Prediction of Putative Epitope Peptides against BaeR Associated with TCS Adaptation in <i>Acinetobacter baumannii</i> Using an In Silico Approach
<i>Background and Objectives</i>: The BaeR protein is involved in the adaptation system of <i>A. baumannii</i> and is associated with virulence factors responsible for systemic infections in hospitalized patients. This study was conducted to characterize putative epitope pept...
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| Format: | Article |
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MDPI AG
2023-02-01
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| Series: | Medicina |
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| Online Access: | https://www.mdpi.com/1648-9144/59/2/343 |
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| author | A. S. Smiline Girija Shoba Gunasekaran Saman Habib Mohammed Aljeldah Basim R. Al Shammari Ahmad A. Alshehri Ameen S. S. Alwashmi Safaa A. Turkistani Abdulsalam Alawfi Amer Alshengeti Mohammed Garout Sara Alwarthan Roua A. Alsubki Nouran M. Moustafa Ali A. Rabaan |
| author_facet | A. S. Smiline Girija Shoba Gunasekaran Saman Habib Mohammed Aljeldah Basim R. Al Shammari Ahmad A. Alshehri Ameen S. S. Alwashmi Safaa A. Turkistani Abdulsalam Alawfi Amer Alshengeti Mohammed Garout Sara Alwarthan Roua A. Alsubki Nouran M. Moustafa Ali A. Rabaan |
| author_sort | A. S. Smiline Girija |
| collection | DOAJ |
| description | <i>Background and Objectives</i>: The BaeR protein is involved in the adaptation system of <i>A. baumannii</i> and is associated with virulence factors responsible for systemic infections in hospitalized patients. This study was conducted to characterize putative epitope peptides for the design of vaccines against BaeR protein, using an immune-informatic approach. <i>Materials and Methods</i>: FASTA sequences of BaeR from five different strains of <i>A. baumannii</i> were retrieved from the UNIPROT database and evaluated for their antigenicity, allergenicity and vaccine properties using BepiPred, Vaxijen, AlgPred, AntigenPro and SolPro. Their physio-chemical properties were assessed using the Expasy Protparam server. Immuno-dominant B-cell and T-cell epitope peptides were predicted using the IEDB database and MHC cluster server with a final assessment of their interactions with TLR-2. Results: A final selection of two peptide sequences (36aa and 22aa) was made from the 38 antigenic peptides. E1 was considered a soluble, non-allergenic antigen, and possessed negative GRAVY values, substantiating the hydrophilic nature of the proteins. Further analysis on the T-cell epitopes, class I immunogenicity and HLA allele frequencies yielded T-cell immuno-dominant peptides. The protein–peptide interactions of the TLR-2 receptor showed good similarity scores in terms of the high number of hydrogen bonds compared to other protein-peptide interactions. <i>Conclusions</i>: The two epitopes predicted from <i>BaeR</i> in the present investigation are promising vaccine candidates for targeting the TCS of <i>A. baumannii</i> in systemic and nosocomial infections. This study also demonstrates an alternative strategy to tackling and mitigating MDR strains of <i>A. baumannii</i> and provides a useful reference for the design and construction of novel vaccine candidates against this bacteria. |
| first_indexed | 2024-03-11T08:27:32Z |
| format | Article |
| id | doaj.art-9f6c7033d1a54868982a2eb6dfaab085 |
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| language | English |
| last_indexed | 2024-03-11T08:27:32Z |
| publishDate | 2023-02-01 |
| publisher | MDPI AG |
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| series | Medicina |
| spelling | doaj.art-9f6c7033d1a54868982a2eb6dfaab0852023-11-16T22:00:29ZengMDPI AGMedicina1010-660X1648-91442023-02-0159234310.3390/medicina59020343Prediction of Putative Epitope Peptides against BaeR Associated with TCS Adaptation in <i>Acinetobacter baumannii</i> Using an In Silico ApproachA. S. Smiline Girija0Shoba Gunasekaran1Saman Habib2Mohammed Aljeldah3Basim R. Al Shammari4Ahmad A. Alshehri5Ameen S. S. Alwashmi6Safaa A. Turkistani7Abdulsalam Alawfi8Amer Alshengeti9Mohammed Garout10Sara Alwarthan11Roua A. Alsubki12Nouran M. Moustafa13Ali A. Rabaan14Department of Microbiology, Saveetha Dental College and Hospitals, Saveetha Institute of Medical and Technical Sciences [SIMATS], Saveetha University, P.H. Road, Chennai 600077, IndiaDepartment of Biotechnology, DG Vaishnav College, Chennai 600106, IndiaDepartment of Medical Education, King Edward Medical University, Lahore 54000, PakistanDepartment of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hafr Al Batin, Hafr Al Batin 39831, Saudi ArabiaDepartment of Clinical Laboratory Sciences, College of Applied Medical Sciences, University of Hafr Al Batin, Hafr Al Batin 39831, Saudi ArabiaDepartment of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran 61441, Saudi ArabiaDepartment of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi ArabiaDepartment of Medical Laboratory Sciences, Fakeeh College for Medical Science, Jeddah 21134, Saudi ArabiaDepartment of Pediatrics, College of Medicine, Taibah University, Al-Madinah 41491, Saudi ArabiaDepartment of Pediatrics, College of Medicine, Taibah University, Al-Madinah 41491, Saudi ArabiaDepartment of Community Medicine and Health Care for Pilgrims, Faculty of Medicine, Umm Al-Qura University, Makkah 21955, Saudi ArabiaDepartment of Internal Medicine, College of Medicine, Imam Abdulrahman Bin Faisal University, Dammam 34212, Saudi ArabiaDepartment of Clinical Laboratory Sciences, College of Applied Medical Sciences, King Saud University, Riyadh 11362, Saudi ArabiaBasic Medical Science Department, College of Medicine, Dar Al Uloom University, Riyadh 12922, Saudi ArabiaMolecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran 31311, Saudi Arabia<i>Background and Objectives</i>: The BaeR protein is involved in the adaptation system of <i>A. baumannii</i> and is associated with virulence factors responsible for systemic infections in hospitalized patients. This study was conducted to characterize putative epitope peptides for the design of vaccines against BaeR protein, using an immune-informatic approach. <i>Materials and Methods</i>: FASTA sequences of BaeR from five different strains of <i>A. baumannii</i> were retrieved from the UNIPROT database and evaluated for their antigenicity, allergenicity and vaccine properties using BepiPred, Vaxijen, AlgPred, AntigenPro and SolPro. Their physio-chemical properties were assessed using the Expasy Protparam server. Immuno-dominant B-cell and T-cell epitope peptides were predicted using the IEDB database and MHC cluster server with a final assessment of their interactions with TLR-2. Results: A final selection of two peptide sequences (36aa and 22aa) was made from the 38 antigenic peptides. E1 was considered a soluble, non-allergenic antigen, and possessed negative GRAVY values, substantiating the hydrophilic nature of the proteins. Further analysis on the T-cell epitopes, class I immunogenicity and HLA allele frequencies yielded T-cell immuno-dominant peptides. The protein–peptide interactions of the TLR-2 receptor showed good similarity scores in terms of the high number of hydrogen bonds compared to other protein-peptide interactions. <i>Conclusions</i>: The two epitopes predicted from <i>BaeR</i> in the present investigation are promising vaccine candidates for targeting the TCS of <i>A. baumannii</i> in systemic and nosocomial infections. This study also demonstrates an alternative strategy to tackling and mitigating MDR strains of <i>A. baumannii</i> and provides a useful reference for the design and construction of novel vaccine candidates against this bacteria.https://www.mdpi.com/1648-9144/59/2/343nosocomial infectionsbioinformaticsBaeRepitope peptidesin silico |
| spellingShingle | A. S. Smiline Girija Shoba Gunasekaran Saman Habib Mohammed Aljeldah Basim R. Al Shammari Ahmad A. Alshehri Ameen S. S. Alwashmi Safaa A. Turkistani Abdulsalam Alawfi Amer Alshengeti Mohammed Garout Sara Alwarthan Roua A. Alsubki Nouran M. Moustafa Ali A. Rabaan Prediction of Putative Epitope Peptides against BaeR Associated with TCS Adaptation in <i>Acinetobacter baumannii</i> Using an In Silico Approach Medicina nosocomial infections bioinformatics BaeR epitope peptides in silico |
| title | Prediction of Putative Epitope Peptides against BaeR Associated with TCS Adaptation in <i>Acinetobacter baumannii</i> Using an In Silico Approach |
| title_full | Prediction of Putative Epitope Peptides against BaeR Associated with TCS Adaptation in <i>Acinetobacter baumannii</i> Using an In Silico Approach |
| title_fullStr | Prediction of Putative Epitope Peptides against BaeR Associated with TCS Adaptation in <i>Acinetobacter baumannii</i> Using an In Silico Approach |
| title_full_unstemmed | Prediction of Putative Epitope Peptides against BaeR Associated with TCS Adaptation in <i>Acinetobacter baumannii</i> Using an In Silico Approach |
| title_short | Prediction of Putative Epitope Peptides against BaeR Associated with TCS Adaptation in <i>Acinetobacter baumannii</i> Using an In Silico Approach |
| title_sort | prediction of putative epitope peptides against baer associated with tcs adaptation in i acinetobacter baumannii i using an in silico approach |
| topic | nosocomial infections bioinformatics BaeR epitope peptides in silico |
| url | https://www.mdpi.com/1648-9144/59/2/343 |
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