Structure-based design of new anticancer N3-Substituted quinazolin-4-ones as type I ATP-competitive inhibitors targeting the deep hydrophobic pocket of EGFR

Abstract

Epidermal growth factor receptor (EGFR) is amongst the earliest targeted kinases by small-molecule inhibitors for the management of EGFR-positive cancer types. While a few inhibitors are granted FDA approval for clinical use, discovery of new inhibitors is still of merit to enhance ligand-binding stability and subsequent enzyme inhibition. Thus, a structure-based design approach was adopted to devise a new series of twenty-nine N3-substituted quinazolin-4-ones as type I ATP-competitive inhibitors targeting the deep hydrophobic pocket of EGFR. The most active compounds demonstrated potent IC₅₀s against MDA-MB-231 and HepG2 cancer cells being comparable to or better than the reference drugs erlotinib and lapatinib. IC₅₀s of 5f and 15a against MDA-MB-231 were 3.34 and 4.99, whilst those against HepG2 were 6.37 and 2.18 μM, respectively. Also, members of this series demonstrated selective cytotoxicity against cancer cell lines showing low toxicity on human skin fibroblast normal cells hFB-4. Both 5f and 15a also effectively inhibited EGFR with sub-micromolar respective IC₅₀s of 0.07 and 0.12 μM. The two derivatives halted the cell cycle progression of treated cancer cells and induced apoptosis as affirmed by flow cytometry along with RT-PCR-determined overexpression of the pro-apoptotic genes p53, Caspase 3, and Bax. Notably, docking and molecular dynamics simulations of members of this series of quinazolin-4-one derivatives showed that analogs with a short linker at the N3 position of the quinazoline ring exemplified by 5f bind to the active form of EGFR with their terminal aryl ring dwelling in the BPI pocket similar to erlotinib, while those with a longer linker represented by 15a bind to the inactive form in a comparable manner to lapatinib lodging the terminal phenyl in the BPII pocket.

Keywords: Anticancer; Cytotoxic agents; Deep hydrophobic pocket; EGFR ATP-Competitive inhibitors.