scholarly journals Molecular Docking Studies of Phytochemicals of Allophylus serratus Against Cyclooxygenase-2 Enzyme

2019 ◽  
Author(s):  
Kero Jemal
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
Cyclooxygenase 2 ◽  
Molecular Docking Study ◽  
Leaf Extracts ◽  
Sulfurous Acid ◽  
Lipinski’S Rule ◽  
Phytochemical Compounds ◽  
Cox 2 ◽  
Anti Inflammatory

AbstractAllophylus serratus is a medicinal plant used traditionally as anti-inflammatory agent. The main objectives of this study are to identify phytochemical compounds that have anti-inflammatory properties from the leaf extracts of Allophylus serratus and to search for cyclooxygenase-2 (COX-2) enzyme inhibitors through molecular docking. From the GC-MS analysis of leaf extracts of this plant, various phytochemicals were identified. About 10of these phytochemical compounds were analyzed for their drug likeliness based on Lipinski’s rule of five and inhibitor property against the cyclooxygenase (COX-2) enzyme, a protein responsible for inflammation The phytochemical compounds which satisfy the Lipinski’s rule such as 1H-Benzocycloheptene, 2,4a,5,6,7,8-hexahydro-3,5,5,9-tetramethyl-,(R) and Sulfurous acid, dipentyl ester were subjected to docking experiments using AutoDock Vina. The results from molecular docking study revealed that 1H-Benzocycloheptene, 2,4a,5,6,7,8-hexahydro-3,5,5,9-tetramethyl-, (R)-, Sulfurous acid, dipentyl ester and 1,2-Benzenedicarboxylic acid, bis(2-methylpropyl) ester bind effectively to the active site region of COX-2 with a binding energy of −8.9, −8.4, and −7.9, respectively. The binding energy of the phyto-compounds were compared with the known antiinflammatory drug Diclofenac that inhibit COX-2 enzyme. It was found that the phytochemical compounds from leaf extracts of Allophylus serratus have strong inhibitory effect on COX-2 enzyme and as a result they have potential anti-inflammatory medicinal values. Thus the study puts forth experimental validation for traditional antidote and these phyto-compounds could be further promoted as potential lead molecule.

scholarly journals Molecular docking study of the phytol and its derivatives against COX-2 induced inflammation: A combined density functional study

2020 ◽  
pp. 1-5
Author(s):  
Muhammad Torequl Islam ◽  
Pranta Ray ◽  
Abul Bashar Ripon Khalipha ◽  
SM Hafiz Hassan ◽  
Md. Roich Khan ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
Density Functional ◽  
Chemical Reactivity ◽  
Docking Study ◽  
Functional Study ◽  
Molecular Docking Study ◽  
Study Results ◽  
Homo And Lumo ◽  
Cox 2

This study aimed to determine the activity of PYT and its derivatives against COX-2, including 5IKR protein induced inflammation by using the computational tools. PYT and its derivatives have been designed by utilizing density functional theory (DFT) and the performance of the drugs was also evaluated by molecular docking study. Results suggest that the NH2 derivative of PYT (D-NH2) showed binding energy -6.4 (Kcal/mol) with protein 5IKR of COX-2 compared to the main drug (D) that showed binding energy -5.1 (Kcal/mol) with the same protein. HOMO and LUMO energy values were also calculated to determine the chemical reactivity of all the modified drugs. Non-covalent interactions of PYT and its derivatives were essential in improving the performance. In conclusion, D-NH2 showed better preference in inhibiting to the protein 5IKR of COX-2 compared to other modified drugs and it can be claimed that D-NH2 will be the best conformer for COX-2 induced inflammation.

scholarly journals In silico study of anthocyanin and ternatin flavonoids for the treatment of inflammation-related diseases using molecular docking analysis

Food Research ◽  
2020 ◽  
Vol 4 (3) ◽  
pp. 780-785
Author(s):  
Y.T. Wijaya ◽  
A. Yulandi ◽  
A.W. Gunawan ◽  
Yanti
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
Active Site ◽  
In Silico ◽  
Protein Crystal ◽  
Drug Candidate ◽  
Inflammatory Drugs ◽  
Cox 2 ◽  
Anti Inflammatory ◽  
Cox 1

Inflammatory markers such as cyclooxygenase (COX)-2, inducible nitric oxide synthase (iNOS), myeloperoxidase (MPO), and prostaglandin (PEG) are widely known as major targets in discovering natural anti-inflammatory drugs for the treatment of inflammationrelated diseases. Non-steroidal anti-inflammatory drugs (NSAIDs) such as ibuprofen and aspirin are mostly used at present, however, some NSAIDS have been reported to cause gastrointestinal side effect due to ligand-protein interaction. Molecular docking is a promising tool to study such modes of interaction. In this study, we evaluated the potential use of anthocyanin and ternatin flavonoids as natural anti-inflammatory agents for treatment of inflammatory-related diseases using in silico molecular docking assay. Automated docking study using Protein-Ligand ANT System (PLANTS) and AutoDock Vina was performed with various ligand molecules, including ibuprofen, anthocyanin, and ternatin against the protein crystal structures of COX-1, COX-2, iNOS, and MPO. The in silico data demonstrated that ibuprofen bound effectively to the active site of COX-1 and MPO with minimum binding energy, yet the compound required more energy to bind the active site of COX-2. Ternatin flavonoid was bound to COX-2 and iNOS with minimum binding energy. In terms of binding energy, anthocyanin flavonoid was found to be effective for inhibiting COX-1, COX-2, and iNOS. These results suggested that anthocyanin and ternatin flavonoids may potentially be developed as anti-inflammatory drug candidate for the treatment of inflammatory-related diseases.

Synthesis of new hexahydropyrimido[1,2-a]azepine derivatives bearing functionalized aryl and heterocyclic moieties as anti-inflammatory agents

2021 ◽  
Author(s):  
Hassanein H Hassanein ◽  
Doaa E Abdel Rahman ◽  
Marwa A Fouad ◽  
Rehab F Ahmed
Keyword(s):  
Molecular Docking ◽  
Binding Sites ◽  
Docking Study ◽  
In Vivo Studies ◽  
Molecular Docking Study ◽  
Cox 2 ◽  
Anti Inflammatory ◽  
Cox 1

New hexahydropyrimido[1,2- a]azepine derivatives bearing functionalized aryl and heterocyclic moieties were synthesized as anti-inflammatory agents with better safety profiles. All synthesized compounds were assessed in vitro for their COX-1 and COX-2 inhibition activities. The most selective compounds, 2f, 5 and 6, were further evaluated for their in vivo anti-inflammatory activity and PGE2 inhibitory activity. To rationalize their selectivity, molecular docking within COX-1 and COX-2 binding sites was performed. Their physicochemical properties and drug-like nature profile were also calculated. The good activity and selectivity of compounds 2f, 5 and 6 were rationalized using a molecular docking study and supported by in vivo studies. These promising findings are encouraging for performing future investigations of these derivatives.

Identification of natural compounds with analgesic and anti-inflammatory properties using machine learning and molecular docking studies

2021 ◽  
Vol 18 ◽  
Author(s):  
Mohammad Firoz Khan ◽  
Ridwan Bin Rashid ◽  
Mohammad A. Rashid
Keyword(s):  
Machine Learning ◽  
Natural Products ◽  
Molecular Docking ◽  
High Throughput ◽  
In Silico ◽  
Docking Study ◽  
Molecular Docking Study ◽  
Natural Sources ◽  
Cox 2 ◽  
Anti Inflammatory

Background: Natural products have been a rich source of compounds for drug discovery. Usually, compounds obtained from natural sources have little or no side effects, thus searching for new lead compounds from traditionally used plant species is still a rational strategy. Introduction: Natural products serve as a useful repository of compounds for new drugs; however, their use has been decreasing, in part because of technical barriers to screening natural products in high-throughput assays against molecular targets. To address this unmet demand, we have developed and validated a high throughput in silico machine learning screening method to identify potential compounds from natural sources. Methods: In the current study, three machine learning approaches, including Support Vector Machine (SVM), Random Forest (RF) and Gradient Boosting Machine (GBM) have been applied to develop the classification model. The model was generated using the cyclooxygenase-2 (COX-2) inhibitors reported in the ChEMBL database. The developed model was validated by evaluating the accuracy, sensitivity, specificity, Matthews correlation coefficient and Cohen’s kappa statistic of the test set. The molecular docking study was conducted on AutoDock vina and the results were analyzed in PyMOL. Results: The accuracy of the model for SVM, RF and GBM was found to be 75.40 %, 74.97 % and 74.60 %, respectively which indicates the good performance of the developed model. Further, the model has demonstrated good sensitivity (61.25 % - 68.60 %) and excellent specificity (77.72 %- 81.41 %). Application of the model on the NuBBE database, a repository of natural compounds, led us to identify a natural compound, enhydrin possessing analgesic and anti-inflammatory activities. The ML methods and the molecular docking study suggest that enhydrin likely demonstrates its analgesic and anti-inflammatory actions by inhibiting COX-2. Conclusion: Our developed and validated in silico high throughput ML screening methods may assist in identifying drug-like compounds from natural sources.

scholarly journals In Silico Molecular Docking Studies of Lichen Metabolites against Cyclooxygenase-2 Enzyme

2015 ◽  
Vol 18 (2) ◽  
pp. 90-96 ◽  
Author(s):  
Mohammad Firoz Khan ◽  
Sabreena Aleem Nabila ◽  
Ridwan Bin Rashid ◽  
Mohammad Sharifur Rahman ◽  
Abu Asad Chowdhury ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Binding Affinity ◽  
Usnic Acid ◽  
Cyclooxygenase 2 ◽  
Therapeutic Effects ◽  
Lichen Metabolites ◽  
Cox 2 ◽  
Anti Inflammatory ◽  
Cox 2 Inhibitors

Cyclooxygenase-2 (COX-2) is an inducible enzyme that causes inflammation. COX-2 inhibitors are clinically effective anti-inflammatory agents with less gastrointestinal and renal toxicities. However, they lack anti-thrombotic activity and hence lead to increased incidences of adverse cardiovascular thrombotic events, including myocardial infarction. Therefore, there is still need to develop COX-2 inhibitors with better therapeutic effects and tolerability. The aim of the present study is to explore the anti-inflammatory activity of five lichen metabolites by conducting virtual screenings. In this regard, molecular docking simulations were carried out for the lichen metabolites namely atranorin, diffractic acid, lecanoric acid, salazinic acid and usnic acid with human COX-2 enzyme and the docked results were compared with the standard reference ligands (Celecoxib and Rofecoxib). Among all the docked ligands, the lecanoric acid demonstrated best binding affinity -9.83 kcal/mol followed by atranorin (-8.7 kcal/mol) and diffractic acid (-8.6 kcal/mol) which are comparable to the reference ligands celecoxib (-12.3 kcal/mol) and rofecoxib (-11.2 kcal/mol). The salazinic acid and usnic acid has shown binding affinity of -7.9 kcal/mol and -4.7 kcal/mol, respectively. Moreover, all the ligands except atranorin and diffractic acid satisfied Lipinski’s rule of 5. From the docking results it was revealed that the lichen metabolites might have inhibitory activity against COX-2 enzyme, and are expected to be useful in conducting in vivo anti-inflammatory screenings on animal model which may lead to the development of more effective and potent new chemical entities with anti-inflammatory properties.Bangladesh Pharmaceutical Journal 18(2): 90-96, 2015

scholarly journals Molecular Docking Study of 3, 4- Dihydropyrimidone Derivatives as Novel Anti-inflammatory Agents

2021 ◽  
pp. 481-487
Author(s):  
Amit N. Panaskar ◽  
Ashish Jain ◽  
Pradeep Kumar Mohanty
Keyword(s):  
Molecular Docking ◽  
Active Site ◽  
Docking Study ◽  
Protein Data Bank Code ◽  
Molecular Docking Study ◽  
Docking Score ◽  
Enzyme Active Site ◽  
Cox 2 ◽  
Anti Inflammatory

Aim: Currently, researchers have developed a lot of new active substances as anti-inflammatory agents. One of the target proteins for anti-inflammatory agents is the selective COX-2 active site. Selective COX-2 inhibition is the regulator of the inflammatory reaction cascade. In this research, 3, 4- Dihydropyrimidone derivatives were used to design the anti-inflammatory agent through a selective COX-2 inhibition. The potential activity of 3, 4- Dihydropyrimidone derivatives maybe increase due to the preparation of the Schiff base with aromatic aldehydes. Selective COX-2 inhibition was required to predict their anti-inflammatory activity so, the aim in the present study, molecular docking study of 3,4- dihydropyrimidone derivatives have performed using COX-2 enzyme active site. Methodology: The molecular docking of 3, 4-dihydropyrimidone derivatives were carried out using AutoDock vina Ver.1.1.2. Twenty 3,4-dihydropyrimidone derivatives were docked into the COX-2 active site with Protein data bank code 3LN1. The interactions were evaluated based on the docking score. Celecoxib was used as the reference standard for this study. Results: Twenty 3, 4- dihydropyrimidone derivatives showed the approximate docking score -8.4 to -10.1 kcal/mol. Fourteen 3,4-dihydropyrimidone derivatives have a greater docking score compared to celecoxib used as a standard compound. Derivative D-1 had higher binding energy than other 3,4-dihydropyrimidone derivatives because it has the smallest docking score. Conclusion: All new 3,4-dihydropyrimidone derivatives are feasible to synthesize and performed their in-vitro evaluation.

scholarly journals In-silico molecular docking analysis of some plant derived molecules for anti-inflammatory inhibitory activity

2021 ◽  
pp. 22-27
Author(s):  
L. Thamaraiselvi ◽  
T. Selvankumar ◽  
E.G. Wesely ◽  
N. Vinod Kumar
Keyword(s):  
Molecular Docking ◽  
Binding Energy ◽  
In Silico ◽  
Novel Drugs ◽  
In Silico Study ◽  
Low Toxicity ◽  
Cox 2 ◽  
Anti Inflammatory ◽  
In Silico Molecular Docking ◽  
Oxide Synthase

Herbs are essential resources for drug discovery. However, numerous challenges stand in front of the scientific community to discover novel drugs from herbs. To explore the validation behind the precious knowledge of traditional medicine, we focused on achieving virtual screening to detect the potential medicines from the herbs.  Five bioactive compounds from known anti-inflammatory medicinal plants were examined through molecular docking against  cyclooxygenase-2 (COX-2) and inducible Nitric Oxide Synthase (iNOS), using AutoDock 4.2. The docking of selected ligands with COX-2 showed the binding energy varying from -6.15 Kcal/mol to ‑11.24 Kcal/mol. The docking energies of identified ligands with iNOS were generated ranges from -3.85kcal/mol to -6.99 kcal/mol.  Among the tested ligands, it was noted that 6 urs-12-en-24-oic acid showed the best binding energy than other compounds with the lowest binding energy and highest binding affinity with both anti-inflammatory target proteins COX-2 and iNOS. The in silico study validates the potential phytochemical compound of the medicinal herb that contribute to anti-inflammatory activity with low toxicity and minimal side effects.

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