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Elrashedy A, Nayel M, Salama A, Salama MM, Hasan ME. Bioinformatics approach for structure modeling, vaccine design, and molecular docking of Brucella candidate proteins BvrR, OMP25, and OMP31. Sci Rep 2024; 14:11951. [PMID: 38789443 PMCID: PMC11126717 DOI: 10.1038/s41598-024-61991-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 05/13/2024] [Indexed: 05/26/2024] Open
Abstract
Brucellosis is a zoonotic disease with significant economic and healthcare costs. Despite the eradication efforts, the disease persists. Vaccines prevent disease in animals while antibiotics cure humans with limitations. This study aims to design vaccines and drugs for brucellosis in animals and humans, using protein modeling, epitope prediction, and molecular docking of the target proteins (BvrR, OMP25, and OMP31). Tertiary structure models of three target proteins were constructed and assessed using RMSD, TM-score, C-score, Z-score, and ERRAT. The best models selected from AlphaFold and I-TASSER due to their superior performance according to CASP 12 - CASP 15 were chosen for further analysis. The motif analysis of best models using MotifFinder revealed two, five, and five protein binding motifs, however, the Motif Scan identified seven, six, and eight Post-Translational Modification sites (PTMs) in the BvrR, OMP25, and OMP31 proteins, respectively. Dominant B cell epitopes were predicted at (44-63, 85-93, 126-137, 193-205, and 208-237), (26-46, 52-71, 98-114, 142-155, and 183-200), and (29-45, 58-82, 119-142, 177-198, and 222-251) for the three target proteins. Additionally, cytotoxic T lymphocyte epitopes were detected at (173-181, 189-197, and 202-210), (61-69, 91-99, 159-167, and 181-189), and (3-11, 24-32, 167-175, and 216-224), while T helper lymphocyte epitopes were displayed at (39-53, 57-65, 150-158, 163-171), (79-87, 95-108, 115-123, 128-142, and 189-197), and (39-47, 109-123, 216-224, and 245-253), for the respective target protein. Furthermore, structure-based virtual screening of the ZINC and DrugBank databases using the docking MOE program was followed by ADMET analysis. The best five compounds of the ZINC database revealed docking scores ranged from (- 16.8744 to - 15.1922), (- 16.0424 to - 14.1645), and (- 14.7566 to - 13.3222) for the BvrR, OMP25, and OMP31, respectively. These compounds had good ADMET parameters and no cytotoxicity, while DrugBank compounds didn't meet Lipinski's rule criteria. Therefore, the five selected compounds from the ZINC20 databases may fulfill the pharmacokinetics and could be considered lead molecules for potentially inhibiting Brucella's proteins.
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Affiliation(s)
- Alyaa Elrashedy
- Department of Animal Medicine and Infectious Diseases (Infectious Diseases), Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Egypt.
| | - Mohamed Nayel
- Department of Animal Medicine and Infectious Diseases (Infectious Diseases), Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Egypt
| | - Akram Salama
- Department of Animal Medicine and Infectious Diseases (Infectious Diseases), Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Egypt
| | - Mohammed M Salama
- Physics Department, Medical Biophysics Division, Faculty of Science, Helwan University, Cairo, Egypt
| | - Mohamed E Hasan
- Bioinformatics Department, Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City, Egypt
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Development of a Monoclonal Antibody to a Vibriophage as a Proxy for Vibrio cholerae Detection. Infect Immun 2022; 90:e0016122. [PMID: 35862704 PMCID: PMC9387236 DOI: 10.1128/iai.00161-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Cholera is an acute watery, diarrheal disease that causes high rates of morbidity and mortality without treatment. Early detection of the etiologic agent of toxigenic Vibrio cholerae is important to mobilize treatment and mitigate outbreaks. Monoclonal antibody (mAb) based rapid diagnostic tests (RDTs) enable early detection in settings without laboratory capacity. However, the odds of an RDT testing positive are reduced by nearly 90% when the common virulent bacteriophage ICP1 is present. We hypothesize that adding a mAb for the common, and specific, virulent bacteriophage ICP1 as a proxy for V. cholerae to an RDT will increase diagnostic sensitivity when virulent ICP1 phage is present. In this study, we used an in-silico approach to identify immunogenic ICP1 protein targets that were conserved across disparate time periods and locations. Specificity of targets to cholera patients with known ICP1 was determined, and specific targets were used to produce mAbs in a murine model. Candidate mAbs to the head protein demonstrated specificity to ICP1 by Enzyme linked immunosorbent assay (ELISA) and an ICP1 phage neutralization assay. The limit of detection of the final mAb candidate for ICP1 phage particles spiked into cholera stool matrix was 8 × 105 PFU by Western blotting analysis. This mAb will be incorporated into a RDT prototype for evaluation in a future diagnostic study to test the guiding hypothesis behind this study.
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Sulong P, Anudit N, Nuanualsuwan S, Mariela S, Khantasup K. Application of phage display technology for the production of antibodies against Streptococcus suis serotype 2. PLoS One 2021; 16:e0258931. [PMID: 34699547 PMCID: PMC8547629 DOI: 10.1371/journal.pone.0258931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 10/08/2021] [Indexed: 11/20/2022] Open
Abstract
Streptococcus suis (S. suis) serotype 2 infection is a problem in the swine industry and responsible for most cases of human infection worldwide. Since current multiplex PCR cannot differentiate between serotypes 2 and 1/2, then serotype-specific antibodies (Abs) are required for serotype identification to confirm infection by serotype 2. This study aimed to generate Abs specific to S. suis serotype 2 by phage display from a human heavy chain variable domain (VH) antibody library. For biopanning, whole cells of S. suis serotype 2 were used as the target antigen. With increasing selection stringency, we could select the VH Abs that specifically bound to a S. suis serotype 2 surface antigen, which was identified as the capsular polysaccharide (CPS). From ELISA analysis, the specific phage clone 47B3 VH with the highest binding activity to S. suis serotype 2 was selected and shown to have no cross-reactivity with S. suis serotypes 1/2, 1, and 14 that shared a common epitope with serotype 2 and occasionally cause infections in human. Moreover, no cross-reactivity with other bacteria that can be found in septic blood specimens was also observed. Then, 47B3 VH was successfully expressed as soluble 47B3 VH in E. coli TG1. The soluble 47B3 VH crude extract was further tested for its binding ability in a dose-dependent ELISA assay. The results indicated that the activity of phage clone 47B3 was still retained even when the Ab occurred in the soluble form. A quellung reaction demonstrated that the soluble 47B3 VH Ab could show bioactivity by differentiation between S. suis serotypes 2 and 1/2. Thus, it will be beneficial to use this VH Ab in the diagnosis of disease or discrimination of S. suis serotypes Furthermore, the results described here could motivate the use of phage display VH platform to produce serotyping antibodies.
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Affiliation(s)
- Pattarawadee Sulong
- The Medical Microbiology Program, Graduate School, Chulalongkorn University, Bangkok, Thailand
| | - Natsinee Anudit
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Suphachai Nuanualsuwan
- Department of Veterinary Public Health, Faculty of Veterinary Sciences, Chulalongkorn University, Bangkok, Thailand
- Food Risk Hub, Research Unit of Chulalongkorn University, Bangkok, Thailand
| | - Segura Mariela
- Laboratory of Immunology, Faculty of Veterinary Medicine, University of Montreal, St-Hyacinthe, Quebec, Canada
| | - Kannika Khantasup
- Department of Biochemistry and Microbiology, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
- Food Risk Hub, Research Unit of Chulalongkorn University, Bangkok, Thailand
- Vaccines and Therapeutic Proteins Research Group, the Special Task Force for Activating Research (STAR), Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, Thailand
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Thibau A, Dichter AA, Vaca DJ, Linke D, Goldman A, Kempf VAJ. Immunogenicity of trimeric autotransporter adhesins and their potential as vaccine targets. Med Microbiol Immunol 2020; 209:243-263. [PMID: 31788746 PMCID: PMC7247748 DOI: 10.1007/s00430-019-00649-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 11/19/2019] [Indexed: 12/15/2022]
Abstract
The current problem of increasing antibiotic resistance and the resurgence of numerous infections indicate the need for novel vaccination strategies more than ever. In vaccine development, the search for and the selection of adequate vaccine antigens is the first important step. In recent years, bacterial outer membrane proteins have become of major interest, as they are the main proteins interacting with the extracellular environment. Trimeric autotransporter adhesins (TAAs) are important virulence factors in many Gram-negative bacteria, are localised on the bacterial surface, and mediate the first adherence to host cells in the course of infection. One example is the Neisseria adhesin A (NadA), which is currently used as a subunit in a licensed vaccine against Neisseria meningitidis. Other TAAs that seem promising vaccine candidates are the Acinetobacter trimeric autotransporter (Ata), the Haemophilus influenzae adhesin (Hia), and TAAs of the genus Bartonella. Here, we review the suitability of various TAAs as vaccine candidates.
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Affiliation(s)
- Arno Thibau
- Institute for Medical Microbiology and Infection Control, University Hospital, Goethe-University, Paul-Ehrlich-Str. 40, 60596 Frankfurt am Main, Germany
| | - Alexander A. Dichter
- Institute for Medical Microbiology and Infection Control, University Hospital, Goethe-University, Paul-Ehrlich-Str. 40, 60596 Frankfurt am Main, Germany
| | - Diana J. Vaca
- Institute for Medical Microbiology and Infection Control, University Hospital, Goethe-University, Paul-Ehrlich-Str. 40, 60596 Frankfurt am Main, Germany
| | - Dirk Linke
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | - Adrian Goldman
- Astbury Centre for Structural Molecular Biology, School of Biomedical Sciences, University of Leeds, Leeds, UK
- Molecular and Integrative Biosciences Program, University of Helsinki, Helsinki, Finland
| | - Volkhard A. J. Kempf
- Institute for Medical Microbiology and Infection Control, University Hospital, Goethe-University, Paul-Ehrlich-Str. 40, 60596 Frankfurt am Main, Germany
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Forde TL, Kollanandi Ratheesh N, Harvey WT, Thomson JR, Williamson S, Biek R, Opriessnig T. Genomic and Immunogenic Protein Diversity of Erysipelothrix rhusiopathiae Isolated From Pigs in Great Britain: Implications for Vaccine Protection. Front Microbiol 2020; 11:418. [PMID: 32231655 PMCID: PMC7083082 DOI: 10.3389/fmicb.2020.00418] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 02/27/2020] [Indexed: 12/30/2022] Open
Abstract
Erysipelas, caused by the bacterium Erysipelothrix rhusiopathiae, is re-emerging in swine and poultry production systems worldwide. While the global genomic diversity of this species has been characterized, how much of this genomic and functional diversity is maintained at smaller scales is unclear. Specifically, while several key immunogenic surface proteins have been identified for E. rhusiopathiae, little is known about their presence among field strains and their divergence from vaccines, which could result in vaccine failure. Here, a comparative genomics approach was taken to determine the diversity of E. rhusiopathiae strains in pigs in Great Britain over nearly three decades, as well as to assess the field strains’ divergence from the vaccine strain most commonly used in British pigs. In addition, the presence/absence and variability of 13 previously described immunogenic surface proteins was determined, including SpaA which is considered a key immunogen. We found a high diversity of E. rhusiopathiae strains in British pigs, similar to the situation described in European poultry but in contrast to swine production systems in Asia. Of the four clades of E. rhusiopathiae found globally, three were represented among British pig isolates, with Clade 2 being the most common. All British pig isolates had one amino acid difference in the immunoprotective domain of the SpaA protein compared to the vaccine strain. However, we were able to confirm using in silico structural protein analyses that this difference is unlikely to compromise vaccine protection. Of 12 other known immunogenic surface proteins of E. rhusiopathiae examined, 11 were found to be present in all British pig isolates and the vaccine strain, but with highly variable degrees of conservation at the amino acid sequence level, ranging from 0.3 to 27% variant positions. Moreover, the phylogenetic incongruence of these proteins suggests that horizontal transfer of genes encoding for antigens is commonplace for this bacterium. We hypothesize that the sequence variants in these proteins could be responsible for differences in the efficacy of the immune response. Our results provide the necessary basis for testing this hypothesis through in vitro and in vivo studies.
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Affiliation(s)
- Taya L Forde
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Nichith Kollanandi Ratheesh
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - William T Harvey
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Jill R Thomson
- Disease Surveillance Centre, SAC Veterinary Services, Scotland's Rural College, Edinburgh, United Kingdom
| | - Susanna Williamson
- Surveillance Intelligence Unit, Animal and Plant Health Agency, Bury St Edmunds, United Kingdom
| | - Roman Biek
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow, United Kingdom
| | - Tanja Opriessnig
- The Roslin Institute, The University of Edinburgh, Midlothian, United Kingdom
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Bacteriophages as Potential Tools for Detection and Control of Salmonella spp. in Food Systems. Microorganisms 2019; 7:microorganisms7110570. [PMID: 31744260 PMCID: PMC6920764 DOI: 10.3390/microorganisms7110570] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 11/14/2019] [Accepted: 11/15/2019] [Indexed: 01/21/2023] Open
Abstract
The global problem of antibiotic resistance in bacteria is quickly developing in most antibiotics used in hospitals and livestock. Recently, the infections with multi-drug resistant (MDR) bacteria become a major cause of death worldwide. Current antibiotics are not very effective in treating MDR Salmonella infections, which have become a public health threat. Therefore, novel approaches are needed to rapidly detect and effectively control antibiotic-resistant pathogens. Bacteriophages (phages) have seen renewed attention for satisfying those requirements due to their host-specific properties. Therefore, this review aims to discuss the possibility of using phages as a detection tool for recognizing bacterial cell surface receptors and an alternative approach for controlling antibiotic-resistant pathogens in food systems.
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Zhu W, Cai C, Li J, Zhang Q, Huang J, Jin M. Characterization of protective antigen CbpB as an adhesin and a plasminogen-binding protein of Erysipelothrix rhusiopathiae. Res Vet Sci 2019; 124:352-356. [PMID: 31060015 DOI: 10.1016/j.rvsc.2019.04.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 01/31/2019] [Accepted: 04/07/2019] [Indexed: 10/27/2022]
Abstract
Erysipelothrix rhusiopathiae is the causative agent of animal erysipelas and human erysipeloid. E. rhusiopathiae CbpB has been reported to be a protective antigen, but its pathogenic roles are not known. The aim of this study was to evaluate the ability of CbpB to act as an adhesin in E. rhusiopathiae adhesion to porcine endothelial cells as well as a host plasminogen- and fibronectin- binding protein. Recombinant CbpB (rCbpB) was successfully obtained, and it was found that E. rhusiopathiae CbpB was located on the cell surface of E. rhusiopathiae. Moreover, CbpB exhibited binding activity to porcine endothelial cells. Recombinant CbpB successfully bound to host plasminogen but was unable to bind to fibronectin. In conclusion, our work suggested that CbpB is a virulence factor of E. rhusiopathiae.
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Affiliation(s)
- Weifeng Zhu
- Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, China; College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Chengzhi Cai
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Wuhan, China
| | - Jingtao Li
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Qiang Zhang
- Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China; College of Life Sciences & Technology, Huazhong Agricultural University, Wuhan, China
| | - Jingjing Huang
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Wuhan, China
| | - Meilin Jin
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China; Key Laboratory of Development of Veterinary Diagnostic Products, Ministry of Agriculture, Wuhan, China; Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China.
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De Plano LM, Fazio E, Rizzo MG, Franco D, Carnazza S, Trusso S, Neri F, Guglielmino SPP. Phage-based assay for rapid detection of bacterial pathogens in blood by Raman spectroscopy. J Immunol Methods 2018; 465:45-52. [PMID: 30552870 DOI: 10.1016/j.jim.2018.12.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 12/11/2018] [Accepted: 12/11/2018] [Indexed: 01/08/2023]
Abstract
Sepsis is a systemic inflammatory response ensuing from presence and persistence of microorganisms in the bloodstream. The possibility to identify them at low concentrations may improve the problem of human health and therapeutic outcomes. So, sensitive and rapid diagnostic systems are essential to evaluate bacterial infections during the time, also reducing the cost. In this study, from random M13 phage display libraries, we selected phage clones that specifically bind surface of Staphyloccocus aureus, Pseudomonas aeruginosa and Escherichia coli. Then, commercial magnetic beads were functionalized with phage clones through covalent bond and used as capture and concentrating of pathogens from blood. We found that phage-magnetic beads complex represents a network which enables a cheap, high sensitive and specific detection of the bacteria involved in sepsis by micro-Raman spectroscopy. The enter process required 6 h and has the limit of detection of 10 Colony Forming Units on 7 ml of blood (CFU/7 ml).
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Affiliation(s)
- Laura M De Plano
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Enza Fazio
- Department of Mathematical and Computer Sciences, Physical Sciences and Earth Sciences, University of Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Maria Giovanna Rizzo
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Domenico Franco
- Department of Mathematical and Computer Sciences, Physical Sciences and Earth Sciences, University of Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Santina Carnazza
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Sebastiano Trusso
- IPCF-CNR Institute for Chemical-Physical Processes, Viale Ferdinando Stagno d'Alcontres 37, 98158 Messina, Italy
| | - Fortunato Neri
- Department of Mathematical and Computer Sciences, Physical Sciences and Earth Sciences, University of Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Salvatore P P Guglielmino
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy.
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Sun S, Zhang D, Zhang J, Huang C, Xiong Y. High activity chimeric snake gamma-type phospholipase A2 inhibitor created by DNA shuffling. Toxicon 2018; 153:32-38. [DOI: 10.1016/j.toxicon.2018.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Revised: 08/24/2018] [Accepted: 08/27/2018] [Indexed: 11/28/2022]
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