Accelerated Hit Identification and Optimization of a Novel Class of Cellularly Active QPCT/L Inhibitors

Abstract QPCT and its Golgi-bound analogue QPCTL catalyze the conversion of N-terminal glutamines into pyroglutamates, a modification that influences diverse biological processes, including Aβ oligomerization, chemokine stabilization, and CD47-SIRPα signaling. Consequently, QPCT/L inhibitors have therapeutic potential in Alzheimer’s disease, cancer, and fibrosis. Here, we describe the identification of QPCT/L inhibitors using a virtual screening strategy in which less than 0.1% of our in-house compound library was selected based on similarity to the bioactive conformations of known QPCT/L inhibitors. This approach yielded previously unknown QPCT/L inhibitor chemotypes and substantially accelerated hit discovery. Structure-guided optimization of one quinazolidinone series afforded a potent cellular tool compound BI-3614 with improved activity over previously reported inhibitors, which is available free of charge on opnMe.com. The campaign provided valuable insights, revealing the critical impact of water networks on binding-mode prediction and the profound influence of subtle electronic changes on π-stacking interactions, emphasizing the importance of experimental validation of computational design hypotheses.