Tyrosine kinase BCR-ABL1 is the underlying cause of chronic myeloid leukaemia (CML). The frontline treatment for CML patients rely on ATP-competitive tyrosine kinase inhibitors (TKIs). Over the course of treatment, 20−30% of patients manifest drug resistance associated with point mutations within the drug-binding site of BCR-ABL1. We developed a strategy to overcome drug resistance by targeting the substrate-binding site of BCR-ABL1 kinase instead.1 In the current study, a substrate-based kinase inhibitor was designed by grafting a sequence derived from the optimal substrate abltide onto a reengineered cyclotide scaffold,2 namely MCo-CTP, with improved cellular internalisation efficiency. The lead molecule displayed antiproliferative activities against CML cell lines including cells harboring multidrug-resistant mutations, T315I, V299L or G250E, in the low micromolar range, while showed no effect on peripheral blood mononuclear cells and other cancerous cell lines including HeLa and MM96L. The serum stability and cell internalisation studies confirmed that the cyclotide scaffold provides enzymatic stability and cell-penetrating properties to the lead molecule. Taken together, our study highlights that incorporating an abltide-derived sequence onto a reengineered cyclotide framework could potentially be developed as a new strategy to tackle CML.