In silico screening, SAR and kinetic studies of naturally occurring flavonoids against SARS CoV-2 main protease
The Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) pandemic has become a global challenge based on its replication within the host cells that relies on non-structural proteins, protease (Mpro). Flavonoids, an important class of naturally occurring compounds with medicinal importance, are...
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2022-01-01
|
| Series: | Arabian Journal of Chemistry |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S1878535221004883 |
| _version_ | 1819238952999059456 |
|---|---|
| author | Muhammad Imran Sana Iqbal Ajaz Hussain Jalal Uddin Mohsin Shahzad Tanwir Khaliq Abdul Razzaq Ahmed Laiba Mushtaq Muhammad Kashif Khalid Mahmood |
| author_facet | Muhammad Imran Sana Iqbal Ajaz Hussain Jalal Uddin Mohsin Shahzad Tanwir Khaliq Abdul Razzaq Ahmed Laiba Mushtaq Muhammad Kashif Khalid Mahmood |
| author_sort | Muhammad Imran |
| collection | DOAJ |
| description | The Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) pandemic has become a global challenge based on its replication within the host cells that relies on non-structural proteins, protease (Mpro). Flavonoids, an important class of naturally occurring compounds with medicinal importance, are frequently available within fruits and vegetables. Herein, we report the in silico studies on naturally occurring flavonoids consisting of molecular docking studies and evaluation of theoretical kinetics. In this study, we prepared a library of nine different classes of naturally occurring flavonoids and screened them on Autodock and Autodockvina. The pharmacokinetic properties of most promising compounds have been predicted through ADMET SAR, inhibition constants, ligand efficiency and ligand fit quality have been worked out theoretically. The results revealed that naturally occurring flavonoids could fit well in the receptor's catalytic pocket, interact with essential amino acid residues and could be useful for future drug candidates through in vitro and in vivo studies. Moreover, MD simulation studies were conducted for two most promising flavonoids and the protein–ligand complexes were found quite stable. The selected natural flavonoids are free from any toxic effects and can be consumed as a preventive measure against SARS CoV-2. |
| first_indexed | 2024-12-23T13:44:24Z |
| format | Article |
| id | doaj.art-27d297a610ec492e8c45a2d7509b444a |
| institution | Directory Open Access Journal |
| issn | 1878-5352 |
| language | English |
| last_indexed | 2024-12-23T13:44:24Z |
| publishDate | 2022-01-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Arabian Journal of Chemistry |
| spelling | doaj.art-27d297a610ec492e8c45a2d7509b444a2022-12-21T17:44:45ZengElsevierArabian Journal of Chemistry1878-53522022-01-01151103473In silico screening, SAR and kinetic studies of naturally occurring flavonoids against SARS CoV-2 main proteaseMuhammad Imran0Sana Iqbal1Ajaz Hussain2Jalal Uddin3Mohsin Shahzad4Tanwir Khaliq5Abdul Razzaq Ahmed6Laiba Mushtaq7Muhammad Kashif8Khalid Mahmood9Department of Chemistry, Faculty of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi ArabiaInstitute of Chemical Sciences, Bahauddin Zakariya University, Multan 60800, PakistanInstitute of Chemical Sciences, Bahauddin Zakariya University, Multan 60800, Pakistan; Corresponding authors.Department of Pharmaceutical Chemistry, College of Pharmacy, King Khalid University, P.O. Box 9004, Abha 62529, Saudi Arabia; Corresponding authors.Department of Molecular Biology and Biochemistry, Shaheed Zulfiqar Ali Bhutto Medical University Islamabad, PakistanDepartment of Molecular Biology and Biochemistry, Shaheed Zulfiqar Ali Bhutto Medical University Islamabad, PakistanDepartment of Prosthodontics, College of Dentistry, King Khalid University, 62529 Abha, Kingdom of Saudi ArabiaDepartment of Chemistry, Faculty of Science, King Khalid University, P.O. Box 9004, Abha 61413, Saudi ArabiaGovernment Emerson College, Bosan Road Multan, 60000, PakistanInstitute of Chemical Sciences, Bahauddin Zakariya University, Multan 60800, PakistanThe Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV-2) pandemic has become a global challenge based on its replication within the host cells that relies on non-structural proteins, protease (Mpro). Flavonoids, an important class of naturally occurring compounds with medicinal importance, are frequently available within fruits and vegetables. Herein, we report the in silico studies on naturally occurring flavonoids consisting of molecular docking studies and evaluation of theoretical kinetics. In this study, we prepared a library of nine different classes of naturally occurring flavonoids and screened them on Autodock and Autodockvina. The pharmacokinetic properties of most promising compounds have been predicted through ADMET SAR, inhibition constants, ligand efficiency and ligand fit quality have been worked out theoretically. The results revealed that naturally occurring flavonoids could fit well in the receptor's catalytic pocket, interact with essential amino acid residues and could be useful for future drug candidates through in vitro and in vivo studies. Moreover, MD simulation studies were conducted for two most promising flavonoids and the protein–ligand complexes were found quite stable. The selected natural flavonoids are free from any toxic effects and can be consumed as a preventive measure against SARS CoV-2.http://www.sciencedirect.com/science/article/pii/S1878535221004883SARS-CoV-2FlavonoidsMolecular dockingKineticsStructure activity relationship |
| spellingShingle | Muhammad Imran Sana Iqbal Ajaz Hussain Jalal Uddin Mohsin Shahzad Tanwir Khaliq Abdul Razzaq Ahmed Laiba Mushtaq Muhammad Kashif Khalid Mahmood In silico screening, SAR and kinetic studies of naturally occurring flavonoids against SARS CoV-2 main protease Arabian Journal of Chemistry SARS-CoV-2 Flavonoids Molecular docking Kinetics Structure activity relationship |
| title | In silico screening, SAR and kinetic studies of naturally occurring flavonoids against SARS CoV-2 main protease |
| title_full | In silico screening, SAR and kinetic studies of naturally occurring flavonoids against SARS CoV-2 main protease |
| title_fullStr | In silico screening, SAR and kinetic studies of naturally occurring flavonoids against SARS CoV-2 main protease |
| title_full_unstemmed | In silico screening, SAR and kinetic studies of naturally occurring flavonoids against SARS CoV-2 main protease |
| title_short | In silico screening, SAR and kinetic studies of naturally occurring flavonoids against SARS CoV-2 main protease |
| title_sort | in silico screening sar and kinetic studies of naturally occurring flavonoids against sars cov 2 main protease |
| topic | SARS-CoV-2 Flavonoids Molecular docking Kinetics Structure activity relationship |
| url | http://www.sciencedirect.com/science/article/pii/S1878535221004883 |
| work_keys_str_mv | AT muhammadimran insilicoscreeningsarandkineticstudiesofnaturallyoccurringflavonoidsagainstsarscov2mainprotease AT sanaiqbal insilicoscreeningsarandkineticstudiesofnaturallyoccurringflavonoidsagainstsarscov2mainprotease AT ajazhussain insilicoscreeningsarandkineticstudiesofnaturallyoccurringflavonoidsagainstsarscov2mainprotease AT jalaluddin insilicoscreeningsarandkineticstudiesofnaturallyoccurringflavonoidsagainstsarscov2mainprotease AT mohsinshahzad insilicoscreeningsarandkineticstudiesofnaturallyoccurringflavonoidsagainstsarscov2mainprotease AT tanwirkhaliq insilicoscreeningsarandkineticstudiesofnaturallyoccurringflavonoidsagainstsarscov2mainprotease AT abdulrazzaqahmed insilicoscreeningsarandkineticstudiesofnaturallyoccurringflavonoidsagainstsarscov2mainprotease AT laibamushtaq insilicoscreeningsarandkineticstudiesofnaturallyoccurringflavonoidsagainstsarscov2mainprotease AT muhammadkashif insilicoscreeningsarandkineticstudiesofnaturallyoccurringflavonoidsagainstsarscov2mainprotease AT khalidmahmood insilicoscreeningsarandkineticstudiesofnaturallyoccurringflavonoidsagainstsarscov2mainprotease |