Pharmacophore model, docking, QSAR, and molecular dynamics simulation studies of substituted cyclic imides and herbal medicines as COX-2 inhibitors
Cyclooxygenase-2 (COX-2) enzyme inhibitors have not eliminated the necessity for developed drugs not only in the nonsteroidal anti-inflammatory drug (NSAIDs) area, but also in other therapeutic applications including prevention of cancer and Alzheimer's disease. A series of novel substituted cy...
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| Format: | Article |
| Language: | English |
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Elsevier
2021-04-01
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| Series: | Heliyon |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2405844021007088 |
| _version_ | 1818573384935538688 |
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| author | Nathalie Moussa Ahmad Hassan Sajjad Gharaghani |
| author_facet | Nathalie Moussa Ahmad Hassan Sajjad Gharaghani |
| author_sort | Nathalie Moussa |
| collection | DOAJ |
| description | Cyclooxygenase-2 (COX-2) enzyme inhibitors have not eliminated the necessity for developed drugs not only in the nonsteroidal anti-inflammatory drug (NSAIDs) area, but also in other therapeutic applications including prevention of cancer and Alzheimer's disease. A series of novel substituted cyclic imides have been reported as selective COX-2 inhibitors. To understand the structural features responsible for their activity, a 3D validated pharmacophore and quantitative structure−activity relationship (QSAR) model have been developed. The values of enrichment factor (EF), goodness of hit score (GH), area under the ROC curve (AUC), sensitivity, and specificity refer to the good ability of the pharmacophore model to identify active compounds. Multiple linear regression (MLR) produced statistically significant QSAR model with (R2 training = 0.763, R2test = 0.96) and predictability (Q2training = 0.66, Q2test = 0.84). Then, using the pharmacophore and QSAR models, eight authenticated botanicals in two herbal medicines and the ZINC compounds database, were virtually screened for ligands to COX-2. The retrieved hits which also obey lipinski's rule of five (RO5) were docked in the COX-2 3D structure to investigate their binding mode and affinity. Finally, based on the docking results, nine molecules were prioritized as promising hits that could be used as leads to discover novel COX-2 inhibitors. COX-2 inhibition of most of these hits has not been reported previously. Ten-nanosecond molecular dynamics simulation (10-ns MD) was performed on the initial structure COX-2 complex with ZINC000113253375 and ZINC000043170560 resulted from the docking. Our utilization of the 3D pharmacophore model, QSAR, molecular docking, and molecular dynamics simulation trials can be a potent strategy to successfully predict activity, efficiently design drugs, and screen large numbers of new compounds as active drug candidates. |
| first_indexed | 2024-12-15T00:10:27Z |
| format | Article |
| id | doaj.art-1d9a0dc6d49a492594a5fbe336e9f5c3 |
| institution | Directory Open Access Journal |
| issn | 2405-8440 |
| language | English |
| last_indexed | 2024-12-15T00:10:27Z |
| publishDate | 2021-04-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Heliyon |
| spelling | doaj.art-1d9a0dc6d49a492594a5fbe336e9f5c32022-12-21T22:42:35ZengElsevierHeliyon2405-84402021-04-0174e06605Pharmacophore model, docking, QSAR, and molecular dynamics simulation studies of substituted cyclic imides and herbal medicines as COX-2 inhibitorsNathalie Moussa0Ahmad Hassan1Sajjad Gharaghani2Department of Pharmaceutical Chemistry and Quality Control of Medicaments, Faculty of Pharmacy, Damascus University, Damascus, Syria; Corresponding author.Department of Pharmaceutical Chemistry and Quality Control of Medicaments, Faculty of Pharmacy, Damascus University, Damascus, Syria; Corresponding author.Laboratory of Bioinformatics and Drug Design, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, IranCyclooxygenase-2 (COX-2) enzyme inhibitors have not eliminated the necessity for developed drugs not only in the nonsteroidal anti-inflammatory drug (NSAIDs) area, but also in other therapeutic applications including prevention of cancer and Alzheimer's disease. A series of novel substituted cyclic imides have been reported as selective COX-2 inhibitors. To understand the structural features responsible for their activity, a 3D validated pharmacophore and quantitative structure−activity relationship (QSAR) model have been developed. The values of enrichment factor (EF), goodness of hit score (GH), area under the ROC curve (AUC), sensitivity, and specificity refer to the good ability of the pharmacophore model to identify active compounds. Multiple linear regression (MLR) produced statistically significant QSAR model with (R2 training = 0.763, R2test = 0.96) and predictability (Q2training = 0.66, Q2test = 0.84). Then, using the pharmacophore and QSAR models, eight authenticated botanicals in two herbal medicines and the ZINC compounds database, were virtually screened for ligands to COX-2. The retrieved hits which also obey lipinski's rule of five (RO5) were docked in the COX-2 3D structure to investigate their binding mode and affinity. Finally, based on the docking results, nine molecules were prioritized as promising hits that could be used as leads to discover novel COX-2 inhibitors. COX-2 inhibition of most of these hits has not been reported previously. Ten-nanosecond molecular dynamics simulation (10-ns MD) was performed on the initial structure COX-2 complex with ZINC000113253375 and ZINC000043170560 resulted from the docking. Our utilization of the 3D pharmacophore model, QSAR, molecular docking, and molecular dynamics simulation trials can be a potent strategy to successfully predict activity, efficiently design drugs, and screen large numbers of new compounds as active drug candidates.http://www.sciencedirect.com/science/article/pii/S2405844021007088Cyclooxygenase-2DockingQSARPharmacophoreMolecular dynamics simulationVirtual screening |
| spellingShingle | Nathalie Moussa Ahmad Hassan Sajjad Gharaghani Pharmacophore model, docking, QSAR, and molecular dynamics simulation studies of substituted cyclic imides and herbal medicines as COX-2 inhibitors Heliyon Cyclooxygenase-2 Docking QSAR Pharmacophore Molecular dynamics simulation Virtual screening |
| title | Pharmacophore model, docking, QSAR, and molecular dynamics simulation studies of substituted cyclic imides and herbal medicines as COX-2 inhibitors |
| title_full | Pharmacophore model, docking, QSAR, and molecular dynamics simulation studies of substituted cyclic imides and herbal medicines as COX-2 inhibitors |
| title_fullStr | Pharmacophore model, docking, QSAR, and molecular dynamics simulation studies of substituted cyclic imides and herbal medicines as COX-2 inhibitors |
| title_full_unstemmed | Pharmacophore model, docking, QSAR, and molecular dynamics simulation studies of substituted cyclic imides and herbal medicines as COX-2 inhibitors |
| title_short | Pharmacophore model, docking, QSAR, and molecular dynamics simulation studies of substituted cyclic imides and herbal medicines as COX-2 inhibitors |
| title_sort | pharmacophore model docking qsar and molecular dynamics simulation studies of substituted cyclic imides and herbal medicines as cox 2 inhibitors |
| topic | Cyclooxygenase-2 Docking QSAR Pharmacophore Molecular dynamics simulation Virtual screening |
| url | http://www.sciencedirect.com/science/article/pii/S2405844021007088 |
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