Identification of Novel Inhibitors of Organic Anion Transporting Polypeptides 1B1 and 1B3 (OATP1B1 and OATP1B3) Using a Consensus Vote of Six Classification Models

Abstract

Organic anion transporting polypeptides 1B1 and 1B3 are transporters selectively expressed on the basolateral membrane of the hepatocyte. Several studies reveal that they are involved in drug–drug interactions, cancer, and hyperbilirubinemia. In this study, we developed a set of classification models for OATP1B1 and 1B3 inhibition based on more than 1700 carefully curated compounds from literature, which were validated via cross-validation and by use of an external test set. After combining several sets of descriptors and classifiers, the 6 best models were selected according to their statistical performance and were used for virtual screening of DrugBank. Consensus scoring of the screened compounds resulted in the selection and purchase of nine compounds as potential dual inhibitors and of one compound as potential selective OATP1B3 inhibitor. Biological testing of the compounds confirmed the validity of the models, yielding an accuracy of 90% for OATP1B1 and 80% for OATP1B3, respectively. Moreover, at least half of the new identified inhibitors are associated with hyperbilirubinemia or hepatotoxicity, implying a relationship between OATP inhibition and these severe side effects.

Introduction

Detoxification mainly takes place in the hepatocyte and is accomplished by a diverse series of transferase-mediated conjugation reactions with charged moieties such as glutathione, glucuronide, and sulfate, resulting in negatively charged, amphiphilic compounds that are efficiently secreted into bile or urine. The hepatocyte is an epithelial cell which comprises two membrane domains, the basolateral (sinusoidal) and the apical (canalicular) membrane.^1,2 Together with metabolizing enzymes, transmembrane transporters are important determinants regarding drug metabolism and drug clearance by the liver. Their significant role has been increasingly recognized in terms of drug and metabolite pharmacokinetics.^2,3 Transport proteins in the basolateral membrane of the liver cause drugs to enter the hepatocyte, where metabolism takes place, while in the apical membrane of the hepatocyte the residing ATP-dependent efflux pumps transfer drugs and metabolites from the hepatocyte to bile. Among the transporters residing on the basolateral (sinusoidal) membrane of human hepatocytes are organic anion transporting polypeptides (OATP1B1, 1B3, and 2B1), NTCP, OAT2, and OCT1. Among the canalicular transporters are MRPs (1, 2, 3, and 6), MDRs (1 and 3), BSEP (ABCB11), and BCRP (ABCG2).^2,4,5

OATPs are encoded by the genes of the SLCO/Slco (SLCO for humans/Slco for rodents) superfamily.^3,6−9 The particular superfamily was originally named SLC21A. However, the nomenclature of its members was updated and standardized in 2004 on the basis of phylogenetic relationships, resulting in its being renamed SLCO, the solute carrier family of OATPs.^3,6,7,9 11 human OATPs have been identified, which are organized in 6 distinct families: OATP1, OATP2, OATP3, OATP4, OATP5, and OATP6. These might be split further into subfamilies (OATP1A, OATP1B, and OATP1C).^7,10−13 OATP1B1 (encoded by the SLCO1B1 gene) and OATP1B3 (encoded by the SLCO1B3 gene) are transporters exclusively expressed on the basolateral membrane of the hepatocyte.⁶ They have a wide and overlapping range of substrates and inhibitors, including various endobiotics, such as bilirubin, estradiol-17β-glucuronide, thyroxine (T4), cholate, and taurocholate. In the liver, OATPs take up bile acids, thus helping in preservation of a circulating pool of bile acids, an important factor for bile flow. This way they contribute to the bile acids and cholesterol homeostasis.^14,15 Furthermore, OATPs are among the transmembrane transporters that regulate the uptake of thyroid hormones into their target cells throughout the body, as well as from the mother to the fetus.^14,16−19 Apart from endogenous compounds, OATPs can transport many marketed drugs, such as erythromycin, levofloxacin, imatinib, pitavastatin, and enalapril (substrates) and cyclosporine, atorvastatin, telmisartan, and diazepam (inhibitors). Due to their wide range of substrates and inhibitors, they are implicated in various drug–drug interactions.²⁰⁻²⁴

Additionally, they are closely associated with cancer, as many anticancer agents are OATP1B1 and 1B3 substrates or/and inhibitors. Therefore, they affect the intracellular concentration of these drugs and alter their effectiveness.²⁵⁻²⁷ The association between OATPs and cancer is also based on the fact that the localization and the expression level of these transporters alters in cancer tissues, which further influences the uptake and exposure of drugs.^25,28−30Moreover, since these influx transporters are working together with efflux transporters and metabolizing enzymes, they are suspected to play an important role in chemoresistance during chemotherapy.^25,31,32

Last, but not least, OATPs are correlated to hyperbilirubinemia, a condition of accumulation of bilirubin in the body. Hyperbilirubinemia has been extensively studied in terms of neurotoxicity, where it appeared that bilirubin may change synaptic potentials and functions of neurotransmitters. It can also interfere with oxidative phosphorylation, enhance DNA instability, interrupt protein synthesis, and block the activity of mitochondrial enzymes. Therefore, apart from neurotoxicity, bilirubin may lead to non-neural organ dysfunctions. Moreover, hyperbilirubinemia can be considered as an early warning of possible adverse effects such as hepatotoxicity, since hepatotoxicity is often accompanied by elevated levels of bilirubin.³³⁻³⁵

Bilirubin is taken up to the hepatocyte by OATP1B1 and 1B3 and is subsequently metabolized into mono- and diglucuronide conjugates by UGT1A1 (UDP-glucuronosyltransferase 1A1). These conjugated bilirubin-glucuronides are excreted into bile by the hepatobiliary ABC-transporter MRP2 (multidrug resistance protein 2), as well as, to a smaller extent, by BCRP.^5,36 In the case of impaired biliary excretion, as a compensatory pathway, the glucuronidated bilirubin may also be secreted back to the sinusoidal blood by MRP3.^5,33,36,37 Thus, since bilirubin is imported by OATP1B1 and 1B3, a potential inhibition of those transporters can lead to the increase of unconjugated bilirubin in the blood and eventually cause hyperbilirubinemia.

Considering the multifactorial role of OATP1B1 and OATP1B3 for drug uptake, efficacy, and metabolism, they also have been included in the table of “Selected Transporter-Mediated Clinical Significant Drug–Drug Interactions (7/28/2011)” of the FDA.³⁸ Therefore, predictive models allowing the assessment of risk for a compound to interact with OATP1B1 and OATP1B3 would be useful tools at the early stage of drug development. Classification models for OATP1B1 and B3 inhibition are already available in the literature.³⁹⁻⁴¹ Karlgren et al.⁴⁰ generated a computational model for OATP1B1, based on 146 compounds (98 in the training set and 48 in the test set) using orthogonal partial least-squares projection to latent structures discriminant analysis (OPLS-DA) based on a set of molecular descriptors. As a follow-up,⁴¹ they also published a model for OATP1B1 and OATP1B3 inhibition, based on 225 compounds (two-thirds randomly assigned as a training set and one-third as a test set), using multivariate partial least-squares (PLS) regression and physicochemical descriptors. De Bruyn et al.³⁹ followed a proteochemometric modeling approach, using almost 2000 compounds for their training set and 54 compounds as an external test set, combining protein-based and ligand-based molecular descriptors and using Random Forest as a classifier. After careful manual curation and removal of compounds that showed contradictory class labels, we used these data sets to develop a set of in silico classification models suitable for virtual screening of compound libraries. This was followed by virtual screening of DrugBank and subsequent biological evaluation of the top ranked compounds, in order to identify existent inhibitors among drugs that are currently on the market or in the stage of clinical trials.

Experimental Section

In Silico Modeling for the Prediction of OATP1B1 and OATP1B3 Inhibition

Selection and Curation of Data Sets

High quality data sets are key for statistical modeling.⁴²⁻⁴⁵ For our study we used two recently published large data sets for the inhibition of OATP1B1 and 1B3, one containing 2000 compounds³⁹ and one consisting of 225 compounds.⁴¹ The first data set was used as a training set and the second data set as an external test set. The external test set was downloaded from ChEMBL,⁴⁶ and the training set was kindly provided by Gerard J. P. van Westen. Subsequently, both data sets were curated according to a set of protocols, which have been developed in house:⁴⁷

• •Inorganic compounds, salt parts as well as compounds containing metals and rare or special atoms were removed (MOE 2013.0801).⁴⁸
• •The chemotypes were standardized using an in-house Pipeline Pilot (version 9.1.0.13)⁴⁹ workflow.
• •Duplicates and permanently charged compounds were removed.
• •3D structures were generated using CORINA (version 3.4),⁵⁰ and their energy was minimized with MOE 2013.0801, using default settings with an extra setting of preserving the existing chirality and changing the gradient to 0.05 RMS kcal/mol/A².

Finally, the training and the test set were checked for duplicates. In total, 68 and 70 overlapping compounds were identified for OATP1B1 and OATP1B3, respectively. In most cases, the overlapping compounds were of the same class (using 50% (±10%) inhibition as threshold, as defined by the initial authors). For these cases, since the overlapping compounds were mostly noninhibitors, we decided to remove them from the training set and keep them in the test instead. Those compounds showing contradictory class labels (10 compounds for OATP1B1 and 2 compounds for OATP1B3) were removed from both data sets.

This procedure finally led to a training set of 1708 compounds (190 inhibitors and 1518 noninhibitors) for OATP1B1 and of 1725 compounds (124 inhibitors and 1601 noninhibitors) for OATP1B3, respectively. The external test set contained 201 compounds for OATP1B1 (64 inhibitors and 137 noninhibitors) and 209 compounds for OATP1B3 (40 inhibitors and 169 noninhibitors).

Generation of Statistical Models

Algorithms Used

The open-source software WEKA (version 3-7-10)⁵¹ served as the basis for generating classification models. The following classifiers were explored: Naive Bayes, k Nearest Neighbors (k = 5), Decision Tree (J48 in WEKA), Random Forest, and Support Vector Machines (SMO in WEKA). Furthermore, because of the highly imbalanced training set, the meta-classifiers MetaCost and CostSensitive Classifier, as implemented in WEKA, were used. They are both cost-sensitive meta-classifiers that artificially balance the training set. In each case, the cost matrix was set according to the ratio of noninhibitors vs inhibitors. In the case of OATP1B1 the ratio noninhibitors/inhibitors was equal to 8, thus the matrix used during the application of cost was [0.0, 1.0; 8.0, 0.0]. For OATP1B3 the respective ratio was equal to 13, thus the respective cost matrix was [0.0, 1.0; 13.0, 0.0].

The best results were obtained using MetaCost⁵² as meta-classifier and Random Forest (RF) and Support Vector Machines (SMO) as base-classifiers.

Molecular Descriptors

Using MOE 2013.0801,⁴⁸ all the available 2D and selected 3D molecular descriptors (like the whole series of Volsurf descriptors) were calculated. Additionally, in order to generate models with open-source descriptors, an analogous set of descriptors was calculated with PaDEL-Descriptor (version 2.18).⁵³ Additionally, several fingerprints such as MACCS-keys using PaDEL and ECFPs using RDkit were also calculated.

In a first run, a set of basic physicochemical descriptors were used for model generation. This should allow us to derive basic physicochemical properties driving OATP1B inhibition. For MOE, these comprised a_acc (number of H-bond acceptors), a_don (number of H-bond donors), logP (o/w) (lipophilicity), mr (molecular refractivity), TPSA (topological polar surface area), and weight (molecular weight, MW). The analogous descriptors calculated with PaDEL included nHBAcc_Lipinski, nHBDon_Lipinski, CrippenLogP, CrippenMR, TopoPSA, and MW. The absolute values were not fully identical to those calculated with MOE, as slightly different algorithms are used by the two software packages. In order to further enrich the original set of the six descriptors, a few topological descriptors were additionally calculated, thus leading to a third set comprising 11 molecular descriptors: nHBAcc_Lipinski, nHBDon_Lipinski (number of H-bond donors and acceptors according to Lipinski), CrippenLogP, CrippenMR (Wildman–Crippen logP and mr), TopoPSA, MW, nRotB (number of rotable bonds), topoRadius (topological radius), topoDiameter (topological diameter), topoShape (topological shape), and globalTopoChargeIndex (global topological charge index).

Finally, combining the three sets of descriptors with the two base-classifier methods selected, six models were generated for each transporter. A detailed description of the model settings is given in the Supporting Information.

Model Validation

The statistical models were validated using 5-fold and 10-fold cross-validation, as well as with the external test set. The parameters used comprised Accuracy, Sensitivity (True Positive Rate), Specificity, Mathews Correlation Coefficient (MCC), and Receiver Operating Characteristic (ROC) Area.⁵⁴ A detailed description of all parameters is provided in the Supporting Information. The cost for the MetaCost meta-classifier was applied based on a standard confusion matrix.

The performance of all models was relatively equivalent with total accuracy values and ROC areas for the test set in the range of 0.81–0.86 and of 0.81–0.92, respectively. Generally, the OATP1B3 models performed slightly better than the ones for OATP1B1. In order to retain as much information as possible, all models were subsequently used for the virtual screening of DrugBank, implementing a consensus scoring approach. Therefore, the prediction score of each classification model for every compound was summed up, giving a float score prediction number between 0 and 6.

In Silico Screening of DrugBank

In order to perform a prospective assessment of the predictivity of our models, DrugBank (Version 4.1)⁵⁵ (http://www.drugbank.ca/), which contains 7740 drug entries including 1584 FDA-approved small molecule drugs, 157 FDA-approved biotech (protein/peptide) drugs, 89 nutraceuticals, and over 6000 experimental drugs, was virtually screened, and the top ranked compounds were purchased and experimentally tested. The in silico screen was restricted to the small molecules (either approved or experimental), since this is the chemical space upon which the models were generated. Before the screening, the compounds underwent the same curation process as the compounds from the training and test sets. This resulted in a screening set of 6279 compounds in total. For each screened compound we obtained two scores for each model: (i) a binary score, 0 if the compound was predicted as noninhibitor and 1 if the compound was predicted as inhibitor; and (ii) a float-number score between 0 and 1, [0, 0.5] if the compound is predicted as noninhibitor and [0.5, 1] if the compound is predicted as inhibitor. The individual binary and the float-number scores for each model were added up and gave a consensus class prediction (integer consensus score) and a predictive score (float consensus score) for each compound, which were afterward ranked from inhibitors to noninhibitors according to these additive scores. In general, a compound was considered as being an inhibitor if it was predicted as inhibitor by at least 3 out of the 6 models for each transporter, while the float-number score was also taken into consideration.

Selection of Compounds for Biological Testing

For the selection and purchase of potential inhibitors, those compounds having an integer consensus score of 6 were taken and ranked according to their float consensus score. Subsequently, a similarity search based on MACCS fingerprints and the Tanimoto coefficient was performed with MOE, comparing the selected screening hits from DrugBank with the compounds included in the training and in the external test set. Thus, any high ranked compound in DrugBank showing a Tanimoto similarity higher than 0.85 to inhibitors from the training set or the test set was excluded from the shopping list. Furthermore, compounds that are known OATP1B1 and/or OATP1B3 inhibitors were also excluded. Last but not least, the final selection of compounds for purchase was influenced by their commercial availability and the respective costs. The ten compounds that were finally selected were purchased from Glentham Life Sciences, U.K. (http://www.glenthamls.com/, 6 compounds) and from Sigma-Aldrich (https://www.sigmaaldrich.com, 4 compounds). The purity of all compounds was ≥95%. Out of the ten compounds, nine were predicted as inhibitors for both OATP1B1 and OATP1B3 and one was predicted as selective OATP1B3 inhibitor with a binary score of 6 for OATP1B3 and of 1 for OATP1B1.

Inhibition Assay for OATP1B1 and OATP1B3

Chinese hamster ovary (CHO) cells that were stably transfected with OATP1B1 or OATP1B3 and wild-type CHO cells were provided by the University of Zurich, Switzerland, and have been extensively characterized previously.^24,56,57 Cells were grown in Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% FCS, 50 μg/mL l-proline, 100 U/mL penicillin, and 100 μg/mL streptomycin. The culture media of the transfected CHO cells additionally contained 500 μg/mL Geneticin sulfate (G418) (Sigma-Aldrich, Munich, Germany). Media and supplements were obtained from Invitrogen (Karlsruhe, Germany). Cells were incubated at 5% CO₂ and 37 °C. For uptake experiments, CHO cells were seeded in 24-well plates (BD Biosciences, Heidelberg, Germany) at a density of 25,000 cells/well. Uptake assays were generally performed on day 3 after seeding, when the cells had grown to confluence. 24 h before starting the transport experiments, cells were additionally treated with 5 mM sodium butyrate (Sigma-Aldrich, Munich, Germany) to induce gene expression. Prior to the uptake experiments, cells were rinsed twice with 2 mL of prewarmed (37 °C) uptake buffer (116.4 mM NaCl, 5.3 mM KCL, 1 mM NaH₂PO₄, 0.8 mM MgSO₄, 5.5 mM d-glucose, and 20 mM Hepes, pH adjusted to 7.4). Uptake was initiated by adding 0.5 mL of uptake buffer containing 5 μM of the fluorescent OATP1B1/1B3 substrate FMTX⁵⁸ in the presence or absence of inhibitors. After 10 min culture at 37 °C, uptake was stopped by removing the uptake solution and washing the cells 3 times with ice-cold uptake buffer. The cells were then lysed with 0.5 mL of 0.5% Triton X-100 solution dissolved in PBS and placed on a plate shaker for 30 min. Fluorescence was measured in an Enspire Multimode plate reader (PerkinElmer, Waltham, MA) at an excitation wavelength of 485 and an emission wavelength of 528 nm.

IC₅₀ values were determined by plotting the log inhibitor concentration against the net uptake rate and nonlinear regression of the data set using the equation

in which y is the net uptake rate (pmol/μg of protein/min), I is the inhibitor concentration (μM), s is the slope at the point of inversion, and a and b are the maximum and minimum values for cellular uptake (GraphPad Software, San Diego, CA, USA) . Net uptake was calculated for each inhibitor concentration as the difference in the uptake rates of the transporter-expressing and wild-type cell lines. Unless otherwise indicated, values are expressed as mean ± SD of three individual experiments. Significant differences from control values were determined using a Student’s paired t test at a significance level of p < 0.05.

Results and Discussion

The Problem of Imbalanced Data Sets

One of the major challenges when dealing with real life scenarios is the imbalance of data sets. While most classification studies published in the literature show an equal number of actives and inactives, our data sets comprised a ratio of 8/1 for noninhibitors/inhibitors for OATP1B1 and of 13/1 for OATP1B3, respectively (Figure 1). This resulted in a very poor performance when applying base classifiers directly on the training set, with sensitivity values lower than 0.2 (data not shown).

Figure 1.

Graphical representation of the numeric gap between inhibitors and noninhibitors of OATP1B1 and OATP1B3 for both the training and the test set.

There are several methods for dealing with imbalanced data when using machine learning techniques.⁵⁹⁻⁶¹ Indicatively, they comprise undersampling, oversampling, bagging, boosting, and application of costs. In our case, the application of a cost for misclassification of the minority class, using the meta-classifier MetaCost in WEKA, yielded the best results.

Classification Models for OATP1B1 and OATP1B3

Combining several sets of descriptors with various base- and meta-classifiers resulted in a cluster of models, based on Random Forest and Support Vector Machines (SMO) in combination with MetaCost as a cost-sensitive meta-classifier. All models present in the final cluster were validated via 5- and 10-fold cross-validation, as well as with the use of an external test set, composed of 201 and 209 compounds for OATP1B1 and OATP1B3, respectively.⁴¹ Although the latter data set has been measured under different assay conditions than the respective one used in the training set, a comparison of the overlapping compounds showed high consistency. The statistical results of all models were quite similar and are presented in Tables 1 and 2.

Table 1. Detailed Statistical Results of OATP1B1 Inhibition Models.

model	validation	accuracy	sensitivity	specificity	precision	MCC	ROC area
B1_6MOE_RF	test set	0.846	0.719	0.905	0.780	0.638	0.815
	10-fold CV	0.843	0.611	0.872	0.374	0.394	0.795
	5-fold CV	0.858	0.621	0.888	0.410	0.428	0.790
B1_6MOE_SMO	test set	0.841	0.672	0.920	0.796	0.622	0.869
	10-fold CV	0.862	0.489	0.909	0.403	0.366	0.808
	5-fold CV	0.862	0.495	0.908	0.402	0.368	0.791
B1_6PaD_SMO	test set	0.811	0.719	0.854	0.697	0.568	0.814
	10-fold CV	0.841	0.626	0.868	0.373	0.399	0.790
	5-fold CV	0.843	0.605	0.872	0.372	0.390	0.787
B1_6PaD_SMO	test set	0.821	0.609	0.920	0.780	0.570	0.851
	10-fold CV	0.867	0.453	0.919	0.411	0.357	0.806
	5-fold CV	0.864	0.453	0.915	0.400	0.348	0.799
	test set	0.831	0.719	0.833	0.742	0.607	0.845
B1_11PaD_RF	10-fold CV	0.854	0.579	0.889	0.394	0.398	0.797
	5-fold CV	0.853	0.595	0.885	0.394	0.404	0.801
B1_11PaD_SMO	test set	0.821	0.547	0.949	0.833	0.568	0.868
	10-fold CV	0.861	0.505	0.905	0.400	0.371	0.801
	5-fold CV	0.861	0.500	0.906	0.401	0.370	0.790
consensus model							0.859

Table 2. Detailed Statistical Results of OATP1B3 Inhibition Models.

model	validation	accuracy	sensitivity	specificity	precision	MCC	ROC area
B3_6MOE_RF	test set	0.847	0.775	0.864	0.574	0.574	0.847
	10-fold CV	0.876	0.677	0.891	0.326	0.412	0.842
	5-fold CV	0.871	0.661	0.887	0.312	0.394	0.821
B3_6MOE_SMO	test set	0.852	0.825	0.858	0.579	0.603	0.919
	10-fold CV	0.900	0.597	0.923	0.376	0.422	0.866
	5-fold CV	0.893	0.589	0.916	0.353	0.401	0.852
B3_6PaD_RF	test set	0.828	0.825	0.828	0.532	0.563	0.877
	10-fold CV	0.870	0.677	0.884	0.312	0.400	0.844
	5-fold CV	0.863	0.669	0.878	0.299	0.385	0.814
B3_6PaD_SMO	test set	0.847	0.725	0.876	0.580	0.554	0.925
	10-fold CV	0.894	0.516	0.923	0.342	0.365	0.853
	5-fold CV	0.896	0.508	0.926	0.348	0.366	0.840
B3_11PaD_RF	test set	0.842	0.775	0.858	0.564	0.565	0.886
	10-fold CV	0.866	0.629	0.884	0.295	0.368	0.832
	5-fold CV	0.863	0.645	0.880	0.294	0.372	0.825
B3_11PaD_SMO	test set	0.866	0.750	0.893	0.625	0.602	0.924
	10-fold CV	0.881	0.581	0.904	0.320	0.372	0.849
	5-fold CV	0.883	0.613	0.904	0.332	0.394	0.844
consensus model							0.917

As can be seen in Tables 1 and 2, all six models for each transporter showed approximately the same performance. Thus, we decided to implement a consensus scoring approach to allow input of all models when screening DrugBank, since it has been often suggested in the literature that consensus modeling outperforms single modeling approaches.⁶²⁻⁶⁶ This would also increase our confidence regarding the selection of potential OATP1B1 and 1B3 inhibitors for experimental testing, especially in the case of contradictory results among different models. For getting the consensus score, the prediction scores of all models were summed up in order to get a final prediction. The validity of this approach was partially confirmed by calculating the ROC area of the consensus models based on the results of the external test set, as well as by plotting the respective ROC curves, using R⁶⁷ (Figure 2). Although for both transporters the consensus models did not exhibit the highest AUC, the consensus model for OATP1B3 had the steepest ROC curve vs all the individual ones and was thus selected as the best solution for the subsequent in silico screen of DrugBank. In the case of OATP1B1, the ROC curve was steeper than the curves of five of the individual models, while there was one model, the SMO_11 PaD_B1, which had a slightly steeper curve. However, also for this case the consensus model was used for screening, since the difference was almost insignificant and we were in favor of using a majority vote for screening and compound selection rather than relying on a single model.

Figure 2.

Comparative ROC plots of individual and consensus models for each transporter: (a) total OATP1B1 models ROC plot, (b) OATP1B1 models zoom ROC plot (TP rate [0.0, 0.5] and FP rate [0.0, 0.1]), (c) total OATP1B3 models ROC plot, and (d) OATP1B3 models zoom ROC plot (TP rate [0.0, 0.5] and FP rate [0.0, 0.1]). Black continuous line represents the performance of the consensus model, with red 6MOE_RF, with green 6MOE_SMO, with dark blue 6 PaD_RF, with yellow 6 PaD_SMO, with cyan 11 PaD_RF, with violet 11 PaD_SMO, and with dashed brown line a random performance of 50%.

In Silico Screening of DrugBank

In order to prospectively validate the in silico models, DrugBank was virtually screened using all of the six classification models for each transporter, and the compounds were ranked according to the probability score of being an inhibitor. For OATP1B1, 5371/6279 compounds of DrugBank were predicted as noninhibitors by the consensus vote of the 6 models (85.5%), while 908/6279 were predicted as inhibitors. From the predicted inhibitors, 271 compounds were given an integer score of 6, i.e., they were predicted as inhibitors by all 6 classification models (4.36% of whole DrugBank). For OATP1B3, the overall figures were quite identical (905/6279 compounds were predicted as inhibitors, with 407 compounds showing a consensus score of 6/6). Integer and float consensus scores of all compounds are provided in the Supporting Information.

Besides validation of our models by identification of new, hitherto unknown inhibitors of OATP1B1 and OATP1B3 from DrugBank, we also aimed at identifying subtype selective inhibitors. Unfortunately, the development of a 4-class classification model gave poor statistical results (data not shown). Thus, for each compound we compared the predictive scores for both transporters. However, this was quite challenging, since most of the compounds either were presenting the same inhibition profile for both transporters or they were already known OATP1B1 or 1B3 selective inhibitors. Finally, with an integer consensus score of 1 and a float consensus score of 2.062 for OATP1B1 vs 6 (integer score) and 4.430 (float score) for OATP1B3, flavin adenine dinucleotide was proposed as potential selective OATP1B3 inhibitor. As we could not identify a suitable OATP1B1 selective inhibitor, the remaining nine compounds that were selected for biological testing were predicted to inhibit both transporters. All of the selected OATP1B1/1B3 inhibitors, as well as their assay results, are presented in Table 3.

Table 3. Inhibition of OATP1B1 and OATP1B3.

Results of the Inhibition Assay

Since the model’s threshold for inhibitors was 10 μM, compounds with IC₅₀ values less than 1 μM were considered as strong inhibitors (+++), compounds with IC₅₀ values between 1 and 5 μM as moderately strong inhibitors (++), compounds with IC₅₀ values between 5 and 10 μM as moderate inhibitors (+), and compounds having IC₅₀ values above 10 μM as slight inhibitors as long as an IC₅₀ value could be obtained. In cases in which it was impossible to obtain an IC₅₀ value, the compound was considered as noninhibitor.

Considering that the classification models were generated on a threshold of 10 μM, the obtained results are very encouraging regarding the predictive capabilities of the models. The consensus model for OATP1B1 was correct for 9/9 inhibitors, while it was mistaken for the case of the selective OATP1B3 inhibitor. Flavin adenine dinucleotide was also an OATP1B1 inhibitor, which renders it a false negative. For OATP1B3, the respective consensus model was able to predict correctly 8/10 compounds. The two remaining compounds (lapatinib and trametinib) that were predicted as inhibitors had IC₅₀ values above the threshold of the model.

Searching in the literature for any association between these newly identified OATP inhibitors and hepatotoxicity manifestations, such as hyperbilirubinemia, revealed the following findings: Carfilzomib was specifically reported as nonhepatotoxic,⁶⁸ and we could not find any association to hepatotoxicity for flavin adenine dinucleotide, gliquidone, and N,O-didansyl-l-tyrosine. Flavin adenine dinucleotide is a redox factor, important for the function of many flavoenzymes,⁶⁹ thus it could not be particularly toxic, while gliquidone is considered a safe antidiabetic drug and has actually been found to improve liver injury in diabetic patients.⁷⁰N,O-Didansyl-l-tyrosine is an antibacterial agent, still in the experimental stage, so it is quite unlikely to have already reports regarding its toxicity. For trametinib, no reports for hyperbilirubinemia were found. However, it is known for elevating hepatic serum enzymes.⁷¹ Finally, dronedarone, fosinopril, lapatinib, rapamycin, and zafirlukast are reported for causing hyperbilirubinemia, when checking in online sources⁷² and in the literature,⁷³ while there are also some literature reports for hepatotoxicity of these compounds.^68,73−78

During the preparation of this manuscript, an additional OATP1B1 classification model was published by van de Steeg et al.⁷⁹ Their Bayesian model was based on a training set of 437 compounds (37 inhibitors and 400 noninhibitors) and an internal set of 155 compounds for validation (12 inhibitors and 143 noninhibitors), resulting from the screening of a commercial library of 640 FDA-approved drugs. Among the 20 strongest OATP1B1 and OATP1B3 inhibitors are rapamycin and fosinopril, which were also in our hit list. For the rest of the compounds we tested, to the best of our knowledge, they are reported for the first time in our study as OATP1B1 and/or 1B3 inhibitors. Moreover, the analysis of the top 20 compounds from van de Steeg et al. further confirmed the validity and high predictivity of our models. For OATP1B1, 5 compounds were not virtually screened by us, either because they did not exist in DrugBank or because they were removed in some stage of the data set curation. Another 7 compounds (cyclosporin A, atazanavir, dipyridamiole, telmisartan, nicardipine, estradiol, spironolactone) were already included either in our training set or in the test set (6/7 predicted correctly as inhibitors). For the remaining 6 compounds, 5/6 are predicted correctly as inhibitors by our consensus model (bromocriptine mesylate, pranlukast, suramin, troglitazone and docetaxel), while sulfasalazine is predicted as noninhibitor. However, for sulfasalazine we must note that it was initially part of both the De Bruyn³⁹ data set and the Karlgren⁴¹ data set. As De Bruyn et al. annotated it as noninhibitor, and Karlgren et al. evaluated it as inhibitor, it was removed from both data sets. Nevertheless, we must emphasize that De Bruyn et al. and Karlgren et al. use different assays. The assay we used is similar to the one from De Bruyn et al. (the source of our training set), while van de Steeg et al. use an assay similar to the one by Karlgren et al. (the source of our test set). This implies that the particular compound might give different results for different assays, and that this is a probable reason for its misclassification by our model.

For OATP1B3, an analogous picture occurs. Six compounds were not virtually screened because of their absence in DrugBank, 7 compounds (cyclosporin A, atazanavir, dipyridamiole, telmisartan, mifepristone, fluvastatin, clarithromycin) were included either in our training set or our test set, and for the remaining 5 compounds we had an accuracy of 100% by our consensus model (suramin, docetaxel, clobetasol propionate, bromocriptine mesylate, and losartan).

Conclusions

The transportome of the liver is most probably the most complex one in the human body. It comprises numerous uptake and efflux transporters that regulate the concentrations of metabolites and endogenous substrates, such as bile acids and bilirubin. Thus, perturbation of this system by drugs might lead to symptoms such as cholestasis or hyperbilirubinemia. With this manuscript we introduce a set of in silico models which aid in the potential early detection of hepatotoxicity manifestations, such as hyperbilirubinemia, by predicting the probability of a compound to block OATP1B1 and OATP1B3 mediated transport of bilirubin. The models have been derived on the basis of a large, manually curated data set, and have been extensively validated by statistical methods, as well as by in silico screening of DrugBank followed by experimental testing of top ranked hits. Among the 9/10 hits confirmed as OATP inhibitors, five are reported for causing hyperbilirubinemia. These results strongly support the use of validated in silico models for prioritizing compounds in the hit triaging process.

Glossary

Abbreviations Used

OATP1B1

organic anion transporting polypeptide 1B1

OATP1B3

organic anion transporting polypeptide 1B3

IC₅₀

half maximal inhibitory concentration

OATP2B1

organic anion transporting polypeptide 2B1

NTCP

Na⁺-taurocholate cotransporting polypeptide

OAT2

organic anion transporter 2

OCT1

organic cation transporter 1

MRPs

multidrug resistance associated proteins

MDRs

multidrug resistance proteins

ABC transporters

ATP-binding cassette transporters

BSEP

bile salt export pump

BCRP

breast cancer resistance protein

UGT1A1

UDP-glucuronosyltransferase 1A1

E1S

estrone sulfate

DHEAS

dehydroepiandrosterone sulfate

RF

Random Forest

SVM

Support Vector Machines

SMO

sequential minimal optimization

FMTX

fluoro-methotrexate

CHO cells

Chinese hamster ovary cells

Supporting Information Available

The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acs.molpharmaceut.5b00583.

• Settings for classification model generation (PDF)

• Training and test set for OATP1B1 and OATP1B3 (SMILES format); scores for DrugBank compounds (XLSX)

The authors declare no competing financial interest.