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Parigger L, Krassnigg A, Grabuschnig S, Gruber K, Steinkellner G, Gruber CC. AI-assisted structural consensus-proteome prediction of human monkeypox viruses isolated within a year after the 2022 multi-country outbreak. Microbiol Spectr 2023; 11:e0231523. [PMID: 37874150 PMCID: PMC10714838 DOI: 10.1128/spectrum.02315-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 09/09/2023] [Indexed: 10/25/2023] Open
Abstract
IMPORTANCE The 2022 outbreak of the monkeypox virus already involves, by April 2023, 110 countries with 86,956 confirmed cases and 119 deaths. Understanding an emerging disease on a molecular level is essential to study infection processes and eventually guide drug discovery at an early stage. To support this, we provide the so far most comprehensive structural proteome of the monkeypox virus, which includes 210 structural models, each computed with three state-of-the-art structure prediction methods. Instead of building on a single-genome sequence, we generated our models from a consensus of 3,713 high-quality genome sequences sampled from patients within 1 year of the outbreak. Therefore, we present an average structural proteome of the currently isolated viruses, including mutational analyses with a special focus on drug-binding sites. Continuing dynamic mutation monitoring within the structural proteome presented here is essential to timely predict possible physiological changes in the evolving virus.
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Affiliation(s)
- Lena Parigger
- Innophore, Graz, Austria
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | | | | | - Karl Gruber
- Innophore, Graz, Austria
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- Austrian Centre of Industrial Biotechnology, Graz, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Austria
| | - Georg Steinkellner
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Austria
- Innophore, San Francisco, California, USA
| | - Christian C. Gruber
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- Austrian Centre of Industrial Biotechnology, Graz, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Austria
- Innophore, San Francisco, California, USA
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Kannan SR, Reddy AS, Burris DM, Byrareddy SN, Singh K. Missing subunits of Mpox replication complex: Possible impact on structural organization. J Infect 2023; 87:445-447. [PMID: 37625552 PMCID: PMC10720701 DOI: 10.1016/j.jinf.2023.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 08/21/2023] [Indexed: 08/27/2023]
Affiliation(s)
- Saathvik R Kannan
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | | | - Dana M Burris
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Siddappa N Byrareddy
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, NE 68198, USA.
| | - Kamal Singh
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA; Department of Veterinary Pathobiology, University of Missouri, Columbia, MO 65211, USA.
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Lv Z, Ji F, Song J, Li P, Chen M, Chang J. Predicting the spatial structure of membrane protein and B-cell epitopes of the MPXV_VEROE6 strain of monkeypox virus. Heliyon 2023; 9:e20386. [PMID: 37767496 PMCID: PMC10520823 DOI: 10.1016/j.heliyon.2023.e20386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 08/31/2023] [Accepted: 09/20/2023] [Indexed: 09/29/2023] Open
Abstract
By targeting the membrane (M) proteins of monkeypox virus (MPXV) strain VEROE6, we analyzed its evolutionary hierarchy and predicted its dominant antigenic B-cell epitope to provide a theoretical basis for the development of MPXV epitope vaccines and related monoclonal antibodies. In this study, phylogenetic trees were constructed based on the nucleic acid sequences of MPXV and the amino acid sequences of M proteins. The 3D structure of the MPXV_VEROE6 M proteins was predicted with AlphaFold v2.0 and the dominant antigenic B-cell epitopes were comprehensively predicted by analyzing parameters such as flexible segments, the hydrophilic index, the antigenic index, and the protein surface probability. The results showed that the M protein of MPXV_VEROE6 contained 377 amino acids, and their spatial configuration was relatively regular with a turning and random coil structure. The results of a comprehensive multiparameter analysis indicated that possible B-cell epitopes were located in the 23-28, 57-63, 67-78, 80-93, 98-105, 125-131, 143-149, 201-206, 231-237, 261-270, 291-303, and 346-362 amino acid segments. This study elucidated the structural and evolutionary characteristics of MPXV membrane proteins with the aim of providing theoretical information for the development of epitope vaccines, rapid diagnostic reagents, and monoclonal antibodies for monkeypox virus.
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Affiliation(s)
- Zhiyuan Lv
- The Xinjiang Key Laboratory of Natural Medicine Active Components and Drug Release Technology, College of Pharmacy, Xinjiang Medical University, Urumqi Xinjiang 830011, China
| | - Feng Ji
- Zhongda Hospital, Medical School, Southeast University, Nanjing 210009, China
| | - Jianzhong Song
- The Xinjiang Key Laboratory of Natural Medicine Active Components and Drug Release Technology, College of Pharmacy, Xinjiang Medical University, Urumqi Xinjiang 830011, China
- Department of Pharmacy, Affiliated Tumor Hospital of Xinjiang Medical University, Urumqi 830011,China
| | - Panpan Li
- The Xinjiang Key Laboratory of Natural Medicine Active Components and Drug Release Technology, College of Pharmacy, Xinjiang Medical University, Urumqi Xinjiang 830011, China
| | - Ming Chen
- Zhongda Hospital, Medical School, Southeast University, Nanjing 210009, China
| | - Junmin Chang
- The Xinjiang Key Laboratory of Natural Medicine Active Components and Drug Release Technology, College of Pharmacy, Xinjiang Medical University, Urumqi Xinjiang 830011, China
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Mehmood A, Nawab S, Jia G, Kaushik AC, Wei DQ. Supervised screening of Tecovirimat-like compounds as potential inhibitors for the monkeypox virus E8L protein. J Biomol Struct Dyn 2023:1-14. [PMID: 37561169 DOI: 10.1080/07391102.2023.2245042] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/26/2023] [Indexed: 08/11/2023]
Abstract
Monkeypox virus (MPXV) is a budding public health threat worldwide, and there lacks a personalized drug availability to treat MPXV infections. Tecovirimat, an antiviral drug against pox viruses, is recently confirmed to be effective against the MPXV in vitro using nanomolar concentrations. Therefore, the current study considers Tecovirimat as a reference compound for a machine learning-based guided screening to scan bioactive compounds from the DrugBank with similar chemical features or moieties as the Tecovirimat to inhibit the MPXV E8L surface binding protein. We used AlphaFold2 to model the E8L's 3D structure, followed by the conformational activity investigation of shortlisted drugs through computational structural biology approaches, including molecular docking and molecular dynamics simulations. As a result, we have shortlisted five drugs named ABX-1431, Alflutinib, Avacopan, Caspitant, and Darapalib that effectively engage the MPXV surface binding protein. Furthermore, the affinity of the proposed drugs is relatively higher than the Tecovirimat by having higher docking scores, establishing more hydrogen and hydrophobic bonds, engaging key residues in the target's structure, and exhibiting stable molecular dynamics.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Aamir Mehmood
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Sadia Nawab
- State Key Laboratory of Microbial Metabolism and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Guihua Jia
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- School of Pharmaceutical Sciences, Jilin University, Changchun, China
| | - Aman Chandra Kaushik
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Dong-Qing Wei
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint International Research Laboratory of Metabolic & Developmental Sciences and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China
- Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Nanyang, P.R. China
- Peng Cheng Laboratory, Shenzhen, P.R. China
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Rabaan AA, Alasiri NA, Aljeldah M, Alshukairiis AN, AlMusa Z, Alfouzan WA, Abuzaid AA, Alamri AA, Al-Afghani HM, Al-Baghli N, Alqahtani N, Al-Baghli N, Almoutawa MY, Mahmoud Alawi M, Alabdullah M, Bati NAA, Alsaleh AA, Tombuloglu H, Arteaga-Livias K, Al-Ahdal T, Garout M, Imran M. An Updated Review on Monkeypox Viral Disease: Emphasis on Genomic Diversity. Biomedicines 2023; 11:1832. [PMID: 37509470 PMCID: PMC10376458 DOI: 10.3390/biomedicines11071832] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Revised: 06/20/2023] [Accepted: 06/23/2023] [Indexed: 07/30/2023] Open
Abstract
Monkeypox virus has remained the most virulent poxvirus since the elimination of smallpox approximately 41 years ago, with distribution mostly in Central and West Africa. Monkeypox (Mpox) in humans is a zoonotically transferred disease that results in a smallpox-like disease. It was first diagnosed in 1970 in the Democratic Republic of the Congo (DRC), and the disease has spread over West and Central Africa. The purpose of this review was to give an up-to-date, thorough, and timely overview on the genomic diversity and evolution of a re-emerging infectious disease. The genetic profile of Mpox may also be helpful in targeting new therapeutic options based on genes, mutations, and phylogeny. Mpox has become a major threat to global health security, necessitating a quick response by virologists, veterinarians, public health professionals, doctors, and researchers to create high-efficiency diagnostic tests, vaccinations, antivirals, and other infection control techniques. The emergence of epidemics outside of Africa emphasizes the disease's global significance. Increased monitoring and identification of Mpox cases are critical tools for obtaining a better knowledge of the ever-changing epidemiology of this disease.
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Affiliation(s)
- Ali A Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
- Department of Public Health and Nutrition, The University of Haripur, Haripur 22610, Pakistan
| | - Nada A Alasiri
- Monitoring and Risk Assessment Department, Saudi Food and Drug Authority, Riyadh 13513, Saudi Arabia
| | - Mohammed Aljeldah
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hafr Al Batin, Hafr Al Batin 39831, Saudi Arabia
| | - Abeer N Alshukairiis
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
- Department of Medicine, King Faisal Specialist Hospital and Research Center, Jeddah 21499, Saudi Arabia
| | - Zainab AlMusa
- Infectious Disease Section, Internal Medicine Department, King Fahad Specialist Hospital, Dammam 32253, Saudi Arabia
| | - Wadha A Alfouzan
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat 13110, Kuwait
- Microbiology Unit, Department of Laboratories, Farwania Hospital, Farwania 85000, Kuwait
| | - Abdulmonem A Abuzaid
- Medical Microbiology Department, Security Forces Hospital Programme, Dammam 32314, Saudi Arabia
| | - Aref A Alamri
- Molecular Microbiology and Cytogenetics Department, Riyadh Regional Laboratory, Riyadh 11425, Saudi Arabia
| | - Hani M Al-Afghani
- Laboratory Department, Security Forces Hospital, Makkah 24269, Saudi Arabia
- iGene Center for Research and Training, Jeddah 2022, Saudi Arabia
| | - Nadira Al-Baghli
- Directorate of Public Health, Dammam Network, Eastern Health Cluster, Dammam 31444, Saudi Arabia
| | - Nawal Alqahtani
- Directorate of Public Health, Dammam Network, Eastern Health Cluster, Dammam 31444, Saudi Arabia
| | - Nadia Al-Baghli
- Directorate of Health Affairs, Al-Ahsa Health Cluster, Ministry of Health, Al-Ahsa 31982, Saudi Arabia
| | - Mashahed Y Almoutawa
- Primary Healthcare, Qatif Health Network, Eastern Health Cluster, Safwa 32833, Saudi Arabia
| | - Maha Mahmoud Alawi
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University Hospital, Jeddah 22254, Saudi Arabia
- Infection Control and Environmental Health Unit, King Abdulaziz University Hospital, Jeddah 22254, Saudi Arabia
| | - Mohammed Alabdullah
- Department of Infectious Diseases, Almoosa Specialist Hospital, Al Mubarraz 36342, Saudi Arabia
| | - Neda A Al Bati
- Medical and Clinical Affairs, Rural Health Network, Eastern Health Cluster, Dammam 31444, Saudi Arabia
| | - Abdulmonem A Alsaleh
- Clinical Laboratory Science Department, Mohammed Al-Mana College for Medical Sciences, Dammam 34222, Saudi Arabia
| | - Huseyin Tombuloglu
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, Dammam 34221, Saudi Arabia
| | - Kovy Arteaga-Livias
- Escuela de Medicina-Filial Ica, Universidad Privada San Juan Bautista, Ica 11000, Peru
- Escuela de Medicina, Universidad Nacional Hermilio Valdizán, Huanuco 10000, Peru
| | - Tareq Al-Ahdal
- Research Associate, Institute of Global Health, Heidelberg University, Neuenheimerfeld130/3, 69120 Heidelberg, Germany
| | - Mohammed Garout
- Department of Community Medicine and Health Care for Pilgrims, Faculty of Medicine, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Mohd Imran
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Northern Border University, Rafha 91911, Saudi Arabia
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Sen Gupta PS, Panda SK, Nayak AK, Rana MK. Identification and Investigation of a Cryptic Binding Pocket of the P37 Envelope Protein of Monkeypox Virus by Molecular Dynamics Simulations. J Phys Chem Lett 2023; 14:3230-3235. [PMID: 36972468 DOI: 10.1021/acs.jpclett.3c00087] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
The spread of the monkeypox virus has surged during the unchecked COVID-19 epidemic. The most crucial target is the viral envelope protein, p37. However, lacking p37's crystal structure is a significant hurdle to rapid therapeutic discovery and mechanism elucidation. Structural modeling and molecular dynamics (MD) of the enzyme with inhibitors reveal a cryptic pocket occluded in the unbound structure. For the first time, the inhibitor's dynamic flip from the active to the cryptic site enlightens p37's allosteric site, which squeezes the active site, impairing its function. A large force is needed for inhibitor dissociation from the allosteric site, ushering in its biological importance. In addition, hot spot residues identified at both locations and discovered drugs more potent than tecovirimat may enable even more robust inhibitor designs against p37 and accelerate the development of monkeypox therapies.
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Affiliation(s)
- Parth Sarthi Sen Gupta
- School of Biosciences and Bioengineering, D Y Patil International University (DYPIU), Akurdi, Pune 411044, Maharashtra, India
| | - Saroj Kumar Panda
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Berhampur, Odisha 760010, India
| | - Abhijit Kumar Nayak
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Berhampur, Odisha 760010, India
| | - Malay Kumar Rana
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER), Berhampur, Odisha 760010, India
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Yang Z, Zeng X, Zhao Y, Chen R. AlphaFold2 and its applications in the fields of biology and medicine. Signal Transduct Target Ther 2023; 8:115. [PMID: 36918529 PMCID: PMC10011802 DOI: 10.1038/s41392-023-01381-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/27/2022] [Accepted: 02/16/2023] [Indexed: 03/16/2023] Open
Abstract
AlphaFold2 (AF2) is an artificial intelligence (AI) system developed by DeepMind that can predict three-dimensional (3D) structures of proteins from amino acid sequences with atomic-level accuracy. Protein structure prediction is one of the most challenging problems in computational biology and chemistry, and has puzzled scientists for 50 years. The advent of AF2 presents an unprecedented progress in protein structure prediction and has attracted much attention. Subsequent release of structures of more than 200 million proteins predicted by AF2 further aroused great enthusiasm in the science community, especially in the fields of biology and medicine. AF2 is thought to have a significant impact on structural biology and research areas that need protein structure information, such as drug discovery, protein design, prediction of protein function, et al. Though the time is not long since AF2 was developed, there are already quite a few application studies of AF2 in the fields of biology and medicine, with many of them having preliminarily proved the potential of AF2. To better understand AF2 and promote its applications, we will in this article summarize the principle and system architecture of AF2 as well as the recipe of its success, and particularly focus on reviewing its applications in the fields of biology and medicine. Limitations of current AF2 prediction will also be discussed.
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Affiliation(s)
- Zhenyu Yang
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Xiaoxi Zeng
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Yi Zhao
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041, China.
- Key Laboratory of Intelligent Information Processing, Advanced Computer Research Center, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China.
| | - Runsheng Chen
- West China Biomedical Big Data Center, West China Hospital, Sichuan University, Chengdu, 610041, China.
- Key Laboratory of RNA Biology, Center for Big Data Research in Health, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
- Pingshan Translational Medicine Center, Shenzhen Bay Laboratory, Shenzhen, 518118, China.
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Han C, Ren P, Mamtimin M, Kruk L, Sarukhanyan E, Li C, Anders HJ, Dandekar T, Krueger I, Elvers M, Goebel S, Adler K, Münch G, Gudermann T, Braun A, Mammadova-Bach E. Minimal Collagen-Binding Epitope of Glycoprotein VI in Human and Mouse Platelets. Biomedicines 2023; 11:biomedicines11020423. [PMID: 36830959 PMCID: PMC9952969 DOI: 10.3390/biomedicines11020423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/22/2023] [Accepted: 01/25/2023] [Indexed: 02/04/2023] Open
Abstract
Glycoprotein VI (GPVI) is a platelet-specific receptor for collagen and fibrin, regulating important platelet functions such as platelet adhesion and thrombus growth. Although the blockade of GPVI function is widely recognized as a potent anti-thrombotic approach, there are limited studies focused on site-specific targeting of GPVI. Using computational modeling and bioinformatics, we analyzed collagen- and CRP-binding surfaces of GPVI monomers and dimers, and compared the interacting surfaces with other mammalian GPVI isoforms. We could predict a minimal collagen-binding epitope of GPVI dimer and designed an EA-20 antibody that recognizes a linear epitope of this surface. Using platelets and whole blood samples donated from wild-type and humanized GPVI transgenic mice and also humans, our experimental results show that the EA-20 antibody inhibits platelet adhesion and aggregation in response to collagen and CRP, but not to fibrin. The EA-20 antibody also prevents thrombus formation in whole blood, on the collagen-coated surface, in arterial flow conditions. We also show that EA-20 does not influence GPVI clustering or receptor shedding. Therefore, we propose that blockade of this minimal collagen-binding epitope of GPVI with the EA-20 antibody could represent a new anti-thrombotic approach by inhibiting specific interactions between GPVI and the collagen matrix.
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Affiliation(s)
- Chao Han
- Walther-Straub-Institute for Pharmacology and Toxicology, Ludwig-Maximilian-University, 80336 Munich, Germany
- Division of Nephrology, Department of Medicine IV, Hospital of the Ludwig-Maximilian-University, 80336 Munich, Germany
| | - Pengxuan Ren
- School of Life Science and Technology, Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, Shanghai 201210, China
| | - Medina Mamtimin
- Walther-Straub-Institute for Pharmacology and Toxicology, Ludwig-Maximilian-University, 80336 Munich, Germany
- Division of Nephrology, Department of Medicine IV, Hospital of the Ludwig-Maximilian-University, 80336 Munich, Germany
| | - Linus Kruk
- Walther-Straub-Institute for Pharmacology and Toxicology, Ludwig-Maximilian-University, 80336 Munich, Germany
- Division of Nephrology, Department of Medicine IV, Hospital of the Ludwig-Maximilian-University, 80336 Munich, Germany
| | - Edita Sarukhanyan
- Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Chenyu Li
- Division of Nephrology, Department of Medicine IV, Hospital of the Ludwig-Maximilian-University, 80336 Munich, Germany
| | - Hans-Joachim Anders
- Division of Nephrology, Department of Medicine IV, Hospital of the Ludwig-Maximilian-University, 80336 Munich, Germany
| | - Thomas Dandekar
- Department of Bioinformatics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Irena Krueger
- Department of Vascular and Endovascular Surgery, Heinrich-Heine University Medical Center, 40225 Düsseldorf, Germany
| | - Margitta Elvers
- Department of Vascular and Endovascular Surgery, Heinrich-Heine University Medical Center, 40225 Düsseldorf, Germany
| | | | | | - Götz Münch
- AdvanceCOR GmbH, 82152 Martinsried, Germany
| | - Thomas Gudermann
- Walther-Straub-Institute for Pharmacology and Toxicology, Ludwig-Maximilian-University, 80336 Munich, Germany
- German Center for Lung Research (DZL), 80336 Munich, Germany
| | - Attila Braun
- Walther-Straub-Institute for Pharmacology and Toxicology, Ludwig-Maximilian-University, 80336 Munich, Germany
- Correspondence: (A.B.); (E.M.-B.)
| | - Elmina Mammadova-Bach
- Walther-Straub-Institute for Pharmacology and Toxicology, Ludwig-Maximilian-University, 80336 Munich, Germany
- Division of Nephrology, Department of Medicine IV, Hospital of the Ludwig-Maximilian-University, 80336 Munich, Germany
- Correspondence: (A.B.); (E.M.-B.)
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Chen ZR, Lv QL, Peng HW, Liu XY, Hu WL, Hu JF. Drug screening against F13 protein, the target of tecovirimat, as potential therapies for monkeypox virus. J Infect 2022; 86:154-225. [PMID: 36442658 PMCID: PMC9694522 DOI: 10.1016/j.jinf.2022.11.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 11/16/2022] [Indexed: 11/27/2022]
Affiliation(s)
- Zhang-Ren Chen
- Department of pharmacy, The First Affiliated Hospital of Nanchang University, Nanchang, China.
| | - Qiao-Li Lv
- Jiangxi Key Laboratory of Translational Cancer Research, Department of Head and Neck Surgery, Jiangxi Cancer Hospital of Nanchang University, Nanchang, China
| | - Hong-Wei Peng
- Department of pharmacy, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xiao-Yi Liu
- Department of pharmacy, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Wen-Lei Hu
- Department of pharmacy, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jin-Fang Hu
- Department of pharmacy, The First Affiliated Hospital of Nanchang University, Nanchang, China.
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Preet G, Oluwabusola ET, Milne BF, Ebel R, Jaspars M. Computational Repurposing of Mitoxantrone-Related Structures against Monkeypox Virus: A Molecular Docking and 3D Pharmacophore Study. Int J Mol Sci 2022; 23. [PMID: 36430762 DOI: 10.3390/ijms232214287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 11/03/2022] [Accepted: 11/08/2022] [Indexed: 11/19/2022] Open
Abstract
Monkeypox is caused by a DNA virus known as the monkeypox virus (MPXV) belonging to the Orthopoxvirus genus of the Poxviridae family. Monkeypox is a zoonotic disease where the primary significant hosts are rodents and non-human primates. There is an increasing global incidence with a 2022 outbreak that has spread to Europe in the middle of the COVID-19 pandemic. The new outbreak has novel, previously undiscovered mutations and variants. Currently, the US Food and Drug Administration (FDA) approved poxvirus treatment involving the use of tecovirimat. However, there has otherwise been limited research interest in monkeypox. Mitoxantrone (MXN), an anthracycline derivative, an FDA-approved therapeutic for treating cancer and multiple sclerosis, was previously reported to exhibit antiviral activity against the vaccinia virus and monkeypox virus. In this study, virtual screening, molecular docking analysis, and pharmacophore ligand-based modelling were employed on anthracene structures (1-13) closely related to MXN to explore the potential repurposing of multiple compounds from the PubChem library. Four chemical structures (2), (7), (10) and (12) show a predicted high binding potential to suppress viral replication.
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Abstract
After the COVID-19 disease, monkeypox disease has emerged today and has started to be seen almost everywhere in the world in a short time. Monkeypox causes symptoms such as fever, chills, and headache in people. In addition, rashes are seen on the skin and lumps are formed. Early diagnosis and treatment of monkeypox, which is a contagious disease, are of great importance. An expert interpretation and clinical examination are usually needed to detect monkeypox. This may cause the treatment process to be slow. Furthermore, monkeypox is sometimes confused with warts. This leads to incorrect diagnosis and treatment. Because of these disadvantages, in this study, the DNA sequences of HPV causing warts and MPV causing monkeypox were analyzed and the classification of these sequences was performed with a deep learning algorithm. The study consisted of four stages. In the first stage, DNA sequences of viruses that cause warts and monkeypox were obtained. In the second stage, these sequences were mapped using various DNA-mapping methods. In the third stage, the mapped sequences were classified using a deep learning algorithm. At the last stage, the performances of DNA-mapping methods were compared by calculating accuracy and F1-score. At the end of the study, an average accuracy of 96.08% and an F1-score of 99.83% were obtained. These results showed that these two diseases can be effectively classified according to their DNA sequences.
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