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Research Articles

In silico identification of potential inhibitors from Cinnamon against main protease and spike glycoprotein of SARS CoV-2

ORCID Icon, ORCID Icon, , , ORCID Icon &
Pages 4618-4632 | Received 29 Apr 2020, Accepted 02 Jun 2020, Published online: 22 Jun 2020

References

  • Aanouz, I., Belhassan, A., El Khatabi, K., Lakhlifi, T., El Idrissi, M., & Bouachrine, M. (2020). Moroccan medicinal plants as inhibitors of COVID-19: Computational investigations. Journal of Biomolecular Structure and Dynamics, 1–12. https://doi.org/10.1080/07391102.2020.1758790
  • Agostino, M., Jene, C., Boyle, T., Ramsland, P. A., & Yuriev, E. (2009). Molecular docking of carbohydrate ligands to antibodies: Structural validation against crystal structures. Journal of Chemical Information and Modeling, 49(12), 2749–2760. https://doi.org/10.1021/ci900388a
  • Benigni, R., & Bossa, C. (2011). Mechanisms of chemical carcinogenicity and mutagenicity: A review with implications for predictive toxicology. Chemical Reviews, 111(4), 2507–2536. https://doi.org/10.1021/cr100222q
  • Boopathi, S., Poma, A. B., & Kolandaivel, P. (2020). Novel 2019 Coronavirus structure, mechanism of action, antiviral drug promises and rule out against its treatment. Journal of Biomolecular Structure and Dynamics, 1–14. https://doi.org/10.1080/07391102.2020.1758788
  • 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. The Lancet, 395(10223), 514–523. https://doi.org/10.1016/S0140-6736(20)30154-9
  • Chaudhuri, S., Symons, J. A., & Deval, J. (2018). Innovation and trends in the development and approval of antiviral medicines: 1987–2017 and beyond. Antiviral Research, 155, 76–88. https://doi.org/10.1016/j.antiviral.2018.05.005
  • Cheng, F., Li, W., Zhou, Y., Shen, J., Wu, Z., Liu, G., & Tang, Y. (2012). admetSAR: A comprehensive source and free tool for assessment of chemical ADMET properties. ACS Publications.
  • Corman, V., Lienau, J., & Witzenrath, M. (2019). Coronaviruses as the cause of respiratory infections. Der Internist, 60(11), 1136–1145.
  • Cosconati, S., Forli, S., Perryman, A. L., Harris, R., Goodsell, D. S., & Olson, A. J. (2010). Virtual screening with AutoDock: Theory and practice. Expert Opinion on Drug Discovery, 5(6), 597–607. https://doi.org/10.1517/17460441.2010.484460
  • Dallakyan, S., & Olson, A. J. (2015). Small-molecule library screening by docking with PyRx. In Chemical biology (pp. 243–250). Springer.
  • de Wit, E., van Doremalen, N., Falzarano, D., & Munster, V. J. (2016). SARS and MERS: Recent insights into emerging coronaviruses. Nature Reviews. Microbiology, 14(8), 523–534. https://doi.org/10.1038/nrmicro.2016.81
  • Design, L. (2014). Pharmacophore and ligand-based design with Biovia Discovery Studio®.
  • Elfiky, A. A. (2020). Natural products may interfere with SARS-CoV-2 attachment to the host cell. Journal of Biomolecular Structure and Dynamics, 1–16. https://doi.org/10.1080/07391102.2020.1761881
  • Elfiky, A. A., & Azzam, E. B. (2020). Novel guanosine derivatives against MERS CoV polymerase: An in silico perspective. Journal of Biomolecular Structure and Dynamics, 1–12. https://doi.org/10.1080/07391102.2020.1758789
  • Elmezayen, A. D., Al-Obaidi, A., Şahin, A. T., & Yelekçi, K. (2020). Drug repurposing for coronavirus (COVID-19): In silico screening of known drugs against coronavirus 3CL hydrolase and protease enzymes. Journal of Biomolecular Structure and Dynamics, 1–12. https://doi.org/10.1080/07391102.2020.1758791
  • Enayatkhani, M., Hasaniazad, M., Faezi, S., Guklani, H., Davoodian, P., Ahmadi, N., Ali Einakian, M., Karmostaji, A., Ahmadi, K. (2020). Reverse vaccinology approach to design a novel multi-epitope vaccine candidate against COVID-19: An in silico study. Journal of Biomolecular Structure and Dynamics, 1–19. https://doi.org/10.1080/07391102.2020.1756411
  • Enmozhi, S. K., Raja, K., Sebastine, I., & Joseph, J. (2020). Andrographolide as a potential inhibitor of SARS-CoV-2 main protease: An in silico approach. Journal of Biomolecular Structure and Dynamics, 1–10. https://doi.org/10.1080/07391102.2020.1760136
  • Ertl, P., Rohde, B., & Selzer, P. (2000). Fast calculation of molecular polar surface area as a sum of fragment-based contributions and its application to the prediction of drug transport properties. Journal of Medicinal Chemistry, 43(20), 3714–3717. https://doi.org/10.1021/jm000942e
  • Fehr, A. R., Channappanavar, R., & Perlman, S. (2017). Middle East respiratory syndrome: Emergence of a pathogenic human coronavirus. Annual Review of Medicine, 68, 387–399. https://doi.org/10.1146/annurev-med-051215-031152
  • Gangadharappa, B. S., Sharath, R., Revanasiddappa, P. D., Chandramohan, V., Balasubramaniam, M., & Vardhineni, T. P. (2019). Structural insights of metallo-beta-lactamase revealed an effective way of inhibition of enzyme by natural inhibitors. Journal of Biomolecular Structure and Dynamics, 1–15. https://doi.org/10.1080/07391102.2019.1667265
  • Ge, X.-Y., Li, J.-L., Yang, X.-L., Chmura, A. A., Zhu, G., Epstein, J. H., Mazet, J. K., Hu, B., Zhang, W., Peng, C., Zhang, Y.-J., Luo, C.-M., Tan, B., Wang, N., Zhu, Y., Crameri, G., Zhang, S.-Y., Wang, L.-F., Daszak, P., & Shi, Z.-L. (2013). Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor. Nature, 503(7477), 535–538. https://doi.org/10.1038/nature12711
  • Glowacka, I., Bertram, S., Müller, M. A., Allen, P., Soilleux, E., Pfefferle, S., Steffen, I., Tsegaye, T. S., He, Y., Gnirss, K., Niemeyer, D., Schneider, H., Drosten, C., & Pöhlmann, S. (2011). Evidence that TMPRSS2 activates the severe acute respiratory syndrome coronavirus spike protein for membrane fusion and reduces viral control by the humoral immune response. Journal of Virology, 85(9), 4122–4134. https://doi.org/10.1128/JVI.02232-10
  • Goel, R. K., Singh, D., Lagunin, A., & Poroikov, V. (2011). PASS-assisted exploration of new therapeutic potential of natural products. Medicinal Chemistry Research, 20(9), 1509–1514. https://doi.org/10.1007/s00044-010-9398-y
  • Guan, Y., Zheng, B. J., He, Y. Q., Liu, X. L., Zhuang, Z. X., Cheung, C. L., Luo, S. W., Li, P. H., Zhang, L. J., Guan, Y. J., Butt, K. M., Wong, K. L., Chan, K. W., Lim, W., Shortridge, K. F., Yuen, K. Y., Peiris, J. S. M., & Poon, L. L. M. (2003). Isolation and characterization of viruses related to the SARS coronavirus from animals in southern China. Science (New York, N.Y.), 302(5643), 276–278. https://doi.org/10.1126/science.1087139
  • Gupta, M. K., Vemula, S., Donde, R., Gouda, G., Behera, L., & Vadde, R. (2020). In-silico approaches to detect inhibitors of the human severe acute respiratory syndrome coronavirus envelope protein ion channel. Journal of Biomolecular Structure and Dynamics, 1–17. https://doi.org/10.1080/07391102.2020.1751300
  • Hall, D. C., Jr., & 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. https://doi.org/10.1016/j.tmaid.2020.101646
  • Hasan, A., Paray, B. A., Hussain, A., Qadir, F. A., Attar, F., Aziz, F. M., Sharifi, M., Derakhshankhah, H., Rasti, B., Mehrabi, M., Shahpasand, K., Saboury, A. A., Falahati, F. (2020). A review on the cleavage priming of the spike protein on coronavirus by angiotensin-converting enzyme-2 and furin. Journal of Biomolecular Structure and Dynamics, 1–13. https://doi.org/10.1080/07391102.2020.1754293
  • Hilgenfeld, R. (2014). From SARS to MERS: Crystallographic studies on coronaviral proteases enable antiviral drug design. The FEBS Journal, 281(18), 4085–4096. https://doi.org/10.1111/febs.12936
  • Hoffmann, M., Kleine-Weber, H., Schroeder, S., Krüger, N., Herrler, T., Erichsen, S., Schiergens, T. S., Herrler, G., Wu, N.-H., Nitsche, A., Müller, M. A., Drosten, C., & Pöhlmann, S. (2020). SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor. Cell, 181(2), 271–280. https://doi.org/10.1016/j.cell.2020.02.052
  • 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. The Lancet, 395(10223), 497–506. https://doi.org/10.1016/S0140-6736(20)30183-5
  • Islam, R., Parves, R., Paul, A. S., Uddin, N., Rahman, M. S., Mamun, A. A., Hossain, M. N., Ali, M. A., Halim, M. A. (2020). A molecular modeling approach to identify effective antiviral phytochemicals against the main protease of SARS-CoV-2. Journal of Biomolecular Structure and Dynamics, 1–20. https://doi.org/10.1080/07391102.2020.1761883
  • Joshi, R. S., Jagdale, S. S., Bansode, S. B., Shankar, S. S., Tellis, M. B., Pandya, V. K., Chugh, A., Giri, A. P., Kulkarni, M. J. (2020). Discovery of potential multi-target-directed ligands by targeting host-specific SARS-CoV-2 structurally conserved main protease$. Journal of Biomolecular Structure and Dynamics, 1–16. https://doi.org/10.1080/07391102.2020.1760137
  • Khan, R. J., Jha, R. K., Amera, G., Jain, M., Singh, E., Pathak, A., Singh, R. P., Muthukumaran, J., Singh, A. K. (2020). Targeting SARS-Cov-2: A systematic drug repurposing approach to identify promising inhibitors against 3C-like Proteinase and 2’-O-RiboseMethyltransferase. Journal of Biomolecular Structure and Dynamics, 1–40. https://doi.org/10.1080/07391102.2020.1753577
  • Khan, S. A., Zia, K., Ashraf, S., Uddin, R., & Ul-Haq, Z. (2020). Identification of chymotrypsin-like protease inhibitors of SARS-CoV-2 via integrated computational approach. Journal of Biomolecular Structure and Dynamics, 1–13. https://doi.org/10.1080/07391102.2020.1751298
  • Khurana, N., Ishar, M. P. S., Gajbhiye, A., & Goel, R. K. (2011). PASS assisted prediction and pharmacological evaluation of novel nicotinic analogs for nootropic activity in mice. European Journal of Pharmacology, 662(1–3), 22–30. https://doi.org/10.1016/j.ejphar.2011.04.048
  • Kumari, R., Open Source Drug Discovery Consortium, Kumar, R., & Lynn, A. (2014). g_mmpbsa-a GROMACS tool for high-throughput MM-PBSA calculations. Journal of Chemical Information and Modeling, 54(7), 1951–1962. https://doi.org/10.1021/ci500020m
  • Lai, K., Shen, H., Zhou, X., Qiu, Z., Cai, S., Huang, K., Wang, Q., Wang, C., Lin, J., Hao, C., Kong, L., Zhang, S., Chen, Y., Luo, W., Jiang, M., Xie, J., & Zhong, N. (2018). Clinical practice guidelines for diagnosis and management of cough-Chinese Thoracic Society (CTS) Asthma Consortium. Journal of Thoracic Disease, 10(11), 6314–6351. https://doi.org/10.21037/jtd.2018.09.153
  • Lau, S. K. P., Woo, P. C. Y., Li, K. S. M., Huang, Y., Tsoi, H.-W., Wong, B. H. L., Wong, S. S. Y., Leung, S.-Y., Chan, K.-H., & Yuen, K.-Y. (2005). Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats. Proceedings of the National Academy of Sciences of the United States of America, 102(39), 14040–14045. https://doi.org/10.1073/pnas.0506735102
  • Li, F., Li, W., Farzan, M., & Harrison, S. C. (2005). Structure of SARS coronavirus spike receptor-binding domain complexed with receptor. Science (New York, N.Y.), 309(5742), 1864–1868. https://doi.org/10.1126/science.1116480
  • Li, W., Moore, M. J., Vasilieva, N., Sui, J., Wong, S. K., Berne, M. A., Somasundaran, M., Sullivan, J. L., Luzuriaga, K., Greenough, T. C., Choe, H., & Farzan, M. (2003). Angiotensin-converting enzyme 2 is a functional receptor for the SARS coronavirus. Nature, 426(6965), 450–454. https://doi.org/10.1038/nature02145
  • Liebler, D. C., & Guengerich, F. P. (2005). Elucidating mechanisms of drug-induced toxicity. Nature Reviews. Drug Discovery, 4(5), 410–420. https://doi.org/10.1038/nrd1720
  • Lin, L.-T., Hsu, W.-C., & Lin, C.-C. (2014). Antiviral natural products and herbal medicines. Journal of Traditional and Complementary Medicine, 4(1), 24–35. https://doi.org/10.4103/2225-4110.124335
  • Martinez, J., Sasse, F., Brönstrup, M., Diez, J., & Meyerhans, A. (2015). Antiviral drug discovery: Broad-spectrum drugs from nature. Natural Product Reports, 32(1), 29–48. https://doi.org/10.1039/C4NP00085D
  • Menachery, V. D., Dinnon, K. H., Yount, B. L., McAnarney, E. T., Gralinski, L. E., Hale, A., Graham, R. L., Scobey, T., Anthony, S. J., Wang, L., Graham, B., Randell, S. H., Lipkin, W. I., & Baric, R. S. (2019). Trypsin treatment unlocks barrier for zoonotic bat coronavirus infection. Journal of Virology, 94(5), e01774-19. https://doi.org/10.1128/JVI.01774-19
  • Mittal, M., Goel, R. K., Bhargava, G., & Mahajan, M. P. (2008). PASS-assisted exploration of antidepressant activity of 1, 3, 4-trisubstituted-β-lactam derivatives. Bioorganic & Medicinal Chemistry Letters, 18(20), 5347–5349. https://doi.org/10.1016/j.bmcl.2008.09.064
  • Mohankumar, T., Chandramohan, V., Lalithamba, H. S., Jayaraj, R. L., Kumaradhas, P., Sivanandam, M., Hunday, G., Vijayakumar, R., Balakrishnan, R., Manimaran, D., & Elangovan, N. (2020). Design and molecular dynamic Investigations of 7,8-dihydroxyflavone derivatives as potential neuroprotective agents against alpha-synuclein. Scientific Reports, 10(1), 599. https://doi.org/10.1038/s41598-020-57417-9
  • Mohanraj, K., Karthikeyan, B. S., Vivek-Ananth, R., Chand, R. B., Aparna, S., Mangalapandi, P., & Samal, A. (2018). IMPPAT: A curated database of Indian medicinal plants, phytochemistry and therapeutics. Scientific Reports, 8(1), 1–17. https://doi.org/10.1038/s41598-018-22631-z
  • Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30(16), 2785–2791. https://doi.org/10.1002/jcc.21256
  • Munster, V. J., Koopmans, M., van Doremalen, N., van Riel, D., & de Wit, E. (2020). A novel coronavirus emerging in China—key questions for impact assessment. New England Journal of Medicine, 382(8), 692–694. https://doi.org/10.1056/NEJMp2000929
  • Muralidharan, N., Sakthivel, R., Velmurugan, D., & Gromiha, M. M. (2020). Computational studies of drug repurposing and synergism of lopinavir, oseltamivir and ritonavir binding with SARS-CoV-2 protease against COVID-19. Journal of Biomolecular Structure and Dynamics, 1–7. https://doi.org/10.1080/07391102.2020.1752802
  • O'Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., & Hutchison, G. R. (2011). Open Babel: An open chemical toolbox. Journal of Cheminformatics, 3(1), 33. https://doi.org/10.1186/1758-2946-3-33
  • Pangastuti, A., Amin, I. F., Amin, A. Z., & Amin, M. (2016). Natural bioactive compound from Moringa oleiferaagainst cancer based on in silico screening. Jurnal Teknologi, 78(5), 1–4. https://doi.org/10.11113/jt.v78.8328
  • Pant, S., Singh, M., Ravichandiran, V., Murty, U., & Srivastava, H. K. (2020). Peptide-like and small-molecule inhibitors against Covid-19. Journal of Biomolecular Structure and Dynamics, 1–15. https://doi.org/10.1080/07391102.2020.1757510
  • Sarma, P., Sekhar, N., Prajapat, M., Avti, P., Kaur, H., Kumar, S., Singh, S., Kumar, H., Dhibar, D. P., Medhi, B. (2020). In-silico homology assisted identification of inhibitor of RNA binding against 2019-nCoV N-protein (N terminal domain). Journal of Biomolecular Structure and Dynamics, 1–11. https:doi.org/10.1080/07391102.2020.1753580
  • Seeliger, D., & de Groot, B. L. (2010). Ligand docking and binding site analysis with PyMOL and Autodock/Vina. Journal of Computer-Aided Molecular Design, 24(5), 417–422. https://doi.org/10.1007/s10822-010-9352-6
  • Sinha, S. K., Shakya, A., Prasad, S. K., Singh, S., Gurav, N. S., Prasad, R. S., & Gurav, S. S. (2020). An in-silico evaluation of different Saikosaponins for their potency against SARS-CoV-2 using NSP15 and fusion spike glycoprotein as targets. Journal of Biomolecular Structure and Dynamics, 1–13. http://doi.org/10.1080/07391102.2020.1762741
  • To, K. K., Hung, I. F., Chan, J. F., & Yuen, K.-Y. (2013). From SARS coronavirus to novel animal and human coronaviruses. Journal of Thoracic Disease, 5(Suppl 2), S103.
  • Townsend, E. A., Siviski, M. E., Zhang, Y., Xu, C., Hoonjan, B., & Emala, C. W. (2013). Effects of ginger and its constituents on airway smooth muscle relaxation and calcium regulation. American Journal of Respiratory Cell and Molecular Biology, 48(2), 157–163. https://doi.org/10.1165/rcmb.2012-0231OC
  • Wahedi, H. M., Ahmad, S., & Abbasi, S. W. (2020). Stilbene-based natural compounds as promising drug candidates against COVID-19. Journal of Biomolecular Structure and Dynamics, 1–16. http://doi.org/10.1080/07391102.2020.1762743
  • Wang, C., Horby, P. W., Hayden, F. G., & Gao, G. F. (2020). A novel coronavirus outbreak of global health concern. The Lancet, 395(10223), 470–473. https://doi.org/10.1016/S0140-6736(20)30185-9
  • WHO. (2003). Summary of probable SARS cases with onset of illness from 1 November 2002 to 31 July 2003. World Health Organization.
  • WHO. (2020). Coronavirus disease 2019 (COVID-19): Situation report, 74.
  • Yang, H., Lou, C., Sun, L., Li, J., Cai, Y., Wang, Z., Li, W., Liu, G., & Tang, Y. (2019). admetSAR 2.0: Web-service for prediction and optimization of chemical ADMET properties. Bioinformatics (Oxford, England), 35(6), 1067–1069. https://doi.org/10.1093/bioinformatics/bty707
  • 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 α-ketoamide inhibitors. Science, 368(6489), 409–412.
  • Zhou, Y., Hou, Y., Shen, J., Huang, Y., Martin, W., & Cheng, F. (2020). Network-based drug repurposing for novel coronavirus 2019-nCoV/SARS-CoV-2. Cell Discovery, 6(1), 14–18. https://doi.org/10.1038/s41421-020-0153-3
  • Zhu, N., Zhang, D., Wang, W., Li, X., Yang, B., Song, J., Zhao, X., Huang, B., Shi, W., Lu, R., Niu, P., Zhan, F., Ma, X., Wang, D., Xu, W., Wu, G., Gao, G. F., & Tan, W. (2020). A novel coronavirus from patients with pneumonia in China, 2019. The New England Journal of Medicine, 382(8), 727–733. https://doi.org/10.1056/NEJMoa2001017

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