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Nomburg J, Doherty EE, Price N, Bellieny-Rabelo D, Zhu YK, Doudna JA. Birth of protein folds and functions in the virome. Nature 2024:10.1038/s41586-024-07809-y. [PMID: 39187718 DOI: 10.1038/s41586-024-07809-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 07/10/2024] [Indexed: 08/28/2024]
Abstract
The rapid evolution of viruses generates proteins that are essential for infectivity and replication but with unknown functions, due to extreme sequence divergence1. Here, using a database of 67,715 newly predicted protein structures from 4,463 eukaryotic viral species, we found that 62% of viral proteins are structurally distinct and lack homologues in the AlphaFold database2,3. Among the remaining 38% of viral proteins, many have non-viral structural analogues that revealed surprising similarities between human pathogens and their eukaryotic hosts. Structural comparisons suggested putative functions for up to 25% of unannotated viral proteins, including those with roles in the evasion of innate immunity. In particular, RNA ligase T-like phosphodiesterases were found to resemble phage-encoded proteins that hydrolyse the host immune-activating cyclic dinucleotides 3',3'- and 2',3'-cyclic GMP-AMP (cGAMP). Experimental analysis showed that RNA ligase T homologues encoded by avian poxviruses similarly hydrolyse cGAMP, showing that RNA ligase T-mediated targeting of cGAMP is an evolutionarily conserved mechanism of immune evasion that is present in both bacteriophage and eukaryotic viruses. Together, the viral protein structural database and analyses presented here afford new opportunities to identify mechanisms of virus-host interactions that are common across the virome.
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Affiliation(s)
- Jason Nomburg
- Gladstone-UCSF Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Erin E Doherty
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA
| | - Nathan Price
- Gladstone-UCSF Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Daniel Bellieny-Rabelo
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA
| | - Yong K Zhu
- Gladstone-UCSF Institute of Data Science and Biotechnology, San Francisco, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Jennifer A Doudna
- Gladstone-UCSF Institute of Data Science and Biotechnology, San Francisco, CA, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA.
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA, USA.
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA.
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2
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Zuiani A, Dulberger CL, De Silva NS, Marquette M, Lu YJ, Palowitch GM, Dokic A, Sanchez-Velazquez R, Schlatterer K, Sarkar S, Kar S, Chawla B, Galeev A, Lindemann C, Rothenberg DA, Diao H, Walls AC, Addona TA, Mensa F, Vogel AB, Stuart LM, van der Most R, Srouji JR, Türeci Ö, Gaynor RB, Şahin U, Poran A. A multivalent mRNA monkeypox virus vaccine (BNT166) protects mice and macaques from orthopoxvirus disease. Cell 2024; 187:1363-1373.e12. [PMID: 38366591 DOI: 10.1016/j.cell.2024.01.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 11/13/2023] [Accepted: 01/12/2024] [Indexed: 02/18/2024]
Abstract
In response to the 2022 outbreak of mpox driven by unprecedented human-to-human monkeypox virus (MPXV) transmission, we designed BNT166, aiming to create a highly immunogenic, safe, accessible, and scalable next-generation vaccine against MPXV and related orthopoxviruses. To address the multiple viral forms and increase the breadth of immune response, two candidate multivalent mRNA vaccines were evaluated pre-clinically: a quadrivalent vaccine (BNT166a; encoding the MPXV antigens A35, B6, M1, H3) and a trivalent vaccine (BNT166c; without H3). Both candidates induced robust T cell responses and IgG antibodies in mice, including neutralizing antibodies to both MPXV and vaccinia virus. In challenge studies, BNT166a and BNT166c provided complete protection from vaccinia, clade I, and clade IIb MPXV. Furthermore, immunization with BNT166a was 100% effective at preventing death and at suppressing lesions in a lethal clade I MPXV challenge in cynomolgus macaques. These findings support the clinical evaluation of BNT166, now underway (NCT05988203).
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Özlem Türeci
- BioNTech SE, Mainz, Germany; HI-TRON - Helmholtz Institute for Translational Oncology Mainz by DKFZ, Mainz, Germany
| | | | - Uğur Şahin
- BioNTech SE, Mainz, Germany; TRON gGmbH - Translational Oncology at the University Medical Center of the Johannes Gutenberg University, Mainz, Germany.
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3
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Giorgi FM, Pozzobon D, Di Meglio A, Mercatelli D. Genomic and transcriptomic analysis of the recent Mpox outbreak. Vaccine 2024; 42:1841-1849. [PMID: 38311533 DOI: 10.1016/j.vaccine.2023.12.086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 12/06/2023] [Accepted: 12/18/2023] [Indexed: 02/06/2024]
Abstract
The Mpox (formerly named Monkeypox) virus is the etiological cause of a recent multi-country outbreak, with thousands of distinct cases detected outside the endemic areas of Africa as of December 2023. In this article, we analyze the sequences of full genomes of Mpox virus from Europe and compare them with all available Mpox sequences of historical relevance, annotated by year and geographic origin, as well as related Cowpox and Variola (smallpox) virus sequences. Our results show that the recent outbreak is most likely originating from the West African clade of Mpox, with >99 % sequence identity with sequences derived from historical and recent cases, dating from 1971 to 2017. We analyze specific mutations occurring in viral proteins between the current outbreak, previous Mpox and Cowpox sequences, and the historical Variola virus. Genome-wide sequence analysis of the recent outbreak and other Mpox/Cowpox/Variola viruses shows a very high conservation, with 97.9 % (protein-based) and 97.8 % (nucleotide-based) sequence identity. We identified significant correlation in human transcriptional responses as well, with a conserved immune pathway response induced in human cell cultures by the three families of Pox virus. The similarities identified between the major strains of Pox viruses, as well as within the Mpox clades, both at the genomic and transcriptomic levels, provide a molecular basis for the observed efficacy of Variola vaccines in other Poxviruses.
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Affiliation(s)
- Federico M Giorgi
- Department of Pharmacy and Biotechnology, University of Bologna, Via Selmi 3, 40126 Bologna, Italy.
| | - Daniele Pozzobon
- Department of Pharmacy and Biotechnology, University of Bologna, Via Selmi 3, 40126 Bologna, Italy
| | - Antonio Di Meglio
- Department of Pharmacy and Biotechnology, University of Bologna, Via Selmi 3, 40126 Bologna, Italy
| | - Daniele Mercatelli
- Department of Pharmacy and Biotechnology, University of Bologna, Via Selmi 3, 40126 Bologna, Italy
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4
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Zeng GG, Jiang WL, Yu J, Nie GY, Lu YR, Xiao CK, Wang C, Zheng K. The Potential Relationship Between Cardiovascular Diseases and Monkeypox. Curr Probl Cardiol 2024; 49:102116. [PMID: 37802168 DOI: 10.1016/j.cpcardiol.2023.102116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 09/30/2023] [Indexed: 10/08/2023]
Abstract
Mpox, a novel epidemic disease, has broken out the period of coronavirus disease 2019 since May 2022, which was caused by the mpox virus. Up to 12 September 2023, there are more than 90,439 confirmed mpox cases in over 115 countries all over the world. Moreover, the outbreak of mpox in 2022 was verified to be Clade II rather than Clade I. Highlighting the significance of this finding, a growing body of literature suggests that mpox may lead to a series of cardiovascular complications, including myocarditis and pericarditis. It is indeed crucial to acquire more knowledge about mpox from a perspective from the clinical cardiologist. In this review, we would discuss the epidemiological characteristics and primary treatments of mpox to attempt to provide a framework for cardiovascular physicians.
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Affiliation(s)
- Guang-Gui Zeng
- Department of Clinical Laboratory, Hengyang Central Hospital, Hengyang, Hunan, China; Institute of Pathogenic Biology, Hengyang Medical College, University of South China, Hengyang, Hunan, China; Institute of Cardiovascular Disease, Key Laboratory for Arteriosclerology of Hunan Province, 2020 Grade Excellent Doctor Class of Hengyang Medical College, University of South China, Hengyang, Hunan, China
| | - Wan-Li Jiang
- Institute of Cardiovascular Disease, Key Laboratory for Arteriosclerology of Hunan Province, 2020 Grade Excellent Doctor Class of Hengyang Medical College, University of South China, Hengyang, Hunan, China
| | - Jiang Yu
- Institute of Cardiovascular Disease, Key Laboratory for Arteriosclerology of Hunan Province, 2020 Grade Excellent Doctor Class of Hengyang Medical College, University of South China, Hengyang, Hunan, China
| | - Gui-Ying Nie
- Institute of Cardiovascular Disease, Key Laboratory for Arteriosclerology of Hunan Province, 2020 Grade Excellent Doctor Class of Hengyang Medical College, University of South China, Hengyang, Hunan, China
| | - Yu-Ru Lu
- Department of Emergency Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China; Department of Intensive Care Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Chang-Kai Xiao
- Department of Urology, Hengyang Medical School, The First Affiliated Hospital, University of South China, Hengyang, Hunan, China
| | - Chuan Wang
- Institute of Pathogenic Biology, Hengyang Medical College, University of South China, Hengyang, Hunan, China.
| | - Kang Zheng
- Department of Clinical Laboratory, Hengyang Central Hospital, Hengyang, Hunan, China.
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5
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Riccardo V, Pablo GC. Neutralization Determinants on Poxviruses. Viruses 2023; 15:2396. [PMID: 38140637 PMCID: PMC10747254 DOI: 10.3390/v15122396] [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: 11/10/2023] [Revised: 12/04/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
Smallpox was a highly contagious disease caused by the variola virus. The disease affected millions of people over thousands of years and variola virus ranked as one of the deadliest viruses in human history. The complete eradication of smallpox in 1980, a major triumph in medicine, was achieved through a global vaccination campaign using a less virulent poxvirus, vaccinia virus. Despite this success, the herd immunity established by this campaign has significantly waned, and concerns are rising about the potential reintroduction of variola virus as a biological weapon or the emergence of zoonotic poxviruses. These fears were further fueled in 2022 by a global outbreak of monkeypox virus (mpox), which spread to over 100 countries, thereby boosting interest in developing new vaccines using molecular approaches. However, poxviruses are complex and creating modern vaccines against them is challenging. This review focuses on the structural biology of the six major neutralization determinants on poxviruses (D8, H3, A27, L1, B5, and A33), the localization of epitopes targeted by neutralizing antibodies, and their application in the development of subunit vaccines.
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Affiliation(s)
| | - Guardado-Calvo Pablo
- Structural Biology of Infectious Diseases Unit, Institut Pasteur, Université Paris Cité, F-75015 Paris, France;
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6
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Therrien C, Prévost J, Blais AC, Turcotte S, Gendron-Lepage G, Finzi A, Fafard J. Development and validation of a highly specific in-house chemiluminescent-based serological assay for the detection of antibodies directed against the human monkeypox virus. J Virol Methods 2023; 322:114836. [PMID: 37890729 DOI: 10.1016/j.jviromet.2023.114836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/23/2023] [Accepted: 10/24/2023] [Indexed: 10/29/2023]
Affiliation(s)
- Christian Therrien
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada; Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada
| | - Jérémie Prévost
- Centre de Recherche du CHUM, Montréal, QC, Canada; Université de Montréal, Montréal, QC, Canada
| | | | - Sonia Turcotte
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada; Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada
| | | | - Andrés Finzi
- Centre de Recherche du CHUM, Montréal, QC, Canada; Université de Montréal, Montréal, QC, Canada
| | - Judith Fafard
- Laboratoire de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada; Institut National de Santé Publique du Québec, Sainte-Anne-de-Bellevue, QC, Canada.
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7
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Xia A, Wang X, He J, Wu W, Jiang W, Xue S, Zhang Q, Gao Y, Han Y, Li Y, Peng X, Xie M, Mayer CT, Liu J, Hua C, Sha Y, Xu W, Huang J, Ying T, Jiang S, Xie Y, Cai Q, Lu L, Silva IT, Yuan Z, Zhang Y, Wang Q. Cross-reactive antibody response to Monkeypox virus surface proteins in a small proportion of individuals with and without Chinese smallpox vaccination history. BMC Biol 2023; 21:205. [PMID: 37784185 PMCID: PMC10546712 DOI: 10.1186/s12915-023-01699-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 09/11/2023] [Indexed: 10/04/2023] Open
Abstract
BACKGROUND After the eradication of smallpox in China in 1979, vaccination with the vaccinia virus (VACV) Tiantan strain for the general population was stopped in 1980. As the monkeypox virus (MPXV) is rapidly spreading in the world, we would like to investigate whether the individuals with historic VACV Tiantan strain vaccination, even after more than 40 years, could still provide ELISA reactivity and neutralizing protection; and whether the unvaccinated individuals have no antibody reactivity against MPXV at all. RESULTS We established serologic ELISA to measure the serum anti-MPXV titer by using immunodominant MPXV surface proteins, A35R, B6R, A29L, and M1R. A small proportion of individuals (born before 1980) with historic VACV Tiantan strain vaccination exhibited serum ELISA cross-reactivity against these MPXV surface proteins. Consistently, these donors also showed ELISA seropositivity and serum neutralization against VACV Tiantan strain. However, surprisingly, some unvaccinated young adults (born after 1980) also showed potent serum ELISA activity against MPXV proteins, possibly due to their past infection by some self-limiting Orthopoxvirus (OPXV). CONCLUSIONS We report the serum ELISA cross-reactivity against MPXV surface protein in a small proportion of individuals both with and without VACV Tiantan strain vaccination history. Combined with our serum neutralization assay against VACV and the recent literature about mice vaccinated with VACV Tiantan strain, our study confirmed the anti-MPXV cross-reactivity and cross-neutralization of smallpox vaccine using VACV Tiantan strain. Therefore, it is necessary to restart the smallpox vaccination program in high risk populations.
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Affiliation(s)
- Anqi Xia
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Xiaojie Wang
- The Interdisciplinary Research Center on Biology and Chemistry, Chinese Academy of Sciences, Shanghai, China
| | - Jiaying He
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Wei Wu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Weiyu Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Song Xue
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Qianqian Zhang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yidan Gao
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yuru Han
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yaming Li
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Xiaofang Peng
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Minxiang Xie
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Christian T Mayer
- Experimental Immunology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jie Liu
- Department of Respiratory and Critical Care Medicine, Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi People's Hospital, Wuxi Medical Center, Nanjing Medical University, Wuxi, 214023, Jiangsu, China
| | - Chen Hua
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Yiou Sha
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Wei Xu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Jinghe Huang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Tianlei Ying
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Shibo Jiang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Youhua Xie
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Qiliang Cai
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Lu Lu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| | - Israel T Silva
- Laboratory of Bioinformatics and Computational Biology, A. C. Camargo Cancer Center, São Paulo, SP, 01509-010, Brazil.
| | - Zhenghong Yuan
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| | - Yixiao Zhang
- The Interdisciplinary Research Center on Biology and Chemistry, Chinese Academy of Sciences, Shanghai, China.
| | - Qiao Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microbes and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
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8
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Noy-Porat T, Tamir H, Alcalay R, Rosenfeld R, Epstein E, Cherry L, Achdout H, Erez N, Politi B, Yahalom-Ronen Y, Weiss S, Melamed S, Israely T, Mazor O, Paran N, Makdasi E. Generation of recombinant mAbs to vaccinia virus displaying high affinity and potent neutralization. Microbiol Spectr 2023; 11:e0159823. [PMID: 37737634 PMCID: PMC10581037 DOI: 10.1128/spectrum.01598-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/23/2023] [Indexed: 09/23/2023] Open
Abstract
Members of the Orthopoxvirus genus can cause severe infections in humans. Global vaccination against smallpox, caused by the variola virus, resulted in the eradication of the disease in 1980. Shortly thereafter, vaccination was discontinued, and as a result, a large proportion of the current population is not protected against orthopoxviruses. The concerns that the variola virus or other engineered forms of poxviruses may re-emerge as bioweapons and the sporadic outbreaks of zoonotic members of the family, such as Mpox, which are becoming more frequent and prevalent, also emphasize the need for an effective treatment against orthopoxviruses. To date, the most effective way to prevent or control an orthopoxvirus outbreak is through vaccination. However, the traditional vaccinia-based vaccine may cause severe side effects. Vaccinia immune globulin was approved by the U.S. Food and Drug Administration (FDA) for the treatment of vaccine adverse reactions and was also used occasionally for the treatment of severe orthopoxvirus infections. However, this treatment carries many disadvantages and is also in short supply. Thus, a recombinant alternative is highly needed. In this study, two non-human primates were immunized with live vaccinia virus, producing a robust and diverse antibody response. A phage-display library was constructed based on the animal's lymphatic organs, and a panel of neutralizing monoclonal antibodies (mAbs), recognizing diverse proteins of the vaccinia virus, was selected and characterized. These antibodies recognized both mature virion and enveloped virion forms of the virus and exhibited high affinity and potent in vitro neutralization capabilities. Furthermore, these monoclonal antibodies were able to neutralize Mpox 2018 and 2022 strains, suggesting a potential for cross-species protection. We suggest that a combination of these mAbs has the potential to serve as recombinant therapy both for vaccinia vaccine adverse reactions and for orthopoxvirus infections. IMPORTANCE In this manuscript, we report the isolation and characterization of several recombinant neutralizing monoclonal antibodies (mAbs) identified by screening a phage-display library constructed from lymphatic cells collected from immunized non-human primates. The antibodies target several different antigens of the vaccinia virus, covering both mature virion and extracellular enveloped virion forms of the virus. We document strong evidence indicating that they exhibit excellent affinity to their respective antigens and, most importantly, optimal in vitro neutralization of the virus, which exceeded that of vaccinia immune globulin. Furthermore, we present the ability of these novel isolated mAbs (as well as the sera collected from vaccinia-immunized animals) to neutralize two Mpox strains from the 2018 to 2022 outbreaks. We believe that these antibodies have the potential to be used for the treatment of vaccinia vaccine adverse reactions, for other orthopoxvirus infections, and in cases of unexpected bioterror scenarios.
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Affiliation(s)
- Tal Noy-Porat
- Israel Institute for Biological Research, Ness Ziona, Israel
| | - Hadas Tamir
- Israel Institute for Biological Research, Ness Ziona, Israel
| | - Ron Alcalay
- Israel Institute for Biological Research, Ness Ziona, Israel
| | - Ronit Rosenfeld
- Israel Institute for Biological Research, Ness Ziona, Israel
| | - Eyal Epstein
- Israel Institute for Biological Research, Ness Ziona, Israel
| | - Lilach Cherry
- Israel Institute for Biological Research, Ness Ziona, Israel
| | - Hagit Achdout
- Israel Institute for Biological Research, Ness Ziona, Israel
| | - Noam Erez
- Israel Institute for Biological Research, Ness Ziona, Israel
| | - Boaz Politi
- Israel Institute for Biological Research, Ness Ziona, Israel
| | | | - Shay Weiss
- Israel Institute for Biological Research, Ness Ziona, Israel
| | - Sharon Melamed
- Israel Institute for Biological Research, Ness Ziona, Israel
| | - Tomer Israely
- Israel Institute for Biological Research, Ness Ziona, Israel
| | - Ohad Mazor
- Israel Institute for Biological Research, Ness Ziona, Israel
| | - Nir Paran
- Israel Institute for Biological Research, Ness Ziona, Israel
| | - Efi Makdasi
- Israel Institute for Biological Research, Ness Ziona, Israel
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9
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Podduturi S, Vemula D, Singothu S, Bhandari V. In-silico investigation of E8 surface protein of the monkeypox virus to identify potential therapeutic agents. J Biomol Struct Dyn 2023:1-14. [PMID: 37555596 DOI: 10.1080/07391102.2023.2245041] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 07/30/2023] [Indexed: 08/10/2023]
Abstract
The re-emergence of the monkeypox virus (MPXV) in 2022 has become a global issue. The virus was first found in Denmark in 1958. The first human MPXV disease was reported in 1980 in Congo, caused by a rare zoonotic virus belonging to the genus Orthopoxvirus and the family Poxviridae. Like SARS-CoV, there are no specific drugs to treat this infection. Taking cues from the successful implementation of drug repositioning for the Covid-19 pandemic using in silico drug discovery. We employed structure-based drug design in the study to repurpose the existing drug and natural product derivatives libraries against MPXV. The E8 protein was chosen as a therapeutic target because it is a surface membrane protein involved in viral entry and adhesion to the host cell surface membrane. Our study was bifurcated into the following steps; determining and analyzing the structure of the E8, followed by structure-based virtual screening of different datasets (natural products obtained from bacteria and fungi and FDA-approved drugs) to identify the hits. Based on the best binding affinities and protein-ligand interactions, we further proceeded for molecular dynamic (MD) studies of the identified hits, which revealed Gabosine D (docking score = -8.469 kcal/mol, MM/GBSA dG bind = -41.6729 kcal/mol) and Edoxudine (docking score = -6.372 kcal/mol, MM/GBSA dG bind = -35.8291 kcal/mol) as the best lead molecules. MD simulation for 100 ns was performed in triplicate, and post MM/GBSA analysis was conducted, which proves the stability of the identified leads. In addition, their ADME profiles also confirmed their suitability as therapeutic options for the treatment of monkeypox.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shourya Podduturi
- National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana, India
| | - Divya Vemula
- National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana, India
| | - Siva Singothu
- National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana, India
| | - Vasundhra Bhandari
- National Institute of Pharmaceutical Education and Research, Hyderabad, Telangana, India
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10
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Patel P, Nandi A, Verma SK, Kaushik N, Suar M, Choi EH, Kaushik NK. Zebrafish-based platform for emerging bio-contaminants and virus inactivation research. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 872:162197. [PMID: 36781138 PMCID: PMC9922160 DOI: 10.1016/j.scitotenv.2023.162197] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/23/2023] [Accepted: 02/08/2023] [Indexed: 05/27/2023]
Abstract
Emerging bio-contaminants such as viruses have affected health and environment settings of every country. Viruses are the minuscule entities resulting in severe contagious diseases like SARS, MERS, Ebola, and avian influenza. Recent epidemic like the SARS-CoV-2, the virus has undergone mutations strengthen them and allowing to escape from the remedies. Comprehensive knowledge of viruses is essential for the development of targeted therapeutic and vaccination treatments. Animal models mimicking human biology like non-human primates, rats, mice, and rabbits offer competitive advantage to assess risk of viral infections, chemical toxins, nanoparticles, and microbes. However, their economic maintenance has always been an issue. Furthermore, the redundancy of experimental results due to aforementioned aspects is also in examine. Hence, exploration for the alternative animal models is crucial for risk assessments. The current review examines zebrafish traits and explores the possibilities to monitor emerging bio-contaminants. Additionally, a comprehensive picture of the bio contaminant and virus particle invasion and abatement mechanisms in zebrafish and human cells is presented. Moreover, a zebrafish model to investigate the emerging viruses such as coronaviridae and poxviridae has been suggested.
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Affiliation(s)
- Paritosh Patel
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, 01897 Seoul, South Korea
| | - Aditya Nandi
- School of Biotechnology, KIIT University, Bhubaneswar 751024, Odisha, India
| | - Suresh K Verma
- School of Biotechnology, KIIT University, Bhubaneswar 751024, Odisha, India; Condensed Matter Theory Group, Materials Theory Division, Department of Physics and Astronomy, Uppsala University, Box 516, SE-751 20 Uppsala, Sweden
| | - Neha Kaushik
- Department of Biotechnology, College of Engineering, The University of Suwon, 18323 Hwaseong, Republic of Korea
| | - Mrutyunjay Suar
- School of Biotechnology, KIIT University, Bhubaneswar 751024, Odisha, India
| | - Eun Ha Choi
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, 01897 Seoul, South Korea.
| | - Nagendra Kumar Kaushik
- Plasma Bioscience Research Center, Department of Electrical and Biological Physics, Kwangwoon University, 01897 Seoul, South Korea.
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11
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Gupta K. Functional characterization of hypothetical proteins from Monkeypox virus. J Genet Eng Biotechnol 2023; 21:46. [PMID: 37099065 PMCID: PMC10133424 DOI: 10.1186/s43141-023-00505-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 04/20/2023] [Indexed: 04/27/2023]
Abstract
BACKGROUND Monkeypox virus is a small, double-stranded DNA virus that causes a zoonotic disease called Monkeypox. The disease has spread from Central and West Africa to Europe and North America and created havoc in some countries all around the world. The complete genome of the Monkeypox virus Zaire-96-I-16 has been sequenced. The viral strain contains 191 protein-coding genes with 30 hypothetical proteins whose structure and function are still unknown. Hence, it is imperative to functionally and structurally annotate the hypothetical proteins to get a clear understanding of novel drug and vaccine targets. The purpose of the study was to characterize the 30 hypothetical proteins through the determination of physicochemical properties, subcellular characterization, function prediction, functional domain prediction, structure prediction, structure validation, structural analysis, and ligand binding sites using Bioinformatics tools. RESULTS The structural and functional analysis of 30 hypothetical proteins was carried out in this research. Out of these, 3 hypothetical functions (Q8V547, Q8V4S4, Q8V4Q4) could be assigned a structure and function confidently. Q8V547 protein in Monkeypox virus Zaire-96-I-16 is predicted as an apoptosis regulator which promotes viral replication in the infected host cell. Q8V4S4 is predicted as a nuclease responsible for viral evasion in the host. The function of Q8V4Q4 is to prevent host NF-kappa-B activation in response to pro-inflammatory cytokines like TNF alpha or interleukin 1 beta. CONCLUSIONS Out of the 30 hypothetical proteins of Monkeypox virus Zaire-96-I-16, 3 were annotated using various bioinformatics tools. These proteins function as apoptosis regulators, nuclease, and inhibitors of NF-Kappa-B activator. The functional and structural annotation of the proteins can be used to perform a docking with potential leads to discover novel drugs and vaccines against the Monkeypox. In vivo research can be carried out to identify the complete potential of the annotated proteins.
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Affiliation(s)
- Kajal Gupta
- Department of Biochemistry, Daulat Ram College, University of Delhi, Delhi, India.
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12
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The emergence of novel Iranian variants in sheeppox and goatpox viral envelope proteins with remarkably altered putative binding affinities with the host receptor. Virus Genes 2023; 59:437-448. [PMID: 36913064 DOI: 10.1007/s11262-023-01987-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 02/28/2023] [Indexed: 03/14/2023]
Abstract
The outbreak of Sheep and goat pox (SGP) viral infections have increasingly been reported despite vaccinating the majority of sheep populations in Iran. The objective of this study was to predict the impacts of the SGP P32/envelope variations on the binding with host receptors as a candidate tool to assess this outbreak. The targeted gene was amplified in a total of 101 viral samples, and the PCR products were subjected to Sanger sequencing. The polymorphism and phylogenetic interactions of the identified variants were assessed. Molecular docking was performed between the identified P32 variants and the host receptor and the effects of these variants were evaluated. Eighteen variations were identified in the investigated P32 gene with variable silent and missense effects on the envelope protein. Five groups (G1-G5) of amino acid variations were identified. While there were no amino acid variations in the G1 (wild-type) viral protein, G2, G3, G4, and G5 proteins had seven, nine, twelve, and fourteen SNPs, respectively. Based on the observed amino acid substitutions, multiple distinct phylogenetic places were occupied from the identified viral groups. Dramatic alterations were identified between G2, G4, and G5 variants with their proteoglycan receptor, while the highest binding was revealed between goatpox G5 variant with the same receptor. It was suggested that the higher severity of goatpox viral infection originated from its higher affinity to bind with its cognate receptor. This firm binding may be explained by the observed higher severity of the SGP cases from which G5 samples were isolated.
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13
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Hogwood J, Mulloy B, Lever R, Gray E, Page CP. Pharmacology of Heparin and Related Drugs: An Update. Pharmacol Rev 2023; 75:328-379. [PMID: 36792365 DOI: 10.1124/pharmrev.122.000684] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 11/04/2022] [Accepted: 11/08/2022] [Indexed: 02/17/2023] Open
Abstract
Heparin has been used extensively as an antithrombotic and anticoagulant for close to 100 years. This anticoagulant activity is attributed mainly to the pentasaccharide sequence, which potentiates the inhibitory action of antithrombin, a major inhibitor of the coagulation cascade. More recently it has been elucidated that heparin exhibits anti-inflammatory effect via interference of the formation of neutrophil extracellular traps and this may also contribute to heparin's antithrombotic activity. This illustrates that heparin interacts with a broad range of biomolecules, exerting both anticoagulant and nonanticoagulant actions. Since our previous review, there has been an increased interest in these nonanticoagulant effects of heparin, with the beneficial role in patients infected with SARS2-coronavirus a highly topical example. This article provides an update on our previous review with more recent developments and observations made for these novel uses of heparin and an overview of the development status of heparin-based drugs. SIGNIFICANCE STATEMENT: This state-of-the-art review covers recent developments in the use of heparin and heparin-like materials as anticoagulant, now including immunothrombosis observations, and as nonanticoagulant including a role in the treatment of SARS-coronavirus and inflammatory conditions.
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Affiliation(s)
- John Hogwood
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (B.M., E.G., C.P.P.); National Institute for Biological Standards and Control, South Mimms, Hertfordshire, United Kingdom (J.H., E.G.) and School of Pharmacy, University College London, London, United Kingdom (R.L.)
| | - Barbara Mulloy
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (B.M., E.G., C.P.P.); National Institute for Biological Standards and Control, South Mimms, Hertfordshire, United Kingdom (J.H., E.G.) and School of Pharmacy, University College London, London, United Kingdom (R.L.)
| | - Rebeca Lever
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (B.M., E.G., C.P.P.); National Institute for Biological Standards and Control, South Mimms, Hertfordshire, United Kingdom (J.H., E.G.) and School of Pharmacy, University College London, London, United Kingdom (R.L.)
| | - Elaine Gray
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (B.M., E.G., C.P.P.); National Institute for Biological Standards and Control, South Mimms, Hertfordshire, United Kingdom (J.H., E.G.) and School of Pharmacy, University College London, London, United Kingdom (R.L.)
| | - Clive P Page
- Sackler Institute of Pulmonary Pharmacology, Institute of Pharmaceutical Science, King's College London, London, United Kingdom (B.M., E.G., C.P.P.); National Institute for Biological Standards and Control, South Mimms, Hertfordshire, United Kingdom (J.H., E.G.) and School of Pharmacy, University College London, London, United Kingdom (R.L.)
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14
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Monkeypox infection elicits strong antibody and B cell response against A35R and H3L antigens. iScience 2023; 26:105957. [PMID: 36687315 PMCID: PMC9838220 DOI: 10.1016/j.isci.2023.105957] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/19/2022] [Accepted: 01/09/2023] [Indexed: 01/14/2023] Open
Abstract
Monkeypox virus (MPXV) resides in two forms; mature and enveloped, and depending on it, distinct proteins are displayed on the viral surface. Here, we expressed two MPXV antigens from the mature, and one from the enveloped form, and tested their reactivity to sera of 11 MPXV recoverees while comparing to sera from recently and past vaccinated individuals. 8 out of 11 recoverees exhibited detectable neutralization levels against Vaccinia Lister. Sera from all recoverees bound strongly to A35R and H3L antigens. Moreover, the responses to A35R were significantly higher within the recoverees compared to both recently and past vaccinated donors. Lastly, A35R- and H3L-specific IgG+ B cells ranging from 0.03-0.46% and 0.11-0.36%, respectively, were detected in all recoverees (A35R), and in 9 out of 11 recoverees (H3L). Therefore, A35R and H3L represent MPXV immune targets and could be used in a heat-inactivated serological ELISA for the identification of recent MPXV infection.
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15
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Gulati P, Chadha J, Harjai K, Singh S. Targeting envelope proteins of poxviruses to repurpose phytochemicals against monkeypox: An in silico investigation. Front Microbiol 2023; 13:1073419. [PMID: 36687601 PMCID: PMC9849581 DOI: 10.3389/fmicb.2022.1073419] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 12/16/2022] [Indexed: 01/07/2023] Open
Abstract
The monkeypox virus (MPXV) has become a major threat due to the increasing global caseload and the ongoing multi-country outbreak in non-endemic territories. Due to limited research in this avenue and the lack of intervention strategies, the present study was aimed to virtually screen bioactive phytochemicals against envelope proteins of MPXV via rigorous computational approaches. Molecular docking, molecular dynamic (MD) simulations, and MM/PBSA analysis were used to investigate the binding affinity of 12 phytochemicals against three envelope proteins of MPXV, viz., D13, A26, and H3. Silibinin, oleanolic acid, and ursolic acid were computationally identified as potential phytochemicals that showed strong binding affinity toward all the tested structural proteins of MPXV through molecular docking. The stability of the docked complexes was also confirmed by MD simulations and MM/PBSA calculations. Results from the iMODS server also complemented the findings from molecular docking and MD simulations. ADME analysis also computationally confirmed the drug-like properties of the phytochemicals, thereby asserting their suitability for consumption. Hence, this study envisions the candidature of bioactive phytochemicals as promising inhibitors against the envelope proteins of the MPXV, serving as template molecules that could further be experimentally evaluated for their efficacy against monkeypox.
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Affiliation(s)
- Pallavi Gulati
- Department of Microbiology, University of Delhi, New Delhi, India
| | - Jatin Chadha
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Kusum Harjai
- Department of Microbiology, Panjab University, Chandigarh, India
| | - Sandeepa Singh
- Department of Botany, Maitreyi College, University of Delhi, New Delhi, India,*Correspondence: Sandeepa Singh, ✉
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16
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Gong Q, Wang C, Chuai X, Chiu S. Monkeypox virus: a re-emergent threat to humans. Virol Sin 2022; 37:477-482. [PMID: 35820590 PMCID: PMC9437600 DOI: 10.1016/j.virs.2022.07.006] [Citation(s) in RCA: 100] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 07/05/2022] [Indexed: 12/17/2022] Open
Abstract
Human monkeypox (MPX) is a rare zoonotic infection characterized by smallpox-like signs and symptoms. It is caused by monkeypox virus (MPXV), a double stranded DNA virus belonging to the genus Orthopoxvirus. MPX was first identified in 1970 and mostly prevailed in the rural rainforests of Central and West Africa in the past. Outside Africa, MPX was reported in the United Kingdom, the USA, Israel, and Singapore. In 2022, the resurgence of MPX in Europe and elsewhere posed a potential threat to humans. MPXV was transmitted by the animals-human or human-human pathway, and the symptoms of MPXV infection are similar to that of smallpox, but in a milder form and with lower mortality (1%-10%). Although the smallpox vaccination has been shown to provide 85% protection against MPXV infection, and two anti-smallpox virus drugs have been approved to treat MPXV, there are still no specific vaccines and drugs against MPXV infection. Therefore it is urgent to take active measures including the adoption of novel anti-MPXV strategies to control the spread of MPXV and prevent MPX epidemic. In this review, we summarize the biological features, epidemiology, pathogenicity, laboratory diagnosis, and prevention and treatment strategies on MPXV. This review provides the basic knowledge for prevention and control of future outbreaks of this emerging infection.
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Affiliation(s)
- Qizan Gong
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China
| | - Changle Wang
- Department of Pathogenic Biology, Hebei Medical University, Shijiazhuang, Hebei, 050017, China
| | - Xia Chuai
- Department of Pathogenic Biology, Hebei Medical University, Shijiazhuang, Hebei, 050017, China.
| | - Sandra Chiu
- Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230026, China.
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17
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New p35 (H3L) Epitope Involved in Vaccinia Virus Neutralization and Its Deimmunization. Viruses 2022; 14:v14061224. [PMID: 35746695 PMCID: PMC9227246 DOI: 10.3390/v14061224] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/02/2022] [Accepted: 06/03/2022] [Indexed: 01/07/2023] Open
Abstract
Vaccinia virus (VACV) is a promising oncolytic agent because it exhibits many characteristic features of an oncolytic virus. However, its effectiveness is limited by the strong antiviral immune response induced by this virus. One possible approach to overcome this limitation is to develop deimmunized recombinant VACV. It is known that VACV p35 is a major protein for B- and T-cell immune response. Despite the relevance of p35, its epitope structure remains insufficiently studied. To determine neutralizing epitopes, a panel of recombinant p35 variants was designed, expressed, and used for mice immunization. Plaque-reduction neutralization tests demonstrated that VACV was only neutralized by sera from mice that were immunized with variants containing both N- and C- terminal regions of p35. This result was confirmed by the depletion of anti-p35 mice sera with recombinant p35 variants. At least nine amino acid residues affecting the immunogenic profile of p35 were identified. Substitutions of seven residues led to disruption of B-cell epitopes, whereas substitutions of two residues resulted in the recognition of the mutant p35 solely by non-neutralizing antibodies.
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18
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Ebrahimi-Jam MH, Keyvanfar H, Varshovi HR, Seyfi Abad Shapoori MR, Lotfi M. Development and Evaluation of an Indirect Capripoxvirus ELISA Based on Truncated P32 Protein Expressed in E. coli. ARCHIVES OF RAZI INSTITUTE 2021; 76:471-485. [PMID: 34824741 PMCID: PMC8605838 DOI: 10.22092/ari.2020.343355.1501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 07/14/2020] [Indexed: 06/13/2023]
Abstract
As notifiable diseases, lumpy skin disease (LSD), sheep pox (SPP), and goat pox (GTP) are associated with a profound effect on cattle, sheep, and goat farming industries. Development of the ELISA method could effectively facilitate serodiagnosis of the infected animals. This study aimed to develop an ELISA system based on the recombinant full-length and truncated P32 protein (Tr.P32) of goat pox virus. The P32 protein was expressed in Rosetta strain of E. coli using pET24a+ vector and evaluated by SDS-PAGE and Western blotting. Then, Tr.P32 was purified by Ni-NTA affinity chromatography under denaturing conditions and used to develop a capripoxvirus-specific ELISA. Checkerboard titration and receiver-operating characteristic (ROC) analysis were used to optimize the ELISA system and determine diagnostic specificity and sensitivity, respectively. The diagnostic potential of the developed ELISA was evaluated using positive and negative control sera collected from goat, sheep, and cattle. Results showed that the expression level of full-length P32 recombinant protein was negligible, while Tr.P32, a ~ 31 kDa recombinant protein, was expressed up to 0.270-0.300 mg/200 mL of culture media. The results of checkerboard titration revealed that 675 ng/well of Tr.P32 antigen and 1:10 dilution of control sera (anti GTPV HIS and healthy goat sera) caused maximum difference in absorbance between positive and negative goat sera. The recombinant Tr.P32 showed good reactions with antibodies against GTP virus (GTPV), SPP virus (SPPV), and LSD virus (LSDV), whereas no cross-reactions with anti-Orf virus antibodies were detected. By comparing with the neutralization index (NI), cut off, diagnostic sensitivity and specificity of the developed indirect-ELISA were estimated, 0.397, 94% and 96.6%, respectively. These findings indicate that the ELISA system based on Tr.P32 protein could potentially be used in sero-surveillance of all capripoxviruses; however, further investigations are required.
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Affiliation(s)
- M H Ebrahimi-Jam
- Department of Pathobiology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - H Keyvanfar
- Department of Animal Viral Vaccine, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - H R Varshovi
- Department of Animal Viral Vaccine, Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - M R Seyfi Abad Shapoori
- Department of Microbiology Faculty of Veterinary Medicine of Shahid Chamran, University of Ahvaz, Ahvaz, Iran
| | - M Lotfi
- Razi Vaccine and Serum Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
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19
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Song K, Viskovska M. Design and Engineering of Deimmunized Vaccinia Viral Vectors. Biomedicines 2020; 8:E491. [PMID: 33187060 PMCID: PMC7697509 DOI: 10.3390/biomedicines8110491] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 11/08/2020] [Accepted: 11/09/2020] [Indexed: 12/31/2022] Open
Abstract
Vaccinia viral (VV) vectors are increasingly used in oncolytic virus therapy and vaccine development for cancer and infectious diseases. However, their effectiveness is hindered by the strong anti-viral immune response induced by the viral vector. In this review, we discuss the strategies to deimmunize vaccinia viral vector. One approach is to mask the virus from the neutralization antibody responses by mapping and eliminating of B-cell epitopes on the viral membrane proteins. The recombinant VVs contain one or more viral glycoproteins with mutations in the neutralizing antibody epitopes, resulting in viral escape from neutralization. In addition, a regulator of complement activation (e.g., CD55) can be expressed on the surface of the virus particle, leading to increased resistance to complement-mediated neutralization.
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Affiliation(s)
| | - Mariya Viskovska
- Icell Kealex Therapeutics, 2450 Holcombe Blvd Suite J, JALBS@TMC, Houston, TX 77021, USA;
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20
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Sumana K, Revanaiah Y, Shivachandra SB, Mothay D, Apsana R, Saminathan M, Basavaraj S, Reddy GBM. Molecular phylogeny of Capripoxviruses based on major immunodominant protein (P32) reveals circulation of host specific sheeppox and goatpox viruses in small ruminants of India. INFECTION GENETICS AND EVOLUTION 2020; 85:104472. [PMID: 32711078 DOI: 10.1016/j.meegid.2020.104472] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 07/16/2020] [Accepted: 07/18/2020] [Indexed: 11/26/2022]
Abstract
Sheeppox and goatpox are highly contagious viral diseases of small ruminants causing severe economic losses to the livestock farmers. The disease is enzootic in Asia including India, Middle East and African countries. In the present study, a total of 28 isolates from twenty five sheeppox and goatpox disease outbreaks were phylogenetically analyzed based on P32 gene/protein along with homology modeling and docking using heparan sulfate and UDP-glucose. Three distinct lineage-specific clusters as per their host origin were recorded. Multiple sequence analysis of P32 gene revealed that genetically similar sheeppox virus (SPPV) and goatpox virus (GTPV) strains are circulating in India. Phylogenetically, Lumpy skin disease (LSDV) and SPPV had a closer genetic relationship than GTPV. Comparative sequence alignment indicated conservation of various motifs such as glycosaminoglycan (GAG), chemokine like motif (CX3C) and Asp-Glu-any other residue-Asp (D/ExD), as well as viral specific signature residues in SPPV and GTPV isolates. Structurally, P32 protein of SPPV and GTPV with mixed α helices and β sheets resembled with crystal structure of homologue vaccinia virus H3L protein. Docking studies in P32 protein of SPPV and GTPV revealed conserved binding pattern with heparan sulfate which is involved in the virus attachment and varied glycosyltransferase fold with UDP-glucose. These findings may help in development of suitable vaccines/diagnostics and therapeutics against capripoxviruses.
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Affiliation(s)
- K Sumana
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Yelahanka, Bengaluru 560064, Karnataka, India; Department of Microbiology and Biotechnology, JAIN (Deemed to be University), School of Sciences, Jayanagar 3rd Block, Bengaluru 560011, Karnataka, India
| | - Yogisharadhya Revanaiah
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Yelahanka, Bengaluru 560064, Karnataka, India
| | | | - Dipti Mothay
- Department of Microbiology and Biotechnology, JAIN (Deemed to be University), School of Sciences, Jayanagar 3rd Block, Bengaluru 560011, Karnataka, India
| | - R Apsana
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Yelahanka, Bengaluru 560064, Karnataka, India
| | - M Saminathan
- ICAR-Indian Veterinary Research Institute, Bareilly, U.P, India
| | - S Basavaraj
- ICAR-Indian Veterinary Research Institute, Bareilly, U.P, India
| | - G B Manjunatha Reddy
- ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Yelahanka, Bengaluru 560064, Karnataka, India.
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21
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Block J. High risk genotypes for schizophrenia may have been adaptive in the context of smallpox. Med Hypotheses 2020; 137:109556. [DOI: 10.1016/j.mehy.2020.109556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 01/05/2020] [Indexed: 10/25/2022]
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22
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Mirzakhanyan Y, Gershon P. The Vaccinia virion: Filling the gap between atomic and ultrastructure. PLoS Pathog 2019; 15:e1007508. [PMID: 30615658 PMCID: PMC6336343 DOI: 10.1371/journal.ppat.1007508] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 01/17/2019] [Accepted: 12/06/2018] [Indexed: 01/19/2023] Open
Abstract
We have investigated the molecular-level structure of the Vaccinia virion in situ by protein-protein chemical crosslinking, identifying 4609 unique-mass crosslink ions at an effective FDR of 0.33%, covering 2534 unique pairs of crosslinked protein positions, 625 of which were inter-protein. The data were statistically non-random and rational in the context of known structures, and showed biological rationality. Crosslink density strongly tracked the individual proteolytic maturation products of p4a and p4b, the two major virion structural proteins, and supported the prediction of transmembrane domains within membrane proteins. A clear sub-network of four virion structural proteins provided structural insights into the virion core wall, and proteins VP8 and A12 formed a strongly-detected crosslinked pair with an apparent structural role. A strongly-detected sub-network of membrane proteins A17, H3, A27 and A26 represented an apparent interface of the early-forming virion envelope with structures added later during virion morphogenesis. Protein H3 seemed to be the central hub not only for this sub-network but also for an 'attachment protein' sub-network comprising membrane proteins H3, ATI, CAHH(D8), A26, A27 and G9. Crosslinking data lent support to a number of known interactions and interactions within known complexes. Evidence is provided for the membrane targeting of genome telomeres. In covering several orders of magnitude in protein abundance, this study may have come close to the bottom of the protein-protein crosslinkome of an intact organism, namely a complex animal virus.
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Affiliation(s)
- Yeva Mirzakhanyan
- Department of Molecular Biology & Biochemistry, UC-Irvine, Irvine, California, United States of America
| | - Paul Gershon
- Department of Molecular Biology & Biochemistry, UC-Irvine, Irvine, California, United States of America
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Medvedev KE, Kinch LN, Grishin NV. Functional and evolutionary analysis of viral proteins containing a Rossmann-like fold. Protein Sci 2018; 27:1450-1463. [PMID: 29722076 PMCID: PMC6153405 DOI: 10.1002/pro.3438] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 04/30/2018] [Accepted: 05/01/2018] [Indexed: 11/17/2022]
Abstract
Viruses are the most abundant life form and infect practically all organisms. Consequently, these obligate parasites are a major cause of human suffering and economic loss. Rossmann-like fold is the most populated fold among α/β-folds in the Protein Data Bank and proteins containing Rossmann-like fold constitute 22% of all known proteins 3D structures. Thus, analysis of viral proteins containing Rossmann-like domains could provide an understanding of viral biology and evolution as well as could propose possible targets for antiviral therapy. We provide functional and evolutionary analysis of viral proteins containing a Rossmann-like fold found in the evolutionary classification of protein domains (ECOD) database developed in our lab. We identified 81 protein families of bacterial, archeal, and eukaryotic viruses in light of their evolution-based ECOD classification and Pfam taxonomy. We defined their functional significance using enzymatic EC number assignments as well as domain-level family annotations.
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Affiliation(s)
- Kirill E. Medvedev
- Departments of Biophysics and BiochemistryUniversity of Texas Southwestern Medical CenterDallasTexas
| | - Lisa N. Kinch
- Howard Hughes Medical Institute, University of Texas Southwestern Medical CenterDallasTexas
| | - Nick V. Grishin
- Departments of Biophysics and BiochemistryUniversity of Texas Southwestern Medical CenterDallasTexas
- Howard Hughes Medical Institute, University of Texas Southwestern Medical CenterDallasTexas
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24
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Comparative sequence and structural analysis of Indian orf viruses based on major envelope immuno-dominant protein (F1L), an homologue of pox viral p35/H3 protein. Gene 2018; 663:72-82. [DOI: 10.1016/j.gene.2018.04.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 04/07/2018] [Accepted: 04/11/2018] [Indexed: 11/23/2022]
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25
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Amsacta moorei entomopoxvirus encodes a functional heparin-binding glycosyltransferase (AMV248). Virus Genes 2018; 54:438-445. [DOI: 10.1007/s11262-018-1561-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 04/09/2018] [Indexed: 12/21/2022]
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26
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Khlusevich Y, Matveev A, Baykov I, Bulychev L, Bormotov N, Ilyichev I, Shevelev G, Morozova V, Pyshnyi D, Tikunova N. Phage display antibodies against ectromelia virus that neutralize variola virus: Selection and implementation for p35 neutralizing epitope mapping. Antiviral Res 2018; 152:18-25. [DOI: 10.1016/j.antiviral.2018.02.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 01/09/2018] [Accepted: 02/05/2018] [Indexed: 11/24/2022]
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27
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Inan C, Muratoglu H, Arif BM, Demirbag Z. Transcriptional analysis of the putative glycosyltransferase gene (amv248) of the Amsacta moorei entomopoxvirus. Virus Res 2017; 243:25-30. [PMID: 29020603 DOI: 10.1016/j.virusres.2017.10.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 10/05/2017] [Accepted: 10/07/2017] [Indexed: 11/17/2022]
Abstract
Amsacta moorei entomopoxvirus (AMEV), the most studied member of the genus Betaentomopoxvirus, was initially isolated from Red Hairy caterpillar larvae, Amsacta moorei. According to genome sequence and previous studies it was shown that amv248 encodes a putative glycosyltransferase that is the only conserved attachment protein in betaentomopoxviruses. Transcriptional analysis of the amv248 gene by RT-PCR and qPCR showed that transcription starts at 6h post infection (hpi). Also, transcription was not affected by a DNA replication inhibitor but was severely curtailed by a protein synthesis inhibitor. These results indicate that amv248 belongs to the intermediate class of gene expression. 5' and 3' untranslated regions analysis revealed that transcription initiates at position -126 relative to the translational start site, and ends between 50 and 83 bases after the stop codon. To narrow down the size and location of the gene's promoter, the upstream region as well as several different sized deletions thereof were generated and cloned upstream of a luciferase reporter gene. The constructs were used to measure the Firefly and Renilla luciferase activities in dual assays. The results showed that luciferase activity decreased when bases -198 to -235 of amv248 upstream region were missing. Sequence analysis among the intermediate gene promoters of AMEV showed that TTTAT(T/A)TT(T/A)2TTA is possibly a common motif, however, further investigations are needed to confirm this conclusion.
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Affiliation(s)
- Cihan Inan
- Department of Biology, Faculty of Sciences, Karadeniz Technical University, Trabzon, Turkey; Department of Molecular Biology and Genetics, Faculty of Sciences, Karadeniz Technical University, Trabzon, Turkey
| | - Hacer Muratoglu
- Department of Molecular Biology and Genetics, Faculty of Sciences, Karadeniz Technical University, Trabzon, Turkey
| | - Basil M Arif
- Laboratory for Molecular Virology, Great Lakes Forestry Centre, Sault Ste. Marie, Ontario, Canada
| | - Zihni Demirbag
- Department of Biology, Faculty of Sciences, Karadeniz Technical University, Trabzon, Turkey.
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Honarmand Ebrahimi K, Carr SB, McCullagh J, Wickens J, Rees NH, Cantley J, Armstrong FA. The radical-SAM enzyme Viperin catalyzes reductive addition of a 5'-deoxyadenosyl radical to UDP-glucose in vitro. FEBS Lett 2017; 591:2394-2405. [PMID: 28752893 DOI: 10.1002/1873-3468.12769] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 07/24/2017] [Accepted: 07/25/2017] [Indexed: 12/11/2022]
Abstract
Viperin, a radical-S-adenosylmethionine (SAM) enzyme conserved from fungi to humans, can restrict replication of many viruses. Neither the molecular mechanism underlying the antiviral activity of Viperin, nor its exact physiological function, is understood: most importantly, no radical-SAM activity has been discovered for Viperin. Here, using electron paramagnetic resonance (EPR) spectroscopy, mass spectrometry, and NMR spectroscopy, we show that uridine diphosphate glucose (UDP-glucose) is a substrate of a fungal Viperin (58% pairwise identity with human Viperin at the amino acid level) in vitro. Structural homology modeling and docking experiments reveal a highly conserved binding pocket in which the position of UDP-glucose is consistent with our experimental data regarding catalytic addition of a 5'-deoxyadenosyl radical and a hydrogen atom to UDP-glucose.
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Affiliation(s)
| | - Stephen B Carr
- Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Oxford, Didcot, UK.,Department of Biochemistry, University of Oxford, UK
| | | | | | | | - James Cantley
- Department of Physiology, Anatomy, and Genetics, University of Oxford, UK
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