Molecular docking analysis of imidazole derivatives and polybenzimidazole analogs as inhibitors of superoxide dismutase (SOD) and xanthine oxidase (XO)

Vijayakumar, V.; Narayanaswamy, Radhakrishnan; Chidambaram, Rameshkumar

doi:10.1109/icstm.2017.8089213

Cited by 3 publications

(7 citation statements)

References 8 publications

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“…The 3D structure of hSOD (PDB ID: 2C9Vwith a resolution of 1.07 Aᵒ); hPDE 9 (PDB ID: 4Y86 with a resolution of 2.01 Aᵒ) and hDPP 4 (PDB ID: 4A5S with a resolution of 1.62 Aᵒ) was retrieved from PDB database. “A” chain of these enzymes was prepared individually by removing other chains, ligands and even crystallographically observed water molecules by applying the UCSF Chimera software tool (Regents, University of California, San Francisco, USA) [ 13 ].…”

Section: Methodsmentioning

confidence: 99%

In Silico Analysis of Selected Glycyrrhiza glabra (Licorice) Constituents: Exploring Their Modulatory Effects on Human Superoxide Dismutase, Human Phosphodiesterase-9 and Human Dipeptidyl Peptidase-4

Tamilarasu,

Narayanaswamy,

Prabhakaran

2024

Cureus

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Background Glycyrrhiza glabra (Licorice) has been known for its various biological activities. In the current investigation, we aimed to evaluate 11 (10 natural and one synthetic) selected constituents of G. glabra as potent modulatory agents of human superoxide dismutase (hSOD), human phosphodiesterase-9 (hPDE 9) and human dipeptidyl peptidase-4 (hDPP 4) using in silico method. Methodology The 11 selected constituents of G. glabra (Licorice) were investigated on the docking behaviour of hSOD, hPDE 9 and hDPP 4 by using the PatchDock method. In addition to docking, toxicity analysis was also carried out using the pkCSM free online server (University of Melbourne, Melbourne, AUS). Results Toxicity analysis has shown that four ligands (36%) of G. glabra (Licorice) are predicted to have human ether-a-go-go-related gene-2 (hERG 2) inhibition activity. The docking analysis showed that glabridin (-224.13 kcal/mol) has shown the highest atomic contact binding energy with the hSOD enzyme, whereas carbenoxolone has shown the maximum atomic contact binding energy with both the hPDE 9 and hDPP 4 enzymes (-239.57 and -173.50 kcal/mol) respectively. Conclusion Thus the present finding provides new information about 11 selected ligands of G. glabra (Licorice) as potent modulatory agents of hSOD, hPDE 9 and hDPP 4.

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Section: Methodsmentioning

confidence: 99%

In Silico Analysis of Selected Glycyrrhiza glabra (Licorice) Constituents: Exploring Their Modulatory Effects on Human Superoxide Dismutase, Human Phosphodiesterase-9 and Human Dipeptidyl Peptidase-4

Tamilarasu,

Narayanaswamy,

Prabhakaran

2024

Cureus

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“…Chemical structures of 25 ligands ( P. pusilla fruit constituents) namely (i) 6‐oxabicyclo [3,1,0] hexan‐2‐one (CID 242082), (ii) 4H‐pyran‐4‐one, 2,3‐dihydro‐3,5‐dihydroxy‐6‐methyl (CID 119838), (iii) 1‐butoxypropan‐2‐yl 2‐methylbutanoate (CID 91693251), (iv) glycerin (CID 753), (v) dimethylamine, N ‐(neopentyloxy) (CID 548341), (vi) tricyclo [2,2,1,0 (2,6)] heptane, 1,3,3‐trimethyl (CID 79022), (vii) benzene, 1‐ethynyl‐4‐fluoro (CID 11171265), (viii) 5‐hydroxymethylfurfural (CID 237332), (ix) phenol, 2‐methoxy‐3‐(2‐propenyl) (CID 596373), (x) cetene (CID 12395), (xi) 7‐epi‐ trans ‐sesquisabinene hydrate (CID 100930863), (xii) Z‐10‐pentadecen‐1‐ol (CID 5364483), (xiii) dodecanoic acid, methyl ester (CID 8139), (xiv) trichloroacetic acid, 4‐tetradecyl ester (CID 534423), (xv) decanoic acid, 3‐methyl (CID 143696), (xvi) methyl tetradecanoate (CID 31284), (xvii) 3‐deoxy‐ d ‐mannoic lactone (CID 541561), (xviii) hexadecanoic acid, methyl ester (CID 8181), (xix) benzenepropanoic acid, 3,5‐ bis (1,1‐dimethylethyl)‐4‐hydroxy‐, methyl ester (CID 62603), (xx) n ‐hexadecanoic acid (CID 985), (xxi) 1‐formyl‐2,5‐dimethoxy‐6,9,10‐trimethyl‐anthracene (CID 626348), (xxii) 9‐octadecenoic acid, methyl ester (CID 5280590), (xxiii) methyl stearate (CID 8201), and (xxiv) 9,12‐octadecadienoic acid (Z,Z) were downloaded from PubMed. One more unavailable structure of ligand (β‐allyloxypropionic acid) and the selected 24 ligands were drawn by using ChemBio Draw Ultra 12.0 and the molecular mechanics (MM2) energy minimization of ligands was performed by ChemBio 3D Ultra 12.0, according to the reported protocol (Vijayakumar et al, 2017). Furthermore, the prepared ligands were converted into the pdbqt file format using the Open Babel free software.…”

Section: Methodsmentioning

confidence: 99%

“…Chemical structures of 25 ligands (P. pusilla fruit constituents) namely (i) 6-oxabicyclo [3,1,0] hexan-2-one (CID 242082), (ii) 4Hpyran-4-one, 2,3-dihydro-3,5-dihydroxy-6-methyl (CID 119838), (iii) 1-butoxypropan-2-yl 2-methylbutanoate (CID 91693251), 1-formyl-2,5-dimethoxy-6,9,10-trimethyl-anthracene (CID 626348), (xxii) 9-octadecenoic acid, methyl ester (CID 5280590), (xxiii) methyl stearate (CID 8201), and (xxiv) 9,12-octadecadienoic acid (Z,Z) were downloaded from PubMed. One more unavailable structure of ligand (β-allyloxypropionic acid) and the selected 24 ligands were drawn by using ChemBio Draw Ultra 12.0 and the molecular mechanics (MM2) energy minimization of ligands was performed by ChemBio 3D Ultra 12.0, according to the reported protocol (Vijayakumar et al, 2017).…”

Section: Ligand Preparationmentioning

confidence: 99%

GC‐MS, alpha‐amylase, and alpha‐glucosidase inhibition and molecular docking analysis of selected phytoconstituents of small wild date palm fruit (Phoenix pusilla)

Srinivasan

Altemimi

Narayanaswamy

et al. 2023

Food Science & Nutrition

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Phoenix pusilla (Arecaceae), commonly known as “small wild date palm”, is regarded as one of the underutilized fruit crops in South India. Methanol extract of P. pusilla ripened fruits (PPRF) was analyzed for in vitro porcine pancreatic alpha‐amylase (PPAA) and rat small intestine alpha‐glucosidase (RIAG) inhibition activities, and through gas chromatography–mass spectrometry (GC‐MS) analysis. The GC‐MS analysis showed the presence of 25 phytoconstituents from PPRF which was further assessed on the docking behavior of five targeted enzymes diabetes mellitus (DM) namely (i) human aldose reductase, (ii) protein tyrosine phosphatase 1B, (iii) pancreatic alpha‐amylase, (iv) peroxisome proliferator‐activated receptor gamma, and (v) dipeptidyl peptidase IV by using the AutoDock Vina method. In addition to this physicochemical, bioactivity score, absorption, distribution, metabolism, excretion, and toxicity (ADMET) analysis was performed using the Molinspiration and pkCSM free online servers. Methanolic extract of PPRF showed 50% inhibition concentration (IC50) at 69.86 and 72.60 μg/mL levels against PPAA and RIAG enzymes activities, respectively. Interestingly in the present study, GC‐MS analysis showed the presence of 25 phytoconstituents from PPRF. Physicochemical analysis of PPRF has exhibited that 13 ligands have complied well with Lipinski's Rule of Five (RoF). With regard to ADMET analysis, one ligand (9,12‐octadecadienoic acid [Z,Z]) has predicated to possess both the hepatotoxicity (HT) and skin sensitization (SS) effect. The docking studies showed that 1‐formyl‐2,5‐dimethoxy‐6,9,10‐trimethyl‐anthracene exhibited the maximum atomic contact energy (ACE) for all the five target enzymes of DM. Thus, the current study suggested that the methanolic extract of PPRF and its phytoconstituents could be considered as potent antidiabetic agents.

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“…pubchem.com). Then the selected ligands were drawn by using ChemBioDraw Ultra 12.0 and the molecular mechanics (MM2) energy minimization of ligands was performed by ChemBio 3D Ultra 12.0, according to the reported protocol 24 . These minimized energy structures were used for further AutoDock study.…”

Section: Methodsmentioning

confidence: 99%

“…In silico experimental analysis ligands was performed by ChemBio 3D Ultra 12.0, according to the reported protocol. 24 These minimized energy structures were used for further AutoDock study.…”

Section: 7mentioning

confidence: 99%

Identification of novel inhibitor against human phosphoethanolamine cytidylyltransferase from phytochemicals of Citrus sinensis peel extract by in vitro and in silico approach

Victor¹,

Narayanaswamy²,

Kadry³

et al. 2023

Biotech and App Biochem

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Kidney stone is a major global menace that demands research on nonsurgical treatment involving biological compounds for the benefit of the patients. Among the biological extracts, citric acid is traditionally used to dissolve kidney stones. The current research focuses on evaluating the in vitro anti‐urolithiatic activity and in silico study of ethanolic extract of Citrus sinensis (ECS) peel against c: phosphoethanolamine cytidylyltransferase (PCYT). The diuretic activity was evaluated using in vitro model against the synthesized calcium oxalate crystals and cytotoxicity study in Madin–Darby canine kidney cell lines. The phytochemicals were identified using gas chromatography–mass spectroscopy. The interaction mechanism was studied using computational docking studies to confirm their involvement in the dissolution of calcium oxalate kidney stones. Further molecular properties, drug‐likeness, ADME (absorption, distribution, metabolism, and excretion), and toxicity analysis were followed for the ligands using software tools. 5‐Hydroxymethylfurfural, 2,4‐di‐tert‐butylphenol, 2‐methoxy‐4‐vinylphenol, 6‐octen‐1‐ol, 3,7‐dimethyl‐, acetate (citronellyl acetate), 3′,5′‐dimethoxyacetophenone, and ethyl alpha‐d‐glucopyranoside showed good binding affinities against PCYT. Moreover, the docking studies showed the ligand 3′,5′‐dimethoxyacetophenone has the highest binding energy (−6.68 kcal/mol) for human CTP. The present investigation concludes that these compounds of C. sinensis peel extract compounds are responsible as novel inhibitors against human CTP and extend their use in the pharmaceutical drug development process.

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Molecular docking analysis of imidazole derivatives and polybenzimidazole analogs as inhibitors of superoxide dismutase (SOD) and xanthine oxidase (XO)

Cited by 3 publications

References 8 publications

In Silico Analysis of Selected Glycyrrhiza glabra (Licorice) Constituents: Exploring Their Modulatory Effects on Human Superoxide Dismutase, Human Phosphodiesterase-9 and Human Dipeptidyl Peptidase-4

In Silico Analysis of Selected Glycyrrhiza glabra (Licorice) Constituents: Exploring Their Modulatory Effects on Human Superoxide Dismutase, Human Phosphodiesterase-9 and Human Dipeptidyl Peptidase-4

GC‐MS, alpha‐amylase, and alpha‐glucosidase inhibition and molecular docking analysis of selected phytoconstituents of small wild date palm fruit (Phoenix pusilla)

Identification of novel inhibitor against human phosphoethanolamine cytidylyltransferase from phytochemicals of Citrus sinensis peel extract by in vitro and in silico approach

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