Predictive chemoproteomics and functional validation reveal Coeae6g-mediated insecticide cross-resistance in the malaria vector Anopheles gambiae

Sustaining malaria control in Africa is imperilled by the rapid evolution of insecticide resistance in the major vector Anopheles gambiae. Although current genomic and transcriptomic approaches map known resistance alleles, they often lack predictive power to anticipate liabilities to new insecticides. We present a predictive functional chemoproteomic framework integrating competitive activity-based protein profiling with functional validation to identify enzyme-mediated resistance mechanisms before they arise in field populations. Applied to a susceptible Anopheles gambiae strain, fluorophosphonate probe profiling with pirimiphos-methyl-oxon, the bioactive metabolite of the organophosphate pirimiphos-methyl, revealed 18 active serine hydrolases. The carboxylesterase Coeae6g was selected for further functional analysis because it had previously been shown to be associated with pyrethroid and carbamate resistance. Functional assays confirmed Coeae6g confers resistance to pirimiphos-methyl and mediates cross-resistance to malathion, bendiocarb, and permethrin. These findings bridge genotype–phenotype gaps, align with emerging field genomic signatures, and establish a scalable framework to complement genomic surveillance and guide insecticide management in malaria vector control.