Investigation of Some Antiviral N-Heterocycles as COVID 19 Drug: Molecular Docking and DFT Calculations.
Identifieur interne : 001525 ( Main/Curation ); précédent : 001524; suivant : 001526Investigation of Some Antiviral N-Heterocycles as COVID 19 Drug: Molecular Docking and DFT Calculations.
Auteurs : Mohamed Hagar [Arabie saoudite, Égypte] ; Hoda A. Ahmed [Égypte] ; Ghadah Aljohani [Arabie saoudite] ; Omaima A. Alhaddad [Arabie saoudite]Source :
- International journal of molecular sciences [ 1422-0067 ] ; 2020.
Descripteurs français
- KwdFr :
- Amides (composition chimique), Amides (pharmacologie), Amodiaquine (composition chimique), Amodiaquine (pharmacologie), Antiviraux (composition chimique), Antiviraux (pharmacologie), Cysteine endopeptidases (composition chimique), Cysteine endopeptidases (métabolisme), Inhibiteurs de protéases (composition chimique), Inhibiteurs de protéases (pharmacologie), Liaison aux protéines (MeSH), Protéines virales non structurales (composition chimique), Protéines virales non structurales (métabolisme), Pyrazines (composition chimique), Pyrazines (pharmacologie), Ribavirine (composition chimique), Ribavirine (pharmacologie), Simulation de docking moléculaire (MeSH), Sites de fixation (MeSH).
- MESH :
- composition chimique : Amides, Amodiaquine, Antiviraux, Cysteine endopeptidases, Inhibiteurs de protéases, Protéines virales non structurales, Pyrazines, Ribavirine.
- métabolisme : Cysteine endopeptidases, Protéines virales non structurales.
- pharmacologie : Amides, Amodiaquine, Antiviraux, Inhibiteurs de protéases, Pyrazines, Ribavirine.
- Liaison aux protéines, Simulation de docking moléculaire, Sites de fixation.
English descriptors
- KwdEn :
- Amides (chemistry), Amides (pharmacology), Amodiaquine (chemistry), Amodiaquine (pharmacology), Antiviral Agents (chemistry), Antiviral Agents (pharmacology), Binding Sites (MeSH), Coronavirus 3C Proteases (MeSH), Cysteine Endopeptidases (chemistry), Cysteine Endopeptidases (metabolism), Molecular Docking Simulation (MeSH), Protease Inhibitors (chemistry), Protease Inhibitors (pharmacology), Protein Binding (MeSH), Pyrazines (chemistry), Pyrazines (pharmacology), Ribavirin (chemistry), Ribavirin (pharmacology), Viral Nonstructural Proteins (chemistry), Viral Nonstructural Proteins (metabolism).
- MESH :
- chemical , chemistry : Amides, Amodiaquine, Antiviral Agents, Cysteine Endopeptidases, Protease Inhibitors, Pyrazines, Ribavirin, Viral Nonstructural Proteins.
- chemical , metabolism : Cysteine Endopeptidases, Viral Nonstructural Proteins.
- chemical , pharmacology : Amides, Amodiaquine, Antiviral Agents, Protease Inhibitors, Pyrazines, Ribavirin.
- Binding Sites, Coronavirus 3C Proteases, Molecular Docking Simulation, Protein Binding.
Abstract
The novel coronavirus, COVID-19, caused by SARS-CoV-2, is a global health pandemic that started in December 2019. The effective drug target among coronaviruses is the main protease Mpro, because of its essential role in processing the polyproteins that are translated from the viral RNA. In this study, the bioactivity of some selected heterocyclic drugs named Favipiravir (1), Amodiaquine (2), 2'-Fluoro-2'-deoxycytidine (3), and Ribavirin (4) was evaluated as inhibitors and nucleotide analogues for COVID-19 using computational modeling strategies. The density functional theory (DFT) calculations were performed to estimate the thermal parameters, dipole moment, polarizability, and molecular electrostatic potential of the present drugs; additionally, Mulliken atomic charges of the drugs as well as the chemical reactivity descriptors were investigated. The nominated drugs were docked on SARS-CoV-2 main protease (PDB: 6LU7) to evaluate the binding affinity of these drugs. Besides, the computations data of DFT the docking simulation studies was predicted that the Amodiaquine (2) has the least binding energy (-7.77 Kcal/mol) and might serve as a good inhibitor to SARS-CoV-2 comparable with the approved medicines, hydroxychloroquine, and remdesivir which have binding affinity -6.06 and -4.96 Kcal/mol, respectively. The high binding affinity of 2 was attributed to the presence of three hydrogen bonds along with different hydrophobic interactions between the drug and the critical amino acids residues of the receptor. Finally, the estimated molecular electrostatic potential results by DFT were used to illustrate the molecular docking findings. The DFT calculations showed that drug 2 has the highest of lying HOMO, electrophilicity index, basicity, and dipole moment. All these parameters could share with different extent to significantly affect the binding affinity of these drugs with the active protein sites.
DOI: 10.3390/ijms21113922
PubMed: 32486229
PubMed Central: PMC7312990
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pubmed:32486229Le document en format XML
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<term>Amodiaquine (pharmacology)</term>
<term>Antiviral Agents (chemistry)</term>
<term>Antiviral Agents (pharmacology)</term>
<term>Binding Sites (MeSH)</term>
<term>Coronavirus 3C Proteases (MeSH)</term>
<term>Cysteine Endopeptidases (chemistry)</term>
<term>Cysteine Endopeptidases (metabolism)</term>
<term>Molecular Docking Simulation (MeSH)</term>
<term>Protease Inhibitors (chemistry)</term>
<term>Protease Inhibitors (pharmacology)</term>
<term>Protein Binding (MeSH)</term>
<term>Pyrazines (chemistry)</term>
<term>Pyrazines (pharmacology)</term>
<term>Ribavirin (chemistry)</term>
<term>Ribavirin (pharmacology)</term>
<term>Viral Nonstructural Proteins (chemistry)</term>
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<term>Pyrazines (pharmacologie)</term>
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<front><div type="abstract" xml:lang="en">The novel coronavirus, COVID-19, caused by SARS-CoV-2, is a global health pandemic that started in December 2019. The effective drug target among coronaviruses is the main protease M<sup>pro</sup>
, because of its essential role in processing the polyproteins that are translated from the viral RNA. In this study, the bioactivity of some selected heterocyclic drugs named Favipiravir (<b>1</b>
), Amodiaquine (<b>2</b>
), 2'-Fluoro-2'-deoxycytidine (<b>3</b>
), and Ribavirin (<b>4</b>
) was evaluated as inhibitors and nucleotide analogues for COVID-19 using computational modeling strategies. The density functional theory (DFT) calculations were performed to estimate the thermal parameters, dipole moment, polarizability, and molecular electrostatic potential of the present drugs; additionally, Mulliken atomic charges of the drugs as well as the chemical reactivity descriptors were investigated. The nominated drugs were docked on SARS-CoV-2 main protease (PDB: 6LU7) to evaluate the binding affinity of these drugs. Besides, the computations data of DFT the docking simulation studies was predicted that the Amodiaquine (<b>2</b>
) has the least binding energy (-7.77 Kcal/mol) and might serve as a good inhibitor to SARS-CoV-2 comparable with the approved medicines, hydroxychloroquine, and remdesivir which have binding affinity -6.06 and -4.96 Kcal/mol, respectively. The high binding affinity of <b>2</b>
was attributed to the presence of three hydrogen bonds along with different hydrophobic interactions between the drug and the critical amino acids residues of the receptor. Finally, the estimated molecular electrostatic potential results by DFT were used to illustrate the molecular docking findings. The DFT calculations showed that drug <b>2</b>
has the highest of lying HOMO, electrophilicity index, basicity, and dipole moment. All these parameters could share with different extent to significantly affect the binding affinity of these drugs with the active protein sites.</div>
</front>
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<Title>International journal of molecular sciences</Title>
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<ArticleTitle>Investigation of Some Antiviral <i>N</i>
-Heterocycles as COVID 19 Drug: Molecular Docking and DFT Calculations.</ArticleTitle>
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<Abstract><AbstractText>The novel coronavirus, COVID-19, caused by SARS-CoV-2, is a global health pandemic that started in December 2019. The effective drug target among coronaviruses is the main protease M<sup>pro</sup>
, because of its essential role in processing the polyproteins that are translated from the viral RNA. In this study, the bioactivity of some selected heterocyclic drugs named Favipiravir (<b>1</b>
), Amodiaquine (<b>2</b>
), 2'-Fluoro-2'-deoxycytidine (<b>3</b>
), and Ribavirin (<b>4</b>
) was evaluated as inhibitors and nucleotide analogues for COVID-19 using computational modeling strategies. The density functional theory (DFT) calculations were performed to estimate the thermal parameters, dipole moment, polarizability, and molecular electrostatic potential of the present drugs; additionally, Mulliken atomic charges of the drugs as well as the chemical reactivity descriptors were investigated. The nominated drugs were docked on SARS-CoV-2 main protease (PDB: 6LU7) to evaluate the binding affinity of these drugs. Besides, the computations data of DFT the docking simulation studies was predicted that the Amodiaquine (<b>2</b>
) has the least binding energy (-7.77 Kcal/mol) and might serve as a good inhibitor to SARS-CoV-2 comparable with the approved medicines, hydroxychloroquine, and remdesivir which have binding affinity -6.06 and -4.96 Kcal/mol, respectively. The high binding affinity of <b>2</b>
was attributed to the presence of three hydrogen bonds along with different hydrophobic interactions between the drug and the critical amino acids residues of the receptor. Finally, the estimated molecular electrostatic potential results by DFT were used to illustrate the molecular docking findings. The DFT calculations showed that drug <b>2</b>
has the highest of lying HOMO, electrophilicity index, basicity, and dipole moment. All these parameters could share with different extent to significantly affect the binding affinity of these drugs with the active protein sites.</AbstractText>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Hagar</LastName>
<ForeName>Mohamed</ForeName>
<Initials>M</Initials>
<AffiliationInfo><Affiliation>Chemistry Department, College of Sciences, Yanbu, Taibah University, Yanbu 30799, Saudi Arabia.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>Chemistry Department, Faculty of Science, Alexandria University, Alexandria 21321, Egypt.</Affiliation>
</AffiliationInfo>
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<Author ValidYN="Y"><LastName>Ahmed</LastName>
<ForeName>Hoda A</ForeName>
<Initials>HA</Initials>
<Identifier Source="ORCID">0000-0003-3966-7024</Identifier>
<AffiliationInfo><Affiliation>Department of Chemistry, Faculty of Science, Cairo University, Cairo 12613, Egypt.</Affiliation>
</AffiliationInfo>
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<Author ValidYN="Y"><LastName>Aljohani</LastName>
<ForeName>Ghadah</ForeName>
<Initials>G</Initials>
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<AffiliationInfo><Affiliation>Chemistry Department, College of Sciences, Al-Madina Al-Munawarah, Taibah University, Al-Madina 30002, Saudi Arabia.</Affiliation>
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<Author ValidYN="Y"><LastName>Alhaddad</LastName>
<ForeName>Omaima A</ForeName>
<Initials>OA</Initials>
<AffiliationInfo><Affiliation>Chemistry Department, College of Sciences, Al-Madina Al-Munawarah, Taibah University, Al-Madina 30002, Saudi Arabia.</Affiliation>
</AffiliationInfo>
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