Benzanilide-Biphenyl Replacement: A Bioisosteric Approach to Quinoline Carboxamide-Type ABCG2 Modulators

Using Jupyter Notebooks for re-training machine learning models

Machine learning (ML) models require an extensive, user-driven selection of molecular descriptors in order to learn from chemical structures to predict actives and inactives with a high reliability. In addition, privacy concerns often restrict the access to sufficient data, leading to models with a narrow chemical space. Therefore, we propose a framework of re-trainable models that can be transferred from one local instance to another, and further allow a less extensive descriptor selection. The models are shared via a Jupyter Notebook, allowing the evaluation and implementation of a broader chemical space by keeping most of the tunable parameters pre-defined. This enables the models to be updated in a decentralized, facile, and fast manner. Herein, the method was evaluated with six transporter datasets (BCRP, BSEP, OATP1B1, OATP1B3, MRP3, P-gp), which revealed the general applicability of this approach.

A new porphyrin as selective substrate-based inhibitor of breast cancer resistance protein (BCRP/ABCG2)

The ABCG2 transporter plays a pivotal role in multidrug resistance, however, no clinical trial using specific ABCG2 inhibitors have been successful. Although ABC transporters actively extrude a wide variety of substrates, photodynamic therapeutic agents with porphyrinic scaffolds are exclusively transported by ABCG2. In this work, we describe for the first time a porphyrin derivative (4B) inhibitor of ABCG2 and capable to overcome multidrug resistance in vitro. The inhibition was time-dependent and 4B was not itself transported by ABCG2. Independently of the substrate, the porphyrin 4B showed an IC₅₀ value of 1.6 μM and a mixed type of inhibition. This compound inhibited the ATPase activity and increased the binding of the conformational-sensitive antibody 5D3. A thermostability assay confirmed allosteric protein changes triggered by the porphyrin. Long-timescale molecular dynamics simulations revealed a different behavior between the ABCG2 porphyrinic substrate pheophorbide a and the porphyrin 4B. Pheophorbide a was able to bind in three different protein sites but 4B showed one binding conformation with a strong ionic interaction with GLU446. The inhibition was selective toward ABCG2, since no inhibition was observed for P-glycoprotein and MRP1. Finally, this compound successfully chemosensitized cells that overexpress ABCG2. These findings reinforce that substrates may be a privileged source of chemical scaffolds for identification of new inhibitors of multidrug resistance-linked ABC transporters.

Uptake, intracellular dissolution, and cytotoxicity of silver nanowires in cell models

The uptake, intracellular dissolution, and cytotoxicity of silver nanowires (AgNWs) in two cell models (human keratinocytes - HaCaT cells and murine macrophages) were systemically investigated for the first time. Cellular uptake of AgNWs occurred mainly via pathways of clathrin-dependent endocytosis, caveolae-dependent endocytosis, and phagocytosis. AgNWs could be internalized by two types of cells with numerous lysosomal vesicles detected in close vicinity to AgNWs. Meanwhile, AgNWs exposure caused lysosomal permeabilization and release of cathepsisn B into cytoplasm. Furthermore, for the first time, this study found that AgNWs exposure inhibited the transmembrane ATP binding cassette (ABC) efflux transporter activity, which could make AgNWs as chemosensitizers to increase the toxicity of other xenobiotic pollutants. Toxicity assays evaluating reactive oxygen species production and mitochondrial activity indicated that cytotoxicity differed for different cell types and particles. The intracellular presence of AgNWs with different diameters induced similar toxic events but to different extents. AgNWs were absorbed by macrophages more efficiently than HaCaT cells, while AgNWs exhibited only marginal cytotoxicity towards macrophages compared to HaCaT cells. Using an Ag⁺ fluorescence probe, it was found that a fraction of AgNWs was dissolved inside the lysosomes. A higher amount of released Ag⁺ was detected in HaCaT cells than in macrophages, which might partially contribute to their higher cytotoxicity in HaCaT cells. The toxicity of AgNWs in HaCaT cells and macrophages is due to the high-aspect nature of the nanowires rather than the extracellular release of Ag⁺. This study may be useful for risk assessments of AgNWs in their practical applications in the biomedical field.

Structural Basis of Drug Recognition by the Multidrug Transporter ABCG2

ABCG2 is an ATP-binding cassette (ABC) transporter whose function affects the pharmacokinetics of drugs and contributes to multidrug resistance of cancer cells. While its interaction with the endogenous substrate estrone-3-sulfate (E₁S) has been elucidated at a structural level, the recognition and recruitment of exogenous compounds is not understood at sufficiently high resolution. Here we present three cryo-EM structures of nanodisc-reconstituted, human ABCG2 bound to anticancer drugs tariquidar, topotecan and mitoxantrone. To enable structural insight at high resolution, we used Fab fragments of the ABCG2-specific monoclonal antibody 5D3, which binds to the external side of the transporter but does not interfere with drug-induced stimulation of ATPase activity. We observed that the binding pocket of ABCG2 can accommodate a single tariquidar molecule in a C-shaped conformation, similar to one of the two tariquidar molecules bound to ABCB1, where tariquidar acts as an inhibitor. We also found single copies of topotecan and mitoxantrone bound between key phenylalanine residues. Mutagenesis experiments confirmed the functional importance of two residues in the binding pocket, F439 and N436. Using 3D variability analyses, we found a correlation between substrate binding and reduced dynamics of the nucleotide binding domains (NBDs), suggesting a structural explanation for drug-induced ATPase stimulation. Our findings provide additional insight into how ABCG2 differentiates between inhibitors and substrates and may guide a rational design of new modulators and substrates.

More Than Resveratrol: New Insights into Stilbene-Based Compounds

The concept of a scaffold concerns many aspects at different steps on the drug development path. In medicinal chemistry, the choice of relevant "drug-likeness" scaffold is a starting point for the design of the structure dedicated to specific molecular targets. For many years, the chemical uniqueness of the stilbene structure has inspired scientists from different fields such as chemistry, biology, pharmacy, and medicine. In this review, we present the outstanding potential of the stilbene-based derivatives. Naturally occurring stilbenes, together with powerful synthetic chemistry possibilities, may offer an excellent approach for discovering new structures and identifying their therapeutic targets. With the development of scientific tools, sophisticated equipment, and a better understanding of the disease pathogenesis at the molecular level, the stilbene scaffold has moved innovation in science. This paper mainly focuses on the stilbene-based compounds beyond resveratrol, which are particularly attractive due to their biological activity. Given the "fresh outlook" about different stilbene-based compounds starting from stilbenoids with particular regard to isorhapontigenin and methoxy- and hydroxyl- analogues, the update about the combretastatins, and the very often overlooked and underestimated benzanilide analogues, we present a new story about this remarkable structure.

More Than Resveratrol: New Insights into Stilbene-Based Compounds

The concept of a scaffold concerns many aspects at different steps on the drug development path. In medicinal chemistry, the choice of relevant "drug-likeness" scaffold is a starting point for the design of the structure dedicated to specific molecular targets. For many years, the chemical uniqueness of the stilbene structure has inspired scientists from different fields such as chemistry, biology, pharmacy, and medicine. In this review, we present the outstanding potential of the stilbene-based derivatives. Naturally occurring stilbenes, together with powerful synthetic chemistry possibilities, may offer an excellent approach for discovering new structures and identifying their therapeutic targets. With the development of scientific tools, sophisticated equipment, and a better understanding of the disease pathogenesis at the molecular level, the stilbene scaffold has moved innovation in science. This paper mainly focuses on the stilbene-based compounds beyond resveratrol, which are particularly attractive due to their biological activity. Given the "fresh outlook" about different stilbene-based compounds starting from stilbenoids with particular regard to isorhapontigenin and methoxy- and hydroxyl- analogues, the update about the combretastatins, and the very often overlooked and underestimated benzanilide analogues, we present a new story about this remarkable structure.

ADMET evaluation in drug discovery. 20. Prediction of breast cancer resistance protein inhibition through machine learning

Breast cancer resistance protein (BCRP/ABCG2), an ATP-binding cassette (ABC) efflux transporter, plays a critical role in multi-drug resistance (MDR) to anti-cancer drugs and drug–drug interactions. The prediction of BCRP inhibition can facilitate evaluating potential drug resistance and drug–drug interactions in early stage of drug discovery. Here we reported a structurally diverse dataset consisting of 1098 BCRP inhibitors and 1701 non-inhibitors. Analysis of various physicochemical properties illustrates that BCRP inhibitors are more hydrophobic and aromatic than non-inhibitors. We then developed a series of quantitative structure–activity relationship (QSAR) models to discriminate between BCRP inhibitors and non-inhibitors. The optimal feature subset was determined by a wrapper feature selection method named rfSA (simulated annealing algorithm coupled with random forest), and the classification models were established by using seven machine learning approaches based on the optimal feature subset, including a deep learning method, two ensemble learning methods, and four classical machine learning methods. The statistical results demonstrated that three methods, including support vector machine (SVM), deep neural networks (DNN) and extreme gradient boosting (XGBoost), outperformed the others, and the SVM classifier yielded the best predictions (MCC = 0.812 and AUC = 0.958 for the test set). Then, a perturbation-based model-agnostic method was used to interpret our models and analyze the representative features for different models. The application domain analysis demonstrated the prediction reliability of our models. Moreover, the important structural fragments related to BCRP inhibition were identified by the information gain (IG) method along with the frequency analysis. In conclusion, we believe that the classification models developed in this study can be regarded as simple and accurate tools to distinguish BCRP inhibitors from non-inhibitors in drug design and discovery pipelines.

Tariquidar-related triazoles as potent, selective and stable inhibitors of ABCG2 (BCRP)

Tariquidar derivatives have been described as potent and selective ABCG2 inhibitors. However, their susceptibility to hydrolysis limits their applicability. The current study comprises the synthesis and characterization of novel tariquidar-related inhibitors, obtained by bioisosteric replacement of the labile moieties in our previous tariquidar analog UR-ME22-1 (9). CuAAC ("click" reaction) gave convenient access to a triazole core as a substitute for the labile amide group and the labile ester moiety was replaced by different acyl groups in a Sugasawa reaction. A stability assay proved the enhancement of the stability in blood plasma. Compounds UR-MB108 (57) and UR-MB136 (59) inhibited ABCG2 in a Hoechst 33342 transport assay with an IC₅₀ value of about 80 nM and belong to the most potent ABCG2 inhibitors described so far. Compound 57 was highly selective, whereas its PEGylated analog 59 showed some potency at ABCB1. Both 57 and 59 produced an ABCG2 ATPase-depressing effect which is in agreement with our precedent cryo-EM study identifying 59 as an ATPase inhibitor that exerts its effect via locking the inward-facing conformation. Thermostabilization of ABCG2 by 57 and 59 can be taken as a hint to comparable binding to ABCG2. As reference substances, compounds 57 and 59 allow additional mechanistic studies on ABCG2 inhibition. Due to their stability in blood plasma, they are also applicable in vivo. The highly specific inhibitor 57 is suited for PET labeling, helping to further elucidate the (patho)physiological role of ABCG2, e.g. at the BBB.

Tariquidar-Related Chalcones and Ketones as ABCG2 Modulators

ABC transporters, including ABCG2, play a vital role in defending the human body against the vast range of xenobiotics. Even though this is beneficial for human health, these protein transporters have been implicated in the emerging resistance of cancer cells to a variety of structurally and functionally diverse anticancer drugs. In order to investigate their role in resistance, potent and selective ABCG2 modulators have been described in the literature. A leading class of modulators are the tariquidar analogues; however, their susceptibility to hydrolysis limits their applicable use. To overcome this, we synthesized a novel series of chalcone- and ketone-based compounds inspired by reported tariquidar analogues. Compounds were characterized and evaluated for their ABCG2 modulatory activity and ABC transporter selectivity. When compared to transporters ABCB1 and ABCC1, the chalcone-based compounds exhibited selectivity for ABCG2, while the ketone-based compounds showed only a slight preference for ABCG2. From the former series, chalcone 16d (UR-DP48) displayed similar activity to the reference fumitremorgin C, both producing comparable maximal effects. The compound exhibited marked antiproliferative activity, while cytotoxicity was less pronounced for the most active compound 17f from the ketone series. Chalcone-containing tariquidar analogues are promising modulators to aid in functional investigations of ABCG2 transporters.

Structural basis of small-molecule inhibition of human multidrug transporter ABCG2

ABCG2 is an ATP-binding cassette (ABC) transporter that protects tissues against xenobiotics, affects the pharmacokinetics of drugs and contributes to multidrug resistance. Although many inhibitors and modulators of ABCG2 have been developed, understanding their structure-activity relationship requires high-resolution structural insight. Here, we present cryo-EM structures of human ABCG2 bound to synthetic derivatives of the fumitremorgin C-related inhibitor Ko143 or the multidrug resistance modulator tariquidar. Both compounds are bound to the central, inward-facing cavity of ABCG2, blocking access for substrates and preventing conformational changes required for ATP hydrolysis. The high resolutions allowed for de novo building of the entire transporter and also revealed tightly bound phospholipids and cholesterol interacting with the lipid-exposed surface of the transmembrane domains (TMDs). Extensive chemical modifications of the Ko143 scaffold combined with in vitro functional analyses revealed the details of ABCG2 interactions with this compound family and provide a basis for the design of novel inhibitors and modulators.

Cytotoxicity and Efflux Pump Inhibition Induced by Molybdenum Disulfide and Boron Nitride Nanomaterials with Sheetlike Structure

Sheetlike molybdenum disulfide (MoS₂) and boron nitride (BN) nanomaterials have attracted attention in the past few years due to their unique material properties. However, information on adverse effects and their underlying mechanisms for sheetlike MoS₂ and BN nanomaterials is rare. In this study, cytotoxicities of sheetlike MoS₂ and BN nanomaterials on human hepatoma HepG2 cells were systematically investigated at different toxic end points. Results showed that MoS₂ and BN nanomaterials decreased cell viability at 30 μg/mL and induced adverse effects on intracellular ROS generation (≥2 μg/mL), mitochondrial depolarization (≥4 μg/mL), and membrane integrity (≥8 μg/mL for MoS₂ and ≥2 μg/mL for BN). Furthermore, this study first found that low exposure concentrations (0.2-2 μg/mL) of MoS₂ and BN nanomaterials could increase plasma membrane fluidity and inhibit transmembrane ATP binding cassette (ABC) efflux transporter activity, which make both nanomaterials act as a chemosensitizer (increasing arsenic toxicity). Damage to plasma membrane and release of soluble Mo or B species might be two reasons that both nanomaterials inhibit efflux pump activities. This study provides a systematic understanding of the cytotoxicity of sheetlike MoS₂ and BN nanomaterials at different exposure levels, which is important for their safe use.

ABCG2/BCRP: Specific and Nonspecific Modulators

Multidrug resistance (MDR) in cancer cells is the development of resistance to a variety of structurally and functionally nonrelated anticancer drugs. This phenomenon has become a major obstacle to cancer chemotherapy seriously affecting the clinical outcome. MDR is associated with increased drug efflux from cells mediated by an energy-dependent mechanism involving the ATP-binding cassette (ABC) transporters, mainly P-glycoprotein (ABCB1), the MDR-associated protein-1 (ABCC1), and the breast cancer resistance protein (ABCG2). The first two transporters have been widely studied already and reviews summarized the results. The ABCG2 protein has been a subject of intense study since its discovery as its overexpression has been detected in resistant cell lines in numerous types of human cancers. To date, a long list of modulators of ABCG2 exists and continues to increase. However, little is known about the clinical consequences of ABCG2 modulation. This makes the design of novel, potent, and nontoxic inhibitors of this efflux protein a major challenge to reverse MDR and thereby increase the success of chemotherapy. The aim of the present review is to describe and highlight specific and nonspecific modulators of ABCG2 reported to date based on the selectivity of the compounds, as many of them are effective against one or more ABC transport proteins.

Flavonoid derivatives as selective ABCC1 modulators: Synthesis and functional characterization

A series of chromones, bearing substituted amino groups or N-substituted carboxamide moieties in position 2, was synthesized and characterized in cellular assays for modulation of the ABC transporters ABCC1 (MDCKII-MRP1 cells), ABCB1 (Kb-V1 cells) and ABCG2 (MCF-7/Topo cells). The most potent ABCC1 modulators identified among these flavonoid-type compounds were comparable to the reference compound reversan regarding potency, but superior in terms of selectivity concerning ABCB1 and ABCG2 (2-[4-(Benzo[c][1,2,5]oxadiazol-5-ylmethyl)piperazin-1-yl]-5,7-dimethoxy-4H-chromen-4-one (51): ABCC1, IC50 11.3 μM; inactive at ABCB1 and ABCG2). Compound 51 was as effective as reversan in reverting ABCC1-mediated resistance to cytostatics in MDCKII-MRP1 cells and proved to be stable in mouse plasma and cell culture medium. Modulators, such as compound 51, are of potential value as pharmacological tools for the investigation of the (patho)physiological role of ABCC1.

Copper oxide and zinc oxide nanomaterials act as inhibitors of multidrug resistance transport in sea urchin embryos: their role as chemosensitizers

The ability of engineered nanomaterials (NMs) to act as inhibitors of ATP-binding cassette (ABC) efflux transporters in embryos of white sea urchin (Lytechinus pictus) was studied. Nanocopper oxide (nano-CuO), nanozinc oxide (nano-ZnO), and their corresponding metal ions (CuSO4 and ZnSO4) were used as target chemicals. The results showed that nano-CuO, nano-ZnO, CuSO4, and ZnSO4, even at relatively low concentrations (0.5 ppm), significantly increased calcein-AM (CAM, an indicator of ABC transporter activity) accumulation in sea urchin embryos at different stages of development. Exposure to nano-CuO, a very low solubility NM, at increasing times after fertilization (>30 min) decreased CAM accumulation, but nano-ZnO (much more soluble NM) did not, indicating that metal ions could cross the hardened fertilization envelope, but not undissolved metal oxide NMs. Moreover, nontoxic levels (0.5 ppm) of nano-CuO and nano-ZnO significantly increased developmental toxicity of vinblastine (an established ABC transporter substrate) and functioned as chemosensitizers. The multidrug resistance associated protein (MRP, one of ABC transporters) inhibitor MK571 significantly increased copper concentrations in embryos, indicating ABC transporters are important in maintaining low intracellular copper levels. We show that low concentrations of nano-CuO and nano-ZnO can make embryos more susceptible to other contaminants, representing a potent amplification of nanomaterial-related developmental toxicity.

Synthesis and ABCG2 inhibitory evaluation of 5-N-acetylardeemin derivatives

An efficient and versatile synthesis of 5-N-acetylardeemin (1a) and sixteen 2-, 3- and 13-substituted derivatives 1b-q was achieved through Ugi three-component reaction of 3,3a,8,8a-tetrahydropyrrolo[2,3-b]indole and cyclization/epimerization. Their inhibitory activity on the drug efflux of breast cancer resistance protein (ABCG2) was evaluated by flow cytometric analysis of accumulation of Hoechst 33342 stain in Flp-In-293/ABCG2 cells. Most of the derivatives exhibited a stronger ABCG2 inhibitory effect compared with natural product 1a. The derivative 1m with a 4-tolyl substituent at the C-13 position exhibited the most potent ABCG2 inhibition. This preliminary structure-activity relationship study indicates that an electron-rich aryl moiety as the 13-substituent is key to increasing the inhibitory activity.