System biology-based investigation of Silymarin to trace hepatoprotective effect

Computational investigation of benzalacetophenone derivatives against SARS-CoV-2 as potential multi-target bioactive compounds

“…The best-docked conformations from the three different targets were selected and subjected to all-atom molecular dynamics (MD) simulation for 150 ns in explicit solvent to investigate their structural stabilities and intermolecular interactions. We used GROMACS ( https://www.gromacs.org/ ) 2021.3 software package to perform MD simulations with the Amber ff99SB-ildn force field [ 25 , 26 ]. The partial charges of the small molecules were generated by performing quantum calculation using an antechamber with a ‘ bcc ’ charge model and topology parameters of the ligands and whole complex were generated using the xleap module of AmberTools ( https://ambermd.org/AmberTools.php ).…”

“…The relative binding energy of a ligand-protein complex is used in MD simulations and thermodynamic computations to explore the binding affinities. In the present work, the ‘ g_mmpbsa ’ tool [ 26 ] was used to calculate the relative binding energy and its contribution to single residues using the MM-PBSA approach. The parameters used to calculate the binding energy were considered from earlier studies [ 28 , 29 ].…”

The favorable impacts of silibinin polyphenols as adjunctive therapy in reducing the complications of COVID-19: A review of research evidence and underlying mechanisms

“…We hypothesized to identify fusion inhibitors from the NPACT library of anticancer phytochemicals. molecular docking experiments Patel, Kumar, Pandya, Rawal [21] CoV-2 hemagglutinin-acetylesterase (HE) glycoprotein as Docking analysis Silymarin, as potential hemagglutinin-acetylesterase (HE) glycoprotein inhibitors with better binding energy. In vitro Aguilar‑Lemarroy, López‑Uribe, Sánchez‑Corona, Jave‑suárez [22] HaCaT, DOK, A549, H1299 and Lenti-X 293 T cells transcrip¬tion quantitative PCR Use of viral particles containing SARS CoV 2 ORF3a and bioinformatics silymarin significantly decrease the level of ACE2 expression a In addition, silymarin treatment markedly decreased IL-6, TNF-α RPL18, RPL32 interleukin‑18 mRNA levels.…”

“…In this regard, polyphenol and flavonoid compounds' anti-inflammatory and antioxidant activity have been confirmed strongly [19] , [20] . Silymarin is a complex polyphenolic compound derived from the seed of the milk thistle plant, and it is known for its anti-inflammatory, antiviral, anti-oxidative, and immunomodulatory effects [21] , [22] , [23] . Silymarin was reported to inhibit the hepatitis C virus in vivo and in vitro by inhibiting hepatitis C virus entry, viral protein expression, RNA synthesis, and virus replication.…”

Mechanisms of action of Zishen Yutai pills in treating premature ovarian failure determined by integrating UHPLC-Q-TOF-MS and network pharmacology analysis

“…The node size and colors in the network were set as “ high values to large size ” and “ high values to dark colors ” respectively on basis of the edge count for both settings [ 24 , 25 ]. Thirdly, the Go enrichment analysis gene ontology (GO) and KEGG enrichment were conducted using the functional annotation tool of DAVID Bioinformatics Resources 6.7 ( http://david.abcc.ncifcri.gov/ ) and Bioinformatics ( http://www.bioinformatics.com.cn/ ), respectively [ 26 – 29 ] .…”