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Reverse Vaccinology Approach to Design a Novel Multi-Epitope Vaccine Candidate Against COVID-19: an in Silico Study

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Reverse Vaccinology Approach to Design a Novel Multi-Epitope Vaccine Candidate Against COVID-19: an in Silico Study Journal of Biomolecular Structure and Dynamics ISSN: 0739-1102 (Print) 1538-0254 (Online) Journal homepage: https://www.tandfonline.com/loi/tbsd20 Reverse vaccinology approach to design a novel multi-epitope vaccine candidate against COVID-19: an in silico study Maryam Enayatkhani, Mehdi Hasaniazad, Sobhan Faezi, Hamed Guklani, Parivash Davoodian, Nahid Ahmadi, Mohammad Ali Einakian, Afsaneh Karmostaji & Khadijeh Ahmadi To cite this article: Maryam Enayatkhani, Mehdi Hasaniazad, Sobhan Faezi, Hamed Guklani, Parivash Davoodian, Nahid Ahmadi, Mohammad Ali Einakian, Afsaneh Karmostaji & Khadijeh Ahmadi (2020): Reverse vaccinology approach to design a novel multi-epitope vaccine candidate against COVID-19: an insilico study, Journal of Biomolecular Structure and Dynamics, DOI: 10.1080/07391102.2020.1756411 To link to this article: https://doi.org/10.1080/07391102.2020.1756411 Accepted author version posted online: 15 Submit your article to this journal Apr 2020. Published online: 02 May 2020. Article views: 3727 View related articles View Crossmark data Citing articles: 2 View citing articles Full Terms & Conditions of access and use can be found at https://www.tandfonline.com/action/journalInformation?journalCode=tbsd20 JOURNAL OF BIOMOLECULAR STRUCTURE AND DYNAMICS https://doi.org/10.1080/07391102.2020.1756411 Reverse vaccinology approach to design a novel multi-epitope vaccine candidate against COVID-19: an in silico study Maryam Enayatkhania, Mehdi Hasaniazada, Sobhan Faezib , Hamed Guklania, Parivash Davoodiana, Nahid Ahmadic, Mohammad Ali Einakiand, Afsaneh Karmostajia and Khadijeh Ahmadia aInfectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran; bMedical Biotechnology Research Center, School of Paramedicine, Guilan University of Medical Sciences, Rasht, Iran; cDepartment of pharmaceutical chemistry, School of Pharmacy, Shahid Beheshti University of Medical Sciences, Tehran, Iran; dFood Health Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, Iran Communicated by Ramaswamy H. Sarma ABSTRACT ARTICLE HISTORY At present, novel Coronavirus (2019-nCoV, the causative agent of COVID-19) has caused worldwide Received 29 March 2020 social and economic disruption. The disturbing statistics of this infection promoted us to develop an Accepted 8 April 2020 effective vaccine candidate against the COVID-19. In this study, bioinformatics approaches were KEYWORDS employed to design and introduce a novel multi-epitope vaccine against 2019-nCoV that can poten- 4þ 8þ COVID-19; Coronavirus; tially trigger both CD and CD T-cell immune responses and investigated its biological activities by Vaccine; Epitope; computational tools. Three known antigenic proteins (Nucleocapsid, ORF3a, and Membrane protein, Immunoinformatics hereafter called NOM) from the virus were selected and analyzed for prediction of the potential immunogenic B and T-cell epitopes and then validated using bioinformatics tools. Based on in silico analysis, we have constructed a multi-epitope vaccine candidate (NOM) with five rich-epitopes domain including highly scored T and B-cell epitopes. After predicting and evaluating of the third structure of the protein candidate, the best 3 D predicted model was applied for docking studies with Toll-like à receptor 4 (TLR4) and HLA-A 11:01. In the next step, molecular dynamics (MD) simulation was used to à evaluate the stability of the designed fusion protein with TLR4 and HLA-A 11:01 receptors. MD studies à demonstrated that the NOM-TLR4 and NOM-HLA-A 11:01 docked models were stable during simula- tion time. In silico evaluation showed that the designed chimeric protein could simultaneously elicit humoral and cell-mediated immune responses. Abbreviations: TLR4: Toll-like receptor4; MD: Molecular dynamics; WHO: World Health Organization; SARS: Severe Acute Respiratory Syndrome; MERS: Middle East Respiratory Syndrome; ORF: Open read- ing frame; MHC: Major histocompatibility complex; CTL: Cytotoxic T-lymphocytes; HTL: Helper T-lym- phocytes; RMSD: Root mean square deviation; ns: Nanoseconds 1. Introduction Betacoronavirus of the Coronaviridae family (Al-Tawfiq et al., 2014). So far, the novel COVID-19 has caused more than Coronavirus disease COVID-19 outbreak began in late 700,000 illnesses and more than 33,000 deaths worldwide December 2019 in Wuhan, the capital of Hubei Province, (W.H.O., 2020). The genome size of this virus is about 30 kb China (Wang et al., 2020). Scientists from all over the world and encodes structural and non-structural proteins like other are attempting to investigate this novel virus, known as coronaviruses. Structural proteins include S protein (Spike), E 2019-nCoV, which is highly contagious, and to discover protein (Envelope), M protein (Membrane), and N protein effective interventions to control and prevent the disease (Nucleocapsid) (Ahmed et al., 2020). The increasing rate of (Heymann, 2020; Huang et al., 2020). Coronaviruses are posi- þ COVID-19 disease and the high morbidity necessitate the tive-sense single-stranded RNA viruses (ssRNA ) belonging to development of a specific and safe vaccine candidate as the Coronaviridae family. Human Coronaviruses HCoV-229E, soon as possible. There is very little known actually about HCoV-NL63, HCoV-OC43, and HCoV-HKU1 are observed in the pathogenesis of the virus; therefore, an immunoinfor- almost one-third of the common cold (Lim et al., 2016). matics-based approach to investigate the immunogenic epit- However, recently some cases of human coronavirus infec- opes and vaccine design using data from proteins tions have led to fatal endemics, including SARS (Severe sequencing of the COVID-19 is required. Acute Respiratory Syndrome), MERS (Middle East Respiratory N protein is the only structural protein that associates Syndrome) and COVID-19 that are common diseases with replicase-transcriptase complexes and binds with gen- between humans and animals whose belong to the genus omic RNA in coronaviruses (Cong et al., 2017). This protein is CONTACT Khadijeh Ahmadi [email protected] Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran. ß 2020 Informa UK Limited, trading as Taylor & Francis Group 2 M. ENAYATKHANI ET AL. multifunctional and one of the most crucial structural com- desirable candidates for vaccine development due to their ponents of coronaviruses. N protein is a structural and anti- relatively easy production, chemical stability, and lack of genic protein that is involved in packaging, transcription, infectious potential (Patronov & Doytchinova, 2013). The and replication coronaviruses (4). This data showed that N experimental design and production of multi-epitope vac- protein is a suitable candidate for targeting drug and vaccine cines have improved dramatically in recent years. These vac- þ design because this protein is conserved, antigenic and cines are mainly made up of B-cell, CD8 cytolytic T-cell þ multifunctional (6). Leung and et al. concluded that N pro- (CTLs) and CD4 helper T-cells (HTLs) epitopes (Chiarella tein can be a suitable vaccine candidate against SARS-Cov et al., 2009). Since the antigenic epitopes of a protein could because induce strong antibody and this process may trigger be predicted and detected, therefore the whole protein is cytokine production (Leung et al., 2004). Coronaviruses M not suitable to stimulate an immune response (Testa & protein also has a key role in the assembly of virions. The Philip, 2012; Zheng et al., 2017). During the development of SARS-CoV M protein can interact with N protein and make a a vaccine candidate against COVID-19, complex pathogenic network of interactions with the genomic RNA (He et al., mechanisms and numerous pathogenic factors should be 2004). Ong and et al. the COVID-19 antigens such as S, N considered in vaccine formulation. and M proteins introduced as a vaccine candidate (6). This In the present study, we aimed to design a novel multi- protein has also been studied as an epitope vaccine candi- epitope fusion protein (Nucleocapsid, ORF3a, and Membrane date against SARS-CoV (7). protein or NOM) containing more efficient antigenic epito- Open reading frame 3a (ORF3a) is required for viral repli- pes-rich domains. The biological activity of the engineered cation and virulence of SARS CoV. Severe induction of proin- fusion protein was assessed by bioinformatics tools using the flammatory cytokine is a sign of SARS-CoV and MERS-CoV interaction between the vaccine candidate and the innate b immune system receptor (TLR4) and cellular immune system infections. ORF3a activates both pro-IL-1 gene expression à and IL-1b secretion and leads to severe lung injury. (Siu receptor (HLA-A 11:01). We strongly believe that the out- et al., 2019). Also, ORF3a has an important role in SARS-CoV come of the present report will provide a potential vaccine assembly or budding with the participation of M and E pro- candidate against 2019-nCoV. teins (McBride & Fielding, 2012). These proteins are not only involved in the pathogenesis of the COVID-19 virus but also 2. Materials and methods have high antigenicity (Chan et al., 2020; Siu et al., 2019;Xu et al., 2020). In this study E, M, N, ORF10, ORF8, ORF3a and In this study, we designed a suitable vaccine candidate M proteins were evaluated by available bioinformatics tools against COVID-19, by exploiting the programs of reverse vac- for designing an efficient multi-epitope
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