Proteolysis-targeting chimeras (PROTACs) offer a novel therapeutic strategy for degrading disease-causing proteins, but designing effective degraders remains challenging. PROTACs function by inducing a ternary complex between the target protein and an E3 ligase, requiring structural insights for rational design. Key factors include linker optimization, attachment points, and warhead refinement. Computational approaches, particularly protein-protein docking, are essential for modeling ternary complexes and predicting critical interactions. However, existing docking methods struggle with cereblon (CRBN)-based ternary complexes. To address this, we introduce a computational approach combining HADDOCK protein-protein docking with induced fit PROTAC docking. Validated against 26 crystal structures from the Protein Data Bank (PDB), this method demonstrated high accuracy, especially for CRBN-based complexes. Additionally, molecular dynamics (MD) simulations of CRBN-BRD4-BD1 complexes (PDB IDs 6BN7, 6BOY) provided insights into complex stability through buried surface area and radius of gyration calculations. This validated approach was then applied to five Ataxia telangiectasia and RAD3-related (ATR) kinase PROTACs, enabling modeling in the absence of experimental structures. Our method provides a robust framework for optimizing and designing novel PROTACs targeting diverse proteins.

New quinazoline derivatives were designed and synthesized to target VEGFR-2, aiming to identify potential anticancer agents. The synthesized compounds underwent in vitro screening to evaluate their cytotoxic effects across 60 cancer cells following the NCI protocol. The most promising derivatives, 3i and 3j, underwent further evaluation via a five-dose test to assess broad-spectrum anticancer activity. Their VEGFR-2 inhibitory potential was compared to sorafenib. Cell cycle analyses, annexin V-FITC, and apoptotic markers were used to examine HT-29 colon cancer cells after treatment with 3j for cell cycle arrest and apoptosis induction. Molecular docking and MD simulations explored binding interactions, while ADMET studies assessed pharmacokinetics. Compounds 3i and 3j exhibited potent to moderate cytotoxic activity, with compound 3j showing the highest activity against colon cancer cell lines (GI₅₀ = 3.29 μM). Both compounds demonstrated promising VEGFR-2 inhibitory activity (IC₅₀ = 0.120 and 0.197 µM, respectively), comparable to sorafenib (IC₅₀ = 0.088 µM). Cell cycle analysis displayed G1 phase arrest and pro-apoptotic effects. Docking studies confirmed favorable VEGFR-2 binding affinity (-7.57 and -7.83 kcal/mol). ADMET profiling indicated promising drug-like properties. Compounds 3i and 3j exhibit promising VEGFR-2 inhibitory properties and significant anticancer activity, warranting further investigation.

The oncogenic transcription factor MYC is a key driver of the development and progression of various types of cancer, but its intrinsically disordered structure and dependence on protein–protein interactions make it a difficult therapeutic target. Proteolysis-targeting chimeras (PROTACs) are bifunctional molecules that can induce the selective degradation of disease-relevant proteins. In this study, we report the synthesis and biological testing of a series of novel MYC-targeted PROTACs derived from the MYC inhibitor EN4. These ligands were conjugated to cereblon (CRBN) or von Hippel–Lindau (VHL) E3 ligase recruiters using different linker architectures and connection sites. The resulting PROTACs were synthesized in high purity and characterized analytically. Cellular evaluation in HEK293T, Panc-1 and HCT-116 cancer cells revealed only moderate reductions in cell viability. Unfortunately, none of the synthesized PROTACs showed detectable MYC degradation at biologically relevant concentrations. Testing the stability of the PROTACs in microsomes showed rapid degradation, which may be a reason for the observed inactivity in cells. These results underscore the significant challenges associated with the targeted protein degradation of intrinsically disordered transcription factors such as MYC. Further studies are necessary to identify additional causes for the lack of MYC degradation and to optimize the chemical structures accordingly.

The Ataxia telangiectasia and RAD3-related (ATR) kinase is a key regulator of DNA replication stress responses and DNA-damage checkpoints. Several potent and selective ATR inhibitors are reported and four of them are currently in clinical trials in combination with radio- or chemotherapy. Based on the idea of degrading target proteins rather than inhibiting them, we designed, synthesized and biologically characterized a library of ATR-targeted proteolysis targeting chimera (PROTACs). Among the synthesized compounds, the lenalidomide-based PROTAC 42i was the most promising. In pancreatic and cervix cancer cells cancer cells (MIA PaCa-2), it reduced ATR to 40% of the levels in untreated cells. 42i selectively degraded ATR through the proteasome, dependent on the E3 ubiquitin ligase component cereblon, and without affecting the associated kinases ATM and DNA-PKcs. 42i may be a promising candidate for further optimization and biological characterization in various cancer cells.