Targeting CAPON to modulate the CAPON–NOS Axis: a computational approach

The carboxy-terminal PDZ ligand of neuronal nitric oxide synthase (CAPON) serves as a critical regulatory protein controlling nitric oxide (NO) signaling across multiple physiological and pathological processes which encompass neurological, cardiac and metabolic functions. These diverse physiological roles of CAPON marks it as a key therapeutic target for conditions associated with its dysregulation. Despite this therapeutic potential there are no specific CAPON or nNOS/CAPON modulators which have been developed to date, highlighting a significant gap in targeted drug discovery. Herein, we report the first strategy specifically focused on disrupting the nNOS/CAPON protein-protein interface. Through screening of a chemical library composed of 4.6 million compounds and 13 molecular dynamics simulations, nine potential hit compounds were identified. This work represents a foundational step toward developing targeted therapies for CAPON-mediated disorders. Beyond identifying these promising hits, our approach introduces three python-based drug discovery tools: (i) a Python-based toolset for NMR structural analysis, clustering and visualization, (ii) accelerated ligand preparation toolkit, (iii) Automated hit prioritization pipeline based on multi-method consensus scoring approach that takes in account docking scores and MMGBSA. Collectively, these tools form an accelerated drug discovery pipeline that automates most of the virtual screening process and offers a scalable computational framework to support future drug discovery targeting protein-protein interactions.