In-silico identification of natural antiviral drug against SARS-CoV-2 and comparison with potential FDA approved drug targets

Sarra Akermi, Neha Lohar, Subrata Sinha, Subrahi Johari, Sunil Jayant, Anshul Nigam


Antimalarial drugs Chloroquine and Hydroxychloroquine have garnered most attention recently as a successful remedy for COVID19. However, the use of these drugs is still questionable due to its undetermined efficacy and side effects. The present study utilizes in-silico high throughput screening of FDA approved antiviral compounds and secondary plant metabolites against spike protein of novel coronavirus (SARS-CoV-2). This target was chosen because it is instrumental in entry of virus into human cells. It is observed that the plant compound Tocopheryl-curcumin has more affinity for spike protein of SARS-CoV-2 in comparison to the majority of FDA approved drugs. Tocopheryl-curcumin binds with the binding site of RBD domain of spike protein (6VSB, chain A) with free energy (∆G) of binding of -11.20 kcal/mol and makes strong hydrogen bonds with amino acid residues of S366, V367, L368, S373, and K529. Among the FDA approved drugs, Pibrentasvir obtains top rank with free energy (∆G) of binding of -9.69 kcal/mol. whereas; surprisingly Chloroquine (-6.87 kcal/mol) and Hydroxychloroquine (-7.24 kcal/mol) ranked lower in our docking study. The toxicity prediction by VEGA predicts that tocopheryl-curcumin shows no toxicity as compared to FDA approved drugs. Therefore, we infer that the plant-based tocopheryl-curcumin could be considered as potential and safer drug against COVID 19 disease as compared to chemical based drugs.


Cava C, Bertoli G, Castiglioni I (2020); In-Silico discovery of candidate drugs against COVID-19. Viruses 12(4): 404.

Clark DR, Jonathan EM, Kenneth B (2020); Clinical evidence does not support corticosteroid treatment for 2019-nCoV lung injury. Lancet 395(10223): 473-475.

Dong L, Hu S, Gao J (2020); Discovering drugs to treat coronavirus disease 2019 (COVID-19). Drug Discoveries & Therapeutics 14(1): 58–60.

Gao J, Tian Z, Yang X (2020); Breakthrough: Chloroquine phosphate has shown apparent efficacy in treatment of COVID-19 associated pneumonia in clinical studies. Bioscience Trends 14(1): 72–73.

Huang C, Wang Y, Li X, Ren L, Zhao J, Hu Y, Zhang L, Fan G, Xu J, Gu X, Cheng Z, Yu , 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.

Kolifarhood G, Aghaali M, Mozafar Saadati H, Taherpour N, Rahimi S, Izadi N, Hashemi Nazari S S (2020); Epidemiological and Clinical Aspects of COVID-19; a Narrative Review. Archives of Academic Emergency Medicine 8(1): e41.

Long SS, Pickering LK, Prober CG (2012); Principles and Practice of Pediatric Infectious Disease. Elsevier Health Sciences.

Mark PL and Paul M (2020); Ongoing Clinical Trials for the Management of the COVID-19 Pandemic. Trends in Pharmacological Sciences Elsevier: 1-29.

Manli W, Ruiyuan C, Leike Z, Xinglou Y, Jia L, Mingyue X, Zhengli S, Zhihong H, Wu Z, Gengfu X (2020); Remdesivir and chloroquine effectively inhibit the recently emerged novel coronavirus (2019-nCoV) in vitro. Cell Research 30: 269–271.

Morris GM, Huey R, Lindstrom W, Sanner MF, Belew RK, Goodsell DS, Olson AJ (2009); Autodock4 and AutoDockTools4: automated docking with selective receptor flexiblity. J. Computational Chemistry 16: 2785-91.

Poon LLM, Guan Y, Nicholls JM, Yuen KY, Peiris JSM (2004); The aetiology, origins, and diagnosis of severe acute respiratory syndrome. The Lancet Infectious Diseases 4(11): 663–671.

Repici A, Maselli R, Colombo M, Gabbiadini R, Spadaccini M, Anderloni A, Carrara S, Fugazza A, Di Leo M, Galtieri PA, Pellegatta G, Ferrara EC, Azzolini E, Lagioia M (2020); Coronavirus (COVID-19) outbreak: what the department of endoscopy should know. Gastrointestinal Endoscopy :(20)30245-5.

Renhong Y,Yuanyuan Z,Yaning L,Lu X,Yingying G,Qiang Z (2020); Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2. Science 367 (6485): 1444-1448.

Roman AL, James DW, Janet MT (2005); ProFunc: a server for predicting protein function from 3D structure. Nucleic Acids Res. 1(33): W89–W93.

Sheahan TP, Sims AC, Graham RL, Menachery VD, Gralinski LE, Case JB, Leist SR, Pyrc K, Feng JY, Trantcheva I, Bannister R, Park Y, Babusis D, Clarke MO, Mackman RL, Spahn JE, Palmiotti CA, Siegel D, Ray AS, Baric RS (2017); Broad-spectrum antiviral GS-5734 inhibits both epidemic and zoonotic coronaviruses. Science Translational Medicine, 9(396): 3653.

Wilson JG, Liu KD, Zhuo H, Caballero L, McMillan M, Fang X, Cosgrove K, Vojnik R, Calfee CS, Lee JW, Rogers AJ, Levitt J, Wiener-Kronish J, Bajwa EK, Leavitt A, McKenna D, Thompson BT, Matthay MA (2015); Mesenchymal stem (stromal) cells for treatment of ARDS: a phase 1 clinical trial. The Lancet Respiratory Medicine 3(1): 24–32.

Wu F, Zhao S, Yu B, Chen YM, Wang W, Song ZG, Hu Y, Tao ZW, Tian JH, Pei YY, Yuan ML, Zhang YL, Dai FH, Liu Y, Wang QM, Zheng JJ, Xu L, Holmes EC, Zhang YZ (2020); A new coronavirus associated with human respiratory disease in China. Nature 579(7798): 265–269.

Yang Y, Islam MS, Wang J, Li Y, Chen X (2020); Traditional Chinese Medicine in the Treatment of Patients Infected with 2019-New Coronavirus (SARS-CoV-2): A Review and Perspective. International Journal of Biological Sciences 16(10):1708–1717.

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(14).

Zikuan L, Rongjia Z, Wei H, Yingmei F, Yanlei Y, Qin H, Guangliang S, Fanyan M, Dongshu D, Shihua W, Junfen F, Wenjing W, Luchan D, Hongbo S, Hongjun L, Zhongjie H, Fengchun Z, Jinming G, Hongjian L, Xiaoxia L, Yangyang Z, Kan Y, Xijing H, Zhengchao G, Yibin W, Bo Y, Ronghua J, Ilia S, Lee WL,Huanxing S, Alexey M, Antonio C, Sasanka C, Kyung-JM, Georgina EH, Calogero C, Kunlin J, Robert CZ (2020); Transplantation of ACE2-mesenchymal stem cells improves the outcome of patients with COVID-19 pneumonia. Aging and Disease Journal. 11(2):216-228.


  • There are currently no refbacks.

Published by:

 Indian Science and Technology Foundation (ISTF)

 C-1/31, Yamuna Vihar, New Delhi-110053