Elucidating the molecular basis of ATP synthase inhibition: A virtual screening framework for next-gen selective acaricides

The rational design of pesticides that selectively target harmful species while sparing beneficial organisms remains a major challenge in sustainable agriculture. Progress in this field has been limited by an incomplete understanding of the molecular basis of selectivity and the lack of effective strategies to exploit specific targets. Here, we provide direct molecular evidence that naturally occurring polymorphisms in the CV-a subunit of mitochondrial adenosine 5′-triphosphate (ATP) synthase are the primary determinants of differential sensitivity between pest mites and predatory mites. Structural modeling and sequence analysis identified the key functional residues (Leu 186 in Tetranychus cinnabarinus and Ala 200 in Neoseiulus barkeri ) that modulate the binding affinity of the inhibitor. Using these mechanistic insights, we developed a structure-based virtual screening pipeline to identify selective small-molecule inhibitors, including Vepdegestrant (ARV-471) and ICG-001, that exploit binding-site variation to achieve robust species specificity. This target-centric discovery framework not only advances the mechanistic understanding of ATP synthase inhibition but also establishes a scalable strategy for the rational design of environmentally safe and precision-oriented acaricides.