About: QM/QM studies for Michael reaction in coronavirus main protease (3CL(Pro))

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

Attributes	Values
type	Academic Article research paper schema:ScholarlyArticle
isDefinedBy	Covid-on-the-Web dataset
has title	QM/QM studies for Michael reaction in coronavirus main protease (3CL(Pro))
Creator	Avery, Mitchell Carvalho, Paulo Taranto, Alex
Source	Elsevier; Medline; PMC
abstract	Severe acute respiratory syndrome (SARS) is an illness caused by a novel corona virus wherein the main proteinase called 3CL(Pro) has been established as a target for drug design. The mechanism of action involves nucleophilic attack by Cys145 present in the active site on the carbonyl carbon of the scissile amide bond of the substrate and the intermediate product is stabilized by hydrogen bonds with the residues of the oxyanion hole. Based on the X-ray structure of 3CL(Pro) co-crystallized with a trans-α,β-unsaturated ethyl ester (Michael acceptor), a set of QM/QM and QM/MM calculations were performed, yielding three models with increasingly higher the number of atoms. A previous validation step was performed using classical theoretical calculation and PROCHECK software. The Michael reaction studies show an exothermic process with −4.5 kcal/mol. During the reaction pathway, an intermediate is formed by hydrogen and water molecule migration from a histidine residue and solvent, respectively. In addition, similar with experimental results, the complex between N3 and 3CL(Pro) is 578 kcal/mol more stable than N1-3CL(Pro) using Own N-layer Integrated molecular Orbital molecular Mechanics (ONIOM) approach. We suggest 3CL(Pro) inhibitors need small polar groups to decrease the energy barrier for alkylation reaction. These results can be useful for the development of new compounds against SARS.
has issue date	2008-05-09(xsd:dateTime)
bibo:doi	10.1016/j.jmgm.2008.05.002
bibo:pmid	18567519
has license	no-cc
sha1sum (hex)	d55e637f236eb9452e2b248b0e48ba584927c908
schema:url	https://doi.org/10.1016/j.jmgm.2008.05.002
resource representing a document's title	QM/QM studies for Michael reaction in coronavirus main protease (3CL(Pro))
has PubMed Central identifier	PMC7110475
has PubMed identifier	18567519
schema:publication	J Mol Graph Model
resource representing a document's body	covid:d55e637f236eb9452e2b248b0e48ba584927c908#body_text
is schema:about of	named entity 'Michael reaction' named entity 'CORONAVIRUS' named entity 'MICHAEL REACTION' named entity 'PROTEASE' named entity 'MAIN' named entity 'STUDIES' named entity 'PRO' named entity 'd orbitals' named entity 'Mulliken charges' named entity 'molecular mechanics' named entity 'transition state structure' named entity 'carbonyl carbon' named entity 'negatively charged' named entity 'kcal/mol' named entity 'active site' named entity 'ligand' named entity 'nucleophile' named entity 'solvent' named entity 'lowest unoccupied molecular orbital' named entity 'kcal/mol' named entity 'active site' named entity 'alkylation' named entity 'enzyme' named entity 'endothermic process' named entity 'hydrogen bonds' named entity 'complexation' named entity 'molecular Mechanics' named entity 'atom' named entity 'proteinase' named entity 'ONIOM' named entity 'dihedral angle' named entity 'correlation' named entity 'coronavirus' named entity 'Rasmol' named entity '1.10' named entity 'ONIOM' named entity 'kcal' named entity 'enzyme' named entity 'virus' named entity '10.7' named entity 'X-ray' named entity 'molecular Orbital' named entity 'alkylation process' named entity 'kcal/mol' named entity 'trans' named entity 'water molecule' named entity 'proteinase inhibitors' named entity 'Atomic charges' named entity 'electrostatic potential' named entity 'QM/MM' named entity 'B3LYP' named entity 'classical force' named entity 'active site' named entity 'Monte Carlo' named entity 'reaction path' named entity 'ligand' named entity 'substrate' named entity 'tetrahedral intermediate' named entity 'MEP' named entity 'cysteine protease' named entity 'oxyanion hole' named entity 'Semiempirical' named entity 'universal force field' named entity 'SARS' named entity 'acquired immune deficiency syndrome' named entity 'stereochemical' named entity 'papain' named entity 'correlation' named entity 'geometry optimization' named entity 'intermolecular interactions' named entity 'active site' named entity 'trans' named entity 'basis set' named entity 'stereochemical' named entity 'PDB' named entity 'negative charge' named entity 'protomer' named entity 'electrostatic interactions' named entity 'protein'

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