In silico modeling and molecular docking insights of kaempferitrin for colon cancer-related molecular targets

Govindarasu, Mydhili; Ganeshan, Shalini; Ansari, Mohammad Azam; Alomary, Mohammad N.; Alyahya, Sami A.; Alghamdi, Saad; Almehmadi, Mazen; Rajakumar, Govindasamy; Thiruvengadam, Muthu; Vaiyapuri, Manju

doi:10.1016/j.jscs.2021.101319

Cited by 23 publications

(11 citation statements)

References 124 publications

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“…According to the results obtained from biological studies, compounds 10d and 16 have been chosen to carry out molecular docking studies on gastric cancer (PDB = 2BID ) and colon cancer (PDB = 2A4L ). According to the literature, the two proteins were selected [ 46 , 47 , 49 ]. Fig 7 explains 2D and 3D snapshots of the hydrophilicity interaction to PDB = 2BID and the results obtained for Gastric cancer ( PDB = 2BID ) receptor.…”

Section: Resultsmentioning

confidence: 99%

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Indenyl-thiazole and indenyl-formazan derivatives: Synthesis, anticancer screening studies, molecular-docking, and pharmacokinetic/ molin-spiration properties

2023

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Two new series of thiazole and formazan linked to 5-Bromo-indan were synthesized, and their structures were assured based on all possible analytical techniques. The size of the tested derivatives was calculated from the XRD technique and found five derivatives 3, 10a, 14a, 15, and 16 on the nanosized scale. The two series were tested for their efficacy and toxicity as anti-colon and stomach cancers. Derivative 10d showed activity more than the two reference drugs used in the case of SNU-16. Surpislly, in the case of COLO205, five derivatives 4, 6c, 6d, 6e, and 10a are better than the two benchmarks used, and two derivatives, 14a and 14b more potent than cisplatin. All potent derivatives showed a strong fit with the active site of the two tested proteins (gastric cancer (PDB = 2BID) and colon cancer (PDB = 2A4L)) in the molecular docking study. The Pharmacophore and ADME studies of the new derivatives showed that most derivatives revealed promising bioactivity, which indicates the drug-likeness properties against kinase inhibitors, protease, and enzyme inhibitors. In addition, the ProTox-II showed that the four compounds 10d, 16, 6d, and 10a are predicted to have oral LD50 values ranging from 335 to 3500 mg/kg in a rat model with (1 s,4 s)-Eucalyptol bearing the highest values and quercetin holding the lowest one.

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Section: Resultsmentioning

confidence: 99%

“…Cell culture reagents were obtained from Lonza (Basel, Switzerland). The anticancer activity of the rested compounds was evaluated against Gastric (SNU-16) Patch number (ATCC CRL-5822) (Gastric cancer) and COLO205 cells (colon cancer) [ 47 , 49 ].…”

Section: Methodsmentioning

confidence: 99%

Indenyl-thiazole and indenyl-formazan derivatives: Synthesis, anticancer screening studies, molecular-docking, and pharmacokinetic/ molin-spiration properties

2023

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“…The hydrogen bond interactions were found in the Asp148 and Glu91 residues, besides that it also has hydrophobic interactions with 9 residues from the receptor (Table 5). five interactions of hydrogen bond with essential amino acids Asp100 (bond length, 2,050 Å), Tyr199 (bond length, 2,647 Å), Asn140 (bond length, 2,281 Å), Arg143 (bond length, 2,033 Å), Asp108 (bond length, 2,136 Å) (Govindarasu et al 2021). Based from the results of this study, these residues were found to be involved in the docking of receptors and red betel leaves test compounds.…”

Section: Ligand Docking To Chek1 Receptormentioning

confidence: 99%

“…Previous reasearch showed that in XP docking kaempferitrin with BCl-2 (PDBID: 4LXD), there were correlations of hydrogen bonds with vital amino acids Ser88 (bond length, 2,054 Å), Tyr86 (length, 2,037 Å), Asp94 (bond length, 2,106 Å), Cys87 (bond length, 2,233 Å), Glu85 (bond length, 2,526 Å), Asp148 (bond length, 2,505 Å), Glu55 (length, 1.84 bond4 Å), Lys38 (bond length, 2,293 Å) (Govindarasu et al 2021). Based on the results of previous studies, some of these residues are broadly involved in the interaction with red betel leaves test ligands, including with test ligand that interacted best with it.…”

Section: Ligand Docking To Bcl 2 Navitoclax Analog Receptormentioning

confidence: 99%

In Silico Study of Anticancer Activity of Red Betel Leaves Bioactive Compounds against Colon Cancer Marker Proteins

2022

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Colon cancer or colorectal cancer is one of the major health problems in the world. Previous research has proven that red betel leaves extract has anticancer activity against breast cancer cells. The study aimed to look at the potential of compounds contained in red betel ethyl acetate fraction as anticancer substances for colon cancer by conducting in silico tests through the docking of three colon cancer biomarker receptors against eight red betel leaves compounds. The parameters of binding affinity energy and inhibition constant used in the molecular docking analysis showed that there are several compounds that have the potential as inhibitors against colon cancer marker proteins to inhibit the development of colorectal cancer and have high bioavalibility as oral drugs. Based on in silico test it is known that the compound N-1,N-9-Bis [E-(2-nitophenyl) methylene] non anedihydrazide has the highest inhibition of human leukotriene A4 hydrolase receptor with binding affinity energy of 11.3160 Kcal/mol. The next compound is 4-({4,6-Bis[3R,5S)-3,5-diamino-1-piperydinyl]-1,3,5-traizin-2-yl}amino) benzenosulfon amide which has the highest inhibition in Chek1 with binding affinity energy of 9.7110 Kcal/mol, and the compound 4-(4-methoxy-phenylamino)-2,3-dihydro-1H-4a, 9-diaza-cyclopenta (b) fluorine-10-carbonitrile has the highest inhibition in the Bcl 2 navitoclax analog receptor with binding affinity energy of 8.4470 Kcal/mol.

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“…Electronic properties of these boron compounds are investigated using contour diagram of frontier moleculer orbitals, molecular electrostatic potential (MEP) maps and MEP contours. Finally, molecular docking analysis which is the popular analysis in the recent time to determine the biological activity of chemicals are performed between target proteins and selected compounds [9][10][11]. Target proteins are main protease, RNA polymerase, and spike glycoproteins of SARS-CoV-2.…”

Section: Introductionmentioning

confidence: 99%

Structural, Electronic, ADME and p450 Analyses of Boron Containing Compounds against Omicron Variant (B.1.1.529) in SARS-CoV-2

Sayın

Ataseven

2023

Cumhuriyet Science Journal

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Eight boron compounds are investigated in this study. Structural and spectral characterization is done at M062X/6-311G(d) level in the water. Active sites of these compounds are determined using contour plots of frontier molecular orbital, molecular electrostatic potential (MEP) maps and MEP contour.. Electrophilic and nucleophilic attack regions are determined. We aimed to determine whether boron compounds inhibitor used in the treatment of omicron variant of SARS-CoV-2. Since SARS-CoV-2 is a worldwide health problem, anti-viral properties of studied boron compounds were investigated using in silico techniques. Bioavaliability analyses were performed using ADME and p450. It was found that compound B7 can be good drug candidate against omicron variant of SARS-CoV-2.

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In silico modeling and molecular docking insights of kaempferitrin for colon cancer-related molecular targets

Cited by 23 publications

References 124 publications

Indenyl-thiazole and indenyl-formazan derivatives: Synthesis, anticancer screening studies, molecular-docking, and pharmacokinetic/ molin-spiration properties

Indenyl-thiazole and indenyl-formazan derivatives: Synthesis, anticancer screening studies, molecular-docking, and pharmacokinetic/ molin-spiration properties

In Silico Study of Anticancer Activity of Red Betel Leaves Bioactive Compounds against Colon Cancer Marker Proteins

Structural, Electronic, ADME and p450 Analyses of Boron Containing Compounds against Omicron Variant (B.1.1.529) in SARS-CoV-2

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