Olası terapötikler için SARS-CoV-2’nin spike, zarf ve membran proteinlerinin modelleri

Öz

Amaç: Şiddetli akut solunum sendromu ile ilişkili SARS-CoV-2, yüksek morbidite ve mortaliteye sahip, yaygın, hızla büyüyen bir enfeksiyon hastalığıdır. Bu virüsün üç yapısal proteininin dizisindeki mutasyonlar, pandeminin ilerlemesi üzerinde önemli bir etkiye sahip olabilir.

Bu çalışmada, söz konusu SARS-CoV-2'nin beş varyantındaki mutasyonlar modellenip analiz edilerek, gelecekteki ilaç ve aşı araştırmaları için olası hedeflerin ortaya çıkarılması amaçlanmıştır.

Materyal ve Metot: DSÖ tarafından Endişe Verici Varyantlar (VoC) olarak tanımlanan beş varyantın RNA dizileri NCBI'den elde edildi. Bu dizilerin amino asit dizisine çevrilmesi, dizi hizalaması ve varyantlar arasında dizi karşılaştırması, 2020 çalışmasına referansla RStudio 1.4.1717'de gerçekleştirilmiştir.

Wuhan varyantının yapısal proteinleri ve PDB dosyaları, I-TASSER sunucusu ile yapılan çalışmalardan indirildi. Yapısal proteinlerin 3D görüntüleri LLC, Schrödinger, PyMOL Molecular Graphics System 1.2r3pre'de gerçekleştirilmiştir.

Sonuçlar: VoC ve Wuhan soyuna ait üç yapısal proteinin amino asit dizileri ve mutasyonlar gösterilmiştir. Alfa, Beta, Delta ve Gama'daki mutasyon sayıları ise şu şekildeydi; 10, 8, 10 ve 12. Zarf ve zar proteinleri sırasıyla Beta ve Delta'da birer mutasyona sahipti.

Sonuçlar: Sonuçlar, SARS-CoV-2 varyantlarının spike proteinlerinde birkaç mutasyon meydana geldiğini göstermektedir. Zarf ve zar proteinlerinde sadece az sayıda mutasyon gözlenir. Gelecekteki aşı ve ilaç geliştirme çalışmaları için daha az mutasyona uğramış yapısal proteinlere odaklanmak faydalı olabilir.

Anahtar Kelimeler

• R programlama dili
• SARS-CoV-2
• Dizi Hizalama
• Yapı Proteinleri
• Moleküler Modelleme

Models of spike, envelope and membrane proteins of SARS-CoV-2 variants for possible therapeutics

Öz

Background: SARS-CoV-2 associated with severe acute respiratory syndrome is a common, rapidly growing infectious disease with high morbidity and mortality. Mutations in the sequence of the three structural proteins of this virus may have a significant impact on the progression of the pandemic.

In this study, it was aimed to reveal possible targets for future drug and vaccine research by modeling and analyzing mutations in five variants of SARS-CoV-2 of concern.

Materials and Methods: RNA sequences of five variants identified by WHO as Variants of Concern (VoC) were obtained from NCBI. The translation of these sequences to amino acid sequence, sequence alignment and sequence comparison between variants was performed in RStudio 1.4.1717 with reference to 2020 study. Structural proteins and PDB files of the Wuhan variant were downloaded from studies conducted with the I-TASSER server. 3D representations of structural proteins were performed in LLC, Schrödinger, PyMOL Molecular Graphics System 1.2r3pre.

Results: The amino acid sequences of three structural proteins belonging to the VoC and the Wuhan lineage and the mutations are shown. The mutation numbers in Alpha, Beta, Delta and Gamma were as follows; 10, 8, 10 and 12. The envelope and membrane proteins had one mutation each in Beta and Delta, respectively.

Conclusions: The results show that several mutations occur the spike proteins of the SARS-CoV-2 variants. Only a small number of mutations are observed in envelope and membrane proteins. It may be beficial to focus on less mutated structural proteins for future vaccine and drug development studies. 

Anahtar Kelimeler

• R programming language
• SARS-CoV-2
• Sequence alignment
• Structural proteins
• Molecular modelling

Kaynakça

1. Alsulami, A. F., Thomas, S. E., Jamasb, A. R., Beaudoin, C. A., Moghul, I., Bannerman, B., Copoiu, L., Vedithi, S. C., Torres, P., & Blundell, T. L. (2021). SARS-CoV-2 3D database: Understanding the coronavirus proteome and evaluating possible drug targets. Briefings in Bioinformatics, 22(2), 769–780. https://doi.org/10.1093/bib/bbaa404
2. Arabi, Y. M., Asiri, A. Y., Assiri, A. M., Balkhy, H. H., Al Bshabshe, A., Al Jeraisy, M., Mandourah, Y., Azzam, M. H. A., Bin Eshaq, A. M., Al Johani, S., Al Harbi, S., Jokhdar, H. A. A., Deeb, A. M., Memish, Z. A., Jose, J., Ghazal, S., Al Faraj, S., Al Mekhlafi, G. A., Sherbeeni, N. M., … Saudi Critical Care Trials Group. (2020). Interferon Beta-1b and Lopinavir-Ritonavir for Middle East Respiratory Syndrome. The New England Journal of Medicine, 383(17), 1645–1656. https://doi.org/10.1056/NEJMoa2015294
3. Bayrakdar, F., Cosgun, Y., Yalcin, S., & Korukluoglu, G. (2021). HCoV-19/Turkey/HSGM-F10304/2021 (GISAID EpiCoV EPI_ISL_8082633). Ministry of Health Turkey. https://www.epicov.org/epi3/frontend#3f63b7
4. Buxbaum, E. (2015). Protein Structure. In E. Buxbaum, Fundamentals of Protein Structure and Function (pp. 15–64). Springer International Publishing. https://doi.org/10.1007/978-3-319-19920-7_2
5. Cao, Y., Wang, J., Jian, F., Xiao, T., Song, W., Yisimayi, A., Huang, W., Li, Q., Wang, P., An, R., Wang, J., Wang, Y., Niu, X., Yang, S., Liang, H., Sun, H., Li, T., Yu, Y., Cui, Q., … Xie, X. S. (2021). Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies. Nature. https://doi.org/10.1038/d41586-021-03796-6
6. Cao, Y., Yang, R., Lee, I., Zhang, W., Sun, J., Wang, W., & Meng, X. (2021). Characterization of the SARS-CoV-2 E Protein: Sequence, Structure, Viroporin, and Inhibitors. Protein Science, 30(6), 1114–1130. https://doi.org/10.1002/pro.4075
7. Classification of Omicron (B.1.1.529): SARS-CoV-2 Variant of Concern. (n.d.). Retrieved 27 December 2021, from https://www.who.int/news/item/26-11-2021-classification-of-omicron-(b.1.1.529)-sars-cov-2-variant-of-concern
8. Cubuk, J., Alston, J. J., Incicco, J. J., Singh, S., Stuchell-Brereton, M. D., Ward, M. D., Zimmerman, M. I., Vithani, N., Griffith, D., Wagoner, J. A., Bowman, G. R., Hall, K. B., Soranno, A., & Holehouse, A. S. (2021). The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA. Nature Communications, 12(1), 1936. https://doi.org/10.1038/s41467-021-21953-3

9. de Oliveira, O. V., Rocha, G. B., Paluch, A. S., & Costa, L. T. (2021). Repurposing approved drugs as inhibitors of SARS-CoV-2 S-protein from molecular modeling and virtual screening. Journal of Biomolecular Structure and Dynamics, 39(11), 3924–3933. https://doi.org/10.1080/07391102.2020.1772885
10. Enjuanes, L., Smerdou, C., Castilla, J., Antón, I. M., Torres, J. M., Sola, I., Golvano, J., Sánchez, J. M., & Pintado, B. (1995). Development of protection against coronavirus induced diseases. A review. Advances in Experimental Medicine and Biology, 380, 197–211. https://doi.org/10.1007/978-1-4615-1899-0_34
11. Good, D. J. (2020). A low-cost, in silico nutritional genomics course-based undergraduate research experience applicable to multiple disciplines. Biochemistry and Molecular Biology Education, 48(4), 320–328. https://doi.org/10.1002/bmb.21352
12. Huang, Y., Yang, C., Xu, X., Xu, W., & Liu, S. (2020). Structural and functional properties of SARS-CoV-2 spike protein: Potential antivirus drug development for COVID-19. Acta Pharmacologica Sinica, 41(9), 1141–1149. https://doi.org/10.1038/s41401-020-0485-4
13. Iannarella, R., Lattanzi, C., Cannata, G., Argentiero, A., Neglia, C., Fainardi, V., Pisi, G., & Esposito, S. (2020). Coronavirus infections in children: From SARS and MERS to COVID-19, a narrative review of epidemiological and clinical features. Acta Biomedica Atenei Parmensis, 91(3), e2020032–e2020032. https://doi.org/10.23750/abm.v91i3.10294
14. Kardani, K., Bolhassani, A., & Namvar, A. (2020). An overview of in silico vaccine design against different pathogens and cancer. Expert Review of Vaccines, 19(8), 699–726. https://doi.org/10.1080/14760584.2020.1794832
15. Lee, C. H., & Koohy, H. (2020). In silico identification of vaccine targets for 2019-nCoV. F1000Research, 9, 145. https://doi.org/10.12688/f1000research.22507.2
16. Li, Y., Zhang, Z., Yang, L., Lian, X., Xie, Y., Li, S., Xin, S., Cao, P., & Lu, J. (2020). The MERS-CoV Receptor DPP4 as a Candidate Binding Target of the SARS-CoV-2 Spike. IScience, 23(6), 101160. https://doi.org/10.1016/j.isci.2020.101160
17. McIntosh, K., Dees, J. H., Becker, W. B., Kapikian, A. Z., & Chanock, R. M. (1967). Recovery in tracheal organ cultures of novel viruses from patients with respiratory disease. Proceedings of the National Academy of Sciences of the United States of America, 57(4), 933–940. https://doi.org/10.1073/pnas.57.4.933
18. Mousavizadeh, L., & Ghasemi, S. (2021). Genotype and phenotype of COVID-19: Their roles in pathogenesis. Journal of Microbiology, Immunology and Infection, 54(2), 159–163. https://doi.org/10.1016/j.jmii.2020.03.022
19. Omrani, A. S., Saad, M. M., Baig, K., Bahloul, A., Abdul-Matin, M., Alaidaroos, A. Y., Almakhlafi, G. A., Albarrak, M. M., Memish, Z. A., & Albarrak, A. M. (2014). Ribavirin and interferon alfa-2a for severe Middle East respiratory syndrome coronavirus infection: A retrospective cohort study. The Lancet. Infectious Diseases, 14(11), 1090–1095. https://doi.org/10.1016/S1473-3099(14)70920-X
20. Portelli, S., Olshansky, M., Rodrigues, C. H. M., D’Souza, E. N., Myung, Y., Silk, M., Alavi, A., Pires, D. E. V., & Ascher, D. B. (2020). Exploring the structural distribution of genetic variation in SARS-CoV-2 with the COVID-3D online resource. Nature Genetics, 52(10), 999–1001. https://doi.org/10.1038/s41588-020-0693-3
21. Pulliam, J. R. C., Schalkwyk, C. van, Govender, N., Gottberg, A. von, Cohen, C., Groome, M. J., Dushoff, J., Mlisana, K., & Moultrie, H. (2021). Increased risk of SARS-CoV-2 reinfection associated with emergence of the Omicron variant in South Africa (p. 2021.11.11.21266068). https://doi.org/10.1101/2021.11.11.21266068
22. Raghav, S., Ghosh, A., Turuk, J., Kumar, S., Jha, A., Madhulika, S., Priyadarshini, M., Biswas, V. K., Shyamli, P. S., Singh, B., Singh, N., Singh, D., Datey, A., Avula, K., Smita, S., Sabat, J., Bhattacharya, D., Kshatri, J. S., Vasudevan, D., … Sherpa, T. (2020). Analysis of Indian SARS-CoV-2 Genomes Reveals Prevalence of D614G Mutation in Spike Protein Predicting an Increase in Interaction With TMPRSS2 and Virus Infectivity. Frontiers in Microbiology, 11, 2847. https://doi.org/10.3389/fmicb.2020.594928
23. Scudellari, M. (2021). How the coronavirus infects cells—And why Delta is so dangerous. Nature, 595(7869), 640–644. https://doi.org/10.1038/d41586-021-02039-y
24. Shamsi, A., Mohammad, T., Anwar, S., Amani, S., Khan, M. S., Husain, F. M., Rehman, Md. T., Islam, A., & Hassan, M. I. (2021). Potential drug targets of SARS-CoV-2: From genomics to therapeutics. International Journal of Biological Macromolecules, 177, 1–9. https://doi.org/10.1016/j.ijbiomac.2021.02.071
25. Shen, L., Bard, J. D., Triche, T. J., Judkins, A. R., Biegel, J. A., & Gai, X. (2021). Emerging variants of concern in SARS-CoV-2 membrane protein: A highly conserved target with potential pathological and therapeutic implications. Emerging Microbes & Infections, 10(1), 885–893. https://doi.org/10.1080/22221751.2021.1922097
26. Siu, Y. L., Teoh, K. T., Lo, J., Chan, C. M., Kien, F., Escriou, N., Tsao, S. W., Nicholls, J. M., Altmeyer, R., Peiris, J. S. M., Bruzzone, R., & Nal, B. (2008). The M, E, and N structural proteins of the severe acute respiratory syndrome coronavirus are required for efficient assembly, trafficking, and release of virus-like particles. Journal of Virology, 82(22), 11318–11330. https://doi.org/10.1128/JVI.01052-08
27. Swain, S. S., Rout, S. S., Sahoo, A., Oyedemi, S. O., & Hussain, T. (2021). Antituberculosis, antioxidant and cytotoxicity profiles of quercetin: A systematic and cost-effective in silico and in vitro approach. Natural Product Research, 0(0), 1–5. https://doi.org/10.1080/14786419.2021.2008387
28. Toparslan, E., Karabag, K., & Bilge, U. (2020). A workflow with R: Phylogenetic analyses and visualizations using mitochondrial cytochrome b gene sequences. PLOS ONE, 15(12), e0243927. https://doi.org/10.1371/journal.pone.0243927
29. Tracking SARS-CoV-2 variants. (2022, May 3). https://www.who.int/activities/tracking-SARS-CoV-2-variants
30. Troyano-Hernáez, P., Reinosa, R., & Holguín, Á. (2021). Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week. Viruses, 13(2), 243. https://doi.org/10.3390/v13020243
31. Vilar, S., & Isom, D. G. (2021). One Year of SARS-CoV-2: How Much Has the Virus Changed? Biology, 10(2), 91. https://doi.org/10.3390/biology10020091
32. Wormser, G. P., & Aitken, C. (2010). Clinical Virology, 3rd Edition Edited by D. D. Richman, R. J. Whitley, and F. G. Hayden Washington, DC: ASM Press, 2009. 1408 pp, Illustrated. $259.59 (hardcover). Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America, 50(12), 1692. https://doi.org/10.1086/652862
33. Zhang, C., Zheng, W., Huang, X., Bell, E. W., Zhou, X., & Zhang, Y. (2020). Protein Structure and Sequence Reanalysis of 2019-nCoV Genome Refutes Snakes as Its Intermediate Host and the Unique Similarity between Its Spike Protein Insertions and HIV-1. Journal of Proteome Research, 19(4), 1351–1360. https://doi.org/10.1021/acs.jproteome.0c00129
34. Zheng, W., Zhang, C., Li, Y., Pearce, R., Bell, E. W., & Zhang, Y. (2021). Folding non-homologous proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. Cell Reports Methods, 1(3), 100014. https://doi.org/10.1016/j.crmeth.2021.100014