Evaluation of Phytochemicals of Cassia occidentalis L. for their Binding Affinities to SARS-CoV-2 3C-Like Protease: An in Silico Approach

Main Article Content

Tohmina Afroze Bondhon
Md. Aynal Haque Rana
Anamul Hasan
Rownak Jahan
Khoshnur Jannat
Mohammed Rahmatullah


Aims: Corona virus SARS-CoV-2, otherwise known as COVID-19 has created a pandemic resulting in social and financial crisis throughout the world. The virus has no known drugs or vaccines for preventive or therapeutic purposes. The objective of the present study was to screen phytochemicals from Cassia occidentalis L. in virtual screening (in silico) studies to evaluate their potential of binding to the main 3C-like protease of the virus and so stop its replication.

Study Design: Molecular docking approach was used for virtual screening studies.

Place and Duration of Study: University of Development Alternative between April and July 2020.

Methodology: Molecular docking (blind) were done with the help of Autodock Vina. We have used the pdb file (6LU7) of the main protease of SARS-CoV-2 3C-like protease or SARS-CoV-2 3CLpro (monomeric form) to study binding of the phytochemicals.

Results: Of the nine phytochemicals studied, the C-glycosidic flavonoids, cassiaoccidentalins A-C demonstrated excellent binding affinities to the protease. The compounds bound to the active site of the protease with binding energy values of -8.2 to-8.4 kcal/mol.

Conclusion: The in silico studies suggest that the compounds merit actual COVID-19 inhibitory tests and have potential for anti-COVID-19 use.

COVID-19, molecular docking, Cassia occidentalis, phytochemicals, 3C-like protease.

Article Details

How to Cite
Bondhon, T. A., Rana, M. A. H., Hasan, A., Jahan, R., Jannat, K., & Rahmatullah, M. (2020). Evaluation of Phytochemicals of Cassia occidentalis L. for their Binding Affinities to SARS-CoV-2 3C-Like Protease: An in Silico Approach. Asian Journal of Research in Infectious Diseases, 4(4), 8-14. https://doi.org/10.9734/ajrid/2020/v4i430152
Original Research Article


Unhale SS, Ansar QB, Sanap S, Thakhre S, Wadatkar S, Bairagi R et al. A review on corona virus (COVID-19). World J Pharm Life Sci. 2020;6(4):109-15.

Anonymous. COVID-19 Coronavirus pandemic.

Available:[https://www.worldometers.info/coronavirus/, accessed July 25, 2020]

Hilgenfeld R. From SARS to MERS: Crystallographic studies on coronaviral proteases enable antiviral drug design. FEBS J. 2014;281(18):4085–96.


Thiel V, Ivanov KA, Putics A, Hertzig T, Schelle B, Bayer S et al. Mechanisms and enzymes involved in SARS coronavirus genome expression. J Gen Virol. 2003; 84(Pt 9):2305-15.


Yang H, Yang M, Ding Y, Liu Y, Lou Z, Zhou Z et al. The crystal structures of Severe Acute Respiratory Syndrome virus main protease and its complex with an inhibitor. Proc Natl Acad Sci USA. 2003; 100(23):13190-5.


Joshi T, Joshi T, Sharma P, Mathpal S, Pundir H, Bhatt V et al. In silico screening of natural compounds against COVID-19 by targeting Mpro and ACE2 using molecular docking. Eur Rev Med Pharmacol Sci. 2020;24(8):4529-36.

DOI: 10.26355/eurrev_202004_21036

Gilani AH, Rahman Atta-ur. Trends in ethnopharmacology. J Ethnopharmacol. 2005;100(1-2):43-9.


Pushpa R, Nishant R, Navin K, Pankaj G. Antiviral potential of medicinal plants: An overview. Int Res J Pharm. 2013;4(6): 8-16.


Liao F. Discovery of artemisinin (Qinghaosu). Molecules. 2009;14:5362-6.


Vijayalakshmi S, Ranjitha J, Devi Rajeswari V, Bhagiyalakshmi M. Pharmacological profile of Cassia occidentalis L. – A review. Int J Pharm Pharm Sci. 2013;5(3):29-33.

Liu X, Zhang B, Jin Z, Yang H, Rao Z. The crystal structure of COVID-19 main protease in complex with an inhibitor N3.

Available:https://www.rcsb.org/structure/6LU7, accessed Apr 19, 2020.


O’Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR. Open Babel: An open chemical toolbox. J Cheminf. 2011;3:33.


Li SW, Yang TC, Lai CC, Huang SH, Liao JM, Wan L et al. Antiviral activity of aloe-emodin against influenza A virus via galectin-3 up-regulation. Eur J Pharmacol. 2014;738:125-32.


Umesh, Kundu D, Selvaraj C, Singh SK, Dubey VK. Identification of new anti-nCoV drug chemical compounds from Indian spices exploiting SARS-CoV-2 main protease as target. J Biomol Struct Dyn. 2020;1-9.


Prateeksha, Yusuf MA, Singh BN, Sudheer S, Kharwar RN, Siddiqui S et al. Chrysophanol: A natural anthraquinone with multifaceted biotherapeutic potential. Biomolecules. 2019;9:68.


Liu Z, Nian MA, Zhong Y, Yang ZQ. Antiviral effect of emodin from Rheum palmatum against Coxsackievirus B5 and human respiratory syncytial virus in vitro. J Huazhong Univ Sci Technol [Med Sci]. 2015;35(6):916-22.


Ogbole OO, Akinleye TE, Faleye TOC, Adeniji AJ. Enterovirus inhibiting activities of two lupane triterpenoids and anthraquinones from Senna siamea stem bark against three serotypes of echovirus. Acta Pharm Sci. 2019;57(3):105-115.


Wang QW, Su Y, Sheng JT, Gu LM, Zhao Y, Chen XX et al. Anti-influenza A virus activity of rhein through regulating oxidative stress, TLR4, Akt, MAPK, and NF-B signal pathways. PLoS One. 2018; 13(1):e0191793.