In order to reach their pharmacologic targets, successful central nervous system (CNS) drug candidates have to cross a complex protective barrier separating brain from the blood. Being able to predict a priori which molecules can successfully penetrate this barrier could be of significant value in CNS drug discovery. Herein we report a new computational approach that combines two mechanism-based models, for passive permeation and for active efflux by P-glycoprotein, to provide insight into the multiparameter optimization problem of designing small molecules able to access the CNS. Our results indicate that this approach is capable of distinguishing compounds with high/low efflux ratios as well as CNS+/CNS− compounds and provides advantage over estimating P-glycoprotein efflux or passive permeability alone when trying to predict these emergent properties. We also demonstrate that this method could be useful for rank-ordering chemically similar compounds and that it can provide detailed mechanistic insight into the relationship between chemical structure and efflux ratios and/or CNS penetration, offering guidance as to how compounds could be modified to improve their access into the brain. KEYWORDS: P-glycoprotein, CNS drugs, blood brain barrier, BBB, efflux ratio prediction, structure-based ADME prediction O ne of the unique challenges of developing drugs for the central nervous system (CNS) is overcoming the bloodbrain barrier (BBB), a cellular and enzymatic barrier that tightly regulates passage of molecules from blood into the brain. Formed by the endothelium of the cerebral blood capillaries, it has several distinct features. Tight junctions between the endothelial cells prevent paracellular transport or diffusion of molecules in the space between the cells, which effectively limits molecular access to the brain to transcellular permeation.3 Another feature is highly expressed active efflux transporters that expel diffusing molecules back into the blood. Among these, P-glycoprotein (also referred to by its gene name MDR1 or ABCB1) is the most abundant and is known to efflux molecules of a wide variety of shapes and sizes with no one single pharmacophore. 4 A recently published structure of mouse P-glycoprotein, Figure 1, revealed a large hydrophobic cavity in the transmembrane region lined with various hydrophobic and flexible side-chains with no clearly defined subsites, offering an explanation for the broad substrate specificity. 5,6 Several in vitro methods have been developed to predict brain penetration of CNS drug candidates. The most widely used assays employ cell monolayers, such as the MDR-MDCK, that is, Madin-Darby canine kidney cells that have been modified to overexpress P-glycoprotein, which localizes on the apical cell surface. In such assays, transport rates of molecules are measured in both directions, basal-to-apical and apical-tobasal, across the single layer of cells. The ratio or difference of the two rates in opposite directions is used to identify P-gp substrates and to predict...