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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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Berta D, Badaoui M, Martino SA, Buigues PJ, Pisliakov AV, Elghobashi-Meinhardt N, Wells G, Harris SA, Frezza E, Rosta E. Modelling the active SARS-CoV-2 helicase complex as a basis for structure-based inhibitor design. Chem Sci 2021; 12:13492-13505. [PMID: 34777769 PMCID: PMC8528070 DOI: 10.1039/d1sc02775a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 09/01/2021] [Indexed: 01/18/2023] Open
Abstract
The RNA helicase (non-structural protein 13, NSP13) of SARS-CoV-2 is essential for viral replication, and it is highly conserved among the coronaviridae family, thus a prominent drug target to treat COVID-19. We present here structural models and dynamics of the helicase in complex with its native substrates based on thorough analysis of homologous sequences and existing experimental structures. We performed and analysed microseconds of molecular dynamics (MD) simulations, and our model provides valuable insights to the binding of the ATP and ssRNA at the atomic level. We identify the principal motions characterising the enzyme and highlight the effect of the natural substrates on this dynamics. Furthermore, allosteric binding sites are suggested by our pocket analysis. Our obtained structural and dynamical insights are important for subsequent studies of the catalytic function and for the development of specific inhibitors at our characterised binding pockets for this promising COVID-19 drug target.
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Affiliation(s)
- Dénes Berta
- Department of Physics and Astronomy, University College London London WC1E 6BT UK
- Department of Chemistry, King's College London London SE1 1DB UK
| | - Magd Badaoui
- Department of Physics and Astronomy, University College London London WC1E 6BT UK
- Department of Chemistry, King's College London London SE1 1DB UK
| | - Sam Alexander Martino
- Department of Physics and Astronomy, University College London London WC1E 6BT UK
- Department of Chemistry, King's College London London SE1 1DB UK
| | - Pedro J Buigues
- Department of Physics and Astronomy, University College London London WC1E 6BT UK
- Department of Chemistry, King's College London London SE1 1DB UK
| | - Andrei V Pisliakov
- Computational Biology, School of Science and Engineering, School of Life Sciences, University of Dundee Dow Street Dundee DD1 5EH UK
| | | | - Geoff Wells
- UCL School of Pharmacy, University College London 29/39 Brunswick Square London WC1N 1AX UK
| | - Sarah A Harris
- School of Physics & Astronomy, University of Leeds Leeds LS2 9JT UK
| | - Elisa Frezza
- Université de Paris, CiTCoM, CNRS F-75006 Paris France
| | - Edina Rosta
- Department of Physics and Astronomy, University College London London WC1E 6BT UK
- Department of Chemistry, King's College London London SE1 1DB UK
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Abstract
Coronaviruses are animal and human pathogens that can cause lethal zoonotic infections like SARS and MERS. They have polycistronic plus-stranded RNA genomes and belong to the order Nidovirales, a diverse group of viruses for which common ancestry was inferred from the common principles underlying their genome organization and expression, and from the conservation of an array of core replicase domains, including key RNA-synthesizing enzymes. Coronavirus genomes (~ 26–32 kilobases) are the largest RNA genomes known to date and their expansion was likely enabled by acquiring enzyme functions that counter the commonly high error frequency of viral RNA polymerases. The primary functions that direct coronavirus RNA synthesis and processing reside in nonstructural protein (nsp) 7 to nsp16, which are cleavage products of two large replicase polyproteins translated from the coronavirus genome. Significant progress has now been made regarding their structural and functional characterization, stimulated by technical advances like improved methods for bioinformatics and structural biology, in vitro enzyme characterization, and site-directed mutagenesis of coronavirus genomes. Coronavirus replicase functions include more or less universal activities of plus-stranded RNA viruses, like an RNA polymerase (nsp12) and helicase (nsp13), but also a number of rare or even unique domains involved in mRNA capping (nsp14, nsp16) and fidelity control (nsp14). Several smaller subunits (nsp7–nsp10) act as crucial cofactors of these enzymes and contribute to the emerging “nsp interactome.” Understanding the structure, function, and interactions of the RNA-synthesizing machinery of coronaviruses will be key to rationalizing their evolutionary success and the development of improved control strategies.
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Affiliation(s)
- E J Snijder
- Leiden University Medical Center, Leiden, The Netherlands.
| | - E Decroly
- Aix-Marseille Université, AFMB UMR 7257, Marseille, France; CNRS, AFMB UMR 7257, Marseille, France
| | - J Ziebuhr
- Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany.
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Lehmann KC, Snijder EJ, Posthuma CC, Gorbalenya AE. What we know but do not understand about nidovirus helicases. Virus Res 2014; 202:12-32. [PMID: 25497126 PMCID: PMC7114383 DOI: 10.1016/j.virusres.2014.12.001] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 11/28/2014] [Accepted: 12/01/2014] [Indexed: 01/24/2023]
Abstract
The ubiquitous nidovirus helicase is a multi-functional enzyme of superfamily 1. Its unique N-terminal domain is most similar to the Upf1 multinuclear zinc-binding domain. It has been implicated in replication, transcription, virion biogenesis, translation and post-transcriptional viral RNA processing. Four different classes of antiviral compounds targeting the helicase have been identified.
Helicases are versatile NTP-dependent motor proteins of monophyletic origin that are found in all kingdoms of life. Their functions range from nucleic acid duplex unwinding to protein displacement and double-strand translocation. This explains their participation in virtually every metabolic process that involves nucleic acids, including DNA replication, recombination and repair, transcription, translation, as well as RNA processing. Helicases are encoded by all plant and animal viruses with a positive-sense RNA genome that is larger than 7 kb, indicating a link to genome size evolution in this virus class. Viral helicases belong to three out of the six currently recognized superfamilies, SF1, SF2, and SF3. Despite being omnipresent, highly conserved and essential, only a few viral helicases, mostly from SF2, have been studied extensively. In general, their specific roles in the viral replication cycle remain poorly understood at present. The SF1 helicase protein of viruses classified in the order Nidovirales is encoded in replicase open reading frame 1b (ORF1b), which is translated to give rise to a large polyprotein following a ribosomal frameshift from the upstream ORF1a. Proteolytic processing of the replicase polyprotein yields a dozen or so mature proteins, one of which includes a helicase. Its hallmark is the presence of an N-terminal multi-nuclear zinc-binding domain, the nidoviral genetic marker and one of the most conserved domains across members of the order. This review summarizes biochemical, structural, and genetic data, including drug development studies, obtained using helicases originating from several mammalian nidoviruses, along with the results of the genomics characterization of a much larger number of (putative) helicases of vertebrate and invertebrate nidoviruses. In the context of our knowledge of related helicases of cellular and viral origin, it discusses the implications of these results for the protein's emerging critical function(s) in nidovirus evolution, genome replication and expression, virion biogenesis, and possibly also post-transcriptional processing of viral RNAs. Using our accumulated knowledge and highlighting gaps in our data, concepts and approaches, it concludes with a perspective on future research aimed at elucidating the role of helicases in the nidovirus replication cycle.
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Affiliation(s)
- Kathleen C Lehmann
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Eric J Snijder
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Clara C Posthuma
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Alexander E Gorbalenya
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands; Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Russia.
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Development of chemical inhibitors of the SARS coronavirus: viral helicase as a potential target. Biochem Pharmacol 2012; 84:1351-8. [PMID: 22935448 PMCID: PMC7092843 DOI: 10.1016/j.bcp.2012.08.012] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Revised: 08/14/2012] [Accepted: 08/15/2012] [Indexed: 11/21/2022]
Abstract
Severe acute respiratory syndrome (SARS) was the first pandemic in the 21st century to claim more than 700 lives worldwide. However, effective anti-SARS vaccines or medications are currently unavailable despite being desperately needed to adequately prepare for a possible SARS outbreak. SARS is caused by a novel coronavirus, and one of its components, a viral helicase, is emerging as a promising target for the development of chemical SARS inhibitors. In the following review, we describe the characterization, family classification, and kinetic movement mechanisms of the SARS coronavirus (SCV) helicase—nsP13. We also discuss the recent progress in the identification of novel chemical inhibitors of nsP13 in the context of our recent discovery of the strong inhibition of the SARS helicase by natural flavonoids, myricetin and scutellarein. These compounds will serve as important resources for the future development of anti-SARS medications.
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Nowosielski M, Hoffmann M, Wyrwicz LS, Stepniak P, Plewczynski DM, Lazniewski M, Ginalski K, Rychlewski L. Detailed Mechanism of Squalene Epoxidase Inhibition by Terbinafine. J Chem Inf Model 2011; 51:455-62. [DOI: 10.1021/ci100403b] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | - Marcin Hoffmann
- Quantum Chemistry Group, Department of Chemistry, Adam Mickiewicz University, Grunwaldzka 6, 60-780 Poznań, Poland
| | - Lucjan S. Wyrwicz
- BioInfoBank Institute, Limanowskiego 24A, 60-744 Poznań, Poland
- Laboratory of Bioinformatics and Systems Biology, M. Sklodowska-Curie Cancer Center and Institute of Oncology, WK Roentgena 5, 02-781 Warsaw, Poland
| | - Piotr Stepniak
- BioInfoBank Institute, Limanowskiego 24A, 60-744 Poznań, Poland
| | - Dariusz M. Plewczynski
- Laboratory of Bioinformatics and Systems Biology, Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Michal Lazniewski
- Laboratory of Bioinformatics and Systems Biology, Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
- Department of Physical Chemistry, Faculty of Pharmacy, Medical University of Warsaw, Banacha 1, 02-097 Warsaw, Poland
| | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Pawinskiego 5a, 02-106 Warsaw, Poland
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Lee NR, Kwon HM, Park K, Oh S, Jeong YJ, Kim DE. Cooperative translocation enhances the unwinding of duplex DNA by SARS coronavirus helicase nsP13. Nucleic Acids Res 2010; 38:7626-36. [PMID: 20671029 PMCID: PMC2995068 DOI: 10.1093/nar/gkq647] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
SARS coronavirus encodes non-structural protein 13 (nsP13), a nucleic acid helicase/NTPase belonging to superfamily 1 helicase, which efficiently unwinds both partial-duplex RNA and DNA. In this study, unwinding of DNA substrates that had different duplex lengths and 5'-overhangs was examined under single-turnover reaction conditions in the presence of excess enzyme. The amount of DNA unwound decreased significantly as the length of the duplex increased, indicating a poor in vitro processivity. However, the quantity of duplex DNA unwound increased as the length of the single-stranded 5'-tail increased for the 50-bp duplex. This enhanced processivity was also observed for duplex DNA that had a longer single-stranded gap in between. These results demonstrate that nsP13 requires the presence of a long 5'-overhang to unwind longer DNA duplexes. In addition, enhanced DNA unwinding was observed for gapped DNA substrates that had a 5'-overhang, indicating that the translocated nsP13 molecules pile up and the preceding helicase facilitate DNA unwinding. Together with the propensity of oligomer formation of nsP13 molecules, we propose that the cooperative translocation by the functionally interacting oligomers of the helicase molecules loaded onto the 5'-overhang account for the observed enhanced processivity of DNA unwinding.
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Affiliation(s)
- Na-Ra Lee
- Department of Bio and Nanochemistry, Kookmin University, Seoul 136-702, Republic of Korea
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ATP Hydrolysis Analysis of Severe Acute Respiratory Syndrome (SARS) Coronavirus Helicase. B KOREAN CHEM SOC 2009. [DOI: 10.5012/bkcs.2009.30.8.1724] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Chen JY, Chen WN, Poon KMV, Zheng BJ, Lin X, Wang YX, Wen YM. Interaction between SARS-CoV helicase and a multifunctional cellular protein (Ddx5) revealed by yeast and mammalian cell two-hybrid systems. Arch Virol 2009; 154:507-12. [PMID: 19224332 PMCID: PMC7087151 DOI: 10.1007/s00705-009-0323-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2008] [Accepted: 01/12/2009] [Indexed: 02/04/2023]
Abstract
To reveal the putative cellular factors involved in SARS coronavirus replication, the helicase (Hel, nsp13) of SARS coronavirus was used to screen the cDNA library of rat pulmonary epithelial cells using the yeast two-hybrid system. Positively interacting proteins were further tested using a mammalian cell hybrid system and co-immunoprecipitation in the human A549 cell line, which has been shown to support SARS coronavirus replication. Out of the seven positive clones observed by yeast two-hybrid assay, only the Ddx5 (Asp-Glu-Ala-Asp box polypeptide 5) protein showed specific interaction with SARS-CoV helicase. When expression of DdX5 was knocked down by small interfering RNA (siRNA), SARS coronavirus replication was significantly inhibited in fetal rhesus kidney (FRhK-4) cells. Since Ddx5 is a multifunctional protein that plays important roles in transcriptional regulation, its interaction with SARS coronavirus helicase provides interesting clues for studying virus–host cell interactions in SARS-CoV infections.
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Affiliation(s)
- Jin-Yan Chen
- Key Laboratory of Infection and Oncology, Research Center of Molecular Medicine, Fujian Medical University, 350004, Fuzhou, People's Republic of China
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The interactome: predicting the protein-protein interactions in cells. Cell Mol Biol Lett 2008; 14:1-22. [PMID: 18839074 PMCID: PMC6275871 DOI: 10.2478/s11658-008-0024-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2008] [Accepted: 04/03/2008] [Indexed: 12/03/2022] Open
Abstract
The term Interactome describes the set of all molecular interactions in cells, especially in the context of protein-protein interactions. These interactions are crucial for most cellular processes, so the full representation of the interaction repertoire is needed to understand the cell molecular machinery at the system biology level. In this short review, we compare various methods for predicting protein-protein interactions using sequence and structure information. The ultimate goal of those approaches is to present the complete methodology for the automatic selection of interaction partners using their amino acid sequences and/or three dimensional structures, if known. Apart from a description of each method, details of the software or web interface needed for high throughput prediction on the whole genome scale are also provided. The proposed validation of the theoretical methods using experimental data would be a better assessment of their accuracy.
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Recent antiviral strategies against human coronavirus-related respiratory illnesses. Curr Opin Pulm Med 2008; 14:248-53. [PMID: 18427249 DOI: 10.1097/mcp.0b013e3282f7646f] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
PURPOSE OF REVIEW The main purpose of this review is to summarize the current research (2006-2007) concerning the development of novel anticoronaviral strategies and compounds. RECENT FINDINGS Recent research led to the identification of several novel agents inhibiting coronaviral replication. The most promising compounds include carbohydrate-binding agents, neutralizing antibodies and drugs targeting a coronaviral envelope protein. SUMMARY Although initial outbreaks of coronavirus that causes severe acute respiratory syndrome (SARS-CoV) were controlled by public health measures, the development of vaccines and antiviral agents for SARS-CoV is essential for improving control and treatment of future outbreaks. Four years after the SARS-CoV epidemic, several compounds with an anticoronaviral activity have been identified.
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