Discovery and Characterization of Cell-Permeable Inhibitors of <i>Leishmania mexicana</i> CLK1 Using an In-Cell Target Engagement Assay

Leishmaniasis is a neglected tropical disease with limited treatment options and significant unmet medical need. Here, we report the development of a bioluminescence resonance energy transfer (BRET)-based target engagement assay in live cells to identify and validate cell-permeable, ATP-competitive inhibitors of <i>Leishmania mexicana</i> (Lmx)CLK1. LmxCLK2, a closely related paralog with an identical protein kinase domain, is also considered in our analysis. Genetic and pharmacological evidence indicates that simultaneous deletion or inhibition of both LmxCLK1/2 is lethal to the parasite. Using our newly developed assay, we screened a library of human kinase inhibitors and identified WZ8040, a third-generation EGFR inhibitor, as a potent LmxCLK1 ligand. WZ8040 demonstrated robust target engagement in both promastigotes and macrophage-internalized amastigotes, with an EC₅₀ value of 2.1 μM for amastigote killing and minimal toxicity to host macrophages. Biochemical assays confirmed that WZ8040 covalently binds and inhibits LmxCLK1, with mass spectrometry identifying Cys172 as the primary site of modification. Genetic validation using overexpression and knockout lines supports LmxCLK1 as the primary target of WZ8040. However, the retained activity of WZ8040 in mutant lines with the Cys172Ala substitution suggests that covalent binding is not essential for compound efficacy. Our findings highlight the utility of BRET-based assays for target validation in kinetoplastid parasites and underscore the potential of CLK1/2 as druggable kinases in <i>Leishmania</i>. This integrated approach provides a framework for accelerating the discovery of novel antileishmanial agents through target engagement-guided strategies.