In Silico Identification of Potentially Effective Herbal Inhibitors of SARS-Cov-2 Main Protease by Virtual Screening Method Potential Anti-COVID-19 Molecules
School of Medicine Students' Journal,
Vol. 2 No. 3 (2020),
1 July 2020
Background: The COVID-19 pandemic is a global health emergency caused by SARS-CoV-2. Unfortunately, no effective drugs have been found to date. There is also a major need for new therapies to treat this disease. The main protease is an attractive drug target among coronaviruses due to its important role in the processing of viral RNA-translated polyproteins. Objective of This study was conducted to screen databases of herbal compounds for potential main protease inhibitors.
Material and Methods: Natural products from 3 database banks were first tested and filtered by ADME / toxicity, then their molecular energy was minimized, and finally, they were docked into the SARS-CoV-2 main protease and compared with indinavir.
Results: The binding energies of 6570 molecules from different herbal compounds comprising databases were tested and five of the molecules with the highest binding energies for SARS-CoV-2 main protease docking were selected and key interactions were studied.
Conclusion: In conclusion, five herbal compounds including Sodwanone B, Cyclomulberrin, and a glycosylated derivative of kaempferol had lower docking energy compared to indinavir and were suggested for further research.
How to Cite
Zhang L, Lin D, Sun X, Curth U, Drosten C, Sauerhering L, et al.Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors.Science.2020.
Ortega JT, Serrano ML, Pujol FH and Rangel HR.Unrevealing sequence and structural features of novel coronavirus using in silico approaches: The main protease as molecular target.EXCLI Journal.2020;19:400.
Cheraghi Z, Moradi M and Ziai SA.Potential pharmacologic treatments for COVID-19 patients: A review study.School of Medicine Students’ Journal.2020;2(2):14-20.
Novick PA, Ortiz OF, Poelman J, Abdulhay AY and Pande VS.SWEETLEAD: an in silico database of approved drugs, regulated chemicals, and herbal isolates for computer-aided drug discovery.PLoS One.2013;8(11).
Hatherley R, Brown DK, Musyoka TM, Penkler DL, Faya N, Lobb KA, et al.SANCDB: a South African natural compound database.Journal of cheminformatics.2015;7(1):29.
Wu Y, Zhang F, Yang K, Fang S, Bu D, Li H, et al.SymMap: an integrative database of traditional Chinese medicine enhanced by symptom mapping.Nucleic acids research.2019;47(D1):D1110-D17.
O’Boyle N, Banck M, James C, Morley C, Vandermeersch T and Hutchison G. Open babel: an open chemical toolbox. J Cheminf 3 (1): 33. 2011.
Lagorce D, Bouslama L, Becot J, Miteva MA and Villoutreix BO.FAF-Drugs4: free ADME-tox filtering computations for chemical biology and early stages drug discovery.Bioinformatics.2017;33(22):3658-60.
Trott O and Olson AJ.AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading.Journal of computational chemistry.2010;31(2):455-61.
Chang Y-C, Tung Y-A, Lee K-H, Chen T-F, Hsiao Y-C, Chang H-C, et al.Potential therapeutic agents for COVID-19 based on the analysis of protease and RNA polymerase docking.2020.
Bon CFL, Berrué F, Thomas O, Reyes F and Amade P.Sodwanone S, a triterpene from the marine sponge Axinella weltneri.Journal of natural products.2005.
Rho HS, Ghimeray AK, Yoo DS, Ahn SM, Kwon SS, Lee KH, et al.Kaempferol and kaempferol rhamnosides with depigmenting and anti-inflammatory properties.Molecules.2011;16(4):3338-44.
Tatsimo SJN, de Dieu Tamokou J, Havyarimana L, Csupor D, Forgo P, Hohmann J, et al.Antimicrobial and antioxidant activity of kaempferol rhamnoside derivatives from Bryophyllum pinnatum.BMC Research notes.2012;5(1):158.
M Calderon-Montano J, Burgos-Morón E, Pérez-Guerrero C and López-Lázaro M.A review on the dietary flavonoid kaempferol.Mini reviews in medicinal chemistry.2011;11(4):298-344.
Kashyap D, Sharma A, Tuli HS, Sak K, Punia S and Mukherjee TK.Kaempferol–A dietary anticancer molecule with multiple mechanisms of action: Recent trends and advancements.Journal of functional foods.2017;30:203-19.
Jo S, Kim S, Shin DH and Kim M-S.Inhibition of SARS-CoV 3CL protease by flavonoids.Journal of enzyme inhibition and medicinal chemistry.2020;35(1):145-51.
Cid-Ortega S and Monroy-Rivera JA.Pregledni prikaz ekstrakcije kempferola i njegovih glikozida iz biljaka pomoću superkritičnih tekućina.Food Technology and Biotechnology.2018;56(4):480-93.
Commission CP. A Colored Identification Atlas of Chinese Materia Medica and Plants as Specified in the Pharmacopoeia of the People’s Republic of China: People’s Medical Publishing House; 2010.
Ma D and Cai W.Sangbaipi decoction on acute exacerbation of chronic obstructive pulmonary disease (phlegm-heat obstructing lung) clinical efficacy and prognosis.J Zhejiang Univ Tradit Chin Med.2013;37:691-94.
Chun-Nan L, Wen-Liang S, Feng-Nien K and Che-Ming T.Antiplatelet activity of some prenylflavonoids.Biochemical pharmacology.1993;45(2):509-12.
Dat N and Binh P.TP Quynh le, C. Van Minh, HT Huong and JJ Lee.Fitoterapia.2010;81:1224-27.
LIOU SS, SHIEH WL, CHENG TH, WON SJ and LIN CN.γ-Pyrone compounds as potential anti-cancer drugs.Journal of pharmacy and pharmacology.1993;45(9):791-94.
Lee H and Lee T.Lyu da.H, Koo, U, Lee, SJ, Hong, SS, Kim, K, Kim, KH, Lee, D and Mar, W.2011:1373-80.
- Abstract Viewed: 126 times
- PDF Downloaded: 55 times
- Figures Downloaded: 0 times