Fragment-based investigation of thiourea derivatives as VEGFR-2 inhibitors: a cross-validated approach of ligand-based and structure-based molecular modeling studies

Discovery of Novel 1-Phenylpiperidine Urea-Containing Derivatives Inhibiting β-Catenin/BCL9 Interaction and Exerting Antitumor Efficacy through the Activation of Antigen Presentation of cDC1 Cells

Aberrant activation of the Wnt/β-catenin signaling is associated with tumor development, and blocking β-catenin/BCL9 is a novel strategy for oncogenic Wnt/β-catenin signaling. Herein, we presented two novel β-catenin variations and exposed conformational dynamics in several β-catenin crystal structures at the BCL9 binding site. Furthermore, we identified a class of novel urea-containing compounds targeting β-catenin/BCL9 interaction. Notably, the binding modalities of inhibitors were greatly affected by the conformational dynamics of β-catenin. Among them, 28 had a strong affinity for β-catenin (Kd = 82 nM), the most potent inhibitor reported. In addition, 13 and 35 not only activate T cells but also promote the antigen presentation of cDC1, showing robust antitumor efficacy in the CT26 model. Collectively, our study demonstrated a series of potent small-molecule inhibitors targeting β-catenin/BCL9, which can enhance antigen presentation and activate cDC1 cells, delivering a potential strategy for boosting innate and adaptive immunity to overcome immunotherapy resistance.

In silico insights into design of novel VEGFR-2 inhibitors: SMILES-based QSAR modelling, and docking studies on substituted benzo-fused heteronuclear derivatives

Eight QSAR models (M1-M8) were developed from a dataset of 118 benzo-fused heteronuclear derivatives targeting VEGFR-2 by Monte Carlo optimization method of CORALSEA 2023 software. Models were generated with hybrid optimal descriptors using both SMILES and Graphs with zero- and first-order Morgan extended connectivity index from a training set of 103 derivatives. All statistical parameters for model validation were within the prescribed limits, establishing the models to be robust and of excellent quality. Among all models, split-2 of M5 was the best-fit as reflected by   r v a lidation 2 ,   Q v a lidation 2 and MAE . Mechanistic interpretation of this model assisted the identification of structural descriptors as promoters and hinderers for VEGFR-2 inhibition. These descriptors were utilized to design novel VEGFR-2 inhibitors (YS01-YS07) by bringing modifications in compound MS90 in the dataset. Docking of all designed compounds, MS90 and sorafenib with VEGFR-2 binding site revealed favourable binding interactions. Docking score of YS07 was higher than that of MS90 and sorafenib. Molecular dynamics simulation study revealed sustained interactions of YS07 with key amino acids of VEGFR-2 at a run time of 100 ns. This study concludes the development of a best fit QSAR model which can assist the design of new anticancer agents targeting VEGFR-2.

Computational evaluation of 1,2,3-triazole-based VEGFR-2 inhibitors: anti-angiogenesis potential and pharmacokinetic assessment

The vascular endothelial growth factor (VEGF) and its cell surface receptor, as well as the human VEGFR-2 domain kinase, are some of the signaling pathways that have received the most attention in this field. This study aimed to identify novel molecules as VEGFR-2 inhibitors using 3D-QSAR modeling based on 1,2,3-triazole. Docking studies and dynamic simulations were performed to analyze novel interactions with the inhibitors and validate the molecular docking, dynamic simulations, and ADMET analyses. The optimized CoMSIA/SEH model showed good statistical results, and molecular docking and molecular dynamics simulations demonstrated stability of M3 ligand with the receptor and provided insight into ligand-receptor interactions. The newly developed compounds performed well in ADMET evaluations and showed promising results using Lipinski's rule of five, suggesting that the molecule M3 could be a useful anti-angiogenesis agent. In conclusion, this study provides insights into the structure-activity relationship of VEGFR-2 inhibitors and identifies M3 as a potential new anti-angiogenesis drug. The methodology used in this study can be applied to other similar drug targets to discover new and potent inhibitors.Communicated by Ramaswamy H. Sarma.

New nicotinamide derivatives as potential anticancer agents targeting VEGFR-2: design, synthesis, in vitro, and in silico studies

Herin, new nicotinamide candidates were designed and synthesized as VEGFR-2 inhibitors. In vitro antiproliferative activities were assessed against MCF-7, HepG-2 and HCT-116 cancer cell lines. The top cytotoxic members 15a, 15b, 16, 18a, and 18b were estimated against their selected target (VEGFR-2). Further mechanistic tests were studied for the most potent cytotoxic candidate 18a, these studies revealed the ability of compound 18a to hinder the progression of HCT-116 cells at S and Pre-G1phases besides boosting early and late apoptosis. Also compound 18a was found to significantly decrease the levels immunomodulatory proteins TNF-α and IL-6 while showing a four-fold rise in an apoptotic marker caspase-3 when compared to control cells. The therapeutic index of the designed derivatives was evaluated by computational ADMET and toxicity calculations as well as their potentiality to occupy the VEGFR-2 active site was signposted by molecular docking assessments. Finally, molecular dynamic simulation studies of compound 18a-VEGFR-2 complex indicated the high steadiness of compound 18a in the VEGFR-2 active site. This study presents compound 18a as a lead candidate that can be optimized to get a strong VEGFR-2 inhibitor.Communicated by Ramaswamy H. Sarma.