Rational design-aided discovery of novel 1,2,4-oxadiazole derivatives as potential EGFR inhibitors.

A molecular dynamics-based sampling of epidermal growth factor receptor tyrosine kinase (EGFR-TK) was carried out to search for energetically more stable protein, which was then used for molecular docking of a series of 1,2,4-oxadiazole derivatives previously reported from our laboratory. A total of 14 compounds were docked, where compounds 6a and 6b showed better binding to EGFR in silico. Further, physicochemical properties of all the compounds were calculated, which suggested that all the molecules obeyed Lipinski's rule of 5 and had favorable polar surface area and CaCO2 permeability along with the low potential for HERG inhibition. All the compounds were then screened for their ability to produce cytotoxicity in four different cell lines overexpressing EGFR (A549, HCT-116, HEPG2, MCF-7) and one EGFR negative cancer cell line (SW620); at three concentrations: 10, 1, and 0.1 µM. None of the compounds showed activity against SW620, which suggested that the compounds show cytotoxicity through inhibition of EGFR. Compounds that showed promise in this 3-concentration screen were further subjected to multiple dose-response curves to identify the IC50 values for the shortlisted eight compounds. It was encouraging to see 6a and 6b showing the best IC50 values against almost all the cell-lines which further suggests that our design protocol can be applied to optimize this lead (which are currently in the low micromolar range) to design the homologous compounds to achieve the desired potency in the nanomolar range and also to achieve selectivity across a range of kinases.

Identification of 1,2,4-Oxadiazoles-Based Novel EGFR Inhibitors: Molecular Dynamics Simulation-Guided Identification and in vitro ADME Studies.

Background: In this work, we have identified heterocyclic derivatives with 1,2,4 oxadiazole scaffold mimicking the functions of tyrosine kinase inhibitors. Fourteen molecules that displayed the best fit were picked from the library of compounds and studied under in-silico and in-vitro conditions. Four compounds were selected for further cytotoxicity and ADME (Absorption, Distribution, Metabolism, Elimination) profiling showing IC50 (from 8-13 µM) values against EGFR positive cancer cell line (MCF7). Methods: A molecular dynamics simulation study was performed to understand the correlation of non-covalent binding energies with biological activity. The drug-like properties of the selected four compounds (7a, 7b, 7e, and 7m) were evaluated by in-vitro ADME studies. Compounds 7a, 7b, and 7m were the active compounds in the molecular dynamics simulations study. Further, EGFR binding activity was confirmed with EGFRWT and EGFRT790M kinase assay using a luminescence-based method. Results: These compounds (7a, 7b, and 7m) showed activity against EGFRWT and mutant EGFRT790M, exhibiting IC50 values of <10 and <50 micromolar, respectively. These compounds also possess moderate aqueous solubility in 40-70 µg/mL at pH 7.4 and 30-100 µg/mL at pH 4.0. Further, 7a, 7b, and 7m showed balanced lipophilicity with Log D values ranging from 1-3. They demonstrated a good correlation in Caco-2 permeability with Apparent permeability (Papp) 1 to 5 × 10-6 cm/s in comparison with 7e, which was found to be highly lipophilic (Log D >5) and showed high permeability (Papp 17 × 10-6 cm/s). Lastly, all these compounds were moderately stable in liver microsomes at alkaline pH with a half-life of 30-60 min, while at a highly acidic pH (2.0), the compounds were stable up to 15-20 min. Conclusion: Overall, in-vitro ADME results of these molecules showed good drug-like properties, which are well correlated with the in-silico ADME data, making them ideal for developing an oral drug delivery formulation.

Identification of RP-6685, an Orally Bioavailable Compound that Inhibits the DNA Polymerase Activity of Polθ.

DNA polymerase theta (Polθ) is an attractive synthetic lethal target for drug discovery, predicted to be efficacious against breast and ovarian cancers harboring BRCA-mutant alleles. Here, we describe our hit-to-lead efforts in search of a selective inhibitor of human Polθ (encoded by POLQ). A high-throughput screening campaign of 350,000 compounds identified an 11 micromolar hit, giving rise to the N2-substituted fused pyrazolo series, which was validated by biophysical methods. Structure-based drug design efforts along with optimization of cellular potency and ADME ultimately led to the identification of RP-6685: a potent, selective, and orally bioavailable Polθ inhibitor that showed in vivo efficacy in an HCT116 BRCA2-/- mouse tumor xenograft model.

Coumarin-carbazole based functionalized pyrazolines: synthesis, characterization, anticancer investigation and molecular docking.

A series of novel pyrazoline scaffolds from coumarin-carbazole chalcones were synthesized. We explored various acetyl, amide, and phenyl substituents at the N-1 position of the pyrazoline core. The synthesized compounds were characterized by FTIR, 1H-NMR, 13C-NMR, DEPT, and mass spectroscopic techniques. The in vitro cytotoxicity study of all the synthesized compounds was evaluated against HeLa, NCI-H520 and NRK-52E cell lines. Compounds 4a and 7b became the most active compounds and exhibited their potential to arrest the cell cycle progression and induce apoptosis in both the cell lines. In addition, molecular docking studies revealed a higher binding affinity of both the molecules with CDK2 protein. Based on the obtained results, a comprehensive analysis is warranted to establish the role of compounds 4a and 7b as promising cancer therapeutic agents.