The natural product neocarzilin A (NCA) was discovered decades ago and despite its potent cytotoxic effects no mode of action studies were performed up to date. Synthesis of neocarzilins A, B, C and a stereoisomer of NCA provided insights into structural preferences as well as access to probes for functional studies. NCA pertained as the most active member and was not only effective against cell proliferation but also migration, a novel and so far overlooked activity. The potent anti-migratory effects could also be confirmed in an in vivo breast carcinoma mouse model. To decipher the molecular mode of action, we applied chemical proteomics for target discovery and revealed that NCA interrogates cancer cell migration via irreversible binding to the largely uncharacterized synaptic vesicle membrane protein VAT-1. A corresponding knockout of the protein confirmed the phenotype and pull-down studies showed the interaction with an intricate network of key migration mediators such as Talin-1. Overall, we introduce VAT-1 as a promising novel target for the development of selective migration inhibitors with the perspective to limit toxicity in absence of anti-proliferative effects.