Designing novel peptides for detecting the Omicron variant, specifying SARS-CoV-2, and simultaneously screening coronavirus infections

References

• Pang, J., Wang, M. X., Ang, I. Y. H., Tan, S. H. X., Lewis, R. F., Chen, J. I.-P., Gutierrez, R. A., Gwee, S. X. W., Chua, P. E. Y., Yang, Q., Ng, X. Y., Yap, R. K., Tan, H. Y., Teo, Y. Y., Tan, C. C., Cook, A. R., Yap, J. C.-H., & Hsu, L. Y. (2020). Potential rapid diagnostics, vaccine and therapeutics for 2019 novel coronavirus (2019-nCoV): A systematic review. Journal of Clinical Medicine, 9(3), 623. https://doi.org/10.3390/jcm9030623
   PubMed Web of Science ®Google Scholar
• Ahmed, S. F., Quadeer, A. A., & McKay, M. R. (2020). Preliminary identification of potential vaccine targets for the COVID-19 coronavirus (SARS-CoV-2) based on SARS-CoV immunological studies. Viruses, 12(3), 254. https://doi.org/10.3390/v12030254
   PubMed Web of Science ®Google Scholar
• Alhazzani, W., Evans, L., Alshamsi, F., Møller, M. H., Ostermann, M., Prescott, H. C., Arabi, Y. M., Loeb, M., Ng Gong, M., Fan, E., Oczkowski, S., Levy, M. M., Derde, L., Dzierba, A., Du, B., Machado, F., Wunsch, H., Crowther, M., Cecconi, M., … Rhodes, A. (2021). Surviving sepsis campaign guidelines on the management of adults with coronavirus disease 2019 (COVID-19) in the ICU: First update. Critical Care Medicine, 49(3), e219–e34. https://doi.org/10.1097/CCM.0000000000004899
   PubMed Web of Science ®Google Scholar
• Banfield, M., King, D., Mountain, A., & Brady, R. (1997). VL: VH domain rotations in engineered antibodies: Crystal structures of the Fab fragments from two murine antitumor antibodies and their engineered human constructs. Proteins: Structure, Function, and Genetics, 29(2), 161–171. https://doi.org/10.1002/(SICI)1097-0134(199710)29:2<161::AID-PROT4>3.0.CO;2-G
   PubMed Web of Science ®Google Scholar
• Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., & Bourne, P. E. (2000). The protein data bank. Nucleic Acids Research, 28(1), 235–242. https://doi.org/10.1093/nar/28.1.235
   PubMed Web of Science ®Google Scholar
• Best, R. B., Zhu, X., Shim, J., Lopes, P. E. M., Mittal, J., Feig, M., & Mackerell, A. D. (2012). Optimization of the additive CHARMM all-atom protein force field targeting improved sampling of the backbone ϕ, ψ and side-chain χ1 and χ2 dihedral angles. Journal of Chemical Theory and Computation, 8(9), 3257–3273. https://doi.org/10.1021/ct300400x
   PubMed Web of Science ®Google Scholar
• Bosch, B. J., van der Zee, R., de Haan, C. A., & Rottier, P. J. (2003). The coronavirus spike protein is a class I virus fusion protein: Structural and functional characterization of the fusion core complex. Journal of Virology, 77(16), 8801–8811. https://doi.org/10.1128/jvi.77.16.8801-8811.2003
   PubMed Web of Science ®Google Scholar
• Can, H., Köseoğlu, A. E., Erkunt Alak, S., Güvendi, M., Döşkaya, M., Karakavuk, M., Gürüz, A. Y., & Ün, C. (2020). 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. Scientific Reports, 10(1), 1–16. https://doi.org/10.1038/s41598-020-79645-9
   PubMed Web of Science ®Google Scholar
• Chan, J. F.-W., Yuan, S., Kok, K.-H., To, K. K.-W., Chu, H., Yang, J., Xing, F., Liu, J., Yip, C. C.-Y., Poon, R. W.-S., Tsoi, H.-W., Lo, S. K.-F., Chan, K.-H., Poon, V. K.-M., Chan, W.-M., Ip, J. D., Cai, J.-P., Cheng, V. C.-C., Chen, H., Hui, C. K.-M., & Yuen, K.-Y. (2020). A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster. Lancet (London, England), 395(10223), 514–523. https://doi.org/10.1016/S0140-6736(20)30154-9
   PubMed Web of Science ®Google Scholar
• Chen, N., Zhou, M., Dong, X., Qu, J., Gong, F., Han, Y., Qiu, Y., Wang, J., Liu, Y., Wei, Y., Xia, J., Yu, T., Zhang, X., & Zhang, L. (2020). Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study. Lancet (London, England), 395(10223), 507–513. https://doi.org/10.1016/S0140-6736(20)30211-7
   PubMed Web of Science ®Google Scholar
• Choe, J. ‐Y., Kim, J. ‐W., Kwon, H. H., Hong, H. ‐L., Jung, C. Y., Jeon, C. ‐H., Park, E. ‐J., & Kim, S. ‐K. (2020). Diagnostic performance of immunochromatography assay for rapid detection of IgM and IgG in coronavirus disease 2019. Journal of Medical Virology, 92(11), 2567–2572. https://doi.org/10.1002/jmv.26060
   PubMed Web of Science ®Google Scholar
• Choudhary, O. P., Dhawan., & M., Priyanka. (2022). Omicron variant (B. 1.1. 529) of SARS-CoV-2: Threat assessment and plan of action. International Journal of Surgery (London, England), 97, 106187. https://doi.org/10.1016/j.ijsu.2021.106187
   PubMed Web of Science ®Google Scholar
• Colovos, C., & Yeates, T. O. (1993). Verification of protein structures: Patterns of nonbonded atomic interactions. Protein Science: A Publication of the Protein Society, 2(9), 1511–1519. https://doi.org/10.1002/pro.5560020916
   PubMed Web of Science ®Google Scholar
• COVaraints. (2022). [2022-01-11:[Available from: https://covariants.org/variants/21K.Omicron.
   Google Scholar
• Demir, A. B., Benvenuto, D., Abacioğlu, Y. H., Angeletti, S., & Ciccozzi, M. (2020). Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey. Turkish Journal of Biology = Turk Biyoloji Dergisi, 44(3), 178–184. https://doi.org/10.3906/biy-2005-69
   PubMed Web of Science ®Google Scholar
• Di Mascio, D., Khalil, A., Saccone, G., Rizzo, G., Buca, D., Liberati, M., Vecchiet, J., Nappi, L., Scambia, G., Berghella, V., & D'Antonio, F. (2020). Outcome of Coronavirus spectrum infections (SARS, MERS, COVID 1-19) during pregnancy: A systematic review and meta-analysis. American Journal of Obstetrics & Gynecology MFM, 2(2), 100107. https://doi.org/10.1016/j.ajogmf.2020.100107
   PubMed Web of Science ®Google Scholar
• Emini, E. A., Hughes, J. V., Perlow, D., & Boger, J. (1985). Induction of hepatitis A virus-neutralizing antibody by a virus-specific synthetic peptide. Journal of Virology, 55(3), 836–839. https://doi.org/10.1128/JVI.55.3.836-839.1985
   PubMed Web of Science ®Google Scholar
• Faria, A. R., de Castro Veloso, L., Coura-Vital, W., Reis, A. B., Damasceno, L. M., Gazzinelli, R. T., & Andrade, H. M. (2015). Novel recombinant multiepitope proteins for the diagnosis of asymptomatic Leishmania infantum-infected dogs. PLoS Neglected Tropical Diseases, 9(1), e3429. https://doi.org/10.1371/journal.pntd.0003429
   PubMed Web of Science ®Google Scholar
• Ferré, V. M., Peiffer-Smadja, N., Visseaux, B., Descamps, D., Ghosn, J., & Charpentier, C. (2022). Omicron SARS-CoV-2 variant: What we know and what we don’t. Anaesthesia. Critical Care & Pain Medicine, 41(1), 100998.
   Web of Science ®Google Scholar
• Guarner, J. (2020). Three emerging coronaviruses in two decades: The story of SARS, MERS, and now COVID-19. Oxford University Press US.
   Google Scholar
• Hajighahramani, N., Nezafat, N., Eslami, M., Negahdaripour, M., Rahmatabadi, S. S., & Ghasemi, Y. (2017). Immunoinformatics analysis and in silico designing of a novel multi-epitope peptide vaccine against Staphylococcus aureus. Infection, Genetics and Evolution: Journal of Molecular Epidemiology and Evolutionary Genetics in Infectious Diseases, 48, 83–94. https://doi.org/10.1016/j.meegid.2016.12.010
   PubMed Web of Science ®Google Scholar
• Huang, C., Wang, Y., Li, X., Ren, L., Zhao, J., Hu, Y., Zhang, L., Fan, G., Xu, J., Gu, X., Cheng, Z., Yu, T., Xia, J., Wei, Y., Wu, W., Xie, X., Yin, W., Li, H., Liu, M., … Cao, B. (2020). Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China. Lancet (London, England), 395(10223), 497–506. https://doi.org/10.1016/S0140-6736(20)30183-5
   PubMed Web of Science ®Google Scholar
• Jespersen, M. C., Peters, B., Nielsen, M., & Marcatili, P. (2017). BepiPred-2.0: Improving sequence-based B-cell epitope prediction using conformational epitopes. Nucleic Acids Research, 45(W1), W24–W29. https://doi.org/10.1093/nar/gkx346
   PubMed Web of Science ®Google Scholar
• Keighobadi, M., Emami, S., Lagzian, M., Fakhar, M., Rafiei, A., & Valadan, R. (2018). Molecular modeling and structural stability of wild-type and mutant CYP51 from leishmania major: In vitro and in silico analysis of a laboratory strain. Molecules, 23(3), 696. https://doi.org/10.3390/molecules23030696
   PubMed Web of Science ®Google Scholar
• Kelley, L. A., Mezulis, S., Yates, C. M., Wass, M. N., & Sternberg, M. J. (2015). The Phyre2 web portal for protein modeling, prediction and analysis. Nature Protocols, 10(6), 845–858. https://doi.org/10.1038/nprot.2015.053
   PubMed Web of Science ®Google Scholar
• Ko, J., Park, H., Heo, L., & Seok, C. (2012). GalaxyWEB server for protein structure prediction and refinement. Nucleic Acids Research, 40(Web Server issue), W294–W297. https://doi.org/10.1093/nar/gks493
   PubMed Web of Science ®Google Scholar
• Laureano, A. F. S., & Riboldi, M. (2020). The different tests for the diagnosis of COVID-19-A review in Brazil so far. JBRA Assisted Reproduction, 24(3), 340.
   PubMed Web of Science ®Google Scholar
• Mahtarin, R., Islam, S., Islam, M. J., Ullah, M. O., Ali, M. A., & Halim, M. A. (2022). Structure and dynamics of membrane protein in SARS-CoV-2. Journal of Biomolecular Structure and Dynamics. 40(10), 4725–4738. https://doi.org/10.1080/07391102.2020.1861983
   PubMed Web of Science ®Google Scholar
• Mathews, D. H., Disney, M. D., Childs, J. L., Schroeder, S. J., Zuker, M., & Turner, D. H. (2004). Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proceedings of the National Academy of Sciences of the United States of America, 101(19), 7287–7292. https://doi.org/10.1073/pnas.0401799101
   PubMed Web of Science ®Google Scholar
• Miao, M., Clercq, E. D., & Li, G. (2021). Genetic Diversity of SARS-CoV-2 over a One-Year Period of the COVID-19 Pandemic: A Global Perspective. Biomedicines, 9(4), 412. https://doi.org/10.3390/biomedicines9040412
   PubMed Web of Science ®Google Scholar
• Mousavizadeh, L., & Ghasemi, S. (2020). Genotype and phenotype of COVID-19: Their roles in pathogenesis. Journal of Microbiology, Immunology and Infection, 54(2), 159-163.
   Google Scholar
• Peeri, N. C., Shrestha, N., Rahman, M. S., Zaki, R., Tan, Z., Bibi, S., et al. (2020). The SARS, MERS and novel coronavirus (COVID-19) epidemics, the newest and biggest global health threats: What lessons have we learned? International Journal of Epidemiology, 49(3), 717-726.
   Google Scholar
• Peiris, J. S. M., Lai, S. T., Poon, L. L. M., Guan, Y., Yam, L. Y. C., Lim, W., Nicholls, J., Yee, W. K. S., Yan, W. W., Cheung, M. T., Cheng, V. C. C., Chan, K. H., Tsang, D. N. C., Yung, R. W. H., Ng, T. K., & Yuen, K. Y. (2003). Coronavirus as a possible cause of severe acute respiratory syndrome. The Lancet, 361(9366), 1319–1325. https://doi.org/10.1016/S0140-6736(03)13077-2
   PubMed Web of Science ®Google Scholar
• Peverengo, L. M., Garcia, V., Rodeles, L. M., Mendicino, D., Vicco, M., Lagier, C., Gonzalez, V., Gugliotta, L., & Marcipar, I. (2018). Development and assessment of an improved recombinant multiepitope antigen-based immunoassay to diagnose chronic Chagas disease. Parasitology, 145(12), 1594–1599. https://doi.org/10.1017/S0031182018000458
   PubMed Web of Science ®Google Scholar
• Poh, C. M., Carissimo, G., Wang, B., Amrun, S. N., Lee, C. Y.-P., Chee, R. S.-L., Fong, S.-W., Yeo, N. K.-W., Lee, W.-H., Torres-Ruesta, A., Leo, Y.-S., Chen, M. I.-C., Tan, S.-Y., Chai, L. Y. A., Kalimuddin, S., Kheng, S. S. G., Thien, S.-Y., Young, B. E., Lye, D. C., … Ng, L. F. P. (2020). Two linear epitopes on the SARS-CoV-2 spike protein that elicit neutralising antibodies in COVID-19 patients. Nature Communications, 11(1), 1–7. https://doi.org/10.1038/s41467-020-16638-2
   PubMed Web of Science ®Google Scholar
• Ponomarenko, J., Bui, H.-H., Li, W., Fusseder, N., Bourne, P. E., Sette, A., et al. (2008). ElliPro: A new structure-based tool for the prediction of antibody epitopes. BMC Bioinformatics, 9(1), 514.
   PubMed Web of Science ®Google Scholar
• Prompetchara, E., Ketloy, C., & Palaga, T. (2020). Immune responses in COVID-19 and potential vaccines: Lessons learned from SARS and MERS epidemic. Asian Pacific Journal of Allergy and Immunology, 38(1), 1–9.
   PubMed Web of Science ®Google Scholar
• Rahman, M. S., Hoque, M. N., Islam, M. R., Akter, S., Rubayet Ul Alam, A. S. M., Siddique, M. A., Saha, O., Rahaman, M. M., Sultana, M., Crandall, K. A., & Hossain, M. A. (2020). Epitope-based chimeric peptide vaccine design against S, M and E proteins of SARS-CoV-2, the etiologic agent of COVID-19 pandemic: An in silico approach. PeerJ. 8, e9572. https://doi.org/10.7717/peerj.9572
   PubMed Web of Science ®Google Scholar
• Romero-López, J., Carnalla-Cortés, M., Pacheco-Olvera, D., Ocampo, M., Oliva-Ramírez, J., & Moreno-Manjón, J. (2020). Prediction of SARS-CoV2 spike protein epitopes reveals HLA-associated susceptibility.
   Google Scholar
• Sahin, A. R., Erdogan, A., Agaoglu, P. M., Dineri, Y., Cakirci, A. Y., & Senel, M. E. (2020). 2019 novel coronavirus (COVID-19) outbreak: A review of the current literature. Eurasian Journal of Medicine and Oncology, 4(1), 1–7. (https://doi.org/10.14744/ejmo.2020.12220
   Google Scholar
• Singanayagam, A., Patel, M., Charlett, A., Bernal, J. L., Saliba, V., Ellis, J., et al. (2020). Duration of infectiousness and correlation with RT-PCR cycle threshold values in cases of COVID-19, England, January to May 2020. Euro Surveill, 25(32), 2001483.
   PubMedGoogle Scholar
• Stein, R. A. (2020). The 2019 coronavirus: Learning curves, lessons, and the weakest link. International Journal of Clinical Practice, 74(4), e13488.
   PubMed Web of Science ®Google Scholar
• Thomas, S. (2020). The structure of the membrane protein of sars-cov-2 resembles the sugar transporter semisweet. Pathogens & Immunity, 5(1), 342–363. https://doi.org/10.20411/pai.v5i1.377
   PubMedGoogle Scholar
• Ul Qamar, M. T., Alqahtani, S. M., Alamri, M. A., & Chen, L.-L. (2020). Structural basis of SARS-CoV-2 3CLpro and anti-COVID-19 drug discovery from medicinal plants. Journal of Pharmaceutical Analysis, 10(4), 313–319. https://doi.org/10.1016/j.jpha.2020.03.009
   PubMed Web of Science ®Google Scholar
• Wijsman, L., Molenkamp, R., Reusken, C., & Meijer, A. (2020). Comparison of seven commercial RT-PCR diagnostic kits for COVID-19. J. Clin. Virol, 128, 104412.
   PubMed Web of Science ®Google Scholar
• World Health Organization. (2021). Classification of Omicron (B. 1.1. 529): SARS-CoV-2 variant of concern. World Health Organization https://www who int/news/item/26-11-2021-classification-of-omicron-(b 11 529)-sars-cov-2-variant-of-concern Published 202Accessed November. 2021;28.
   Google Scholar
• Wrapp, D., Wang, N., Corbett, K. S., Goldsmith, J. A., Hsieh, C.-L., Abiona, O., Graham, B. S., & McLellan, J. S. (2020). Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation. Science (New York, N.Y.), 367(6483), 1260–1263. https://doi.org/10.1126/science.abb2507
   PubMed Web of Science ®Google Scholar
• Yan, Y., Tao, H., He, J., & Huang, S.-Y. (2020). The HDOCK server for integrated protein–protein docking. Nature Protocols, 15(5), 1829–1852. https://doi.org/10.1038/s41596-020-0312-x
   PubMed Web of Science ®Google Scholar
• Yan, Y., Zhang, D., Zhou, P., Li, B., & Huang, S.-Y. (2017). HDOCK: A web server for protein–protein and protein–DNA/RNA docking based on a hybrid strategy. Nucleic Acids Research, 45(W1), W365–W373. https://doi.org/10.1093/nar/gkx407
   PubMed Web of Science ®Google Scholar
• Yazdani, Z., Rafiei, A., Ghoreyshi, M., & Abediankenari, S. (2023). In Silico Analysis of a Candidate Multi-epitope Peptide Vaccine Against Human Brucellosis. Molecular Biotechnology, 65(3), 1–15. https://doi.org/10.1007/s12033-023-00698-y
   PubMedGoogle Scholar
• Yazdani, Z., Rafiei, A., Irannejad, H., Yazdani, M., & Valadan, R. (2022). Designing a novel multiepitope peptide vaccine against melanoma using immunoinformatics approach. Journal of Biomolecular Structure & Dynamics, 40(7), 3312–3324. https://doi.org/10.1080/07391102.2020.1846625
   PubMed Web of Science ®Google Scholar
• Yazdani, Z., Rafiei, A., Valadan, R., Ashrafi, H., Pasandi, M., & Kardan, M. (2020). Designing a potent L1 protein-based HPV peptide vaccine: A bioinformatics approach. Computational Biology and Chemistry, 85, 107209. https://doi.org/10.1016/j.compbiolchem.2020.107209
   PubMed Web of Science ®Google Scholar
• Yazdani, Z., Rafiei, A., Yazdani, M., & Valadan, R. (2020). Design an efficient multi-epitope peptide vaccine candidate against SARS-CoV-2: An in silico analysis. Infection and Drug Resistance, 13, 3007–3022. https://doi.org/10.2147/IDR.S264573
   PubMed Web of Science ®Google Scholar
• Yin, Y., & Wunderink, R. G. (2018). MERS, SARS and other coronaviruses as causes of pneumonia. Respirology (Carlton, Vic.), 23(2), 130–137. https://doi.org/10.1111/resp.13196
   PubMed Web of Science ®Google Scholar
• Yurkovetskiy, L., Wang, X., Pascal, K. E., Tomkins-Tinch, C., Nyalile, T. P., Wang, Y., Baum, A., Diehl, W. E., Dauphin, A., Carbone, C., Veinotte, K., Egri, S. B., Schaffner, S. F., Lemieux, J. E., Munro, J. B., Rafique, A., Barve, A., Sabeti, P. C., Kyratsous, C. A., … Luban, J. (2020). Structural and functional analysis of the D614G SARS-CoV-2 spike protein variant. Cell, 183(3), 739–751. e8. https://doi.org/10.1016/j.cell.2020.09.032
   PubMed Web of Science ®Google Scholar
• Zheng, M., & Song, L. (2020). Novel antibody epitopes dominate the antigenicity of spike glycoprotein in SARS-CoV-2 compared to SARS-CoV. Cellular & Molecular Immunology, 17(5), 536–538. https://doi.org/10.1038/s41423-020-0385-z
   PubMed Web of Science ®Google Scholar