The present study aimed to work out a peptide-based multi-epitope vaccine against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We predicted different B-cell and T-cell epitopes by using the Immune Epitopes Database (IEDB). Homology modeling of the construct was done using SWISS-MODEL and then docked with different toll-like-receptors (TLR4, TLR7, and TLR8) using PatchDock, HADDOCK, and FireDock, respectively. From the overlapped epitopes, we designed five vaccine constructs C1-C5. Based on antigenicity, allergenicity, solubility, different physiochemical properties, and molecular docking scores, we selected the vaccine construct 1 (C1) for further processing. Docking of C1 with TLR4, TLR7, and TLR8 showed striking interactions with global binding energy of -43.48, -65.88, and -60.24 Kcal/mol, respectively. The docked complex was further simulated, which revealed that both molecules remain stable with minimum RMSF. Activation of TLRs induces downstream pathways to produce pro-inflammatory cytokines against viruses and immune system simulation shows enhanced antibody production after the booster dose. In conclusion, C1 was the best vaccine candidate among all designed constructs to elicit an immune response SARS-CoV-2 and combat the coronavirus disease (COVID-19).

Centre for Applied Molecular Biology University of the Punjab Lahore 53700 Pakistan

Department of Biochemistry Hazara University Mansehra 21120 Pakistan

Department of Biotechnology Virtual University of Pakistan Lahore 54000 Pakistan

Department of Chemistry Faculty of Science University of Hradec Kralove 50005 Hradec Kralove Czech Republic

Department of Pharmacy Abdul Wali Khan University Mardan Mardan 23200 Pakistan

Faculty of Sciences University of Reims Champagne Ardenne CEDEX 2 51687 Reims France

H E J Research Institute of Chemistry International Center for Chemical and Biological Sciences University of Karachi Karachi 75270 Pakistan

Jamil ur Rahman Center for Genome Research PCMD ICCBS University of Karachi Karachi 75270 Pakistan

See more in PubMed

Lu R., Zhao X., Li J., Niu P., Yang B., Wu H., Wang W., Song H., Huang B., Zhu N., et al. Articles Genomic characterisation and epidemiology of 2019 novel coronavirus: Implications for virus origins and receptor binding. Lancet. 2020;6736:1–10. doi: 10.1016/S0140-6736(20)30251-8. PubMed DOI PMC

Alejandra Tortorici M., Walls A.C., Lang Y., Wang C., Li Z., Koerhuis D., Boons G.J., Bosch B.J., Rey F.A., de Groot R.J., et al. Structural basis for human coronavirus attachment to sialic acid receptors. Nat. Struct. Mol. Biol. 2019;26:481–489. doi: 10.1038/s41594-019-0233-y. PubMed DOI PMC

Lu G., Wang Q., Gao G.F. Bat-to-human: Spike features determining “host jump” of coronaviruses SARS-CoV, MERS-CoV, and beyond. Trends Microbiol. 2015;23:468–478. doi: 10.1016/j.tim.2015.06.003. PubMed DOI PMC

Ge X.Y., Li J.L., Yang X.-L., Chmura A.A., Zhu G., Epstein J.H., Mazet J.K., Hu B., Zhang W., Peng C., et al. Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor. Nature. 2013;503:535–538. doi: 10.1038/nature12711. PubMed DOI PMC

Haagmans B.L., Al Dhahiry S.H.S., Reusken C.B.E.M., Raj V.S., Galiano M., Myers R., Godeke G.J., Jonges M., Farag E., Diab A., et al. Middle East respiratory syndrome coronavirus in dromedary camels: An outbreak investigation. Lancet Infect. Dis. 2014;14:140–145. doi: 10.1016/S1473-3099(13)70690-X. PubMed DOI PMC

Su S., Wong G., Shi W., Liu J., Lai A.C.K., Zhou J., Liu W., Bi Y., Gao G.F. Epidemiology, Genetic Recombination, and Pathogenesis of Coronaviruses. Trends Microbiol. 2016;24:490–502. doi: 10.1016/j.tim.2016.03.003. PubMed DOI PMC

Walls A.C., Park Y.J., Tortorici M.A., Wall A., McGuire A.T., Veesler D. Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein. Cell. 2020;181:281–292.e6. doi: 10.1016/j.cell.2020.02.058. PubMed DOI PMC

Zheng M., Song L. Novel antibody epitopes dominate the antigenicity of spike glycoprotein in SARS-CoV-2 compared to SARS-CoV. Cell. Mol. Immunol. 2020;17:536–538. doi: 10.1038/s41423-020-0385-z. PubMed DOI PMC

Yuan M., Wu N.C., Zhu X., Lee C.C.D., So R.T.Y., Lv H., Mok C.K.P., Wilson I.A. A highly conserved cryptic epitope in the receptor binding domains of SARS-CoV-2 and SARS-CoV. Science. 2020;368:630–633. doi: 10.1126/science.abb7269. PubMed DOI PMC

Rahman N., Basharat Z., Yousuf M., Castaldo G., Rastrelli L. Virtual Screening of Natural Products Against Type II Transmembrane Serine Protease (TMPRSS2), the Priming Agent of Coronavirus 2 (SARS-CoV-2) Molecules. 2020;25:2271. doi: 10.3390/molecules25102271. PubMed DOI PMC

Li Z., Tomlinson A.C.A., Wong A.H.M., Zhou D., Desforges M., Talbot P.J., Benlekbir S., Rubinstein J.L., Rini J.M. The human coronavirus HCoV-229E S-protein structure and receptor binding. Elife. 2019;8:1–22. doi: 10.7554/eLife.51230. PubMed DOI PMC

Walls A.C., Tortorici M.A., Bosch B.J., Frenz B., Rottier P.J.M., DiMaio F., Rey F.A., Veesler D. Cryo-electron microscopy structure of a coronavirus spike glycoprotein trimer. Nature. 2016;531:114–117. doi: 10.1038/nature16988. PubMed DOI PMC

Shey R.A., Ghogomu S.M., Esoh K.K., Nebangwa N.D., Shintouo C.M., Nongley N.F., Asa B.F., Ngale F.N., Vanhamme L., Souopgui J. In-silico design of a multi-epitope vaccine candidate against onchocerciasis and related filarial diseases. Sci. Rep. 2019;9:1–18. doi: 10.1038/s41598-019-40833-x. PubMed DOI PMC

Fleri W., Paul S., Dhanda S.K., Mahajan S., Xu X., Peters B., Sette A. The immune epitope database and analysis resource in epitope discovery and synthetic vaccine design. Front. Immunol. 2017;8:278. doi: 10.3389/fimmu.2017.00278. PubMed DOI PMC

Wang P., Sidney J., Dow C., Mothé B., Sette A., Peters B. A Systematic Assessment of MHC Class II Peptide Binding Predictions and Evaluation of a Consensus Approach. PLoS Comput. Biol. 2008;4:e1000048. doi: 10.1371/journal.pcbi.1000048. PubMed DOI PMC

Kim Y., Ponomarenko J., Zhu Z., Tamang D., Wang P., Greenbaum J., Lundegaard C., Sette A., Lund O., Bourne P.E., et al. Immune epitope database analysis resource. Nucleic Acids Res. 2012;40:W525–W530. doi: 10.1093/nar/gks438. PubMed DOI PMC

Rahman N., Ajmal A., Ali F., Rastrelli L. Core proteome mediated therapeutic target mining and multi-epitope vaccine design for Helicobacter pylori. Genomics. 2020 doi: 10.1016/j.ygeno.2020.06.026. PubMed DOI

El-manzalawy Y., Dobbs D., Honavar V. Predicting linear B-cell epitopes using string kernels. J. Mol. Recognit. Interdiscip. J. 2008;21:243–255. doi: 10.1002/jmr.893. PubMed DOI PMC

Jespersen M.C., Peters B., Nielsen M., Marcatili P. BepiPred-2.0: Improving sequence-based B-cell epitope prediction using conformational epitopes. Nucleic Acids Res. 2017;45:W24–W29. doi: 10.1093/nar/gkx346. PubMed DOI PMC

Hajighahramani N., Nezafat N., Eslami M., Negahdaripour M., Rahmatabadi S.S., Ghasemi Y. Immunoinformatics analysis and in silico designing of a novel multi-epitope peptide vaccine against Staphylococcus aureus. Infect. Genet. Evol. 2017;48:83–94. doi: 10.1016/j.meegid.2016.12.010. PubMed DOI

Ahmad T.A., Eweida A.E., Sheweita S.A. B-cell epitope mapping for the design of vaccines and effective diagnostics. Trials Vaccinol. 2016;5:71–83. doi: 10.1016/j.trivac.2016.04.003. DOI

Rosa D.S., Tzelepis F., Cunha M.G., Soares I.S., Rodrigues M.M. The pan HLA DR-binding epitope improves adjuvant-assisted immunization with a recombinant protein containing a malaria vaccine candidate. Immunol. Lett. 2004;92:259–268. doi: 10.1016/j.imlet.2004.01.006. PubMed DOI

Jung D., Jeong S.K., Lee C.M., Noh K.T., Heo D.R., Shin Y.K., Yun C.H., Koh W.J., Akira S., Whang J., et al. Enhanced efficacy of therapeutic cancer vaccines produced by Co-treatment with mycobacterium tuberculosis heparin-binding hemagglutinin, a novel TLR4 agonist. Cancer Res. 2011;71:2858–2870. doi: 10.1158/0008-5472.CAN-10-3487. PubMed DOI

Ferris L.K., Mburu Y.K., Mathers A.R., Fluharty E.R., Larregina A.T., Ferris R.L., Falo L.D. Human beta-defensin 3 induces maturation of human langerhans cell-like dendritic cells: An antimicrobial peptide that functions as an endogenous adjuvant. J. Invest. Dermatol. 2013;133:460–468. doi: 10.1038/jid.2012.319. PubMed DOI PMC

Park H.J., Jang G.Y., Kim Y.S., Park J.H., Lee S.E., Vo M.C., Lee J.J., Han H.D., Jung I.D., Kang T.H., et al. A novel TLR4 binding protein, 40S ribosomal protein S3, has potential utility as an adjuvant in a dendritic cell-based vaccine. J. Immunother. Cancer. 2019;7:1–13. doi: 10.1186/s40425-019-0539-7. PubMed DOI PMC

Mizel S.B., Bates J.T. Flagellin as an Adjuvant: Cellular Mechanisms and Potential. J. Immunol. 2010;185:5677–5682. doi: 10.4049/jimmunol.1002156. PubMed DOI PMC

Gnjatic S., Sawhney N.B., Bhardwaj N. Toll-Like Receptor Agonists. Cancer J. 2010;16:382–391. doi: 10.1097/PPO.0b013e3181eaca65. PubMed DOI PMC

Nezafat N., Ghasemi Y., Javadi G., Khoshnoud M.J., Omidinia E. A novel multi-epitope peptide vaccine against cancer: An in silico approach. J. Theor. Biol. 2014;349:121–134. doi: 10.1016/j.jtbi.2014.01.018. PubMed DOI

Solanki V., Tiwari V. Subtractive proteomics to identify novel drug targets and reverse vaccinology for the development of chimeric vaccine against Acinetobacter baumannii. Sci. Rep. 2018;8 doi: 10.1038/s41598-018-26689-7. PubMed DOI PMC

Doytchinova I., Flower D.R. Bioinformatic approach for identifying parasite and fungal candidate subunit vaccines. Open Vaccine J. 2008;1:4.:4. doi: 10.2174/1875035400801010022. DOI

Saha S., Raghava G.P.S. AlgPred: Prediction of allergenic proteins and mapping of IgE epitopes. Nucleic Acids Res. 2006;34:W202–W209. doi: 10.1093/nar/gkl343. PubMed DOI PMC

Magnan C.N., Randall A., Baldi P. SOLpro: Accurate sequence-based prediction of protein solubility. Bioinformatics. 2009;25:2200–2207. doi: 10.1093/bioinformatics/btp386. PubMed DOI

Gasteiger E., Gattiker A., Hoogland C., Ivanyi I., Appel R.D., Bairoch A. ExPASy: The proteomics server for in-depth protein knowledge and analysis. Nucleic Acids Res. 2003;31:3784–3788. doi: 10.1093/nar/gkg563. PubMed DOI PMC

Modelos C. Trabajo práctico N 13. Varianzas en función de variable independiente categórica. Nat. Protoc. 2016;10:845–858.

Rahman N., Muhammad I., Nayab G.E., Khan H., Aschner M., Filosa R., Daglia M. Molecular Docking of Isolated Alkaloids for Possible α-Glucosidase Inhibition. Biomolecules. 2019;9:544. doi: 10.3390/biom9100544. PubMed DOI PMC

Muhammad I., Rahman N., Nayab G.E., Niaz S., Shah M., Afridi S.G., Khan H., Daglia M., Capanoglu E. The Molecular Docking of Flavonoids Isolated from Daucus carota as a Dual Inhibitor of MDM2 and MDMX. Recent Pat. Anticancer. Drug Discov. 2020;15:1–11. doi: 10.2174/1574892815666200226112506. PubMed DOI

Mashiach E., Schneidman-Duhovny D., Andrusier N., Nussinov R., Wolfson H.J. FireDock: A web server for fast interaction refinement in molecular docking. Nucleic Acids Res. 2008;36:229–232. doi: 10.1093/nar/gkn186. PubMed DOI PMC

Kaba S.A., Karch C.P., Seth L., Ferlez K.M.B., Storme C.K., Pesavento D.M., Laughlin P.Y., Bergmann-Leitner E.S., Burkhard P., Lanar D.E. Self-assembling protein nanoparticles with built-in flagellin domains increases protective efficacy of a Plasmodium falciparum based vaccine. Vaccine. 2018;36:906–914. doi: 10.1016/j.vaccine.2017.12.001. PubMed DOI

Rapin N., Lund O., Bernaschi M., Castiglione F. Computational immunology meets bioinformatics: The use of prediction tools for molecular binding in the simulation of the immune system. PLoS ONE. 2010;5 doi: 10.1371/journal.pone.0009862. PubMed DOI PMC

Grote A., Hiller K., Scheer M., Münch R., Nörtemann B., Hempel D.C., Jahn D. JCat: A novel tool to adapt codon usage of a target gene to its potential expression host. Nucleic Acids Res. 2005;33:526–531. doi: 10.1093/nar/gki376. PubMed DOI PMC

Kyte J., Doolittle R.F., Diego S., Jolla L. A Simple Method for Displaying the Hydropathic Character of a Protein. J. Mol. Biol. 1982;157:105–132. doi: 10.1016/0022-2836(82)90515-0. PubMed DOI

Wilkins M.R., Gasteiger E., Bairoch A., Sanchez J., Williams K.L., Appel R.D., Hochstrasser D.F. The Proteomics Protocols Handbook. Volume 112. Humana Press; Totowa, NJ, USA: 2005. Protein Identification and Analysis Tools in the ExPASy Server; pp. 531–552. PubMed

Mohan R., Venugopal S. Computational structural and functional analysis of hypothetical proteins of Staphylococcus aureus. Bioinformation. 2012;8:722. doi: 10.6026/97320630008722. PubMed DOI PMC

Miyazawa S., Jernigan R.L. Residue-residue potentials with a favorable contact pair term and an unfavorable high packing density term, for simulation and threading. J. Mol. Biol. 1996;256:623–644. doi: 10.1006/jmbi.1996.0114. PubMed DOI

Thanh Le T., Andreadakis Z., Kumar A., Gómez Román R., Tollefsen S., Saville M., Mayhew S. The COVID-19 vaccine development landscape. Nat. Rev. Drug Discov. 2020:1–7. doi: 10.1038/d41573-020-00073-5. PubMed DOI

Ghaffari-Nazari H., Tavakkol-Afshari J., Jaafari M.R., Tahaghoghi-Hajghorbani S., Masoumi E., Jalali S.A. Improving multi-epitope long peptide vaccine potency by using a strategy that enhances CD4+ T Help in BALB/c mice. PLoS ONE. 2015;10 doi: 10.1371/journal.pone.0142563. PubMed DOI PMC

Yang Y., Sun W., Guo J., Zhao G., Sun S., Yu H., Guo Y., Li J., Jin X., Du L., et al. In silico design of a DNA-based HIV-1 multi-epitope vaccine for Chinese populations. Hum. Vaccines Immunother. 2015;11:795–805. doi: 10.1080/21645515.2015.1012017. PubMed DOI PMC

Swati S., Ashok S. Bioinformatics approaches for structural and functional analysis of proteins in secondary metabolism in Withania somnifera. Mol. Biol. Rep. 2014 doi: 10.1007/s11033-014-3618-3. PubMed DOI

Guruprasad K., Reddy B.V.B., Pandit M.W. Correlation between stability of a protein and its dipeptide composition: A novel approach for predicting in vivo stability of a protein from its primary sequence. Protein Eng. Des. Sel. 1990;4:155–161. doi: 10.1093/protein/4.2.155. PubMed DOI

Lester S.N., Li K. Toll-like receptors in antiviral innate immunity. J. Mol. Biol. 2014;426:1246–1264. doi: 10.1016/j.jmb.2013.11.024. PubMed DOI PMC

Olejnik J., Hume A.J., Mühlberger E. Toll-like receptor 4 in acute viral infection: Too much of a good thing. PLoS Pathog. 2018;14 doi: 10.1371/journal.ppat.1007390. PubMed DOI PMC

Gorden K.B., Gorski K.S., Gibson S.J., Kedl R.M., Kieper W.C., Qiu X., Tomai M.A., Alkan S.S., Vasilakos J.P. Synthetic TLR Agonists Reveal Functional Differences between Human TLR7 and TLR8. J. Immunol. 2005;174:1259–1268. doi: 10.4049/jimmunol.174.3.1259. PubMed DOI

Craft N., Bruhn K.W., Nguyen B.D., Prins R., Lin J.W., Liau L.M., Miller J.F. The TLR7 Agonist Imiquimod Enhances the Anti-Melanoma Effects of a Recombinant Listeria monocytogenes Vaccine. J. Immunol. 2005;175:1983–1990. doi: 10.4049/jimmunol.175.3.1983. PubMed DOI

Wille-Reece U., Flynn B.J., Loré K., Koup R.A., Kedl R.M., Mattapallil J.J., Weiss W.R., Roederer M., Seder R.A. HIV Gag protein conjugated to a Toll-like receptor 7/8 agonist improves the magnitude and quality of Th1 and CD8+ T cell responses in nonhuman primates. Proc. Natl. Acad. Sci. USA. 2005;102:15190–15194. doi: 10.1073/pnas.0507484102. PubMed DOI PMC