Identifications of good and bad structural fragments of hydrazone/2,5-disubstituted-1,3,4-oxadiazole hybrids with correlation intensity index and consensus modelling using Monte Carlo based QSAR studies, their molecular docking and ADME analysis

Monte Carlo Optimization Method Based QSAR Modeling of Placental Barrier Permeability

PURPOSE

In order to ensure that drug administration is safe during pregnancy, it is crucial to have the possibility to predict the placental permeability of drugs in humans. The experimental method which is most widely used for the said purpose is in vitro human placental perfusion, though the approach is highly expensive and time consuming. Quantitative structure-activity relationship (QSAR) modeling represents a powerful tool for the assessment of the drug placental transfer, and can be successfully employed to be an alternative in in vitro experiments.

METHODS

The conformation-independent QSAR models covered in the present study were developed through the use of the SMILES notation descriptors and local molecular graph invariants. What is more, the Monte Carlo optimization method, was used in the test sets and the training sets as the model developer with three independent molecular splits.

RESULTS

A range of different statistical parameters was used to validate the developed QSAR model, including the standard error of estimation, mean absolute error, root-mean-square error (RMSE), correlation coefficient, cross-validated correlation coefficient, Fisher ratio, MAE-based metrics and the correlation ideality index. Once the mentioned statistical methods were employed, an excellent predictive potential and robustness of the developed QSAR model was demonstrated. In addition, the molecular fragments, which are derived from the SMILES notation descriptors accounting for the decrease or increase in the investigated activity, were revealed.

CONCLUSION

The presented QSAR modeling can be an invaluable tool for the high-throughput screening of the placental permeability of drugs.

Thiazolidinedione-triazole conjugates: design, synthesis and probing of the α-amylase inhibitory potential

Aim: The primary objective of this investigation was the synthesis, spectral interpretation and evaluation of the α-amylase inhibition of rationally designed thiazolidinedione-triazole conjugates (7a-7aa). Materials & methods: The designed compounds were synthesized by stirring a mixture of thiazolidine-2,4-dione, propargyl bromide, cinnamaldehyde and azide derivatives in polyethylene glycol-400. The α-amylase inhibitory activity of the synthesized conjugates was examined by integrating in vitro and in silico studies. Results: The investigated derivatives exhibited promising α-amylase inhibitory activity, with IC50 values ranging between 0.028 and 0.088 μmol ml-1. Various computational approaches were employed to get detailed information about the inhibition mechanism. Conclusion: The thiazolidinedione-triazole conjugate 7p, with IC50 = 0.028 μmol ml-1, was identified as the best hit for inhibiting α-amylase.

Parsing structural fragments of thiazolidin-4-one based α-amylase inhibitors: A combined approach employing in vitro colorimetric screening and GA-MLR based QSAR modelling supported by molecular docking, molecular dynamics simulation and ADMET studies

α-Amylase (EC.3.2.1.1) is a ubiquitous digestive endoamylase. The abrupt rise in blood glucose levels due to the hydrolysis of carbohydrates by α-amylase at a faster rate is one of the main reasons for type 2 diabetes. The inhibitors prevent the action of digestive enzymes, slowing the digestion of carbs and eventually assisting in the management of postprandial hyperglycemia. In the course of developing α-amylase inhibitors, we have screened 2-aryliminothiazolidin-4-one based analogs for their in vitro α-amylase inhibitory potential and employed various in silico approaches for the detailed exploration of the bioactivity. The DNSA bioassay revealed that compounds 5c, 5e, 5h, 5j, 5m, 5o and 5t were more potent than the reference drug (IC₆₀ value = 22.94 ± 0.24 μg mL^-1). The derivative 5o with -NO₂ group at both the rings was the most potent analog with an IC₆₀ value of 19.67 ± 0.20 μg mL^-1 whereas derivative 5a with unsubstituted aromatic rings showed poor inhibitory potential with an IC₆₀ value of 33.40 ± 0.15 μg mL^-1. The reliable QSAR models were developed using the QSARINS software. The high value of R²_ext = 0.9632 for model IM-9 showed that the built model can be applied to predict the α-amylase inhibitory activity of the untested molecules. A consensus modelling approach was also employed to test the reliability and robustness of the developed QSAR models. Molecular docking and molecular dynamics were employed to validate the bioassay results by studying the conformational changes and interaction mechanisms. A step further, these compounds also exhibited good ADMET characteristics and bioavailability when tested for in silico pharmacokinetics prediction parameters.

QSAR study of tetrahydropteridin derivatives as polo-like kinase 1(PLK1) Inhibitors with molecular docking and dynamics study

PLK1 is the key target for dealing with different cancer because it plays an important role in cell proliferation. According to the regulation of OECD, a QSAR model was developed from a dataset of 68 tetrahydropteridin derivatives. Three descriptors (maxHaaCH, ATSC7i, AATS7m) were considered for the development of the QSAR model. The reliability and predictability of the developed QSAR model were evaluated by various statistical parameters (r² = 0.8213, r²_ext = 0.8771 and CCC_ext = 0.9364). The maxHaaCH descriptor is positively correlated to pIC₅₀ whereas, the ATSC7i and AATS7m are negatively correlated with pIC₅₀. The QSAR model explains all the structural features and shows a good correlation with the activity. Based on molecular modelling techniques, five compounds (D1-D5) were designed. Molecular docking and dynamics studies of the most active compound were performed with PDB ID: 2RKU. The results of the present investigation may be employed to identify and develop effective inhibitors for the treatment of PLK1-related pathophysiological disorders.