Structure- and Ligand-Based Discovery of Novel Non-Arginine-Based DDAH1 Inhibitors with Anti-Triple-Negative Breast...

Dimethylarginine dimethylaminohydrolase 1 (DDAH1) regulates nitric oxide (NO) synthesis, a key mediator of abnormal neovascularisation, i.e., vasculogenic mimicry, in triple negative breast cancer (TNBC). DDAH1 inhibitors have shown to suppress vasculogenic mimicry; however, they are mostly arginine-based and have limited bioavailability. In this study, we used ligand- and structure-based approaches to discover novel nonarginine-based DDAH1 inhibitors. Computational screening of over 1 million compounds led to the selection of 52 candidates for experimental testing, of which four showed more than 40% inhibition of DDAH1, with two inhibitors, A8 and C8, having IC₅₀ values below 180 μM. In triple-negative breast cancer cells, A8 and C8 significantly suppressed vasculogenic mimicry equivalent to previously known potent DDAH1 inhibitors. Molecular dynamics simulations of A8 in complex with DDAH1 demonstrate significant remodelling of the binding pocket, leading to novel binding interactions with DDAH1 not observed with previously reported inhibitors.