Structure of human drug transporters OATP1B1 and OATP1B3.

The organic anion transporting polypeptides OATP1B1 and OATP1B3 are membrane proteins that mediate uptake of drugs into the liver for subsequent conjugation and biliary excretion, a key step in drug elimination from the human body. Polymorphic variants of these transporters can cause reduced drug clearance and adverse drug effects such as statin-induced rhabdomyolysis, and co-administration of OATP substrates can lead to damaging drug-drug interaction. Despite their clinical relevance in drug disposition and pharmacokinetics, the structure and mechanism of OATPs are unknown. Here we present cryo-EM structures of human OATP1B1 and OATP1B3 bound to synthetic Fab fragments and in functionally distinct states. A single estrone-3-sulfate molecule is bound in a pocket located in the C-terminal half of OATP1B1. The shape and chemical nature of the pocket rationalize the preference for diverse organic anions and allow in silico docking of statins. The structure of OATP1B3 is determined in a drug-free state but reveals a bicarbonate molecule bound to the conserved signature motif and a histidine residue that is prevalent in OATPs exhibiting pH-dependent activity.

Cryo-EM structures of human organic anion transporting polypeptide OATP1B1.

Members of the solute carrier organic anion transporting polypeptide (OATPs) family function as transporters for a large variety of amphipathic organic anions including endogenous metabolites and clinical drugs, such as bile salts, steroids, thyroid hormones, statins, antibiotics, antivirals, and anticancer drugs. OATP1B1 plays a vital role in transporting such substances into the liver for hepatic clearance. FDA and EMA recommend conducting in vitro testing of drug-drug interactions (DDIs) involving OATP1B1. However, the structure and working mechanism of OATPs still remains elusive. In this study, we determined cryo-EM structures of human OATP1B1 bound with representative endogenous metabolites (bilirubin and estrone-3-sulfate), a clinical drug (simeprevir), and a fluorescent indicator (2',7'-dichlorofluorescein), in both outward- and inward-open states. These structures reveal major and minor substrate binding pockets and conformational changes during transport. In combination with mutagenesis studies and molecular dynamics simulations, our work comprehensively elucidates the transport mechanism of OATP1B1 and provides the structural basis for DDI predictions involving OATP1B1, which will greatly promote our understanding of OATPs.

Development of predictive QSAR models for the substrates/inhibitors of OATP1B1 by deep neural networks.

The organic anion transporting polypeptide 1B1 (OATP1B1) is an important hepatic uptake transporter. Inhibition of its normal function could lead to drug-drug interactions. In silico prediction is an effective means to identify potential OATP1B1 inhibitors and quantitative structure-activity relationship (QSAR) modeling is extensively used. As the structures of OATP1B1 substrates/inhibitors are quite diverse, machine learning based methods should be a good option for their QSAR analysis. In the present study, deep neural networks (DNNs) were employed to develop QSAR models for the substrates/inhibitors of OATP1B1 with different molecular fingerprints. Our results showed that QSAR models based on 4-hidden layer DNNs and ECFP4/FCFP4 fingerprints had the best generalization performance. The correlation coefficients (R2) of test set for ECFP4 and FCFP4 models were 0.641 and 0.653, respectively. Model application domain (AD) was calculated with Euclidean distance-based method, and AD could improve the performance of ECFP4 model but has little effect on FCFP4 model. Finally, the prediction of additional 8 compounds that not included in the data set further demonstrated that our QSAR models had a good predictive ability (averaged prediction accuracy >92%). The developed QSAR models could be used to screen large data sets and discover novel inhibitors for OATP1B1.

Organic Anion Transporting Polypeptide 1B1 Is a Potential Reporter for Dual MR and Optical Imaging.

Membrane proteins responsible for transporting magnetic resonance (MR) and fluorescent contrast agents are of particular importance because they are potential reporter proteins in noninvasive molecular imaging. Gadobenate dimeglumine (Gd-BOPTA), a liver-specific MR contrast agent, has been used globally for more than 10 years. However, the corresponding molecular transportation mechanism has not been validated. We previously reported that the organic anion transporting polypeptide (OATP) 1B3 has an uptake capability for both MR agents (Gd-EOB-DTPA) and indocyanine green (ICG), a clinically available near-infrared (NIR) fluorescent dye. This study further evaluated OATP1B1, another polypeptide of the OATP family, to determine its reporter capability. In the OATP1B1 transfected 293T transient expression model, both Gd-BOPTA and Gd-EOB-DTPA uptake were confirmed through 1.5 T MR imaging. In the constant OAPT1B1 and OATP1B3 expression model in the HT-1080 cell line, both HT-1080-OAPT1B1 and HT-1080-OATP1B3 were observed to ingest Gd-BOPTA and Gd-EOB-DTPA. Lastly, we validated the ICG uptake capability of both OATP1B1 and OATP1B3. OAPT1B3 exhibited a superior ICG uptake capability to that of OAPT1B1. We conclude that OATP1B1 is a potential reporter for dual MR and NIR fluorescent molecular imaging, especially in conjunction with Gd-BOPTA.

Investigation of the interactions between flavonoids and human organic anion transporting polypeptide 1B1 using fluorescent substrate and 3D-QSAR analysis.

Organic anion transporting polypeptide 1B1 (OATP1B1) is a key hepatic uptake transporter whose inhibition could lead to adverse drug-drug and drug-food interactions. Flavonoids are widely distributed in food and beverages and thus our bodies are frequently exposed to them. Therefore, investigation of the interactions between OATP1B1 and flavonoids could be of great significance. In the present study, 25 common flavonoids were investigated for their interactions with OATP1B1 using the fluorescent substrate 2',7'-dichlorofluorescein (DCF) and three-dimensional quantitative structure-activity relationship (3D-QSAR) analysis. Kinetic study showed that OATP1B1-mediated DCF uptake exhibited a monophasic saturation kinetics with a Km value of 9.7 ± 2.4 µM. Inhibition assay for flavonoids on OATP1B1-mediated DCF uptake was performed and their IC50 values were determined upon which reliable and predictive CoMFA (q2 = 0.604, r2 = 0.841) and CoMSIA (q2 = 0.534, r2 = 0.807) models were developed. Our experimental and computational results showed that flavonoid aglycones interacted with OATP1B1 much stronger than their glycosides such as 3-O- and 7-O-glycosides as bulky hydrophilic and hydrogen-bond forming substituents at C-3 and C-7 positions on rings A and C were unfavorable for their binding. On the other hand, the presence of hydrogen-bond forming groups on ring B was beneficial as long as the number of hydroxyl groups was not >2. Our results also indicated that flavones usually interacted with OATP1B1 much stronger than their 3-hydroxyflavone counterparts (flavonols). The obtained information and 3D-QSAR models could be useful for elucidating and predicting the interactions between flavonoids and human OATP1B1.

Gly45 and Phe555 in Transmembrane Domains 1 and 10 Are Critical for the Activation of Organic Anion Transporting Polypeptide 1B3 by Epigallocatechin Gallate.

Organic anion transporting polypeptides (OATPs) 1B1 and 1B3 are two highly homologous transporters expressed in the human liver. However, epigallocatechin gallate (EGCG), which is the most predominant catechin in green tea, has opposite effects on the function of OATP1B1 and OATP1B3. In the present study, the critical structural domains and amino acid residues for the activation of OATP1B3 by EGCG have been determined by characterizing the function of a series of OATP1B3-derived chimeric transporters, site-directed mutagenesis, and kinetic studies. Our results showed that G45 and F555 in transmembrane domains 1 and 10 are the most important amino acid residues for OATP1B3 activation. Kinetic studies showed that the activation of OATP1B3 by EGCG at a low substrate concentration was due to its increased substrate binding affinity. However, EGCG caused increased Km and decreased Vmax for 1B3-G45A and 1B3-F555H. The flexibility at position 45 and aromaticity at position 555 might be important for OATP1B3 activation. While 1B3-G45A and 1B3-F555H could not be activated by EGCG, their transport activity for EGCG was comparable to that of wild-type OATP1B3. In conclusion, the present study elucidated the molecular mechanism for OATP1B3 activation by EGCG.

The intracellular NPxY motif is critical in maintaining the function and expression of human organic anion transporting polypeptide 1B1.

Organic anion transporting polypeptides (OATPs, gene symbol SLCO) mediate sodium-independent transport of endogenous compounds such as bile salts, hormones and their conjugates as well as toxins and drugs. OATP1B1 is the major OATP specifically expressed at the basolateral membrane of human hepatocytes and many clinically important drugs have been shown to be substrates of the transporter. According to the computer-based hydropathy analysis, a large intracellular loop 3 (IL3) is situated between transmembrane domain 6 and 7 of OATPs, in which a conserved NPxY motif is found. In the current study, HEK293 cells expressing the HA-tagged OATP1B1 was utilized to investigate the role of the NPxY motif for the function and expression of the transporter. Alanine replacement of N335 or P336 retained substantial uptake function; while simultaneous mutation of these residues resulted in a double mutant that lost almost all the transport activity. On the other hand, Y338A showed >80% reduction for estrone-3-sulfate uptake. Plasma membrane protein analysis revealed that N335/P336A completely lost its cell surface protein expression; while that of Y338A is dramatically reduced. Further investigation with pharmacological inhibitors and immunocytochemistry demonstrated that N335/336A is detained in the Golgi apparatus and Y338A exhibited accelerated protein degradation rate compared to that of the wild-type. Conservative replacement of Y338 with phenylalanine fully recovered uptake and expression of the transporter. In summary, a new role was observed for the NPxY motif located in the IL3 of OATP1B1, which may affect processing and stability of the transporter.

In Silico and in Vitro Assessment of OATP1B1 Inhibition in Drug Discovery.

The organic anion-transporting polypeptide 1B1 transporter belongs to the solute carrier superfamily and is highly expressed at the basolateral membrane of hepatocytes. Several clinical studies show drug-drug interactions involving OATP1B1, thereby prompting the International Transporter Consortium to label OATP1B1 as a critical transporter that can influence a compound's disposition. To examine OATP1B1 inhibition early in the drug discovery process, we established a medium-throughput concentration-dependent OATP1B1 assay. To create an in silico OATP1B1 inhibition model, deliberate in vitro assay enrichment was performed with publically known OATP1B1 inhibitors, noninhibitors, and compounds from our own internal chemistry. To date, approximately 1200 compounds have been tested in the assay with 60:40 distribution between noninhibitors and inhibitors. Bagging, random forest, and support vector machine fingerprint (SVM-FP) quantitative structure-activity relationship classification models were created, and each method showed positive and negative predictive values >90%, sensitivity >80%, specificity >95%, and Matthews correlation coefficient >0.8 on a prospective test set indicating the ability to distinguish inhibitors from noninhibitors. A SVMF-FP regression model was also created that showed an R2 of 0.39, Spearman's rho equal to 0.76, and was capable of predicting 69% of the prospective test set within the experimental variability of the assay (3-fold). In addition to the in silico quantitative structure-activity relationship (QSAR) models, physicochemical trends were examined to provide structure activity relationship guidance to early discovery teams. A JMP partition tree analysis showed that among the compounds with calculated logP >3.5 and ≥1 negatively charged atom, 94% were identified as OATP1B1 inhibitors. The combination of the physicochemical trends along with an in silico QSAR model provides discovery project teams a valuable tool to identify and address drug-drug interaction liability due to OATP1B1 inhibition.

Analysis of amino acid residues in the predicted transmembrane pore influencing transport kinetics of the hepatic drug transporter organic anion transporting polypeptide 1B1 (OATP1B1).

The hepatic uptake transporters OATP1B1 (SLCO1B1) and OATP1B3 (SLCO1B3) mediate the uptake of endogenous metabolites and drugs from blood into hepatocytes. Alterations of transport function are accompanied with variations in drug plasma concentrations and the risk of adverse drug effects. Thus, knowledge on amino acids determining substrate recognition or transport kinetics are important to predict alterations in transport kinetics. Therefore, we analyzed the charged amino acids His54 and Tyr169, both located at the extracellular entry of the predicted transmembrane pore of OATP1B1. Based on a computational analysis we established HEK293 cell lines overexpressing the mutant OATP1B1 proteins HEK-OATP1B1p.H54Q, -p.H54A, -p.Y169H and -p.Y169A and analyzed protein expression, localization and transport kinetics of the four OATP1B1 substrates bromosulfophthalein, estradiaol-17ß-glucuronide, taurocholate and pravastatin. Consequences on transport were detected for all mutants and these were different for each amino acid exchange and for each substrate tested. For example, the exchange H54Q resulted in reduced transport for BSP (78% of wildtype OATP1B1 transport at 0.05µM, P<0.01) with reduced affinity to this substrate (Km value increases from 0.76µM to 8.04µM) but in stimulated E217ßG transport (138% compared to wildtype transport at 10µM, P<0.001). Investigating amino acid exchanges located at the extracellular entry of the transport pore of the OATP1B1 protein we demonstrated that these residues are involved in modulating transport kinetics and this participation strongly depends on the substrate and not on the physicochemical character of the investigated amino acid.

A novel biochromatographic Oatp2 column to study the transmembrane transport of statins.

In a previous paper, using a biophysical model system to study the passive diffusion of the statin molecules through the cell membrane, our group demonstrated that statins could cross biological membrane by passive diffusion (Sarr et al. [40]). However, in the liver, the uptake of statins would also be mediated by organic anion transporting polypeptides (Oatps) like Oatp2 a member of this family. Thus, a novel biochromatographic approach was developed in our laboratory to study the transmembrane transport of statins and an Oatp2 inhibitor via this carrier family. For this, the Oatp2 protein was immobilized via its amino groups on a chromatographic support using an "in situ" immobilization technique. For the first time, using this novel biochromatographic concept, the effect of magnesium chloride salt (MgCl(2)) on the pharmacomolecule-Oatp2 binding was investigated. It was shown an Mg(2+)-dependent pharmacomolecule-protein association and a potential facilitated diffusion of these pharmacomolecules into biological membrane. This association process was due to the central positive potential pore of the Oatp2. Indeed, at pH 7.4, all the pharmacomolecules studied were ionized (i.e. negatively charged) and so interact with this positive potential pore. However, an increase of the Mg(2+) concentration led a decrease of the pharmacomolecule-Oatp2 association attributed to ion pair formations between the Mg(2+) cation and molecules. Moreover, the decrease of this affinity could be explained by an ion attraction between the Cl(-) anion of the MgCl(2) salt and the positively charged pore of the protein. This novel biochromatographic column could be useful to find a specific reversible inhibitor for these transporters and so open new perspectives to be investigated.

Functional analysis of the extracellular cysteine residues in the human organic anion transporting polypeptide, OATP2B1.

Organic anion transporting polypeptide (OATP) superfamily member 2B1 (OATP2B1) mediates the uptake of steroid hormone precursors and selected drugs in the placenta, liver, mammary gland, brain, and intestine. This action is modulated by sulfhydryl reagents. Common to all OATPs is a large extracellular loop between transmembrane domains IX and X with 10 conserved cysteines. To elucidate the structure-function relationship of this cysteine rich ectodomain, a truncated OATP2B1 lacking 10 extracellular cysteines (OATP2B1(Delta489-557)) and 10 OATP2B1 mutants containing individual Cys-to-Ala substitutions were generated and expressed in CHO-K1 cells. The immunolocalization, cell-surface expression, transport activity, and free cysteine labeling with N-biotinoylaminoethylmethane-thiosulfonate of mutant proteins and wild-type OATP2B1 were compared. OATP2B1(Delta489-557) accumulated intracellularly. Nine Cys-to-Ala substitutions, C489A, C495A, C504A, C516A, C520A, C539A, C541A, C553A, and C557A, were misprocessed, appearing predominantly as core-glycosylated, 60-kDa proteins and as 180-kDa complexes. Only C493A was a fully glycosylated 75-kDa protein expressed at the cell surface. Thapsigargin partially corrected the misprocessing of mutants. Compared with OATP2B1, C493A and C557A transported estrone-3-sulfate and dehydroepiandrosterone sulfate less efficiently, whereas all other mutants were functionally impaired. MTSEA labeled free cysteines in all Cys-to-Ala mutants but not in OATP2B1, suggesting that all 10 extracellular cysteines are normally disulfide-bonded. Our findings show that the trafficking and function of OATP2B1 is vulnerable to changes in the cysteine residues of extracellular loop IX-X.

Comparative pharmacophore modeling of organic anion transporting polypeptides: a meta-analysis of rat Oatp1a1 and human OATP1B1.

The organic anion transporting polypeptides OATPs are key membrane transporters for which crystal structures are not currently available. They transport a diverse array of xenobiotics and are expressed at the interface of hepatocytes, renal tubular cells, enterocytes, and the choroid plexus. To aid the understanding of the key molecular features for substrate-transporter interactions, pharmacophore models were produced for the two OATPs that have been most extensively studied, namely rat Oatp1a1 and human OATP1B1. Literature data from Chinese hamster ovary, HeLa, human embryonic kidney 293 cells, and Xenopus laevis oocytes were used to construct pharmacophores for each individual transporter which were later merged to show similarities across cell lines for the same transporter. Additionally, meta-pharmacophores were generated from the combined datasets of each cell system used with the same transporter. The pharmacophores for each transporter consisted of hydrogen bond acceptor and hydrophobic features. There was good agreement between the merged and meta-pharmacophores containing two hydrogen bond acceptors and two or three hydrophobic features for Oatp1a1 and OATP1B1. External test sets were used to validate the individual pharmacophores. The meta-pharmacophores were also used to make predictions for molecules not included in the models and provided new molecular insight into the key features for these OATP transporters. This approach can be extended to other transporters for which limited data are available.

Polymorphisms in human organic anion-transporting polypeptide 1A2 (OATP1A2): implications for altered drug disposition and central nervous system drug entry.

Organic anion-transporting polypeptide 1A2 (OATP1A2) is a drug uptake transporter known for broad substrate specificity, including many drugs in clinical use. Therefore, genetic variation in SLCO1A2 may have important implications to the disposition and tissue penetration of substrate drugs. In the present study, we demonstrate OATP1A2 protein expression in human brain capillary and renal distal nephron using immunohistochemistry. We also determined the extent of single nucleotide polymorphisms in SLCO1A2 upon analyses of ethnically defined genomic DNA samples (n = 95 each for African-, Chinese-, European-, and Hispanic-Americans). We identified six nonsynonymous polymorphisms within the coding region of SLCO1A2 (T38C (I13T), A516C (E172D), G559A (A187T), A382T (N128Y), A404T (N135I), and C2003G (T668S)), the allelic frequencies of which appeared to be ethnicity-dependent. In vitro functional assessment revealed that the A516C and A404T variants had markedly reduced capacity for mediating the cellular uptake of OATP1A2 substrates, estrone 3-sulfate and two delta-opioid receptor agonists, deltorphin II, and [D-penicillamine(2,5)]-enkephalin. On the other hand, the G559A and C2003G variants appeared to have substrate-dependent changes in transport activity. Cell surface biotinylation and immunofluorescence confocal microscopy suggested that altered plasma membrane expression of the transporter may contribute to reduced transport activity associated with the A516C, A404T, and C2003G variants. The A404T (N135I) variant also showed a shift in the apparent molecular size, indicative of alterations in glycosylation status. Taken together, these data suggest that SLCO1A2 polymorphisms may be an important yet unrecognized contributor to inter-individual variability in drug disposition and central nervous system entry of substrate drugs.

A naturally occurring mutation in the SLC21A6 gene causing impaired membrane localization of the hepatocyte uptake transporter.

The organic anion transporter SLC21A6 (also known as OATP2, OATP-C, or LST-1) is involved in the hepatocellular uptake of a variety of endogenous and xenobiotic substances and drugs. We analyzed 81 human liver samples by immunoblotting and found one with a strongly reduced amount of SLC21A6 protein suggesting mutations in the SLC21A6 gene. The SLC21A6 cDNA from this sample contained five base pair changes in one allele; three of the mutations resulted in amino acid substitutions designated SLC21A6-N130D, SLC21A6-P155T, and SLC21A6-L193R. The former two were polymorphisms (SLC21A6*1b and SLC21A6*4), whereas SLC21A6-L193R represents the first naturally occurring mutation identified in one allele of the SLC21A6 gene, which affects protein maturation and organic anion transport. We introduced each of the mutations into the SLC21A6 cDNA and established stably transfected MDCKII cells expressing the respective mutant SLC21A6 protein. Immunofluorescence microscopy and uptake measurements were used to study localization and transport properties of the mutated proteins. Both proteins carrying the polymorphisms were sorted to the lateral membrane like wild-type SLC21A6, but their transport properties for the substrates cholyltaurine and 17beta-glucuronosyl estradiol were altered. Importantly, most of the mutant protein SLC21A6-L193R was retained intracellularly, and this single amino acid exchange abolished transport function.