Dataset on the DFT-QSAR, and docking approaches for anticancer activities of 1, 2, 3-triazole-pyrimidine derivatives against human esophageal carcinoma (EC-109)

Abstract

The investigation of the novel hybrid, 1, 2, 3-triazole moiety combined with pyrimidine derivatives against human esophageal carcinoma is an unexplored field of theoretical/computational chemistry. Also, the development of new drugs still remains a major challenge, cost-intensive and time-consuming, thus making the computational approach now a hot topic due to its ability to hasten up and aid the process of drug designs. Here, the use of the quantum chemical method via density functional theory (DFT) was employed in calculating molecular descriptors for developing the quantitative structure-activity relation (QSAR) model which predicts bioactivity of the selected 1, 2, 3-triazole-pyrimidine derivatives. Quantum chemical method implemented in Spartan 14, was used in calculating the molecular descriptors. The obtained results were imputed into Gretl and SPSS (software package for social sciences) to generate a novel QSAR model equation for human esophageal carcinoma (EC-109) through multiple linear regression. The relationship between the experimental and predicted inhibition efficiency (IC 50 ) of 1,2,3-triazole-pyrimidine with EC-109 was calculated which gives good correlation results. QSAR was validated using CV.R 2 . Fitting value (R 2 ) of 0.999 with an adjusted fitting value of 0.995 was obtained and the result of validating QSAR performance gave CV.R 2 and value that is greater than 0.6, signifying its appropriateness and dependability. Molecular docking through simulation using Discovery Studio 4.1, Autodock Tool 1.5.6 and AutodockVina 1.1.2 was also carried out to calculate the free energy of ligand-receptor interactions as well as ligand conformation in the receptor-binding site. The results obtained revealed the presence of hydrogen bond interaction of the ligands with the amino acids residue in the binding sites of the receptor. Conformation of the ligands was essential property for binding ligand with the receptor. Critical examination and the correlations between the IC 50 and binding energy showed the activeness of ligand conformation in the gouge of the receptor with binding energy greater than the 5-fluorouracil (5- Fu) that was used as the standard compound.

Synthesis, structural insights, and biological screening of DNA targeted Ru(ii)(η6-p-cymene) complexes containing bioactive amino-benzothiazole ligand scaffolds

“…The electronic structures and the bonding attributes of drug candidates 1 and 2 were calculated using DFT calculations by employing the Spartan 18 (Win/64b) version programme and the molecular electrostatic potential (MEP) plotted onto the van der Waals surface was calculated for each complex to explore electron-rich (red) and poor regions of the complex. 33 The negative MEP was found to be situated on the Cl atoms (180–190 kcal M −1 ) and the positive MEP was at the peripheral aromatic hydrogens of the cymene ring (120–130 kcal M −1 ) indicated by the blue colour in both the complexes (Fig. 4).…”

QSAR and Molecular Docking Studies on Nitro (Triazole/Imidazole)-Based Compounds as Anti-Tubercular Agents

“…As reported by Adegoke et al, 2020, any developed QSAR model with R 2 ≥ 0.5, Adj R 2 ≥ 0.6 and CVR 2 ≥ 0.5 is considered to be predictive; thus, as shown in Table 4, the developed QSAR model is proved to be predictive and efficient in predicting biological activity of the studied compounds. 27…”

In-Silico Study on Anti-bacteria and Anti-fungal Activities of 3,4-Dihydropyrimidin-2(1H)-One Urea Derivatives

“…In this present study, 2D structure of sixteen molecular compounds (Table 1) were accomplished using CHEMDRAW ultra 8.0 version and were optimized using density functional theory with 6-31G* (B3LYP) as basis set via Spartan'14 [30][31][32][33][34]. The studied compounds were optimized so as to generate descriptors that describe anti-1,4α-demethylase and anti-bacteria activities.…”