Immunoinformatic exploration of a multi-epitope-based peptide vaccine candidate targeting emerging variants of SARS-CoV-2

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; Muntazir Mushtaq

doi:10.3389/fmicb.2023.1251716

Immunoinformatic exploration of a multi-epitope-based peptide vaccine candidate targeting emerging variants of SARS-CoV-2

Front Microbiol. 2023 Oct 17:14:1251716. doi: 10.3389/fmicb.2023.1251716. eCollection 2023.

Authors

Affiliations

¹ Department of Bioinformatics, Pondicherry University, Pondicherry, India.
² Department of Studies and Research in Microbiology, Mangalore University, Chikka Aluvara, Kodagu, Karnataka, India.
³ Biotechnology Department, Dayananda Sagar College of Engineering, Dr. C.D Sagar Centre for Life Sciences, Dayananda Sagar Institutions, Bengaluru, India.
⁴ Centre for Incubation, Innovation, Research and Consultancy (CIIRC®), Jyothy Institute of Technology, Bengaluru, Karnataka, India.
⁵ Department of Microbiology, St. Pius X College, Rajapuram, Kerala, India.
⁶ Department of Biotechnology, Ramaiah Institute of Technology, Bengaluru, Karnataka, India.
⁷ Department of Biochemistry, PSG College of Arts and Science, Coimbatore, Tamil Nadu, India.
⁸ Department of Pharmaceutical Sciences, College of Pharmacy, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia.
⁹ Physiology Department, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh, Egypt.
¹⁰ Department of Economic Entomology and Pesticides, Faculty of Agriculture, Cairo University, Giza, Egypt.
¹¹ Department of Science and Technology, University College-Ranyah, Taif University, Taif, Saudi Arabia.
¹² MS Swaminathan School of Agriculture, Shoolini University of Biotechnology and Management Sciences, Solan, Himachal Pradesh, India.

Abstract

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.

Keywords: MD simulation; SARS-CoV-2; immune response profiling; in-silico modeling; peptide-protein docking; vaccine design.