<italic style="font-style: italic">In Silico</italic> Screening of Natural Products as Potential Inhibitors of SARS-CoV-2 Using Molecular Docking Simulation

Rajib Hossain; Chandan Sarkar; Shardar Mohammad Hafiz Hassan; Rasel Ahmed Khan; Mohammad Arman; Pranta Ray; Muhammad Torequl Islam; Sevgi Durna Daștan; Javad Sharifi-Rad; Zainab M. Almarhoon; Miquel Martorell; William N. Setzer; Daniela Calina

doi:10.1007/s11655-021-3504-5

Your Location：

Home >

Browse articles >

In Silico Screening of Natural Products as Potential Inhibitors of SARS-CoV-2 Using Molecular Docking Simulation

Original Article | Updated：2022-03-18

- In Silico Screening of Natural Products as Potential Inhibitors of SARS-CoV-2 Using Molecular Docking Simulation
- In Silico Screening of Natural Products as Potential Inhibitors of SARS-CoV-2 Using Molecular Docking Simulation
- Chinese Journal of Integrative Medicine 2022年28卷第3期页码：249-256
- Affiliations：
  
  1.Department of Pharmacy, Life Science Faculty, Bangabandhu Sheikh Mujibur Rahman Science and Technology University,Gopalganj (8100), Bangladesh
  2.Harmacy Discipline, Life Science School, Khulna University, Khulna-9280, Bangladesh
  3.Department of Pharmacy, International Islamic University,Chittagong, Bangladesh
  4.Department of Biomedical Engineering, Huazhong University of Science and Technology,Wuhan (430074), China
  5.Department of Biology, Faculty of Science, Sivas Cumhuriyet University, Sivas (58140), Turkey
  6.Beekeeping Development Application and Research Center,Sivas Cumhuriyet University, Sivas (58140), Turkey
  7.School of Medicine, University of Azuay, Cuenca, Ecuador
  8.Department of Chemistry, College of Science, King Saud University, Riyadh(11451), Saudi Arabia
  9.Department of Nutrition and Dietetics,Faculty of Pharmacy, and Centre for Healthy Living, University of Concepción, Concepción (4070386), Chile
  10.Department of Chemistry, University of Alabama in Huntsville, Huntsville,AL (35899), USA
  11.Aromatic Plant Research Center, 230 N 1200 E, Suite 100, Lehi, UT (84043), USA
  12.Department of Clinical Pharmacy, University of Medicine and Pharmacy of Craiova, Craiova (200349), Romania
- Author bio：
  
  Prof. Javad Sharifi-Rad, E-mail: javad.sharifirad@gmail.com
- Funds：
- DOI：10.1007/s11655-021-3504-5
  中图分类号：
- 纸质出版日期：2022-03-01，
  
  网络出版日期：2021-12-15，
  
  录用日期：2021-01-13
Scan for full text
Rajib Hossain, Chandan Sarkar, Shardar Mohammad Hafiz Hassan, 等. In Silico Screening of Natural Products as Potential Inhibitors of SARS-CoV-2 Using Molecular Docking Simulation[J]. Chinese Journal of Integrative Medicine, 2022,28(3):249-256.

Rajib Hossain, Chandan Sarkar, Shardar Mohammad Hafiz Hassan, et al. In Silico Screening of Natural Products as Potential Inhibitors of SARS-CoV-2 Using Molecular Docking Simulation[J]. Chinese Journal of Integrative Medicine, 2022,28(3):249-256.
Rajib Hossain, Chandan Sarkar, Shardar Mohammad Hafiz Hassan, 等. In Silico Screening of Natural Products as Potential Inhibitors of SARS-CoV-2 Using Molecular Docking Simulation[J]. Chinese Journal of Integrative Medicine, 2022,28(3):249-256. DOI： 10.1007/s11655-021-3504-5.

Rajib Hossain, Chandan Sarkar, Shardar Mohammad Hafiz Hassan, et al. In Silico Screening of Natural Products as Potential Inhibitors of SARS-CoV-2 Using Molecular Docking Simulation[J]. Chinese Journal of Integrative Medicine, 2022,28(3):249-256. DOI： 10.1007/s11655-021-3504-5.

摘要

Abstract

Objective:

To explore potential natural products against severe acute respiratory syndrome coronavirus (SARS-CoV-2) via the study of structural and non-structural proteins of human coronaviruses.

Methods:

In this study

we performed an

in-silico

survey of 25 potential natural compounds acting against SARS-CoV-2. Molecular docking studies were carried out using compounds against 3-chymotrypsin-like protease (3CL

PRO

)

papain-like protease (PL

PRO

)

RNA-dependent RNA polymerase (RdRp)

non-structural protein (nsp)

human angiotensin converting enzyme 2 receptor (hACE2R)

spike glycoprotein (S protein)

abelson murine leukemia viral oncogene homolog 1 (ABL1)

calcineurin-nuclear factor of activated T-cells (NFAT) and transmembrane protease serine 2.

Results:

Among the screened compounds

amentoflavone showed the best binding affinity with the 3CL

PRO

RdRp

nsp13

nsp15

hACE2R¸ ABL1 and calcineurin-NFAT; berbamine with hACE2R and ABL1; cepharanthine with nsp10

nsp14

nsp16

S protein and ABL1; glucogallin with nsp15; and papyriflavonol A with PL

PRO

protein. Other good interacting compounds were juglanin

betulinic acid

betulonic acid

broussooflavan A

tomentin A

B and E

7-methoxycryptopleurine

aloe emodin

quercetin

tanshinone Ⅰ

tylophorine and furruginol

which also showed excellent binding affinity towards a number of target proteins. Most of these compounds showed better binding affinities towards the target proteins than the standard drugs used in this study.

Conclusion:

Natural products or their derivatives may be one of the potential targets to fight against SARS-CoV-2.

关键词

Keywords

SARS-CoV-2natural products-derived anti-SARS-CoV-2 candidatesstructural proteinsnonstructural proteinsmolecular docking

references

Elfiky AA, Mahdy SM, Elshemey WM. Quantitative structure-activity relationship and molecular docking revealed a potency of anti-hepatitis C virus drugs against human corona viruses. J Med Virol 2017;89:1040-1047.

Robson B. Computers and viral diseases. Preliminary bioinformatics studies on the design of a synthetic vaccine and a preventative peptidomimetic antagonist against the SARS-CoV-2 (2019-nCoV, COVID-19) coronavirus.Comput Biol Med 2020;119:103670.

Calina D, Docea AO, Petrakis D, Egorov AM,Ishmukhametov AA, Gabibov AG, et al. Towards effective COVID-19 vaccines: updates, perspectives and challenges.Int J Mol Med 2020;46:3-16.

Hilgenfeld R. From SARS to MERS: crystallographic studies on coronaviral proteases enable antiviral drug design. FEBS J 2014;281:4085-4096.

Elfiky AA. Ribavirin, remdesivir, sofosbuvir, galidesivir,and tenofovir against SARS-CoV-2 RNA dependent RNA polymerase (RdRp): a molecular docking study. Life Sci 2020;253:117592.

Ratia K, Saikatendu KS, Santarsiero BD, Barretto N,Baker SC, Stevens RC, et al. Severe acute respiratory syndrome coronavirus papain-like protease: structure of a viral deubiquitinating enzyme. Proc Natl Acad Sci USA 2006;103:5717-5722.

Wu C, Liu Y, Yang Y, Zhang P, Zhong W, Wang Y, et al. Analysis of therapeutic targets for SARS-CoV-2 and discovery of potential drugs by computational methods.Acta Pharm Sin B 2020;10:766-788.

Báez-Santos YM, St John SE, Mesecar AD. The SARS-coronavirus papain-like protease: structure, function and inhibition by designed antiviral compounds. Antivir Res 2015;115:21-38.

Ivanov KA, Ziebuhr J. Human coronavirus 229E nonstructural protein 13: characterization of duplex-unwinding, nucleoside triphosphatase, and RNA 5'-triphosphatase activities. J Virol 2004;78:7833-7838.

Jin X, Chen Y, Sun Y, Zeng C, Wang Y, Tao J, et al.Characterization of the guanine-N7 methyltransferase activity of coronavirus nsp14 on nucleotide GTP. Virus Res 2013;176:45-52.

Bouvet M, Imbert I, Subissi L, Gluais L, Canard B, Decroly E. RNA 3'-end mismatch excision by the severe acute respiratory syndrome coronavirus nonstructural protein nsp10/nsp14 exoribonuclease complex. Proc Natl Acad Sci USA 2012;109:9372-9377.

Ricagno S, Egloff M-P, Ulferts R, Coutard B, Nurizzo D,Campanacci V, et al. Crystal structure and mechanistic determinants of SARS coronavirus nonstructural protein 15 define an endoribonuclease family. Proc Natl Acad Sci USA 2006;103:11892.

Decroly E, Imbert I, Coutard B, Bouvet M, Selisko B,Alvarez K, et al. Coronavirus nonstructural protein 16 is a cap-0 binding enzyme possessing (nucleoside-2'O)-methyltransferase activity. J Virol 2008;82:8071-8084.

van der Hoek L, Pyrc K, Jebbink MF, Vermeulen-Oost W,Berkhout RJ, Wolthers KC, et al. Identification of a new human coronavirus. Nat Med 2004;10:368-373.

Berry M, Fielding BC, Gamieldien J. Potential broad spectrum inhibitors of the coronavirus 3CLPRO: a virtual screening and structure-based drug design study. Viruses 2015;7:6642-6660.

Ortega JT, Serrano ML, Pujol FH, Rangel HR. Role of changes in SARS-CoV-2 spike protein in the interaction with the human ACE2 receptor: an in silico analysis. EXCLI J 2020;19:410-417.

Zhao X, Chen D, Szabla R, Zheng M, Li G, Du P, et al.Broad and differential animal angiotensin-converting enzyme 2 receptor usage by SARS-CoV-2. J Virol 2020;94:e00940-e00920.

Bouricha EM, Hakmi M, Akachar J, Belyamani L, Ibrahimi A. In silico analysis of ACE2 orthologues to predict animal host range with high susceptibility to SARS-CoV-2. Biotech 2020;10:483.

Islam MT, Sarkar C, El-Kersh DM, Jamaddar S, Uddin SJ, Shilpi JA, et al. Natural products and their derivatives against coronavirus: a review of the non-clinical and pre-clinical data. Phytother Res 2020;34:2471-2492.

Singh D, Gawande DY, Singh T, Poroikov V, Goel RK.Revealing pharmacodynamics of medicinal plants using in silico approach: a case study with wet lab validation.Comput Biol Med 2014;47:1-6.

Aziz MA, Mehedi M, Akter MI, Sajon SR, Mazumder K,Rana MS. In vivo and in silico evaluation of analgesic activity of Lippia alba. Clin Phytosci 2019;5:38.

Shen L, Niu J, Wang C, Huang B, Wang W, Zhu N, et al.High-throughput screening and identification of potent broad-spectrum inhibitors of coronaviruses. J Virol 2019;93:e00023-e00019.

Jassim SA, Naji MA. Novel antiviral agents: a medicinal plant perspective. J Appl Microbiol 2003;95:412-427.

Wu K, Chen L, Peng G, Zhou W, Pennell CA, Mansky LM, et al. A virus-binding hot spot on human angiotensin-converting enzyme 2 is critical for binding of two different coronaviruses. J Virol 2011;85:5331-5337.

Ryu YB, Jeong HJ, Kim JH, Kim YM, Park JY, Kim D, et al.Biflavonoids from Torreya nucifera displaying SARS-CoV 3CL (pro) inhibition. Bioorg Med Chem 2010;18:7940-7947.

Zhang CH, Wang YF, Liu XJ, Lu JH, Qian CW, Wan ZY, et al. Antiviral activity of cepharanthine against severe acute respiratory syndrome coronavirus in vitro. Chin Med J 2005;118:493-496.

Park JY, Yuk HJ, Ryu HW, Lim SH, Kim KS, Park KH, et al.Evaluation of polyphenols from Broussonetia papyrifera as coronavirus protease inhibitors. J Enzyme Inhib Med Chem 2017;32:504-515.

Schwarz S, Sauter D, Wang K, Zhang R, Sun B, Karioti A, et al. Kaempferol derivatives as antiviral drugs against the 3a channel protein of coronavirus. Planta Med 2014;80:177-182.

Yi L, Li Z, Yuan K, Qu X, Chen J, Wang G, et al.Small molecules blocking the entry of severe acute respiratory syndrome coronavirus into host cells. J Virol 2004;78:11334-11339.

Wen CC, Kuo YH, Jan JT, Liang PH, Wang SY, Liu HG,et al. Specific plant terpenoids and lignoids possess potent antiviral activities against severe acute respiratory syndrome coronavirus. J Med Chem 2007;50:4087-4095.

Park JY, Kim JH, Kim YM, Jeong HJ, Kim DW, Park KH,et al. Tanshinones as selective and slow-binding inhibitors for SARS-CoV cysteine proteases. Bioorg Med Chem 2012;20:5928-5935.

Cho JK, Curtis-Long MJ, Lee KH, Kim DW, Ryu HW, Yuk HJ, et al. Geranylated flavonoids displaying SARS-CoV papain-like protease inhibition from the fruits of Paulownia tomentosa. Bioorg Med Chem 2013;21:3051-3057.

Lin CW, Tsai FJ, Tsai CH, Lai CC, Wan L, Ho TY, et al.Anti-SARS coronavirus 3C-like protease effects of Isatis indigotica root and plant-derived phenolic compounds.Antivir Res 2005;68:36-42.

Yang CW, Lee YZ, Kang IJ, Barnard DL, Jan JT, Lin D, et al. Identification of phenanthroindolizines and phenanthroquinolizidines as novel potent anti-coronaviral agents for porcine enteropathogenic coronavirus transmissible gastroenteritis virus and human severe acute respiratory syndrome coronavirus. Antivir Res 2010;88:160-168.

Shulla A, Heald-Sargent T, Subramanya G, Zhao J, Perlman S, Gallagher T. A transmembrane serine protease is linked to the severe acute respiratory syndrome coronavirus receptor and activates virus entry. J Virol 2011;85:873-882.

Zang R, Gomez Castro MF, McCune BT, Zeng Q, Rothlauf PW, Sonnek NM, et al. TMPRSS2 and TMPRSS4 promote SARS-CoV-2 infection of human small intestinal enterocytes. Sci Immunol 2020;5:eabc3582.

More>

浏览量

Downloads

CSCD

文章被引用时，请邮件提醒。

Submit

工具集

关联资源

Inhibitory Effect of Resveratrol on LPS-Induced Glomerular Mesangial Cells Proliferation and TGF-β1 Expression via Sphingosine Kinase 1 Pathway

Therapeutic Mechanism of Kai Xin San on Alzheimer's Disease Based on Network Pharmacology and Experimental Validation

Mechanism of Key Ingredient of Astragalus membranaceus on Lung Adenocarcinoma via PI3K/AKT Signaling Clarified by Utilizing Network Pharmacology Approach and Experimental Validation

Active Ingredients of Reduning Injection Maintain High Potency against SARS-CoV-2 Variants

Chinese Medicine, Which Targets Body's Response State, Is An Effective Way to Treat Epidemic Infectious Diseases

In Silico Screening of Natural Products as Potential Inhibitors of SARS-CoV-2 Using Molecular Docking Simulation

In Silico Screening of Natural Products as Potential Inhibitors of SARS-CoV-2 Using Molecular Docking Simulation

DOI：10.1007/s11655-021-3504-5

摘要

Abstract

关键词

Keywords

references