Predicting Efflux Ratios and Blood-Brain Barrier Penetration from Chemical Structure: Combining Passive Permeability with Active Efflux by P-Glycoprotein

Abstract

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...

Development, maintenance and disruption of the blood-brain barrier

“…The number of suitable mouse and rat models is continuously increasing 145 , but alternative model organisms such as grasshopper, fruit fly, and zebrafish also hold promise for studying this complex barrier in vivo while being less labor- and cost-intensive than vertebrate models 146 . In silico approaches can also assist in designing drugs that can efficiently penetrate the BBB – a prerequisite for the successful treatment of CNS diseases 147 , and those studies can help to better understand the functionality of this highly selective barrier. In vitro models represent another sophisticated method for BBB research.…”

Reversing cancer multidrug resistance: insights into the efflux by ABC transports from in silico studies

“…Also addressing passive permeability and ERs, a method able to distinguish between high and low ERs as well as compounds with a higher probability to surpass the blood–brain barrier was proposed . Based on induced‐fit docking scores by GlideXP, the compound's apparent affinity toward P‐gp was determined and combined with an estimation of the relative passive permeability allowing discrimination between molecules with high (81%) or low (71%) efflux rates.…”

GM1 Oligosaccharide Crosses the Human Blood–Brain Barrier In Vitro by a Paracellular Route

“…Bidirectional transport analysis represents a common indirect strategy to evaluate the implication of active transport in drug absorption [36,[43][44][45][46][47]. For this purpose, many indices and coefficients can be calculated and compared with other data to characterize the transport of a drug across an epithelial-type barrier [32,46,[48][49][50][51]. Thus, OligoGM1 was administered to the hBLECs in the basolateral compartment or apical compartment of the transwell system.…”