Evaluation of therapeutic potentials of some bioactive compounds in selected African plants targeting main protease (Mpro) in SARS-CoV-2: a molecular docking study
Ishola Abeeb Akinwumi, Barakat Olamide Ishola, Oluwatosin Maryam Adeyemo, Adefolarin Phebean Owojuyigbe
Egyptian Journal of Medical Human Genetics, doi:10.1186/s43042-023-00456-4
Background Coronavirus disease 2019 is an infectious disease brought on by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a global treat in early 2020. Despite worldwide research proving different medications used to treat COVID-19, the infection still affects the human race; we need to continue researching the virus to protect humanity and reduce the complications that some medications might cause. This study focuses on finding another promising therapeutic compound against SARS-CoV-2. Twenty-four (24) bioactive compounds were selected from the following African plants' Adansonia digitata L, Aframomum melegueta K. Schum, Ageratum conyzoides (L.) L, and Boswellia dalzielii, and Remdesivir was used as the control medication. The PubChem web server acquired the 3D structures of bioactive compounds in the plant and the control medication. The SARS-CoV-2 main protease (M pro ) crystal structure was obtained using the Protein Data Bank (PDB). Using the SwissADME web server, the bioactive compounds' drug-likeness was assessed, and AutoDock was employed for the molecular docking with the M pro . The Proteins Plus and Protein-Ligand Interaction Profiler web servers were used to analyse the docked complexes. Furthermore, the admetSAR website was utilized to predict the ligands' absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties.
Results Based on the drug-likeness screening, Rutin violated more than one of the Lipinski rules of five, while Remdesivir violated two. Molecular docking analysis results indicated that Catechin, Epicatechin, Vitexin, Quercetin, Kaempferol, Gamma-Sitosterol, and Kaur-16-ene exhibited a stronger binding affinity with M pro , with binding scores of -7.1, -7.1, -8.0, -7.3, -7.2, -6.8, and -6.5 kcal/mol, respectively, compared to Remdesivir's binding score of -6.3 kcal/mol. Consequently, binding scores of bioactive compounds suggest their potential biological activity against the SARS-CoV-2 main protease. Additionally, these bioactive compounds exhibited favourable ADMET properties. Vitexin also has a plasma protein binding below 90%, a promising medication distribution feature.
Conclusions This study shows that Catechin, Epicatechin, Vitexin, Quercetin, Kaempferol, Gamma-Sitosterol, and Kaur-16-ene have better binding affinities with M pro than Remdesivir. Molecular dynamics simulation in vitro and in vivo investigation is required to support this study.
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Declarations Ethics approval and consent to participate Not applicable.
Consent for publication Not applicable.
Competing interests The authors declare that they have no competing interests.
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'abstract': '<jats:title>Abstract</jats:title><jats:sec>\n'
' <jats:title>Background</jats:title>\n'
' <jats:p>Coronavirus disease 2019 (COVID-19) is an infectious disease brought '
'on by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a global treat in '
'early 2020. Despite worldwide research proving different medications used to treat COVID-19, '
'the infection still affects the human race; we need to continue researching the virus to '
'protect humanity and reduce the complications that some medications might cause. This study '
'focuses on finding another promising therapeutic compound against SARS-CoV-2. Twenty-four '
"(24) bioactive compounds were selected from the following African plants'\xa0"
'<jats:italic>Adansonia digitata L, Aframomum melegueta K. Schum, Ageratum conyzoides (L.) '
'L</jats:italic>, and <jats:italic>Boswellia dalzielii, and</jats:italic> Remdesivir was used '
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'compounds in the plant and the control medication. The SARS-CoV-2 main protease '
'(M<jats:sup>pro</jats:sup>) crystal structure was obtained using the Protein Data Bank (PDB). '
"Using the SwissADME web server, the bioactive compounds' drug-likeness was assessed, and "
'AutoDock was employed for the molecular docking with the M<jats:sup>pro</jats:sup>. The '
'Proteins Plus and Protein–Ligand Interaction Profiler web servers were used to analyse the '
"docked complexes. Furthermore, the admetSAR website was utilized to predict the ligands' "
'absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties.</jats:p>\n'
' </jats:sec><jats:sec>\n'
' <jats:title>Results</jats:title>\n'
' <jats:p>Based on the drug-likeness screening, Rutin violated more than one of '
'the Lipinski rules of five, while Remdesivir violated two. Molecular docking analysis results '
'indicated that Catechin, Epicatechin, Vitexin, Quercetin, Kaempferol, Gamma-Sitosterol, and '
'Kaur-16-ene exhibited a stronger binding affinity with M<jats:sup>pro</jats:sup>, with '
'binding scores of −\xa07.1, −\xa07.1, −\xa08.0, −\xa07.3, −\xa07.2, −\xa06.8, and −\xa06.5\xa0'
"kcal/mol, respectively, compared to Remdesivir's binding score of −\xa06.3\xa0kcal/mol. "
'Consequently, binding scores of bioactive compounds suggest their potential biological '
'activity against the SARS-CoV-2 main protease. Additionally, these bioactive compounds '
'exhibited favourable ADMET properties. Vitexin also has a plasma protein binding below 90%, a '
'promising medication distribution feature.</jats:p>\n'
' </jats:sec><jats:sec>\n'
' <jats:title>Conclusions</jats:title>\n'
' <jats:p>This study shows that Catechin, Epicatechin, Vitexin, Quercetin, '
'Kaempferol, Gamma-Sitosterol, and Kaur-16-ene have better binding affinities with '
'M<jats:sup>pro</jats:sup> than Remdesivir. Molecular dynamics simulation\xa0in vitro\xa0'
'and\xa0in vivo\xa0investigation is required to support this study.</jats:p>\n'
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