Immunoinformatic exploration of a multi-epitope-based peptide vaccine candidate targeting emerging variants of SARS-CoV-2
Many countries around the world are facing severe challenges due to the recently emerging variants of SARS-CoV-2. Over the last few months, scientists have been developing treatments, drugs, and vaccines to subdue the virus and prevent its transmission. In this context, a peptide-based vaccine const...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2023-10-01
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| Series: | Frontiers in Microbiology |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2023.1251716/full |
| _version_ | 1797658876784410624 |
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| author | K. M. Kumar Yalpi Karthik D. Ramakrishna S. Balaji Sinosh Skariyachan T. P. Krishna Murthy Kunnathur Murugesan Sakthivel Badriyah S. Alotaibi Mustafa Shukry Samy M. Sayed Samy M. Sayed Muntazir Mushtaq |
| author_facet | K. M. Kumar Yalpi Karthik D. Ramakrishna S. Balaji Sinosh Skariyachan T. P. Krishna Murthy Kunnathur Murugesan Sakthivel Badriyah S. Alotaibi Mustafa Shukry Samy M. Sayed Samy M. Sayed Muntazir Mushtaq |
| author_sort | K. M. Kumar |
| collection | DOAJ |
| description | Many countries around the world are facing severe challenges due to the recently emerging variants of SARS-CoV-2. Over the last few months, scientists have been developing treatments, drugs, and vaccines to subdue the virus and prevent its transmission. In this context, a peptide-based vaccine construct containing pathogenic proteins of the virus known to elicit an immune response was constructed. An analysis of the spike protein-based epitopes allowed us to design an “epitope-based subunit vaccine” against coronavirus using the approaches of “reverse vaccinology” and “immunoinformatics.” Computational experimentation and a systematic, comprehensive protocol were followed with an aim to develop and design a multi-epitope-based peptide (MEBP) vaccine candidate. Our study attempted to predict an MEBP vaccine by introducing mutations of SARS-CoV-2 (Delta, Lambda, Iota, Omicron, and Kappa) in Spike glycoprotein and predicting dual-purpose epitopes (B-cell and T-cell). This was followed by screening the selected epitopes based on antigenicity, allergenicity, and population coverage and constructing them into a vaccine by using linkers and adjuvants. The vaccine construct was analyzed for its physicochemical properties and secondary structure prediction, and a 3D structure was built, refined, and validated. Furthermore, the peptide-protein interaction of the vaccine construct with Toll-like receptor (TLR) molecules was performed. Immune profiling was performed to check the immune response. Codon optimization of the vaccine construct was performed to obtain the GC content before cloning it into the E. coli genome, facilitating its progression it into a vector. Finally, an in-silico simulation of the vaccine–protein complex was performed to comprehend its stability and conformational behavior. |
| first_indexed | 2024-03-11T18:05:39Z |
| format | Article |
| id | doaj.art-f4efb840dca2438da67b9db5434cb42b |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-03-11T18:05:39Z |
| publishDate | 2023-10-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-f4efb840dca2438da67b9db5434cb42b2023-10-17T07:43:06ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2023-10-011410.3389/fmicb.2023.12517161251716Immunoinformatic exploration of a multi-epitope-based peptide vaccine candidate targeting emerging variants of SARS-CoV-2K. M. Kumar0Yalpi Karthik1D. Ramakrishna2S. Balaji3Sinosh Skariyachan4T. P. Krishna Murthy5Kunnathur Murugesan Sakthivel6Badriyah S. Alotaibi7Mustafa Shukry8Samy M. Sayed9Samy M. Sayed10Muntazir Mushtaq11Department of Bioinformatics, Pondicherry University, Pondicherry, IndiaDepartment of Studies and Research in Microbiology, Mangalore University, Chikka Aluvara, Kodagu, Karnataka, IndiaBiotechnology Department, Dayananda Sagar College of Engineering, Dr. C.D Sagar Centre for Life Sciences, Dayananda Sagar Institutions, Bengaluru, IndiaCentre for Incubation, Innovation, Research and Consultancy (CIIRC®), Jyothy Institute of Technology, Bengaluru, Karnataka, IndiaDepartment of Microbiology, St. Pius X College, Rajapuram, Kerala, IndiaDepartment of Biotechnology, Ramaiah Institute of Technology, Bengaluru, Karnataka, IndiaDepartment of Biochemistry, PSG College of Arts and Science, Coimbatore, Tamil Nadu, IndiaDepartment of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint Abdulrahman University, Riyadh, Saudi ArabiaPhysiology Department, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh, Egypt0Department of Economic Entomology and Pesticides, Faculty of Agriculture, Cairo University, Giza, Egypt1Department of Science and Technology, University College-Ranyah, Taif University, Taif, Saudi Arabia2MS Swaminathan School of Agriculture, Shoolini University of Biotechnology and Management Sciences, Solan, Himachal Pradesh, IndiaMany countries around the world are facing severe challenges due to the recently emerging variants of SARS-CoV-2. Over the last few months, scientists have been developing treatments, drugs, and vaccines to subdue the virus and prevent its transmission. In this context, a peptide-based vaccine construct containing pathogenic proteins of the virus known to elicit an immune response was constructed. An analysis of the spike protein-based epitopes allowed us to design an “epitope-based subunit vaccine” against coronavirus using the approaches of “reverse vaccinology” and “immunoinformatics.” Computational experimentation and a systematic, comprehensive protocol were followed with an aim to develop and design a multi-epitope-based peptide (MEBP) vaccine candidate. Our study attempted to predict an MEBP vaccine by introducing mutations of SARS-CoV-2 (Delta, Lambda, Iota, Omicron, and Kappa) in Spike glycoprotein and predicting dual-purpose epitopes (B-cell and T-cell). This was followed by screening the selected epitopes based on antigenicity, allergenicity, and population coverage and constructing them into a vaccine by using linkers and adjuvants. The vaccine construct was analyzed for its physicochemical properties and secondary structure prediction, and a 3D structure was built, refined, and validated. Furthermore, the peptide-protein interaction of the vaccine construct with Toll-like receptor (TLR) molecules was performed. Immune profiling was performed to check the immune response. Codon optimization of the vaccine construct was performed to obtain the GC content before cloning it into the E. coli genome, facilitating its progression it into a vector. Finally, an in-silico simulation of the vaccine–protein complex was performed to comprehend its stability and conformational behavior.https://www.frontiersin.org/articles/10.3389/fmicb.2023.1251716/fullSARS-CoV-2vaccine designin-silico modelingpeptide-protein dockingimmune response profilingMD simulation |
| spellingShingle | K. M. Kumar Yalpi Karthik D. Ramakrishna S. Balaji Sinosh Skariyachan T. P. Krishna Murthy Kunnathur Murugesan Sakthivel Badriyah S. Alotaibi Mustafa Shukry Samy M. Sayed Samy M. Sayed Muntazir Mushtaq Immunoinformatic exploration of a multi-epitope-based peptide vaccine candidate targeting emerging variants of SARS-CoV-2 Frontiers in Microbiology SARS-CoV-2 vaccine design in-silico modeling peptide-protein docking immune response profiling MD simulation |
| title | Immunoinformatic exploration of a multi-epitope-based peptide vaccine candidate targeting emerging variants of SARS-CoV-2 |
| title_full | Immunoinformatic exploration of a multi-epitope-based peptide vaccine candidate targeting emerging variants of SARS-CoV-2 |
| title_fullStr | Immunoinformatic exploration of a multi-epitope-based peptide vaccine candidate targeting emerging variants of SARS-CoV-2 |
| title_full_unstemmed | Immunoinformatic exploration of a multi-epitope-based peptide vaccine candidate targeting emerging variants of SARS-CoV-2 |
| title_short | Immunoinformatic exploration of a multi-epitope-based peptide vaccine candidate targeting emerging variants of SARS-CoV-2 |
| title_sort | immunoinformatic exploration of a multi epitope based peptide vaccine candidate targeting emerging variants of sars cov 2 |
| topic | SARS-CoV-2 vaccine design in-silico modeling peptide-protein docking immune response profiling MD simulation |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2023.1251716/full |
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