This study was designed 1) to examine the effects of bloodbrain barrier (BBB) permeability [quantified as permeabilitysurface area product (PS)], unbound fraction in plasma (f u,plasma ), and brain tissue (f u,brain ) on the time to reach equilibrium between brain and plasma and 2) to investigate the drug discovery strategies to design and select compounds that can rapidly penetrate the BBB and distribute to the site of action. The pharmacokinetics of seven model compounds: caffeine, CP-141938 [methoxy-3-[(2-phenyl-piperadinyl-3-aminopropranolol, theobromine, and theophylline in rat brain and plasma after subcutaneous administration were studied. The in vivo log PS and log f u,brain calculated using a physiologically based pharmacokinetic model correlates with in situ log PS (R 2 ϭ 0.83) and in vitro log f u,brain (R 2 ϭ 0.69), where the in situ PS and in vitro f u,brain was determined using in situ brain perfusion and equilibrium dialysis using brain homogenate, respectively. The time to achieve brain equilibrium can be quantitated with a proposed parameter, intrinsic brain equilibrium, where V b is the physiological volume of brain. The in vivo log t 1/2eq,in does not correlate with in situ log PS (R 2 Ͻ 0.01) but correlates inversely with log(PS ⅐ f u,brain ) (R 2 ϭ 0.85). The present study demonstrates that rapid brain equilibration requires a combination of high BBB permeability and low brain tissue binding. A high BBB permeability alone cannot guarantee a rapid equilibration. The strategy to select compounds with rapid brain equilibration in drug discovery should identify compounds with high BBB permeability and low nonspecific binding in brain tissue.The blood-brain barrier (BBB) consists of a continuous layer of endothelial cells joined by tight junctions at the cerebral vasculature. It represents a physical and enzymatic barrier to restrict and regulate the penetration of compounds into and out of the brain and maintain the homeostasis of the brain microenvironment. Brain penetration is essential for compounds where the site of action is within the central nervous system (CNS), whereas BBB penetration needs to be minimized for compounds that target peripheral sites to reduce potential CNS-related side effects. Therefore, it is critical during the drug discovery phase to design and select compounds having appropriate brain penetration properties for drug targets that reside within and outside the CNS (Chen et al., 2003a; Golden and Pollack, 2003).The kinetics of brain penetration consists of the extent of brain equilibrium and the time to achieve brain equilibrium. The extent of brain equilibrium is often quantified by brainplasma partition coefficient (K p ), the ratio of total brain concentration and plasma concentration at steady state. This parameter depends upon drug binding in plasma and brain tissue, the uptake and efflux transporters at BBB, metabolism in the brain, and the bulk flow of cerebrospinal fluid (Hammarlund-Udenaes et al., 1997). If active transporters, brain metabolism and the...