We report the results of a three-dimensional quantitative structure-activity relationship (3D-QSAR)/ comparative molecular field analysis (CoMFA) of the activity of IS bisphosphonates and imidodiphosphate in the inhibition of a mung bean (Vigna radiata L.) vacuolar proton pumping pyrophosphatase (V/H+-PPase; EC 3.6.1.1). We find an experimental versus QSAR predicted pK(i)(app) R-2 value of 0.89, a cross-validated R-2 = 0.77, and a bootstrapped R-2 = 0.89 for 18 bisphosphonates plus imidodiphosphate over the 1.3 muM to 425 muM range of K-i(app) values. We also demonstrate that this approach has predictive utility (a 0.26 pK(i)(app) rms error for three test sets of 3 activity predictions each), corresponding to about a factor of two error in K-i(app) prediction. The 3D-QSAR/CoAWA approach provides a quantitative method for predicting the activity of V/H+-PPase inhibitors and is likely to be of use in the design of novel pharmacological agents since all of the major human disease-causing parasitic protozoa contain large levels of pyrophosphate, together with V-type proton-pumping pyrophosphatases located in plant-like vacuoles (acidocalcisomes), which are absent in their mammalian hosts.