Targeting PfCLK3 with Covalent Inhibitors: A Novel Strategy for Malaria Treatment

Malaria continues to pose a significant global health threat, with the number of deaths exceeding 600,000 annually. Acquired resistance to frontline drugs by the most deadly parasite, Plasmodium falciparum, means this number is increasing each year. There is therefore an urgent unmet need for new medicines with novel mechanisms of action. In this work, we solved the co-crystal structure of the essential malarial kinase PfCLK3 with the reversible inhibitor TCMDC-135051 1. This facilitated the rational design of covalent inhibitors of this validated drug target. An allosteric cysteine residue (Cys368) that is poorly conserved in the human kinome was targeted to improve the selectivity of hit molecules. Structure-based drug design yielded chloroacetamide 4, which displays low nanomolar potency and covalent inhibition in both recombinant protein and P. falciparum killing assays. Efficacy in parasites was maintained when 4 was washed out 6 hours after exposure. Compound 4 showed significantly improved kinase selectivity relative to TCMDC-135051 1, and cell viability experiments in HepG2 cultures also demonstrated an over 500-fold selectivity index relative to P. falciparum parasites. To our knowledge, compound 4 represents the first covalent inhibitor of a malarial kinase. Its covalency, efficacy and selectivity for PfCLK3 makes it a promising lead in the search for a single-dose cure for malaria.