Journal of Advanced Defense Science & Technology

Journal of Advanced Defense Science & Technology

In Silico Design and Construction of an RBD Immunogen Against the Adherence of SARS Cov_2

Document Type : -

Authors
Amir Rezaiei 1
shahram nazarian 2
Seyed Mir Latif Mousavi Gargari 3
Hossein Samiei Abianeh 4
Emad Kordbacheh 4
1 Student in Microbial Biotechnology, Department of Biology, Shahed University, Tehran, Iran.
2 Imam Hossein University
3 Professor in Biology Department, Shahed University, Tehran, Iran
4 Department of Biological Sciences,, Faculty of Sciences, Imam Hossein University, Tehran, Iran
Abstract
The contagious SARS virus CoV_2 spread rapidly around the world. The virus has infected more than 550 million people worldwide and killed about 7 million to date. Regarding the mechanism of infection, the receptor-binding domain (RBD) of the Spike protein plays an important role in the virus entry into the host cell. In this study, with a bioinformatics approach the cassette design, codon compatibility, protein stability and finally the structural accuracy (through examining the protein expression) were investigated. To increase the probability of RBD cassette expression, the gene codons and various parameters were optimized and the thermodynamic analysis of mRNA structure were performed to increase stability. The structure of the third protein was also predicted and the quality of the structures was evaluated. The linear and conformational B-cell epitopes were determined. The recombinant RBD protein showed the highest antigen index. The compatibility index of the recombinant protein codon increased to 0.96. The third predicted structure based on the I_TASSER server showed good quality. Thermodynamic analysis of the mRNA structure showed that the predicted structure is stable. The conformational and linear B-cell epitopes were observed in all three domains of the recombinant protein. Finally, the recombinant protein was expressed in a bacterial host. Immunoinformatics and expression results showed that the designed recombinant construct has a high antigenicity and production potential and can be considered as an immunogenic candidate against SARS CoV_2 virus in the future studies.
Keywords
Vaccine Candidate
Bioinformatics
RBD
Recombinant Protein
SARS CoV_2
Subjects

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  1. Smith, T. R. F.; Patel, A.; Ramos, S.; Elwood, D.; Zhu, X.; Yan, J.; Gary, E. N.; Walker, S. N.; Schultheis, K.; Purwar, M.; Xu, Z.; Walters, J.; Bhojnagarwala, P.; Yang, M.; Chokkalingam, N.; Pezzoli, P.; Parzych, E; Reuschel, E. L.; Doan, A.; Tursi, N.; Vasquez, M.; Choi, J.; Tello-Ruiz, E.; Maricic, I.; Bah, M. A.; Wu, Y.; Amante, D.; Park, D. H.; Dia, Y.; Ali, A. R.; Zaidi, F. I.; Generotti, A.; Kim, K. Y.; Herring, T. A.; Reeder, S.; Andrade, V. M.; Buttigieg, K.; Zhao, G.; Wu, J. M.; Li, D.; Bao, L.; Liu, J;. Deng, W.; Qin, C.; Brown, A. S.; Khoshnejad, M.; Wang, N.; Chu, J.; Wrapp, D.; McLellan, J. S.; Muthumani, K.; Wang, B.; Carroll, M. W.; Kim, J. J.; Boyer, J.; Kulp, D. W.; Humeau, L.; Weiner, D. B.; Broderick, K. E. “Immunogenicity of a DNA Vaccine Candidate for COVID-19”; Nat. Commun. 2020, 11.1, 1-13
  2. Tavakoli, A.; Vahdat, K.; Keshavarz, M.“Novel Coronavirus Disease 2019 (COVID-19): An Emerging Infectious Disease in the 21st Century”; ISMJ, 2020, 22.6, 432-450.
  3. Coutard, B.; Valle, C.; de Lamballerie, X.; Canard, B.; Seidah, N. G.; Decroly, E. “The Spike Glycoprotein of the New Coronavirus 2019-nCoV Contains a Furin-Like Cleavage Site Absent in CoV of the Same Clade”; Antiviral Res. 2020, 176, 104742.
  4. 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, 19.5, 305-306.
  5. Wertheim, J. O.; Chu, D. K.; Peiris, J. S. M.; Kosakovsky Pond, S. L.; Poon, L. L. M. “A Case for the Ancient Origin of Coronaviruses”; J. Virol. 2013, 87.12, 7039-7045.
  6. Giandhari, J.; Pillay, S.; Wilkinson, E.; Tegally, H.; Sinayskiy, I.; Schuld, M.; Lourenco, J.; Chimukangara, B.; Lessells, R.; Moosa, Y.; Gazy, I.; Fish, M.; Singh, L.; Khanyile, K.S.; Fonseca, V.; Giovanetti, M.; Alcantara, L.C.; Petruccione, F.; de Oliveira, T. “Early Transmission of SARS-CoV-2 in South Africa: An Epidemiological and Phylogenetic Report”; Int. J. Infect. Dis. 2020, 103, 234-241.
  7. Zhang, J.; Zeng, H.; Gu, J.; Li, H.; Zheng, L.; Zou, Q. “Progress and Prospects on Vaccine Development Against SARS-CoV-2”; Vaccines (Basel) 2020, 8, 153.
  8. Hussain, A.; Kaler, J.; Tabrez, E.; Tabrez, S.; Tabrez, S. S. M. “Novel COVID-19: A Comprehensive Review of Transmission, Manifestation, and Pathogenesis”; Cureus, 2020, 12.5.
  9. Shereen, M. A.; Khan, S.; Kazmi, A.; Bashir, N.; Siddique, R. “COVID-19 Infection: Origin, Transmission, and Characteristics of Human Coronaviruses”; J. Adv. Res. 2020, 24, 91.
  10. Weiss, S. R.; Navas-Martin, S. “Coronavirus Pathogenesis and the Emerging Pathogen Severe Acute Respiratory Syndrome Coronavirus”; Microbiol. Mol. Biol. Rev. 2005, 69, 635-664.
  11. Farnoosh, G.; Alishiri, G.; Hosseini Zijoud, S. R.; Dorostkar, R.; Jalali Farahani, A. “Understanding the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) and Coronavirus Disease (COVID-19) Based on Available Evidence - A Narrative Review”; J. Military Medicine 2020, 22, 1-11.
  12. Shereen, M. A.; Khan, S.; Kazmi, A., Bashir, N.; Siddique, R. “COVID-19 Infection: Origin, Transmission, and Characteristics of Human Coronaviruses”; J. Adv. Res. 2020, 24, 91.
  13. Nazarian, S.; Gargari, S. L. M.; Rasooli, I.; Amani, J.; Bagheri, S.; Alerasool, M. J. J. O. M. M. “An in Silico Chimeric Multi Subunit Vaccine Targeting Virulence Factors of Enterotoxigenic Escherichia Coli (ETEC) with Its Bacterial Inbuilt Adjuvant”; J. Microbiol. Methods 2012, 90, 36-45.
  14. Daugelaite, J.; O'Driscoll, A.; Sleator, R. D. J. I. S. R. N. “An Overview of Multiple Sequence Aignments and Cloud Computing in Bioinformatics”; Int. Scholarly Res. Not. 2013.
  15. Manikyam, H. K.; Joshi, S. K. J. J. O. P. “Whole Genome Analysis and Targeted Drug Discovery Using Computational Methods and High Throughput Screening Tools for Emerged Novel Coronavirus (2019-nCoV)”; J. Pharm. Drug Res. 2020, 3, 341.
  16. Puigbo, P.; Romeu, A.; Garcia-Vallve, S. J. N. A. R. “HEG-DB: a Database of Predicted Highly Expressed Genes in Prokaryotic Complete Genomes under Translational Selection”; Nucleic Acids Res. 2007, 36, D524-D527.
  17. Srivastava, S.; Verma, S.; Kamthania, M.; Kaur, R.; Badyal, R. K.; Saxena, A. K.; Shin, H. J.; Kolbe, M.; Pandey, K. C. J. B. “Structural Basis to Design Multi-Epitope Vaccines Against Novel Coronavirus 19 (COVID19) Infection, the Ongoing Pandemic Emergency: an In Silico Approach”; BioRxiv, 2020.
  18. Madhugiri, R.; Karl, N.; Petersen, D.; Lamkiewicz, K.; Fricke, M.; Wend,; Scheuer, R.; Marz, M.; Ziebuhr, J. J. V. “Structural and Functional Conservation of Cis-Acting RNA Elements in Coronavirus 5'-terminal Genome Regions”; Virology 2018, 517, 44-55.
  19. Gasteiger, E.; Hoogland, C.; Gattiker, A.; Wilkins, M. R.; Appel, R. D.; Bairoch, A. J. T. P. P. H. “Protein Identification and Analysis Tools on the ExPASy Server”; The Proteomics Protocols Handbook, 2005, 571-607.
  20. Hebditch, M.; Carballo-Amador, M. A.; Charonis, S.; Curtis, R.; Warwicker, J. J. B. “Protein–Sol: A Web Tool for Predicting Protein Solubility from Sequence”; Bioinformatics 2017, 33, 3098-3100.
  21. Ceroni, A.; Passerini, A.; Vullo, A.; Frasconi, P. J. N. A. R. “DISULFIND: A Disulfide Bonding State and Cysteine Connectivity Prediction Server”; Nucleic Acids Res. 2006, 34 , W177-W181.
  22. Magnan, C. N.; Zeller, M.; Kayala, M. A.; Vigil, A.; Randall, A.; Felgner, P. L.; Baldi, P. J. B. “High-Throughput Prediction of Protein Antigenicity Using Protein Microarray Data”; Bioinformatics  2010, 26, 2936-2943.
  23. Chukwudozie, O. S.; Duru, V. C.; Ndiribe, C. C.; Aborode, A.; Oyebanji, V. O.; Emikpe, B. O. J. B.; Insights, B. “The Relevance of Bioinformatics Applications in the Discovery of Vaccine Candidates and Potential Drugs for COVID-19 Treatment”; Bioinf. Biol. Insights 2021, 15, 11779322211002168.
  24. Sadat, S. M.; Aghadadeghi, M. R.; Yousefi, M.; Khodaei, A.; Larijani, M. S.; Bahramali, G. J. M. B. “Bioinformatics Analysis of SARS-CoV-2 to Approach an Effective Vaccine Candidate Against COVID-19”; Mol. Biotech. 2021, 63, 389-409.‏
  25. Dangi, M.; Kumari, R.; Singh, B.; Chhillar, A. K. “Advanced in Silico Tools for Designing of Antigenic Epitope as Potential Vaccine Candidates Against Coronavirus”; Bioinformatics 2018, 329-357.
  26. Yazdani, Z.; Rafiei, A.; Yazdani, M.; Valadan, R. J. I.; Resistance, D. “Design an Efficient Multi-Epitope Peptide Vaccine Candidate Against SARS-CoV-2: An in Silico Analysis”; Infect. Drug Resist. 2020, 13, 3007.
  27. Chen, H. Z.; Tang, L. L.; Yu, X. L.; Zhou, J.; Chang, Y. ; Wu, X. J. I. D. O. P. “Bioinformatics Analysis of Epitope-Based Vaccine Design Against the Novel SARS-CoV-2”; Infect. Dis. Poverty 2020,  9, 1-10.
  28. Can, H.; Köseoğlu, A. E.; Alak, S. E.; Güvendi, M.; Döşkaya, M.; Karakavuk, M.; Gürüz, A. Y.; Ün, C. J. S. R. “In Silico Discovery of Antigenic Proteins and Epitopes of SARS-CoV-2 for the Development of a Vaccine or a Diagnostic Approach for COVID-19”; Sci. Rep. 2020, 10, 1-16.
  29. Yang, J.; Wang, W.; Chen, Z.; Lu, S.; Yang, F.; Bi, Z.; Wei, X. “A Vaccine Targeting the RBD of the S Protein of SARS-CoV-2 Induces Protective Immunity”; Nature 2020, 586, 572-577.‏
  30. Djukic, T.; Mladenovic, M.; Stanic-Vucinic, D.; Radosavljevic, J.; Smiljanic, K.; Sabljic, L.; Velickovic, T. C. “Expression, Purification and Immunological Characterization of Recombinant Nucleocapsid Protein Fragment from SARS-CoV-2”; Virology 2021, 557, 15-22
Journal of Advanced Defense Science & Technology
Volume 13, Issue 2 - Serial Number 48
Summer
Autumn 2022
Pages 79-87

  • Receive Date 01 January 2022
  • Revise Date 01 August 2022
  • Accept Date 11 August 2022
  • Publish Date 22 September 2022