Molecular docking analysis of the BRCA1 protein with compounds from Justica adhatoda L

Jayaraman, Selvaraj; Vishnupriya, V.; Sreekandan, Radhika Nalinakumari; Mohan, Surapaneni Krishna; Suga, Sumetha Suga Deiva; Kamaraj, Devakumar; Mohandoss, Sonaimuthu; Koora, Sravanthi

doi:10.6026/97320630016888

Cited by 3 publications

(1 citation statement)

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“…For the preparation of the protein removal, unwanted things namely all the heteroatoms, H 2 O molecules, ligands, and metal ions, extra chains from the protein by using UCSF Chimera (version 1.14) package were made. As part of the macromolecule preparation applied “Gasteiger’s methods”, the protonation states for “Histidine” and conserver as PDB format for further analysis [ 41 , 42 ].…”

Section: Computational Methodologymentioning

confidence: 99%

Amentoflavone derivatives significantly act towards the main protease (3CLPRO/MPRO) of SARS-CoV-2: in silico admet profiling, molecular docking, molecular dynamics simulation, network pharmacology

Dey

Hossain

Biswas³

et al. 2022

Mol Divers

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SARS-CoV-2 is the foremost culprit of the novel coronavirus disease 2019 (nCoV-19 and/or simply COVID-19) and poses a threat to the continued life of humans on the planet and create pandemic issue globally. The 3-chymotrypsin-like protease (M PRO or 3CL PRO ) is the crucial protease enzyme of SARS-CoV-2, which directly involves the processing and release of translated non-structural proteins (nsps), and therefore involves the development of virus pathogenesis along with outbreak the forecasting of COVID-19 symptoms. Moreover, SARS-CoV-2 infections can be inhibited by plant-derived chemicals like amentoflavone derivatives, which could be used to develop an anti-COVID-19 drug. Our research study is designed to conduct an in silico analysis on derivatives of amentoflavone (isoginkgetin, putraflavone, 4′′′′′′-methylamentoflavone, bilobetin, ginkgetin, sotetsuflavone, sequoiaflavone, heveaflavone, kayaflavone, and sciadopitysin) for targeting the non-structural protein of SARS-CoV-2, and subsequently further validate to confirm their antiviral ability. To conduct all the in silico experiments with the derivatives of amentoflavone against the M PRO protein, both computerized tools and online servers were applied; notably the software used is UCSF Chimera (version 1.14), PyRx, PyMoL, BIOVIA Discovery Studio tool (version 4.5), YASARA (dynamics simulator), and Cytoscape. Besides, as part of the online tools, the SwissDME and pKCSM were employed. The research study was proposed to implement molecular docking investigations utilizing compounds that were found to be effective against the viral primary protease (M PRO ). M PRO protein interacted strongly with 10 amentoflavone derivatives. Every time, amentoflavone compounds outperformed the FDA-approved antiviral medicine that is currently underused in COVID-19 in terms of binding affinity (− 8.9, − 9.4, − 9.7, − 9.1, − 9.3, − 9.0, − 9.7, − 9.3, − 8.8, and − 9.0 kcal/mol, respectively). The best-selected derivatives of amentoflavone also possessed potential results in 100 ns molecular dynamic simulation (MDS) validation. It is conceivable that based on our in silico research these selected amentoflavone derivatives more precisely 4′′′′′′-methylamentoflavone, ginkgetin, and sequoiaflavone have potential for serving as promising lead drugs against SARS-CoV-2 infection. In consequence, it is recommended that additional in vitro as well as in vivo research studies have to be conducted to support the conclusions of this current research study. Graphical abstract

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Section: Computational Methodologymentioning

confidence: 99%