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Abstract

A pandemic coronavirus disease of 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has now been declared a global pandemic by the World Health Organization. The search for new drugs, especially by utilizing antiviral peptides is a very potential area. Through this study, protein-peptide docking and protein-protein docking simulations were conducted using in silico methods to identify, evaluate, and explore the molecular affinity and interaction of dermaseptin peptide molecules produced by frogs of the genus Phyllomedusa against the SARS-CoV-2 spike protein macromolecule, and its effect on attachment to the surface of the ACE-2 (Angiotensin Converting Enzyme-2) receptor. Protein-peptide docking simulation results show that dermaseptin-S9 peptide molecule has the best affinity to the active site of SARS- CoV-2 spike protein macromolecule binding site, with a binding free energy value of −792.93 kJ/mol. Then the results of protein-protein docking simulations proved that dermaseptin-S9 peptide molecule was able to prevent the attachment of SARS-CoV-2 spike protein to the surface of the ACE-2 receptor, with a total energy value of 517.85 kJ/mol. Therefore, it is hoped that dermaseptin-S9 peptide molecule can be further studied in the development of novel antiviral peptide candidates for the control of COVID-19 infectious disease.

References

Ahuja, P., & Singh, K. (2016). In silico approach for SAR analysis of the predicted model of DEPDC1B: A novel target for oral cancer. Advances in Bioinformatics, 3136024, 8.

Bergaoui, I., Zaïri, A., Gharsallah, H., Aouni, M., Hammami, A., Hani, K., & Selmi, B. (2013). The in vitro evaluation of anti-chlamydial and cytotoxic properties of dermaseptin S4 and derivatives: Peptides from amphibian skin. Medicinal Chemistry Research, 22(12).

Bergaoui, I., Zairi, A., Tangy, F., Aouni, M., Selmi, B., & Hani, K. (2013). In vitro antiviral activity of dermaseptin S4 and derivatives from amphibian skin against herpes simplex virus type 2. Journal of Medical Virology, 85, 272–281

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. The Lancet, 395(10223).

Das, S., Sarmah, S., Lyndem, S., & Singha Roy, A. (2020). An investigation into the identification of potential inhibitors of SARS-CoV-2 main protease using molecular docking study. Journal of Biomolecular Structure and Dynamics, 1–11.

Gabutti, G., d’Anchera, E., Sandri, F., Savio, M., & Stefanati, A. (2020). Coronavirus: Update Related to the Current Outbreak of COVID-19. In Infectious Diseases and Therapy, 9(2), 1–13.

Hall, D. C., & Ji, H. F. (2020). A search for medications to treat COVID-19 via in silico molecular docking models of the SARS-CoV-2 spike glycoprotein and 3CL protease.Travel Medicine and Infectious Disease, 101646.

Huang, S. Y., & Zou, X. (2007). Ensemble docking of multiple protein structures: Considering protein structural variations in molecular docking. Proteins: Structure, Function and Genetics, 66(2), 399–421.

Huang, S. Y., & Zou, X. (2008). An iterative knowledge- based scoring function for protein-protein recognition. Proteins: Structure, Function and Genetics, 72(2), 557– 579.

Hui, D. S., I Azhar, E., Madani, T. A., Ntoumi, F., Kock, R., Dar, O., Ippolito, G., Mchugh, T. D., Memish, Z. A., Drosten, C., Zumla, A., & Petersen, E. (2020).

The continuing 2019-nCoV epidemic threat of novel coronaviruses to global health — The latest 2019 novel coronavirus outbreak in Wuhan, China. In International Journal of Infectious Diseases, 91, 264–266.

Jiménez-García, B., Pons, C., & Fernández-Recio, J. (2013). pyDockWEB: A web server for rigid- body protein-protein docking using electrostatics and desolvation scoring. Bioinformatics, 29(13), 1698–1699.

Lamiable, A., Thévenet, P., Rey, J., Vavrusa, M., Derreumaux, P., & Tufféry, P. (2016). PEP-FOLD3: faster de novo structure prediction for linear peptides in solution and in complex. Nucleic Acids Research, 44(1), 449–454.

Li, F., Li, W., Farzan, M., & Harrison, S. C. (2005). Structural biology: Structure of SARS coronavirus spike receptor-binding domain complexed with receptor. Science, 309(5742), 1864–1868.

Lu, R., Zhao, X., Li, J., Niu, P., Yang, B., Wu, H., Wang, W., Song, H., Huang, B., Zhu, N., Bi, Y., Ma, X., Zhan, F., Wang, L., Hu, T., Zhou, H., Hu, Z., Zhou, W., Zhao, L., Chen, J., Meng, Y., Wang, J., Lin, Y., Yuan, J., Xie, Z., Ma, J., Liu, W. J., Wang, D., Xu, W., Holmes, E. C., Gao, G.F., Wu, G., Chen, W., Shi, W., & Tan, W. (2020). Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding. The Lancet, 395,565–574.

Maupetit, J., Derreumaux, P., & Tuffery, P. (2009). PEP- FOLD: An online resource for de novo peptide structure prediction. Nucleic Acids Research, 37, 498–503.

Mechlia, M. Ben, Belaid, A., Castel, G., Jallet, C., Mansfield, K. L., Fooks, A. R., Hani, K., & Tordo, N. (2019). Dermaseptins as potential antirabies compounds. Vaccine, 37(33), 4694–4700.

Mustafa, S., Balkhy, H., & Gabere, M. (2019). Peptide-Protein Interaction Studies of Antimicrobial Peptides Targeting Middle East Respiratory Syndrome Coronavirus Spike Protein: An In Silico Approach. Advances in Bioinformatics, 1(87):1–16.

Sable, R., & Jois, S. (2015). Surfing the protein-protein interaction surface using docking methods: Application to the design of PPI inhibitors. In Molecules, 20(6), 11569–11603.

Sah, R., Rodriguez-Morales, A. J., Jha, R., Chu, D. K. W., Gu, H., Peiris, M., Bastola, A., Lal, B. K., Ojha, H. C., Rabaan, A. A., Zambrano, L. I., Costello, A., Morita, K., Pandey, B. D., & Poon, L. L. M. (2020). Complete Genome Sequence of a 2019 Novel Coronavirus (SARS-CoV-2) Strain Isolated in Nepal. Microbiology Resource Announcements, 9(11), 169.

Sharma, S. (2019). Molecular dynamics simulation of nanocomposites using BIOVIA materials studio, lammps and gromacs. In Molecular Dynamics Simulation of Nanocomposites using BIOVIA Materials Studio, Lammps and Gromacs.

Sharma, S., Kumar, P., Chandra, R., Singh, S. P., Mandal, A., & Dondapati, R. S. (2019). Overview of BIOVIA materials studio, LAMMPS, and GROMACS. In Molecular Dynamics Simulation of Nanocomposites using BIOVIA Materials Studio, Lammps and Gromacs.

Shen, Y., Maupetit, J., Derreumaux, P., & Tufféry, P. (2014). Improved PEP-FOLD approach for peptide and miniprotein structure prediction. Journal of Chemical Theory and Computation, 10(10), 4745–4758.

Tahir ul Qamar, M., 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.

Thévenet, P., Shen, Y., Maupetit, J., Guyon, F., Derreumaux, P., & Tufféry, P. (2012). PEP-FOLD: An updated de novo structure prediction server for both linear and disulfide bonded cyclic peptides. Nucleic Acids Research, 40, 288–293.

Ton, A. T., Gentile, F., Hsing, M., Ban, F., & Cherkasov, A. (2020). Rapid Identification of Potential Inhibitors of SARS-CoV-2 Main Protease by Deep Docking of 1.3 Billion Compounds. Molecular Informatics.

Wang, Q., Zhang, Y., Wu, L., Niu, S., Song, C., Zhang, Z., Lu, G., Qiao, C., Hu, Y., Yuen, K. Y., Wang, Q., Zhou, H., Yan, J., & Qi, J. (2020). Structural and Functional Basis of SARS-CoV-2 Entry by Using Human ACE2. Cell, 581, 221–224.

Wu, C., Liu, Y., Yang, Y., Zhang, P., Zhong, W., Wang, Y., Wang, Q., Xu, Y., Li, M., Li, X., Zheng, M., Chen, L., & Li, H. (2020). Analysis of therapeutic targets for SARS-CoV-2 and discovery of potential drugs by computational methods. Acta Pharmaceutica Sinica B.

Xu, X., Chen, P., Wang, J., Feng, J., Zhou, H., Li, X., Zhong, W., & Hao, P. (2020). Evolution of the novel coronavirus from the ongoing Wuhan outbreak and modeling of its spike protein for risk of human transmission. In Science China Life Sciences, 63(3), 457–460.

Yan, Y., Zhang, D., & Huang, S. Y. (2017). Efficient conformational ensemble generation of protein-bound peptides. Journal of Cheminformatics, 9(1), 59.

Zhang, L., Lin, D., Sun, X., Curth, U., Drosten, C., Sauerhering, L., Becker, S., Rox, K., & Hilgenfeld, R. (2020). Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved a-ketoamide inhibitors. Science, 368(6489), 409–412.

Zhou, P., Jin, B., Li, H., & Huang, S. Y. (2018). HPEPDOCK: A web server for blind peptide-protein docking based on a hierarchical algorithm. Nucleic Acids Research, 46, 443–450.

Zhou, P., Li, B., Yan, Y., Jin, B., Wang, L., & Huang, S. Y. (2018). Hierarchical Flexible Peptide Docking by Conformer Generation and Ensemble Docking of Peptides. Journal of Chemical Information and Modeling, 58(6), 1292–1302.

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