Epitope-based chimeric peptide vaccine design against S, M and E proteins of SARS-CoV-2 etiologic agent of global pandemic COVID-19: an in silico approach

M. Shaminur Rahman; M. Nazmul Hoque; M. Rafiul Islam; Salma Akter; A. S. M. Rubayet-Ul-Alam; Mohammad Anwar Siddique; Otun Saha; Md. Mizanur Rahaman; Munawar Sultana; M. Anwar Hossain

After codon optimization and mRNA secondary structure analysis, the sequence of the 388 chimeric peptide vaccine production does not involve virus replication, therefore reduce the cost 416 of production. Hence, a low cost strategy should be adopted for developing a highly demanded 417 vaccine for the mankind. Heterologous expression of any vaccine candidate protein has very 418 promising scopes for developing such low cost vaccine, providing that all essential properties for 419 antigenicity, immunogenicity and functional configuration are being conserved to mimic the 420 structural and functional property of the actual antigen 34 . Construction of a vaccine candidate 421 with multiple potential epitopes can obviously potentiate the multi-valency of the antigen to 422 develop immune response against a number of epitopes of any pathogen. Also, rational 423 engineering of epitopes for increased potency and magnitude, ability to enhance immune 424 . CC-BY 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.30.015164 doi: bioRxiv preprint response in conserved epitopes, increased safety and absence of unnecessary viral materials and 425 cost effectiveness all these cumulatively include potential benefit to multi-epitope recombinant 426 protein based vaccine 20 . This study was designed to assist with the initial phase of multi-epitope 427 vaccine candidate selection. Thereby, safe and effective vaccine development by providing 428 recommendations of epitopes that may potentially be considered for incorporation in vaccine 429 design for SARS-CoV-2. Vaccine design is improved through the use of specialized spacer sequences 39 . To 461 designing the CoV-RMEN (vaccine candidate) GG and EGGE linkers were incorporated 462 between the predicted epitopes to produce sequences with minimized junctional 463 immunogenicity, thereby, allowing the rational design construction of a potent multi-epitope 464 vaccine 21,38 . The molecular weight of our vaccine candidate, the CoV-RMEN is 46.8 kDa with a 465 predicted theoretical pI of 8.71, indicating that the protein is basic in nature. Also, the predicted 466 instability index indicates that the protein will be stable upon expression, thus further 467 strengthening its potential for use. The aliphatic index showed that the protein contains aliphatic 468 side chains, indicating potential hydrophobicity. All these parameters indicate that the 469 . CC-BY 4.0 International license author/funder. It is made available under a The copyright holder for this preprint (which was not peer-reviewed) is the . https://doi.org/10.1101/2020.03.30.015164 doi: bioRxiv preprint recombinant protein is thermally stable, hence would be best suited for use in different endemic 470 areas worldwide 6,21 . 471