Crystal structure, chemical reactivity, kinetic and thermodynamic studies of new ligand derived from 4-hydroxycoumarin: Interaction with SARS-CoV-2.
Identifieur interne : 001178 ( Main/Exploration ); précédent : 001177; suivant : 001179Crystal structure, chemical reactivity, kinetic and thermodynamic studies of new ligand derived from 4-hydroxycoumarin: Interaction with SARS-CoV-2.
Auteurs : Chafia Ait-Ramdane-Terbouche [Algérie] ; Hasnia Abdeldjebar [Algérie] ; Achour Terbouche [Algérie] ; Houria Lakhdari [Algérie] ; Khaldoun Bachari [Algérie] ; Thierry Roisnel ; Didier HauchardSource :
- Journal of molecular structure [ 0022-2860 ] ; 2020.
Abstract
Currently, Covid-19 pandemic infects staggering number of people around the globe and causes a high rate of mortality. In order to fight this disease, a new coumarin derivative ligand (4-[(pyridin-3-ylmethyl) amino]-2H-chromen-2-one) (LTA) has been synthesized and characterized by single-crystal X-ray diffraction, NMR, ATR, UV-Visible and cyclic voltammetry. Chemical reactivity, kinetic and thermodynamic studies were investigated using DFT method. The possible binding mode between LTA and Main protease (Mpro) of SARS-CoV-2 and their reactivity were studied using molecular docking simulation. Single crystal X-ray diffraction showed that LTA crystallizes in a monoclinic system with P2 1 space group. The reactivity descriptors such as nucleophilic index confirm that LTA is more nucleophile, inducing complexation with binding species like biomolecules. The kinetic and thermodynamic parameters showed that the mechanism of crystal formation is moderately exothermic. The binding energy of the SARS-CoV-2/Mpro-LTA complex and the calculated inhibition constant using docking simulation showed that the active LTA molecule has the ability to inhibit SARS-CoV-2.
DOI: 10.1016/j.molstruc.2020.128918
PubMed: 32834114
PubMed Central: PMC7363612
Affiliations:
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kinetic and thermodynamic studies of new ligand derived from 4-hydroxycoumarin: Interaction with SARS-CoV-2.</title><author><name sortKey="Ait Ramdane Terbouche, Chafia" sort="Ait Ramdane Terbouche, Chafia" uniqKey="Ait Ramdane Terbouche C" first="Chafia" last="Ait-Ramdane-Terbouche">Chafia Ait-Ramdane-Terbouche</name><affiliation wicri:level="1"><nlm:affiliation>Centre de Recherche Scientifique et Technique en Analyses Physico-chimiques(CRAPC), BP384, Bou-Ismail, RP 42004, Tipasa, Algeria.</nlm:affiliation><country xml:lang="fr">Algérie</country><wicri:regionArea>Centre de Recherche Scientifique et Technique en Analyses Physico-chimiques(CRAPC), BP384, Bou-Ismail, RP 42004, Tipasa</wicri:regionArea><wicri:noRegion>Tipasa</wicri:noRegion></affiliation></author><author><name sortKey="Abdeldjebar, Hasnia" sort="Abdeldjebar, Hasnia" uniqKey="Abdeldjebar H" first="Hasnia" last="Abdeldjebar">Hasnia Abdeldjebar</name><affiliation wicri:level="1"><nlm:affiliation>Centre de Recherche Scientifique et Technique en Analyses Physico-chimiques(CRAPC), BP384, Bou-Ismail, RP 42004, Tipasa, Algeria.</nlm:affiliation><country xml:lang="fr">Algérie</country><wicri:regionArea>Centre de Recherche Scientifique et Technique en Analyses Physico-chimiques(CRAPC), BP384, Bou-Ismail, RP 42004, Tipasa</wicri:regionArea><wicri:noRegion>Tipasa</wicri:noRegion></affiliation></author><author><name sortKey="Terbouche, Achour" sort="Terbouche, Achour" uniqKey="Terbouche A" first="Achour" last="Terbouche">Achour Terbouche</name><affiliation wicri:level="1"><nlm:affiliation>Centre de Recherche Scientifique et Technique en Analyses Physico-chimiques(CRAPC), BP384, Bou-Ismail, RP 42004, Tipasa, Algeria.</nlm:affiliation><country xml:lang="fr">Algérie</country><wicri:regionArea>Centre de Recherche Scientifique et Technique en Analyses Physico-chimiques(CRAPC), BP384, Bou-Ismail, RP 42004, Tipasa</wicri:regionArea><wicri:noRegion>Tipasa</wicri:noRegion></affiliation></author><author><name sortKey="Lakhdari, Houria" sort="Lakhdari, Houria" uniqKey="Lakhdari H" first="Houria" last="Lakhdari">Houria Lakhdari</name><affiliation wicri:level="1"><nlm:affiliation>Centre de Recherche Scientifique et Technique en Analyses Physico-chimiques(CRAPC), BP384, Bou-Ismail, RP 42004, Tipasa, Algeria.</nlm:affiliation><country xml:lang="fr">Algérie</country><wicri:regionArea>Centre de Recherche Scientifique et Technique en Analyses Physico-chimiques(CRAPC), BP384, Bou-Ismail, RP 42004, Tipasa</wicri:regionArea><wicri:noRegion>Tipasa</wicri:noRegion></affiliation></author><author><name sortKey="Bachari, Khaldoun" sort="Bachari, Khaldoun" uniqKey="Bachari K" first="Khaldoun" last="Bachari">Khaldoun Bachari</name><affiliation wicri:level="1"><nlm:affiliation>Centre de Recherche Scientifique et Technique en Analyses Physico-chimiques(CRAPC), BP384, Bou-Ismail, RP 42004, Tipasa, Algeria.</nlm:affiliation><country xml:lang="fr">Algérie</country><wicri:regionArea>Centre de Recherche Scientifique et Technique en Analyses Physico-chimiques(CRAPC), BP384, Bou-Ismail, RP 42004, Tipasa</wicri:regionArea><wicri:noRegion>Tipasa</wicri:noRegion></affiliation></author><author><name sortKey="Roisnel, Thierry" sort="Roisnel, Thierry" uniqKey="Roisnel T" first="Thierry" last="Roisnel">Thierry Roisnel</name><affiliation><nlm:affiliation>Univ Rennes CNRS ISCR (Institut des Sciences Chimiques de Rennes)-UMR 6226 F-35000 Rennes France.</nlm:affiliation><wicri:noCountry code="no comma">Univ Rennes CNRS ISCR (Institut des Sciences Chimiques de Rennes)-UMR 6226 F-35000 Rennes France.</wicri:noCountry></affiliation></author><author><name sortKey="Hauchard, Didier" sort="Hauchard, Didier" uniqKey="Hauchard D" first="Didier" last="Hauchard">Didier Hauchard</name><affiliation><nlm:affiliation>Univ Rennes Ecole Nationale Supérieure de Chimie de Rennes CNRS ISCR (Institut des Sciences Chimiques de Rennes)-UMR 6226 F-35000 Rennes France.</nlm:affiliation><wicri:noCountry code="no comma">Univ Rennes Ecole Nationale Supérieure de Chimie de Rennes CNRS ISCR (Institut des Sciences Chimiques de Rennes)-UMR 6226 F-35000 Rennes France.</wicri:noCountry></affiliation></author></analytic><series><title level="j">Journal of molecular structure</title><idno type="ISSN">0022-2860</idno><imprint><date when="2020" type="published">2020</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Currently, Covid-19 pandemic infects staggering number of people around the <i>globe</i> and causes a high rate of mortality. In order to fight this disease, a new coumarin derivative ligand (4-[(<i>pyridin</i>-3-<i>ylmethyl</i>) <i>amino</i>]-2<i>H</i>-chromen-2-one) (L<sub>TA</sub>) has been synthesized and characterized by single-crystal X-ray diffraction, NMR, ATR, UV-Visible and cyclic voltammetry. Chemical reactivity, kinetic and thermodynamic studies were investigated using DFT method. The possible binding mode between L<sub>TA</sub> and Main protease (Mpro) of SARS-CoV-2 and their reactivity were studied using molecular docking simulation. Single crystal X-ray diffraction showed that L<sub>TA</sub> crystallizes in a monoclinic system with <i>P</i>2 <i><sub>1</sub></i> space group. The reactivity descriptors such as nucleophilic index confirm that L<sub>TA</sub> is more nucleophile, inducing complexation with binding species like biomolecules. The kinetic and thermodynamic parameters showed that the mechanism of crystal formation is moderately exothermic. The binding energy of the SARS-CoV-2/Mpro-L<sub>TA</sub> complex and the calculated inhibition constant using docking simulation showed that the active L<sub>TA</sub> molecule has the ability to inhibit SARS-CoV-2.</div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">32834114</PMID><DateRevised><Year>2020</Year><Month>08</Month><Day>24</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">0022-2860</ISSN><JournalIssue CitedMedium="Print"><Volume>1222</Volume><PubDate><Year>2020</Year><Month>Dec</Month><Day>15</Day></PubDate></JournalIssue><Title>Journal of molecular structure</Title><ISOAbbreviation>J Mol Struct</ISOAbbreviation></Journal><ArticleTitle>Crystal structure, chemical reactivity, kinetic and thermodynamic studies of new ligand derived from 4-hydroxycoumarin: Interaction with SARS-CoV-2.</ArticleTitle><Pagination><MedlinePgn>128918</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.molstruc.2020.128918</ELocationID><Abstract><AbstractText>Currently, Covid-19 pandemic infects staggering number of people around the <i>globe</i> and causes a high rate of mortality. In order to fight this disease, a new coumarin derivative ligand (4-[(<i>pyridin</i>-3-<i>ylmethyl</i>) <i>amino</i>]-2<i>H</i>-chromen-2-one) (L<sub>TA</sub>) has been synthesized and characterized by single-crystal X-ray diffraction, NMR, ATR, UV-Visible and cyclic voltammetry. Chemical reactivity, kinetic and thermodynamic studies were investigated using DFT method. The possible binding mode between L<sub>TA</sub> and Main protease (Mpro) of SARS-CoV-2 and their reactivity were studied using molecular docking simulation. Single crystal X-ray diffraction showed that L<sub>TA</sub> crystallizes in a monoclinic system with <i>P</i>2 <i><sub>1</sub></i> space group. The reactivity descriptors such as nucleophilic index confirm that L<sub>TA</sub> is more nucleophile, inducing complexation with binding species like biomolecules. The kinetic and thermodynamic parameters showed that the mechanism of crystal formation is moderately exothermic. The binding energy of the SARS-CoV-2/Mpro-L<sub>TA</sub> complex and the calculated inhibition constant using docking simulation showed that the active L<sub>TA</sub> molecule has the ability to inhibit SARS-CoV-2.</AbstractText><CopyrightInformation>© 2020 Elsevier B.V. All rights reserved.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Ait-Ramdane-Terbouche</LastName><ForeName>Chafia</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Centre de Recherche Scientifique et Technique en Analyses Physico-chimiques(CRAPC), BP384, Bou-Ismail, RP 42004, Tipasa, Algeria.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Abdeldjebar</LastName><ForeName>Hasnia</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Centre de Recherche Scientifique et Technique en Analyses Physico-chimiques(CRAPC), BP384, Bou-Ismail, RP 42004, Tipasa, Algeria.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Terbouche</LastName><ForeName>Achour</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Centre de Recherche Scientifique et Technique en Analyses Physico-chimiques(CRAPC), BP384, Bou-Ismail, RP 42004, Tipasa, Algeria.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Lakhdari</LastName><ForeName>Houria</ForeName><Initials>H</Initials><AffiliationInfo><Affiliation>Centre de Recherche Scientifique et Technique en Analyses Physico-chimiques(CRAPC), BP384, Bou-Ismail, RP 42004, Tipasa, Algeria.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Bachari</LastName><ForeName>Khaldoun</ForeName><Initials>K</Initials><AffiliationInfo><Affiliation>Centre de Recherche Scientifique et Technique en Analyses Physico-chimiques(CRAPC), BP384, Bou-Ismail, RP 42004, Tipasa, Algeria.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Roisnel</LastName><ForeName>Thierry</ForeName><Initials>T</Initials><AffiliationInfo><Affiliation>Univ Rennes CNRS ISCR (Institut des Sciences Chimiques de Rennes)-UMR 6226 F-35000 Rennes France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hauchard</LastName><ForeName>Didier</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Univ Rennes Ecole Nationale Supérieure de Chimie de Rennes CNRS ISCR (Institut des Sciences Chimiques de Rennes)-UMR 6226 F-35000 Rennes France.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2020</Year><Month>07</Month><Day>16</Day></ArticleDate></Article><MedlineJournalInfo><Country>Netherlands</Country><MedlineTA>J Mol Struct</MedlineTA><NlmUniqueID>0141747</NlmUniqueID><ISSNLinking>0022-2860</ISSNLinking></MedlineJournalInfo><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Chemical reactivity</Keyword><Keyword MajorTopicYN="N">Coumarin derivative</Keyword><Keyword MajorTopicYN="N">Crystal structure</Keyword><Keyword MajorTopicYN="N">Interaction SARS-CoV-2/Mpro-LTA</Keyword><Keyword MajorTopicYN="N">Thermodynamic properties</Keyword></KeywordList><CoiStatement>The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.</CoiStatement></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2020</Year><Month>05</Month><Day>12</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2020</Year><Month>06</Month><Day>30</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>07</Month><Day>15</Day></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2020</Year><Month>8</Month><Day>25</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2020</Year><Month>8</Month><Day>25</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2020</Year><Month>8</Month><Day>25</Day><Hour>6</Hour><Minute>1</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">32834114</ArticleId><ArticleId IdType="doi">10.1016/j.molstruc.2020.128918</ArticleId><ArticleId IdType="pii">S0022-2860(20)31243-6</ArticleId><ArticleId IdType="pii">128918</ArticleId><ArticleId IdType="pmc">PMC7363612</ArticleId></ArticleIdList><pmc-dir>pmcsd</pmc-dir>
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