An In-Silico Investigation to Design a Multi-Epitopes Vaccine against Multi-Drug Resistant <i>Hafnia alvei</i>
Antimicrobial resistance has become a significant health issue because of the misuse of antibiotics in our daily lives, resulting in high rates of morbidity and mortality. <i>Hafnia alvei</i> is a rod-shaped, Gram-negative and facultative anaerobic bacteria. The medical community has emp...
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| Format: | Article |
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MDPI AG
2022-07-01
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| Series: | Vaccines |
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| Online Access: | https://www.mdpi.com/2076-393X/10/7/1127 |
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| author | Fahad M. Alshabrmi Faris Alrumaihi Sahar Falah Alrasheedi Wafa Abdullah I. Al-Megrin Ahmad Almatroudi Khaled S. Allemailem |
| author_facet | Fahad M. Alshabrmi Faris Alrumaihi Sahar Falah Alrasheedi Wafa Abdullah I. Al-Megrin Ahmad Almatroudi Khaled S. Allemailem |
| author_sort | Fahad M. Alshabrmi |
| collection | DOAJ |
| description | Antimicrobial resistance has become a significant health issue because of the misuse of antibiotics in our daily lives, resulting in high rates of morbidity and mortality. <i>Hafnia alvei</i> is a rod-shaped, Gram-negative and facultative anaerobic bacteria. The medical community has emphasized <i>H. alvei</i>’s possible association with gastroenteritis. As of now, there is no licensed vaccine for <i>H. alvei</i>, and as such, computer aided vaccine design approaches could be an ideal approach to highlight the potential vaccine epitopes against this bacteria. By using bacterial pan-genome analysis (BPGA), we were able to study the entire proteomes of <i>H. alvei</i> with the aim of developing a vaccine. Based on the analysis, 20,370 proteins were identified as core proteins, which were further used in identifying potential vaccine targets based on several vaccine candidacy parameters. The prioritized vaccine targets against the bacteria are; type 1 fimbrial protein, flagellar hook length control protein (FliK), flagellar hook associated protein (FlgK), curli production assembly/transport protein (CsgF), fimbria/pilus outer membrane usher protein, fimbria/pilus outer membrane usher protein, molecular chaperone, flagellar filament capping protein (FliD), TonB-dependent hemoglobin /transferrin/lactoferrin family receptor, Porin (OmpA), flagellar basal body rod protein (FlgF) and flagellar hook-basal body complex protein (FliE). During the epitope prediction phase, different antigenic, immunogenic, non-Allergenic, and non-Toxic epitopes were predicted for the above-mentioned proteins. The selected epitopes were combined to generate a multi-epitope vaccine construct and a cholera toxin B subunit (adjuvant) was added to enhance the vaccine’s antigenicity. Downward analyses of vaccines were performed using a vaccine three-dimensional model. Docking studies have confirmed that the vaccine strongly binds with MHC-I, MHC-II, and TLR-4 immune cell receptors. Additionally, molecular dynamics simulations confirmed that the vaccine epitopes were exposed to nature and to the host immune system and interpreted strong intermolecular binding between the vaccine and receptors. Based on the results of the study, the model vaccine construct seems to have the capacity to produce protective immune responses in the host, making it an attractive candidate for further in vitro and in vivo studies. |
| first_indexed | 2024-03-09T05:43:04Z |
| format | Article |
| id | doaj.art-51e0d0722cc04333b1cb90ff28d505ef |
| institution | Directory Open Access Journal |
| issn | 2076-393X |
| language | English |
| last_indexed | 2024-03-09T05:43:04Z |
| publishDate | 2022-07-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Vaccines |
| spelling | doaj.art-51e0d0722cc04333b1cb90ff28d505ef2023-12-03T12:23:23ZengMDPI AGVaccines2076-393X2022-07-01107112710.3390/vaccines10071127An In-Silico Investigation to Design a Multi-Epitopes Vaccine against Multi-Drug Resistant <i>Hafnia alvei</i>Fahad M. Alshabrmi0Faris Alrumaihi1Sahar Falah Alrasheedi2Wafa Abdullah I. Al-Megrin3Ahmad Almatroudi4Khaled S. Allemailem5Department of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi ArabiaDepartment of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi ArabiaDepartment of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi ArabiaDepartment of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi ArabiaDepartment of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi ArabiaDepartment of Medical Laboratories, College of Applied Medical Sciences, Qassim University, Buraydah 51452, Saudi ArabiaAntimicrobial resistance has become a significant health issue because of the misuse of antibiotics in our daily lives, resulting in high rates of morbidity and mortality. <i>Hafnia alvei</i> is a rod-shaped, Gram-negative and facultative anaerobic bacteria. The medical community has emphasized <i>H. alvei</i>’s possible association with gastroenteritis. As of now, there is no licensed vaccine for <i>H. alvei</i>, and as such, computer aided vaccine design approaches could be an ideal approach to highlight the potential vaccine epitopes against this bacteria. By using bacterial pan-genome analysis (BPGA), we were able to study the entire proteomes of <i>H. alvei</i> with the aim of developing a vaccine. Based on the analysis, 20,370 proteins were identified as core proteins, which were further used in identifying potential vaccine targets based on several vaccine candidacy parameters. The prioritized vaccine targets against the bacteria are; type 1 fimbrial protein, flagellar hook length control protein (FliK), flagellar hook associated protein (FlgK), curli production assembly/transport protein (CsgF), fimbria/pilus outer membrane usher protein, fimbria/pilus outer membrane usher protein, molecular chaperone, flagellar filament capping protein (FliD), TonB-dependent hemoglobin /transferrin/lactoferrin family receptor, Porin (OmpA), flagellar basal body rod protein (FlgF) and flagellar hook-basal body complex protein (FliE). During the epitope prediction phase, different antigenic, immunogenic, non-Allergenic, and non-Toxic epitopes were predicted for the above-mentioned proteins. The selected epitopes were combined to generate a multi-epitope vaccine construct and a cholera toxin B subunit (adjuvant) was added to enhance the vaccine’s antigenicity. Downward analyses of vaccines were performed using a vaccine three-dimensional model. Docking studies have confirmed that the vaccine strongly binds with MHC-I, MHC-II, and TLR-4 immune cell receptors. Additionally, molecular dynamics simulations confirmed that the vaccine epitopes were exposed to nature and to the host immune system and interpreted strong intermolecular binding between the vaccine and receptors. Based on the results of the study, the model vaccine construct seems to have the capacity to produce protective immune responses in the host, making it an attractive candidate for further in vitro and in vivo studies.https://www.mdpi.com/2076-393X/10/7/1127antimicrobial resistancevaccine<i>Hafnia alvei</i>molecular dynamics simulations |
| spellingShingle | Fahad M. Alshabrmi Faris Alrumaihi Sahar Falah Alrasheedi Wafa Abdullah I. Al-Megrin Ahmad Almatroudi Khaled S. Allemailem An In-Silico Investigation to Design a Multi-Epitopes Vaccine against Multi-Drug Resistant <i>Hafnia alvei</i> Vaccines antimicrobial resistance vaccine <i>Hafnia alvei</i> molecular dynamics simulations |
| title | An In-Silico Investigation to Design a Multi-Epitopes Vaccine against Multi-Drug Resistant <i>Hafnia alvei</i> |
| title_full | An In-Silico Investigation to Design a Multi-Epitopes Vaccine against Multi-Drug Resistant <i>Hafnia alvei</i> |
| title_fullStr | An In-Silico Investigation to Design a Multi-Epitopes Vaccine against Multi-Drug Resistant <i>Hafnia alvei</i> |
| title_full_unstemmed | An In-Silico Investigation to Design a Multi-Epitopes Vaccine against Multi-Drug Resistant <i>Hafnia alvei</i> |
| title_short | An In-Silico Investigation to Design a Multi-Epitopes Vaccine against Multi-Drug Resistant <i>Hafnia alvei</i> |
| title_sort | in silico investigation to design a multi epitopes vaccine against multi drug resistant i hafnia alvei i |
| topic | antimicrobial resistance vaccine <i>Hafnia alvei</i> molecular dynamics simulations |
| url | https://www.mdpi.com/2076-393X/10/7/1127 |
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