1
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Soper N, Yardumian I, Chen E, Yang C, Ciervo S, Oom AL, Desvignes L, Mulligan MJ, Zhang Y, Lupoli TJ. A Repurposed Drug Interferes with Nucleic Acid to Inhibit the Dual Activities of Coronavirus Nsp13. ACS Chem Biol 2024; 19:1593-1603. [PMID: 38980755 PMCID: PMC11267572 DOI: 10.1021/acschembio.4c00244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/31/2024] [Accepted: 06/10/2024] [Indexed: 07/11/2024]
Abstract
The recent pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) highlighted a critical need to discover more effective antivirals. While therapeutics for SARS-CoV-2 exist, its nonstructural protein 13 (Nsp13) remains a clinically untapped target. Nsp13 is a helicase responsible for unwinding double-stranded RNA during viral replication and is essential for propagation. Like other helicases, Nsp13 has two active sites: a nucleotide binding site that hydrolyzes nucleoside triphosphates (NTPs) and a nucleic acid binding channel that unwinds double-stranded RNA or DNA. Targeting viral helicases with small molecules, as well as the identification of ligand binding pockets, have been ongoing challenges, partly due to the flexible nature of these proteins. Here, we use a virtual screen to identify ligands of Nsp13 from a collection of clinically used drugs. We find that a known ion channel inhibitor, IOWH-032, inhibits the dual ATPase and helicase activities of SARS-CoV-2 Nsp13 at low micromolar concentrations. Kinetic and binding assays, along with computational and mutational analyses, indicate that IOWH-032 interacts with the RNA binding interface, leading to displacement of nucleic acid substrate, but not bound ATP. Evaluation of IOWH-032 with microbial helicases from other superfamilies reveals that it is selective for coronavirus Nsp13. Furthermore, it remains active against mutants representative of observed SARS-CoV-2 variants. Overall, this work provides a new inhibitor for Nsp13 and provides a rationale for a recent observation that IOWH-032 lowers SARS-CoV-2 viral loads in human cells, setting the stage for the discovery of other potent viral helicase modulators.
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Affiliation(s)
- Nathan Soper
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - Isabelle Yardumian
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - Eric Chen
- Department
of Chemistry, New York University, New York, New York 10003, United States
- Simons
Center for Computational Physical Chemistry at New York University, New York, New York 10003, United States
| | - Chao Yang
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - Samantha Ciervo
- Department
of Chemistry, New York University, New York, New York 10003, United States
| | - Aaron L. Oom
- NYU
Langone Vaccine Center, Department of Medicine, New York University Grossman School of Medicine, New York, New York 10016, United States
| | - Ludovic Desvignes
- NYU
Langone Vaccine Center, Department of Medicine, New York University Grossman School of Medicine, New York, New York 10016, United States
- High
Containment Laboratories, Office of Science and Research, NYU Langone Health, New York, New York 10016, United States
| | - Mark J. Mulligan
- NYU
Langone Vaccine Center, Department of Medicine, New York University Grossman School of Medicine, New York, New York 10016, United States
| | - Yingkai Zhang
- Department
of Chemistry, New York University, New York, New York 10003, United States
- Simons
Center for Computational Physical Chemistry at New York University, New York, New York 10003, United States
| | - Tania J. Lupoli
- Department
of Chemistry, New York University, New York, New York 10003, United States
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2
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Hussein HAM, Thabet AA, Wardany AA, El-Adly AM, Ali M, Hassan MEA, Abdeldayem MAB, Mohamed ARMA, Sobhy A, El-Mokhtar MA, Afifi MM, Fathy SM, Sultan S. SARS-CoV-2 outbreak: role of viral proteins and genomic diversity in virus infection and COVID-19 progression. Virol J 2024; 21:75. [PMID: 38539202 PMCID: PMC10967059 DOI: 10.1186/s12985-024-02342-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 03/12/2024] [Indexed: 05/15/2024] Open
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection is the cause of coronavirus disease 2019 (COVID-19); a severe respiratory distress that has emerged from the city of Wuhan, Hubei province, China during December 2019. COVID-19 is currently the major global health problem and the disease has now spread to most countries in the world. COVID-19 has profoundly impacted human health and activities worldwide. Genetic mutation is one of the essential characteristics of viruses. They do so to adapt to their host or to move to another one. Viral genetic mutations have a high potentiality to impact human health as these mutations grant viruses unique unpredicted characteristics. The difficulty in predicting viral genetic mutations is a significant obstacle in the field. Evidence indicates that SARS-CoV-2 has a variety of genetic mutations and genomic diversity with obvious clinical consequences and implications. In this review, we comprehensively summarized and discussed the currently available knowledge regarding SARS-CoV-2 outbreaks with a fundamental focus on the role of the viral proteins and their mutations in viral infection and COVID-19 progression. We also summarized the clinical implications of SARS-CoV-2 variants and how they affect the disease severity and hinder vaccine development. Finally, we provided a massive phylogenetic analysis of the spike gene of 214 SARS-CoV-2 isolates from different geographical regions all over the world and their associated clinical implications.
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Affiliation(s)
- Hosni A M Hussein
- Department of Microbiology, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt.
| | - Ali A Thabet
- Department of Zoology, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt
| | - Ahmed A Wardany
- Department of Microbiology, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt
| | - Ahmed M El-Adly
- Department of Microbiology, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt
| | - Mohamed Ali
- Department of Microbiology, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt
| | - Mohamed E A Hassan
- Department of Microbiology, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt
| | - Mohamed A B Abdeldayem
- Department of Microbiology, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt
| | | | - Ali Sobhy
- Department of Clinical Pathology, Faculty of Medicine, Al-Azhar University, 71524, Assiut, Egypt
| | - Mohamed A El-Mokhtar
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Assiut University, Assiut, Egypt
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos Campus, Lebanon
| | - Magdy M Afifi
- Department of Botany and Microbiology, Faculty of Science, Al-Azhar University, Nasr City 11884, Cairo, Egypt
| | - Samah M Fathy
- Department of Zoology, Faculty of Science, Fayoum University, Fayoum, Egypt.
| | - Serageldeen Sultan
- Department of Microbiology, Virology Division, Faculty of Veterinary medicine, South Valley University, 83523, Qena, Egypt.
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3
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Stoll GA, Nikolopoulos N, Zhai H, Zhang L, Douse CH, Modis Y. Crystal structure and biochemical activity of the macrodomain from rubella virus p150. J Virol 2024; 98:e0177723. [PMID: 38289106 PMCID: PMC10878246 DOI: 10.1128/jvi.01777-23] [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: 11/14/2023] [Accepted: 12/22/2023] [Indexed: 02/13/2024] Open
Abstract
Rubella virus encodes a nonstructural polyprotein with RNA polymerase, methyltransferase, and papain-like cysteine protease activities, along with a putative macrodomain of unknown function. Macrodomains bind ADP-ribose adducts, a post-translational modification that plays a key role in host-virus conflicts. Some macrodomains can also remove the mono-ADP-ribose adduct or degrade poly-ADP-ribose chains. Here, we report high-resolution crystal structures of the macrodomain from rubella virus nonstructural protein p150, with and without ADP-ribose binding. The overall fold is most similar to macroD-type macrodomains from various nonviral species. The specific composition and structure of the residues that coordinate ADP-ribose in the rubella virus macrodomain are most similar to those of macrodomains from alphaviruses. Isothermal calorimetry shows that the rubella virus macrodomain binds ADP-ribose in solution. Enzyme assays show that the rubella virus macrodomain can hydrolyze both mono- and poly-ADP-ribose adducts. Site-directed mutagenesis identifies Asn39 and Cys49 required for mono-ADP-ribosylhydrolase (de-MARylation) activity.IMPORTANCERubella virus remains a global health threat. Rubella infections during pregnancy can cause serious congenital pathology, for which no antiviral treatments are available. Our work demonstrates that, like alpha- and coronaviruses, rubiviruses encode a mono-ADP-ribosylhydrolase with a structurally conserved macrodomain fold to counteract MARylation by poly (ADP-ribose) polymerases (PARPs) in the host innate immune response. Our structural data will guide future efforts to develop novel antiviral therapeutics against rubella or infections with related viruses.
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Affiliation(s)
- Guido A. Stoll
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Nikos Nikolopoulos
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Haoming Zhai
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Liao Zhang
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | | | - Yorgo Modis
- Molecular Immunity Unit, Department of Medicine, University of Cambridge, MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, Cambridge, United Kingdom
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4
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Sobotka AA, Tempera I. PARP1 as an Epigenetic Modulator: Implications for the Regulation of Host-Viral Dynamics. Pathogens 2024; 13:131. [PMID: 38392869 PMCID: PMC10891851 DOI: 10.3390/pathogens13020131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
The principal understanding of the Poly(ADP-ribose) polymerase (PARP) regulation of genomes has been focused on its role in DNA repair; however, in the past few years, an additional role for PARPs and PARylation has emerged in regulating viral-host interactions. In particular, in the context of DNA virus infection, PARP1-mediated mechanisms of gene regulations, such as the involvement with cellular protein complexes responsible for the folding of the genome into the nucleus, the formation of chromatin loops connecting distant regulatory genomic regions, and other methods of transcriptional regulation, provide additional ways through which PARPs can modulate the function of both the host and the viral genomes during viral infection. In addition, potential viral amplification of the activity of PARPs on the host genome can contribute to the pathogenic effect of viral infection, such as viral-driven oncogenesis, opening the possibility that PARP inhibition may represent a potential therapeutic approach to target viral infection. This review will focus on the role of PARPs, particularly PARP1, in regulating the infection of DNA viruses.
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Affiliation(s)
- Asher A. Sobotka
- Wistar Institute, Philadelphia, PA 19104, USA
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
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5
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Li X, Song Y. Targeting SARS-CoV-2 nonstructural protein 3: Function, structure, inhibition, and perspective in drug discovery. Drug Discov Today 2024; 29:103832. [PMID: 37977285 PMCID: PMC10872262 DOI: 10.1016/j.drudis.2023.103832] [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: 09/22/2023] [Revised: 11/06/2023] [Accepted: 11/13/2023] [Indexed: 11/19/2023]
Abstract
As a highly contagious human pathogen, severe acute respiratory syndrome-associated coronavirus-2 (SARS-CoV-2) has infected billions of people worldwide with more than 6 million deaths. With several effective vaccines and antiviral drugs now available, the SARS-CoV-2 pandemic been brought under control. However, a new pathogenic coronavirus could emerge in the future, given the zoonotic nature of this virus. Natural evolution and drug-induced mutations of SARS-CoV-2 also require continued efforts for new anti-coronavirus drugs. Nonstructural protein (nsp) 3 of CoVs is a large, multifunctional protein, containing a papain-like protease (PLpro) and a macrodomain (Mac1), which are essential for viral replication. Here, we provide a comprehensive review of the function, structure, and inhibition of SARS-CoV/-CoV-2 PLpro and Mac1. We also discuss advances in, and challenges to, the discovery of drugs against these targets.
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Affiliation(s)
- Xin Li
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA.
| | - Yongcheng Song
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA; Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA.
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6
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Zimmermann L, Zhao X, Makroczyova J, Wachsmuth-Melm M, Prasad V, Hensel Z, Bartenschlager R, Chlanda P. SARS-CoV-2 nsp3 and nsp4 are minimal constituents of a pore spanning replication organelle. Nat Commun 2023; 14:7894. [PMID: 38036567 PMCID: PMC10689437 DOI: 10.1038/s41467-023-43666-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 11/16/2023] [Indexed: 12/02/2023] Open
Abstract
Coronavirus replication is associated with the remodeling of cellular membranes, resulting in the formation of double-membrane vesicles (DMVs). A DMV-spanning pore was identified as a putative portal for viral RNA. However, the exact components and the structure of the SARS-CoV-2 DMV pore remain to be determined. Here, we investigate the structure of the DMV pore by in situ cryo-electron tomography combined with subtomogram averaging. We identify non-structural protein (nsp) 3 and 4 as minimal components required for the formation of a DMV-spanning pore, which is dependent on nsp3-4 proteolytic cleavage. In addition, we show that Mac2-Mac3-DPUP-Ubl2 domains are critical for nsp3 oligomerization and crown integrity which influences membrane curvature required for biogenesis of DMVs. Altogether, SARS-CoV-2 nsp3-4 have a dual role by driving the biogenesis of replication organelles and assembly of DMV-spanning pores which we propose here to term replicopores.
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Affiliation(s)
- Liv Zimmermann
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University, 69120, Heidelberg, Germany
| | - Xiaohan Zhao
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University, 69120, Heidelberg, Germany
| | - Jana Makroczyova
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University, 69120, Heidelberg, Germany
| | - Moritz Wachsmuth-Melm
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University, 69120, Heidelberg, Germany
| | - Vibhu Prasad
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120, Heidelberg, Germany
| | - Zach Hensel
- ITQB NOVA, Universidade NOVA de Lisboa, 2780-157, Oeiras, Portugal
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University, 69120, Heidelberg, Germany
- Division Virus-Associated Carcinogenesis, German Cancer Research Center (DKFZ), 69120, Heidelberg, Germany
- German Center for Infection Research (DZIF), Heidelberg partner site, 69120, Heidelberg, Germany
| | - Petr Chlanda
- Schaller Research Group, Department of Infectious Diseases, Virology, Heidelberg University, 69120, Heidelberg, Germany.
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7
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Yazdani B, Sirous H, Brogi S, Calderone V. Structure-Based High-Throughput Virtual Screening and Molecular Dynamics Simulation for the Discovery of Novel SARS-CoV-2 NSP3 Mac1 Domain Inhibitors. Viruses 2023; 15:2291. [PMID: 38140532 PMCID: PMC10747130 DOI: 10.3390/v15122291] [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: 10/17/2023] [Revised: 11/16/2023] [Accepted: 11/21/2023] [Indexed: 12/24/2023] Open
Abstract
Since the emergence of SARS-CoV-2, many genetic variations within its genome have been identified, but only a few mutations have been found in nonstructural proteins (NSPs). Among this class of viral proteins, NSP3 is a multidomain protein with 16 different domains, and its largest domain is known as the macrodomain or Mac1 domain. In this study, we present a virtual screening campaign in which we computationally evaluated the NCI anticancer library against the NSP3 Mac1 domain, using Molegro Virtual Docker. The top hits with the best MolDock and Re-Rank scores were selected. The physicochemical analysis and drug-like potential of the top hits were analyzed using the SwissADME data server. The binding stability and affinity of the top NSC compounds against the NSP3 Mac1 domain were analyzed using molecular dynamics (MD) simulation, using Desmond software, and their interaction energies were analyzed using the MM/GBSA method. In particular, by applying subsequent computational filters, we identified 10 compounds as possible NSP3 Mac1 domain inhibitors. Among them, after the assessment of binding energies (ΔGbind) on the whole MD trajectories, we identified the four most interesting compounds that acted as strong binders of the NSP3 Mac1 domain (NSC-358078, NSC-287067, NSC-123472, and NSC-142843), and, remarkably, it could be further characterized for developing innovative antivirals against SARS-CoV-2.
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Affiliation(s)
- Behnaz Yazdani
- Bioscience Department, Faculty of Science and Technology (FCT), Universitat de Vic—Universitat Central de Catalunya (Uvic-UCC), 08500 Vic, Spain;
| | - Hajar Sirous
- Bioinformatics Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan 81746-73461, Iran
| | - Simone Brogi
- Bioinformatics Research Center, School of Pharmacy and Pharmaceutical Sciences, Isfahan University of Medical Sciences, Isfahan 81746-73461, Iran
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy;
| | - Vincenzo Calderone
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy;
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8
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Ortega Granda O, Alvarez K, Mate-Perez MJ, Canard B, Ferron F, Rabah N. Macro1 domain residue F156: A hallmark of SARS-CoV-2 de-MARylation specificity. Virology 2023; 587:109845. [PMID: 37517331 DOI: 10.1016/j.virol.2023.109845] [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: 07/07/2023] [Accepted: 07/17/2023] [Indexed: 08/01/2023]
Abstract
SARS-CoV-2 is a large, enveloped and positive sense single stranded RNA virus. Its genome codes for 16 non-structural proteins. The largest protein of this complex is nsp3, that contains a well conserved Macro1 domain. Viral Macro domains were shown to bind to mono-ADP-ribose (MAR) and poly-ADP-ribose (PAR) in their free form or conjugated to protein substrates. They carry ADP-ribose hydrolase activities implicated in the regulation of innate immunity. SARS-CoV-2 and SARS-CoV show widely different induction and handling of the host interferon response. Herein, we have conducted a mutational study on the key amino-acid residue F156 in SARS-CoV-2, pinpointed by bioinformatic and structural studies, and its cognate residue N157 in SARS-CoV. Our data suggest that the exchange of these residues slightly modifies ADP-ribose binding, but drastically impacts de-MARylation activity. Alanine substitutions at this position hampers PAR binding, abolishes MAR hydrolysis of SARS-CoV-2, and reduces by 70% this activity in the case of SARS-CoV.
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Affiliation(s)
| | - Karine Alvarez
- Aix Marseille Université, CNRS, AFMB UMR 7257, Marseille, France
| | | | - Bruno Canard
- Aix Marseille Université, CNRS, AFMB UMR 7257, Marseille, France
| | - François Ferron
- Aix Marseille Université, CNRS, AFMB UMR 7257, Marseille, France
| | - Nadia Rabah
- Aix Marseille Université, CNRS, AFMB UMR 7257, Marseille, France; Previous Affiliation: Université de Toulon, 83130, La Garde, France.
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9
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Mohammad A, Alshawaf E, Arefanian H, Marafie SK, Khan A, Wei DQ, Al-Mulla F, Abubaker J. Targeting SARS-CoV-2 Macrodomain-1 to Restore the Innate Immune Response Using In Silico Screening of Medicinal Compounds and Free Energy Calculation Approaches. Viruses 2023; 15:1907. [PMID: 37766313 PMCID: PMC10538035 DOI: 10.3390/v15091907] [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: 07/17/2023] [Revised: 08/31/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Among the different drug targets of SARS-CoV-2, a multi-domain protein known as NSP3 is a critical element of the translational and replication machinery. The macrodomain-I, in particular, has been reported to have an essential role in the viral attack on the innate immune response. In this study, we explore natural medicinal compounds and identify potential inhibitors to target the SARS-CoV-2-NSP3 macrodomain-I. Computational modeling and simulation tools were utilized to investigate the structural-dynamic properties using triplicates of 100 ns MD simulations. In addition, the MM/GBSA method was used to calculate the total binding free energy of each inhibitor bound to macrodomain-I. Two significant hits were identified: 3,5,7,4'-tetrahydroxyflavanone 3'-(4-hydroxybenzoic acid) and 2-hydroxy-3-O-beta-glucopyranosyl-benzoic acid. The structural-dynamic investigation of both compounds with macrodomain-I revealed stable dynamics and compact behavior. In addition, the total binding free energy for each complex demonstrated a robust binding affinity, of ΔG -61.98 ± 0.9 kcal/mol for Compound A, while for Compound B, the ΔG was -45.125 ± 2.8 kcal/mol, indicating the inhibitory potential of these compounds. In silico bioactivity and dissociation constant (KD) determination for both complexes further validated the inhibitory potency of each compound. In conclusion, the aforementioned natural products have the potential to inhibit NSP3, to directly rescue the host immune response. The current study provides the basis for novel drug development against SARS-CoV-2 and its variants.
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Affiliation(s)
- Anwar Mohammad
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Dasman 15462, Kuwait; (E.A.); (S.K.M.); (J.A.)
| | - Eman Alshawaf
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Dasman 15462, Kuwait; (E.A.); (S.K.M.); (J.A.)
| | - Hossein Arefanian
- Department of Immunology and Microbiology, Dasman Diabetes Institute, Dasman 15462, Kuwait;
| | - Sulaiman K. Marafie
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Dasman 15462, Kuwait; (E.A.); (S.K.M.); (J.A.)
| | - Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (A.K.); (D.-Q.W.)
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China; (A.K.); (D.-Q.W.)
| | - Fahd Al-Mulla
- Department of Genetics and Bioinformatics, Dasman Diabetes Institute, Dasman 15462, Kuwait;
- Translational Research Department, Dasman Diabetes Institute, Dasman 15462, Kuwait
| | - Jehad Abubaker
- Department of Biochemistry and Molecular Biology, Dasman Diabetes Institute, Dasman 15462, Kuwait; (E.A.); (S.K.M.); (J.A.)
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10
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Abstract
Biomolecular condensates are reversible compartments that form through a process called phase separation. Post-translational modifications like ADP-ribosylation can nucleate the formation of these condensates by accelerating the self-association of proteins. Poly(ADP-ribose) (PAR) chains are remarkably transient modifications with turnover rates on the order of minutes, yet they can be required for the formation of granules in response to oxidative stress, DNA damage, and other stimuli. Moreover, accumulation of PAR is linked with adverse phase transitions in neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. In this review, we provide a primer on how PAR is synthesized and regulated, the diverse structures and chemistries of ADP-ribosylation modifications, and protein-PAR interactions. We review substantial progress in recent efforts to determine the molecular mechanism of PAR-mediated phase separation, and we further delineate how inhibitors of PAR polymerases may be effective treatments for neurodegenerative pathologies. Finally, we highlight the need for rigorous biochemical interrogation of ADP-ribosylation in vivo and in vitro to clarify the exact pathway from PARylation to condensate formation.
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Affiliation(s)
- Kevin Rhine
- Program in Cell, Molecular, Developmental Biology, and Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Biology, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Hana M Odeh
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, United States
| | - James Shorter
- Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania 19104, United States
| | - Sua Myong
- Program in Cell, Molecular, Developmental Biology, and Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Physics Frontier Center (Center for the Physics of Living Cells), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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11
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Kakavandi S, Zare I, VaezJalali M, Dadashi M, Azarian M, Akbari A, Ramezani Farani M, Zalpoor H, Hajikhani B. Structural and non-structural proteins in SARS-CoV-2: potential aspects to COVID-19 treatment or prevention of progression of related diseases. Cell Commun Signal 2023; 21:110. [PMID: 37189112 DOI: 10.1186/s12964-023-01104-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 03/15/2023] [Indexed: 05/17/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is caused by a new member of the Coronaviridae family known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). There are structural and non-structural proteins (NSPs) in the genome of this virus. S, M, H, and E proteins are structural proteins, and NSPs include accessory and replicase proteins. The structural and NSP components of SARS-CoV-2 play an important role in its infectivity, and some of them may be important in the pathogenesis of chronic diseases, including cancer, coagulation disorders, neurodegenerative disorders, and cardiovascular diseases. The SARS-CoV-2 proteins interact with targets such as angiotensin-converting enzyme 2 (ACE2) receptor. In addition, SARS-CoV-2 can stimulate pathological intracellular signaling pathways by triggering transcription factor hypoxia-inducible factor-1 (HIF-1), neuropilin-1 (NRP-1), CD147, and Eph receptors, which play important roles in the progression of neurodegenerative diseases like Alzheimer's disease, epilepsy, and multiple sclerosis, and multiple cancers such as glioblastoma, lung malignancies, and leukemias. Several compounds such as polyphenols, doxazosin, baricitinib, and ruxolitinib could inhibit these interactions. It has been demonstrated that the SARS-CoV-2 spike protein has a stronger affinity for human ACE2 than the spike protein of SARS-CoV, leading the current study to hypothesize that the newly produced variant Omicron receptor-binding domain (RBD) binds to human ACE2 more strongly than the primary strain. SARS and Middle East respiratory syndrome (MERS) viruses against structural and NSPs have become resistant to previous vaccines. Therefore, the review of recent studies and the performance of current vaccines and their effects on COVID-19 and related diseases has become a vital need to deal with the current conditions. This review examines the potential role of these SARS-CoV-2 proteins in the initiation of chronic diseases, and it is anticipated that these proteins could serve as components of an effective vaccine or treatment for COVID-19 and related diseases. Video Abstract.
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Affiliation(s)
- Sareh Kakavandi
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Iman Zare
- Research and Development Department, Sina Medical Biochemistry Technologies Co. Ltd., Shiraz, 7178795844, Iran
| | - Maryam VaezJalali
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Masoud Dadashi
- Department of Microbiology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
- Non-Communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran
| | - Maryam Azarian
- Department of Radiology, Charité - Universitätsmedizin Berlin, 10117, Berlin, Germany
| | - Abdullatif Akbari
- Shiraz Neuroscience Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran
| | - Marzieh Ramezani Farani
- Department of Biological Sciences and Bioengineering, Nano Bio High-Tech Materials Research Center, Inha University, Incheon, 22212, Republic of Korea
| | - Hamidreza Zalpoor
- Shiraz Neuroscience Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Tehran, Iran.
| | - Bahareh Hajikhani
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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12
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Delgado-Rodriguez SE, Ryan AP, Daugherty MD. Recurrent Loss of Macrodomain Activity in Host Immunity and Viral Proteins. Pathogens 2023; 12:674. [PMID: 37242344 PMCID: PMC10221186 DOI: 10.3390/pathogens12050674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 04/29/2023] [Accepted: 04/30/2023] [Indexed: 05/28/2023] Open
Abstract
Protein post-translational modifications (PTMs) are an important battleground in the evolutionary arms races that are waged between the host innate immune system and viruses. One such PTM, ADP-ribosylation, has recently emerged as an important mediator of host antiviral immunity. Important for the host-virus conflict over this PTM is the addition of ADP-ribose by PARP proteins and removal of ADP-ribose by macrodomain-containing proteins. Interestingly, several host proteins, known as macroPARPs, contain macrodomains as well as a PARP domain, and these proteins are both important for the host antiviral immune response and evolving under very strong positive (diversifying) evolutionary selection. In addition, several viruses, including alphaviruses and coronaviruses, encode one or more macrodomains. Despite the presence of the conserved macrodomain fold, the enzymatic activity of many of these proteins has not been characterized. Here, we perform evolutionary and functional analyses to characterize the activity of macroPARP and viral macrodomains. We trace the evolutionary history of macroPARPs in metazoans and show that PARP9 and PARP14 contain a single active macrodomain, whereas PARP15 contains none. Interestingly, we also reveal several independent losses of macrodomain enzymatic activity within mammalian PARP14, including in the bat, ungulate, and carnivore lineages. Similar to macroPARPs, coronaviruses contain up to three macrodomains, with only the first displaying catalytic activity. Intriguingly, we also reveal the recurrent loss of macrodomain activity within the alphavirus group of viruses, including enzymatic loss in insect-specific alphaviruses as well as independent enzymatic losses in two human-infecting viruses. Together, our evolutionary and functional data reveal an unexpected turnover in macrodomain activity in both host antiviral proteins and viral proteins.
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Affiliation(s)
| | | | - Matthew D. Daugherty
- Department of Molecular Biology, School of Biological Sciences, University of California—San Diego, La Jolla, CA 92093, USA
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13
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Costanzo M, De Giglio MAR, Roviello GN. Deciphering the Relationship between SARS-CoV-2 and Cancer. Int J Mol Sci 2023; 24:ijms24097803. [PMID: 37175509 PMCID: PMC10178366 DOI: 10.3390/ijms24097803] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/17/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
Some viruses are known to be associated with the onset of specific cancers. These microorganisms, oncogenic viruses or oncoviruses, can convert normal cells into cancer cells by modulating the central metabolic pathways or hampering genomic integrity mechanisms, consequently inhibiting the apoptotic machinery and/or enhancing cell proliferation. Seven oncogenic viruses are known to promote tumorigenesis in humans: human papillomavirus (HPV), hepatitis B and C viruses (HBV, HCV), Epstein-Barr virus (EBV), human T-cell leukemia virus 1 (HTLV-1), Kaposi sarcoma-associated herpesvirus (KSHV), and Merkel cell polyomavirus (MCPyV). Recent research indicates that SARS-CoV-2 infection and COVID-19 progression may predispose recovered patients to cancer onset and accelerate cancer development. This hypothesis is based on the growing evidence regarding the ability of SARS-CoV-2 to modulate oncogenic pathways, promoting chronic low-grade inflammation and causing tissue damage. Herein, we summarize the main relationships known to date between virus infection and cancer, providing a summary of the proposed biochemical mechanisms behind the cellular transformation. Mechanistically, DNA viruses (such as HPV, HBV, EBV, and MCPyV) encode their virus oncogenes. In contrast, RNA viruses (like HCV, HTLV-1) may encode oncogenes or trigger host oncogenes through cis-/-trans activation leading to different types of cancer. As for SARS-CoV-2, its role as an oncogenic virus seems to occur through the inhibition of oncosuppressors or controlling the metabolic and autophagy pathways in the infected cells. However, these effects could be significant in particular scenarios like those linked to severe COVID-19 or long COVID. On the other hand, looking at the SARS-CoV-2─cancer relationship from an opposite perspective, oncolytic effects and anti-tumor immune response were triggered by SARS-CoV-2 infection in some cases. In summary, our work aims to recall comprehensive attention from the scientific community to elucidate the effects of SARS-CoV-2 and, more in general, β-coronavirus infection on cancer susceptibility for cancer prevention or supporting therapeutic approaches.
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Affiliation(s)
- Michele Costanzo
- Department of Molecular Medicine and Medical Biotechnology, School of Medicine, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
- CEINGE-Biotecnologie Avanzate Franco Salvatore s.c.ar.l., Via G. Salvatore 486, 80145 Naples, Italy
| | | | - Giovanni Nicola Roviello
- Institute of Biostructures and Bioimaging, Italian National Council for Research (IBB-CNR), Via P. Castellino 111, 80131 Naples, Italy
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14
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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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15
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Schuller M, Zarganes-Tzitzikas T, Bennett J, De Cesco S, Fearon D, von Delft F, Fedorov O, Brennan PE, Ahel I. Discovery and Development Strategies for SARS-CoV-2 NSP3 Macrodomain Inhibitors. Pathogens 2023; 12:324. [PMID: 36839595 PMCID: PMC9965906 DOI: 10.3390/pathogens12020324] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/03/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
The worldwide public health and socioeconomic consequences caused by the COVID-19 pandemic highlight the importance of increasing preparedness for viral disease outbreaks by providing rapid disease prevention and treatment strategies. The NSP3 macrodomain of coronaviruses including SARS-CoV-2 is among the viral protein repertoire that was identified as a potential target for the development of antiviral agents, due to its critical role in viral replication and consequent pathogenicity in the host. By combining virtual and biophysical screening efforts, we discovered several experimental small molecules and FDA-approved drugs as inhibitors of the NSP3 macrodomain. Analogue characterisation of the hit matter and crystallographic studies confirming binding modes, including that of the antibiotic compound aztreonam, to the active site of the macrodomain provide valuable structure-activity relationship information that support current approaches and open up new avenues for NSP3 macrodomain inhibitor development.
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Affiliation(s)
- Marion Schuller
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
| | | | - James Bennett
- Centre for Medicines Discovery, University of Oxford, Headington OX3 7DQ, UK
| | - Stephane De Cesco
- Centre for Medicines Discovery, University of Oxford, Headington OX3 7DQ, UK
| | - Daren Fearon
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Frank von Delft
- Centre for Medicines Discovery, University of Oxford, Headington OX3 7DQ, UK
- Diamond Light Source Ltd., Harwell Science and Innovation Campus, Didcot OX11 0DE, UK
- Research Complex at Harwell, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
- Structural Genomics Consortium, University of Oxford, Headington OX3 7DQ, UK
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa
| | - Oleg Fedorov
- Centre for Medicines Discovery, University of Oxford, Headington OX3 7DQ, UK
| | - Paul E. Brennan
- Centre for Medicines Discovery, University of Oxford, Headington OX3 7DQ, UK
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, UK
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16
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The Discovery of Novel Ferulic Acid Derivatives Incorporating Substituted Isopropanolamine Moieties as Potential Tobacco Mosaic Virus Helicase Inhibitors. Int J Mol Sci 2022; 23:ijms232213991. [PMID: 36430473 PMCID: PMC9698358 DOI: 10.3390/ijms232213991] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 11/02/2022] [Accepted: 11/03/2022] [Indexed: 11/16/2022] Open
Abstract
Target-based drug design, a high-efficiency strategy used to guide the development of novel pesticide candidates, has attracted widespread attention. Herein, various natural-derived ferulic acid derivatives incorporating substituted isopropanolamine moieties were designed to target the tobacco mosaic virus (TMV) helicase. Bioassays demonstrating the optimized A19, A20, A29, and A31 displayed excellent in vivo antiviral curative abilities, affording corresponding EC50 values of 251.1, 336.2, 347.1, and 385.5 μg/mL, which visibly surpassed those of commercial ribavirin (655.0 μg/mL). Moreover, configurational analysis shows that the R-forms of target compounds were more beneficial to aggrandize antiviral profiles. Mechanism studies indicate that R-A19 had a strong affinity (Kd = 5.4 μM) to the TMV helicase and inhibited its ability to hydrolyze ATP (50.61% at 200 μM). Meanwhile, A19 could down-regulate the expression of the TMV helicase gene in the host to attenuate viral replication. These results illustrate the excellent inhibitory activity of A19 towards the TMV helicase. Additionally, docking simulations uncovered that R-A19 formed more hydrogen bonds with the TMV helicase in the binding pocket. Recent studies have unambiguously manifested that these designed derivatives could be considered as promising potential helicase-based inhibitors for plant disease control.
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17
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Hagino R, Mozaki K, Komura N, Imamura A, Ishida H, Ando H, Tanaka HN. Straightforward Synthesis of the Poly(ADP-ribose) Branched Core Structure. ACS OMEGA 2022; 7:32795-32804. [PMID: 36119971 PMCID: PMC9476175 DOI: 10.1021/acsomega.2c04732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
Poly(ADP-ribosyl)ation is a post-translational modification that produces poly(ADP-ribose) with a branched structure every 20-50 units; such branching structure has been previously suggested to be involved in regulating chromatin remodeling. To elucidate its detailed functions, we developed a straightforward method for the synthesis of the poly(ADP-ribose) branched core structure, α-d-ribofuranosyl-(1‴ → 2″)-α-d-ribofuranosyl-(1″ → 2')-adenosine 5',5'',5‴-trisphosphate 1, from 6-chloropurine ribofuranoside 4 in 10 steps and 6.1% overall yield. The structure poses synthetic challenges for constructing iterative α-1,2-cis-glycosidic bonds in the presence of a purine base and the installation of three phosphate groups at primary hydroxyl groups. Iterative glycosidic bonds were formed by α-1,2-cis-selective ribofuranosylation using 2-O-(2-naphthylmethyl)-protected thioglycoside donor 6 and a thiophilic bismuth promoter. After the construction of diribofuranosyl adenosine 5 had been constructed, it was chemo- and regioselectively phosphorylated at a later stage. Subsequent deprotection provided the synthetic target 1.
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Affiliation(s)
- Rui Hagino
- The
United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
- Department
of Applied Bioorganic Chemistry, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Keita Mozaki
- Department
of Applied Bioorganic Chemistry, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Naoko Komura
- Institute
for Glyco-core Research (iGCORE), Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Akihiro Imamura
- Institute
for Glyco-core Research (iGCORE), Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
- The
United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
- Department
of Applied Bioorganic Chemistry, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Hideharu Ishida
- Institute
for Glyco-core Research (iGCORE), Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
- The
United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
- Department
of Applied Bioorganic Chemistry, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Hiromune Ando
- Institute
for Glyco-core Research (iGCORE), Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
- The
United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
| | - Hide-Nori Tanaka
- Institute
for Glyco-core Research (iGCORE), Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
- The
United Graduate School of Agricultural Science, Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
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18
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Wang Z, Belecciu T, Eaves J, Reimers M, Bachmann MH, Woldring D. Phytochemical drug discovery for COVID-19 using high-resolution computational docking and machine learning assisted binder prediction. J Biomol Struct Dyn 2022:1-21. [PMID: 35993534 DOI: 10.1080/07391102.2022.2112976] [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: 10/15/2022]
Abstract
The COVID-19 pandemic has resulted in millions of deaths around the world. Multiple vaccines are in use, but there are many underserved locations that do not have adequate access to them. Variants may emerge that are highly resistant to existing vaccines, and therefore cheap and readily obtainable therapeutics are needed. Phytochemicals, or plant chemicals, can possibly be such therapeutics. Phytochemicals can be used in a polypharmacological approach, where multiple viral proteins are inhibited and escape mutations are made less likely. Finding the right phytochemicals for viral protein inhibition is challenging, but in-silico screening methods can make this a more tractable problem. In this study, we screen a wide range of natural drug products against a comprehensive set of SARS-CoV-2 proteins using a high-resolution computational workflow. This workflow consists of a structure-based virtual screening (SBVS), where an initial phytochemical library was docked against all selected protein structures. Subsequently, ligand-based virtual screening (LBVS) was employed, where chemical features of 34 lead compounds obtained from the SBVS were used to predict 53 lead compounds from a larger phytochemical library via supervised learning. A computational docking validation of the 53 predicted leads obtained from LBVS revealed that 28 of them elicit strong binding interactions with SARS-CoV-2 proteins. Thus, the inclusion of LBVS resulted in a 4-fold increase in the lead discovery rate. Of the total 62 leads, 18 showed promising pharmacokinetic properties in a computational ADME screening. Collectively, this study demonstrates the advantage of incorporating machine learning elements into a virtual screening workflow.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Zirui Wang
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA.,Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA
| | - Theodore Belecciu
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA.,Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA
| | - Joelle Eaves
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA.,Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA
| | - Mark Reimers
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA.,Department of Biomedical Engineering, Michigan State University, East Lansing, MI, USA
| | - Michael H Bachmann
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA.,Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Daniel Woldring
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing, MI, USA.,Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI, USA
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19
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Sherrill LM, Joya EE, Walker A, Roy A, Alhammad YM, Atobatele M, Wazir S, Abbas G, Keane P, Zhuo J, Leung AKL, Johnson DK, Lehtiö L, Fehr AR, Ferraris D. Design, synthesis and evaluation of inhibitors of the SARS-CoV-2 nsp3 macrodomain. Bioorg Med Chem 2022; 67:116788. [PMID: 35597097 PMCID: PMC9093066 DOI: 10.1016/j.bmc.2022.116788] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 01/25/2023]
Abstract
A series of amino acid based 7H-pyrrolo[2,3-d]pyrimidines were designed and synthesized to discern the structure activity relationships against the SARS-CoV-2 nsp3 macrodomain (Mac1), an ADP-ribosylhydrolase that is critical for coronavirus replication and pathogenesis. Structure activity studies identified compound 15c as a low-micromolar inhibitor of Mac1 in two ADP-ribose binding assays. This compound also demonstrated inhibition in an enzymatic assay of Mac1 and displayed a thermal shift comparable to ADPr in the melting temperature of Mac1 supporting binding to the target protein. A structural model reproducibly predicted a binding mode where the pyrrolo pyrimidine forms a hydrogen bonding network with Asp22 and the amide backbone NH of Ile23 in the adenosine binding pocket and the carboxylate forms hydrogen bonds to the amide backbone of Phe157 and Asp156, part of the oxyanion subsite of Mac1. Compound 15c also demonstrated notable selectivity for coronavirus macrodomains when tested against a panel of ADP-ribose binding proteins. Together, this study identified several low MW, low µM Mac1 inhibitors to use as small molecule chemical probes for this potential anti-viral target and offers starting points for further optimization.
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Affiliation(s)
- Lavinia M Sherrill
- McDaniel College, Department of Chemistry, 2 College Hill, Westminster, MD 21157, USA
| | - Elva E Joya
- McDaniel College, Department of Chemistry, 2 College Hill, Westminster, MD 21157, USA
| | - AnnMarie Walker
- McDaniel College, Department of Chemistry, 2 College Hill, Westminster, MD 21157, USA
| | - Anuradha Roy
- Infectious Disease Assay Development Laboratory/HTS, University of Kansas, Lawrence, KS 66047, USA
| | - Yousef M Alhammad
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA
| | - Moriama Atobatele
- Infectious Disease Assay Development Laboratory/HTS, University of Kansas, Lawrence, KS 66047, USA
| | - Sarah Wazir
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - George Abbas
- McDaniel College, Department of Chemistry, 2 College Hill, Westminster, MD 21157, USA
| | - Patrick Keane
- McDaniel College, Department of Chemistry, 2 College Hill, Westminster, MD 21157, USA
| | - Junlin Zhuo
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
| | - Anthony K L Leung
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA; Department of Oncology, McKusick-Nathans Department of Genetic Medicine and Department of Molecular Biology and Genetics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
| | - David K Johnson
- Molecular Graphics and Modeling Laboratory and the Computational Chemical Biology Core, University of Kansas, Lawrence, KS 66047, USA
| | - Lari Lehtiö
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Anthony R Fehr
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA.
| | - Dana Ferraris
- McDaniel College, Department of Chemistry, 2 College Hill, Westminster, MD 21157, USA.
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20
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Gao K, Wang R, Chen J, Cheng L, Frishcosy J, Huzumi Y, Qiu Y, Schluckbier T, Wei X, Wei GW. Methodology-Centered Review of Molecular Modeling, Simulation, and Prediction of SARS-CoV-2. Chem Rev 2022; 122:11287-11368. [PMID: 35594413 PMCID: PMC9159519 DOI: 10.1021/acs.chemrev.1c00965] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Despite tremendous efforts in the past two years, our understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), virus-host interactions, immune response, virulence, transmission, and evolution is still very limited. This limitation calls for further in-depth investigation. Computational studies have become an indispensable component in combating coronavirus disease 2019 (COVID-19) due to their low cost, their efficiency, and the fact that they are free from safety and ethical constraints. Additionally, the mechanism that governs the global evolution and transmission of SARS-CoV-2 cannot be revealed from individual experiments and was discovered by integrating genotyping of massive viral sequences, biophysical modeling of protein-protein interactions, deep mutational data, deep learning, and advanced mathematics. There exists a tsunami of literature on the molecular modeling, simulations, and predictions of SARS-CoV-2 and related developments of drugs, vaccines, antibodies, and diagnostics. To provide readers with a quick update about this literature, we present a comprehensive and systematic methodology-centered review. Aspects such as molecular biophysics, bioinformatics, cheminformatics, machine learning, and mathematics are discussed. This review will be beneficial to researchers who are looking for ways to contribute to SARS-CoV-2 studies and those who are interested in the status of the field.
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Affiliation(s)
- Kaifu Gao
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Rui Wang
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Jiahui Chen
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Limei Cheng
- Clinical
Pharmacology and Pharmacometrics, Bristol
Myers Squibb, Princeton, New Jersey 08536, United States
| | - Jaclyn Frishcosy
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuta Huzumi
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Yuchi Qiu
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Tom Schluckbier
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Xiaoqi Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
| | - Guo-Wei Wei
- Department
of Mathematics, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Electrical and Computer Engineering, Michigan State University, East Lansing, Michigan 48824, United States
- Department
of Biochemistry and Molecular Biology, Michigan
State University, East Lansing, Michigan 48824, United States
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21
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Discovery of compounds that inhibit SARS-CoV-2 Mac1-ADP-ribose binding by high-throughput screening. Antiviral Res 2022; 203:105344. [PMID: 35598780 PMCID: PMC9119168 DOI: 10.1016/j.antiviral.2022.105344] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/10/2022] [Accepted: 05/16/2022] [Indexed: 01/17/2023]
Abstract
The emergence of several zoonotic viruses in the last twenty years, especially the pandemic outbreak of SARS-CoV-2, has exposed a dearth of antiviral drug therapies for viruses with pandemic potential. Developing a diverse drug portfolio will be critical to rapidly respond to novel coronaviruses (CoVs) and other viruses with pandemic potential. Here we focus on the SARS-CoV-2 conserved macrodomain (Mac1), a small domain of non-structural protein 3 (nsp3). Mac1 is an ADP-ribosylhydrolase that cleaves mono-ADP-ribose (MAR) from target proteins, protects the virus from the anti-viral effects of host ADP-ribosyltransferases, and is critical for the replication and pathogenesis of CoVs. In this study, a luminescent-based high-throughput assay was used to screen ∼38,000 small molecules for those that could inhibit Mac1-ADP-ribose binding. We identified 5 compounds amongst 3 chemotypes that inhibit SARS-CoV-2 Mac1-ADP-ribose binding in multiple assays with IC50 values less than 100 μM, inhibit ADP-ribosylhydrolase activity, and have evidence of direct Mac1 binding. These chemotypes are strong candidates for further derivatization into highly effective Mac1 inhibitors.
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22
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Correy GJ, Kneller DW, Phillips G, Pant S, Russi S, Cohen AE, Meigs G, Holton JM, Gahbauer S, Thompson MC, Ashworth A, Coates L, Kovalevsky A, Meilleur F, Fraser JS. The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and x-ray diffraction at room temperature. SCIENCE ADVANCES 2022; 8:eabo5083. [PMID: 35622909 PMCID: PMC9140965 DOI: 10.1126/sciadv.abo5083] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/11/2022] [Indexed: 05/04/2023]
Abstract
The nonstructural protein 3 (NSP3) macrodomain of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (Mac1) removes adenosine diphosphate (ADP) ribosylation posttranslational modifications, playing a key role in the immune evasion capabilities of the virus responsible for the coronavirus disease 2019 pandemic. Here, we determined neutron and x-ray crystal structures of the SARS-CoV-2 NSP3 macrodomain using multiple crystal forms, temperatures, and pHs, across the apo and ADP-ribose-bound states. We characterize extensive solvation in the Mac1 active site and visualize how water networks reorganize upon binding of ADP-ribose and non-native ligands, inspiring strategies for displacing waters to increase the potency of Mac1 inhibitors. Determining the precise orientations of active site water molecules and the protonation states of key catalytic site residues by neutron crystallography suggests a catalytic mechanism for coronavirus macrodomains distinct from the substrate-assisted mechanism proposed for human MacroD2. These data provoke a reevaluation of macrodomain catalytic mechanisms and will guide the optimization of Mac1 inhibitors.
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Affiliation(s)
- Galen J. Correy
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Daniel W. Kneller
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, U.S. Department of Energy, Washington, DC 20585, USA
| | - Gwyndalyn Phillips
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, U.S. Department of Energy, Washington, DC 20585, USA
| | - Swati Pant
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, U.S. Department of Energy, Washington, DC 20585, USA
| | - Silvia Russi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Aina E. Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - George Meigs
- Department of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - James M. Holton
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
- Department of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Stefan Gahbauer
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Michael C. Thompson
- Department of Chemistry and Biochemistry, University of California, Merced, Merced, CA 95343, USA
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Leighton Coates
- National Virtual Biotechnology Laboratory, U.S. Department of Energy, Washington, DC 20585, USA
- Second Target Station, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, U.S. Department of Energy, Washington, DC 20585, USA
| | - Flora Meilleur
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695, USA
| | - James S. Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94158, USA
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23
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Lüscher B, Verheirstraeten M, Krieg S, Korn P. Intracellular mono-ADP-ribosyltransferases at the host-virus interphase. Cell Mol Life Sci 2022; 79:288. [PMID: 35536484 PMCID: PMC9087173 DOI: 10.1007/s00018-022-04290-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/15/2022] [Accepted: 04/05/2022] [Indexed: 01/22/2023]
Abstract
The innate immune system, the primary defense mechanism of higher organisms against pathogens including viruses, senses pathogen-associated molecular patterns (PAMPs). In response to PAMPs, interferons (IFNs) are produced, allowing the host to react swiftly to viral infection. In turn the expression of IFN-stimulated genes (ISGs) is induced. Their products disseminate the antiviral response. Among the ISGs conserved in many species are those encoding mono-ADP-ribosyltransferases (mono-ARTs). This prompts the question whether, and if so how, mono-ADP-ribosylation affects viral propagation. Emerging evidence demonstrates that some mono-ADP-ribosyltransferases function as PAMP receptors and modify both host and viral proteins relevant for viral replication. Support for mono-ADP-ribosylation in virus–host interaction stems from the findings that some viruses encode mono-ADP-ribosylhydrolases, which antagonize cellular mono-ARTs. We summarize and discuss the evidence linking mono-ADP-ribosylation and the enzymes relevant to catalyze this reversible modification with the innate immune response as part of the arms race between host and viruses.
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Affiliation(s)
- Bernhard Lüscher
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany.
| | - Maud Verheirstraeten
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany
| | - Sarah Krieg
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany
| | - Patricia Korn
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, RWTH Aachen University, Pauwelsstraße 30, 52074, Aachen, Germany.
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24
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Lubin JH, Zardecki C, Dolan EM, Lu C, Shen Z, Dutta S, Westbrook JD, Hudson BP, Goodsell DS, Williams JK, Voigt M, Sarma V, Xie L, Venkatachalam T, Arnold S, Alfaro Alvarado LH, Catalfano K, Khan A, McCarthy E, Staggers S, Tinsley B, Trudeau A, Singh J, Whitmore L, Zheng H, Benedek M, Currier J, Dresel M, Duvvuru A, Dyszel B, Fingar E, Hennen EM, Kirsch M, Khan AA, Labrie‐Cleary C, Laporte S, Lenkeit E, Martin K, Orellana M, Ortiz‐Alvarez de la Campa M, Paredes I, Wheeler B, Rupert A, Sam A, See K, Soto Zapata S, Craig PA, Hall BL, Jiang J, Koeppe JR, Mills SA, Pikaart MJ, Roberts R, Bromberg Y, Hoyer JS, Duffy S, Tischfield J, Ruiz FX, Arnold E, Baum J, Sandberg J, Brannigan G, Khare SD, Burley SK. Evolution of the SARS-CoV-2 proteome in three dimensions (3D) during the first 6 months of the COVID-19 pandemic. Proteins 2022; 90:1054-1080. [PMID: 34580920 PMCID: PMC8661935 DOI: 10.1002/prot.26250] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 08/26/2021] [Accepted: 09/16/2021] [Indexed: 01/18/2023]
Abstract
Understanding the molecular evolution of the SARS-CoV-2 virus as it continues to spread in communities around the globe is important for mitigation and future pandemic preparedness. Three-dimensional structures of SARS-CoV-2 proteins and those of other coronavirusess archived in the Protein Data Bank were used to analyze viral proteome evolution during the first 6 months of the COVID-19 pandemic. Analyses of spatial locations, chemical properties, and structural and energetic impacts of the observed amino acid changes in >48 000 viral isolates revealed how each one of 29 viral proteins have undergone amino acid changes. Catalytic residues in active sites and binding residues in protein-protein interfaces showed modest, but significant, numbers of substitutions, highlighting the mutational robustness of the viral proteome. Energetics calculations showed that the impact of substitutions on the thermodynamic stability of the proteome follows a universal bi-Gaussian distribution. Detailed results are presented for potential drug discovery targets and the four structural proteins that comprise the virion, highlighting substitutions with the potential to impact protein structure, enzyme activity, and protein-protein and protein-nucleic acid interfaces. Characterizing the evolution of the virus in three dimensions provides testable insights into viral protein function and should aid in structure-based drug discovery efforts as well as the prospective identification of amino acid substitutions with potential for drug resistance.
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Affiliation(s)
- Joseph H. Lubin
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Christine Zardecki
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Elliott M. Dolan
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Changpeng Lu
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Zhuofan Shen
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Shuchismita Dutta
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, Rutgers, The State University of New JerseyNew BrunswickNew JerseyUSA
| | - John D. Westbrook
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, Rutgers, The State University of New JerseyNew BrunswickNew JerseyUSA
| | - Brian P. Hudson
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - David S. Goodsell
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, Rutgers, The State University of New JerseyNew BrunswickNew JerseyUSA
- The Scripps Research InstituteLa JollaCaliforniaUSA
| | - Jonathan K. Williams
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Maria Voigt
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Vidur Sarma
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Lingjun Xie
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Thejasvi Venkatachalam
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Steven Arnold
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | | | | | - Aaliyah Khan
- University of Maryland Baltimore CountyBaltimoreMarylandUSA
| | | | | | | | | | | | | | - Helen Zheng
- Watchung Hills Regional High SchoolWarrenNew JerseyUSA
| | | | | | - Mark Dresel
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | | | | | | | | | | | | | | | | | - Evan Lenkeit
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | | | | | | | | | | | | | - Andrew Sam
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Katherine See
- Rochester Institute of TechnologyRochesterNew YorkUSA
| | | | - Paul A. Craig
- Rochester Institute of TechnologyRochesterNew YorkUSA
| | | | - Jennifer Jiang
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | | | | | | | | | - Yana Bromberg
- Department of Biochemistry and MicrobiologyRutgers, The State University of New JerseyNew BrunswickNew JerseyUSA
| | - J. Steen Hoyer
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological SciencesRutgers, The State University of New JerseyNew BrunswickNew JerseyUSA
| | - Siobain Duffy
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological SciencesRutgers, The State University of New JerseyNew BrunswickNew JerseyUSA
| | - Jay Tischfield
- Department of GeneticsRutgers, The State University of New Jersey, and Human Genetics Institute of New JerseyPiscatawayNew JerseyUSA
| | - Francesc X. Ruiz
- Center for Advanced Biotechnology and MedicineRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Eddy Arnold
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Center for Advanced Biotechnology and MedicineRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Jean Baum
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
| | - Jesse Sandberg
- Center for Computational and Integrative BiologyRutgers, The State University of New JerseyCamdenNew JerseyUSA
| | - Grace Brannigan
- Center for Computational and Integrative BiologyRutgers, The State University of New JerseyCamdenNew JerseyUSA
- Department of PhysicsRutgers, The State University of New JerseyCamdenNew JerseyUSA
| | - Sagar D. Khare
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, Rutgers, The State University of New JerseyNew BrunswickNew JerseyUSA
| | - Stephen K. Burley
- Institute for Quantitative Biomedicine, Rutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Department of Chemistry and Chemical BiologyRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Research Collaboratory for Structural Bioinformatics Protein Data BankRutgers, The State University of New JerseyPiscatawayNew JerseyUSA
- Rutgers Cancer Institute of New Jersey, Robert Wood Johnson Medical School, Rutgers, The State University of New JerseyNew BrunswickNew JerseyUSA
- Research Collaboratory for Structural Bioinformatics Protein Data Bank, San Diego Supercomputer CenterUniversity of CaliforniaSan Diego, La JollaCaliforniaUSA
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25
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Novak Kujundžić R. COVID-19: Are We Facing Secondary Pellagra Which Cannot Simply Be Cured by Vitamin B3? Int J Mol Sci 2022; 23:ijms23084309. [PMID: 35457123 PMCID: PMC9032523 DOI: 10.3390/ijms23084309] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 04/11/2022] [Accepted: 04/12/2022] [Indexed: 02/07/2023] Open
Abstract
Immune response to SARS-CoV-2 and ensuing inflammation pose a huge challenge to the host’s nicotinamide adenine dinucleotide (NAD+) metabolism. Humans depend on vitamin B3 for biosynthesis of NAD+, indispensable for many metabolic and NAD+-consuming signaling reactions. The balance between its utilization and resynthesis is vitally important. Many extra-pulmonary symptoms of COVID-19 strikingly resemble those of pellagra, vitamin B3 deficiency (e.g., diarrhoea, dermatitis, oral cavity and tongue manifestations, loss of smell and taste, mental confusion). In most developed countries, pellagra is successfully eradicated by vitamin B3 fortification programs. Thus, conceivably, it has not been suspected as a cause of COVID-19 symptoms. Here, the deregulation of the NAD+ metabolism in response to the SARS-CoV-2 infection is reviewed, with special emphasis on the differences in the NAD+ biosynthetic pathway’s efficiency in conditions predisposing for the development of serious COVID-19. SARS-CoV-2 infection-induced NAD+ depletion and the elevated levels of its metabolites contribute to the development of a systemic disease. Acute liberation of nicotinamide (NAM) in antiviral NAD+-consuming reactions potentiates “NAM drain”, cooperatively mediated by nicotinamide N-methyltransferase and aldehyde oxidase. “NAM drain” compromises the NAD+ salvage pathway’s fail-safe function. The robustness of the host’s NAD+ salvage pathway, prior to the SARS-CoV-2 infection, is an important determinant of COVID-19 severity and persistence of certain symptoms upon resolution of infection.
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Affiliation(s)
- Renata Novak Kujundžić
- Laboratory for Epigenomics, Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia
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26
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Siddique S, Kumar RP. 3β-Acetoxy-21α-H-hop-22(29)ene, a novel multitargeted phytocompound against SARS-CoV-2: in silico screening. J Biomol Struct Dyn 2022; 41:3884-3891. [PMID: 35377270 DOI: 10.1080/07391102.2022.2058094] [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: 10/18/2022]
Abstract
The present pandemic disease COVID-19 demands an urgent need for more efficient antiviral drugs against SARS-CoV-2. Computational drug designing and discovery enable us to explore ethnomedicinal plants as a source of various lead molecules that can be used against present and future pathogens. Adiantum latifolium Lam., a common fern, is resistant to pathogens mainly due to the presence of various phytochemicals having antimicrobial properties. In our previous study, 3β-acetoxy-21α-H-hop-22(29)ene, a terpenoid has been characterized from the methanol extract of leaves of A. latifolium. The manuscript evaluates the antiviral potency of the compound against SARS-CoV-2 through molecular docking method. Proteins essential for SARS-CoV-2 multiplication in host cells are the target sites. The study revealed strong binding affinity of the compound for all the ten proteins selected, including seven nonstructural proteins, two structural proteins and one receptor protein, with a binding energy of -4.67 to -8.76 kcal/mol. MDS and MMPBSA analysis of the best ranked complex further confirmed the results. The multitargeted compound can be considered as a natural lead molecule in drug designing against COVID-19, but requires wet-lab experimentation and clinical trials.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Simna Siddique
- Department of Zoology, Government College for Women, Thiruvananthapuram, Kerala, India
| | - R Pradeep Kumar
- Department of Zoology, Government College for Women, Thiruvananthapuram, Kerala, India
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27
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Roy A, Alhammad YM, McDonald P, Johnson DK, Zhuo J, Wazir S, Ferraris D, Lehtiö L, Leung AKL, Fehr AR. Discovery of compounds that inhibit SARS-CoV-2 Mac1-ADP-ribose binding by high-throughput screening. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.03.01.482536. [PMID: 35262075 PMCID: PMC8902866 DOI: 10.1101/2022.03.01.482536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The emergence of several zoonotic viruses in the last twenty years, especially the pandemic outbreak of SARS-CoV-2, has exposed a dearth of antiviral drug therapies for viruses with pandemic potential. Developing a diverse drug portfolio will be critical for our ability to rapidly respond to novel coronaviruses (CoVs) and other viruses with pandemic potential. Here we focus on the SARS-CoV-2 conserved macrodomain (Mac1), a small domain of non-structural protein 3 (nsp3). Mac1 is an ADP-ribosylhydrolase that cleaves mono-ADP-ribose (MAR) from target proteins, protects the virus from the anti-viral effects of host ADP-ribosyltransferases, and is critical for the replication and pathogenesis of CoVs. In this study, a luminescent-based high-throughput assay was used to screen ∼38,000 small molecules for those that could inhibit Mac1-ADP-ribose binding. We identified 5 compounds amongst 3 chemotypes that inhibit SARS-CoV-2 Mac1-ADP-ribose binding in multiple assays with IC 50 values less than 100 µ M, inhibit ADP-ribosylhydrolase activity, and have evidence of direct Mac1 binding. These chemotypes are strong candidates for further derivatization into highly effective Mac1 inhibitors.
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28
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An H, Eun M, Yi J, Park J. CRESSP: a comprehensive pipeline for prediction of immunopathogenic SARS-CoV-2 epitopes using structural properties of proteins. Brief Bioinform 2022; 23:6539139. [PMID: 35226074 DOI: 10.1093/bib/bbac056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 01/04/2022] [Accepted: 02/03/2022] [Indexed: 12/16/2022] Open
Abstract
The development of autoimmune diseases following SARS-CoV-2 infection, including multisystem inflammatory syndrome, has been reported, and several mechanisms have been suggested, including molecular mimicry. We developed a scalable, comparative immunoinformatics pipeline called cross-reactive-epitope-search-using-structural-properties-of-proteins (CRESSP) to identify cross-reactive epitopes between a collection of SARS-CoV-2 proteomes and the human proteome using the structural properties of the proteins. Overall, by searching 4 911 245 proteins from 196 352 SARS-CoV-2 genomes, we identified 133 and 648 human proteins harboring potential cross-reactive B-cell and CD8+ T-cell epitopes, respectively. To demonstrate the robustness of our pipeline, we predicted the cross-reactive epitopes of coronavirus spike proteins, which were recognized by known cross-neutralizing antibodies. Using single-cell expression data, we identified PARP14 as a potential target of intermolecular epitope spreading between the virus and human proteins. Finally, we developed a web application (https://ahs2202.github.io/3M/) to interactively visualize our results. We also made our pipeline available as an open-source CRESSP package (https://pypi.org/project/cressp/), which can analyze any two proteomes of interest to identify potentially cross-reactive epitopes between the proteomes. Overall, our immunoinformatic resources provide a foundation for the investigation of molecular mimicry in the pathogenesis of autoimmune and chronic inflammatory diseases following COVID-19.
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Affiliation(s)
- Hyunsu An
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Republic of Korea
| | - Minho Eun
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Republic of Korea
| | - Jawoon Yi
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Republic of Korea
| | - Jihwan Park
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Republic of Korea.,Anti-Virus Research Center, Gwangju Institute of Science and Technology (GIST), Republic of Korea.,Laboratory for cell mechanobiology, Gwangju Institute of Science and Technology (GIST), Republic of Korea
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29
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Sherrill LM, Joya EE, Walker A, Roy A, Alhammad YM, Atobatele M, Wazir S, Abbas G, Keane P, Zhuo J, Leung AKL, Johnson DK, Lehtiö L, Fehr AR, Ferraris D. Design, Synthesis and Evaluation of Inhibitors of the SARS-CoV2 nsp3 Macrodomain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.02.27.482176. [PMID: 35262078 PMCID: PMC8902877 DOI: 10.1101/2022.02.27.482176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A series of amino acid based 7H -pyrrolo[2,3- d ]pyrimidines were designed and synthesized to discern the structure activity relationships against the SARS-CoV-2 nsp3 macrodomain (Mac1), an ADP-ribosylhydrolase that is critical for coronavirus replication and pathogenesis. Structure activity studies identified compound 15c as a low-micromolar inhibitor of Mac1 in two ADP-ribose binding assays. This compound also demonstrated inhibition in an enzymatic assay of Mac1 and displayed a thermal shift comparable to ADPr in the melting temperature of Mac1 supporting binding to the target protein. A structural model reproducibly predicted a binding mode where the pyrrolo pyrimidine forms a hydrogen bonding network with Asp 22 and the amide backbone NH of Ile 23 in the adenosine binding pocket and the carboxylate forms hydrogen bonds to the amide backbone of Phe 157 and Asp 156 , part of the oxyanion subsite of Mac1. Compound 15c also demonstrated notable selectivity for coronavirus macrodomains when tested against a panel of ADP-ribose binding proteins. Together, this study identified several low MW, low μM Mac1 inhibitors to use as small molecule chemical probes for this potential anti-viral target and offers starting points for further optimization.
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30
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Correy GJ, Kneller DW, Phillips G, Pant S, Russi S, Cohen AE, Meigs G, Holton JM, Gahbauer S, Thompson MC, Ashworth A, Coates L, Kovalevsky A, Meilleur F, Fraser JS. The mechanisms of catalysis and ligand binding for the SARS-CoV-2 NSP3 macrodomain from neutron and X-ray diffraction at room temperature. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.02.07.479477. [PMID: 35169801 PMCID: PMC8845425 DOI: 10.1101/2022.02.07.479477] [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: 11/25/2022]
Abstract
The NSP3 macrodomain of SARS CoV 2 (Mac1) removes ADP-ribosylation post-translational modifications, playing a key role in the immune evasion capabilities of the virus responsible for the COVID-19 pandemic. Here, we determined neutron and X-ray crystal structures of the SARS-CoV-2 NSP3 macrodomain using multiple crystal forms, temperatures, and pHs, across the apo and ADP-ribose-bound states. We characterize extensive solvation in the Mac1 active site, and visualize how water networks reorganize upon binding of ADP-ribose and non-native ligands, inspiring strategies for displacing waters to increase potency of Mac1 inhibitors. Determining the precise orientations of active site water molecules and the protonation states of key catalytic site residues by neutron crystallography suggests a catalytic mechanism for coronavirus macrodomains distinct from the substrate-assisted mechanism proposed for human MacroD2. These data provoke a re-evaluation of macrodomain catalytic mechanisms and will guide the optimization of Mac1 inhibitors.
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Affiliation(s)
- Galen J Correy
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Daniel W Kneller
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, USA
| | - Gwyndalyn Phillips
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, USA
| | - Swati Pant
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, USA
| | - Silvia Russi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA
| | - Aina E Cohen
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA
| | - George Meigs
- Department of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, CA 94158, USA
| | - James M Holton
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Center, Menlo Park, CA 94025, USA
- Department of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, CA 94158, USA
| | - Stefan Gahbauer
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Michael C Thompson
- Department of Chemistry and Chemical Biology, University of California Merced, CA 95343, USA
| | - Alan Ashworth
- Helen Diller Family Comprehensive Cancer, University of California San Francisco, CA 94158, USA
| | - Leighton Coates
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, USA
| | - Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, USA
| | - Flora Meilleur
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, NC 27695
| | - James S Fraser
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158, USA
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31
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NAD+ in COVID-19 and Viral Infections. Trends Immunol 2022; 43:283-295. [PMID: 35221228 PMCID: PMC8831132 DOI: 10.1016/j.it.2022.02.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/06/2022] [Accepted: 02/07/2022] [Indexed: 11/24/2022]
Abstract
NAD+, as an emerging regulator of immune responses during viral infections, may be a promising therapeutic target for coronavirus disease 2019 (COVID-19). In this Opinion, we suggest that interventions that boost NAD+ levels might promote antiviral defense and suppress uncontrolled inflammation. We discuss the association between low NAD+ concentrations and risk factors for poor COVID-19 outcomes, including aging and common comorbidities. Mechanistically, we outline how viral infections can further deplete NAD+ and its roles in antiviral defense and inflammation. We also describe how coronaviruses can subvert NAD+-mediated actions via genes that remove NAD+ modifications and activate the NOD-, LRR-, and pyrin domain-containing protein 3 (NLRP3) inflammasome. Finally, we explore ongoing approaches to boost NAD+ concentrations in the clinic to putatively increase antiviral responses while curtailing hyperinflammation.
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32
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Yan W, Zheng Y, Zeng X, He B, Cheng W. Structural biology of SARS-CoV-2: open the door for novel therapies. Signal Transduct Target Ther 2022; 7:26. [PMID: 35087058 PMCID: PMC8793099 DOI: 10.1038/s41392-022-00884-5] [Citation(s) in RCA: 123] [Impact Index Per Article: 61.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/05/2022] [Accepted: 01/10/2022] [Indexed: 02/08/2023] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is the causative agent of the pandemic disease COVID-19, which is so far without efficacious treatment. The discovery of therapy reagents for treating COVID-19 are urgently needed, and the structures of the potential drug-target proteins in the viral life cycle are particularly important. SARS-CoV-2, a member of the Orthocoronavirinae subfamily containing the largest RNA genome, encodes 29 proteins including nonstructural, structural and accessory proteins which are involved in viral adsorption, entry and uncoating, nucleic acid replication and transcription, assembly and release, etc. These proteins individually act as a partner of the replication machinery or involved in forming the complexes with host cellular factors to participate in the essential physiological activities. This review summarizes the representative structures and typically potential therapy agents that target SARS-CoV-2 or some critical proteins for viral pathogenesis, providing insights into the mechanisms underlying viral infection, prevention of infection, and treatment. Indeed, these studies open the door for COVID therapies, leading to ways to prevent and treat COVID-19, especially, treatment of the disease caused by the viral variants are imperative.
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Affiliation(s)
- Weizhu Yan
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, 610041, Chengdu, China
| | - Yanhui Zheng
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, 610041, Chengdu, China
| | - Xiaotao Zeng
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, 610041, Chengdu, China
| | - Bin He
- Department of Emergency Medicine, West China Hospital of Sichuan University, 610041, Chengdu, China.
- The First People's Hospital of Longquanyi District Chengdu, 610100, Chengdu, China.
| | - Wei Cheng
- Division of Respiratory and Critical Care Medicine, Respiratory Infection and Intervention Laboratory of Frontiers Science Center for Disease-Related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital of Sichuan University, 610041, Chengdu, China.
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33
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Dasovich M, Zhuo J, Goodman JA, Thomas A, McPherson RL, Jayabalan AK, Busa VF, Cheng SJ, Murphy BA, Redinger KR, Alhammad YMO, Fehr AR, Tsukamoto T, Slusher BS, Bosch J, Wei H, Leung AKL. High-Throughput Activity Assay for Screening Inhibitors of the SARS-CoV-2 Mac1 Macrodomain. ACS Chem Biol 2022; 17:17-23. [PMID: 34904435 PMCID: PMC8691451 DOI: 10.1021/acschembio.1c00721] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/16/2021] [Indexed: 12/11/2022]
Abstract
Macrodomains are a class of conserved ADP-ribosylhydrolases expressed by viruses of pandemic concern, including coronaviruses and alphaviruses. Viral macrodomains are critical for replication and virus-induced pathogenesis; therefore, these enzymes are a promising target for antiviral therapy. However, no potent or selective viral macrodomain inhibitors currently exist, in part due to the lack of a high-throughput assay for this class of enzymes. Here we developed a high-throughput ADP-ribosylhydrolase assay using the SARS-CoV-2 macrodomain Mac1. We performed a pilot screen that identified dasatinib and dihydralazine as ADP-ribosylhydrolase inhibitors. Importantly, dasatinib inhibits SARS-CoV-2 and MERS-CoV Mac1 but not the closest human homologue, MacroD2. Our study demonstrates the feasibility of identifying selective inhibitors based on ADP-ribosylhydrolase activity, paving the way for the screening of large compound libraries to identify improved macrodomain inhibitors and to explore their potential as antiviral therapies for SARS-CoV-2 and future viral threats.
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Affiliation(s)
- Morgan Dasovich
- Department of Biochemistry and Molecular Biology,
Bloomberg School of Public Health, Johns Hopkins University,
Baltimore, Maryland 21205, United States
- Department of Chemistry, Krieger School of Arts and
Sciences, Johns Hopkins University, Baltimore, Maryland 21218,
United States
| | - Junlin Zhuo
- Department of Biochemistry and Molecular Biology,
Bloomberg School of Public Health, Johns Hopkins University,
Baltimore, Maryland 21205, United States
| | - Jack A. Goodman
- Department of Biochemistry and Molecular Biology,
Bloomberg School of Public Health, Johns Hopkins University,
Baltimore, Maryland 21205, United States
| | - Ajit Thomas
- Johns Hopkins Drug Discovery,
Baltimore, Maryland 21205, United States
- Department of Neurology, School of Medicine,
Johns Hopkins University, Baltimore, Maryland 21205,
United States
| | - Robert Lyle McPherson
- Department of Biochemistry and Molecular Biology,
Bloomberg School of Public Health, Johns Hopkins University,
Baltimore, Maryland 21205, United States
| | - Aravinth Kumar Jayabalan
- Department of Biochemistry and Molecular Biology,
Bloomberg School of Public Health, Johns Hopkins University,
Baltimore, Maryland 21205, United States
| | - Veronica F. Busa
- Department of Biochemistry and Molecular Biology,
Bloomberg School of Public Health, Johns Hopkins University,
Baltimore, Maryland 21205, United States
- McKusick-Nathans Department of Genetics Medicine,
School of Medicine, Johns Hopkins
University, Baltimore, Maryland 21205, United
States
| | - Shang-Jung Cheng
- Department of Biochemistry and Molecular Biology,
Bloomberg School of Public Health, Johns Hopkins University,
Baltimore, Maryland 21205, United States
| | - Brennan A. Murphy
- Johns Hopkins Drug Discovery,
Baltimore, Maryland 21205, United States
| | - Karli R. Redinger
- Center for Global Health and Diseases, Case
Western Reserve University, Cleveland, Ohio 44106, United
States
| | - Yousef M. O. Alhammad
- Department of Molecular Biosciences,
University of Kansas, Lawrence, Kansas 66045, United
States
| | - Anthony R. Fehr
- Department of Molecular Biosciences,
University of Kansas, Lawrence, Kansas 66045, United
States
| | - Takashi Tsukamoto
- Johns Hopkins Drug Discovery,
Baltimore, Maryland 21205, United States
- Department of Neurology, School of Medicine,
Johns Hopkins University, Baltimore, Maryland 21205,
United States
| | - Barbara S. Slusher
- Johns Hopkins Drug Discovery,
Baltimore, Maryland 21205, United States
- Department of Neurology, School of Medicine,
Johns Hopkins University, Baltimore, Maryland 21205,
United States
| | - Jürgen Bosch
- Center for Global Health and Diseases, Case
Western Reserve University, Cleveland, Ohio 44106, United
States
- InterRayBio, LLC,
Cleveland, Ohio 44106, United States
| | - Huijun Wei
- Johns Hopkins Drug Discovery,
Baltimore, Maryland 21205, United States
- Department of Neurology, School of Medicine,
Johns Hopkins University, Baltimore, Maryland 21205,
United States
| | - Anthony K. L. Leung
- Department of Biochemistry and Molecular Biology,
Bloomberg School of Public Health, Johns Hopkins University,
Baltimore, Maryland 21205, United States
- McKusick-Nathans Department of Genetics Medicine,
School of Medicine, Johns Hopkins
University, Baltimore, Maryland 21205, United
States
- Department of Oncology and Department of
Molecular Biology and Genetics, School of Medicine, Johns Hopkins
University, Baltimore, Maryland 21205, United
States
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34
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Leung AKL, Griffin DE, Bosch J, Fehr AR. The Conserved Macrodomain Is a Potential Therapeutic Target for Coronaviruses and Alphaviruses. Pathogens 2022; 11:pathogens11010094. [PMID: 35056042 PMCID: PMC8780475 DOI: 10.3390/pathogens11010094] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 01/07/2022] [Accepted: 01/11/2022] [Indexed: 12/04/2022] Open
Abstract
Emerging and re-emerging viral diseases pose continuous public health threats, and effective control requires a combination of non-pharmacologic interventions, treatment with antivirals, and prevention with vaccines. The COVID-19 pandemic has demonstrated that the world was least prepared to provide effective treatments. This lack of preparedness has been due, in large part, to a lack of investment in developing a diverse portfolio of antiviral agents, particularly those ready to combat viruses of pandemic potential. Here, we focus on a drug target called macrodomain that is critical for the replication and pathogenesis of alphaviruses and coronaviruses. Some mutations in alphavirus and coronaviral macrodomains are not tolerated for virus replication. In addition, the coronavirus macrodomain suppresses host interferon responses. Therefore, macrodomain inhibitors have the potential to block virus replication and restore the host’s protective interferon response. Viral macrodomains offer an attractive antiviral target for developing direct acting antivirals because they are highly conserved and have a structurally well-defined (druggable) binding pocket. Given that this target is distinct from the existing RNA polymerase and protease targets, a macrodomain inhibitor may complement current approaches, pre-empt the threat of resistance and offer opportunities to develop combination therapies for combating COVID-19 and future viral threats.
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Affiliation(s)
- Anthony K. L. Leung
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Oncology, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
- McKusick-Nathans Department of Genetic Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
- Department of Molecular Biology and Genetics, School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA
- Correspondence: (A.K.L.L.); (D.E.G.); (A.R.F.); Tel.: +1-(410)-5028939 (A.K.L.L.); +1-(410)-955-3459 (D.E.G.); +1-(785)-864-6626 (A.R.F.)
| | - Diane E. Griffin
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21205, USA
- Correspondence: (A.K.L.L.); (D.E.G.); (A.R.F.); Tel.: +1-(410)-5028939 (A.K.L.L.); +1-(410)-955-3459 (D.E.G.); +1-(785)-864-6626 (A.R.F.)
| | - Jürgen Bosch
- Center for Global Health and Diseases, Case Western Reserve University, Cleveland, OH 44106, USA;
- InterRayBio, LLC, Cleveland, OH 44106, USA
| | - Anthony R. Fehr
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA
- Correspondence: (A.K.L.L.); (D.E.G.); (A.R.F.); Tel.: +1-(410)-5028939 (A.K.L.L.); +1-(410)-955-3459 (D.E.G.); +1-(785)-864-6626 (A.R.F.)
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35
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Patel DC, Hausman KR, Arba M, Tran A, Lakernick PM, Wu C. Novel inhibitors to ADP ribose phosphatase of SARS-CoV-2 identified by structure-based high throughput virtual screening and molecular dynamics simulations. Comput Biol Med 2022; 140:105084. [PMID: 34891093 PMCID: PMC8629772 DOI: 10.1016/j.compbiomed.2021.105084] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/24/2021] [Accepted: 11/25/2021] [Indexed: 12/16/2022]
Abstract
The outbreak of a new coronavirus (SARS-CoV-2) was first identified in Wuhan, People's Republic of China, in 2019, which has led to a severe, life-threatening form of pneumonia (COVID-19). Research scientists all around the world have been trying to find small molecule drugs to treat COVID-19. In the present study, a conserved macrodomain, ADP Ribose phosphatase (ADRP), of a critical non-structural protein (Nsp3) in all coronaviruses was probed using large-scale Molecular Dynamics (MD) simulations to identify novel inhibitors. In our virtual screening workflow, the recently-solved X-ray complex structure, 6W6Y, with a substrate-mimics was used to screen 17 million ZINC15 compounds using drug property filters and Glide docking scores. The top twenty output compounds each underwent 200 ns MD simulations (i.e. 20 × 200 ns) to validate their individual stability as potential inhibitors. Eight out of the twenty compounds showed stable binding modes in the MD simulations, as well as favorable drug properties from our predctions. Therefore, our computational data suggest that the resulting top eight out of twenty compounds could potentially be novel inhibitors to ADRP of SARS-CoV-2.
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Affiliation(s)
- Dhrumi C Patel
- Department of Molecular & Cellular Biosciences, College of Science and Mathematics, Rowan University, Glassboro, NJ, 08028, United States
| | - Katherine R Hausman
- Department of Molecular & Cellular Biosciences, College of Science and Mathematics, Rowan University, Glassboro, NJ, 08028, United States
| | - Muhammad Arba
- Faculty of Pharmacy, Universitas Halu Oleo, Kendari, 93232, Indonesia
| | - Annie Tran
- Department of Molecular & Cellular Biosciences, College of Science and Mathematics, Rowan University, Glassboro, NJ, 08028, United States
| | - Phillip M Lakernick
- Department of Molecular & Cellular Biosciences, College of Science and Mathematics, Rowan University, Glassboro, NJ, 08028, United States
| | - Chun Wu
- Department of Molecular & Cellular Biosciences, College of Science and Mathematics, Rowan University, Glassboro, NJ, 08028, United States.
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36
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Guerra JVDS, Ribeiro-Filho HV, Jara GE, Bortot LO, Pereira JGDC, Lopes-de-Oliveira PS. pyKVFinder: an efficient and integrable Python package for biomolecular cavity detection and characterization in data science. BMC Bioinformatics 2021; 22:607. [PMID: 34930115 PMCID: PMC8685811 DOI: 10.1186/s12859-021-04519-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/07/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Biomolecular interactions that modulate biological processes occur mainly in cavities throughout the surface of biomolecular structures. In the data science era, structural biology has benefited from the increasing availability of biostructural data due to advances in structural determination and computational methods. In this scenario, data-intensive cavity analysis demands efficient scripting routines built on easily manipulated data structures. To fulfill this need, we developed pyKVFinder, a Python package to detect and characterize cavities in biomolecular structures for data science and automated pipelines. RESULTS pyKVFinder efficiently detects cavities in biomolecular structures and computes their volume, area, depth and hydropathy, storing these cavity properties in NumPy arrays. Benefited from Python ecosystem interoperability and data structures, pyKVFinder can be integrated with third-party scientific packages and libraries for mathematical calculations, machine learning and 3D visualization in automated workflows. As proof of pyKVFinder's capabilities, we successfully identified and compared ADRP substrate-binding site of SARS-CoV-2 and a set of homologous proteins with pyKVFinder, showing its integrability with data science packages such as matplotlib, NGL Viewer, SciPy and Jupyter notebook. CONCLUSIONS We introduce an efficient, highly versatile and easily integrable software for detecting and characterizing biomolecular cavities in data science applications and automated protocols. pyKVFinder facilitates biostructural data analysis with scripting routines in the Python ecosystem and can be building blocks for data science and drug design applications.
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Affiliation(s)
- João Victor da Silva Guerra
- Brazilian Center for Research in Energy and Materials (CNPEM), Brazilian Biosciences National Laboratory (LNBio), R. Giuseppe Máximo Scolfaro, 10000 - Bosque das Palmeiras, Campinas, SP, 13083-100, Brazil. .,Graduate Program in Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, University of Campinas, Campinas, SP, Brazil.
| | - Helder Veras Ribeiro-Filho
- Brazilian Center for Research in Energy and Materials (CNPEM), Brazilian Biosciences National Laboratory (LNBio), R. Giuseppe Máximo Scolfaro, 10000 - Bosque das Palmeiras, Campinas, SP, 13083-100, Brazil
| | - Gabriel Ernesto Jara
- Brazilian Center for Research in Energy and Materials (CNPEM), Brazilian Biosciences National Laboratory (LNBio), R. Giuseppe Máximo Scolfaro, 10000 - Bosque das Palmeiras, Campinas, SP, 13083-100, Brazil
| | - Leandro Oliveira Bortot
- Brazilian Center for Research in Energy and Materials (CNPEM), Brazilian Biosciences National Laboratory (LNBio), R. Giuseppe Máximo Scolfaro, 10000 - Bosque das Palmeiras, Campinas, SP, 13083-100, Brazil
| | - José Geraldo de Carvalho Pereira
- Brazilian Center for Research in Energy and Materials (CNPEM), Brazilian Biosciences National Laboratory (LNBio), R. Giuseppe Máximo Scolfaro, 10000 - Bosque das Palmeiras, Campinas, SP, 13083-100, Brazil
| | - Paulo Sérgio Lopes-de-Oliveira
- Brazilian Center for Research in Energy and Materials (CNPEM), Brazilian Biosciences National Laboratory (LNBio), R. Giuseppe Máximo Scolfaro, 10000 - Bosque das Palmeiras, Campinas, SP, 13083-100, Brazil. .,Graduate Program in Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, University of Campinas, Campinas, SP, Brazil.
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37
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A novel statistical method predicts mutability of the genomic segments of the SARS-CoV-2 virus. QRB DISCOVERY 2021; 3:e1. [PMID: 35106478 PMCID: PMC8795775 DOI: 10.1017/qrd.2021.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 05/28/2021] [Accepted: 11/26/2021] [Indexed: 11/06/2022] Open
Abstract
Abstract
The SARS-CoV-2 virus has made the largest pandemic of the 21st century, with hundreds of millions of cases and tens of millions of fatalities. Scientists all around the world are racing to develop vaccines and new pharmaceuticals to overcome the pandemic and offer effective treatments for COVID-19 disease. Consequently, there is an essential need to better understand how the pathogenesis of SARS-CoV-2 is affected by viral mutations and to determine the conserved segments in the viral genome that can serve as stable targets for novel therapeutics. Here, we introduce a text-mining method to estimate the mutability of genomic segments directly from a reference (ancestral) whole genome sequence. The method relies on calculating the importance of genomic segments based on their spatial distribution and frequency over the whole genome. To validate our approach, we perform a large-scale analysis of the viral mutations in nearly 80,000 publicly available SARS-CoV-2 predecessor whole genome sequences and show that these results are highly correlated with the segments predicted by the statistical method used for keyword detection. Importantly, these correlations are found to hold at the codon and gene levels, as well as for gene coding regions. Using the text-mining method, we further identify codon sequences that are potential candidates for siRNA-based antiviral drugs. Significantly, one of the candidates identified in this work corresponds to the first seven codons of an epitope of the spike glycoprotein, which is the only SARS-CoV-2 immunogenic peptide without a match to a human protein.
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38
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Bhati AP, Wan S, Alfè D, Clyde AR, Bode M, Tan L, Titov M, Merzky A, Turilli M, Jha S, Highfield RR, Rocchia W, Scafuri N, Succi S, Kranzlmüller D, Mathias G, Wifling D, Donon Y, Di Meglio A, Vallecorsa S, Ma H, Trifan A, Ramanathan A, Brettin T, Partin A, Xia F, Duan X, Stevens R, Coveney PV. Pandemic drugs at pandemic speed: infrastructure for accelerating COVID-19 drug discovery with hybrid machine learning- and physics-based simulations on high-performance computers. Interface Focus 2021; 11:20210018. [PMID: 34956592 PMCID: PMC8504892 DOI: 10.1098/rsfs.2021.0018] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2021] [Indexed: 12/13/2022] Open
Abstract
The race to meet the challenges of the global pandemic has served as a reminder that the existing drug discovery process is expensive, inefficient and slow. There is a major bottleneck screening the vast number of potential small molecules to shortlist lead compounds for antiviral drug development. New opportunities to accelerate drug discovery lie at the interface between machine learning methods, in this case, developed for linear accelerators, and physics-based methods. The two in silico methods, each have their own advantages and limitations which, interestingly, complement each other. Here, we present an innovative infrastructural development that combines both approaches to accelerate drug discovery. The scale of the potential resulting workflow is such that it is dependent on supercomputing to achieve extremely high throughput. We have demonstrated the viability of this workflow for the study of inhibitors for four COVID-19 target proteins and our ability to perform the required large-scale calculations to identify lead antiviral compounds through repurposing on a variety of supercomputers.
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Affiliation(s)
- Agastya P. Bhati
- Centre for Computational Science, University College London, Gordon Street, London WC1H 0AJ, UK
| | - Shunzhou Wan
- Centre for Computational Science, University College London, Gordon Street, London WC1H 0AJ, UK
| | - Dario Alfè
- Department of Earth Sciences, London Centre for Nanotechnology and Thomas Young Centre at University College London, University College London, Gower Street, London WC1E 6BT, UK
- Dipartimento di Fisica Ettore Pancini, Università di Napoli Federico II, Monte Sant'Angelo, Napoli 80126, Italy
| | - Austin R. Clyde
- Department of Computer Science, University of Chicago, Chicago, IL, USA
| | - Mathis Bode
- Institute for Combustion Technology, RWTH Aachen University, Aachen 52056, Germany
| | - Li Tan
- Brookhaven National Laboratory, Upton, NY 11973, USA
| | - Mikhail Titov
- Department of Electrical and Computer Engineering, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Andre Merzky
- Department of Electrical and Computer Engineering, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Matteo Turilli
- Department of Electrical and Computer Engineering, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | - Shantenu Jha
- Brookhaven National Laboratory, Upton, NY 11973, USA
- Department of Electrical and Computer Engineering, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA
| | | | - Walter Rocchia
- Concept Lab, Italian Institute of Technology, Via Melen, Genova, Italy
| | - Nicola Scafuri
- Concept Lab, Italian Institute of Technology, Via Melen, Genova, Italy
| | - Sauro Succi
- Center for Life Nanosciences at La Sapienza, Italian Institute of Technology, viale Regina Elena, Roma, Italy
| | - Dieter Kranzlmüller
- Leibniz Supercomputing Centre (LRZ) of the Bavarian Academy of Sciences and Humanities, Boltzmannstrasse 1, Garching bei München 85748, Germany
| | - Gerald Mathias
- Leibniz Supercomputing Centre (LRZ) of the Bavarian Academy of Sciences and Humanities, Boltzmannstrasse 1, Garching bei München 85748, Germany
| | - David Wifling
- Leibniz Supercomputing Centre (LRZ) of the Bavarian Academy of Sciences and Humanities, Boltzmannstrasse 1, Garching bei München 85748, Germany
| | | | | | | | - Heng Ma
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Anda Trifan
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Arvind Ramanathan
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Tom Brettin
- Computing, Environment and Life Sciences Directorate, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Alexander Partin
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Fangfang Xia
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Xiaotan Duan
- Department of Computer Science, University of Chicago, Chicago, IL, USA
| | - Rick Stevens
- Computing, Environment and Life Sciences Directorate, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Peter V. Coveney
- Centre for Computational Science, University College London, Gordon Street, London WC1H 0AJ, UK
- Institute for Informatics, University of Amsterdam, Science Park 904, Amsterdam 1098 XH, The Netherlands
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39
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Hardenbrook NJ, Zhang P. A structural view of the SARS-CoV-2 virus and its assembly. Curr Opin Virol 2021; 52:123-134. [PMID: 34915287 PMCID: PMC8642146 DOI: 10.1016/j.coviro.2021.11.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 11/11/2021] [Accepted: 11/22/2021] [Indexed: 12/15/2022]
Abstract
Structural biology plays a vital role in SARS-CoV-2 vaccine and treatment. High-resolution structures of SARS-CoV-2 proteins and complexes have been obtained. In situ structures of SARS-CoV-2 virus and its assembly are visualized by cryoET.
The SARS-CoV-2 pandemic that struck in 2019 has left the world crippled with hundreds of millions of cases and millions of people dead. During this time, we have seen unprecedented support and collaboration amongst scientists to respond to this deadly disease. Advances in the field of structural biology, in particular cryoEM and cryo-electron tomography, have allowed unprecedented structural analysis of SARS-CoV-2. Here, we review the structural work on the SARS-CoV-2 virus and viral components, as well as its cellular assembly process, highlighting some important structural findings that have made significant impact on the protection from and treatment of emerging viral infections.
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Affiliation(s)
- Nathan J Hardenbrook
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
| | - Peijun Zhang
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK; Electron Bio-Imaging Centre, Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, UK; Chinese Academy of Medical Sciences Oxford Institute, University of Oxford, Oxford, OX3 7BN, UK.
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40
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Selvaraj C, Dinesh DC, Krafcikova P, Boura E, Aarthy M, Pravin MA, Singh SK. Structural Understanding of SARS-CoV-2 Drug Targets, Active Site Contour Map Analysis and COVID-19 Therapeutics. Curr Mol Pharmacol 2021; 15:418-433. [PMID: 34488601 DOI: 10.2174/1874467214666210906125959] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 03/11/2021] [Accepted: 03/17/2021] [Indexed: 11/22/2022]
Abstract
The most iconic word of the year 2020 is 'COVID-19', the shortened name for coronavirus disease 2019. The pandemic, caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), is responsible for multiple worldwide lockdowns, an economic crisis, and a substantial increase in hospitalizations for viral pneumonia along with respiratory failure and multiorgan dysfunctions. Recently, the first few vaccines were approved by World Health Organization (WHO) and can eventually save millions of lives. Even though, few emergency use drugs like Remdesivir and several other repurposed drugs, still there is no approved drug for COVID-19. The coronaviral encoded proteins involved in host-cell entry, replication, and host-cell invading mechanism are potentially therapeutic targets. This perspective review provides the molecular overview of SARS-CoV-2 life cycle for summarizing potential drug targets, structural insights, active site contour map analyses of those selected SARS-CoV-2 protein targets for drug discovery, immunology, and pathogenesis.
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Affiliation(s)
- Chandrabose Selvaraj
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi-630004, Tamil Nadu. India
| | | | - Petra Krafcikova
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Flemingovo nam. 2, 166 10 Prague 6. Czech Republic
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Flemingovo nam. 2, 166 10 Prague 6. Czech Republic
| | - Murali Aarthy
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi-630004, Tamil Nadu. India
| | - Muthuraja Arun Pravin
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi-630004, Tamil Nadu. India
| | - Sanjeev Kumar Singh
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi-630004, Tamil Nadu. India
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Bhavaniramya S, Ramar V, Vishnupriya S, Palaniappan R, Sibiya A, Baskaralingam V. Comprehensive analysis of SARS-COV-2 drug targets and pharmacological aspects in treating the COVID-19. Curr Mol Pharmacol 2021; 15:393-417. [PMID: 34382513 DOI: 10.2174/1874467214666210811120635] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/27/2021] [Accepted: 02/22/2021] [Indexed: 11/22/2022]
Abstract
Corona viruses are enveloped, single-stranded RNA (Ribonucleic acid) viruses and they cause pandemic diseases having a devastating effect on both human healthcare and the global economy. To date, six corona viruses have been identified as pathogenic organisms which are significantly responsible for the infection and also cause severe respiratory diseases. Among them, the novel SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) caused a major outbreak of corona virus diseases 2019 (COVID-19). Coronaviridae family members can affects both humans and animals. In human, corona viruses cause severe acute respiratory syndrome with mild to severe outcomes. Several structural and genomics have been investigated, and the genome encodes about 28 proteins most of them with unknown function though it shares remarkable sequence identity with other proteins. There is no potent and licensed vaccine against SARS-CoV-2 and several trials are underway to investigate the possible therapeutic agents against viral infection. However, some of the antiviral drugs that have been investigated against SARS-CoV-2 are under clinical trials. In the current review we comparatively emphasize the emergence and pathogenicity of the SARS-CoV-2 and their infection and discuss the various putative drug targets of both viral and host receptors for developing effective vaccines and therapeutic combinations to overcome the viral outbreak.
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Affiliation(s)
- Sundaresan Bhavaniramya
- Biomaterials and Biotechnology in Animal Health Lab, Department of Animal Health and Management, Alagappa University, Karaikudi 630004, Tamil Nadu. India
| | - Vanajothi Ramar
- Department of Biomedical Science, Bharathidasan University, Tiruchirappalli, Tamil Nadu, 620024. India
| | - Selvaraju Vishnupriya
- College of Food and Dairy Technology, Tamil Nadu Veterinary and Animal Sciences University, Chennai 600052. India
| | - Ramasamy Palaniappan
- Research and Development Wing, Sree Balaji Medical College and Hospital, Bharath Institute of Higher Education (BIHER), Chennai-600044, Tamilnadu. India
| | - Ashokkumar Sibiya
- Biomaterials and Biotechnology in Animal Health Lab, Department of Animal Health and Management, Alagappa University, Karaikudi 630004, Tamil Nadu. India
| | - Vaseeharan Baskaralingam
- Biomaterials and Biotechnology in Animal Health Lab, Department of Animal Health and Management, Alagappa University, Karaikudi 630004, Tamil Nadu. India
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Halder UC. Predicted antiviral drugs Darunavir, Amprenavir, Rimantadine and Saquinavir can potentially bind to neutralize SARS-CoV-2 conserved proteins. JOURNAL OF BIOLOGICAL RESEARCH (THESSALONIKE, GREECE) 2021; 28:18. [PMID: 34344455 PMCID: PMC8331326 DOI: 10.1186/s40709-021-00149-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 07/14/2021] [Indexed: 12/12/2022]
Abstract
BACKGROUND Novel Coronavirus disease 2019 or COVID-19 has become a threat to human society due to fast spreading and increasing mortality. It uses vertebrate hosts and presently deploys humans. Life cycle and pathogenicity of SARS-CoV-2 have already been deciphered and possible drug target trials are on the way. RESULTS The present study was aimed to analyze Non-Structural Proteins that include conserved enzymes of SARS-CoV-2 like papain-like protease, main protease, Replicase, RNA-dependent RNA polymerase, methyltransferase, helicase, exoribonuclease and endoribonucleaseas targets to all known drugs. A bioinformatic based web server Drug ReposeER predicted several drug binding motifs in these analyzed proteins. Results revealed that anti-viral drugs Darunavir,Amprenavir, Rimantadine and Saquinavir were the most potent to have 3D-drug binding motifs that were closely associated with the active sites of the SARS-CoV-2 enzymes . CONCLUSIONS Repurposing of the antiviral drugs Darunavir, Amprenavir, Rimantadine and Saquinavir to treat COVID-19 patients could be useful that can potentially prevent human mortality.
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Affiliation(s)
- Umesh C Halder
- Department of Zoology, Raniganj Girls' College, Searsole -Rajbari, Paschim Bardhaman, Raniganj, 713358, West Bengal, India.
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Kim C, Mahasenan KV, Bhardwaj A, Wiest O, Chang M, Mobashery S. Production of Proteins of the SARS-CoV-2 Proteome for Drug Discovery. ACS OMEGA 2021; 6:19983-19994. [PMID: 34337272 PMCID: PMC8315141 DOI: 10.1021/acsomega.1c02984] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 07/06/2021] [Indexed: 05/09/2023]
Abstract
The severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is the causative agent of the coronavirus disease of 2019 (COVID-19). Its genome encodes two open reading frames for two large proteins, PP1a and PP1ab. Within the two polypeptide stretches, there are two proteases that process the large proteins into 15 discrete proteins essential for the assembly of the virion during its replication. We describe herein the cloning of the genes for these discrete proteins optimized for expression in Escherichia coli, production of the proteins, and their purification to homogeneity. These included all but six: NSP6, which possesses eight transmembrane regions, and five that are small proteins/peptides (E, ORF3b, ORF6, ORF7b, and ORF10). These proteins are intended for experimental validation of small-molecule binders as molecular template hits. The proof of concept was established with the ADP-ribosylhydrolase (ARH) domain of NSP3 in discovery of small-molecule templates that could serve as the basis for further optimization. The hit molecules include one submicromolar and a few low-micromolar binders to the ARH domain. Availability of these proteins in soluble forms opens up the opportunity for discoveries of novel templates with the potential for anti-COVID-19 pharmaceuticals.
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Lanjanian H, Nematzadeh S, Hosseini S, Torkamanian-Afshar M, Kiani F, Moazzam-Jazi M, Aydin N, Masoudi-Nejad A. High-throughput analysis of the interactions between viral proteins and host cell RNAs. Comput Biol Med 2021; 135:104611. [PMID: 34246161 PMCID: PMC8252845 DOI: 10.1016/j.compbiomed.2021.104611] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 06/20/2021] [Accepted: 06/23/2021] [Indexed: 01/18/2023]
Abstract
RNA-protein interactions of a virus play a major role in the replication of RNA viruses. The replication and transcription of these viruses take place in the cytoplasm of the host cell; hence, there is a probability for the host RNA-viral protein and viral RNA-host protein interactions. The current study applies a high-throughput computational approach, including feature extraction and machine learning methods, to predict the affinity of protein sequences of ten viruses to three categories of RNA sequences. These categories include RNAs involved in the protein-RNA complexes stored in the RCSB database, the human miRNAs deposited at the mirBase database, and the lncRNA deposited in the LNCipedia database. The results show that evolution not only tries to conserve key viral proteins involved in the replication and transcription but also prunes their interaction capability. These proteins with specific interactions do not perturb the host cell through undesired interactions. On the other hand, the hypermutation rate of NSP3 is related to its affinity to host cell RNAs. The Gene Ontology (GO) analysis of the miRNA with affiliation to NSP3 suggests that these miRNAs show strongly significantly enriched GO terms related to the known symptoms of COVID-19. Docking and MD simulation study of the obtained miRNA through high-throughput analysis suggest a non-coding RNA (an RNA antitoxin, ToxI) as a natural aptamer drug candidate for NSP5 inhibition. Finally, a significant interplay of the host RNA-viral protein in the host cell can disrupt the host cell's system by influencing the RNA-dependent processes of the host cells, such as a differential expression in RNA. Furthermore, our results are useful to identify the side effects of mRNA-based vaccines, many of which are caused by the off-label interactions with the human lncRNAs.
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Affiliation(s)
- Hossein Lanjanian
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Sajjad Nematzadeh
- Department of Computer Technologies, Beykent University, Istanbul, Turkey; Department of Computer Engineering, Faculty of Electrical and Electronics, Yildiz Technical University, Istanbul, Turkey.
| | - Shadi Hosseini
- Department of Medicinal Chemistry, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran.
| | - Mahsa Torkamanian-Afshar
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran; Nisantasi University, Faculty of Engineering and Architecture, Department of Computer Engineering, Turkey.
| | - Farzad Kiani
- Department of Software Engineering, Engineering and Natural Sciences Faculty, Istinye University, Istanbul, Turkey.
| | - Maryam Moazzam-Jazi
- Cellular and Molecular Endocrine Research Center, Research Institute for Endocrine Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Nizamettin Aydin
- Department of Computer Engineering, Faculty of Electrical and Electronics, Yildiz Technical University, Istanbul, Turkey.
| | - Ali Masoudi-Nejad
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran. http://lbb.ut.ac.ir/
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Cotten M, Robertson DL, Phan MVT. Unique protein features of SARS-CoV-2 relative to other Sarbecoviruses. Virus Evol 2021; 7:veab067. [PMID: 34527286 PMCID: PMC8385934 DOI: 10.1093/ve/veab067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 06/30/2021] [Accepted: 08/06/2021] [Indexed: 01/08/2023] Open
Abstract
Defining the unique properties of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) protein sequences has potential to explain the range of Coronavirus Disease 2019 severity. To achieve this we compared proteins encoded by all Sarbecoviruses using profile Hidden Markov Model similarities to identify protein features unique to SARS-CoV-2. Consistent with previous reports, a small set of bat- and pangolin-derived Sarbecoviruses show the greatest similarity to SARS-CoV-2 but are unlikely to be the direct source of SARS-CoV-2. Three proteins (nsp3, spike, and orf9) showed regions differing between the bat Sarbecoviruses and SARS-CoV-2 and indicate virus protein features that might have evolved to support human infection and/or transmission. Spike analysis identified all regions of the protein that have tolerated change and revealed that the current SARS-CoV-2 variants of concern have sampled only a fraction (∼31 per cent) of the possible spike domain changes which have occurred historically in Sarbecovirus evolution. This result emphasises the evolvability of these coronaviruses and the potential for further change in virus replication and transmission properties over the coming years.
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Affiliation(s)
- Matthew Cotten
- MRC/UVRI & LSHTM Uganda Research Unit, Plot 51-59 Nakiwogo Road, P.O Box 49, Entebbe, Uganda
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Garscube Campus, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, Sir Michael Stoker Building, Garscube Campus, 464 Bearsden Road, Glasgow G61 1QH, UK
| | - My V T Phan
- MRC/UVRI & LSHTM Uganda Research Unit, Plot 51-59 Nakiwogo Road, P.O Box 49, Entebbe, Uganda
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Lin Z, Qing H, Li R, Zheng L, Yao H. Evolution trace of SARS-CoV-2 from January 19 to March 12, 2020, in the United States. J Med Virol 2021; 93:6595-6604. [PMID: 34292617 PMCID: PMC8426869 DOI: 10.1002/jmv.27225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 07/13/2021] [Indexed: 01/18/2023]
Abstract
As a kind of human betacoronavirus, SARS‐CoV‐2 has endangered globally public health. As of January 2021, the virus had resulted in 2,209,195 deaths. By studying the evolution trend and characteristics of 265 SARS‐CoV‐2 strains in the United States from January to March, it is found that the strains can be divided into six clades, USA clade‐1, USA clade‐2, USA clade‐3, USA clade‐4, USA clade‐5, and USA clade‐6, in which US clade‐1 may be the most ancestral clade, USA clade‐2 is an interim clade of USA clade‐1 and USA clade‐3, the other three clades have similar codon usage pattern, while USA clade‐6 is the newest and most adaptable clade. Mismatch analysis and protein alignment showed that the evolution of the clades arises from some special mutations in viral proteins, which may help the strain to invade, replicate, transcribe and so on. Compared with previous research and classifications, we suggest that clade O in GISAID should not be an independent clade and Wuhan‐Hu‐1 (EPI_ISL_402125) should not be an ancestral reference sequence. Our study decoded the evolutionary dynamic of SARS‐CoV‐2 in the early stage from the United States, which give some clues to infer the current evolution trend of SARS‐CoV‐2 and study the function of viral mutational protein. Basing on decoding the characteristics and evolution process of SARS‐CoV‐2 in the early stage of the USA, it is suggested that the clade O in GISAID should not be as an independent evolutionary clade by phylogenetic analysis or protein alignment. Secondly, Wuhan‐Hu‐1 (EPI_ISL_402125) should not be as an ancestral reference sequence and its candidate should be EPI_ISL_529213. Thirdly, many unique mutation sites in viral proteins were found to lay foundation to study the function of the mutational protein and to reveal the evolution trend of SARS‐CoV‐2 in coming days.
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Affiliation(s)
- Ziying Lin
- College of Life Science, Sichuan Agriculture University, Ya'an, China
| | - Hua Qing
- College of Life Science, Sichuan Agriculture University, Ya'an, China
| | - Rui Li
- College of Life Science, Sichuan Agriculture University, Ya'an, China
| | | | - Huipeng Yao
- College of Life Science, Sichuan Agriculture University, Ya'an, China
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Fu W, Yao H, Bütepage M, Zhao Q, Lüscher B, Li J. The search for inhibitors of macrodomains for targeting the readers and erasers of mono-ADP-ribosylation. Drug Discov Today 2021; 26:2547-2558. [PMID: 34023495 DOI: 10.1016/j.drudis.2021.05.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 04/13/2021] [Accepted: 05/14/2021] [Indexed: 01/15/2023]
Abstract
Macrodomains are evolutionarily conserved structural elements. Many macrodomains feature as binding modules of ADP-ribose, thus participating in the recognition and removal of mono- and poly-ADP-ribosylation. Macrodomains are involved in the regulation of a variety of physiological processes and represent valuable therapeutic targets. Moreover, as part of the nonstructural proteins of certain viruses, macrodomains are also pivotal for viral replication and pathogenesis. Thus, targeting viral macrodomains with inhibitors is considered to be a promising antiviral intervention. In this review, we summarize our current understanding of human and viral macrodomains that are related to mono-ADP-ribosylation, with emphasis on the search for inhibitors. The advances summarized here will be helpful for the design of macrodomain-specific agents for therapeutic and diagnostic applications.
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Affiliation(s)
- Wei Fu
- College of Chemistry, Fuzhou University, 350116 Fuzhou, China
| | - Huiqiao Yao
- College of Chemistry, Fuzhou University, 350116 Fuzhou, China
| | - Mareike Bütepage
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, 52057 Aachen, Germany
| | - Qianqian Zhao
- College of Chemistry, Fuzhou University, 350116 Fuzhou, China
| | - Bernhard Lüscher
- Institute of Biochemistry and Molecular Biology, Medical School, RWTH Aachen University, 52057 Aachen, Germany.
| | - Jinyu Li
- College of Chemistry, Fuzhou University, 350116 Fuzhou, China.
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Barrantes FJ. The Contribution of Biophysics and Structural Biology to Current Advances in COVID-19. Annu Rev Biophys 2021; 50:493-523. [PMID: 33957057 DOI: 10.1146/annurev-biophys-102620-080956] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Critical to viral infection are the multiple interactions between viral proteins and host-cell counterparts. The first such interaction is the recognition of viral envelope proteins by surface receptors that normally fulfil other physiological roles, a hijacking mechanism perfected over the course of evolution. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of coronavirus disease 2019 (COVID-19), has successfully adopted this strategy using its spike glycoprotein to dock on the membrane-bound metalloprotease angiotensin-converting enzyme 2 (ACE2). The crystal structures of several SARS-CoV-2 proteins alone or in complex with their receptors or other ligands were recently solved at an unprecedented pace. This accomplishment is partly due to the increasing availability of data on other coronaviruses and ACE2 over the past 18 years. Likewise, other key intervening actors and mechanisms of viral infection were elucidated with the aid of biophysical approaches. An understanding of the various structurally important motifs of the interacting partners provides key mechanistic information for the development of structure-based designer drugs able to inhibit various steps of the infective cycle, including neutralizing antibodies, small organic drugs, and vaccines. This review analyzes current progress and the outlook for future structural studies.
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Affiliation(s)
- Francisco J Barrantes
- Biomedical Research Institute (BIOMED), Catholic University of Argentina (UCA)-National Scientific and Technical Research Council, Argentina (CONICET), C1107AFF Buenos Aires, Argentina;
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49
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Altincekic N, Korn SM, Qureshi NS, Dujardin M, Ninot-Pedrosa M, Abele R, Abi Saad MJ, Alfano C, Almeida FCL, Alshamleh I, de Amorim GC, Anderson TK, Anobom CD, Anorma C, Bains JK, Bax A, Blackledge M, Blechar J, Böckmann A, Brigandat L, Bula A, Bütikofer M, Camacho-Zarco AR, Carlomagno T, Caruso IP, Ceylan B, Chaikuad A, Chu F, Cole L, Crosby MG, de Jesus V, Dhamotharan K, Felli IC, Ferner J, Fleischmann Y, Fogeron ML, Fourkiotis NK, Fuks C, Fürtig B, Gallo A, Gande SL, Gerez JA, Ghosh D, Gomes-Neto F, Gorbatyuk O, Guseva S, Hacker C, Häfner S, Hao B, Hargittay B, Henzler-Wildman K, Hoch JC, Hohmann KF, Hutchison MT, Jaudzems K, Jović K, Kaderli J, Kalniņš G, Kaņepe I, Kirchdoerfer RN, Kirkpatrick J, Knapp S, Krishnathas R, Kutz F, zur Lage S, Lambertz R, Lang A, Laurents D, Lecoq L, Linhard V, Löhr F, Malki A, Bessa LM, Martin RW, Matzel T, Maurin D, McNutt SW, Mebus-Antunes NC, Meier BH, Meiser N, Mompeán M, Monaca E, Montserret R, Mariño Perez L, Moser C, Muhle-Goll C, Neves-Martins TC, Ni X, Norton-Baker B, Pierattelli R, Pontoriero L, Pustovalova Y, Ohlenschläger O, Orts J, Da Poian AT, Pyper DJ, Richter C, Riek R, Rienstra CM, Robertson A, Pinheiro AS, Sabbatella R, Salvi N, Saxena K, Schulte L, Schiavina M, Schwalbe H, Silber M, Almeida MDS, Sprague-Piercy MA, Spyroulias GA, Sreeramulu S, Tants JN, Tārs K, Torres F, Töws S, Treviño MÁ, Trucks S, Tsika AC, Varga K, Wang Y, Weber ME, Weigand JE, Wiedemann C, Wirmer-Bartoschek J, Wirtz Martin MA, Zehnder J, Hengesbach M, Schlundt A. Large-Scale Recombinant Production of the SARS-CoV-2 Proteome for High-Throughput and Structural Biology Applications. Front Mol Biosci 2021; 8:653148. [PMID: 34041264 PMCID: PMC8141814 DOI: 10.3389/fmolb.2021.653148] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 02/04/2021] [Indexed: 01/18/2023] Open
Abstract
The highly infectious disease COVID-19 caused by the Betacoronavirus SARS-CoV-2 poses a severe threat to humanity and demands the redirection of scientific efforts and criteria to organized research projects. The international COVID19-NMR consortium seeks to provide such new approaches by gathering scientific expertise worldwide. In particular, making available viral proteins and RNAs will pave the way to understanding the SARS-CoV-2 molecular components in detail. The research in COVID19-NMR and the resources provided through the consortium are fully disclosed to accelerate access and exploitation. NMR investigations of the viral molecular components are designated to provide the essential basis for further work, including macromolecular interaction studies and high-throughput drug screening. Here, we present the extensive catalog of a holistic SARS-CoV-2 protein preparation approach based on the consortium's collective efforts. We provide protocols for the large-scale production of more than 80% of all SARS-CoV-2 proteins or essential parts of them. Several of the proteins were produced in more than one laboratory, demonstrating the high interoperability between NMR groups worldwide. For the majority of proteins, we can produce isotope-labeled samples of HSQC-grade. Together with several NMR chemical shift assignments made publicly available on covid19-nmr.com, we here provide highly valuable resources for the production of SARS-CoV-2 proteins in isotope-labeled form.
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Affiliation(s)
- Nadide Altincekic
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Sophie Marianne Korn
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Nusrat Shahin Qureshi
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Marie Dujardin
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | - Martí Ninot-Pedrosa
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | - Rupert Abele
- Institute for Biochemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Marie Jose Abi Saad
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Caterina Alfano
- Structural Biology and Biophysics Unit, Fondazione Ri.MED, Palermo, Italy
| | - Fabio C. L. Almeida
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Islam Alshamleh
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Gisele Cardoso de Amorim
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Multidisciplinary Center for Research in Biology (NUMPEX), Campus Duque de Caxias Federal University of Rio de Janeiro, Duque de Caxias, Brazil
| | - Thomas K. Anderson
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI, United States
| | - Cristiane D. Anobom
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Chelsea Anorma
- Department of Chemistry, University of California, Irvine, CA, United States
| | - Jasleen Kaur Bains
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Adriaan Bax
- LCP, NIDDK, NIH, Bethesda, MD, United States
| | | | - Julius Blechar
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Anja Böckmann
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | - Louis Brigandat
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | - Anna Bula
- Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Matthias Bütikofer
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | | | - Teresa Carlomagno
- BMWZ and Institute of Organic Chemistry, Leibniz University Hannover, Hannover, Germany
- Group of NMR-Based Structural Chemistry, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Icaro Putinhon Caruso
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Multiuser Center for Biomolecular Innovation (CMIB), Department of Physics, São Paulo State University (UNESP), São José do Rio Preto, Brazil
| | - Betül Ceylan
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Apirat Chaikuad
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Feixia Chu
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Laura Cole
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | - Marquise G. Crosby
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
| | - Vanessa de Jesus
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Karthikeyan Dhamotharan
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Isabella C. Felli
- Magnetic Resonance Centre (CERM), University of Florence, Sesto Fiorentino, Italy
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
| | - Jan Ferner
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Yanick Fleischmann
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Marie-Laure Fogeron
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | | | - Christin Fuks
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Angelo Gallo
- Department of Pharmacy, University of Patras, Patras, Greece
| | - Santosh L. Gande
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Juan Atilio Gerez
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Dhiman Ghosh
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Francisco Gomes-Neto
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratory of Toxinology, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Oksana Gorbatyuk
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | | | | | - Sabine Häfner
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), Jena, Germany
| | - Bing Hao
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | - Bruno Hargittay
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - K. Henzler-Wildman
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI, United States
| | - Jeffrey C. Hoch
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | - Katharina F. Hohmann
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Marie T. Hutchison
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | | | - Katarina Jović
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Janina Kaderli
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Gints Kalniņš
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Iveta Kaņepe
- Latvian Institute of Organic Synthesis, Riga, Latvia
| | - Robert N. Kirchdoerfer
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI, United States
| | - John Kirkpatrick
- BMWZ and Institute of Organic Chemistry, Leibniz University Hannover, Hannover, Germany
- Group of NMR-Based Structural Chemistry, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Robin Krishnathas
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Felicitas Kutz
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Susanne zur Lage
- Group of NMR-Based Structural Chemistry, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Roderick Lambertz
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Andras Lang
- Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), Jena, Germany
| | - Douglas Laurents
- “Rocasolano” Institute for Physical Chemistry (IQFR), Spanish National Research Council (CSIC), Madrid, Spain
| | - Lauriane Lecoq
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | - Verena Linhard
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Frank Löhr
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute of Biophysical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Anas Malki
- Univ. Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | | | - Rachel W. Martin
- Department of Chemistry, University of California, Irvine, CA, United States
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
| | - Tobias Matzel
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Damien Maurin
- Univ. Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Seth W. McNutt
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Nathane Cunha Mebus-Antunes
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Beat H. Meier
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Nathalie Meiser
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Miguel Mompeán
- “Rocasolano” Institute for Physical Chemistry (IQFR), Spanish National Research Council (CSIC), Madrid, Spain
| | - Elisa Monaca
- Structural Biology and Biophysics Unit, Fondazione Ri.MED, Palermo, Italy
| | - Roland Montserret
- Molecular Microbiology and Structural Biochemistry, UMR 5086, CNRS/Lyon University, Lyon, France
| | | | - Celine Moser
- IBG-4, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | | | - Thais Cristtina Neves-Martins
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Xiamonin Ni
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Frankfurt am Main, Germany
| | - Brenna Norton-Baker
- Department of Chemistry, University of California, Irvine, CA, United States
| | - Roberta Pierattelli
- Magnetic Resonance Centre (CERM), University of Florence, Sesto Fiorentino, Italy
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
| | - Letizia Pontoriero
- Magnetic Resonance Centre (CERM), University of Florence, Sesto Fiorentino, Italy
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
| | - Yulia Pustovalova
- Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, United States
| | | | - Julien Orts
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Andrea T. Da Poian
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Dennis J. Pyper
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Christian Richter
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Roland Riek
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Chad M. Rienstra
- Department of Biochemistry and National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, WI, United States
| | | | - Anderson S. Pinheiro
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Nicola Salvi
- Univ. Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Krishna Saxena
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Linda Schulte
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Marco Schiavina
- Magnetic Resonance Centre (CERM), University of Florence, Sesto Fiorentino, Italy
- Department of Chemistry “Ugo Schiff”, University of Florence, Sesto Fiorentino, Italy
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Mara Silber
- IBG-4, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Marcius da Silva Almeida
- National Center of Nuclear Magnetic Resonance (CNRMN, CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
- Institute of Medical Biochemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marc A. Sprague-Piercy
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, United States
| | | | - Sridhar Sreeramulu
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Jan-Niklas Tants
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Kaspars Tārs
- Latvian Biomedical Research and Study Centre, Riga, Latvia
| | - Felix Torres
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Sabrina Töws
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Miguel Á. Treviño
- “Rocasolano” Institute for Physical Chemistry (IQFR), Spanish National Research Council (CSIC), Madrid, Spain
| | - Sven Trucks
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | | | - Krisztina Varga
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH, United States
| | - Ying Wang
- BMWZ and Institute of Organic Chemistry, Leibniz University Hannover, Hannover, Germany
| | - Marco E. Weber
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Julia E. Weigand
- Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Christoph Wiedemann
- Institute of Biochemistry and Biotechnology, Charles Tanford Protein Centre, Martin Luther University Halle-Wittenberg, Halle/Saale, Germany
| | - Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Maria Alexandra Wirtz Martin
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Johannes Zehnder
- Swiss Federal Institute of Technology, Laboratory of Physical Chemistry, ETH Zurich, Zurich, Switzerland
| | - Martin Hengesbach
- Institute for Organic Chemistry and Chemical Biology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Andreas Schlundt
- Center of Biomolecular Magnetic Resonance (BMRZ), Goethe University Frankfurt, Frankfurt am Main, Germany
- Institute for Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
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Mikolčević P, Hloušek-Kasun A, Ahel I, Mikoč A. ADP-ribosylation systems in bacteria and viruses. Comput Struct Biotechnol J 2021; 19:2366-2383. [PMID: 34025930 PMCID: PMC8120803 DOI: 10.1016/j.csbj.2021.04.023] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 04/07/2021] [Accepted: 04/07/2021] [Indexed: 12/30/2022] Open
Abstract
ADP-ribosylation is an ancient posttranslational modification present in all kingdoms of life. The system likely originated in bacteria where it functions in inter- and intra-species conflict, stress response and pathogenicity. It was repeatedly adopted via lateral transfer by eukaryotes, including humans, where it has a pivotal role in epigenetics, DNA-damage repair, apoptosis, and other crucial pathways including the immune response to pathogenic bacteria and viruses. In other words, the same ammunition used by pathogens is adapted by eukaryotes to fight back. While we know quite a lot about the eukaryotic system, expanding rather patchy knowledge on bacterial and viral ADP-ribosylation would give us not only a better understanding of the system as a whole but a fighting advantage in this constant arms race. By writing this review we hope to put into focus the available information and give a perspective on how this system works and can be exploited in the search for therapeutic targets in the future. The relevance of the subject is especially highlighted by the current situation of being amid the world pandemic caused by a virus harbouring and dependent on a representative of such a system.
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Affiliation(s)
- Petra Mikolčević
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | | | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, UK
| | - Andreja Mikoč
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
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