About: Structure-based virtual screening and molecular dynamics simulation of SARS-CoV-2 Guanine-N7 methyltransferase (nsp14) for identifying antiviral inhibitors against COVID-19

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About: Structure-based virtual screening and molecular dynamics simulation of SARS-CoV-2 Guanine-N7 methyltransferase (nsp14) for identifying antiviral inhibitors against COVID-19 Goto Sponge NotDistinct Permalink

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Structure-based virtual screening and molecular dynamics simulation of SARS-CoV-2 Guanine-N7 methyltransferase (nsp14) for identifying antiviral inhibitors against COVID-19
Creator	Singh, Sanjeev Boura, Evzen Abhirami, Rajaram Dinesh, Chandrasekaran Panwar, Umesh Selvaraj, Chandrabose
Source	Medline; PMC
abstract	The recent pandemic caused by Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) calls the whole world into a medical emergency. For tackling Coronavirus Disease 2019 (COVID-19), researchers from around the world are swiftly working on designing and identifying inhibitors against all possible viral key protein targets. One of the attractive drug targets is guanine-N7 methyltransferase which plays the main role in capping the 5′-ends of viral genomic RNA and sub genomic RNAs, to escape the host’s innate immunity. We performed homology modeling and molecular dynamic (MD) simulation, in order to understand the molecular architecture of Guanosine-P3-Adenosine-5’,5’-Triphosphate (G3A) binding with C-terminal N7-MTase domain of nsp14 from SARS-CoV-2. The residue Asn388 is highly conserved in present both in N7-MTase from SARS-CoV and SARS-CoV-2 and displays a unique function in G3A binding. For an in-depth understanding of these substrate specificities, we tried to screen and identify inhibitors from the Traditional Chinese Medicine (TCM) database. The combination of several computational approaches, including screening, MM/GBSA, MD simulations, and PCA calculations, provides the screened compounds that readily interact with the G3A binding site of homology modeled N7-MTase domain. Compounds from this screening will have strong potency towards inhibiting the substrate-binding and efficiently hinder the viral 5’-end RNA capping mechanism. We strongly believe the final compounds can become COVID-19 therapeutics, with huge international support. Communicated by Ramaswamy H. Sarma.
has issue date	2020-06-22(xsd:dateTime)
bibo:doi	10.1080/07391102.2020.1778535
bibo:pmid	32567979
has license	no-cc
sha1sum (hex)	c52c88a75051a4ea4fca5013f8263ff68e9296fe
schema:url	https://doi.org/10.1080/07391102.2020.1778535
resource representing a document's title	Structure-based virtual screening and molecular dynamics simulation of SARS-CoV-2 Guanine-N7 methyltransferase (nsp14) for identifying antiviral inhibitors against COVID-19
has PubMed Central identifier	PMC7332868
has PubMed identifier	32567979
schema:publication	J Biomol Struct Dyn
resource representing a document's body	covid:c52c88a75051a4ea4fca5013f8263ff68e9296fe#body_text
is schema:about of	named entity 'One' named entity 'RNA' named entity 'For' named entity 'Traditional Chinese Medicine (TCM)' named entity 'methyltransferase' named entity 'POSSIBLE' named entity 'MD SIMULATIONS' named entity 'CAUSED BY' named entity 'C-TERMINAL' named entity 'FUNCTION' named entity 'UNDERSTANDING' named entity 'PROTEIN ' named entity 'PRESENT' named entity 'WORKING' named entity 'GUANOSINE' named entity 'COVID-19' named entity 'RESEARCHERS' named entity 'ATTRACTIVE' named entity 'STRUCTURE' named entity 'interact' named entity 'RNA' named entity 'genomic' named entity 'support' named entity 'calls' named entity 'pandemic' named entity 'escape' named entity 'medical emergency' named entity 'domain' named entity 'drug targets' named entity 'COVID-19' named entity 'function' named entity 'virtual screening' named entity 'antiviral inhibitors' named entity 'Coronavirus Disease 2019' named entity 'SARS-CoV-2' named entity 'SARS-CoV-2' named entity 'RNA' named entity 'SARS-CoV-2' named entity 'amino acid' named entity 'murine' named entity 'RMSD' named entity 'ligand' named entity 'alpha helix' named entity 'bond length' named entity 'binding site' named entity 'BLASTp' named entity 'antiviral drug' named entity 'pneumonia' named entity 'RNA' named entity 'TCM' named entity 'ligand' named entity 'protein structure' named entity 'protein' named entity 'Berendsen thermostat' named entity 'beta-turns' named entity 'enzyme complex' named entity 'Hubei' named entity 'genome replication' named entity 'SARS-CoV-2' named entity 'SARS-CoV' named entity 'CoV' named entity 'RMSD' named entity 'SARS-CoV-2' named entity 'Poisson-Boltzmann' named entity 'ribose' named entity 'TCM' named entity 'hydroxyl group' named entity 'TCM' named entity 'exonuclease' named entity 'force field' named entity 'SARS-CoV-2' named entity 'protein' named entity 'root-mean-square deviation' named entity 'OPLS' named entity 'protein' named entity 'ligand'

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