Computational Analysis and Biological Activities of Oxyresveratrol Analogues, the Putative Cyclooxygenase-2 Inhibitors

Jongkon, Nathjanan; Seaho, Boonwiset; Tayana, Ngampuk; Prateeptongkum, Saisuree; Duangdee, Nongnaphat; Jaiyong, Panichakorn

doi:10.3390/molecules27072346

Cited by 7 publications

(3 citation statements)

References 88 publications

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“…As the growing importance of accurately estimating binding affinities in drug design is unforeseeably gaining interest, leading to quantum mechanical (QM) approaches to become incredibly popular for designing drugs [ 58 ]. It has been discovered that certain computation of QM parameters, such as a dipole moment and atomic charges, can help increase the precision of a docking process [ 58 , 59 ]. According to the theory of Gibbs’s free energy, the higher or more negative the Δ G value energy produced from the bonds between the ligands and the receptors, the more stable are the bonds [ 60 ].…”

Section: Discussionmentioning

confidence: 99%

Pharmacophore study, molecular docking and molecular dynamic simulation of virgin coconut oil derivatives as anti-inflammatory agent against COX-2

Jack

Asaruddin

Bhawani

2022

Chem. Biol. Technol. Agric.

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Background Virgin coconut oil is mostly made up of saturated fatty acids in which approximately 72% are medium chain triglycerides. Medium chain triglycerides can be digested into medium chain fatty acids and medium chain monoglycerides which are bioactive components. Therefore, it is very important to study the in-silico ability of some Virgin coconut oil derivatives, namely, medium chain fatty acids and medium chain monoglycerides to inhibit Cyclooxygenase 2 (COX-2) protein for prevention of excessive inflammatory response. Results Pharmacophore study displayed monolaurin with two hydrogen bond donor, three hydrogen bond acceptor and five hydrophobic interactions, while lauric acid presented two hydrogen bond acceptor, five hydrophobic interactions and a negative ion interaction. Molecular docking underlined the ability of monolaurin in the inhibition of COX-2 protein which causes inflammatory action with a decent result of energy binding affinity of − 7.58 kcal/mol and 15 interactions out of which 3 are strong hydrogen bond with TYR385 (3.00 Å), PHE529 (2.77 Å), and GLY533 (3.10 Å) residues of the protein. Monolaurin was employed as hydrogen bond acceptor to the side of residue TYR385 of COX-2 protein with an occupancy of 67.03% and was observed to be long-living during the entire 1000 frames of the molecular dynamic simulation. The analysis of RMSD score of the Monolaurin–COX-2 complex backbone was calculated to be low (1.137 $$\pm$$ ± 0.153 Å) and was in a stable range of 0.480 to 1.520 Å. Redocking of this complex still maintained a strong hydrogen bond (2.87 Å) with the main residue TYR385. AMDET results where promising for medium chain fatty acids and medium chain monoglycerides with good physicochemical drug scores. Conclusions This can be concluded from the results obtained that the monolaurin has strong interactions with COX-2 protein to disrupt its function due to significant hydrogen bonds and hydrophobic interactions with amino acid residues present in the target protein’s active site. These results displayed a very significant anti-inflammatory potential of monolaurin and a new promising drug candidates as anti-inflammatory agent. Graphical Abstract

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Section: Discussionmentioning

confidence: 99%

Pharmacophore study, molecular docking and molecular dynamic simulation of virgin coconut oil derivatives as anti-inflammatory agent against COX-2

Jack

Asaruddin

Bhawani

2022

Chem. Biol. Technol. Agric.

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“…Most of the FDA-approved non-steroidal anti-inflammatory drugs (NSAIDs), whether they are Salicylates [2], Anthranilic acid [3], Arylindoic acid [4], and Oxicame [5] (Scheme 1), possess common structural features of an acidic or amine of an aromatic or heterocyclic ring, and an additional center of lipophilicity mostly aromatic. Their mechanisms are nonselective, inhibiting both COX-I and COX-II isoforms [6,7]. Density-functional theory (DFT) is a computational quantum mechanical method widely used in modern medicinal chemistry to suggest the electronic 3D atoms or molecule structures compute the ground state energy in realistic models of bulky molecules and their surfaces [8,9].…”

Section: Introductionmentioning

confidence: 99%

“…Docking of Anthranilic acid derivatives (compounds[1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16][17][18][19][20] …”

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confidence: 99%

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2023

J. Med. Chem. Sci.

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Nonsteroidal anti-inflammatories (NSAIDs), are very effective agents in relieving mild to moderate pain and inflammation by inhibiting two isoforms of prostaglandin G-H synthetase (I and II). In the present work, anthranilic acid derivatives' electronic and physicochemical properties are reported utilizing quantum chemical calculations that use the density functional theory (DFT), which forecast physicochemical properties. To clarify the type of chemical composition, drug-likeness, and cyclooxygenase inhibitor, ADME and molecular docking were used. The molecule was highly electrophilic and relatively stable from a quantum chemical computation perspective. The contour maps of HOMO-LUMO and molecule electrostatic potential were examined to display the charge density distributions that might be related to the biological activity.

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Ginkgo biloba active compounds can modulate the development of acute mountain sickness and ischemic stroke as discovered by network pharmacology and molecular docking

Guo,

Kang,

et al. 2024

iLABMED

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BackgroundA combination of molecular docking, molecular dynamics simulations, and herbal network pharmacology was used to investigate the shared key targets and potential mechanisms underlying the preventive effects of Ginkgo biloba active compounds against acute mountain sickness (AMS) and ischemic stroke (IS).Material and MethodsThe Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform was used to screen the main active compounds of Ginkgo biloba and their corresponding targets. We obtained AMS‐related genes by mining several databases and cross‐correlated them with key active compounds of Ginkgo biloba to identify relevant action targets for treating AMS. The STRING database was used to construct a protein–protein interaction network of the effect of Ginkgo biloba active compounds on AMS targets. The expression of genes in the network was analyzed in an IS dataset to identify common key targets of Ginkgo biloba active compounds for both AMS and IS prevention.ResultsThe intersection between the targets of Ginkgo biloba active compounds and AMS‐related genes identified 43 overlapping genes. Analysis of the protein–protein interaction network showed that VEGFA, TP53, SERPINE1, and PTGS2 were among the key hub genes. Analysis of the IS dataset identified significant differences in the expression levels of CAT, TP53, CXCL8, NFKBIA, and PTGS2. These genes were used to construct a visual nomogram prediction model for IS prognosis with promising clinical implications. Molecular docking and molecular dynamics simulations indicated that sesamin stably targeted and bound to PTGS2.ConclusionsActive ingredients of Ginkgo biloba, including luteolin, quercetin, and sesamin, have the potential to modulate the development of AMS and IS through targeted interactions with key proteins, including TP53, CXCL8, NFKBIA, PTGS2, and CAT.

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Computational Analysis and Biological Activities of Oxyresveratrol Analogues, the Putative Cyclooxygenase-2 Inhibitors

Cited by 7 publications

References 88 publications

Pharmacophore study, molecular docking and molecular dynamic simulation of virgin coconut oil derivatives as anti-inflammatory agent against COX-2

Pharmacophore study, molecular docking and molecular dynamic simulation of virgin coconut oil derivatives as anti-inflammatory agent against COX-2

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Ginkgo biloba active compounds can modulate the development of acute mountain sickness and ischemic stroke as discovered by network pharmacology and molecular docking

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