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About:
Virtual screening, molecular dynamics and structure–activity relationship studies to identify potent approved drugs for Covid-19 treatment
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An Entity of Type :
schema:ScholarlyArticle
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covidontheweb.inria.fr
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Academic Article
research paper
schema:ScholarlyArticle
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type
Academic Article
research paper
schema:ScholarlyArticle
isDefinedBy
Covid-on-the-Web dataset
has title
Virtual screening, molecular dynamics and structure–activity relationship studies to identify potent approved drugs for Covid-19 treatment
Creator
Rahman, Md
Al Mamun, Abdulla
Halim, Mohammad
Islam, Rajib
Ali, Ackas
Biswas, Sourav
Hossain, Nayeem
Khan, Maksud
Saha, Titon
Hossen,
Islam, Jahidul
Rahat, Uddin
Suman, Hosen
Source
Medline; PMC
abstract
Computer-aided drug screening by molecular docking, molecular dynamics (MD) and structural–activity relationship (SAR) can offer an efficient approach to identify promising drug repurposing candidates for COVID-19 treatment. In this study, computational screening is performed by molecular docking of 1615 Food and Drug Administration (FDA) approved drugs against the main protease (Mpro) of SARS-CoV-2. Several promising approved drugs, including Simeprevir, Ergotamine, Bromocriptine and Tadalafil, stand out as the best candidates based on their binding energy, fitting score and noncovalent interactions at the binding sites of the receptor. All selected drugs interact with the key active site residues, including His41 and Cys145. Various noncovalent interactions including hydrogen bonding, hydrophobic interactions, pi–sulfur and pi–pi interactions appear to be dominant in drug–Mpro complexes. MD simulations are applied for the most promising drugs. Structural stability and compactness are observed for the drug–Mpro complexes. The protein shows low flexibility in both apo and holo form during MD simulations. The MM/PBSA binding free energies are also measured for the selected drugs. For pattern recognition, structural similarity and binding energy prediction, multiple linear regression (MLR) models are used for the quantitative structural–activity relationship. The binding energy predicted by MLR model shows an 82% accuracy with the binding energy determined by molecular docking. Our details results can facilitate rational drug design targeting the SARS-CoV-2 main protease. Communicated by Ramaswamy H. Sarma
has issue date
2020-07-21
(
xsd:dateTime
)
bibo:doi
10.1080/07391102.2020.1794974
bibo:pmid
32692306
has license
no-cc
sha1sum (hex)
f2de55293b9c5c8c4d538c323df399d8348fb21d
schema:url
https://doi.org/10.1080/07391102.2020.1794974
resource representing a document's title
Virtual screening, molecular dynamics and structure–activity relationship studies to identify potent approved drugs for Covid-19 treatment
has PubMed Central identifier
PMC7441776
has PubMed identifier
32692306
schema:publication
Journal of biomolecular structure & dynamics
resource representing a document's body
covid:f2de55293b9c5c8c4d538c323df399d8348fb21d#body_text
is
schema:about
of
named entity 'hydrophobic interactions'
named entity 'holo'
named entity 'approved drugs'
named entity 'candidates'
named entity 'SARS-CoV-2'
named entity 'approved drugs'
named entity 'BINDING'
named entity 'STRUCTURAL STABILITY'
covid:arg/f2de55293b9c5c8c4d538c323df399d8348fb21d
named entity 'active site'
named entity 'drugs'
named entity 'COVID'
named entity 'Simeprevir'
named entity 'RNA virus'
named entity 'chemometric'
named entity 'long-term'
named entity 'hydrophobic interactions'
named entity 'Remdesivir'
named entity 'protease'
named entity 'Organism'
named entity 'RNA virus'
named entity 'Worldometer'
named entity 'active site'
named entity 'severe acute respiratory syndrome'
named entity 'crystal structure'
named entity 'binding energy'
named entity 'identify'
named entity 'steepest descent'
named entity 'Tadalafil'
named entity 'free energy'
named entity 'BIOVIA'
named entity 'TPSA'
named entity 'protease'
named entity 'PCA'
named entity 'protein'
named entity 'dihedral angles'
named entity 'solvent accessible surface area'
named entity 'Chymotrypsin'
named entity 'Bromocriptine'
named entity 'Bromocriptine'
named entity 'coronavirus'
named entity 'Lopinavir'
named entity 'SAR'
named entity 'crystal structure'
named entity 'China'
named entity 'genus'
named entity 'MLR'
named entity 'protease'
named entity 'Eastern China'
named entity 'protease'
named entity 'Ergotamine'
named entity 'protein'
named entity 'SARS-CoV-2'
named entity 'positive-sense'
named entity 'Mpro'
named entity 'root mean square fluctuation'
named entity 'protease'
named entity 'RNA synthesis'
named entity 'Tadalafil'
named entity 'MLR'
named entity 'van der Waals'
named entity 'QSAR'
named entity 'molecular dynamics'
named entity 'candidates'
named entity 'hydrogen bonding'
named entity 'protease'
named entity 'predicted'
named entity 'FDA'
named entity 'molecular dynamics'
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