About: Investigating the binding affinity, interaction, and structure-activity-relationship of 76 prescription antiviral drugs targeting RdRp and Mpro of SARS-CoV-2

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About: Investigating the binding affinity, interaction, and structure-activity-relationship of 76 prescription antiviral drugs targeting RdRp and Mpro of SARS-CoV-2 Goto Sponge NotDistinct Permalink

An Entity of Type : schema:ScholarlyArticle, within Data Space : covidontheweb.inria.fr associated with source document(s)

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Investigating the binding affinity, interaction, and structure-activity-relationship of 76 prescription antiviral drugs targeting RdRp and Mpro of SARS-CoV-2
Creator	Al Mamun, Abdulla Halim, Mohammad Islam, Rajib Parves, Ahmed, Samina Ahmed, Sinthyia Akter, Shaila Ali, Ackas Hossain, Nayeem Mahtarin, Rumana Sultana, Mossammad Ullah, M
Source	Medline; PMC
abstract	SARS-CoV-2 virus outbreak poses a major threat to humans worldwide due to its highly contagious nature. In this study, molecular docking, molecular dynamics, and structure-activity relationship are employed to assess the binding affinity and interaction of 76 prescription drugs against RNA dependent RNA polymerase (RdRp) and Main Protease (Mpro) of SARS-CoV-2. The RNA-dependent RNA polymerase is a vital enzyme of coronavirus replication/transcription complex whereas the main protease acts on the proteolysis of replicase polyproteins. Among 76 prescription antiviral drugs, four drugs (Raltegravir, Simeprevir, Cobicistat, and Daclatasvir) that are previously used for human immunodeficiency virus (HIV), hepatitis C virus (HCV), Ebola, and Marburg virus show higher binding energy and strong interaction with active sites of the receptor proteins. To explore the dynamic nature of the interaction, 100 ns molecular dynamics (MD) simulation is performed on the selected protein-drug complexes and apo-protein. Binding free energy of the selected drugs is performed by MM/PBSA. Besides docking and dynamics, partial least square (PLS) regression method is applied for the quantitative structure activity relationship to generate and predict the binding energy for drugs. PLS regression satisfactorily predicts the binding energy of the effective antiviral drugs compared to binding energy achieved from molecular docking with a precision of 85%. This study highly recommends researchers to screen these potential drugs in vitro and in vivo against SARS-CoV-2 for further validation of utility.
has issue date	2020-07-28(xsd:dateTime)
bibo:doi	10.1080/07391102.2020.1796804
bibo:pmid	32720571
has license	no-cc
sha1sum (hex)	e54a453638b227dfba3cdcf5e0211551f9dfeb7d
schema:url	https://doi.org/10.1080/07391102.2020.1796804
resource representing a document's title	Investigating the binding affinity, interaction, and structure-activity-relationship of 76 prescription antiviral drugs targeting RdRp and Mpro of SARS-CoV-2
has PubMed Central identifier	PMC7441766
has PubMed identifier	32720571
schema:publication	Journal of biomolecular structure & dynamics
resource representing a document's body	covid:e54a453638b227dfba3cdcf5e0211551f9dfeb7d#body_text
is schema:about of	named entity 'Simeprevir' named entity 'vivo' named entity 'proteins' named entity 'poses' named entity 'explore' named entity 'SARS-CoV-2' named entity 'RNA-dependent RNA polymerase' named entity 'structure-activity relationship' named entity 'ENZYME' named entity 'DYNAMIC NATURE OF' named entity 'SIMEPREVIR' named entity 'EFFECTIVE' named entity 'researchers' named entity 'predict' named entity 'Raltegravir' named entity 'interaction' named entity 'PLS' named entity 'SARS-CoV-2' named entity 'utility' named entity 'polymerase' named entity 'regression' named entity 'dynamic' named entity 'quantitative' named entity 'free energy' named entity 'replicase' named entity 'protein' named entity 'replicase' named entity 'molecular docking' named entity 'HCV' named entity 'RNA-dependent RNA polymerase' named entity 'protease' named entity 'apo' named entity 'binding affinity' named entity 'prescription drugs' named entity 'PLS' named entity 'human immunodeficiency virus' named entity 'structure activity relationship' named entity 'molecular dynamics' named entity '85%' named entity 'antiviral drugs' named entity 'Daclatasvir' named entity 'PLS' named entity 'binding affinity' named entity 'antiviral drugs' named entity 'Protease' named entity 'Hermes' named entity 'molecular docking' named entity 'Mpro' named entity 'RNA dependent RNA polymerase' named entity 'binding affinity' named entity 'RStudio' named entity 'RdRp' named entity 'structural domains' named entity 'protein structure' named entity 'free energy' named entity 'critical role' named entity 'particle Mesh' named entity 'RdRp' named entity 'Molecular Mechanics' named entity 'RMSF' named entity 'free energy' named entity 'Ligand Docking' named entity 'Remdesivir' named entity 'binding energy' named entity 'Principal component analysis' named entity 'coronavirus outbreak' named entity 'Mpro' named entity 'Mpro' named entity 'binding affinity' named entity 'Mpro'

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