Exploration on Shufeng Jiedu Capsule for Treatment of COVID-19 Based on Network Pharmacology and Molecular Docking

Zhao, Yanwu; Hu, Junhui; Jiang, Song; Zhao, Xinhong; Shi, Yanjing; Jiang, Yanping

doi:10.4236/cm.2020.111002

Cited by 6 publications

(2 citation statements)

References 2 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Our findings in this current in silico work through the molecular interaction fingerprints of the lead molecules are in tandem with those of previous studies (Kamaz et al 2020 ; Jin et al 2020 ; Putu et al 2020 ; Zhao et al 2020 ).…”

Section: Resultssupporting

confidence: 90%

Novel Molecules derived from 3-O-(6-galloylglucoside) inhibit Main Protease of SARS-CoV 2 In Silico

et al. 2021

View full text Add to dashboard Cite

The ongoing pandemic caused by the severe acute respiratory syndrome 2 (SARS-CoV 2) has led to more than 168 million confirmed cases with 3.5 million deaths as at 28th May, 2021 across 218 countries. The virus has a cysteine protease called main protease (Mpro) which is significant to it life cycle, tagged as a suitable target for novel antivirals. In this computer-assisted study, we designed 100 novel molecules through an artificial neural network-driven platform called LigDream ( https://playmolecule.org/LigDream/ ) using 3-O-(6-galloylglucoside) as parent molecule for design. Druglikeness screening of the molecules through five (5) different rules was carried out, followed by a virtual screening of those molecules without a single violation of the druglike rules using AutoDock Vina against Mpro. The in silico pharmacokinetic features were predicted and finally, quantum mechanics/molecular mechanics (QM/MM) study was carried out using Molecular Orbital Package 2016 (MOPAC2016) on the overall hit compound with controls to determine the stability and reactivity of the lead molecule. The findings showed that eight (8) novel molecules violated none of the druglikeness rules of which three (3) novel molecules (C33, C35 and C54) showed the utmost binding affinity of −8.3 kcal/mol against Mpro; C33 showed a good in silico pharmacokinetic features with acceptable level of stability and reactively better than our controls based on the quantum chemical descriptors analysis. However, there is an urgent need to carry out more research on these novel molecules for the fight against the disease. Supplementary Information The online version contains supplementary material available at 10.1007/s11696-021-01899-y.

show abstract

Section: Resultssupporting

confidence: 90%

Novel Molecules derived from 3-O-(6-galloylglucoside) inhibit Main Protease of SARS-CoV 2 In Silico

et al. 2021

View full text Add to dashboard Cite

show abstract

“…Throughout this in silico investigation, an exhaustiveness of 10 was used for docking, and the number of modes set to 10 so as to achieve more accurate and reliable results. The interaction between ligands and proteins was then prepared, visualized, and analyzed using PyMOL and Discovery Studio 2016 respectively [ 1 , 30 ].…”

Section: Methodsmentioning

confidence: 99%

Molecular docking studies of some selected gallic acid derivatives against five non-structural proteins of novel coronavirus

Umar

Siraj

Ajayi

et al. 2021

Journal of Genetic Engineering and Biotechnology

View full text Add to dashboard Cite

Background The World Health Organization has recently declared a new coronavirus disease (COVID-19) a pandemic and a global health emergency. The pressure to produce drugs and vaccines against the ongoing pandemic has resulted in the use of some drugs such as azithromycin, chloroquine (sulfate and phosphate), hydroxychloroquine, dexamethasone, favipiravir, remdesivir, ribavirin, ivermectin, and lopinavir/ritonavir. However, reports from some of the clinical trials with these drugs have proved detrimental on some COVID-19 infected patients with side effects more of which cardiomyopathy, cardiotoxicity, nephrotoxicity, macular retinopathy, and hepatotoxicity have been recently reported. Realizing the need for potent and harmless therapeutic compounds to combat COVID-19, we attempted in this study to find promising therapeutic compounds against the imminent threat of this virus. In this current study, 16 derivatives of gallic acid were docked against five selected non-structural proteins of SARS-COV-2 known to be a good target for finding small molecule inhibitors against the virus, namely, nsp3, nsp5, nsp12, nsp13, and nsp14. All the protein crystal structures and 3D structures of the small molecules (16 gallic acid derivatives and 3 control drugs) were retrieved from the Protein database (PDB) and PubChem server respectively. The compounds with lower binding energy than the control drugs were selected and subjected to pharmacokinetics screening using AdmetSAR server. Results 4-O-(6-galloylglucoside) gave binding energy values of − 8.4, − 6.8, − 8.9, − 9.1, and − 7.5 kcal/mol against Mpro, nsp3, nsp12, nsp13, and nsp15 respectively. Based on the ADMET profile, 4-O-(6-galloylglucoside) was found to be metabolized by the liver and has a very high plasma protein binding. Conclusion The result of this study revealed that 4-O-(6-galloylglucoside) could be a promising inhibitor against these SAR-Cov-2 proteins. However, there is still a need for further molecular dynamic simulation, in vivo and in vitro studies to support these findings.

show abstract

Investigation on humic substance and tetracycline interaction mechanism: biophysical and theoretical studies and assessing their effect on biological activity

Nascimento,

de Oliveira Souza,

Guimarães

et al. 2024

Environ Sci Pollut Res

View full text Add to dashboard Cite

Exploration on Shufeng Jiedu Capsule for Treatment of COVID-19 Based on Network Pharmacology and Molecular Docking

Cited by 6 publications

References 2 publications

Novel Molecules derived from 3-O-(6-galloylglucoside) inhibit Main Protease of SARS-CoV 2 In Silico

Novel Molecules derived from 3-O-(6-galloylglucoside) inhibit Main Protease of SARS-CoV 2 In Silico

Molecular docking studies of some selected gallic acid derivatives against five non-structural proteins of novel coronavirus

Investigation on humic substance and tetracycline interaction mechanism: biophysical and theoretical studies and assessing their effect on biological activity

Contact Info

Product

Resources

About