About: Virtual screening and dynamics of potential inhibitors targeting RNA binding domain of nucleocapsid phosphoprotein from SARS-CoV-2

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About: Virtual screening and dynamics of potential inhibitors targeting RNA binding domain of nucleocapsid phosphoprotein from SARS-CoV-2 Goto Sponge NotDistinct Permalink

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

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type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	Virtual screening and dynamics of potential inhibitors targeting RNA binding domain of nucleocapsid phosphoprotein from SARS-CoV-2
Creator	Dhamija, Puneet Handu, Shailendra Imran, Mohammed Suchal, Kapil Yadav, Rohitash
Source	Medline; PMC
abstract	The emergence of the coronavirus disease-2019 pandemic has led to an outbreak in the world. The SARS-CoV-2 is seventh and latest in coronavirus family with unique exonucleases for repairing any mismatches in newly transcribed genetic material. Therefore, drugs with novel additional mechanisms are required to simultaneously target and eliminate the virus. Thus, a newly deciphered N protein is taken as a target that belongs to SARS-CoV-2. They play a vital role in RNA transcription, viral replication and new virion formation. This study used virtual screening, molecular modeling and docking of the 8987 ligands from Asinex and PubChem databases against this novel target protein. Three hotspot sites having DScore ≥1 (Site 1, Site 2 and Site 3) for ligand binding were selected. Subsequently, high throughput screening, standard precision and extra precision docking process and molecular dynamics concluded three best drugs from two libraries. Two antiviral moieties from Asinex databases (5817 and 6799) have docking scores of −10.29 and −10.156; along with their respective free binding energies (ΔG bind) of −51.96 and −64.36 on Site 3. The third drug, Zidovudine, is from PubChem database with docking scores of −9.75 with its binding free energies (ΔG bind) of −59.43 on Site 3. The RMSD and RMSF were calculated for all the three drugs through molecular dynamics simulation studies for 50 ns. Zidovudine shows a very stable interaction with fluctuation starting at 2.4 Å on 2 ns and remained stable at 3 Å from 13 to 50 ns. Thus, paving the way for further biological validation as a potential treatment. Communicated by Ramaswamy H. Sarma
has issue date	2020-06-22(xsd:dateTime)
bibo:doi	10.1080/07391102.2020.1778536
bibo:pmid	32568013
has license	no-cc
sha1sum (hex)	ef9220984560f5a8be33e50146f8b6e3020e8d78
schema:url	https://doi.org/10.1080/07391102.2020.1778536
resource representing a document's title	Virtual screening and dynamics of potential inhibitors targeting RNA binding domain of nucleocapsid phosphoprotein from SARS-CoV-2
has PubMed Central identifier	PMC7332875
has PubMed identifier	32568013
schema:publication	J Biomol Struct Dyn
resource representing a document's body	covid:ef9220984560f5a8be33e50146f8b6e3020e8d78#body_text
is schema:about of	named entity 'SARS-COV-2' named entity 'SITES' named entity 'VIRTUAL SCREENING' named entity 'REQUIRED' named entity 'BINDING' named entity 'MOLECULAR DYNAMICS SIMULATION' named entity 'RMSF' named entity 'NOVEL' named entity 'TRANSCRIBED' named entity 'LATEST' named entity 'SEVENTH' named entity 'STUDIES' named entity '8059' named entity 'LED' named entity 'CORONAVIRUS DISEASE' named entity 'N PROTEIN' named entity 'LIGANDS' named entity 'MOLECULAR MODELING' named entity 'STABLE' named entity 'STUDY' named entity 'VIRAL REPLICATION' named entity 'LIBRARIES' named entity 'PLAY' named entity 'STARTING' named entity 'STANDARD' named entity 'exonucleases' named entity 'ligands' named entity 'ligand binding' named entity 'free energies' named entity 'Zidovudine' named entity 'molecular dynamics' named entity 'binding energies' named entity 'virion' named entity 'protein' named entity 'molecular dynamics simulation' named entity 'RNA binding' named entity 'nucleocapsid' named entity '1, 2' named entity 'protein structure' named entity 'PubChem' named entity 'ligands' named entity 'protein' named entity 'ADME' named entity 'GBSA' named entity 'force field' named entity '3.5' named entity 'SARS-CoV-2' named entity 'protease' named entity 'pyrimidine' named entity 'infectious disease' named entity 'kcal' named entity 'SARS CoV' named entity 'proteases' named entity 'atom' named entity 'ligands' named entity 'protein' named entity 'ligands' named entity 'ligands' named entity 'protein structure' named entity 'Herpes' named entity 'drug designing' named entity 'Ramachandran plot' named entity 'ligands' named entity 'FDA' named entity 'Protein' named entity 'free energy' named entity 'ligand' named entity 'Valganciclovir' named entity 'active site' named entity 'hydrogen bond interactions' named entity 'hydrogen bond' named entity 'angiotensin converting enzyme' named entity 'ligand' named entity 'antiviral drugs' named entity 'cell cycle' named entity 'protein receptor' named entity 'methionine'

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