN NMPylation activity, we extended these earlier studies by characterizing representative alpha- and betacoronavirus NiRAN domains. The study revealed that key features of NiRAN-mediated NMPylation activities, such as protein and nucleotide specificity and metal ion requirements, are very well conserved among genetically divergent coronaviruses, suggesting potential avenues for future antiviral drug development targeting this essential viral enzyme.
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Affiliation(s)
- Heiko Slanina
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | | | - Kai Wenk
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | - Tess Reinke
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | - Karin Schultheiß
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | - Julia Schultheis
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | - Nadja Karl
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
| | - Uwe Linne
- Mass Spectrometry Facility, Department of Chemistry, Philipps University, Marburg, Germany
| | - John Ziebuhr
- Institute of Medical Virology, Justus Liebig University, Giessen, Germany
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26
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Sharifi E, Yousefiasl S, Trovato M, Sartorius R, Esmaeili Y, Goodarzi H, Ghomi M, Bigham A, Moghaddam FD, Heidarifard M, Pourmotabed S, Nazarzadeh Zare E, Paiva-Santos AC, Rabiee N, Wang X, Tay FR. Nanostructures for prevention, diagnosis, and treatment of viral respiratory infections: from influenza virus to SARS-CoV-2 variants. J Nanobiotechnology 2023; 21:199. [PMID: 37344894 PMCID: PMC10283343 DOI: 10.1186/s12951-023-01938-8] [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: 12/21/2022] [Accepted: 05/24/2023] [Indexed: 06/23/2023] Open
Abstract
Viruses are a major cause of mortality and socio-economic downfall despite the plethora of biopharmaceuticals designed for their eradication. Conventional antiviral therapies are often ineffective. Live-attenuated vaccines can pose a safety risk due to the possibility of pathogen reversion, whereas inactivated viral vaccines and subunit vaccines do not generate robust and sustained immune responses. Recent studies have demonstrated the potential of strategies that combine nanotechnology concepts with the diagnosis, prevention, and treatment of viral infectious diseases. The present review provides a comprehensive introduction to the different strains of viruses involved in respiratory diseases and presents an overview of recent advances in the diagnosis and treatment of viral infections based on nanotechnology concepts and applications. Discussions in diagnostic/therapeutic nanotechnology-based approaches will be focused on H1N1 influenza, respiratory syncytial virus, human parainfluenza virus type 3 infections, as well as COVID-19 infections caused by the SARS-CoV-2 virus Delta variant and new emerging Omicron variant.
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Affiliation(s)
- Esmaeel Sharifi
- Department of Tissue Engineering and Biomaterials, School of Advanced Medical Sciences and Technologies, Hamadan University of Medical Sciences, Hamadan, 6517838736, Iran.
| | - Satar Yousefiasl
- Dental Research Center, Dentistry Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Maria Trovato
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council (CNR), 80131, Naples, Italy
| | - Rossella Sartorius
- Institute of Biochemistry and Cell Biology (IBBC), National Research Council (CNR), 80131, Naples, Italy
| | - Yasaman Esmaeili
- School of Advanced Technologies in Medicine, Biosensor Research Center, Isfahan University of Medical Sciences, Isfahan, 8174673461, Iran
| | - Hamid Goodarzi
- Centre de recherche, Hôpital Maisonneuve-Rosemont, Montreal, QC, Canada
- Départment d'Ophtalmologie, Université de Montréal, Montreal, QC, Canada
| | - Matineh Ghomi
- School of Chemistry, Damghan University, Damghan, 36716-45667, Iran
| | - Ashkan Bigham
- Department of Tissue Engineering and Biomaterials, School of Advanced Medical Sciences and Technologies, Hamadan University of Medical Sciences, Hamadan, 6517838736, Iran
| | - Farnaz Dabbagh Moghaddam
- Institute for Photonics and Nanotechnologies, National Research Council, Via Fosso del Cavaliere, 100, 00133, Rome, Italy
| | - Maryam Heidarifard
- Centre de recherche, Hôpital Maisonneuve-Rosemont, Montreal, QC, Canada
- Départment d'Ophtalmologie, Université de Montréal, Montreal, QC, Canada
| | - Samiramis Pourmotabed
- Department of Emergency Medicine, School of Medicine, Hamadan University of Medical Sciences, Hamadan, 6517838736, Iran
| | | | - Ana Cláudia Paiva-Santos
- Department of Pharmaceutical Technology, Faculty of Pharmacy of the University of Coimbra, University of Coimbra, 3000-548, Coimbra, Portugal
- Group of Pharmaceutical Technology, Faculty of Pharmacy of the University of Coimbra, University of Coimbra, 3000-548, Coimbra, Portugal
| | - Navid Rabiee
- School of Engineering, Macquarie University, Sydney, NSW, 2109, Australia
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-ro, Nam-gu, Pohang, Gyeongbuk, 37673, Republic of Korea
| | - Xiangdong Wang
- Department of Pulmonary and Critical Care Medicine, Zhongshan Hospital, Fudan University Shanghai Medical College, Shanghai, 200032, China
| | - Franklin R Tay
- The Graduate School, Augusta University, Augusta, GA, 30912, USA.
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Mehyar N. Coronaviruses SARS-CoV, MERS-CoV, and SARS-CoV-2 helicase inhibitors: A systematic review of in vitro studies. J Virus Erad 2023:100327. [PMID: 37363132 PMCID: PMC10214743 DOI: 10.1016/j.jve.2023.100327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 05/11/2023] [Accepted: 05/22/2023] [Indexed: 06/28/2023] Open
Abstract
Introduction The recent outbreak of SARS-CoV-2 significantly increased the need to find inhibitors that target the essential enzymes for virus replication in the host cells. This systematic review was conducted to identify potential inhibitors of SARS-CoV, MERS-CoV, and SARS-CoV-2 helicases that have been tested by in vitro methods. The inhibition mechanisms of these compounds were discussed in this review, in addition to their cytotoxic and viral infection protection properties. Methods The databases PUBMED/MEDLINE, EMBASE, SCOPUS, and Web of Science were searched using different combinations of the keywords "helicase", "nsp13", "inhibitors", "coronaviridae", "coronaviruses", "virus replication", "replication", and "antagonists and inhibitors". Results By the end of this search, a total of 6854 articles had been identified. Thirty-one articles were included in this review. These studies reported the inhibitory effects of 309 compounds on SARS-CoV, MERS-CoV, and SARS-CoV-2 helicase activities measured by in vitro methods. Helicase inhibitors were categorized according to the type of coronavirus and the type of tested enzymatic activity, nature, approval, inhibition level, cytotoxicity, and viral infection protection effects. These inhibitors are classified according to the site of their interaction with the coronavirus helicases into four types: zinc-binding site inhibitors, nucleic acid binding site inhibitors, nucleotide-binding site inhibitors, and inhibitors with no clear interaction site. Conclusion Evidence from in vitro studies suggests that helicase inhibitors have a high potential as antiviral agents. Several helicase inhibitors tested in vitro showed good antiviral activities while maintaining moderate cytotoxicity. These inhibitors should be clinically investigated to determine their efficiency in treating different coronavirus infections, particularly COVID-19.
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Affiliation(s)
- Nimer Mehyar
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- King Abdullah International Medical Research Center, Riyadh, Saudi Arabia
- King Abdulaziz Medical City, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
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An immunoinformatics approach to study the epitopes of SARS-CoV-2 helicase, Nsp13. VACUNAS 2023. [PMCID: PMC9977615 DOI: 10.1016/j.vacun.2023.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 03/06/2023]
Abstract
Introduction and objective. Vaccines are administered worldwide to control on-going coronavirus disease-19 (COVID-19) pandemic caused by SARS-CoV-2. Vaccine efficacy is largely contributed by the epitopes present on the viral proteins and their alteration might help emerging variants to escape host immune surveillance. Therefore, this study was designed to study SARS-CoV-2 Nsp13 protein, its epitopes and evolution. Methods Clustal Omega was used to identify mutations in Nsp13 protein. Secondary structure and disorder score was predicted by CFSSP and PONDR-VSL2 webservers. Protein stability was predicted by DynaMut webserver. B cell epitopes were predicted by IEDB DiscoTope 2.0 tools and their 3D structures were represented by discovery studio. Antigenicity and allergenicity of epitopes were predicted by Vaxijen2.0 and AllergenFPv.1.0. Physiochemical properties of epitopes were predicted by Toxinpred, HLP webserver tool. Results Our data revealed 182 mutations in Nsp13 among Indian SARS-CoV-2 isolates, which were characterised by secondary structure and per-residue disorderness, stability and dynamicity predictions. To correlate the functional impact of these mutations, we characterised the most prominent B cell and T cell epitopes contributed by Nsp13. Our data revealed twenty-one epitopes, which exhibited antigenicity, stability and interactions with MHC class-I and class-II molecules. Subsequently, the physiochemical properties of these epitopes were analysed. Furthermore, eighteen mutations reside in these Nsp13 epitopes. Conclusions We report appearance of eighteen mutations in the predicted twenty-one epitopes of Nsp13. Among these, at least seven epitopes closely matches with the functionally validated epitopes. Altogether, our study shows the pattern of evolution of Nsp13 epitopes and their probable implications.
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Abstract
SARS-CoV-2, the virus responsible for the COVID-19 pandemic, has been associated with substantial global morbidity and mortality. Despite a tropism that is largely confined to the airways, COVID-19 is associated with multiorgan dysfunction and long-term cognitive pathologies. A major driver of this biology stems from the combined effects of virus-mediated interference with the host antiviral defences in infected cells and the sensing of pathogen-associated material by bystander cells. Such a dynamic results in delayed induction of type I and III interferons (IFN-I and IFN-III) at the site of infection, but systemic IFN-I and IFN-III priming in distal organs and barrier epithelial surfaces, respectively. In this Review, we examine the relationship between SARS-CoV-2 biology and the cellular response to infection, detailing how antagonism and dysregulation of host innate immune defences contribute to disease severity of COVID-19.
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Affiliation(s)
- Judith M Minkoff
- Department of Microbiology, New York University Langone Health, New York, NY, USA
| | - Benjamin tenOever
- Department of Microbiology, New York University Langone Health, New York, NY, USA.
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Yang T, Wang SC, Ye L, Maimaitiyiming Y, Naranmandura H. Targeting viral proteins for restraining SARS-CoV-2: focusing lens on viral proteins beyond spike for discovering new drug targets. Expert Opin Drug Discov 2023; 18:247-268. [PMID: 36723288 DOI: 10.1080/17460441.2023.2175812] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
INTRODUCTION Emergence of highly infectious SARS-CoV-2 variants are reducing protection provided by current vaccines, requiring constant updates in antiviral approaches. The virus encodes four structural and sixteen nonstructural proteins which play important roles in viral genome replication and transcription, virion assembly, release , entry into cells, and compromising host cellular defenses. As alien proteins to host cells, many viral proteins represent potential targets for combating the SARS-CoV-2. AREAS COVERED Based on literature from PubMed and Web of Science databases, the authors summarize the typical characteristics of SARS-CoV-2 from the whole viral particle to the individual viral proteins and their corresponding functions in virus life cycle. The authors also discuss the potential and emerging targeted interventions to curb virus replication and spread in detail to provide unique insights into SARS-CoV-2 infection and countermeasures against it. EXPERT OPINION Our comprehensive analysis highlights the rationale to focus on non-spike viral proteins that are less mutated but have important functions. Examples of this include: structural proteins (e.g. nucleocapsid protein, envelope protein) and extensively-concerned nonstructural proteins (e.g. NSP3, NSP5, NSP12) along with the ones with relatively less attention (e.g. NSP1, NSP10, NSP14 and NSP16), for developing novel drugs to overcome resistance of SARS-CoV-2 variants to preexisting vaccines and antibody-based treatments.
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Affiliation(s)
- Tao Yang
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Si Chun Wang
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Linyan Ye
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yasen Maimaitiyiming
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Zhejiang Province Key Laboratory of Haematology Oncology Diagnosis and Treatment, Hangzhou, Zhejiang, China.,Department of Neurobiology, NHC and CAMS Key Laboratory of Medical Neurobiology, School of Brain Science and Brain Medicine, and MOE Frontier Science Center for Brain Science and Brain-machine Integration, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Hua Naranmandura
- Department of Hematology of First Affiliated Hospital, and Department of Public Health, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Zhejiang Province Key Laboratory of Haematology Oncology Diagnosis and Treatment, Hangzhou, Zhejiang, China.,Cancer Center, Zhejiang University, Hangzhou, Zhejiang, China
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31
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Lessons Learnt from COVID-19: Computational Strategies for Facing Present and Future Pandemics. Int J Mol Sci 2023; 24:ijms24054401. [PMID: 36901832 PMCID: PMC10003049 DOI: 10.3390/ijms24054401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 02/19/2023] [Accepted: 02/21/2023] [Indexed: 02/25/2023] Open
Abstract
Since its outbreak in December 2019, the COVID-19 pandemic has caused the death of more than 6.5 million people around the world. The high transmissibility of its causative agent, the SARS-CoV-2 virus, coupled with its potentially lethal outcome, provoked a profound global economic and social crisis. The urgency of finding suitable pharmacological tools to tame the pandemic shed light on the ever-increasing importance of computer simulations in rationalizing and speeding up the design of new drugs, further stressing the need for developing quick and reliable methods to identify novel active molecules and characterize their mechanism of action. In the present work, we aim at providing the reader with a general overview of the COVID-19 pandemic, discussing the hallmarks in its management, from the initial attempts at drug repurposing to the commercialization of Paxlovid, the first orally available COVID-19 drug. Furthermore, we analyze and discuss the role of computer-aided drug discovery (CADD) techniques, especially those that fall in the structure-based drug design (SBDD) category, in facing present and future pandemics, by showcasing several successful examples of drug discovery campaigns where commonly used methods such as docking and molecular dynamics have been employed in the rational design of effective therapeutic entities against COVID-19.
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32
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Metabolic Activation of PARP as a SARS-CoV-2 Therapeutic Target-Is It a Bait for the Virus or the Best Deal We Could Ever Make with the Virus? Is AMBICA the Potential Cure? Biomolecules 2023; 13:biom13020374. [PMID: 36830743 PMCID: PMC9953159 DOI: 10.3390/biom13020374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 02/10/2023] [Accepted: 02/11/2023] [Indexed: 02/18/2023] Open
Abstract
The COVID-19 pandemic has had a great impact on global health and is an economic burden. Even with vaccines and anti-viral medications we are still scrambling to get a balance. In this perspective, we have shed light upon an extremely feasible approach by which we can control the SARS-CoV-2 infection and the associated complications, bringing some solace to this ongoing turmoil. We are providing some insights regarding an ideal agent which could prevent SARS-CoV-2 multiplication. If we could identify an agent which is an activator of metabolism and is also bioactive, we could prevent corona activation (AMBICA). Some naturally occurring lipid molecules best fit this identity as an agent which has the capacity to replenish our host cells, specifically immune cells, with ATP. It could also act as a source for providing a substrate for host cell PARP family members for MARylation and PARylation processes, leading to manipulation of the viral macro domain function, resulting in curbing the virulence and propagation of SARS-CoV-2. Identification of the right lipid molecule or combination of lipid molecules will fulfill the criteria. This perspective has focused on a unique angle of host-pathogen interaction and will open up a new dimension in treating COVID-19 infection.
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Jia X, Chen J, Qiao C, Li C, Yang K, Zhang Y, Li J, Li Z. Porcine Epidemic Diarrhea Virus nsp13 Protein Downregulates Neonatal Fc Receptor Expression by Causing Promoter Hypermethylation through the NF-κB Signaling Pathway. JOURNAL OF IMMUNOLOGY (BALTIMORE, MD. : 1950) 2023; 210:475-485. [PMID: 36602596 DOI: 10.4049/jimmunol.2200291] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 11/28/2022] [Indexed: 01/06/2023]
Abstract
Porcine epidemic diarrhea virus (PEDV) is a highly pathogenic porcine enteric coronavirus that causes severe watery diarrhea and even death in piglets. The neonatal Fc receptor (FcRn) is the only transport receptor for IgG. FcRn expressed by intestinal epithelial cells can transport IgG from breast milk to piglets to provide immune protection. Previous studies have shown that viral infection affects FcRn expression. In this study, we showed for the first time, to our knowledge, that FcRn expression can be influenced by methyltransferases. In addition, we found that PEDV inhibited FcRn protein synthesis in porcine small intestinal epithelial cells postinfection. Then, we found that PEDV interfered with the transcription of genes through aberrant methylation modification of the FcRn promoter. DNA methyltransferase 3b (DNMT3b) has been implicated in this process. Using a series of PEDV structural and nonstructural protein (nsp) expression plasmids, we showed that nsp13 plays an important role in this aberrant methylation modification. PEDV nsp13 can affect the NF-κB canonical pathway and promote DNMT3b protein expression by facilitating p65 protein binding to chromatin. PEDV caused aberrant methylation of the FcRn promoter via DNMT3b. The same phenomenon was found in animal experiments with large white piglets. IgG transcytosis demonstrated that PEDV nsp13 can inhibit bidirectional IgG transport by FcRn. In addition, the core region of nsp13 (230-597 aa) is critical for FcRn inhibition. Taken together, to our knowledge, our findings revealed a novel immune escape mechanism of PEDV and shed new light on the design and development of vaccines and drugs.
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Affiliation(s)
- Xiangchao Jia
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; and Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Jing Chen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; and Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Chenyuan Qiao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; and Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Chenxi Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; and Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Kang Yang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; and Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Yang Zhang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; and Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Jian Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; and Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Zili Li
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; and Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
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Sommers JA, Loftus LN, Jones MP, Lee RA, Haren CE, Dumm AJ, Brosh RM. Biochemical analysis of SARS-CoV-2 Nsp13 helicase implicated in COVID-19 and factors that regulate its catalytic functions. J Biol Chem 2023; 299:102980. [PMID: 36739951 PMCID: PMC9897874 DOI: 10.1016/j.jbc.2023.102980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/27/2023] [Accepted: 01/29/2023] [Indexed: 02/05/2023] Open
Abstract
Replication of the 30-kilobase genome of SARS-CoV-2, responsible for COVID-19, is a key step in the coronavirus life cycle that requires a set of virally encoded nonstructural proteins such as the highly conserved Nsp13 helicase. However, the features that contribute to catalytic properties of Nsp13 are not well established. Here, we biochemically characterized the purified recombinant SARS-CoV-2 Nsp13 helicase protein, focusing on its catalytic functions, nucleic acid substrate specificity, nucleotide/metal cofactor requirements, and displacement of proteins from RNA molecules proposed to be important for its proofreading role during coronavirus replication. We determined that Nsp13 preferentially interacts with single-stranded DNA compared with single-stranded RNA to unwind a partial duplex helicase substrate. We present evidence for functional cooperativity as a function of Nsp13 concentration, which suggests that oligomerization is important for optimal activity. In addition, under single-turnover conditions, Nsp13 unwound partial duplex RNA substrates of increasing double-stranded regions (16-30 base pairs) with similar efficiency, suggesting the enzyme unwinds processively in this range. We also show Nsp13-catalyzed RNA unwinding is abolished by a site-specific neutralizing linkage in the sugar-phosphate backbone, demonstrating continuity in the helicase-translocating strand is essential for unwinding the partial duplex substrate. Taken together, we demonstrate for the first time that coronavirus helicase Nsp13 disrupts a high-affinity RNA-protein interaction in a unidirectional and ATP-dependent manner. Furthermore, sensitivity of Nsp13 catalytic functions to Mg2+ concentration suggests a regulatory mechanism for ATP hydrolysis, duplex unwinding, and RNA protein remodeling, processes implicated in SARS-CoV-2 replication and proofreading.
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Affiliation(s)
- Joshua A Sommers
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, NIH, NIH Biomedical Research Center, Baltimore, Maryland, USA
| | - Lorin N Loftus
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, NIH, NIH Biomedical Research Center, Baltimore, Maryland, USA
| | - Martin P Jones
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, NIH, NIH Biomedical Research Center, Baltimore, Maryland, USA
| | - Rebecca A Lee
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, NIH, NIH Biomedical Research Center, Baltimore, Maryland, USA
| | - Caitlin E Haren
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, NIH, NIH Biomedical Research Center, Baltimore, Maryland, USA
| | - Adaira J Dumm
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, NIH, NIH Biomedical Research Center, Baltimore, Maryland, USA
| | - Robert M Brosh
- Helicases and Genomic Integrity Section, Translational Gerontology Branch, National Institute on Aging, NIH, NIH Biomedical Research Center, Baltimore, Maryland, USA.
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Imprachim N, Yosaatmadja Y, Newman JA. Crystal structures and fragment screening of SARS-CoV-2 NSP14 reveal details of exoribonuclease activation and mRNA capping and provide starting points for antiviral drug development. Nucleic Acids Res 2023; 51:475-487. [PMID: 36546776 PMCID: PMC9841433 DOI: 10.1093/nar/gkac1207] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 11/23/2022] [Accepted: 12/09/2022] [Indexed: 12/24/2022] Open
Abstract
NSP14 is a dual function enzyme containing an N-terminal exonuclease domain (ExoN) and C-terminal Guanine-N7-methyltransferase (N7-MTase) domain. Both activities are essential for the viral life cycle and may be targeted for anti-viral therapeutics. NSP14 forms a complex with NSP10, and this interaction enhances the nuclease but not the methyltransferase activity. We have determined the structure of SARS-CoV-2 NSP14 in the absence of NSP10 to 1.7 Å resolution. Comparisons with NSP14/NSP10 complexes reveal significant conformational changes that occur within the NSP14 ExoN domain upon binding of NSP10, including helix to coil transitions that facilitate the formation of the ExoN active site and provide an explanation of the stimulation of nuclease activity by NSP10. We have determined the structure of NSP14 in complex with cap analogue 7MeGpppG, and observe conformational changes within a SAM/SAH interacting loop that plays a key role in viral mRNA capping offering new insights into MTase activity. We perform an X-ray fragment screen on NSP14, revealing 72 hits bound to sites of inhibition in the ExoN and MTase domains. These fragments serve as excellent starting point tools for structure guided development of NSP14 inhibitors that may be used to treat COVID-19 and potentially other future viral threats.
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Affiliation(s)
- Nergis Imprachim
- Centre for Medicines Discovery, University of Oxford, South Parks Rd, Oxford OX1 3QU, UK
| | - Yuliana Yosaatmadja
- Centre for Medicines Discovery, University of Oxford, South Parks Rd, Oxford OX1 3QU, UK
| | - Joseph A Newman
- Centre for Medicines Discovery, University of Oxford, South Parks Rd, Oxford OX1 3QU, UK
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36
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Malik A, Kohli M, Jacob NA, Kayal A, Raj TK, Kulkarni N, Chandramohan V. In silico screening of phytochemical compounds and FDA drugs as potential inhibitors for NSP16/10 5' methyl transferase activity. J Biomol Struct Dyn 2023; 41:221-233. [PMID: 34844519 DOI: 10.1080/07391102.2021.2005680] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The recent global pandemic associated with the highly contagious novel coronavirus (SARS-CoV-2) has led to an unpredictable loss of life and economy worldwide, and the discovery of antiviral drugs is an urgent necessity. For the discovery of new drug leads and for the treatment of various diseases, natural products and purified photochemical from medicinal plants are used. The RNA cap was methylated by two S-adenosyl-L-methionine (SAM)-dependent methyltransferases of SARS coronavirus (SARS-CoV-2), catalyzed by NSP16 2'-O-Mtase. Natural substrate SAM, 128 Phytocompounds retrieved from the Phytocompounds database, and 11 standard FDA-approved HIV drugs reclaimed from the PubChem database are subjected to docking analysis. The docking study was done using AutoDock Vina. Further, admetSAR and DruLiTO servers are used to analyze the drug-likeness properties. The NSP16/10 structure and natural substrate SAM, Phytocompounds Withanolide (WTL), and HIV standard drug Dolutegravir (DLT) as hit compounds were identified by molecular dynamics using the Gromacs GPU-enabled package. To examine the effectiveness of the identified drugs versus COVID-19, further in vitro and in vivo studies are required. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Mayank Kohli
- Biotechnology Skill Enhancement Programme, Department of Biotechnology, Siddaganga Institute of Technology, Karnataka, India
| | - Neethu Anju Jacob
- Biotechnology Skill Enhancement Programme, Department of Biotechnology, Siddaganga Institute of Technology, Karnataka, India
| | | | | | | | - Vivek Chandramohan
- Department of Biotechnology, Siddaganga Institute of Technology, Karnataka, India
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Sarkar M, Saha S. Modeling of SARS-CoV-2 Virus Proteins: Implications on Its Proteome. Methods Mol Biol 2023; 2627:265-299. [PMID: 36959453 DOI: 10.1007/978-1-0716-2974-1_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
Abstract
COronaVIrus Disease 19 (COVID-19) is a severe acute respiratory syndrome (SARS) caused by a group of beta coronaviruses, SARS-CoV-2. The SARS-CoV-2 virus is similar to previous SARS- and MERS-causing strains and has infected nearly six hundred and fifty million people all over the globe, while the death toll has crossed the six million mark (as of December, 2022). In this chapter, we look at how computational modeling approaches of the viral proteins could help us understand the various processes in the viral life cycle inside the host, an understanding of which might provide key insights in mitigating this and future threats. This understanding helps us identify key targets for the purpose of drug discovery and vaccine development.
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Affiliation(s)
- Manish Sarkar
- Hochschule für Technik und Wirtschaft (HTW) Berlin, Berlin, Germany
- MedInsights SAS, Paris, France
| | - Soham Saha
- MedInsights, Veuilly la Poterie, France.
- MedInsights SAS, Paris, France.
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Machitani M, Takei J, Kaneko MK, Ueki S, Ohashi H, Watashi K, Kato Y, Masutomi K. Development of novel monoclonal antibodies against nsp12 of SARS-CoV-2. Virol J 2022; 19:213. [PMID: 36496472 PMCID: PMC9736705 DOI: 10.1186/s12985-022-01948-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
A novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused a global pandemic of coronavirus disease 19. Coronaviruses, including SARS-CoV-2, use RNA-dependent RNA polymerase (RdRP) for viral replication and transcription. Since RdRP is a promising therapeutic target for infection of SARS-CoV-2, it would be beneficial to develop new experimental tools for analysis of the RdRP reaction of SARS-CoV-2. Here, we succeeded to develop novel mouse monoclonal antibodies (mAbs) that recognize SARS-CoV-2 nsp12, catalytic subunit of the RdRP. These anti-nsp12 mAbs, RdMab-2, -13, and -20, specifically recognize SARS-CoV-2 nsp12 by western blotting analysis, while they exhibit less or no cross-reactivity to SARS-CoV nsp12. In addition, SARS-CoV-2 nsp12 was successfully immunoprecipitated using RdMab-2 from lysates of cells overexpressing SARS-CoV-2 nsp12. RdMab-2 was able to detect SARS-CoV-2 nsp12 transiently expressed in established culture cells such as HEK293T cells by indirect immunofluorescence technique. These novel mAbs against SARS-CoV-2 nsp12 are useful to elucidate the RdRP reaction of SARS-CoV-2 and biological cell response against it.
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Affiliation(s)
- Mitsuhiro Machitani
- grid.272242.30000 0001 2168 5385Division of Cancer Stem Cell, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045 Japan
| | - Junko Takei
- grid.69566.3a0000 0001 2248 6943Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-Ku, Sendai, Miyagi 980-8575 Japan
| | - Mika K. Kaneko
- grid.69566.3a0000 0001 2248 6943Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-Ku, Sendai, Miyagi 980-8575 Japan
| | - Saori Ueki
- grid.272242.30000 0001 2168 5385Division of Cancer Stem Cell, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045 Japan
| | - Hirofumi Ohashi
- grid.410795.e0000 0001 2220 1880Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku, Tokyo, 162-8640 Japan ,grid.410795.e0000 0001 2220 1880Department of Virology II, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku, Tokyo, 162-8640 Japan
| | - Koichi Watashi
- grid.410795.e0000 0001 2220 1880Research Center for Drug and Vaccine Development, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku, Tokyo, 162-8640 Japan ,grid.410795.e0000 0001 2220 1880Department of Virology II, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku, Tokyo, 162-8640 Japan
| | - Yukinari Kato
- grid.69566.3a0000 0001 2248 6943Department of Antibody Drug Development, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-Ku, Sendai, Miyagi 980-8575 Japan ,grid.69566.3a0000 0001 2248 6943Department of Molecular Pharmacology, Tohoku University Graduate School of Medicine, 2-1 Seiryo-Machi, Aoba-Ku, Sendai, Miyagi 980-8575 Japan
| | - Kenkichi Masutomi
- grid.272242.30000 0001 2168 5385Division of Cancer Stem Cell, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-Ku, Tokyo, 104-0045 Japan
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Chen Z, Ye SY. Research progress on antiviral constituents in traditional Chinese medicines and their mechanisms of action. PHARMACEUTICAL BIOLOGY 2022; 60:1063-1076. [PMID: 35634712 PMCID: PMC9154771 DOI: 10.1080/13880209.2022.2074053] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 04/22/2022] [Accepted: 04/30/2022] [Indexed: 06/15/2023]
Abstract
CONTEXT Viruses have the characteristics of rapid transmission and high mortality. At present, western medicines still lack an ideal antiviral. As natural products, many traditional Chinese medicines (TCM) have certain inhibitory effects on viruses, which has become the hotspot of medical research in recent years. OBJECTIVE The antiviral active ingredients and mechanisms of TCM against viral diseases was studied in combination with the pathogenesis of viral diseases and antiviral effects. MATERIALS AND METHODS English and Chinese literature from 1999 to 2021 was collected from databases including Web of Science, PubMed, Elsevier, Chinese Pharmacopoeia 2020 (CP), and CNKI (Chinese). Traditional Chinese medicines (TCM), active ingredients, antiviral, mechanism of action, and anti-inflammatory effect were used as the key words. RESULTS The antiviral activity of TCM is clarified to put forward a strategy for discovering active compounds against viruses, and provide reference for screening antivirus drugs from TCM. TCM can not only directly kill viruses and inhibit the proliferation of viruses in cells, but also prevent viruses from infecting cells and causing cytophilia. It can also regulate the human immune system, enhance human immunity, and play an indirect antiviral role. DISCUSSION AND CONCLUSION Based on the experimental study and antiviral mechanism of TCM, this paper can provide analytical evidence that supports the effectiveness of TCM in treating virus infections, as well as their mechanisms against viruses. It could be helpful to provide reference for the research and development of innovative TCMs with multiple components, multiple targets and low toxicity.
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Affiliation(s)
- Zhi Chen
- Pharmaceutical College, Shandong University of TCM, Jinan, People’s Republic of China
| | - Si-yong Ye
- Department of Pharmacy, Jinan Second People's Hospital, Jinan, People’s Republic of China
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El Hassab MA, Eldehna WM, Al-Rashood ST, Alharbi A, Eskandrani RO, Alkahtani HM, Elkaeed EB, Abou-Seri SM. Multi-stage structure-based virtual screening approach towards identification of potential SARS-CoV-2 NSP13 helicase inhibitors. J Enzyme Inhib Med Chem 2022; 37:563-572. [PMID: 35012384 PMCID: PMC8757614 DOI: 10.1080/14756366.2021.2022659] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 11/24/2022] Open
Abstract
On account of its crucial role in the virus life cycle, SARS-COV-2 NSP13 helicase enzyme was exploited as a promising target to identify a novel potential inhibitor using multi-stage structure-based drug discovery approaches. Firstly, a 3D pharmacophore was generated based on the collected data from a protein-ligand interaction fingerprint (PLIF) study using key interactions between co-crystallised fragments and the NSP13 helicase active site. The ZINC database was screened through the generated 3D-pharmacophore retrieving 13 potential hits. All the retrieved hits exceeded the benchmark score of the co-crystallised fragments at the molecular docking step and the best five-hit compounds were selected for further analysis. Finally, a combination between molecular dynamics simulations and MM-PBSA based binding free energy calculations was conducted on the best hit (compound FWM-1) bound to NSP13 helicase enzyme, which identified FWM-1 as a potential potent NSP13 helicase inhibitor with binding free energy equals -328.6 ± 9.2 kcal/mol.
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Affiliation(s)
- Mahmoud A. El Hassab
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, King Salman International University (KSIU), Ras Sudr, Egypt
| | - Wagdy M. Eldehna
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Kafrelsheikh University, Kafrelsheikh, Egypt
| | - Sara T. Al-Rashood
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Amal Alharbi
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Razan O. Eskandrani
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Hamad M. Alkahtani
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Eslam B. Elkaeed
- Department of Pharmaceutical Sciences, College of Pharmacy, AlMaarefa University, Riyadh, Saudi Arabia
| | - Sahar M. Abou-Seri
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, Cairo University, Cairo, Egypt
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Ghobain MA, Rebh F, Saad A, Khan AH, Mehyar N, Mashhour A, Islam I, Alobaida Y, Alaskar AS, Boudjelal M, Jeraisy MA. The efficacy of Zafirlukast as a SARS-CoV-2 helicase inhibitor in adult patients with moderate COVID-19 Pneumonia (pilot randomized clinical trial). J Infect Public Health 2022; 15:1546-1550. [PMID: 36436481 PMCID: PMC9673052 DOI: 10.1016/j.jiph.2022.11.016] [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: 09/04/2022] [Revised: 11/07/2022] [Accepted: 11/13/2022] [Indexed: 11/18/2022] Open
Abstract
OBJECTIVE To assess the efficacy of Zafirlukast as a SARS-CoV-2 Helicase Inhibitor in adult patients with moderate COVID-19 symptoms (hospitalized patients with COVID-19 pneumonia who were not admitted to an intensive care unit). METHODS We conducted a randomized, double blind, placebo-controlled, pilot trial with adult patients with moderate COVID-19 pneumonia. The sample was randomized to Zafirlukast 10 mg BD for 10 days plus standard care vs placebo plus standard care. The primary outcome was the complete resolution of all symptoms. The secondary outcomes were the duration of oxygen therapy, and length of hospital stay (LOS). RESULTS In total, 40 patients were randomized (20 to Zafirlukast and 20 to the control). The time to the resolution of clinical symptoms in both groups was not significantly different. Regarding the fever, 0.3 days [95 % CI, - 1.19, 0.69], p = 0.76, for shortness of breath, the difference was 0.4 days [95 % CI, - 2.67, 3.46], p = 0.68, for cough the difference was 0.2 days [95 % CI, - 1.45, 1.95], p = 0.98, for sputum the difference was 0.5 days [95 % CI, - 0.75, 1.85], p = 0.09, for vomiting the difference was 0.1 days [95 % CI, - 0.50, 0.30], p = 0.93, for fatigue the difference was 0.3 days [95 % CI, - 4.32, 3.62], p = 0.64. The LOS per day for the two groups was not significantly different, 1.1 days [95 % CI,- 2.03, 4.28], p = 0.94, nor was the duration of oxygen therapy per days, 1.3 days [95 % CI, - 1.79, 4.49], p = 0.49. Regarding the 7 category ordinary scale, there was no significant difference between the two groups at day 7 (p-value = 0.62), day 14 (p-value = 0.60) and day 28 (p-value = 0.48). CONCLUSION Among adult patients hospitalized with COVID-19 pneumonia, the treatment with Zafirlukast, compared to placebo, did not significantly improve symptoms resolution.
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Affiliation(s)
- M Al Ghobain
- King Abdullah International Medical Research Center, Riyadh, Saudi Arabia, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia.
| | - F Rebh
- Prince Mohammed Bin Abdulaziz Hospital, Ministry of Health, Riyadh, Saudi Arabia
| | - A Saad
- King Abdullah International Medical Research Center, Riyadh, Saudi Arabia, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
| | - A H Khan
- King Abdullah International Medical Research Center, Riyadh, Saudi Arabia, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
| | - N Mehyar
- King Abdullah International Medical Research Center, Riyadh, Saudi Arabia, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
| | - A Mashhour
- King Abdullah International Medical Research Center, Riyadh, Saudi Arabia, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
| | - I Islam
- King Abdullah International Medical Research Center, Riyadh, Saudi Arabia, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
| | - Y Alobaida
- Sudair Pharmaceutical Co, Riyadh, Saudi Arabia
| | - A S Alaskar
- King Abdullah International Medical Research Center, Riyadh, Saudi Arabia, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
| | - M Boudjelal
- King Abdullah International Medical Research Center, Riyadh, Saudi Arabia, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
| | - M Al Jeraisy
- King Abdullah International Medical Research Center, Riyadh, Saudi Arabia, King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia
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Zhai LY, Su AM, Liu JF, Zhao JJ, Xi XG, Hou XM. Recent advances in applying G-quadruplex for SARS-CoV-2 targeting and diagnosis: A review. Int J Biol Macromol 2022; 221:1476-1490. [PMID: 36130641 PMCID: PMC9482720 DOI: 10.1016/j.ijbiomac.2022.09.152] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 08/31/2022] [Accepted: 09/15/2022] [Indexed: 12/05/2022]
Abstract
The coronavirus SARS-CoV-2 has caused a health care crisis all over the world since the end of 2019. Although vaccines and neutralizing antibodies have been developed, rapidly emerging variants usually display stronger immune escape ability and can better surpass vaccine protection. Therefore, it is still vital to find proper treatment strategies. To date, antiviral drugs against SARS-CoV-2 have mainly focused on proteases or polymerases. Notably, noncanonical nucleic acid structures called G-quadruplexes (G4s) have been identified in many viruses in recent years, and numerous G4 ligands have been developed. During this pandemic, literature on SARS-CoV-2 G4s is rapidly accumulating. Here, we first summarize the recent progress in the identification of SARS-CoV-2 G4s and their intervention by ligands. We then introduce the potential interacting proteins of SARS-CoV-2 G4s from both the virus and the host that may regulate G4 functions. The innovative strategy to use G4s as a diagnostic tool in SARS-CoV-2 detection is also reviewed. Finally, we discuss some key questions to be addressed in the future.
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Affiliation(s)
- Li-Yan Zhai
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Ai-Min Su
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Jing-Fan Liu
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Jian-Jin Zhao
- College of Life Sciences, Northwest A&F University, Yangling 712100, China
| | - Xu-Guang Xi
- College of Life Sciences, Northwest A&F University, Yangling 712100, China; ENS Paris-Saclay, Université Paris-Saclay, CNRS UMR8113, IDA FR3242, Laboratory of Biology and Applied Pharmacology (LBPA), 91190 Gif-sur-Yvette, France
| | - Xi-Miao Hou
- College of Life Sciences, Northwest A&F University, Yangling 712100, China.
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Khan MZI, Nazli A, Al-furas H, Asad MI, Ajmal I, Khan D, Shah J, Farooq MA, Jiang W. An overview of viral mutagenesis and the impact on pathogenesis of SARS-CoV-2 variants. Front Immunol 2022; 13:1034444. [PMID: 36518757 PMCID: PMC9742215 DOI: 10.3389/fimmu.2022.1034444] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 11/04/2022] [Indexed: 11/29/2022] Open
Abstract
Viruses are submicroscopic, obligate intracellular parasites that carry either DNA or RNA as their genome, protected by a capsid. Viruses are genetic entities that propagate by using the metabolic and biosynthetic machinery of their hosts and many of them cause sickness in the host. The ability of viruses to adapt to different hosts and settings mainly relies on their ability to create de novo variety in a short interval of time. The size and chemical composition of the viral genome have been recognized as important factors affecting the rate of mutations. Coronavirus disease 2019 (Covid-19) is a novel viral disease that has quickly become one of the world's leading causes of mortality, making it one of the most serious public health problems in recent decades. The discovery of new medications to cope with Covid-19 is a difficult and time-consuming procedure, as new mutations represent a serious threat to the efficacy of recently developed vaccines. The current article discusses viral mutations and their impact on the pathogenicity of newly developed variants with a special emphasis on Covid-19. The biology of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), its mutations, pathogenesis, and treatment strategies are discussed in detail along with the statistical data.
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Affiliation(s)
| | - Adila Nazli
- Faculty of Biological Sciences, Department of Pharmacy, Quaid-i-Azam University, Islamabad, Pakistan
| | - Hawaa Al-furas
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development, Ministry of Education (MOE) of China, Guangzhou City Key Laboratory of Precision Chemical Drug Development, School of Pharmacy, Jinan University, Guangzhou, China
| | - Muhammad Imran Asad
- Faculty of Biological Sciences, Department of Pharmacy, Quaid-i-Azam University, Islamabad, Pakistan
| | - Iqra Ajmal
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, East China Normal University, Shanghai, China
| | - Dildar Khan
- Faculty of Biological Sciences, Department of Pharmacy, Quaid-i-Azam University, Islamabad, Pakistan
| | - Jaffer Shah
- Department of Health, New York, NY, United States,*Correspondence: Jaffer Shah, ; Muhammad Asad Farooq, ; Wenzheng Jiang,
| | - Muhammad Asad Farooq
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, East China Normal University, Shanghai, China,*Correspondence: Jaffer Shah, ; Muhammad Asad Farooq, ; Wenzheng Jiang,
| | - Wenzheng Jiang
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences, East China Normal University, Shanghai, China,*Correspondence: Jaffer Shah, ; Muhammad Asad Farooq, ; Wenzheng Jiang,
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A mechanism for SARS-CoV-2 RNA capping and its inhibition by nucleotide analog inhibitors. Cell 2022; 185:4347-4360.e17. [PMID: 36335936 PMCID: PMC9531661 DOI: 10.1016/j.cell.2022.09.037] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/01/2022] [Accepted: 09/27/2022] [Indexed: 01/26/2023]
Abstract
Decoration of cap on viral RNA plays essential roles in SARS-CoV-2 proliferation. Here, we report a mechanism for SARS-CoV-2 RNA capping and document structural details at atomic resolution. The NiRAN domain in polymerase catalyzes the covalent link of RNA 5' end to the first residue of nsp9 (termed as RNAylation), thus being an intermediate to form cap core (GpppA) with GTP catalyzed again by NiRAN. We also reveal that triphosphorylated nucleotide analog inhibitors can be bonded to nsp9 and fit into a previously unknown "Nuc-pocket" in NiRAN, thus inhibiting nsp9 RNAylation and formation of GpppA. S-loop (residues 50-KTN-52) in NiRAN presents a remarkable conformational shift observed in RTC bound with sofosbuvir monophosphate, reasoning an "induce-and-lock" mechanism to design inhibitors. These findings not only improve the understanding of SARS-CoV-2 RNA capping and the mode of action of NAIs but also provide a strategy to design antiviral drugs.
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Romeo I, Ambrosio FA, Costa G, Corona A, Alkhatib M, Salpini R, Lemme S, Vergni D, Svicher V, Santoro MM, Tramontano E, Ceccherini-Silberstein F, Artese A, Alcaro S. Targeting SARS-CoV-2 nsp13 Helicase and Assessment of Druggability Pockets: Identification of Two Potent Inhibitors by a Multi-Site In Silico Drug Repurposing Approach. Molecules 2022; 27:7522. [PMID: 36364347 PMCID: PMC9654784 DOI: 10.3390/molecules27217522] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 10/21/2022] [Accepted: 10/25/2022] [Indexed: 06/14/2024] Open
Abstract
The SARS-CoV-2 non-structural protein 13 (nsp13) helicase is an essential enzyme for viral replication and has been identified as an attractive target for the development of new antiviral drugs. In detail, the helicase catalyzes the unwinding of double-stranded DNA or RNA in a 5' to 3' direction and acts in concert with the replication-transcription complex (nsp7/nsp8/nsp12). In this work, bioinformatics and computational tools allowed us to perform a detailed conservation analysis of the SARS-CoV-2 helicase genome and to further predict the druggable enzyme's binding pockets. Thus, a structure-based virtual screening was used to identify valuable compounds that are capable of recognizing multiple nsp13 pockets. Starting from a database of around 4000 drugs already approved by the Food and Drug Administration (FDA), we chose 14 shared compounds capable of recognizing three out of four sites. Finally, by means of visual inspection analysis and based on their commercial availability, five promising compounds were submitted to in vitro assays. Among them, PF-03715455 was able to block both the unwinding and NTPase activities of nsp13 in a micromolar range.
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Affiliation(s)
- Isabella Romeo
- Dipartimento di Scienze della Salute, Università degli Studi “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy
- Net4Science Academic Spin-Off, Università degli Studi “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy
| | - Francesca Alessandra Ambrosio
- Dipartimento di Medicina Sperimentale e Clinica, Università degli Studi “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy
| | - Giosuè Costa
- Dipartimento di Scienze della Salute, Università degli Studi “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy
- Net4Science Academic Spin-Off, Università degli Studi “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy
| | - Angela Corona
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, 09124 Cagliari, Italy
| | - Mohammad Alkhatib
- Dipartimento di Medicina Sperimentale, Università Tor Vergata di Roma, Via Montpellier, 1, 00133 Roma, Italy
| | - Romina Salpini
- Dipartimento di Medicina Sperimentale, Università Tor Vergata di Roma, Via Montpellier, 1, 00133 Roma, Italy
| | - Saverio Lemme
- Dipartimento di Medicina Sperimentale, Università Tor Vergata di Roma, Via Montpellier, 1, 00133 Roma, Italy
| | - Davide Vergni
- Istituto per le Applicazioni del Calcolo “Mauro Picone”-CNR, 00185 Rome, Italy
| | - Valentina Svicher
- Dipartimento di Medicina Sperimentale, Università Tor Vergata di Roma, Via Montpellier, 1, 00133 Roma, Italy
| | - Maria Mercedes Santoro
- Dipartimento di Medicina Sperimentale, Università Tor Vergata di Roma, Via Montpellier, 1, 00133 Roma, Italy
| | - Enzo Tramontano
- Department of Life and Environmental Sciences, University of Cagliari, Cittadella Universitaria di Monserrato, 09124 Cagliari, Italy
| | | | - Anna Artese
- Dipartimento di Scienze della Salute, Università degli Studi “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy
- Net4Science Academic Spin-Off, Università degli Studi “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Università degli Studi “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy
- Net4Science Academic Spin-Off, Università degli Studi “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy
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Gangadharan S, Ambrose JM, Rajajagadeesan A, Kullappan M, Patil S, Gandhamaneni SH, Veeraraghavan VP, Nakkella AK, Agarwal A, Jayaraman S, Surapaneni KM. Repurposing of potential antiviral drugs against RNA-dependent RNA polymerase of SARS-CoV-2 by computational approach. J Infect Public Health 2022; 15:1180-1191. [PMID: 36240528 PMCID: PMC9514006 DOI: 10.1016/j.jiph.2022.09.007] [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: 08/10/2022] [Revised: 09/16/2022] [Accepted: 09/20/2022] [Indexed: 01/18/2023] Open
Abstract
The high incidences of COVID-19 cases are believed to be associated with high transmissibility rates, which emphasizes the need for the discovery of evidence-based antiviral therapies for curing the disease. The rationale of repurposing existing classes of antiviral small molecule therapeutics against SARS-CoV-2 infection has been expected to accelerate the tedious and expensive drug development process. While Remdesivir has been recently approved to be the first treatment option for specific groups of COVID-19 patients, combinatory therapy with potential antiviral drugs may be necessary to enhance the efficacy in different populations. Hence, a comprehensive list of investigational antimicrobial drug compounds such as Favipiravir, Fidaxomicin, Galidesivir, GC376, Ribavirin, Rifabutin, and Umifenovir were computationally evaluated in this study. We performed in silico docking and molecular dynamics simulation on the selected small molecules against RNA-dependent RNA polymerase, which is one of the key target proteins of SARS-CoV-2, using AutoDock and GROMACS. Interestingly, our results revealed that the macrocyclic antibiotic, Fidaxomicin, possesses the highest binding affinity with the lowest energy value of -8.97 kcal/mol binding to the same active sites of RdRp. GC376, Rifabutin, Umifenovir and Remdesivir were identified as the next best compounds. Therefore, the above-mentioned compounds could be considered good leads for further preclinical and clinical experimentations as potentially efficient antiviral inhibitors for combination therapies against SARS-CoV-2.
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Affiliation(s)
- Sivakumar Gangadharan
- Department of Chemistry, Panimalar Engineering College, Varadharajapuram, Poonamallee, Chennai 600123, Tamil Nadu, India.
| | - Jenifer Mallavarpu Ambrose
- Department of Research, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Chennai 600123, Tamil Nadu, India.
| | - Anusha Rajajagadeesan
- Department of Biochemistry, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Chennai 600123, Tamil Nadu, India.
| | - Malathi Kullappan
- Department of Research, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Chennai 600123, Tamil Nadu, India.
| | - Shankargouda Patil
- College of Dental Medicine, Roseman University of Health Sciences, South Jordan, UTAH-84095, USA; Centre of Molecular Medicine and Diagnostics ( COMManD), Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai 600077, India.
| | - Sri Harshini Gandhamaneni
- Department of General Medicine, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Chennai 600123, Tamil Nadu, India.
| | - Vishnu Priya Veeraraghavan
- Centre of Molecular Medicine and Diagnostics ( COMManD), Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai 600077, India.
| | - Aruna Kumari Nakkella
- Department of Engineering Chemistry, Dr B R Ambedkar University, Etcherla, Srikakulam 532410, Andhra Pradesh, India.
| | - Alok Agarwal
- Department of Chemistry, Chinmaya Degree College, BHEL, Haridwar 249403, Uttarakhand, India.
| | - Selvaraj Jayaraman
- Centre of Molecular Medicine and Diagnostics ( COMManD), Saveetha Dental College & Hospitals, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai 600077, India.
| | - Krishna Mohan Surapaneni
- Departments of Biochemistry, Molecular Virology, Research, Clinical Skills & Simulation, Panimalar Medical College Hospital & Research Institute, Varadharajapuram, Poonamallee, Chennai 600123, Tamil Nadu, India.
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Lu L, Zheng J, Liu B, Wu H, Huang J, Wu L, Li D. The m7G Modification Level and Immune Infiltration Characteristics in Patients with COVID-19. J Multidiscip Healthc 2022; 15:2461-2472. [PMID: 36320552 PMCID: PMC9618243 DOI: 10.2147/jmdh.s385050] [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: 08/04/2022] [Accepted: 10/14/2022] [Indexed: 11/10/2022] Open
Abstract
Purpose The 7-methylguanosine (m7G)-related genes were used to identify the clinical severity and prognosis of patients with coronavirus disease 2019 (COVID-19) and to identify possible therapeutic targets. Patients and Methods The GSE157103 dataset provides the transcriptional spectrum and clinical information required to analyze the expression of m7G-related genes and the disease subtypes. R language was applied for immune infiltration analysis, functional enrichment analysis, and nomogram model construction. Results Most m7G-related genes were up-regulated in COVID-19 and were closely related to immune cell infiltration. Disease subtypes were grouped using a clustering algorithm. It was found that the m7G-cluster B was associated with higher immune infiltration, lower mechanical ventilation, lower intensive care unit (ICU) status, higher ventilator-free days, and lower m7G scores. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that differentially expressed genes (DEGs) between m7G-cluster A and B were enriched in viral infection and immune-related aspects, including COVID-19 infection; Th17, Th1, and Th2 cell differentiation, and human T-cell leukemia virus 1 infection. Finally, through machine learning, six disease characteristic genes, NUDT4B, IFIT5, LARP1, EIF4E, LSM1, and NUDT4, were screened and used to develop a nomogram model to estimate disease risk. Conclusion The expression of most m7G genes was higher in COVID-19 patients compared with that in non-COVID-19 patients. The m7G-cluster B showed higher immune infiltration and milder symptoms. The predictive nomogram based on the six m7G genes can be used to accurately assess risk.
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Affiliation(s)
- Lingling Lu
- Fuzong Clinical Medical College of Fujian Medical University, The 900th Hospital, Fuzhou, People’s Republic of China
| | - Jiaolong Zheng
- Fuzong Clinical Medical College of Fujian Medical University, The 900th Hospital, Fuzhou, People’s Republic of China,Department of Hepatobiliary Disease, The 900th Hospital of Joint Logistics Support Force, Fuzhou, People’s Republic of China
| | - Bang Liu
- Fuzong Clinical Medical College of Fujian Medical University, The 900th Hospital, Fuzhou, People’s Republic of China
| | - Haicong Wu
- Fuzong Clinical Medical College of Fujian Medical University, The 900th Hospital, Fuzhou, People’s Republic of China,Department of Hepatobiliary Disease, The 900th Hospital of Joint Logistics Support Force, Fuzhou, People’s Republic of China
| | - Jiaofeng Huang
- Fuzong Clinical Medical College of Fujian Medical University, The 900th Hospital, Fuzhou, People’s Republic of China
| | - Liqing Wu
- Department of Hepatobiliary Disease, The 900th Hospital of Joint Logistics Support Force, Fuzhou, People’s Republic of China
| | - Dongliang Li
- Fuzong Clinical Medical College of Fujian Medical University, The 900th Hospital, Fuzhou, People’s Republic of China,Department of Hepatobiliary Disease, The 900th Hospital of Joint Logistics Support Force, Fuzhou, People’s Republic of China,Correspondence: Dongliang Li, Fuzong Clinical Medical College of Fujian Medical University, The 900th Hospital of the People’s Liberation Army Joint Logistics Support Force, No. 156 Xierhuan Road, Fuzhou, Fujian, 350025, People’s Republic of China, Tel/Fax +86 591 22859128, Email
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48
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Shannon A, Sama B, Gauffre P, Guez T, Debart F, Vasseur JJ, Decroly E, Canard B, Ferron F. A second type of N7-guanine RNA cap methyltransferase in an unusual locus of a large RNA virus genome. Nucleic Acids Res 2022; 50:11186-11198. [PMID: 36265859 DOI: 10.1093/nar/gkac876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 09/29/2022] [Indexed: 11/12/2022] Open
Abstract
The order Nidovirales is a diverse group of (+)RNA viruses, with a common genome organization and conserved set of replicative and editing enzymes. In particular, RNA methyltransferases play a central role in mRNA stability and immune escape. However, their presence and distribution in different Nidovirales families is not homogeneous. In Coronaviridae, the best characterized family, two distinct methytransferases perform methylation of the N7-guanine and 2'-OH of the RNA-cap to generate a cap-1 structure (m7GpppNm). The genes of both of these enzymes are located in the ORF1b genomic region. While 2'-O-MTases can be identified for most other families based on conservation of both sequence motifs and genetic loci, identification of the N7-guanine methyltransferase has proved more challenging. Recently, we identified a putative N7-MTase domain in the ORF1a region (N7-MT-1a) of certain members of the large genome Tobaniviridae family. Here, we demonstrate that this domain indeed harbors N7-specific methyltransferase activity. We present its structure as the first N7-specific Rossmann-fold (RF) MTase identified for (+)RNA viruses, making it remarkably different from that of the known Coronaviridae ORF1b N7-MTase gene. We discuss the evolutionary implications of such an appearance in this unexpected location in the genome, which introduces a split-off in the classification of Tobaniviridae.
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Affiliation(s)
- Ashleigh Shannon
- Aix-Marseille Université and CNRS, Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 7257, 13009, Marseille, France
| | - Bhawna Sama
- Aix-Marseille Université and CNRS, Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 7257, 13009, Marseille, France
| | - Pierre Gauffre
- Aix-Marseille Université and CNRS, Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 7257, 13009, Marseille, France
| | - Théo Guez
- IBMM, University of Montpellier, CNRS, ENSCM, Montpellier, France
| | - Françoise Debart
- IBMM, University of Montpellier, CNRS, ENSCM, Montpellier, France
| | | | - Etienne Decroly
- Aix-Marseille Université and CNRS, Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 7257, 13009, Marseille, France
| | - Bruno Canard
- Aix-Marseille Université and CNRS, Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 7257, 13009, Marseille, France.,European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
| | - François Ferron
- Aix-Marseille Université and CNRS, Laboratoire Architecture et Fonction des Macromolécules Biologiques, UMR 7257, 13009, Marseille, France.,European Virus Bioinformatics Center, Leutragraben 1, 07743 Jena, Germany
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49
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Marx SK, Mickolajczyk KJ, Craig JM, Thomas CA, Pfeffer AM, Abell SJ, Carrasco JD, Franzi MC, Huang JR, Kim HC, Brinkerhoff HD, Kapoor TM, Gundlach JH, Laszlo AH. Inhibition of the SARS-CoV-2 helicase at single-nucleotide resolution. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.10.07.511351. [PMID: 36238723 PMCID: PMC9558434 DOI: 10.1101/2022.10.07.511351] [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: 06/16/2023]
Abstract
The genome of SARS-CoV-2 encodes for a helicase called nsp13 that is essential for viral replication and highly conserved across related viruses, making it an attractive antiviral target. Here we use nanopore tweezers, a high-resolution single-molecule technique, to gain detailed insight into how nsp13 turns ATP-hydrolysis into directed motion along nucleic acid strands. We measured nsp13 both as it translocates along single-stranded DNA or unwinds short DNA duplexes. Our data confirm that nsp13 uses the inchworm mechanism to move along the DNA in single-nucleotide steps, translocating at ~1000 nt/s or unwinding at ~100 bp/s. Nanopore tweezers' high spatio-temporal resolution enables observation of the fundamental physical steps taken by nsp13 even as it translocates at speeds in excess of 1000 nucleotides per second enabling detailed kinetic analysis of nsp13 motion. As a proof-of-principle for inhibition studies, we observed nsp13's motion in the presence of the ATPase inhibitor ATPγS. Our data reveals that ATPγS interferes with nsp13's action by affecting several different kinetic processes. The dominant mechanism of inhibition differs depending on the application of assisting force. These advances demonstrate that nanopore tweezers are a powerful method for studying viral helicase mechanism and inhibition.
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Affiliation(s)
- Sinduja K Marx
- Department of Physics, University of Washington, Seattle, WA 98195
| | - Keith J Mickolajczyk
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, New York
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, USA
| | - Jonathan M Craig
- Department of Physics, University of Washington, Seattle, WA 98195
| | | | - Akira M Pfeffer
- Department of Physics, University of Washington, Seattle, WA 98195
| | - Sarah J Abell
- Department of Physics, University of Washington, Seattle, WA 98195
| | | | | | - Jesse R Huang
- Department of Physics, University of Washington, Seattle, WA 98195
| | - Hwanhee C Kim
- Department of Physics, University of Washington, Seattle, WA 98195
| | | | - Tarun M Kapoor
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, New York
| | - Jens H Gundlach
- Department of Physics, University of Washington, Seattle, WA 98195
| | - Andrew H Laszlo
- Department of Physics, University of Washington, Seattle, WA 98195
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50
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Duan X, Lacko LA, Chen S. Druggable targets and therapeutic development for COVID-19. Front Chem 2022; 10:963701. [PMID: 36277347 PMCID: PMC9581228 DOI: 10.3389/fchem.2022.963701] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 07/11/2022] [Indexed: 12/15/2022] Open
Abstract
Coronavirus disease (COVID-19), which is caused by SARS-CoV-2, is the biggest challenge to the global public health and economy in recent years. Until now, only limited therapeutic regimens have been available for COVID-19 patients, sparking unprecedented efforts to study coronavirus biology. The genome of SARS-CoV-2 encodes 16 non-structural, four structural, and nine accessory proteins, which mediate the viral life cycle, including viral entry, RNA replication and transcription, virion assembly and release. These processes depend on the interactions between viral polypeptides and host proteins, both of which could be potential therapeutic targets for COVID-19. Here, we will discuss the potential medicinal value of essential proteins of SARS-CoV-2 and key host factors. We summarize the most updated therapeutic interventions for COVID-19 patients, including those approved clinically or in clinical trials.
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