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Guevara-Vega M, Andrade BS, Palmeira LS, Bernardino SS, Taveira EB, Cardoso-Sousa L, Caixeta DC, Cunha TM, Goulart LR, Jardim ACG, Sabino-Silva R. Chapare virus infection and current perspectives on dentistry. Clin Oral Investig 2024; 28:238. [PMID: 38568249 DOI: 10.1007/s00784-023-05399-z] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 12/04/2023] [Indexed: 04/05/2024]
Abstract
OBJECTIVES This narrative review addresses relevant points about Chapare virus (CHAV) entry in oral cells, CHAV transmission, and preventive strategies in dental clinical settings. It is critical in dentistry due to the frequent presence of gingival hemorrhage occurred in CHAV-infected patients. MATERIALS AND METHODS Studies related to CHAV were searched in MEDLINE/PubMed, Scopus, EMBASE, and Web-of-Science databases without language restriction or year of publication. RESULTS Recently, the PAHO/WHO and CDC indicate a presence of human-to-human transmission of CHAV associated with direct contact with saliva, blood, or urine, and also through droplets or aerosols created in healthcare procedures. CHAV was detected in human oropharyngeal saliva and gingival bleeding was confirmed in all cases of CHAV hemorrhagic fever, including evidence of nosocomial CHAV transmission in healthcare workers. We revisited the human transferrin receptor 1 (TfR1) expression in oral, nasal, and salivary glands tissues, as well as, we firstly identified the critical residues in the pre-glycoprotein (GP) complex of CHAV that interacts with human TfR1 using cutting-edge in silico bioinformatics platforms associated with molecular dynamic analysis. CONCLUSIONS In this multidisciplinary view, we also point out critical elements to provide perspectives on the preventive strategies for dentists and frontline healthcare workers against CHAV, and in the implementation of salivary diagnostic platforms for virus detection, which can be critical to an urgent plan to prevent human-to-human transmission based on current evidence. CLINICAL RELEVANCE The preventive strategies in dental clinical settings are pivotal due to the aerosol-generating procedures in dentistry with infected patients or suspected cases of CHAV infection.
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Affiliation(s)
- Marco Guevara-Vega
- Innovation Center in Salivary Diagnostics and Nanobiotechnology, Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlandia, Minas Gerais, Brazil
- Biomedical Research Group, University of Sucre, Sincelejo, Colombia
| | - Bruno Silva Andrade
- Laboratory of Bioinformatics and Computational Chemistry, Department of Biological Sciences, State University of Southwest of Bahia (UESB), Jequié, Bahia, Brazil.
| | - Lucas Sousa Palmeira
- Laboratory of Bioinformatics and Computational Chemistry, Department of Biological Sciences, State University of Southwest of Bahia (UESB), Jequié, Bahia, Brazil
| | - Sttephany Silva Bernardino
- Innovation Center in Salivary Diagnostics and Nanobiotechnology, Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlandia, Minas Gerais, Brazil
| | - Elisa Borges Taveira
- Innovation Center in Salivary Diagnostics and Nanobiotechnology, Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlandia, Minas Gerais, Brazil
| | - Leia Cardoso-Sousa
- Innovation Center in Salivary Diagnostics and Nanobiotechnology, Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlandia, Minas Gerais, Brazil
| | - Douglas C Caixeta
- Innovation Center in Salivary Diagnostics and Nanobiotechnology, Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlandia, Minas Gerais, Brazil
| | - Thulio M Cunha
- Department of Pulmonology, School of Medicine, Federal University of Uberlandia, Uberlandia, Minas Gerais, Brazil
| | - Luiz R Goulart
- Institute of Biotechnology, Federal University of Uberlandia, Uberlandia, Minas Gerais, Brazil
| | - Ana Carolina Gomes Jardim
- Laboratory of Antiviral Research, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlandia, Minas Gerais, Brazil
| | - Robinson Sabino-Silva
- Innovation Center in Salivary Diagnostics and Nanobiotechnology, Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlandia, Minas Gerais, Brazil.
- Innovation Center in Salivary Diagnostic and Nanotheranostics, Institute of Biomedical Sciences (ICBIM), Federal University of Uberlandia (UFU), Av. Pará, 1720, Campus Umuarama, Uberlandia, MG, CEP 38400-902, Brazil.
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2
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Hassan SS, Bhattacharya T, Nawn D, Jha I, Basu P, Redwan EM, Lundstrom K, Barh D, Andrade BS, Tambuwala MM, Aljabali AA, Hromić-Jahjefendić A, Baetas-da-Cruz W, Serrano-Aroca Á, Uversky VN. SARS-CoV-2 NSP14 governs mutational instability and assists in making new SARS-CoV-2 variants. Comput Biol Med 2024; 170:107899. [PMID: 38232455 DOI: 10.1016/j.compbiomed.2023.107899] [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: 09/26/2023] [Revised: 12/03/2023] [Accepted: 12/23/2023] [Indexed: 01/19/2024]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the rapidly evolving RNA virus behind the COVID-19 pandemic, has spawned numerous variants since its 2019 emergence. The multifunctional Nonstructural protein 14 (NSP14) enzyme, possessing exonuclease and messenger RNA (mRNA) capping capabilities, serves as a key player. Notably, single and co-occurring mutations within NSP14 significantly influence replication fidelity and drive variant diversification. This study comprehensively examines 120 co-mutations, 68 unique mutations, and 160 conserved residues across NSP14 homologs, shedding light on their implications for phylogenetic patterns, pathogenicity, and residue interactions. Quantitative physicochemical analysis categorizes 3953 NSP14 variants into three clusters, revealing genetic diversity. This research underscoresthe dynamic nature of SARS-CoV-2 evolution, primarily governed by NSP14 mutations. Understanding these genetic dynamics provides valuable insights for therapeutic and vaccine development.
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Affiliation(s)
- Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, Paschim Medinipur, 721140, West Bengal, India.
| | - Tanishta Bhattacharya
- Department of Biological Sciences, Indian Institute of Science Education and Research, Berhampur, IISER Berhampur Transit campus (Govt. ITI Building), Engg. School Junction, Berhampur, 760010, Odisha, India.
| | - Debaleena Nawn
- Indian Research Institute for Integrated Medicine (IRIIM), Unsani, Howrah, 711302, West Bengal, India.
| | - Ishana Jha
- Department of Bioinformatics, Pondicherry University, Chinna Kalapet, Kalapet, Puducherry 605014, India.
| | - Pallab Basu
- School of Physics, University of the Witwatersrand, Johannesburg, Braamfontein 2000, 721140, South Africa; Adjunct Faculty, Woxsen School of Sciences, Woxsen University, Telangana, 500 033, India.
| | - Elrashdy M Redwan
- Biological Science Department, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia; Therapeutic and Protective Proteins Laboratory, Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications, New Borg EL-Arab, 21934, Alexandria, Egypt.
| | | | - Debmalya Barh
- Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, 721172, India; Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, 31270-901, Brazil.
| | - Bruno Silva Andrade
- Laboratory of Bioinformatics and Computational Chemistry, Department of Biological Sciences, State University of Southwest of Bahia (UESB), Jequié 45083-900, Brazil.
| | - Murtaza M Tambuwala
- Lincoln Medical School, University of Lincoln, Brayford Pool Campus, Lincoln LN6 7TS, UK; College of Pharmacy, Ras Al Khaimah Medical and Health Sciences University, Ras Al Khaimah, United Arab Emirates.
| | - Alaa A Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Yarmouk University, Irbid 21163, Jordan.
| | - Altijana Hromić-Jahjefendić
- Department of Genetics and Bioengineering, Faculty of Engineering and Natural Sciences, International University of Sarajevo, Hrasnicka cesta 15, 71000 Sarajevo, Bosnia and Herzegovina.
| | - Wagner Baetas-da-Cruz
- Centre for Experimental Surgery, Translational Laboratory in Molecular Physiology, College of Medicine, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
| | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Lab, Centro de Investigación Traslacional San Alberto Magno, Universidad Católica de Valencia San Vicente Mártir, c/Guillem de Castro 94, 46001 Valencia, Spain.
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
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Ferreira MM, Farias KS, Zugaib M, Alves AMM, Amaral GV, Santos MLDC, Freitas ADS, Santana BCG, dos Santos Júnior SL, Mora-Ocampo IY, Santos AS, da Silva MF, Andrade BS, Pirovani CP. TcSERPIN, an inhibitor that interacts with cocoa defense proteins and has biotechnological potential against human pathogens. Front Plant Sci 2024; 15:1337750. [PMID: 38348273 PMCID: PMC10859438 DOI: 10.3389/fpls.2024.1337750] [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] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 01/09/2024] [Indexed: 02/15/2024]
Abstract
In plants, serpins are a superfamily of serine and cysteine protease inhibitors involved in stress and defense mechanisms, with potential for controlling agricultural pests, making them important biotechnological tools. The objective of this study was to characterize a serpin from Theobroma cacao, called TcSERPIN, to identify its endogenous targets and determine its function and biotechnological potential. TcSERPIN has 390 amino acid residues and shows conservation of the main active site, RCL. Cis-elements related to light, stress, hormones, anaerobic induction, cell cycle regulation and defense have been identified in the gene's regulatory region. TcSERPIN transcripts are accumulated in different tissues of Theobroma cacao. Furthermore, in plants infected with Moniliophtora perniciosa and Phytophthora palmivora, the expression of TcSERPIN was positively regulated. The protein spectrum, rTcSERPIN, reveals a typical β-sheet pattern and is thermostable at pH 8, but loses its structure with temperature increases above 66°C at pH 7. At the molar ratios of 0.65 and 0.49, rTcSERPIN inhibited 55 and 28% of the activity of papain from Carica papaya and trypsin from Sus scrofa, respectively. The protease trap containing immobilized rTcSERPIN captured endogenous defense proteins from cocoa extracts that are related to metabolic pathways, stress and defense. The evaluation of the biotechnological potential against geohelminth larvae showed that rTcSERPIN and rTcCYS4 (Theobroma cacao cystatin 4) reduced the movement of larvae after 24 hours. The results of this work show that TcSERPIN has ideal biochemical characteristics for biotechnological applications, as well as potential for studies of resistance to phytopathogens of agricultural crops.
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Affiliation(s)
- Monaliza Macêdo Ferreira
- Centro de Biotecnologia e Genética (CBG), Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz (UESC), Ilhéus, Bahia, Brazil
| | - Keilane Silva Farias
- Centro de Biotecnologia e Genética (CBG), Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz (UESC), Ilhéus, Bahia, Brazil
| | - Maria Zugaib
- Centro de Biotecnologia e Genética (CBG), Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz (UESC), Ilhéus, Bahia, Brazil
| | - Akyla Maria Martins Alves
- Centro de Biotecnologia e Genética (CBG), Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz (UESC), Ilhéus, Bahia, Brazil
| | - Geiseane Velozo Amaral
- Centro de Biotecnologia e Genética (CBG), Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz (UESC), Ilhéus, Bahia, Brazil
| | - Maria Luíza do Carmo Santos
- Centro de Biotecnologia e Genética (CBG), Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz (UESC), Ilhéus, Bahia, Brazil
| | - Andria dos Santos Freitas
- Centro de Biotecnologia e Genética (CBG), Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz (UESC), Ilhéus, Bahia, Brazil
| | - Brenda Conceição Guimarães Santana
- Centro de Biotecnologia e Genética (CBG), Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz (UESC), Ilhéus, Bahia, Brazil
| | - Sérgio Liberato dos Santos Júnior
- Centro de Biotecnologia e Genética (CBG), Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz (UESC), Ilhéus, Bahia, Brazil
| | - Irma Yuliana Mora-Ocampo
- Centro de Biotecnologia e Genética (CBG), Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz (UESC), Ilhéus, Bahia, Brazil
| | - Ariana Silva Santos
- Centro de Biotecnologia e Genética (CBG), Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz (UESC), Ilhéus, Bahia, Brazil
| | - Marcelo Fernandes da Silva
- Centro de Biotecnologia e Genética (CBG), Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz (UESC), Ilhéus, Bahia, Brazil
| | - Bruno Silva Andrade
- Laboratório de Bioinformática e Química Computacional (LBQC), Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia (UESB), Jequié, Bahia, Brazil
| | - Carlos Priminho Pirovani
- Centro de Biotecnologia e Genética (CBG), Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz (UESC), Ilhéus, Bahia, Brazil
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Mirabal B, Andrade BS, Souza SPA, Oliveira IBDS, Melo TS, Barbosa FS, Jaiswal AK, Seyffert N, Portela RW, Soares SDC, Azevedo V, Meyer R, Tiwari S, Castro TLDP. In silico approaches for predicting natural compounds with therapeutic potential and vaccine candidates against Streptococcus equi. J Biomol Struct Dyn 2024:1-15. [PMID: 38239063 DOI: 10.1080/07391102.2023.2301056] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 12/26/2023] [Indexed: 01/26/2024]
Abstract
Equine strangles is a prevalent disease that affects the upper respiratory in horses and is caused by the Gram-positive bacterium Streptococcus equi. In addition to strangles, other clinical conditions are caused by the two S. equi subspecies, equi and zooepidemicus, which present relevant zoonotic potential. Treatment of infections caused by S. equi has become challenging due to the worldwide spreading of infected horses and the unavailability of effective therapeutics and vaccines. Penicillin treatment is often recommended, but multidrug resistance issues arised. We explored the whole genome sequence of 18 S. equi isolates to identify candidate proteins to be targeted by natural drug-like compounds or explored as immunogens. We considered only proteins shared among the sequenced strains of subspecies equi and zooepidemicus, absent in the equine host and predicted to be essential and involved in virulence. Of these, 4 proteins with cytoplasmic subcellular location were selected for molecular docking with a library of 5008 compounds, while 6 proteins were proposed as prominent immunogens against S. equi due to their probabilities of behaving as adhesins. The molecular docking analyses revealed the best ten ligands for each of the 4 drug target candidates, and they were ranked according to their binding affinities and the number of hydrogen bonds for complex stability. Finally, the natural 5-ring compound C25H20F3N5O3 excelled in molecular dynamics simulations for the increased stability in the interaction with UDP-N-acetylenolpyruvoylglucosamine reductase (MurB). This research paves the way to developing new therapeutics to minimize the impacts caused by S. equi infections.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bernardo Mirabal
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Bruno Silva Andrade
- Department of Biological Sciences, State University of Southwest Bahia, Jequié, Brazil
| | | | | | - Tarcisio Silva Melo
- Postgraduate Program in Biotechnology, State University of Feira de Santana (UEFS), Feira de Santana, Brazil
| | - Fabrício Santos Barbosa
- Postgraduate Program in Chemistry, State University of Southwest Bahia (UESB), Jequié, Brazil
| | - Arun Kumar Jaiswal
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Nubia Seyffert
- Institute of Health Sciences, Federal University of Bahia, Salvador, Brazil
| | | | - Siomar de Castro Soares
- Microbiology and Parasitology, Institute of Biological Sciences and Natural Sciences, Federal University of Triângulo Mineiro, Uberaba, Brazil
| | - Vasco Azevedo
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
- School of Veterinary Medicine and Animal Science, Federal University of Bahia, Salvador, Brazil
| | - Roberto Meyer
- Institute of Health Sciences, Federal University of Bahia, Salvador, Brazil
| | - Sandeep Tiwari
- Institute of Health Sciences, Federal University of Bahia, Salvador, Brazil
| | - Thiago Luiz de Paula Castro
- Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
- Institute of Health Sciences, Federal University of Bahia, Salvador, Brazil
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Garcia-Junior MA, Andrade BS, Guevara-Vega M, de Melo IS, Cunha TM, Jardim ACG, Sabino-Silva R. Oral Infection, Oral Pathology and Salivary Diagnostics of Mpox Disease: Relevance in Dentistry and OMICs Perspectives. Int J Mol Sci 2023; 24:14362. [PMID: 37762664 PMCID: PMC10531708 DOI: 10.3390/ijms241814362] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/31/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
In this narrative review, we aim to point out the close relationship between mpox virus (MPXV) infection and the role of saliva as a diagnostic tool for mpox, considering the current molecular approach and in the perspective of OMICs application. The MPXV uses the host cell's rough endoplasmic reticulum, ribosomes, and cytoplasmic proteins to replicate its genome and synthesize virions for cellular exit. The presence of oral mucosa lesions associated with mpox infection is one of the first signs of infection; however, current diagnostic tools find it difficult to detect the virus before the rashes begin. MPXV transmission occurs through direct contact with an infected lesion and infected body fluids, including saliva, presenting a potential use of this fluid for diagnostic purposes. Currently available diagnostic tests for MPXV detection are performed either by real-time quantitative PCR (RT-qPCR) or ELISA, which presents several limitations since they are invasive tests. Despite current clinical trials with restricted sample size, MPXV DNA was detected in saliva with a sensitivity of 85%-100%. In this context, the application of transcriptomics, metabolomics, lipidomics, or proteomics analyses coupled with saliva can identify novel disease biomarkers. Thus, it is important to note that the identification and quantification of salivary DNA, RNA, lipid, protein, and metabolite can provide novel non-invasive biomarkers through the use of OMICs platforms aiding in the early detection and diagnosis of MPXV infection. Untargeted mass spectrometry (MS)-based proteomics reveals that some proteins also expressed in saliva were detected with greater expression differences in blood plasma when comparing mpox patients and healthy subjects, suggesting a promising alternative to be applied in screening or diagnostic platforms for mpox salivary diagnostics coupled to OMICs.
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Affiliation(s)
- Marcelo Augusto Garcia-Junior
- Innovation Center in Salivary Diagnostics and Nanobiotechnology, Laboratory of Nanobiotechnology – “Luiz Ricardo Goulart”, Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlândia 38496-017, Brazil (M.G.-V.)
| | - Bruno Silva Andrade
- Laboratory of Bioinformatics and Computational Chemistry, Department of Biological Sciences, State University of Southwest of Bahia (UESB), Jequié 45083-900, Brazil
| | - Marco Guevara-Vega
- Innovation Center in Salivary Diagnostics and Nanobiotechnology, Laboratory of Nanobiotechnology – “Luiz Ricardo Goulart”, Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlândia 38496-017, Brazil (M.G.-V.)
| | - Igor Santana de Melo
- Department of Histology and Embryology, Institute of Biological Sciences and Health, Federal University of Alagoas (UFAL), Maceió 57072-260, Brazil
| | - Thúlio M. Cunha
- Department of Pulmonology, School of Medicine, Federal University of Uberlandia, Uberlândia 38496-017, Brazil
| | - Ana Carolina Gomes Jardim
- Laboratory of Antiviral Research, Department of Microbiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlândia 38496-017, Brazil
| | - Robinson Sabino-Silva
- Innovation Center in Salivary Diagnostics and Nanobiotechnology, Laboratory of Nanobiotechnology – “Luiz Ricardo Goulart”, Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Uberlândia 38496-017, Brazil (M.G.-V.)
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Grosche VR, Souza LPF, Ferreira GM, Guevara-Vega M, Carvalho T, Silva RRDS, Batista KLR, Abuna RPF, Silva JS, Calmon MDF, Rahal P, da Silva LCN, Andrade BS, Teixeira CS, Sabino-Silva R, Jardim ACG. Mannose-Binding Lectins as Potent Antivirals against SARS-CoV-2. Viruses 2023; 15:1886. [PMID: 37766292 PMCID: PMC10536204 DOI: 10.3390/v15091886] [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: 05/23/2023] [Revised: 08/17/2023] [Accepted: 08/30/2023] [Indexed: 09/29/2023] Open
Abstract
The SARS-CoV-2 entry into host cells is mainly mediated by the interactions between the viral spike protein (S) and the ACE-2 cell receptor, which are highly glycosylated. Therefore, carbohydrate binding agents may represent potential candidates to abrogate virus infection. Here, we evaluated the in vitro anti-SARS-CoV-2 activity of two mannose-binding lectins isolated from the Brazilian plants Canavalia brasiliensis and Dioclea violacea (ConBR and DVL). These lectins inhibited SARS-CoV-2 Wuhan-Hu-1 strain and variants Gamma and Omicron infections, with selectivity indexes (SI) of 7, 1.7, and 6.5, respectively for ConBR; and 25, 16.8, and 22.3, for DVL. ConBR and DVL inhibited over 95% of the early stages of the viral infection, with strong virucidal effect, and also protected cells from infection and presented post-entry inhibition. The presence of mannose resulted in the complete lack of anti-SARS-CoV-2 activity by ConBR and DVL, recovering virus titers. ATR-FTIR, molecular docking, and dynamic simulation between SARS-CoV-2 S and either lectins indicated molecular interactions with predicted binding energies of -85.4 and -72.0 Kcal/Mol, respectively. Our findings show that ConBR and DVL lectins possess strong activities against SARS-CoV-2, potentially by interacting with glycans and blocking virus entry into cells, representing potential candidates for the development of novel antiviral drugs.
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Affiliation(s)
- Victória Riquena Grosche
- Laboratory of Antiviral Research, Institute of Biomedical Science (ICBIM), Federal University of Uberlândia (UFU), Uberlândia 38405-317, Brazil; (V.R.G.); (G.M.F.)
- Institute of Biosciences, Languages, and Exact Sciences (Ibilce), São Paulo State University (Unesp), São José do Rio Preto 15054-000, Brazil; (T.C.); (M.d.F.C.); (P.R.)
| | - Leandro Peixoto Ferreira Souza
- Innovation Center in Salivary Diagnostic and Nanobiotechnology, Institute of Biomedical Science (ICBIM), Federal University of Uberlândia (UFU), Uberlândia 38405-317, Brazil; (L.P.F.S.); (M.G.-V.)
| | - Giulia Magalhães Ferreira
- Laboratory of Antiviral Research, Institute of Biomedical Science (ICBIM), Federal University of Uberlândia (UFU), Uberlândia 38405-317, Brazil; (V.R.G.); (G.M.F.)
| | - Marco Guevara-Vega
- Innovation Center in Salivary Diagnostic and Nanobiotechnology, Institute of Biomedical Science (ICBIM), Federal University of Uberlândia (UFU), Uberlândia 38405-317, Brazil; (L.P.F.S.); (M.G.-V.)
| | - Tamara Carvalho
- Institute of Biosciences, Languages, and Exact Sciences (Ibilce), São Paulo State University (Unesp), São José do Rio Preto 15054-000, Brazil; (T.C.); (M.d.F.C.); (P.R.)
| | | | | | - Rodrigo Paolo Flores Abuna
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil; (R.P.F.A.); (J.S.S.)
- Oswaldo Cruz Foundation (Fiocruz), Bi-Institutional Platform for Translational Medicine, Ribeirão Preto 14049-900, Brazil
| | - João Santana Silva
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, Brazil; (R.P.F.A.); (J.S.S.)
- Oswaldo Cruz Foundation (Fiocruz), Bi-Institutional Platform for Translational Medicine, Ribeirão Preto 14049-900, Brazil
| | - Marília de Freitas Calmon
- Institute of Biosciences, Languages, and Exact Sciences (Ibilce), São Paulo State University (Unesp), São José do Rio Preto 15054-000, Brazil; (T.C.); (M.d.F.C.); (P.R.)
| | - Paula Rahal
- Institute of Biosciences, Languages, and Exact Sciences (Ibilce), São Paulo State University (Unesp), São José do Rio Preto 15054-000, Brazil; (T.C.); (M.d.F.C.); (P.R.)
| | | | - Bruno Silva Andrade
- Laboratory of Bioinformatics and Computational Chemistry, State University of Southwest of Bahia, Jequié 45205-490, Brazil;
| | - Claudener Souza Teixeira
- Center of Agrarian Science and Biodiversity, Federal University of Cariri (UFCA), Crato 63130-025, Brazil; (R.R.d.S.S.); (C.S.T.)
| | - Robinson Sabino-Silva
- Innovation Center in Salivary Diagnostic and Nanobiotechnology, Institute of Biomedical Science (ICBIM), Federal University of Uberlândia (UFU), Uberlândia 38405-317, Brazil; (L.P.F.S.); (M.G.-V.)
| | - Ana Carolina Gomes Jardim
- Laboratory of Antiviral Research, Institute of Biomedical Science (ICBIM), Federal University of Uberlândia (UFU), Uberlândia 38405-317, Brazil; (V.R.G.); (G.M.F.)
- Institute of Biosciences, Languages, and Exact Sciences (Ibilce), São Paulo State University (Unesp), São José do Rio Preto 15054-000, Brazil; (T.C.); (M.d.F.C.); (P.R.)
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7
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Usman M, Ayub A, Habib S, Rana MS, Rehman Z, Zohaib A, Jamal SB, Jaiswal AK, Andrade BS, de Carvalho Azevedo V, Faheem M, Javed A. Vaccinomics Approach for Multi-Epitope Vaccine Design against Group A Rotavirus Using VP4 and VP7 Proteins. Vaccines (Basel) 2023; 11:726. [PMID: 37112638 PMCID: PMC10144065 DOI: 10.3390/vaccines11040726] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 03/15/2023] [Accepted: 03/15/2023] [Indexed: 03/29/2023] Open
Abstract
Rotavirus A is the most common cause of Acute Gastroenteritis globally among children <5 years of age. Due to a segmented genome, there is a high frequency of genetic reassortment and interspecies transmission which has resulted in the emergence of novel genotypes. There are concerns that monovalent (Rotarix: GlaxoSmithKline Biologicals, Rixensart, Belgium) and pentavalent (RotaTeq: MERCK & Co., Inc., Kenilworth, NJ, USA) vaccines may be less effective against non-vaccine strains, which clearly shows the demand for the design of a vaccine that is equally effective against all circulating genotypes. In the present study, a multivalent vaccine was designed from VP4 and VP7 proteins of RVA. Epitopes were screened for antigenicity, allergenicity, homology with humans and anti-inflammatory properties. The vaccine contains four B-cell, three CTL and three HTL epitopes joined via linkers and an N-terminal RGD motif adjuvant. The 3D structure was predicted and refined preceding its docking with integrin. Immune simulation displayed promising results both in Asia and worldwide. In the MD simulation, the RMSD value varied from 0.2 to 1.6 nm while the minimum integrin amino acid fluctuation (0.05-0.1 nm) was observed with its respective ligand. Codon optimization was performed with an adenovirus vector in a mammalian expression system. The population coverage analysis showed 99.0% and 98.47% in South Asia and worldwide, respectively. These computational findings show potential against all RVA genotypes; however, in-vitro/in-vivo screening is essential to devise a meticulous conclusion.
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Affiliation(s)
- Muhammad Usman
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad 44000, Pakistan
- Department of Virology, National Institute of Health, Islamabad 45500, Pakistan
| | - Aaima Ayub
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad 44000, Pakistan
| | - Sabahat Habib
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad 44000, Pakistan
| | | | - Zaira Rehman
- Department of Virology, National Institute of Health, Islamabad 45500, Pakistan
| | - Ali Zohaib
- Department of Microbiology, The Islamia University of Bahawalpur, Baghdad-ul-Jadeed Campus, Bahawalpur 63100, Pakistan
| | - Syed Babar Jamal
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi 46000, Pakistan (M.F.)
| | - Arun Kumar Jaiswal
- Laboratory of Cellular and Molecular Genetics (LGCM), PG Program in Bioinformatics, Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil
| | - Bruno Silva Andrade
- Laboratory of Bioinformatics and Computational Chemistry, State University of Southwest of Bahia, Bahia 45083-900, Brazil
| | - Vasco de Carvalho Azevedo
- Laboratory of Cellular and Molecular Genetics (LGCM), PG Program in Bioinformatics, Department of Genetics, Ecology, and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil
| | - Muhammad Faheem
- Department of Biological Sciences, National University of Medical Sciences, Rawalpindi 46000, Pakistan (M.F.)
| | - Aneela Javed
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad 44000, Pakistan
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8
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de Menezes TA, Aburjaile FF, Quintanilha-Peixoto G, Tomé LMR, Fonseca PLC, Mendes-Pereira T, Araújo DS, Melo TS, Kato RB, Delabie JHC, Ribeiro SP, Brenig B, Azevedo V, Drechsler-Santos ER, Andrade BS, Góes-Neto A. Unraveling the Secrets of a Double-Life Fungus by Genomics: Ophiocordyceps australis CCMB661 Displays Molecular Machinery for Both Parasitic and Endophytic Lifestyles. J Fungi (Basel) 2023; 9:jof9010110. [PMID: 36675931 PMCID: PMC9864599 DOI: 10.3390/jof9010110] [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: 12/06/2022] [Revised: 12/31/2022] [Accepted: 01/09/2023] [Indexed: 01/15/2023] Open
Abstract
Ophiocordyceps australis (Ascomycota, Hypocreales, Ophiocordycipitaceae) is a classic entomopathogenic fungus that parasitizes ants (Hymenoptera, Ponerinae, Ponerini). Nonetheless, according to our results, this fungal species also exhibits a complete set of genes coding for plant cell wall degrading Carbohydrate-Active enZymes (CAZymes), enabling a full endophytic stage and, consequently, its dual ability to both parasitize insects and live inside plant tissue. The main objective of our study was the sequencing and full characterization of the genome of the fungal strain of O. australis (CCMB661) and its predicted secretome. The assembled genome had a total length of 30.31 Mb, N50 of 92.624 bp, GC content of 46.36%, and 8,043 protein-coding genes, 175 of which encoded CAZymes. In addition, the primary genes encoding proteins and critical enzymes during the infection process and those responsible for the host-pathogen interaction have been identified, including proteases (Pr1, Pr4), aminopeptidases, chitinases (Cht2), adhesins, lectins, lipases, and behavioral manipulators, such as enterotoxins, Protein Tyrosine Phosphatases (PTPs), and Glycoside Hydrolases (GHs). Our findings indicate that the presence of genes coding for Mad2 and GHs in O. australis may facilitate the infection process in plants, suggesting interkingdom colonization. Furthermore, our study elucidated the pathogenicity mechanisms for this Ophiocordyceps species, which still is scarcely studied.
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Affiliation(s)
- Thaís Almeida de Menezes
- Department of Biological Sciences, Universidade Estadual de Feira de Santana, Av. Transnordestina, s/n, Novo Horizonte, Feira de Santana 44036-900, BA, Brazil
| | - Flávia Figueira Aburjaile
- Laboratory of Integrative Bioinformatics, Preventive Veterinary Medicine Department, Veterinary School, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil
| | - Gabriel Quintanilha-Peixoto
- Laboratory of Molecular and Computational Biology of Fungi, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte 31270-901, MG, Brazil
| | - Luiz Marcelo Ribeiro Tomé
- Laboratory of Molecular and Computational Biology of Fungi, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte 31270-901, MG, Brazil
| | - Paula Luize Camargos Fonseca
- Laboratory of Molecular and Computational Biology of Fungi, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte 31270-901, MG, Brazil
| | - Thairine Mendes-Pereira
- Laboratory of Molecular and Computational Biology of Fungi, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte 31270-901, MG, Brazil
| | - Daniel Silva Araújo
- Program in Bioinformatics, Loyola University Chicago, Chicago, IL 60660, USA
| | - Tarcisio Silva Melo
- Department of Biological Sciences, Universidade Estadual de Feira de Santana, Av. Transnordestina, s/n, Novo Horizonte, Feira de Santana 44036-900, BA, Brazil
| | - Rodrigo Bentes Kato
- Laboratory of Molecular and Computational Biology of Fungi, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte 31270-901, MG, Brazil
| | - Jacques Hubert Charles Delabie
- Laboratory of Myrmecology, Centro de Pesquisa do Cacau, Ilhéus 45600-000, BA, Brazil
- Department of Agricultural and Environmental Sciences, Universidade Estadual de Santa Cruz, Ilhéus 45600-970, BA, Brazil
| | - Sérvio Pontes Ribeiro
- Laboratory of Ecology of Diseases and Forests, Nucleus of Biological Science, Campus Morro do Cruzeiro, Universidade Federal de Ouro Preto, Ouro Preto 35402-163, MG, Brazil
| | - Bertram Brenig
- Institute of Veterinary Medicine, Burckhardtweg, University of Göttingen, 37073 Göttingen, Germany
| | - Vasco Azevedo
- Laboratory of Cellular and Molecular Genetics, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, MG, Brazil
| | | | - Bruno Silva Andrade
- Department of Biological Sciences, Universidade Federal do Sudoeste da Bahia, Av. José Moreira Sobrinho, s/n, Jequiezinho, Jequié 45205-490, BA, Brazil
| | - Aristóteles Góes-Neto
- Laboratory of Molecular and Computational Biology of Fungi, Institute of Biological Sciences, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha, Belo Horizonte 31270-901, MG, Brazil
- Correspondence: ; Tel.: +55-31-3409-3050
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9
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Barh D, Tiwari S, Rodrigues Gomes LG, Ramalho Pinto CH, Andrade BS, Ahmad S, Aljabali AAA, Alzahrani KJ, Banjer HJ, Hassan SS, Redwan EM, Raza K, Góes-Neto A, Sabino-Silva R, Lundstrom K, Uversky VN, Azevedo V, Tambuwala MM. SARS-CoV-2 Variants Show a Gradual Declining Pathogenicity and Pro-Inflammatory Cytokine Stimulation, an Increasing Antigenic and Anti-Inflammatory Cytokine Induction, and Rising Structural Protein Instability: A Minimal Number Genome-Based Approach. Inflammation 2023; 46:297-312. [PMID: 36215001 PMCID: PMC9549046 DOI: 10.1007/s10753-022-01734-w] [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: 07/19/2022] [Revised: 08/12/2022] [Accepted: 08/23/2022] [Indexed: 11/30/2022]
Abstract
Hyper-transmissibility with decreased disease severity is a typical characteristic of the SARS-CoV-2 Omicron variant. To understand this phenomenon, we used various bioinformatics approaches to analyze randomly selected genome sequences (one each) of the Gamma, Delta, and Omicron variants submitted to NCBI from December 15 to 31, 2021. We report that the pathogenicity of SARS-CoV-2 variants decreases in the order of Wuhan > Gamma > Delta > Omicron; however, the antigenic property follows the order of Omicron > Gamma > Wuhan > Delta. The Omicron spike RBD shows lower pathogenicity but higher antigenicity than other variants. The reported decreased disease severity by the Omicron variant may be due to its decreased pro-inflammatory and IL-6 stimulation and increased IFN-γ and IL-4 induction efficacy. The mutations in the N protein are probably associated with this decreased IL-6 induction and human DDX21-mediated increased IL-4 production for Omicron. Due to the mutations, the stability of S, M, N, and E proteins decreases in the order of Omicron > Gamma > Delta > Wuhan. Although a stronger spike RBD-hACE2 binding of Omicron increases its transmissibility, the lowest stability of its spike protein makes spike RBD-hACE2 interaction weak for systemic infection and for causing severe disease. Finally, the highest instability of the Omicron E protein may also be associated with decreased viral maturation and low viral load, leading to less severe disease and faster recovery. Our findings will contribute to the understanding of the dynamics of SARS-CoV-2 variants and the management of emerging variants. This minimal genome-based method may be used for other similar viruses avoiding robust analysis.
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Affiliation(s)
- Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, West Bengal, 721172, Purba Medinipur, India. .,Laboratory of Cellular and Molecular Genetics (LGCM) and PG Program in Bioinformatics, Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, CEP, 31270-901, Brazil.
| | - Sandeep Tiwari
- Laboratory of Cellular and Molecular Genetics (LGCM) and PG Program in Bioinformatics, Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, CEP 31270-901 Brazil
| | - Lucas Gabriel Rodrigues Gomes
- Laboratory of Cellular and Molecular Genetics (LGCM) and PG Program in Bioinformatics, Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, CEP 31270-901 Brazil
| | - Cecília Horta Ramalho Pinto
- Department of Biochemistry and Immunology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, 31270-901 Brazil
| | - Bruno Silva Andrade
- Laboratory of Bioinformatics and Computational Chemistry, Department of Biological Sciences, State University of Southwest Bahia (UESB), Jequié, 45206-190 Brazil
| | - Shaban Ahmad
- Department of Computer Science, Jamia Millia Islamia, New Delhi, 110025 India
| | - Alaa A. A. Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Yarmouk University, P O BOX 566, Irbid, 21163 Jordan
| | - Khalid J. Alzahrani
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif, 21944 Saudi Arabia
| | - Hamsa Jameel Banjer
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, P.O. Box 11099, Taif, 21944 Saudi Arabia
| | - Sk. Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, 721140 India
| | - Elrashdy M. Redwan
- Department of Biological Science, Faculty of Science, King Abdulazizi University, Jeddah, 21589 Saudi Arabia
| | - Khalid Raza
- Department of Computer Science, Jamia Millia Islamia, New Delhi, 110025 India
| | - Aristóteles Góes-Neto
- Laboratory of Cellular and Molecular Genetics (LGCM) and PG Program in Bioinformatics, Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, CEP 31270-901 Brazil
| | - Robinson Sabino-Silva
- Department of Physiology, Institute of Biomedical Sciences, Federal University of Uberlandia, Minas Gerais, Uberlandia, CEP 38400-902 Brazil
| | | | - Vladimir N. Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612 USA
| | - Vasco Azevedo
- Laboratory of Cellular and Molecular Genetics (LGCM) and PG Program in Bioinformatics, Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, CEP 31270-901 Brazil
| | - Murtaza M. Tambuwala
- Lincoln Medical School, University of Lincoln, Brayford Pool Campus, Lincoln, LN6 7TS UK
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10
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Prado LCDS, Giacchetto Felice A, Rodrigues TCV, Tiwari S, Andrade BS, Kato RB, Oliveira CJF, Silva MV, Barh D, Azevedo VADC, Jaiswal AK, Soares SDC. New putative therapeutic targets against Serratia marcescens using reverse vaccinology and subtractive genomics. J Biomol Struct Dyn 2022; 40:10106-10121. [PMID: 34192477 DOI: 10.1080/07391102.2021.1942211] [Citation(s) in RCA: 4] [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] [Indexed: 12/16/2022]
Abstract
The Gram-negative bacillus Serratia marcescens, a member of Enterobacteriaceae family, is an opportunistic nosocomial pathogen commonly found in hospital outbreaks that can cause infections in the urinary tract, bloodstream, central nervous system and pneumonia. Because S. marcescens strains are resistant to several antibiotics, it is critical the need for effective treatments, including new drugs and vaccines. Here, we applied reverse vaccinology and subtractive genomic approaches for the in silico prediction of potential vaccine and drug targets against 59 strains of S. marcescens. We found 759 core non-host homologous proteins, of which 87 are putative surface-exposed proteins, 183 secreted proteins, and 80 membrane proteins. From these proteins, we predicted seven candidates vaccine targets: a sn-glycerol-3-phosphate-binding periplasmic protein UgpB, a vitamin B12 TonB-dependent receptor, a ferrichrome porin FhuA, a divisome-associated lipoprotein YraP, a membrane-bound lytic murein transglycosylase A, a peptidoglycan lytic exotransglycosylase, and a DUF481 domain-containing protein. We also predicted two drug targets: a N(4)-acetylcytidine amidohydrolase, and a DUF1428 family protein. Using the molecular docking approach for each drug target, we identified and selected ZINC04259491 and ZINC04235390 molecules as the most favorable interactions with the target active site residues. Our findings may contribute to the development of vaccines and new drug targets against S. marcescens. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ligia Carolina da Silva Prado
- Inter-unit Post-Graduate Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Andrei Giacchetto Felice
- Department of Microbiology, Immunology and Parasitology, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro, Uberaba, MG, Brazil
| | - Thaís Cristina Vilela Rodrigues
- Inter-unit Post-Graduate Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Sandeep Tiwari
- Inter-unit Post-Graduate Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Bruno Silva Andrade
- Laboratory of Bioinformatics and Computational Chemistry, State University of Southwest of Bahia, Bahia, Brazil
| | - Rodrigo Bentes Kato
- Inter-unit Post-Graduate Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Carlo José Freire Oliveira
- Department of Microbiology, Immunology and Parasitology, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro, Uberaba, MG, Brazil
| | - Marcos Vinicius Silva
- Department of Microbiology, Immunology and Parasitology, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro, Uberaba, MG, Brazil
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology, Nonakuri, West Bengal, India
| | - Vasco Ariston de Carvalho Azevedo
- Inter-unit Post-Graduate Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Arun Kumar Jaiswal
- Inter-unit Post-Graduate Program in Bioinformatics, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Siomar de Castro Soares
- Department of Microbiology, Immunology and Parasitology, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro, Uberaba, MG, Brazil
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11
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Ribeiro SP, Barh D, Andrade BS, José Santana Silva R, Costa-Rezende DH, Fonseca PLC, Tiwari S, Giovanetti M, Alcantara LCJ, Azevedo VA, Ghosh P, Diniz-Filho JAF, Loyola R, de Almeida MFB, Góes-Neto A. Long-term unsustainable patterns of development rather than recent deforestation caused the emergence of Orthocoronavirinae species. Environ Microbiol 2022; 24:4714-4724. [PMID: 35859337 DOI: 10.1111/1462-2920.16121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 06/22/2022] [Accepted: 06/29/2022] [Indexed: 11/28/2022]
Abstract
We investigated whether a set of phylogeographical tracked emergent events of Orthocoronavirinae were related to developed, urban and polluted environments worldwide. We explored coronavirus records in response to climate (rainfall parameters), population density, CO2 emission, Human Developmental Index (HDI) and deforestation. We contrasted environmental characteristics from regions with spillovers or encounters of wild Orthocoronavirinae against adjacent areas having best-preserved conditions. We used all complete sequenced CoVs genomes deposited in NCBI and GISAID databases until January 2021. Except for Deltacoronavirus, concentrated in Hong Kong and in birds, the other three genera were scattered all over the planet, beyond the original distribution of the subfamily, and found in humans, mammals, fishes and birds, wild or domestic. Spillovers and presence in wild animals were only reported in developed/densely populated places. We found significantly more occurrences reported in places with higher HDI, CO2 emission, or population density, along with more rainfall and more accentuated seasonality. Orthocoronavirinae occurred in areas with significantly higher human populations, CO2 emissions and deforestation rates than in adjacent locations. Intermediately disturbed ecosystems seemed more vulnerable for Orthocoronavirinae emergence than forested regions in frontiers of deforestation. Sadly, people experiencing poverty in an intensely consumerist society are the most vulnerable.
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Affiliation(s)
- Sérvio P Ribeiro
- Laboratório de Ecologia do Adoecimento & Florestas NUPEB/ICEB, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Purba Medinipur, West Bengal, India.,Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Bruno Silva Andrade
- Laboratório de Bioinformática e Química Computacional, Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia (UESB), Jequié, Bahia, Brazil
| | - Raner José Santana Silva
- Departamento de Ciências Biológicas (DCB), Universidade Estadual de Santa Cruz (UESC), Ilhéus, Bahia, Brazil.,Programa de Pós-Graduação em Genética e Biologia Molecular (PPGGBM), Universidade Estadual de Santa Cruz (UESC), Ilhéus, Bahia, Brazil
| | - Diogo Henrique Costa-Rezende
- Programa de Pós-Graduação em Botânica (PPGBot), Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana (UEFS), Feira de Santana, Bahia, Brazil
| | - Paula Luize Camargos Fonseca
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Sandeep Tiwari
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Marta Giovanetti
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.,Laboratório de Flavivírus, Instituto Oswaldo Cruz Fiocruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Luiz Carlos Junior Alcantara
- Laboratório de Genética Celular e Molecular, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil.,Laboratório de Flavivírus, Instituto Oswaldo Cruz Fiocruz, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Vasco Ariston Azevedo
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Preetam Ghosh
- Virginia Commonwealth University, Richmond, Virginia, USA
| | | | - Rafael Loyola
- Departamento de Ecologia, Universidade Federal de Goiás, Goiânia, Goiás, Brazil.,Fundação Brasileira para o Desenvolvimento Sustentável, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Maria Fernanda Brito de Almeida
- Laboratório de Ecologia do Adoecimento & Florestas NUPEB/ICEB, Universidade Federal de Ouro Preto, Ouro Preto, Minas Gerais, Brazil.,Programa de Pós-Graduação em Ecologia, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Aristóteles Góes-Neto
- Laboratório de Biologia Molecular e Computacional de Fungos, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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12
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Moreira BO, Vilar VLS, de Almeida RNS, Morbeck LLB, Andrade BS, Barros RGM, Neves BM, de Carvalho AL, Cruz MP, Yatsuda R, David JM. New dimer and trimer of chalcone derivatives from anti-inflammatory and antinociceptive extracts of Schinopsis brasiliensis roots. J Ethnopharmacol 2022; 289:115089. [PMID: 35143935 DOI: 10.1016/j.jep.2022.115089] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 01/31/2022] [Accepted: 02/04/2022] [Indexed: 06/14/2023]
Abstract
ETHNOPHARMACOLOGY RELEVANCE Schinopsis brasiliensis Engl. is an endemic tree of the Brazilian semi-arid regions belonging to the Anacardiaceae family. It is the main representative of the genus Schinopsis, mostly native to Brazil and popularly known as "braúna" or "baraúna". Different parts of this plant are employed in Brazilian folk medicines to treat inflammation in general, sexual impotence, cough, and influenza. AIM OF THE STUDY This work describes the antinociceptive (acetic acid-induced writhing and formalin-induced nociception) and anti-inflammatory (paw edema and neutrophil migration) activities of the extract of the root of S. brasiliensis. Besides, the evaluation of total phenolic compounds and antioxidant, antimicrobial (including MRSA bacteria), and acetylcholinesterase inhibition activities were also determined. MATERIAL AND METHODS The pure compounds were isolated by different chromatographic techniques and their chemical structures have been unambiguously elucidated based on extensive spectroscopic methods, including 1D (1H, 13C, DEPT, and NOEdiff) and 2D (HSQC, HMBC, and NOESY) NMR experiments, MS data, and comparison with the literature data of similar compounds. The antinociceptive and anti-inflammatory activities were evaluated by acid acetic writhing test, formalin paw edema, and by the investigation of neutrophil migration to the peritoneal cavities of mice. For antimicrobial evaluation were determined MIC and MBC, antioxidant activities were obtained by TPC and DPPH tests, and AChE inhibition by Elmann's methodology. RESULTS The extracts showed antinociceptive and anti-inflammatory activities and two unusual new compounds, a cyclobutanyl chalcone trimer (schinopsone A) and a cyclohexene-containing chalcone dimer (schinopsone B), with six known compounds were isolated from the active extracts. Additionally, the acetylcholinesterase inhibitory activity for isolated compounds was reported for the first time in this study. Molecular docking studies indicated that the isolated compounds are responsible for the interaction with anti-inflammatory targets (COX 1 and 2 and LOX) with variable binding affinities, indicating a possible mechanism of action of these compounds. CONCLUSIONS These findings indicate for the first time the correlation between the anti-inflammatory activity different enriched polyphenol-organic soluble fractions of S. brasiliensis, and it contributes to the understanding of the anti-inflammatory potential of S. brasiliensis.
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Affiliation(s)
- Bruno Oliveira Moreira
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, 45029-094, Vitória da Conquista, BA, Brazil
| | - Vanessa Lima Souza Vilar
- Instituto Federal Catarinense - Campus Concórdia, 89703-720, Concórdia, SC, Brazil; Instituto de Química, Universidade Federal da Bahia, 40170-115, Salvador, BA, Brazil
| | | | - Lorena Lôbo Brito Morbeck
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, 45029-094, Vitória da Conquista, BA, Brazil
| | - Bruno Silva Andrade
- Universidade Estadual do Sudoeste da Bahia, Departamento de Ciências Biológicas, Jequié, 45200-000, BA, Brazil
| | - Rafael Gomes Moreno Barros
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, 45029-094, Vitória da Conquista, BA, Brazil
| | - Breno Magalhães Neves
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, 45029-094, Vitória da Conquista, BA, Brazil
| | - Anaildes Lago de Carvalho
- Departamento de Ciências Naturais, Universidade Estadual do Sudoeste da Bahia, 45083-900, Vitória da Conquista, BA, Brazil
| | - Mariluze Peixoto Cruz
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, 45029-094, Vitória da Conquista, BA, Brazil
| | - Regiane Yatsuda
- Instituto Multidisciplinar em Saúde, Universidade Federal da Bahia, 45029-094, Vitória da Conquista, BA, Brazil
| | - Jorge Mauricio David
- Instituto de Química, Universidade Federal da Bahia, 40170-115, Salvador, BA, Brazil.
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13
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Hassan SS, Kodakandla V, Redwan EM, Lundstrom K, Pal Choudhury P, Abd El-Aziz TM, Takayama K, Kandimalla R, Lal A, Serrano-Aroca Á, Azad GK, Aljabali AA, Palù G, Chauhan G, Adadi P, Tambuwala M, Brufsky AM, Baetas-da-Cruz W, Barh D, Azevedo V, Bazan NG, Andrade BS, Santana Silva RJ, Uversky VN. An issue of concern: unique truncated ORF8 protein variants of SARS-CoV-2. PeerJ 2022; 10:e13136. [PMID: 35341060 PMCID: PMC8944340 DOI: 10.7717/peerj.13136] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [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: 09/16/2021] [Accepted: 02/27/2022] [Indexed: 01/12/2023] Open
Abstract
Open reading frame 8 (ORF8) shows one of the highest levels of variability among accessory proteins in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of Coronavirus Disease 2019 (COVID-19). It was previously reported that the ORF8 protein inhibits the presentation of viral antigens by the major histocompatibility complex class I (MHC-I), which interacts with host factors involved in pulmonary inflammation. The ORF8 protein assists SARS-CoV-2 in evading immunity and plays a role in SARS-CoV-2 replication. Among many contributing mutations, Q27STOP, a mutation in the ORF8 protein, defines the B.1.1.7 lineage of SARS-CoV-2, engendering the second wave of COVID-19. In the present study, 47 unique truncated ORF8 proteins (T-ORF8) with the Q27STOP mutations were identified among 49,055 available B.1.1.7 SARS-CoV-2 sequences. The results show that only one of the 47 T-ORF8 variants spread to over 57 geo-locations in North America, and other continents, which include Africa, Asia, Europe and South America. Based on various quantitative features, such as amino acid homology, polar/non-polar sequence homology, Shannon entropy conservation, and other physicochemical properties of all specific 47 T-ORF8 protein variants, nine possible T-ORF8 unique variants were defined. The question as to whether T-ORF8 variants function similarly to the wild type ORF8 is yet to be investigated. A positive response to the question could exacerbate future COVID-19 waves, necessitating severe containment measures.
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Affiliation(s)
- Sk. Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, India
| | - Vaishnavi Kodakandla
- Department of Life sciences, Sophia College For Women, University of Mumbai, Mumbai, India
| | - Elrashdy M. Redwan
- Faculty of Science, Department of Biological Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | | | - Tarek Mohamed Abd El-Aziz
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Kazuo Takayama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Ramesh Kandimalla
- Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad, India
| | - Amos Lal
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic Rochester, Rochester, NY, United States
| | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Lab, Centro de Investigacion Traslacional San Alberto Magno, Universidad Catolica de Valencia San Vicente Martir, Valencia, Spain
| | | | - Alaa A.A. Aljabali
- Department of Pharmaceutics and Pharmaceutical, Yarmouk University, Irbid, Jordan
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Gaurav Chauhan
- School of Engineering and Sciences, Tecnologico de Monterrey, Monterrey, Mexico
| | - Parise Adadi
- Department of Food Science, University of Otago, University of Otago, Dunedin, New Zealand
| | - Murtaza Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine, UK
| | - Adam M. Brufsky
- Department of Medicine, Division of Hematology/Oncology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Wagner Baetas-da-Cruz
- Translational Laboratory in Molecular Physiology, Centre for Experimental Surgery, College of Medicine, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and 46 Applied Biotechnology (IIOAB), Nonakuri, India
| | - Vasco Azevedo
- Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Nikolas G. Bazan
- Neuroscience Center of Excellence, School of Medicine, LSU Health New Orleans, New Orleans, LA, United States
| | - Bruno Silva Andrade
- Laboratório de Bioinformática e Química Computacional, Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia, Jequié, Brazil
| | - Raner José Santana Silva
- Departamento de Ciencias Biologicas (DCB), Programa de Pos-Graduacao em Genetica e Biologia Molecular (PPGGBM), Universidade Estadual de Santa Cruz (UESC), Ilheus, Brazil
| | - Vladimir N. Uversky
- Department of Molecular Medicine, University of South Florida, Tampa, FL, United States
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14
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Santana de Carvalho D, Trovatti Uetanabaro AP, Kato RB, Aburjaile FF, Jaiswal AK, Profeta R, De Oliveira Carvalho RD, Tiwar S, Cybelle Pinto Gomide A, Almeida Costa E, Kukharenko O, Orlovska I, Podolich O, Reva O, Ramos PIP, De Carvalho Azevedo VA, Brenig B, Andrade BS, de Vera JPP, Kozyrovska NO, Barh D, Góes-Neto A. The Space-Exposed Kombucha Microbial Community Member Komagataeibacter oboediens Showed Only Minor Changes in Its Genome After Reactivation on Earth. Front Microbiol 2022; 13:782175. [PMID: 35369445 PMCID: PMC8970348 DOI: 10.3389/fmicb.2022.782175] [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: 09/23/2021] [Accepted: 02/01/2022] [Indexed: 11/23/2022] Open
Abstract
Komagataeibacter is the dominant taxon and cellulose-producing bacteria in the Kombucha Microbial Community (KMC). This is the first study to isolate the K. oboediens genome from a reactivated space-exposed KMC sample and comprehensively characterize it. The space-exposed genome was compared with the Earth-based reference genome to understand the genome stability of K. oboediens under extraterrestrial conditions during a long time. Our results suggest that the genomes of K. oboediens IMBG180 (ground sample) and K. oboediens IMBG185 (space-exposed) are remarkably similar in topology, genomic islands, transposases, prion-like proteins, and number of plasmids and CRISPR-Cas cassettes. Nonetheless, there was a difference in the length of plasmids and the location of cas genes. A small difference was observed in the number of protein coding genes. Despite these differences, they do not affect any genetic metabolic profile of the cellulose synthesis, nitrogen-fixation, hopanoid lipids biosynthesis, and stress-related pathways. Minor changes are only observed in central carbohydrate and energy metabolism pathways gene numbers or sequence completeness. Altogether, these findings suggest that K. oboediens maintains its genome stability and functionality in KMC exposed to the space environment most probably due to the protective role of the KMC biofilm. Furthermore, due to its unaffected metabolic pathways, this bacterial species may also retain some promising potential for space applications.
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Affiliation(s)
- Daniel Santana de Carvalho
- Laboratory of Molecular and Computational Biology of Fungi, Department of Microbiology, Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
- Laboratory of Cellular and Molecular Genetics, Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ana Paula Trovatti Uetanabaro
- Laboratory of Molecular and Computational Biology of Fungi, Department of Microbiology, Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
- Postgraduate Program in Biology and Biotechnology of Microorganisms, Department of Biological Sciences, State University of Santa Cruz, Ilhéus, Brazil
| | - Rodrigo Bentes Kato
- Laboratory of Molecular and Computational Biology of Fungi, Department of Microbiology, Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
- Laboratory of Cellular and Molecular Genetics, Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Flávia Figueira Aburjaile
- Laboratory of Cellular and Molecular Genetics, Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Arun Kumar Jaiswal
- Laboratory of Cellular and Molecular Genetics, Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Rodrigo Profeta
- Laboratory of Cellular and Molecular Genetics, Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Rodrigo Dias De Oliveira Carvalho
- Laboratory of Cellular and Molecular Genetics, Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Sandeep Tiwar
- Laboratory of Cellular and Molecular Genetics, Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Anne Cybelle Pinto Gomide
- Laboratory of Cellular and Molecular Genetics, Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Eduardo Almeida Costa
- Computational Biology and Biotechnological Information Management Center (NBCGIB), State University of Santa Cruz, Ilhéus, Brazil
| | - Olga Kukharenko
- Institute of Molecular Biology and Genetics of NASU, Kyiv, Ukraine
| | - Iryna Orlovska
- Institute of Molecular Biology and Genetics of NASU, Kyiv, Ukraine
| | - Olga Podolich
- Institute of Molecular Biology and Genetics of NASU, Kyiv, Ukraine
| | - Oleg Reva
- Department of Biochemistry, Genetics and Microbiology, Centre for Bioinformatics and Computational Biology, University of Pretoria, Pretoria, South Africa
| | - Pablo Ivan P. Ramos
- Center for Data and Knowledge Integration for Health (CIDACS), Institute Gonçalo Moniz, Oswaldo Cruz Foundation (FIOCRUZ-Bahia), Salvador, Brazil
| | - Vasco Ariston De Carvalho Azevedo
- Laboratory of Cellular and Molecular Genetics, Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Bertram Brenig
- Institute of Veterinary Medicine, Burckhardtweg, University of Göttingen, Göttingen, Germany
| | - Bruno Silva Andrade
- Laboratory of Bioinformatics and Computational Chemistry, Department of Biological Sciences, State University of Southwest Bahia (UESB), Jequié, Brazil
| | - Jean-Pierre P. de Vera
- German Aerospace Center (DLR) Berlin, Institute of Planetary Research, Planetary Laboratories, Astrobiological Laboratories, Berlin, Germany
| | | | - Debmalya Barh
- Laboratory of Cellular and Molecular Genetics, Department of Genetics, Ecology and Evolution, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology, Purba Medinipur, India
| | - Aristóteles Góes-Neto
- Laboratory of Molecular and Computational Biology of Fungi, Department of Microbiology, Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Brazil
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15
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Hassan SS, Kodakandla V, Redwan EM, Lundstrom K, Pal Choudhury P, Abd El-Aziz TM, Takayama K, Kandimalla R, Lal A, Serrano-Aroca Á, Azad GK, Aljabali AAA, Palù G, Chauhan G, Adadi P, Tambuwala M, Brufsky AM, Baetas-da-Cruz W, Barh D, Azevedo V, Bazan NG, Andrade BS, Santana Silva RJ, Uversky VN. An issue of concern: unique truncated ORF8 protein variants of SARS-CoV-2. PeerJ 2022. [PMID: 35341060 DOI: 10.1101/2021.05.25.445557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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] [Indexed: 04/15/2023] Open
Abstract
Open reading frame 8 (ORF8) shows one of the highest levels of variability among accessory proteins in Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of Coronavirus Disease 2019 (COVID-19). It was previously reported that the ORF8 protein inhibits the presentation of viral antigens by the major histocompatibility complex class I (MHC-I), which interacts with host factors involved in pulmonary inflammation. The ORF8 protein assists SARS-CoV-2 in evading immunity and plays a role in SARS-CoV-2 replication. Among many contributing mutations, Q27STOP, a mutation in the ORF8 protein, defines the B.1.1.7 lineage of SARS-CoV-2, engendering the second wave of COVID-19. In the present study, 47 unique truncated ORF8 proteins (T-ORF8) with the Q27STOP mutations were identified among 49,055 available B.1.1.7 SARS-CoV-2 sequences. The results show that only one of the 47 T-ORF8 variants spread to over 57 geo-locations in North America, and other continents, which include Africa, Asia, Europe and South America. Based on various quantitative features, such as amino acid homology, polar/non-polar sequence homology, Shannon entropy conservation, and other physicochemical properties of all specific 47 T-ORF8 protein variants, nine possible T-ORF8 unique variants were defined. The question as to whether T-ORF8 variants function similarly to the wild type ORF8 is yet to be investigated. A positive response to the question could exacerbate future COVID-19 waves, necessitating severe containment measures.
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Affiliation(s)
- Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, India
| | - Vaishnavi Kodakandla
- Department of Life sciences, Sophia College For Women, University of Mumbai, Mumbai, India
| | - Elrashdy M Redwan
- Faculty of Science, Department of Biological Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | | | - Tarek Mohamed Abd El-Aziz
- Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Kazuo Takayama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto, Japan
| | - Ramesh Kandimalla
- Applied Biology, CSIR-Indian Institute of Chemical Technology, Hyderabad, India
| | - Amos Lal
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic Rochester, Rochester, NY, United States
| | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Lab, Centro de Investigacion Traslacional San Alberto Magno, Universidad Catolica de Valencia San Vicente Martir, Valencia, Spain
| | | | - Alaa A A Aljabali
- Department of Pharmaceutics and Pharmaceutical, Yarmouk University, Irbid, Jordan
| | - Giorgio Palù
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - Gaurav Chauhan
- School of Engineering and Sciences, Tecnologico de Monterrey, Monterrey, Mexico
| | - Parise Adadi
- Department of Food Science, University of Otago, University of Otago, Dunedin, New Zealand
| | - Murtaza Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine, UK
| | - Adam M Brufsky
- Department of Medicine, Division of Hematology/Oncology, University of Pittsburgh School of Medicine, Pittsburgh, PA, United States
| | - Wagner Baetas-da-Cruz
- Translational Laboratory in Molecular Physiology, Centre for Experimental Surgery, College of Medicine, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and 46 Applied Biotechnology (IIOAB), Nonakuri, India
| | - Vasco Azevedo
- Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciencias Biologicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Nikolas G Bazan
- Neuroscience Center of Excellence, School of Medicine, LSU Health New Orleans, New Orleans, LA, United States
| | - Bruno Silva Andrade
- Laboratório de Bioinformática e Química Computacional, Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia, Jequié, Brazil
| | - Raner José Santana Silva
- Departamento de Ciencias Biologicas (DCB), Programa de Pos-Graduacao em Genetica e Biologia Molecular (PPGGBM), Universidade Estadual de Santa Cruz (UESC), Ilheus, Brazil
| | - Vladimir N Uversky
- Department of Molecular Medicine, University of South Florida, Tampa, FL, United States
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16
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Hassan SS, Lundstrom K, Barh D, Silva RJS, Andrade BS, Azevedo V, Choudhury PP, Palu G, Uhal BD, Kandimalla R, Seyran M, Lal A, Sherchan SP, Azad GK, Aljabali AAA, Brufsky AM, Serrano-Aroca Á, Adadi P, Abd El-Aziz TM, Redwan EM, Takayama K, Rezaei N, Tambuwala M, Uversky VN. Implications derived from S-protein variants of SARS-CoV-2 from six continents. Int J Biol Macromol 2021; 191:934-955. [PMID: 34571123 PMCID: PMC8462006 DOI: 10.1016/j.ijbiomac.2021.09.080] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 09/13/2021] [Accepted: 09/13/2021] [Indexed: 01/19/2023]
Abstract
The spike (S) protein is a critical determinant of the infectivity and antigenicity of SARS-CoV-2. Several mutations in the S protein of SARS-CoV-2 have already been detected, and their effect in immune system evasion and enhanced transmission as a cause of increased morbidity and mortality are being investigated. From pathogenic and epidemiological perspectives, S proteins are of prime interest to researchers. This study focused on the unique variants of S proteins from six continents: Asia, Africa, Europe, Oceania, South America, and North America. In comparison to the other five continents, Africa had the highest percentage of unique S proteins (29.1%). The phylogenetic relationship implies that unique S proteins from North America are significantly different from those of the other five continents. They are most likely to spread to the other geographic locations through international travel or naturally by emerging mutations. It is suggested that restriction of international travel should be considered, and massive vaccination as an utmost measure to combat the spread of the COVID-19 pandemic. It is also further suggested that the efficacy of existing vaccines and future vaccine development must be reviewed with careful scrutiny, and if needed, further re-engineered based on requirements dictated by new emerging S protein variants.
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Affiliation(s)
- Sk Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, Paschim Medinipur 721140, West Bengal, India.
| | | | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, WB, India; Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil.
| | - Raner Jośe Santana Silva
- Department of Biological Sciences (DCB), Graduate Program in Genetics and Molecular Biology (PPGGBM), State University of Santa Cruz (UESC), Rodovia Ilheus-Itabuna, km 16, 45662-900 Ilheus, BA, Brazil
| | - Bruno Silva Andrade
- Laboratory of Bioinformatics and Computational Chemistry, Department of Biological Sciences, State University of Southwest Bahia (UESB), Jequié 45206-190, Brazil.
| | - Vasco Azevedo
- Laborat'orio de Geńetica Celular e Molecular, Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciˆencias Biol'ogicas, Universidade Federal de Minas Gerais, Belo Horizonte CEP 31270-901, Brazil.
| | - Pabitra Pal Choudhury
- Applied Statistics Unit, Indian Statistical Institute, 203 B T Road, Kolkata 700108, India
| | - Giorgio Palu
- Department of Molecular Medicine, University of Padova, Via Gabelli 63, 35121 Padova, Italy.
| | - Bruce D Uhal
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA
| | - Ramesh Kandimalla
- Applied Biology, CSIR-Indian Institute of Chemical Technology, Uppal Road, Tarnaka, Hyderabad 500007, India; Department of Biochemistry, Kakatiya Medical College, Warangal, Telangana, India
| | - Murat Seyran
- Doctoral Studies in Natural and Technical Sciences (SPL 44), University of Vienna, W¨ahringer Straße, A-1090 Vienna, Austria
| | - Amos Lal
- Division of Pulmonary and Critical Care Medicine, Mayo Clinic, Rochester, MN, USA
| | - Samendra P Sherchan
- Department of Environmental Health Sciences, Tulane University, New Orleans, LA 70112, USA.
| | | | - Alaa A A Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Yarmouk University, Faculty of Pharmacy, Irbid 566, Jordan.
| | - Adam M Brufsky
- University of Pittsburgh School of Medicine, Department of Medicine, Division of Hematology/Oncology, UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
| | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Lab, Centro de Investigaci'on Traslacional San Alberto Magno, Universidad Cat́olica de Valencia San Vicente Ḿartir, c/Guillem de Castro, 94, 46001 Valencia, Spain.
| | - Parise Adadi
- Department of Food Science, University of Otago, Dunedin 9054, New Zealand
| | - Tarek Mohamed Abd El-Aziz
- Zoology Department, Faculty of Science, Minia University, El-Minia 61519, Egypt; Department of Cellular and Integrative Physiology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229-3900, USA.
| | - Elrashdy M Redwan
- Faculty of Science, Department of Biological Science, King Abdulazizi University, Jeddah 21589, Saudi Arabia; Therapeutic and Protective Proteins Laboratory, Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City for Scientific Research and Technology Applications, New Borg El-Arab, Alexandria 21934, Egypt.
| | - Kazuo Takayama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan.
| | - Nima Rezaei
- Research Center for Immunodeficiencies, Pediatrics Center of Excellence, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran; Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Stockholm, Sweden.
| | - Murtaza Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine BT52 1SA, Northern Ireland, UK.
| | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA; Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, Dolgoprudny, 141700, Russia.
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17
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Barh D, Tiwari S, Gabriel Rodrigues Gomes L, Weener ME, Alzahrani KJ, Alsharif KF, Aljabali AAA, Tambuwala MM, Lundstrom K, Hassan SS, Serrano-Aroca Á, Takayama K, Ghosh P, Redwan EM, Silva Andrade B, Soares SDC, Azevedo V, Uversky VN. Potential Molecular Mechanisms of Rare Anti-Tumor Immune Response by SARS-CoV-2 in Isolated Cases of Lymphomas. Viruses 2021; 13:v13101927. [PMID: 34696358 PMCID: PMC8539762 DOI: 10.3390/v13101927] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/07/2021] [Accepted: 09/22/2021] [Indexed: 12/12/2022] Open
Abstract
Recently, two cases of complete remission of classical Hodgkin lymphoma (cHL) and follicular lymphoma (FL) after SARS-CoV-2 infection were reported. However, the precise molecular mechanism of this rare event is yet to be understood. Here, we hypothesize a potential anti-tumor immune response of SARS-CoV-2 and based on a computational approach show that: (i) SARS-CoV-2 Spike-RBD may bind to the extracellular domains of CD15, CD27, CD45, and CD152 receptors of cHL or FL and may directly inhibit cell proliferation. (ii) Alternately, upon internalization after binding to these CD molecules, the SARS-CoV-2 membrane (M) protein and ORF3a may bind to gamma-tubulin complex component 3 (GCP3) at its tubulin gamma-1 chain (TUBG1) binding site. (iii) The M protein may also interact with TUBG1, blocking its binding to GCP3. (iv) Both the M and ORF3a proteins may render the GCP2-GCP3 lateral binding where the M protein possibly interacts with GCP2 at its GCP3 binding site and the ORF3a protein to GCP3 at its GCP2 interacting residues. (v) Interactions of the M and ORF3a proteins with these gamma-tubulin ring complex components potentially block the initial process of microtubule nucleation, leading to cell-cycle arrest and apoptosis. (vi) The Spike-RBD may also interact with and block PD-1 signaling similar to pembrolizumab and nivolumab- like monoclonal antibodies and may induce B-cell apoptosis and remission. (vii) Finally, the TRADD interacting “PVQLSY” motif of Epstein-Barr virus LMP-1, that is responsible for NF-kB mediated oncogenesis, potentially interacts with SARS-CoV-2 Mpro, NSP7, NSP10, and spike (S) proteins, and may inhibit the LMP-1 mediated cell proliferation. Taken together, our results suggest a possible therapeutic potential of SARS-CoV-2 in lymphoproliferative disorders.
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Affiliation(s)
- Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur 721172, West Bengal, India
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil; (S.T.); (L.G.R.G.); (V.A.)
- Correspondence:
| | - Sandeep Tiwari
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil; (S.T.); (L.G.R.G.); (V.A.)
| | - Lucas Gabriel Rodrigues Gomes
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil; (S.T.); (L.G.R.G.); (V.A.)
| | - Marianna E. Weener
- Clinical Research Center, Oftalmic, CRO, 119334 Bardina Str. 22/4, 119991 Moscow, Russia;
| | - Khalid J. Alzahrani
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (K.J.A.); (K.F.A.)
| | - Khalaf F. Alsharif
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia; (K.J.A.); (K.F.A.)
| | - Alaa A. A. Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Yarmouk University, Irbid 21163, Jordan;
| | - Murtaza M. Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine BT52 1SA, UK;
| | | | - Sk. Sarif Hassan
- Department of Mathematics, Pingla Thana Mahavidyalaya, Maligram, Paschim Medinipur 721140, West Bengal, India;
| | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Lab, Centro de Investigación Traslacional San Alberto Magno, Universidad Católica de Valencia San Vicente Mártir, 46001 Valencia, Spain;
| | - Kazuo Takayama
- Center for iPS Cell Research and Application (CiRA), Kyoto University, Kyoto 606-8507, Japan;
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA 23284, USA;
| | - Elrashdy M. Redwan
- Department of Biological Science, Faculty of Science, King Abdulazizi University, Jeddah 21589, Saudi Arabia;
| | - Bruno Silva Andrade
- Laboratory of Bioinformatics and Computational Chemistry, Department of Biological Sciences, State University of Southwest Bahia (UESB), Jequié 45206-190, Brazil;
| | - Siomar de Castro Soares
- Department of Immunology, Microbiology and Parasitology, Institute of Biological and Natural Sciences, Federal University of Triângulo Mineiro (UFTM), Uberaba 38025-180, Brazil;
| | - Vasco Azevedo
- Department of Genetics, Ecology and Evolution, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte 31270-901, Brazil; (S.T.); (L.G.R.G.); (V.A.)
| | - Vladimir N. Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer’s Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA;
- Research Center for Molecular Mechanisms of Aging and Age-Related Diseases, Moscow Institute of Physics and Technology, Institutskiy pereulok, 9, 141700 Dolgoprudny, Russia
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18
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Kumavath R, Barh D, Andrade BS, Imchen M, Aburjaile FF, Ch A, Rodrigues DLN, Tiwari S, Alzahrani KJ, Góes-Neto A, Weener ME, Ghosh P, Azevedo V. The Spike of SARS-CoV-2: Uniqueness and Applications. Front Immunol 2021; 12:663912. [PMID: 34305894 PMCID: PMC8297464 DOI: 10.3389/fimmu.2021.663912] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 06/16/2021] [Indexed: 12/20/2022] Open
Abstract
The Spike (S) protein of the SARS-CoV-2 virus is critical for its ability to attach and fuse into the host cells, leading to infection, and transmission. In this review, we have initially performed a meta-analysis of keywords associated with the S protein to frame the outline of important research findings and directions related to it. Based on this outline, we have reviewed the structure, uniqueness, and origin of the S protein of SARS-CoV-2. Furthermore, the interactions of the Spike protein with host and its implications in COVID-19 pathogenesis, as well as drug and vaccine development, are discussed. We have also summarized the recent advances in detection methods using S protein-based RT-PCR, ELISA, point-of-care lateral flow immunoassay, and graphene-based field-effect transistor (FET) biosensors. Finally, we have also discussed the emerging Spike mutants and the efficacy of the Spike-based vaccines against those strains. Overall, we have covered most of the recent advances on the SARS-CoV-2 Spike protein and its possible implications in countering this virus.
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Affiliation(s)
- Ranjith Kumavath
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, India
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, West Bengal, India
- Laboratório de Genética Celular e Molecular, Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Bruno Silva Andrade
- Laboratório de Bioinformática e Química Computacional, Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia (UESB), Jequié, Brazil
| | - Madangchanok Imchen
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, India
| | - Flavia Figueira Aburjaile
- Laboratório de Genética Celular e Molecular, Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Athira Ch
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, India
| | - Diego Lucas Neres Rodrigues
- Laboratório de Genética Celular e Molecular, Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Sandeep Tiwari
- Laboratório de Genética Celular e Molecular, Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Khalid J Alzahrani
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Aristóteles Góes-Neto
- Laboratório de Biologia Molecular e Computacional de Fungos, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | | | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, United States
| | - Vasco Azevedo
- Laboratório de Genética Celular e Molecular, Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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19
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Barh D, Aljabali AA, Tambuwala MM, Tiwari S, Serrano-Aroca Á, Alzahrani KJ, Silva Andrade B, Azevedo V, Ganguly NK, Lundstrom K. Predicting COVID-19-Comorbidity Pathway Crosstalk-Based Targets and Drugs: Towards Personalized COVID-19 Management. Biomedicines 2021; 9:556. [PMID: 34067609 PMCID: PMC8156524 DOI: 10.3390/biomedicines9050556] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 05/12/2021] [Accepted: 05/12/2021] [Indexed: 12/11/2022] Open
Abstract
It is well established that pre-existing comorbid conditions such as hypertension, diabetes, obesity, cardiovascular diseases (CVDs), chronic kidney diseases (CKDs), cancers, and chronic obstructive pulmonary disease (COPD) are associated with increased severity and fatality of COVID-19. The increased death from COVID-19 is due to the unavailability of a gold standard therapeutic and, more importantly, the lack of understanding of how the comorbid conditions and COVID-19 interact at the molecular level, so that personalized management strategies can be adopted. Here, using multi-omics data sets and bioinformatics strategy, we identified the pathway crosstalk between COVID-19 and diabetes, hypertension, CVDs, CKDs, and cancers. Further, shared pathways and hub gene-based targets for COVID-19 and its associated specific and combination of comorbid conditions are also predicted towards developing personalized management strategies. The approved drugs for most of these identified targets are also provided towards drug repurposing. Literature supports the involvement of our identified shared pathways in pathogenesis of COVID-19 and development of the specific comorbid condition of interest. Similarly, shared pathways- and hub gene-based targets are also found to have potential implementations in managing COVID-19 patients. However, the identified targets and drugs need further careful evaluation for their repurposing towards personalized treatment of COVID-19 cases having pre-existing specific comorbid conditions we have considered in this analysis. The method applied here may also be helpful in identifying common pathway components and targets in other disease-disease interactions too.
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Affiliation(s)
- Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur 721172, India
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (S.T.); (V.A.)
| | - Alaa A. Aljabali
- Department of Pharmaceutics and Pharmaceutical Technology, Faculty of Pharmacy, Yarmouk University, Irbid 21163, Jordan;
| | - Murtaza M. Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine BT52 1SA, UK;
| | - Sandeep Tiwari
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (S.T.); (V.A.)
| | - Ángel Serrano-Aroca
- Biomaterials and Bioengineering Lab, Centro de Investigación Traslacional San Alberto Magno, Universidad Católica de Valencia San Vicente Mártir, 46001 Valencia, Spain;
| | - Khalid J. Alzahrani
- Department of Clinical Laboratories Sciences, College of Applied Medical Sciences, Taif University, Taif 21944, Saudi Arabia;
| | - Bruno Silva Andrade
- Laboratório de Bioinformática e Química Computacional, Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia (UESB), Jequié 45206-190, Brazil;
| | - Vasco Azevedo
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil; (S.T.); (V.A.)
| | - Nirmal Kumar Ganguly
- National Institute of Immunology, Aruna Asaf Ali Marg, Jawaharlal Nehru University, New Delhi 110067, India;
- Institute of Liver and Biliary Science, New Delhi 110070, India
- Policy Center for Biomedical Research, Translational Health Science & Technology Institute, Faridabad 121001, India
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20
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Barh D, Tiwari S, Andrade BS, Weener ME, Góes-Neto A, Azevedo V, Ghosh P, Blum K, Ganguly NK. A novel multi-omics-based highly accurate prediction of symptoms, comorbid conditions, and possible long-term complications of COVID-19. Mol Omics 2021; 17:317-337. [PMID: 33683246 DOI: 10.1039/d0mo00189a] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Comprehensive clinical pictures, comorbid conditions, and long-term complications of COVID-19 are still unknown. Recently, using a multi-omics-based strategy, we predicted potential drugs for COVID-19 with ∼70% accuracy. Herein, using a novel multi-omics-based bioinformatic approach and three ways of analysis, we identified the symptoms, comorbid conditions, and short-, mid-, and possible long-term complications of COVID-19 with >90% precision including 27 parent, 170 child, and 403 specific conditions. Among the specific conditions, 36 viral, 53 short-term, 62 short-mid-long-term, 194 mid-long-term, and 57 congenital conditions are identified. At a threshold "count of occurrence" of 4, we found that 83-100% (average 92.67%) of enriched conditions are associated with COVID-19. Except for dry cough and loss of taste, all the other COVID-19-associated mild and severe symptoms are enriched. CVDs, and pulmonary, metabolic, musculoskeletal, neuropsychiatric, kidney, liver, and immune system disorders are top comorbid conditions. Specific diseases like myocardial infarction, hypertension, COPD, lung injury, diabetes, cirrhosis, mood disorders, dementia, macular degeneration, chronic kidney disease, lupus, arthritis, etc. along with several other NCDs were found to be top candidates. Interestingly, many cancers and congenital disorders associated with COVID-19 severity are also identified. Arthritis, gliomas, diabetes, psychiatric disorders, and CVDs having a bidirectional relationship with COVID-19 are also identified as top conditions. Based on our accuracy (>90%), the long-term presence of SARS-CoV-2 RNA in human, and our "genetic remittance" assumption, we hypothesize that all the identified top-ranked conditions could be potential long-term consequences in COVID-19 survivors, warranting long-term observational studies.
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Affiliation(s)
- Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, WB, India.
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21
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Andrade BS, Rangel FDS, Santos NO, Freitas ADS, Soares WRDA, Siqueira S, Barh D, Góes-Neto A, Birbrair A, Azevedo VADC. Repurposing Approved Drugs for Guiding COVID-19 Prophylaxis: A Systematic Review. Front Pharmacol 2020; 11:590598. [PMID: 33390967 PMCID: PMC7772842 DOI: 10.3389/fphar.2020.590598] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [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: 09/02/2020] [Accepted: 11/18/2020] [Indexed: 12/17/2022] Open
Abstract
The SARS-CoV-2 outbreak originally appeared in China in December 2019 and became a global pandemic in March 2020. This infectious disease has directly affected public health and the world economy. Several palliative therapeutic treatments and prophylaxis strategies have been used to control the progress of this viral infection, including pre-(PrEP) and post-exposure prophylaxis. On the other hand, research groups around the world are still studying novel drug prophylaxis and treatment using repurposing approaches, as well as vaccination options, which are in different pre-clinical and clinical testing phases. This systematic review evaluated 1,228 articles from the PubMed and Scopus indexing databases, following the Kitchenham bibliographic searching protocol, with the aim to list drug candidates, potentially approved to be used as new options for SARS-CoV-2 prophylaxis clinical trials and medical protocols. In searching protocol, we used the following keywords: "Covid-19 or SARS-CoV-2" or "Coronavirus or 2019 nCoV," "prophylaxis," "prophylactic," "pre-exposure," "COVID-19 or SARS-CoV-2 Chemoprophylaxis," "repurposed," "strategies," "clinical," "trials," "anti-SARS-CoV-2," "anti-covid-19," "Antiviral," "Therapy prevention in vitro," in cells "and" human testing. After all protocol steps, we selected 60 articles that included: 15 studies with clinical data, 22 studies that used in vitro experiments, seven studies using animal models, and 18 studies performed with in silico experiments. Additionally, we included more 22 compounds between FDA approved drugs and drug-like like molecules, which were tested in large-scale screenings, as well as those repurposed approved drugs with new mechanism of actions. The drugs selected in this review can assist clinical studies and medical guidelines on the rational repurposing of known antiviral drugs for COVID-19 prophylaxis.
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Affiliation(s)
- Bruno Silva Andrade
- Laboratório de Bioinformática e Química Computacional, Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia (UESB), Jequié, Brazil
| | - Fernanda de Souza Rangel
- Laboratório de Bioinformática e Química Computacional, Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia (UESB), Jequié, Brazil
- Programa de Pós-graduação em Genética e Biologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus, Brazil
| | - Naiane Oliveira Santos
- Programa de Pós-graduação em Genética e Biologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus, Brazil
| | - Andria dos Santos Freitas
- Laboratório de Bioinformática e Química Computacional, Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia (UESB), Jequié, Brazil
- Programa de Pós-graduação em Genética e Biologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus, Brazil
| | - Wagner Rodrigues de Assis Soares
- Laboratório de Bioinformática e Química Computacional, Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia (UESB), Jequié, Brazil
- Departamento de Saúde II, Universidade Estadual do Sudoeste da Bahia, Jequié, Brazil
| | - Sérgio Siqueira
- Laboratório de Bioinformática e Química Computacional, Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia (UESB), Jequié, Brazil
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Purba Medinipur, India
| | - Aristóteles Góes-Neto
- Laboratório de Biologia Molecular e Computacional de Fungos, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Alexander Birbrair
- Departamento de Patologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Brazil
| | - Vasco Ariston de Carvalho Azevedo
- Laboratório de Genética Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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Barh D, Silva Andrade B, Tiwari S, Giovanetti M, Góes-Neto A, Alcantara LCJ, Azevedo V, Ghosh P. Natural selection versus creation: a review on the origin of SARS-COV-2. Infez Med 2020; 28:302-311. [PMID: 32920565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
SARS-CoV-2 has created a global disaster by infecting millions of people and causing thousands of deaths across hundreds of countries. Currently, the infection is in its exponential phase in several countries and there is no sign of immediate relief from this deadly virus. At the same time, some "conspiracy theories" have arisen on the origin of this virus due to the lack of a "definite origin". To understand if this controversy is also reflected in scientific publications, here, we reviewed the key articles published at initial stages of the COVID-19 pandemic (January 01, 2020 to April 30, 2020) related to the zoonotic origin of SARS-CoV-2 and the articles opposing the "conspiracy theories". We also provide an overview on the current knowledge on SARS-CoV-2 Spike as well as the Coronavirus research domain. Furthermore, a few important points related to the "conspiracy theories" such as "laboratory engineering" or "bioweapon" aspects of SARS-CoV-2 are also reviewed. In this article, we have only considered the peer-reviewed publications that are indexed in PubMed and other official publications, and we have directly quoted the authors' statements from their respective articles to avoid any controversy.
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Affiliation(s)
- Debmalya Barh
- Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, WB, India
| | - Bruno Silva Andrade
- Laboratório de Bioinformática e Química Computacional, Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia (UESB), Jequié, Bahia, Brazil
| | - Sandeep Tiwari
- Laboratório de Genética Celular e Molecular, Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Marta Giovanetti
- Laboratório de Genética Celular e Molecular, Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil; Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Aristóteles Góes-Neto
- Laboratório de Biologia Molecular e Computacional de Fungos, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Luiz Carlos Junior Alcantara
- Laboratório de Genética Celular e Molecular, Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil; Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Vasco Azevedo
- Laboratório de Genética Celular e Molecular, Departamento de Genetica, Ecologia e Evolucao, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, 23284, USA
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23
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Barh D, Tiwari S, Silva Andrade B, Giovanetti M, Almeida Costa E, Kumavath R, Ghosh P, Góes-Neto A, Carlos Junior Alcantara L, Azevedo V. Potential chimeric peptides to block the SARS-CoV-2 spike receptor-binding domain. F1000Res 2020; 9:576. [PMID: 32802318 PMCID: PMC7411520 DOI: 10.12688/f1000research.24074.1] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/27/2020] [Indexed: 12/11/2022] Open
Abstract
Background: There are no known medicines or vaccines to control the COVID-19 pandemic caused by SARS-CoV-2 (nCoV). Antiviral peptides are superior to conventional drugs and may also be effective against COVID-19. Hence, we investigated the SARS-CoV-2 Spike receptor-binding domain (nCoV-RBD) that interacts with hACE2 for viral attachment and entry. Methods: Three strategies and bioinformatics approaches were employed to design potential nCoV-RBD - hACE2 interaction-blocking peptides that may restrict viral attachment and entry. Firstly, the key residues interacting with nCoV-RBD - hACE2 are identified and hACE2 sequence-based peptides are designed. Second, peptides from five antibacterial peptide databases that block nCoV-RBD are identified; finally, a chimeric peptide design approach is used to design peptides that can bind to key nCoV-RBD residues. The final peptides are selected based on their physiochemical properties, numbers and positions of key residues binding, binding energy, and antiviral properties. Results: We found that: (i) three amino acid stretches in hACE2 interact with nCoV-RBD; (ii) effective peptides must bind to three key positions of nCoV-RBD (Gly485/Phe486/Asn487, Gln493, and Gln498/Thr500/Asn501); (iii) Phe486, Gln493, and Asn501 are critical residues; (iv) AC20 and AC23 derived from hACE2 may block two key critical positions; (iv) DBP6 identified from databases can block the three sites of the nCoV-RBD and interacts with one critical position, Gln498; (v) seven chimeric peptides were considered promising, among which cnCoVP-3, cnCoVP-4, and cnCoVP-7 are the top three; and (vi) cnCoVP-4 meets all the criteria and is the best peptide. Conclusions: To conclude, using three different bioinformatics approaches, we identified 17 peptides that can potentially bind to the nCoV-RBD that interacts with hACE2. Binding these peptides to nCoV-RBD may potentially inhibit the virus to access hACE2 and thereby may prevent the infection. Out of 17, 10 peptides have promising potential and need further experimental validation.
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Affiliation(s)
- Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Nonakuri, Purba Medinipur, WB, India
| | - Sandeep Tiwari
- Laboratório de Genética Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Bruno Silva Andrade
- Laboratório de Bioinformática e Química Computacional, Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia (UESB), Jequié, Bahia, Brazil
| | - Marta Giovanetti
- Laboratório de Genética Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil.,Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Eduardo Almeida Costa
- Núcleo de Biologia Computacional e Gestão de Informações Biotecnológicas (NBCGIB), Universidade Estadual de Santa Cruz (UESC), Km 16, Salobrinho, Ilhéus, Bahia, CEP 45662-900, Brazil
| | - Ranjith Kumavath
- Department of Genomic Science, School of Biological Sciences, University of Kerala, Tejaswini Hills, Periya P.O, Kasaragod, Kerala, 671316, India
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Aristóteles Góes-Neto
- Laboratório de Biologia Molecular e Computacional de Fungos, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Luiz Carlos Junior Alcantara
- Laboratório de Genética Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil.,Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Vasco Azevedo
- Laboratório de Genética Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
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24
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Silva Andrade B, Ghosh P, Barh D, Tiwari S, José Santana Silva R, Rodrigues de Assis Soares W, Silva Melo T, Santos Freitas A, González-Grande P, Sousa Palmeira L, Carlos Junior Alcantara L, Giovanetti M, Góes-Neto A, Ariston de Carvalho Azevedo V. Computational screening for potential drug candidates against the SARS-CoV-2 main protease. F1000Res 2020; 9:ISCB Comm J-514. [PMID: 33447372 PMCID: PMC7780344 DOI: 10.12688/f1000research.23829.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/12/2020] [Indexed: 12/13/2022] Open
Abstract
Background: SARS-CoV-2 is the causal agent of the current coronavirus disease 2019 (COVID-19) pandemic. They are enveloped, positive-sense, single-stranded RNA viruses of the Coronaviridae family. Proteases of SARS-CoV-2 are necessary for viral replication, structural assembly, and pathogenicity. The approximately 33.8 kDa M pro protease of SARS-CoV-2 is a non-human homologue and is highly conserved among several coronaviruses, indicating that M pro could be a potential drug target for Coronaviruses. Methods: Herein, we performed computational ligand screening of four pharmacophores (OEW, remdesivir, hydroxychloroquine and N3) that are presumed to have positive effects against SARS-CoV-2 M pro protease (6LU7), and also screened 50,000 natural compounds from the ZINC Database dataset against this protease target. Results: We found 40 pharmacophore-like structures of natural compounds from diverse chemical classes that exhibited better affinity of docking as compared to the known ligands. The 11 best selected ligands, namely ZINC1845382, ZINC1875405, ZINC2092396, ZINC2104424, ZINC44018332, ZINC2101723, ZINC2094526, ZINC2094304, ZINC2104482, ZINC3984030, and ZINC1531664, are mainly classified as beta-carboline, alkaloids, and polyflavonoids, and all displayed interactions with dyad CYS145 and HIS41 from the protease pocket in a similar way as other known ligands. Conclusions: Our results suggest that these 11 molecules could be effective against SARS-CoV-2 protease and may be subsequently tested in vitro and in vivo to develop novel drugs against this virus.
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Affiliation(s)
- Bruno Silva Andrade
- Laboratório de Bioinformática e Química Computacional, Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia (UESB), Jequié, Bahia, 45205-490, Brazil
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Purba Medinipur, India
| | - Sandeep Tiwari
- Laboratório de Genética Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, MG, Brazil
| | - Raner José Santana Silva
- Programa de Pós-graduação em Genética e Biologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus, BA, Brazil
| | | | - Tarcisio Silva Melo
- Laboratório de Bioinformática e Química Computacional, Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia (UESB), Jequié, Bahia, 45205-490, Brazil
| | - Andria Santos Freitas
- Programa de Pós-graduação em Genética e Biologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus, BA, Brazil
| | - Patrícia González-Grande
- Programa de Pós-graduação em Genética e Biologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus, BA, Brazil
| | - Lucas Sousa Palmeira
- Laboratório de Bioinformática e Química Computacional, Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia (UESB), Jequié, Bahia, 45205-490, Brazil
| | - Luiz Carlos Junior Alcantara
- Laboratório de Genética Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, MG, Brazil
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Marta Giovanetti
- Laboratório de Genética Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, MG, Brazil
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Aristóteles Góes-Neto
- Laboratório de Biologia Molecular e Computacional de Fungos, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Vasco Ariston de Carvalho Azevedo
- Laboratório de Genética Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, MG, Brazil
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Silva Andrade B, Ghosh P, Barh D, Tiwari S, José Santana Silva R, Rodrigues de Assis Soares W, Silva Melo T, Santos Freitas A, González-Grande P, Sousa Palmeira L, Carlos Junior Alcantara L, Giovanetti M, Góes-Neto A, Ariston de Carvalho Azevedo V. Computational screening for potential drug candidates against the SARS-CoV-2 main protease. F1000Res 2020; 9:ISCB Comm J-514. [PMID: 33447372 PMCID: PMC7780344 DOI: 10.12688/f1000research.23829.2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/16/2020] [Indexed: 01/04/2023] Open
Abstract
Background: SARS-CoV-2 is the causal agent of the current coronavirus disease 2019 (COVID-19) pandemic. They are enveloped, positive-sense, single-stranded RNA viruses of the Coronaviridae family. Proteases of SARS-CoV-2 are necessary for viral replication, structural assembly, and pathogenicity. The approximately 33.8 kDa M pro protease of SARS-CoV-2 is a non-human homologue and is highly conserved among several coronaviruses, indicating that M pro could be a potential drug target for Coronaviruses. Methods: Herein, we performed computational ligand screening of four pharmacophores (OEW, remdesivir, hydroxychloroquine and N3) that are presumed to have positive effects against SARS-CoV-2 M pro protease (6LU7), and also screened 50,000 natural compounds from the ZINC Database dataset against this protease target. Results: We found 40 pharmacophore-like structures of natural compounds from diverse chemical classes that exhibited better affinity of docking as compared to the known ligands. The 11 best selected ligands, namely ZINC1845382, ZINC1875405, ZINC2092396, ZINC2104424, ZINC44018332, ZINC2101723, ZINC2094526, ZINC2094304, ZINC2104482, ZINC3984030, and ZINC1531664, are mainly classified as beta-carboline, alkaloids, and polyflavonoids, and all displayed interactions with dyad CYS145 and HIS41 from the protease pocket in a similar way as other known ligands. Conclusions: Our results suggest that these 11 molecules could be effective against SARS-CoV-2 protease and may be subsequently tested in vitro and in vivo to develop novel drugs against this virus.
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Affiliation(s)
- Bruno Silva Andrade
- Laboratório de Bioinformática e Química Computacional, Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia (UESB), Jequié, Bahia, 45205-490, Brazil
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, VA, 23284, USA
| | - Debmalya Barh
- Centre for Genomics and Applied Gene Technology, Institute of Integrative Omics and Applied Biotechnology (IIOAB), Purba Medinipur, India
| | - Sandeep Tiwari
- Laboratório de Genética Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, MG, Brazil
| | - Raner José Santana Silva
- Programa de Pós-graduação em Genética e Biologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus, BA, Brazil
| | | | - Tarcisio Silva Melo
- Laboratório de Bioinformática e Química Computacional, Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia (UESB), Jequié, Bahia, 45205-490, Brazil
| | - Andria Santos Freitas
- Programa de Pós-graduação em Genética e Biologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus, BA, Brazil
| | - Patrícia González-Grande
- Programa de Pós-graduação em Genética e Biologia Molecular, Universidade Estadual de Santa Cruz, Ilhéus, BA, Brazil
| | - Lucas Sousa Palmeira
- Laboratório de Bioinformática e Química Computacional, Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia (UESB), Jequié, Bahia, 45205-490, Brazil
| | - Luiz Carlos Junior Alcantara
- Laboratório de Genética Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, MG, Brazil
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Marta Giovanetti
- Laboratório de Genética Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, MG, Brazil
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Aristóteles Góes-Neto
- Laboratório de Biologia Molecular e Computacional de Fungos, Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG, Brazil
| | - Vasco Ariston de Carvalho Azevedo
- Laboratório de Genética Celular e Molecular, Departamento de Biologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, MG, Brazil
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Martins Alves AM, Pereira Menezes S, Matos Lima E, Peres Gramacho K, Silva Andrade B, Macêdo Ferreira M, Pirovani CP, Micheli F. The selenium-binding protein of Theobroma cacao: A thermostable protein involved in the witches' broom disease resistance. Plant Physiol Biochem 2019; 142:472-481. [PMID: 31430675 DOI: 10.1016/j.plaphy.2019.08.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 06/23/2019] [Accepted: 08/08/2019] [Indexed: 06/10/2023]
Abstract
The selenium-binding proteins are known to be inducers of apoptosis in human and animals, and have been studied as target for the treatment of various types of cancer. In plants, SBP expression has been related to abiotic and biotic stress resistance. The SBP from Theobroma cacao (TcSBP) was first identified from a cocoa-Moniliophthora perniciosa cDNA library. The present study provides details on the TcSBP gene and protein structure. Multiple alignments revealed conserved domains between SBP from plants, human and archea. Homology modeling and molecular docking were performed and showed that the TcSBP has affinity to selenite in the active CSSC site. This result was confirmed by circular dichroism of the recombinant TcSBP, which also presented thermostable behavior. RT-qPCR analysis showed that TcSBP was differentially expressed in resistant vs susceptible cacao varieties inoculated by M. perniciosa and its expression was probably due to hormone induction via cis-regulating elements present in its promotor. The presence of the CSSC domain suggested that TcSBP acted by altering oxidation/reduction of proteins during H2O2 production and programmed cell death in the final stages of the witches' broom disease. To our knowledge, this is the first in silico and in vitro analysis of the SBP from cacao.
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Affiliation(s)
- Akyla Maria Martins Alves
- Universidade Estadual de Santa Cruz (UESC), Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Rodovia Ilhéus-Itabuna, km 16, 45662-900, Ilhéus-BA, Brazil
| | - Sara Pereira Menezes
- Universidade Estadual de Santa Cruz (UESC), Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Rodovia Ilhéus-Itabuna, km 16, 45662-900, Ilhéus-BA, Brazil
| | - Eline Matos Lima
- Universidade Estadual de Santa Cruz (UESC), Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Rodovia Ilhéus-Itabuna, km 16, 45662-900, Ilhéus-BA, Brazil
| | | | - Bruno Silva Andrade
- Universidade Estadual do Sudoeste da Bahia (UESB), Av. José Moreira Sobrinho, Jequié, Bahia, 45206-190, Brazil
| | - Monaliza Macêdo Ferreira
- Universidade Estadual de Santa Cruz (UESC), Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Rodovia Ilhéus-Itabuna, km 16, 45662-900, Ilhéus-BA, Brazil
| | - Carlos Priminho Pirovani
- Universidade Estadual de Santa Cruz (UESC), Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Rodovia Ilhéus-Itabuna, km 16, 45662-900, Ilhéus-BA, Brazil
| | - Fabienne Micheli
- Universidade Estadual de Santa Cruz (UESC), Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Rodovia Ilhéus-Itabuna, km 16, 45662-900, Ilhéus-BA, Brazil; CIRAD, UMR AGAP, F-34398, Montpellier, France.
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Araújo Castro J, Gomes Ferreira MD, Santana Silva RJ, Andrade BS, Micheli F. Alternative oxidase (AOX) constitutes a small family of proteins in Citrus clementina and Citrus sinensis L. Osb. PLoS One 2017; 12:e0176878. [PMID: 28459876 PMCID: PMC5411082 DOI: 10.1371/journal.pone.0176878] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 04/18/2017] [Indexed: 11/18/2022] Open
Abstract
The alternative oxidase (AOX) protein is present in plants, fungi, protozoa and some invertebrates. It is involved in the mitochondrial respiratory chain, providing an alternative route for the transport of electrons, leading to the reduction of oxygen to form water. The present study aimed to characterize the family of AOX genes in mandarin (Citrus clementina) and sweet orange (Citrus sinensis) at nucleotide and protein levels, including promoter analysis, phylogenetic analysis and C. sinensis gene expression. This study also aimed to do the homology modeling of one AOX isoform (CcAOXd). Moreover, the molecular docking of the CcAOXd protein with the ubiquinone (UQ) was performed. Four AOX genes were identified in each citrus species. These genes have an open reading frame (ORF) ranging from 852 bp to 1150 bp and a number of exons ranging from 4 to 9. The 1500 bp-upstream region of each AOX gene contained regulatory cis-elements related to internal and external response factors. CsAOX genes showed a differential expression in citrus tissues. All AOX proteins were predicted to be located in mitochondria. They contained the conserved motifs LET, NERMHL, LEEEA and RADE-H as well as several putative post-translational modification sites. The CcAOXd protein was modeled by homology to the AOX of Trypanosona brucei (45% of identity). The 3-D structure of CcAOXd showed the presence of two hydrophobic helices that could be involved in the anchoring of the protein in the inner mitochondrial membrane. The active site of the protein is located in a hydrophobic environment deep inside the AOX structure and contains a diiron center. The molecular docking of CcAOXd with UQ showed that the binding site is a recessed pocket formed by the helices and submerged in the membrane. These data are important for future functional studies of citrus AOX genes and/or proteins, as well as for biotechnological approaches leading to AOX inhibition using UQ homologs.
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Affiliation(s)
- Jacqueline Araújo Castro
- Universidade Estadual de Santa Cruz (UESC), Centro de Biotecnologia e Genética (CBG), Ilhéus, Bahia, Brazil
- Instituto Federal de Educação, Ciência e Tecnologia Baiano (IFBaiano), Santa Inês, Bahia, Brazil
| | | | - Raner José Santana Silva
- Universidade Estadual de Santa Cruz (UESC), Centro de Biotecnologia e Genética (CBG), Ilhéus, Bahia, Brazil
| | - Bruno Silva Andrade
- Universidade Estadual Sudoeste da Bahia (UESB), Av. José Moreira Sobrinho, Jequié, Bahia, Brazil
| | - Fabienne Micheli
- Universidade Estadual de Santa Cruz (UESC), Centro de Biotecnologia e Genética (CBG), Ilhéus, Bahia, Brazil
- CIRAD, UMR AGAP, F-34398 Montpellier, France
- * E-mail:
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Andrade BS, Souza CS, Santos G, Góes-Neto A. Virtual screening reveals a viral-like polymerase inhibitor that complexes with the DNA polymerase of Moniliophthora perniciosa. Genet Mol Res 2016; 15:gmr8190. [PMID: 27323084 DOI: 10.4238/gmr.15028190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The filamentous fungus Moniliophthora perniciosa is a basidiomycota that causes the witches' broom disease in cocoa trees (Theobroma cacao L.). The mitochondrial DNA polymerase of M. perniciosa (MpmitDNApol) is classified within the B family of DNA polymerases, which can be found in viruses and cellular organelles. Using virtual screening processes, accessing KEGG, PubChem, and ZINC databases, we selected the 27 best putative nucleoside viral-like polymerase inhibitors to test against MpmitDNApol. We used Autodock Vina to perform docking simulations of the selected molecules and to return energy values in several ligand conformations. Then, we used Pymol v1.7.4.4 to check the stereochemistry of chiral carbons, hydrogen bonding receptors, absence or presence of hydrogen, sub and superstructure, numbers of rings, rotatable bonds, and donor groups. We selected the Entecavir Hydrate, a drug used to control hepatitis B; subsequently AMBER 14 was used to describe the behavior of polymerase-entecavir complex after setting up 3500 ps of simulation in water at a temperature of 300 K. From the simulation, a graph of Potential Energy was generated revealing that the ligand remains in the catalytic site after 3500 ps with a final energy of -612,587.4214 kcal/mol.
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Affiliation(s)
- B S Andrade
- Departamento de Biologia, Universidade Estadual do Sudoeste da Bahia, Jequié, BA, Brasil.,Programa de Pós-Graduação em Biotecnologia, Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Novo Horizonte, Feira de Santana, BA, Brasil
| | - C S Souza
- Laboratório de Modelagem Molecular, Departamento de Saúde, Universidade Estadual de Feira de Santana, Novo Horizonte, Feira de Santana, BA, Brasil.,Programa de Pós-Graduação em Biotecnologia, Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Novo Horizonte, Feira de Santana, BA, Brasil
| | - G Santos
- Departamento de Biologia, Universidade Estadual do Sudoeste da Bahia, Jequié, BA, Brasil
| | - A Góes-Neto
- Programa de Pós-Graduação em Biotecnologia, Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Novo Horizonte, Feira de Santana, BA, Brasil
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Andrade BS, Góes-Neto A. Phylogenetic analysis of DNA and RNA polymerases from a Moniliophthora perniciosa mitochondrial plasmid reveals probable lateral gene transfer. Genet Mol Res 2015; 14:14105-14. [PMID: 26535725 DOI: 10.4238/2015.october.29.30] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
The filamentous fungus Moniliophthora perniciosa is a hemibiotrophic basidiomycete that causes witches' broom disease of cacao (Theobroma cacao L.). Many fungal mitochondrial plasmids are DNA and RNA polymerase-encoding invertrons with terminal inverted repeats and 5'-linked proteins. The aim of this study was to carry out comparative and phylogenetic analyses of DNA and RNA polymerases for all known linear mitochondrial plasmids in fungi. We performed these analyses at both gene and protein levels and assessed differences between fungal and viral polymerases in order to test the lateral gene transfer (LGT) hypothesis. We analyzed all mitochondrial plasmids of the invertron type within the fungal clade, including five from Ascomycota, seven from Basidiomycota, and one from Chytridiomycota. All phylogenetic analyses generated similar tree topologies regardless of the methods and datasets used. It is likely that DNA and RNA polymerase genes were inserted into the mitochondrial genomes of the 13 fungal species examined in our study as a result of different LGT events. These findings are important for a better understanding of the evolutionary relationships between fungal mitochondrial plasmids.
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Affiliation(s)
- B S Andrade
- Departamento de Ciências Biológicas, Universidade Estadual do Sudoeste da Bahia, Jequié, BA, Brasil
| | - A Góes-Neto
- Laboratório de Pesquisa em Microbiologia, Departamento de Ciências Biológicas, Universidade Estadual de Feira de Santana, Feira de Santana, BA, Brasil
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Pereira Menezes S, de Andrade Silva EM, Matos Lima E, Oliveira de Sousa A, Silva Andrade B, Santos Lima Lemos L, Peres Gramacho K, da Silva Gesteira A, Pirovani CP, Micheli F. The pathogenesis-related protein PR-4b from Theobroma cacao presents RNase activity, Ca(2+) and Mg(2+) dependent-DNase activity and antifungal action on Moniliophthora perniciosa. BMC Plant Biol 2014; 14:161. [PMID: 24920373 PMCID: PMC4079191 DOI: 10.1186/1471-2229-14-161] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2014] [Accepted: 06/06/2014] [Indexed: 05/08/2023]
Abstract
BACKGROUND The production and accumulation of pathogenesis-related proteins (PR proteins) in plants in response to biotic or abiotic stresses is well known and is considered as a crucial mechanism for plant defense. A pathogenesis-related protein 4 cDNA was identified from a cacao-Moniliophthora perniciosa interaction cDNA library and named TcPR-4b. RESULTS TcPR-4b presents a Barwin domain with six conserved cysteine residues, but lacks the chitin-binding site. Molecular modeling of TcPR-4b confirmed the importance of the cysteine residues to maintain the protein structure, and of several conserved amino acids for the catalytic activity. In the cacao genome, TcPR-4b belonged to a small multigene family organized mainly on chromosome 5. TcPR-4b RT-qPCR analysis in resistant and susceptible cacao plants infected by M. perniciosa showed an increase of expression at 48 hours after infection (hai) in both cacao genotypes. After the initial stage (24-72 hai), the TcPR-4b expression was observed at all times in the resistant genotypes, while in the susceptible one the expression was concentrated at the final stages of infection (45-90 days after infection). The recombinant TcPR-4b protein showed RNase, and bivalent ions dependent-DNase activity, but no chitinase activity. Moreover, TcPR-4b presented antifungal action against M. perniciosa, and the reduction of M. perniciosa survival was related to ROS production in fungal hyphae. CONCLUSION To our knowledge, this is the first report of a PR-4 showing simultaneously RNase, DNase and antifungal properties, but no chitinase activity. Moreover, we showed that the antifungal activity of TcPR-4b is directly related to RNase function. In cacao, TcPR-4b nuclease activities may be related to the establishment and maintenance of resistance, and to the PCD mechanism, in resistant and susceptible cacao genotypes, respectively.
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Affiliation(s)
- Sara Pereira Menezes
- Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Universidade Estadual de Santa Cruz (UESC), Rodovia Ilhéus-Itabuna, km 16, 45662-900 Ilhéus, BA, Brazil
| | - Edson Mario de Andrade Silva
- Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Universidade Estadual de Santa Cruz (UESC), Rodovia Ilhéus-Itabuna, km 16, 45662-900 Ilhéus, BA, Brazil
| | - Eline Matos Lima
- Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Universidade Estadual de Santa Cruz (UESC), Rodovia Ilhéus-Itabuna, km 16, 45662-900 Ilhéus, BA, Brazil
| | - Aurizângela Oliveira de Sousa
- Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Universidade Estadual de Santa Cruz (UESC), Rodovia Ilhéus-Itabuna, km 16, 45662-900 Ilhéus, BA, Brazil
| | - Bruno Silva Andrade
- Universidade Estadual do Sudoeste da Bahia (UESB), Av. José Moreira Sobrinho, Jequié, Bahia 45206-190, Brazil
| | | | | | - Abelmon da Silva Gesteira
- Departamento de Biologia Molecular, Embrapa Mandioca e Fruticultura, Rua Embrapa, s/n°, CEP44380-000 Cruz das Almas, Bahia, Brazil
| | - Carlos Priminho Pirovani
- Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Universidade Estadual de Santa Cruz (UESC), Rodovia Ilhéus-Itabuna, km 16, 45662-900 Ilhéus, BA, Brazil
| | - Fabienne Micheli
- Departamento de Ciências Biológicas (DCB), Centro de Biotecnologia e Genética (CBG), Universidade Estadual de Santa Cruz (UESC), Rodovia Ilhéus-Itabuna, km 16, 45662-900 Ilhéus, BA, Brazil
- CIRAD, UMR AGAP, F-34398 Montpellier, France
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31
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Andrade BS, Villela-Dias C, Gomes DS, Micheli F, Góes-Neto A. DNA and RNA polymerase activity in a Moniliophthora perniciosa mitochondrial plasmid and self-defense against oxidative stress. Genet Mol Res 2013; 12:1944-50. [PMID: 23913377 DOI: 10.4238/2013.june.13.3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Moniliophthora perniciosa (Stahel) Aime and Phillips-Mora is a hemibiotrophic basidiomycete (Agaricales, Tricholomataceae) that causes witches' broom disease in cocoa (Theobroma cacao L.). This pathogen carries a stable integrated invertron-type linear plasmid in its mitochondrial genome that encodes viral-like DNA and RNA polymerases related to fungal senescence and longevity. After culturing the fungus and obtaining its various stages of development in triplicate, we carried out total RNA extraction and subsequent complementary DNA synthesis. To analyze DNA and RNA polymerase expression levels, we performed real-time reverse transcriptase polymerase chain reaction for various fungal phases of development. Our results showed that DNA and RNA polymerase gene expression in the primordium phase of M. perniciosa is related to a potential defense mechanism against T. cacao oxidative attack.
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Affiliation(s)
- B S Andrade
- Laboratório de Bioinformática, Departamento de Biologia, Universidade Estadual do Sudoeste da Bahia, Jequié, BA, Brasil.
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