Replacement of hydrogen with fluorine within three pairs of structurally similar small molecule inhibitors of heat shock protein 90 (HSP90) resulted in differences in inhibition constants (K(i)) in vitro as well as marked differences in rat intravenous pharmacokinetic profiles. The difference in pharmacokinetic profiles between lower and higher affinity inhibitors (LAIs and HAIs, respectively) was characterized by remarkably different estimates for steady-state volumes of distribution (V(ss): 1.8-2.0 versus 10-13 l/kg) with comparable clearance estimates (3.2-3.5 l/h per kilogram). When the observed V(ss) estimates were compared with the values predicted with the tissue-composition-based model, the observed V(ss) estimates for HAIs were 4- to 8-fold larger than the predicted values, whereas the V(ss) values for LAIs were comparable. Accordingly, a negative relationship between in vitro HSP90 K(i) versus in vivo V(ss) estimates was observed among these inhibitors. We therefore hypothesized that pharmacokinetic profiles of these inhibitors could be characterized by a target-mediated drugdisposition (TMDD) model. In vivo equilibrium dissociation constant (K(D)) estimates for HAIs due to target binding by TMDD model with rapid binding approximation were 1-6 nM (equivalent to 0.3-2 nM free drug), which appeared comparable to the in vitro K(i) estimates (2-3 nM). In vivo KD values of LAIs were not accurately determined by the TMDD model, likely due to nonspecific binding-dependent tissue distribution obscuring TMDD profiles. Overall, these results suggest that the observed large Vss estimates for potent HSP90 inhibitors are likely due to pharmacological target binding.