Molecular Docking Study on the Interaction of Riboflavin (Vitamin <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M1"><mml:mrow><mml:msub><mml:mtext>B</mml:mtext><mml:mtext>2</mml:mtext></mml:msub></mml:mrow></mml:math>) and Cyanocobalamin (Vitamin <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" id="M2"><mml:mrow><mml:msub><mml:mtext>B</mml:mtext><mml:mtext>12</mml:mtext></mml:msub></mml:mrow></mml:math>) Coenzymes

Hafeez, Amtul; Saify, Zafar Saied; Naz, Afshan; Yasmin, Farzana; Akhtar, Naheed

doi:10.1155/2013/312183

Cited by 13 publications

(7 citation statements)

References 15 publications

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“…The 2D structure of nineexperimental ligands were constructed with Marvin sketch 5.2.5.1 (http://www.chemaxon.com) [33]. The preparation for these ligands was performed inthe same way as the native ligands and the conformers saved in the.…”

Section: Materials Preparationmentioning

confidence: 99%

In Silico Molecular Docking of Xanthone Derivatives as Cyclooxygenase-2 Inhibitor Agents

Miladiyah

Jumina

Haryana

et al. 2017

Int J Pharm Pharm Sci

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Objective: To demonstrate the potential ofdifferent xanthone derivatives as cyclooxygenase-2 (COX-2) inhibitor agents and their selectivity against cycloooxygenase-1 (COX-1) and COX-2 using molecular simulation. Methods:Nine novel xanthone derivatives (compounds A-I) were employed to dock against protein COX-2 (Protein Data Bank/PDB ID: 1CX2) and COX-1 (PDB ID: 3N8Z). Celecoxib, a selective COX-2 inhibitor, was chosen as a control compound. The free binding energy produced by the docking was scored using Protein-Ligand Ant System (PLANTS) and the hydrogen bonds (H-bonds) between ligands and enzymes were visualised using Pymol.Results: Molecular docking studies revealed that celecoxib docked to the active site of COX-2 enzyme, but not to COX-1; where as xanthone derivatives docked to the active site of both COX-2 and COX-1. Free binding energy of xanthone derivatives ranged between-73, 57 to-79,18 and between-73,06 to-79,25 against COX-2 and COX-1, respectively, and-78,13 against celecoxib. H-bonds in the molecule of xanthone derivatives and COX-2 protein were found in amino acid residues Arg 120 , Tyr 355 , Tyr 385 , and Ser 353 . There was an insignificant difference between the free binding energyof xanthone derivatives against COX-2 and against COX-1, suggesting that their inhibition was non-selective. Conclusion:In conclusion, in silico studies showed that xanthone derivatives could be effective as potential inhibitors against COX-2, although they are not selective.

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Section: Materials Preparationmentioning

confidence: 99%

In Silico Molecular Docking of Xanthone Derivatives as Cyclooxygenase-2 Inhibitor Agents

Miladiyah

Jumina

Haryana

et al. 2017

Int J Pharm Pharm Sci

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“…The stability of docked poses was decided by ArgusLab energy functions and the hydrogen bonds formed between receptor and ligands. [ 64 ] Further 3D, figure for BSA‐ C3 interactions, was also generated by “Protein‐Ligand Interaction Profiler.” The tool gave us the idea regarding hydrophobic interaction and π‐stacking interaction. [ 65 ]…”

Section: Resultsmentioning

confidence: 99%

“…The docking algorithm was set as Argus dock with exhaustive search and the grid resolution was fixed to F I G U R E 5 Plot of Fluorescence emission intensity versus wavelength for BSA at increasing concentrations of C1, the arrow shows decrease in the fluorescence intensity with increasing concentration of the complex The stability of docked poses was decided by ArgusLab energy functions and the hydrogen bonds formed between receptor and ligands. [64] Further 3D, figure for BSA-C3 interactions, was also generated by "Protein-Ligand Interaction Profiler." The tool gave us the idea regarding hydrophobic interaction and π-stacking interaction.…”

Section: Docking Studiesmentioning

confidence: 99%

Organoruthenium (II) complexes featuring pyrazole‐linked thiosemicarbazone ligands: Synthesis, DNA/BSA interactions, molecular docking, and cytotoxicity studies

Khanvilkar

Dash

Banerjee

et al. 2021

Applied Organom Chemis

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A series of pyrazol-derived thiosemicarbazone ligands (L1-L4) were synthesized and reacted with [Ru(p-cymene)(μ-Cl)Cl] 2 to yield a series of "piano-stool"-type binuclear ruthenium (II)-arene-thiosemicarbazone complexes (C1-C8) of the general type [(Ru(η 6 -p-cym)L) 2 (μ-im/azpy)] Cl 1-2 (L = diphenylpyrazole thiosemicarbazone; cym = p-cymene; im = imidazole; azpy = 4,4 0 -azopyridine). The thiosemicarbazone ligands act as N and S donors binding to the Ru(II) center via the imine nitrogen and the thione sulfur atoms. The complexes were characterized by NMR, FTIR, UV-Vis spectroscopy, and ESI + mass spectrometry. The binding of the complexes to calf thymus deoxyribonucleic acid (CT-DNA) and bovine serum albumin (BSA) was evaluated, and it has been established that the binuclear complexes have good binding efficacies with DNA (K b = 10 4 -10 5 M À1 ) and BSA (K a = 10 5 -10 6 M À1 ). This is attributed to the arene moieties present in the ligands of the complexes that can have hydrophobic interactions with DNA/BSA. Ethidium bromide (EB) displacement studies and DNA viscosity measurements revealed intercalative interaction of the complexes with DNA. Static interaction of the complexes with BSA was revealed by fluorescence quenching studies. Molecular docking studies confirmed base stacking, H-bonding, and hydrophobic interactions with the biomolecules. In vitro antiproliferative studies of the complexes affirmed that the complexes are cytotoxic towards the HeLa (human cervical cancer) cell line with IC 50 values in range of 17.3-41.3 μM. K E Y W O R D S binuclear ruthenium (II) complexes, DNA/BSA binding interactions, HeLa human cervical carcinoma, pyrazole-derived thiosemicarbazone

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“…The 2D xanthone structure was constructed by using Marvinsketch 5.2.5.1. 27 This ligand preparation was performed in a similar manner as used for the native ligands, and the 10 conformers generated were saved in a .mol2 format for the docking process.…”

Section: Methodsmentioning

confidence: 99%

Biological activity, quantitative structure–activity relationship analysis, and molecular docking of xanthone derivatives as anticancer drugs

Miladiyah

Jumina²,

Haryana³

et al. 2018

DDDT

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BackgroundXanthone derivatives have a wide range of pharmacological activities, such as those involving antibacterial, antiviral, antimalarial, anthelmintic, anti-inflammatory, antiprotozoal, and anticancer properties. Among these, we investigated the anticancer properties of xanthone. This research aimed to analyze the biological activity of ten novel xanthone derivatives, to investigate the most contributing-descriptors for their cytotoxic activities, and to examine the possible mechanism of actions of xanthone compound through molecular docking.Materials and methodsThe cytotoxic tests were carried out on WiDR and Vero cell lines, by a 3-(4,5-dimethylthiazole-2-yl)-2,5-diphenyl-tetrazolium bromide (MTT) assay method. The structural features required for xanthone’s anticancer activity were conducted by using the semi-empirical Austin Model-1 method, and continued with quantitative structure-activity relationship (QSAR) analysis using BuildQSAR program. The study of the possible mechanism of actions of the selected xanthone compound was done through molecular docking with PLANTS.ResultsThe three novel xanthone derivatives (compounds 5, 7, and 8) exhibited cytotoxic activity with compound 5 showed the highest degree of cytotoxicity at concentration 9.23 µg/mL (37.8 µM). The following best equation model was obtained from the BuildQSAR calculation: log 1/IC50 = −8.124 qC1 −35.088 qC2 −6.008 qC3 + 1.831 u + 0.540 logP −9.115 (n = 10, r = 0.976, s = 0.144, F = 15.920, Q2 = 0.651, SPRESS = 0.390). This equation model generated 15 proposed new xanthone compounds with better-predicted anticancer activities. A molecular docking study of compound 5 showed that xanthone formed binding interactions with some receptors involved in cancer pathology, including telomerase, tumor-promoting inflammation (COX-2), and cyclin-dependent kinase-2 (CDK2) inhibitor.ConclusionThe results suggested that compound 5 showed the best cytotoxic activity among the xanthone derivatives tested. QSAR analysis showed that the descriptors contributed to xanthone’s cytotoxic activity were the net atomic charge at qC1, qC2, and qC3 positions, also dipole moment and logP. Compound 5 was suspected to be cytotoxic by its inhibition of telomerase, COX-2, and CDK2 receptors.

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Molecular Docking Study on the Interaction of Riboflavin (Vitamin B2) and Cyanocobalamin (Vitamin B12) Coenzymes

Cited by 13 publications

References 15 publications

In Silico Molecular Docking of Xanthone Derivatives as Cyclooxygenase-2 Inhibitor Agents

In Silico Molecular Docking of Xanthone Derivatives as Cyclooxygenase-2 Inhibitor Agents

Organoruthenium (II) complexes featuring pyrazole‐linked thiosemicarbazone ligands: Synthesis, DNA/BSA interactions, molecular docking, and cytotoxicity studies

Biological activity, quantitative structure–activity relationship analysis, and molecular docking of xanthone derivatives as anticancer drugs

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Molecular Docking Study on the Interaction of Riboflavin (Vitamin B2) and Cyanocobalamin (Vitamin B12) Coenzymes

Cited by 13 publications

References 15 publications

In Silico Molecular Docking of Xanthone Derivatives as Cyclooxygenase-2 Inhibitor Agents

In Silico Molecular Docking of Xanthone Derivatives as Cyclooxygenase-2 Inhibitor Agents

Organoruthenium (II) complexes featuring pyrazole‐linked thiosemicarbazone ligands: Synthesis, DNA/BSA interactions, molecular docking, and cytotoxicity studies

Biological activity, quantitative structure&ndash;activity relationship analysis, and molecular docking of xanthone derivatives as anticancer drugs

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Biological activity, quantitative structure–activity relationship analysis, and molecular docking of xanthone derivatives as anticancer drugs