An online repository of solvation thermodynamic and structural maps of SARS-CoV-2 targets.
Antiviral Agents
/ chemistry
Betacoronavirus
/ chemistry
Binding Sites
COVID-19
Catalytic Domain
Coronavirus Infections
/ drug therapy
Drug Design
Drug Evaluation, Preclinical
Humans
Ligands
Models, Chemical
Models, Molecular
Molecular Dynamics Simulation
Molecular Targeted Therapy
Pandemics
Pneumonia, Viral
/ drug therapy
Protein Conformation
SARS-CoV-2
Small Molecule Libraries
Structure-Activity Relationship
Thermodynamics
Viral Nonstructural Proteins
/ chemistry
Water
COVID-19 Drug Treatment
COVID-19
Drug discovery
Rational lead modification
Solvation thermodynamics
Virtual screening
Journal
Journal of computer-aided molecular design
ISSN: 1573-4951
Titre abrégé: J Comput Aided Mol Des
Pays: Netherlands
ID NLM: 8710425
Informations de publication
Date de publication:
12 2020
12 2020
Historique:
received:
04
06
2020
accepted:
29
08
2020
pubmed:
13
9
2020
medline:
11
11
2020
entrez:
12
9
2020
Statut:
ppublish
Résumé
SARS-CoV-2 recently jumped species and rapidly spread via human-to-human transmission to cause a global outbreak of COVID-19. The lack of effective vaccine combined with the severity of the disease necessitates attempts to develop small molecule drugs to combat the virus. COVID19_GIST_HSA is a freely available online repository to provide solvation thermodynamic maps of COVID-19-related protein small molecule drug targets. Grid inhomogeneous solvation theory maps were generated using AmberTools cpptraj-GIST, 3D reference interaction site model maps were created with AmberTools rism3d.snglpnt and hydration site analysis maps were created using SSTMap code. The resultant data can be applied to drug design efforts: scoring solvent displacement for docking, rational lead modification, prioritization of ligand- and protein- based pharmacophore elements, and creation of water-based pharmacophores. Herein, we demonstrate the use of the solvation thermodynamic mapping data. It is hoped that this freely provided data will aid in small molecule drug discovery efforts to defeat SARS-CoV-2.
Identifiants
pubmed: 32918236
doi: 10.1007/s10822-020-00341-x
pii: 10.1007/s10822-020-00341-x
pmc: PMC7486166
mid: NIHMS1628432
doi:
Substances chimiques
Antiviral Agents
0
Ligands
0
Small Molecule Libraries
0
Viral Nonstructural Proteins
0
Water
059QF0KO0R
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, U.S. Gov't, Non-P.H.S.
Langues
eng
Sous-ensembles de citation
IM
Pagination
1219-1228Subventions
Organisme : NIGMS NIH HHS
ID : SC3 GM095417
Pays : United States
Organisme : NIGMS NIH HHS
ID : R01GM100946
Pays : United States
Organisme : Research Corporation for Science Advancement
ID : 23967
Pays : International
Organisme : National Science Foundation
ID : 1566638
Pays : International
Organisme : NIGMS NIH HHS
ID : R01 GM100946
Pays : United States
Commentaires et corrections
Type : UpdateOf
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