Design, synthesis and biological evaluation of novel glutaminyl cyclase inhibitors targeting the CD47-SIRPα axis in breast cancer cells.

Glutaminyl cyclase isoforms (gQC and sQC) are zinc-dependent metalloenzymes that catalyze the formation of N-terminal pyroglutamate (pE) in peptides and proteins. In human malignancies, gQC drives tumor immune evasion by enhancing CD47 pyroglutamylation, thereby amplifying its "don't eat me" signaling through interactions with SIRPα on immune cells. This establishes QC (particularly gQC isoform) as a compelling therapeutic target for cancer immunotherapy. In this study, we describe the structure-guided design and SAR optimization of a novel series of benzimidazole-based QC inhibitors aimed at disrupting the CD47-SIRPα immune checkpoint in breast cancer. Among these, compound 30 was identified as a potent dual inhibitor of both gQC and sQC, exhibiting nanomolar inhibitory activity with IC50 values of 0.59 μM (gQC) and 0.83 μM (sQC). Molecular docking and 100 ns molecular dynamics simulations revealed that compound 30 with the catalytic zinc ion and forms multiple stabilizing hydrogen bonds within the QC active site, with simulations further confirming the stability of the binding mode. Biological evaluation demonstrated that compound 30 selectively disrupted the CD47-SIRPα interaction, significantly enhancing macrophage-mediated phagocytosis of tumor cells. These findings highlight compound 30 as a promising lead compound and validate QC catalytic inhibition as a potential therapeutic strategy to counteract immune evasion in breast cancer.