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Gao Y, Wei C, Luo L, Tang Y, Yu Y, Li Y, Xing J, Pan X. Membrane-assisted tariquidar access and binding mechanisms of human ATP-binding cassette transporter P-glycoprotein. Front Mol Biosci 2024; 11:1364494. [PMID: 38560519 PMCID: PMC10979361 DOI: 10.3389/fmolb.2024.1364494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 02/20/2024] [Indexed: 04/04/2024] Open
Abstract
The human multidrug transporter P-glycoprotein (P-gp) is physiologically essential and of key relevance to biomedicine. Recent structural studies have shed light on the mode of inhibition of the third-generation inhibitors for human P-gp, but the molecular mechanism by which these inhibitors enter the transmembrane sites remains poorly understood. In this study, we utilized all-atom molecular dynamics (MD) simulations to characterize human P-gp dynamics under a potent inhibitor, tariquidar, bound condition, as well as the atomic-level binding pathways in an explicit membrane/water environment. Extensive unbiased simulations show that human P-gp remains relatively stable in tariquidar-free and bound states, while exhibiting a high dynamic binding mode at either the drug-binding pocket or the regulatory site. Free energy estimations by partial nudged elastic band (PNEB) simulations and Molecular Mechanics Generalized Born Surface Area (MM/GBSA) method identify two energetically favorable binding pathways originating from the cytoplasmic gate with an extended tariquidar conformation. Interestingly, free tariquidar in the lipid membrane predominantly adopts extended conformations similar to those observed at the regulatory site. These results suggest that membrane lipids may preconfigure tariquidar into an active ligand conformation for efficient binding to the regulatory site. However, due to its conformational plasticity, tariquidar ultimately moves toward the drug-binding pocket in both pathways, explaining how it acts as a substrate at low concentrations. Our molecular findings propose a membrane-assisted mechanism for the access and binding of the third-generation inhibitors to the binding sites of human P-gp, and offer deeper insights into the molecule design of more potent inhibitors against P-gp-mediated drug resistance.
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Affiliation(s)
- Yingjie Gao
- Department of Medicinal Chemistry, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
| | - Caiyan Wei
- Department of Medicinal Chemistry, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
| | - Lanxin Luo
- Department of Pathophysiology, School of Basic Medical Science, Southwest Medical University, Luzhou, Sichuan, China
| | - Yang Tang
- Department of Medicinal Chemistry, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
| | - Yongzhen Yu
- Department of Medicinal Chemistry, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
| | - Yaling Li
- Department of Pharmacy, The Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan, China
| | - Juan Xing
- Department of Pathophysiology, School of Basic Medical Science, Southwest Medical University, Luzhou, Sichuan, China
| | - Xianchao Pan
- Department of Medicinal Chemistry, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
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Interaction of a Homologous Series of Amphiphiles with P-glycoprotein in a Membrane Environment-Contributions of Polar and Non-Polar Interactions. Pharmaceutics 2023; 15:pharmaceutics15010174. [PMID: 36678803 PMCID: PMC9862096 DOI: 10.3390/pharmaceutics15010174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/06/2022] [Accepted: 12/26/2022] [Indexed: 01/05/2023] Open
Abstract
The transport of drugs by efflux transporters in biomembranes limits their bioavailability and is a major determinant of drug resistance development by cancer cells and pathogens. A large number of chemically dissimilar drugs are transported, and despite extensive studies, the molecular determinants of substrate specificity are still not well understood. In this work, we explore the role of polar and non-polar interactions on the interaction of a homologous series of fluorescent amphiphiles with the efflux transporter P-glycoprotein. The interaction of the amphiphiles with P-glycoprotein is evaluated through effects on ATPase activity, efficiency in inhibition of [125I]-IAAP binding, and partition to the whole native membranes containing the transporter. The results were complemented with partition to model membranes with a representative lipid composition, and details on the interactions established were obtained from MD simulations. We show that when the total concentration of amphiphile is considered, the binding parameters obtained are apparent and do not reflect the affinity for P-gp. A new formalism is proposed that includes sequestration of the amphiphiles in the lipid bilayer and the possible binding of several molecules in P-gp's substrate-binding pocket. The intrinsic binding affinity thus obtained is essentially independent of amphiphile hydrophobicity, highlighting the importance of polar interactions. An increase in the lipophilicity and amphiphilicity led to a more efficient association with the lipid bilayer, which maintains the non-polar groups of the amphiphiles in the bilayer, while the polar groups interact with P-gp's binding pocket. The presence of several amphiphiles in this orientation is proposed as a mechanism for inhibition of P-pg function.
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Secretion into Milk of the Main Metabolites of the Anthelmintic Albendazole Is Mediated by the ABCG2/BCRP Transporter. Antimicrob Agents Chemother 2022; 66:e0006222. [PMID: 35736132 PMCID: PMC9295555 DOI: 10.1128/aac.00062-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Albendazole (ABZ) is an anthelmintic with a broad-spectrum activity, widely used in human and veterinary medicine. ABZ is metabolized in all mammalian species to albendazole sulfoxide (ABZSO), albendazole sulfone (ABZSO2) and albendazole 2-aminosulphone (ABZSO2-NH2). ABZSO and ABZSO2 are the main metabolites detected in plasma and all three are detected in milk. The ATP-binding cassette transporter G2 (ABCG2) is an efflux transporter that is involved in the active secretion of several compounds into milk. Previous studies have reported that ABZSO was in vitro transported by ABCG2. The aim of this work is to correlate the in vitro interaction between ABCG2 and the other ABZ metabolites with their secretion into milk by this transporter. Using in vitro transepithelial assays with cells transduced with murine Abcg2 and human ABCG2, we show that ABZSO2 and ABZSO2-NH2 are in vitro substrates of both. In vivo assays carried out with wild-type and Abcg2-/- lactating female mice demonstrated that secretion into milk of these ABZ metabolites was mediated by Abcg2. Milk concentrations and milk-to-plasma ratio were higher in wild-type compared to Abcg2-/- mice for all the metabolites tested. We conclude that ABZ metabolites are undoubtedly in vitro substrates of ABCG2 and actively secreted into milk by ABCG2.
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Abdelaal MR, Haffez H. The potential roles of retinoids in combating drug resistance in cancer: implications of ATP-binding cassette (ABC) transporters. Open Biol 2022; 12:220001. [PMID: 35642494 PMCID: PMC9157304 DOI: 10.1098/rsob.220001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Multidrug resistance (MDR) means that tumour cells become unresponsive during or after the course of treatment to one or more of chemotherapeutic drugs. Chemotherapeutic resistance critically limits the treatment outcomes and remains a key challenge for clinicians. The alternation in intracellular drug concentration through the modulation of its transport across the plasma membrane is the major cause for MDR and is adopted by various mediators, including ATP-requiring enzymes (ATPases). Among these ATPases, ABC transporters have been extensively studied, and found to be highly implicated in tumorigenesis and MDR. The present review sheds light on the documented effects of retinoids on ABC enzymes to understand their mechanism in combating cancer cell resistance. This would open the gate to test the mechanism and applicability of different new synthetic retinoids in literature and market as modulators of ATP-dependent efflux pumping activity, and promote their applicability in diminishing anti-cancer drug resistance.
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Affiliation(s)
- Mohamed R. Abdelaal
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy, Helwan University, Cairo 11795, Egypt,Centre of Scientific Excellence ‘Helwan Structural Biology Research (HSBR)’, Helwan University, Cairo 11795, Egypt
| | - Hesham Haffez
- Biochemistry and Molecular Biology Department, Faculty of Pharmacy, Helwan University, Cairo 11795, Egypt,Centre of Scientific Excellence ‘Helwan Structural Biology Research (HSBR)’, Helwan University, Cairo 11795, Egypt
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Huang S, Gao Y, Zhang X, Lu J, Wei J, Mei H, Xing J, Pan X. Development of Simple and Accurate in Silico Ligand-Based Models for Predicting ABCG2 Inhibition. Front Chem 2022; 10:863146. [PMID: 35665065 PMCID: PMC9159808 DOI: 10.3389/fchem.2022.863146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 04/29/2022] [Indexed: 11/13/2022] Open
Abstract
The ATP binding cassette transporter ABCG2 is a physiologically important drug transporter that has a central role in determining the ADMET (absorption, distribution, metabolism, elimination, and toxicity) profile of therapeutics, and contributes to multidrug resistance. Thus, development of predictive in silico models for the identification of ABCG2 inhibitors is of great interest in the early stage of drug discovery. In this work, by exploiting a large public dataset, a number of ligand-based classification models were developed using partial least squares-discriminant analysis (PLS-DA) with molecular interaction field- and fingerprint-based structural description methods, regarding physicochemical and fragmental properties related to ABCG2 inhibition. An in-house dataset compiled from recently experimental studies was used to rigorously validated the model performance. The key molecular properties and fragments favored to inhibitor binding were discussed in detail, which was further explored by docking simulations. A highly informative chemical property was identified as the principal determinant of ABCG2 inhibition, which was utilized to derive a simple rule that had a strong capability for differentiating inhibitors from non-inhibitors. Furthermore, the incorporation of the rule into the best PLS-DA model significantly improved the classification performance, particularly achieving a high prediction accuracy on the independent in-house set. The integrative model is simple and accurate, which could be applied to the evaluation of drug-transporter interactions in drug development. Also, the dominant molecular features derived from the models may help medicinal chemists in the molecular design of novel inhibitors to circumvent ABCG2-mediated drug resistance.
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Affiliation(s)
- Shuheng Huang
- Department of Medicinal Chemistry, School of Pharmacy, Southwest Medical University, Luzhou, China
- Key Laboratory of Biorheological Science and Technology (Ministry of Education), College of Bioengineering, Chongqing University, Chongqing, China
| | - Yingjie Gao
- Department of Medicinal Chemistry, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Xuelian Zhang
- Department of Pathophysiology, School of Basic Medical Science, Southwest Medical University, Luzhou, China
| | - Ji Lu
- Department of Medicinal Chemistry, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Jun Wei
- Department of Medicinal Chemistry, School of Pharmacy, Southwest Medical University, Luzhou, China
| | - Hu Mei
- Key Laboratory of Biorheological Science and Technology (Ministry of Education), College of Bioengineering, Chongqing University, Chongqing, China
| | - Juan Xing
- Department of Pathophysiology, School of Basic Medical Science, Southwest Medical University, Luzhou, China
- *Correspondence: Xianchao Pan, ; Juan Xing,
| | - Xianchao Pan
- Department of Medicinal Chemistry, School of Pharmacy, Southwest Medical University, Luzhou, China
- *Correspondence: Xianchao Pan, ; Juan Xing,
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Singh K, Tarapcsák S, Gyöngy Z, Ritter Z, Batta G, Bosire R, Remenyik J, Goda K. Effects of Polyphenols on P-Glycoprotein (ABCB1) Activity. Pharmaceutics 2021; 13:pharmaceutics13122062. [PMID: 34959345 PMCID: PMC8707248 DOI: 10.3390/pharmaceutics13122062] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 11/09/2021] [Accepted: 11/26/2021] [Indexed: 11/17/2022] Open
Abstract
P-glycoprotein (Pgp, ABCB1) is a member of one of the largest families of active transporter proteins called ABC transporters. Thanks to its expression in tissues with barrier functions and its broad substrate spectrum, it is an important determinant of the absorption, metabolism and excretion of many drugs. Pgp and/or some other drug transporting ABC proteins (e.g., ABCG2, MRP1) are overexpressed in nearly all cancers and cancer stem cells by which cancer cells become resistant against many drugs. Thus, Pgp inhibition might be a strategy for fighting against drug-resistant cancer cells. Previous studies have shown that certain polyphenols interact with human Pgp. We tested the effect of 15 polyphenols of sour cherry origin on the basal and verapamil-stimulated ATPase activity of Pgp, calcein-AM and daunorubicin transport as well as on the conformation of Pgp using the conformation sensitive UIC2 mAb. We found that quercetin, quercetin-3-glucoside, narcissoside and ellagic acid inhibited the ATPase activity of Pgp and increased the accumulation of calcein and daunorubicin by Pgp-positive cells. Cyanidin-3O-sophoroside, catechin, naringenin, kuromanin and caffeic acid increased the ATPase activity of Pgp, while they had only a weaker effect on the intracellular accumulation of fluorescent Pgp substrates. Several tested polyphenols including epicatechin, trans-ferulic acid, oenin, malvin and chlorogenic acid were ineffective in all assays applied. Interestingly, catechin and epicatechin behave differently, although they are stereoisomers. We also investigated the effect of quercetin, naringenin and ellagic acid added in combination with verapamil on the transport activity of Pgp. In these experiments, we found that the transport inhibitory effect of the tested polyphenols and verapamil was additive or synergistic. Generally, our data demonstrate diverse interactions of the tested polyphenols with Pgp. Our results also call attention to the potential risks of drug–drug interactions (DDIs) associated with the consumption of dietary polyphenols concurrently with chemotherapy treatment involving Pgp substrate/inhibitor drugs.
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Affiliation(s)
- Kuljeet Singh
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (K.S.); (S.T.); (Z.G.); (Z.R.); (G.B.); (R.B.)
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, 4032 Debrecen, Hungary
| | - Szabolcs Tarapcsák
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (K.S.); (S.T.); (Z.G.); (Z.R.); (G.B.); (R.B.)
- Utah Center for Genetic Discovery, Eccles Institute of Human Genetics, University of Utah, Salt Lake City, UT 84112, USA
| | - Zsuzsanna Gyöngy
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (K.S.); (S.T.); (Z.G.); (Z.R.); (G.B.); (R.B.)
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, 4032 Debrecen, Hungary
| | - Zsuzsanna Ritter
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (K.S.); (S.T.); (Z.G.); (Z.R.); (G.B.); (R.B.)
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, 4032 Debrecen, Hungary
| | - Gyula Batta
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (K.S.); (S.T.); (Z.G.); (Z.R.); (G.B.); (R.B.)
- Department of Genetics and Applied Microbiology, Faculty of Science of Technology, University of Debrecen, 4032 Debrecen, Hungary
| | - Rosevalentine Bosire
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (K.S.); (S.T.); (Z.G.); (Z.R.); (G.B.); (R.B.)
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, 4032 Debrecen, Hungary
| | - Judit Remenyik
- Institute of Food Technology, Faculty of Agricultural and Food Sciences and Environmental Management, University of Debrecen, 4032 Debrecen, Hungary;
| | - Katalin Goda
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (K.S.); (S.T.); (Z.G.); (Z.R.); (G.B.); (R.B.)
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, 4032 Debrecen, Hungary
- Correspondence:
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7
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Garcia-Lino AM, Gomez-Gomez A, Garcia-Mateos D, de la Fuente A, Alvarez AI, Pozo OJ, Merino G. Analysis of the interaction between tryptophan-related compounds and ATP-binding cassette transporter G2 (ABCG2) using targeted metabolomics. Food Chem 2020; 344:128665. [PMID: 33250293 DOI: 10.1016/j.foodchem.2020.128665] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 11/04/2020] [Accepted: 11/14/2020] [Indexed: 12/19/2022]
Abstract
ATP-binding cassette transporter G2 (ABCG2) is involved in the secretion of several compounds in milk. The in vitro and in vivo interactions between tryptophan-related compounds and ABCG2 were investigated. The tryptophan metabolome was determined by liquid chromatography-tandem mass spectrometry in milk and plasma from wild-type and Abcg2-/- mice as well as dairy cows carrying the ABCG2 Y581S polymorphism (Y/S) and noncarrier animals (Y/Y). The milk-to-plasma ratios of tryptophan, kynurenic acid, kynurenine, anthranilic acid, and xanthurenic acid were higher in wild-type mice than in Abcg2-/- mice. The ratio was 2-fold higher in Y/S than in Y/Y cows for kynurenine. In vitro transport assays confirmed that some of these compounds were in vitro substrates of the transporter and validated the differences observed between the two variants of the bovine protein. These findings show that the secretion of metabolites belonging to the kynurenine pathway into milk is mediated by ABCG2.
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Affiliation(s)
- Alba M Garcia-Lino
- Department of Biomedical Sciences-Physiology, Faculty of Veterinary Medicine, Animal Health Institute (INDEGSAL), University of Leon, Campus de Vegazana, 24071 Leon, Spain
| | - Alex Gomez-Gomez
- Integrative Pharmacology and Systems Neuroscience Group, IMIM-Hospital del Mar Medical Research Institute, 88 Doctor Aiguader, 08003 Barcelona, Spain
| | - Dafne Garcia-Mateos
- Department of Biomedical Sciences-Physiology, Faculty of Veterinary Medicine, Animal Health Institute (INDEGSAL), University of Leon, Campus de Vegazana, 24071 Leon, Spain
| | - Alvaro de la Fuente
- Department of Biomedical Sciences-Physiology, Faculty of Veterinary Medicine, Animal Health Institute (INDEGSAL), University of Leon, Campus de Vegazana, 24071 Leon, Spain
| | - Ana I Alvarez
- Department of Biomedical Sciences-Physiology, Faculty of Veterinary Medicine, Animal Health Institute (INDEGSAL), University of Leon, Campus de Vegazana, 24071 Leon, Spain
| | - Oscar J Pozo
- Integrative Pharmacology and Systems Neuroscience Group, IMIM-Hospital del Mar Medical Research Institute, 88 Doctor Aiguader, 08003 Barcelona, Spain
| | - Gracia Merino
- Department of Biomedical Sciences-Physiology, Faculty of Veterinary Medicine, Animal Health Institute (INDEGSAL), University of Leon, Campus de Vegazana, 24071 Leon, Spain.
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Seelig A. P-Glycoprotein: One Mechanism, Many Tasks and the Consequences for Pharmacotherapy of Cancers. Front Oncol 2020; 10:576559. [PMID: 33194688 PMCID: PMC7649427 DOI: 10.3389/fonc.2020.576559] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 08/31/2020] [Indexed: 12/31/2022] Open
Abstract
P-glycoprotein or multidrug resistance protein (MDR1) is an adenosine triphosphate (ATP) binding cassette transporter (ABCB1) intensely investigated because it is an obstacle to successful pharmacotherapy of cancers. P-glycoprotein prevents cellular uptake of a large number of structurally and functionally diverse compounds, including most cancer therapeutics and in this way causes multidrug resistance (MDR). To overcome MDR, and thus improve cancer treatment, an understanding of P-glycoprotein inhibition at the molecular level is required. With this goal in mind, we propose rules that predict whether a compound is a modulator, substrate, inhibitor, or inducer of P-glycoprotein. This new set of rules is derived from a quantitative analysis of the drug binding and transport properties of P-glycoprotein. We further discuss the role of P-glycoprotein in immune surveillance and cell metabolism. Finally, the predictive power of the proposed rules is demonstrated with a set of FDA approved drugs which have been repurposed for cancer therapy.
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Affiliation(s)
- Anna Seelig
- Biozentrum, University of Basel, Basel, Switzerland
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9
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Horsey AJ, Briggs DA, Holliday ND, Briddon SJ, Kerr ID. Application of fluorescence correlation spectroscopy to study substrate binding in styrene maleic acid lipid copolymer encapsulated ABCG2. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183218. [PMID: 32057756 PMCID: PMC7156912 DOI: 10.1016/j.bbamem.2020.183218] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/28/2020] [Accepted: 01/30/2020] [Indexed: 12/16/2022]
Abstract
ABCG2 is one of a trio of human ATP binding cassette transporters that have the ability to bind and transport a diverse array of chemical substrates out of cells. This so-called "multidrug" transport has numerous physiological consequences including effects on how drugs are absorbed into and eliminated from the body. Understanding how ABCG2 is able to interact with multiple drug substrates remains an important goal in transporter biology. Most drugs are believed to interact with ABCG2 through the hydrophobic lipid bilayer and experimental systems for ABCG2 study need to incorporate this. We have exploited styrene maleic acid to solubilise ABCG2 from HEK293T cells overexpressing the transporter, and confirmed by dynamic light scattering and fluorescence correlation spectroscopy (FCS) that this results in the extraction of SMA lipid copolymer (SMALP) particles that are uniform in size and contain a dimer of ABCG2, which is the predominant physiological state. FCS was further employed to measure the diffusion of a fluorescent ABCG2 substrate (BODIPY-prazosin) in the presence and absence of SMALP particles of purified ABCG2. Autocorrelation analysis of FCS traces enabled the mathematical separation of free BODIPY-prazosin from drug bound to ABCG2 and allowed us to show that combining SMALP extraction with FCS can be used to study specific drug: transporter interactions.
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Affiliation(s)
- Aaron J Horsey
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Deborah A Briggs
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Nicholas D Holliday
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Stephen J Briddon
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK; Centre of Membrane Proteins and Receptors, University of Birmingham and University of Nottingham, The Midlands, UK.
| | - Ian D Kerr
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK.
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10
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Cseke A, Schwarz T, Jain S, Decker S, Vogl K, Urban E, Ecker GF. Propafenone analogue with additional H-bond acceptor group shows increased inhibitory activity on P-glycoprotein. Arch Pharm (Weinheim) 2020; 353:e1900269. [PMID: 31917466 DOI: 10.1002/ardp.201900269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 11/21/2019] [Accepted: 12/08/2019] [Indexed: 11/10/2022]
Abstract
P-glycoprotein (P-gp) is an ATP-dependent efflux pump that has a marked impact on the absorption, distribution, and excretion of therapeutic drugs. As P-gp inhibition can result in drug-drug interactions and altered drug bioavailability, identifying molecular properties that are linked to inhibition is of great interest in drug development. In this study, we combined chemical synthesis, in vitro testing, quantitative structure-activity relationship analysis, and docking studies to investigate the role of hydrogen bond (H-bond) donor/acceptor properties in transporter-ligand interaction. In a previous work, it has been shown that propafenone analogs with a 4-hydroxy-4-piperidine moiety exhibit a generally 10-fold higher P-gp inhibitory activity than expected based on their lipophilicity. Here, we specifically expanded the data set by introducing substituents at position 4 of the 4-phenylpiperidine moiety to assess the importance of H-bond donor/acceptor features in this region. The results suggest that indeed an H-bond acceptor, such as hydroxy and methoxy, increases the affinity by forming a H-bond with Tyr310.
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Affiliation(s)
- Anna Cseke
- Department of Pharmaceutical Chemistry, University of Vienna, Vienna, Austria
| | - Theresa Schwarz
- Department of Pharmaceutical Chemistry, University of Vienna, Vienna, Austria
| | - Sankalp Jain
- Department of Pharmaceutical Chemistry, University of Vienna, Vienna, Austria.,National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Simon Decker
- Department of Pharmaceutical Chemistry, University of Vienna, Vienna, Austria
| | - Kerstin Vogl
- Department of Pharmaceutical Chemistry, University of Vienna, Vienna, Austria
| | - Ernst Urban
- Department of Pharmaceutical Chemistry, University of Vienna, Vienna, Austria
| | - Gerhard F Ecker
- Department of Pharmaceutical Chemistry, University of Vienna, Vienna, Austria
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11
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Al-Ali AAA, Nielsen RB, Steffansen B, Holm R, Nielsen CU. Nonionic surfactants modulate the transport activity of ATP-binding cassette (ABC) transporters and solute carriers (SLC): Relevance to oral drug absorption. Int J Pharm 2019; 566:410-433. [DOI: 10.1016/j.ijpharm.2019.05.033] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Revised: 05/10/2019] [Accepted: 05/11/2019] [Indexed: 01/11/2023]
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12
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Xing J, Mei H, Huang S, Zhang D, Pan X. An Energetically Favorable Ligand Entrance Gate of a Multidrug Transporter Revealed by Partial Nudged Elastic Band Simulations. Comput Struct Biotechnol J 2019; 17:319-323. [PMID: 30899446 PMCID: PMC6406077 DOI: 10.1016/j.csbj.2019.02.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 02/14/2019] [Accepted: 02/15/2019] [Indexed: 11/08/2022] Open
Abstract
P-glycoprotein (P-gp) is a multidrug transporter, which harnesses the chemical energy of ATP to power the efflux of diverse chemotherapeutics out of cells and thus contributes to the development of multidrug resistance (MDR) in cancer. It has been proved that the ligand-binding pocket of P-gp is located at the transmembrane domains (TMDs). However, the access of ligands into the binding pocket remains to be elucidated, which definitely hinder the development of P-gp inhibitors. Herein, the access pathways of a well-known substrate rhodamine-123 and a cyclopeptide inhibitor QZ-Leu were characterized by time-independent partial nudged elastic band (PNEB) simulations. The decreasing free energies along the PNEB-optimized access pathway indicated that TM4/6 cleft may be an energetically favorable entrance gate for ligand entry into the binding pocket of P-gp. The results can be reconciled with a range of experimental studies, further corroborating the reliability of the gate revealed by computational simulations. Our atomic level description of the ligand access pathway provides valuable insights into the gating mechanism for drug uptake and transport by P-gp and other multidrug transporters. P-gp contributes to the development of multidrug resistance in cancer. The entrance of drugs into P-gp binding pocket has yet to be elucidated. An energetically favorable entrance gate was revealed by PNEB simulations. The computational results were reconciled with the experimental data. The atomic simulations provide insights into the gating mechanism of P-gp.
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Affiliation(s)
- Juan Xing
- Key Laboratory of Biorheological Science and Technology (Ministry of Education), College of Bioengineering, Chongqing University, Chongqing 400045, China.,Department of Pathophysiology, College of Basic Medical Science, Southwest Medical University, Luzhou, Sichuan 646000, China
| | - Hu Mei
- Key Laboratory of Biorheological Science and Technology (Ministry of Education), College of Bioengineering, Chongqing University, Chongqing 400045, China
| | - ShuHeng Huang
- Key Laboratory of Biorheological Science and Technology (Ministry of Education), College of Bioengineering, Chongqing University, Chongqing 400045, China
| | - Duo Zhang
- Key Laboratory of Biorheological Science and Technology (Ministry of Education), College of Bioengineering, Chongqing University, Chongqing 400045, China
| | - XianChao Pan
- Key Laboratory of Biorheological Science and Technology (Ministry of Education), College of Bioengineering, Chongqing University, Chongqing 400045, China.,Department of Medicinal Chemistry, College of Pharmacy, Southwest Medical University, Luzhou, Sichuan 646000, China
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13
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Al-Ali AAA, Steffansen B, Holm R, Nielsen CU. Nonionic surfactants increase digoxin absorption in Caco-2 and MDCKII MDR1 cells: Impact on P-glycoprotein inhibition, barrier function, and repeated cellular exposure. Int J Pharm 2018; 551:270-280. [DOI: 10.1016/j.ijpharm.2018.09.039] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 09/16/2018] [Accepted: 09/17/2018] [Indexed: 12/18/2022]
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14
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Residues contributing to drug transport by ABCG2 are localised to multiple drug-binding pockets. Biochem J 2018; 475:1553-1567. [PMID: 29661915 PMCID: PMC5934980 DOI: 10.1042/bcj20170923] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 03/28/2018] [Accepted: 04/16/2018] [Indexed: 01/09/2023]
Abstract
Multidrug binding and transport by the ATP-binding cassette transporter ABCG2 is a factor in the clinical resistance to chemotherapy in leukaemia, and a contributory factor to the pharmacokinetic profiles of many other prescribed drugs. Despite its importance, the structural basis of multidrug transport, i.e. the ability to transport multiple distinct chemicals, has remained elusive. Previous research has shown that at least two residues positioned towards the cytoplasmic end of transmembrane helix 3 (TM3) of the transporter play a role in drug transport. We hypothesised that other residues, either in the longitudinal span of TM3, or a perpendicular slice through the intracellular end of other TM helices would also contribute to drug binding and transport by ABCG2. Single-point mutant isoforms of ABCG2 were made at ∼30 positions and were analysed for effects on protein expression, localisation (western blotting, confocal microscopy) and function (flow cytometry) in a mammalian stable cell line expression system. Our data were interpreted in terms of recent structural data on the ABCG protein subfamily and enabled us to propose a surface-binding site for the drug mitoxantrone (MX) as well as a second, buried site for the same drug. Further mutational analysis of residues that spatially separate these two sites prompts us to suggest a molecular and structural pathway for MX transport by ABCG2.
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15
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Polysorbate 20 alters the oral bioavailability of etoposide in wild type and mdr1a deficient Sprague-Dawley rats. Int J Pharm 2018; 543:352-360. [DOI: 10.1016/j.ijpharm.2018.04.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 03/16/2018] [Accepted: 04/05/2018] [Indexed: 01/03/2023]
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16
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Köhler SC, Vahdati S, Scholz MS, Wiese M. Structure activity relationships, multidrug resistance reversal and selectivity of heteroarylphenyl ABCG2 inhibitors. Eur J Med Chem 2018; 146:483-500. [PMID: 29407974 DOI: 10.1016/j.ejmech.2018.01.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 01/02/2018] [Accepted: 01/04/2018] [Indexed: 10/18/2022]
Abstract
An overexpression of the transmembrane ATP-binding cassette transporter G2 (ABCG2, BCRP) in cancer tissues is supposed to play a role in the multidrug resistance (MDR) of tumors resulting in an inefficient chemotherapy. Therefore, co-administration of selective and non-toxic ABCG2 inhibitors is a promising strategy for improving the efficacy of chemotherapy by blocking ABCG2-mediated export of the cytostatic drugs. In the present study, we designed a small library of 38 novel compounds containing a heteroaryl-phenyl scaffold possessing several (bioisosteric) moieties, and twelve new precursors. We investigated the library for ABCG2 inhibition, for the selectivity against MDR-involved efflux pump ABCB1 (P-gp) and for toxicity. Structure activity relationship (SAR) studies revealed that, at least a phenylheteroaryl-phenylamide scaffold is necessary for observing an ABCG2 inhibition. 4-Methoxy-N-(2-(2-(6-methoxypyridin-3-yl)-2H-tetrazol-5-yl)phenyl)benzamide (43) exhibited a high potency (IC50 = 61 nM)), selectivity, low intrinsic toxicity and reversed the ABCG2-mediated drug resistance in presence of only 0.1 μM.
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Affiliation(s)
- Sebastian C Köhler
- Pharmazeutisches Institut, Rheinische Friedrich-Wilhelms-Universität Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | - Sahel Vahdati
- Pharmazeutisches Institut, Rheinische Friedrich-Wilhelms-Universität Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | - Matthias S Scholz
- Pharmazeutisches Institut, Rheinische Friedrich-Wilhelms-Universität Bonn, An der Immenburg 4, D-53121 Bonn, Germany
| | - Michael Wiese
- Pharmazeutisches Institut, Rheinische Friedrich-Wilhelms-Universität Bonn, An der Immenburg 4, D-53121 Bonn, Germany.
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17
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Structure-function relationships in ABCG2: insights from molecular dynamics simulations and molecular docking studies. Sci Rep 2017; 7:15534. [PMID: 29138424 PMCID: PMC5686161 DOI: 10.1038/s41598-017-15452-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 10/25/2017] [Indexed: 12/29/2022] Open
Abstract
Efflux pumps of the ATP-binding cassette transporters superfamily (ABC transporters) are frequently involved in the multidrug-resistance (MDR) phenomenon in cancer cells. Herein, we describe a new atomistic model for the MDR-related ABCG2 efflux pump, also named breast cancer resistance protein (BCRP), based on the recently published crystallographic structure of the ABCG5/G8 heterodimer sterol transporter, a member of the ABCG family involved in cholesterol homeostasis. By means of molecular dynamics simulations and molecular docking, a far-reaching characterization of the ABCG2 homodimer was obtained. The role of important residues and motifs in the structural stability of the transporter was comprehensively studied and was found to be in good agreement with the available experimental data published in literature. Moreover, structural motifs potentially involved in signal transmission were identified, along with two symmetrical drug-binding sites that are herein described for the first time, in a rational attempt to better understand how drug binding and recognition occurs in ABCG2 homodimeric transporters.
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18
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Abstract
ABCG2 is one of at least three human ATP binding cassette (ABC) transporters which can facilitate the export from cells of a wide range of chemically unrelated drug molecules. This capacity for multidrug transport is not only a confounding factor in chemotherapy, but is also one of the more perplexing phenomena in transporter biochemistry. Since its discovery in the last decade of the 20th century much has been revealed about ABCG2’s localization, physiological function and its broad substrate range. There have also been many investigations of its structure and molecular mechanism. In this mini review article we take a Rumsfeldian approach to ABCG2 and essentially ask what we do know about this transporter, and what we will need to know about this transporter if we wish to use modulation of ABCG2 activity as a therapeutic approach.
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19
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Tarapcsák S, Szalóki G, Telbisz Á, Gyöngy Z, Matúz K, Csősz É, Nagy P, Holb IJ, Rühl R, Nagy L, Szabó G, Goda K. Interactions of retinoids with the ABC transporters P-glycoprotein and Breast Cancer Resistance Protein. Sci Rep 2017; 7:41376. [PMID: 28145501 PMCID: PMC5286421 DOI: 10.1038/srep41376] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 12/20/2016] [Indexed: 01/16/2023] Open
Abstract
Retinoids – derivatives of vitamin A – are important cell permeant signaling molecules that regulate gene expression through activation of nuclear receptors. P-glycoprotein (Pgp) and ABCG2 are plasma membrane efflux transporters affecting the tissue distribution of numerous structurally unrelated lipophilic compounds. In the present work we aimed to study the interaction of the above ABC transporters with retinoid derivatives. We have found that 13-cis-retinoic acid, retinol and retinyl-acetate inhibited the Pgp and ABCG2 mediated substrate transport as well as the substrate stimulated ATPase activity of these transporters. Interestingly, 9-cis-retinoic acid and ATRA (all-trans retinoic acid), both are stereoisomers of 13-cis-retinoic acid, did not have any effect on the transporters’ activity. Our fluorescence anisotropy measurements revealed that 13-cis-retinoic acid, retinol and retinyl-acetate selectively increase the viscosity and packing density of the membrane. Thus, the mixed-type inhibition of both transporters by retinol and ABCG2 by 13-cis-retinoic acid may be the collective result of direct interactions of these retinoids with the substrate binding site(s) and of indirect interactions mediated by their membrane rigidifying effects.
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Affiliation(s)
- Szabolcs Tarapcsák
- Department of Biophysics and Cell Biology, University of Debrecen, Debrecen, H-4002 Egyetem tér 1, P.O.B. 400, Hungary
| | - Gábor Szalóki
- Department of Biophysics and Cell Biology, University of Debrecen, Debrecen, H-4002 Egyetem tér 1, P.O.B. 400, Hungary
| | - Ágnes Telbisz
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, H-1117 Magyar tudósok körútja 2, P.O.B. 286, Hungary
| | - Zsuzsanna Gyöngy
- Department of Biophysics and Cell Biology, University of Debrecen, Debrecen, H-4002 Egyetem tér 1, P.O.B. 400, Hungary
| | - Krisztina Matúz
- Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen, H-4002 Egyetem tér 1, P.O.B. 400, Hungary
| | - Éva Csősz
- Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen, H-4002 Egyetem tér 1, P.O.B. 400, Hungary
| | - Péter Nagy
- Department of Biophysics and Cell Biology, University of Debrecen, Debrecen, H-4002 Egyetem tér 1, P.O.B. 400, Hungary
| | - Imre J Holb
- Institute of Horticulture, University of Debrecen, Debrecen, H-4015 Böszörményi út 138, P.O.B. 400, Hungary.,Plant Protection Institute, Centre for Agricultural Research, Hungarian Academy of Sciences, Budapest, H-1525 Hermann Ottó út 15, P.O.B. 525, Hungary
| | - Ralph Rühl
- MTA-DE, Public Health Research Group of the Hungarian Academy of Sciences, Faculty of Public Health, University of Debrecen, Debrecen, H-4028 Kassai út 26, P.O.B. 400, Hungary
| | - László Nagy
- Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen, H-4002 Egyetem tér 1, P.O.B. 400, Hungary
| | - Gábor Szabó
- Department of Biophysics and Cell Biology, University of Debrecen, Debrecen, H-4002 Egyetem tér 1, P.O.B. 400, Hungary
| | - Katalin Goda
- Department of Biophysics and Cell Biology, University of Debrecen, Debrecen, H-4002 Egyetem tér 1, P.O.B. 400, Hungary
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20
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Rajagopalan N, Halasz A, Lu Y, Liu E, Monteil-Rivera F, Loewen MC. Probing allocrite preferences of 2 naturally occurring variants of the wheat LR34 ABC transporter. Biochem Cell Biol 2016; 94:459-470. [DOI: 10.1139/bcb-2016-0058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
For almost a century, the wheat Lr34 gene has conferred durable resistance against fungal rust diseases. While sequence homology predicts a putative ATP binding cassette transporter, the molecules that are transported (allocrites) by the encoded LR34 variants, and any associated mechanism of resistance, remain enigmatic. Here, the in vitro transport characteristics of 2 naturally occurring Lr34 variants (that differ in their ability to mediate disease resistance; Lr34sus and Lr34res) are investigated. Initially, a method to express and purify recombinant LR34Sus and LR34Res pseudo half-molecules from Saccharomyces cerevisiae, is described. Subsequently, a semi-targeted chlorophyll catabolite (CC) extraction from Lr34res-expressing wheat plants was performed based on previous reports highlighting increased accumulation of CCs in Lr34res-expressing flag leaves. Following partial biochemical characterization, this extract was applied to an LR34 in vitro proteoliposome transport assay. Mass spectroscopic analyses of transported metabolites revealed that LR34Sus imported a wheat metabolite of 618 Da and that the LR34Res transporter did not. While the identity of the LR34Sus transported metabolite remains to be confirmed and any allocrites of LR34Res remain to be detected, this work demonstrates that these variants have different allocrite preferences, a finding that may be relevant to the mechanism of disease resistance.
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Affiliation(s)
| | - Annamaria Halasz
- National Research Council of Canada, 6100 Royalmount Avenue, Montreal, QC H4P 2R2, Canada
| | - Yuping Lu
- National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Enwu Liu
- National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Fanny Monteil-Rivera
- National Research Council of Canada, 6100 Royalmount Avenue, Montreal, QC H4P 2R2, Canada
| | - Michele C. Loewen
- National Research Council of Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
- Department of Biochemistry, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada
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21
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Vasios G, Kosmidi A, Kalantzi OI, Tsantili-Kakoulidou A, Kavantzas N, Theocharis S, Giaginis C. Simple physicochemical properties related with lipophilicity, polarity, molecular size and ionization status exert significant impact on the transfer of drugs and chemicals into human breast milk. Expert Opin Drug Metab Toxicol 2016; 12:1273-1278. [PMID: 27573378 DOI: 10.1080/17425255.2016.1230197] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
OBJECTIVES The transfer of xenobiotic compounds into human breast milk has raised serious concerns in the last few years. The present study is aimed to assess whether simple physicochemical properties exert significant impact on human breast milk transfer of drugs and chemicals. METHODS A large data set of 375 xenobiotic compounds with available experimental milk to plasma (M/P) ratios was systematically compiled from the literature and explored with their physicochemical properties being further analyzed with respect to their extent to transfer into breast milk. RESULTS Xenobiotic compounds with increased breast milk transfer (M/P ≥ 1) were characterized by enhanced lipophilicity and decreased molecular size (p < 0.05). Enhanced polarity and hydrogen bonding capacity were more frequently observed in xenobiotic compounds with reduced breast milk transfer (p < 0.0001). Xenobiotic compounds presenting increased positive charge at pH 7.4 were characterized by enhanced breast milk transfer (p < 0.001). Xenobiotic compounds presenting increased negative charge at pH 7.4 were characterized by decreased breast milk transfer (p < 0.001). CONCLUSIONS The present study supports evidence that simple physicochemical properties related with lipophilicity, polarity, molecular size and ionization status exert significant impact on drugs and chemicals transport into human breast milk.
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Affiliation(s)
- George Vasios
- a Department of Food Science and Nutrition, School of Environment , University of the Aegean , Lemnos , Greece
| | - Aggeliki Kosmidi
- a Department of Food Science and Nutrition, School of Environment , University of the Aegean , Lemnos , Greece
| | - Olga-Ioanna Kalantzi
- b Department of Environment, School of Environment , University of the Aegean , Lesvos , Greece
| | - Anna Tsantili-Kakoulidou
- c Department of Pharmaceutical Chemistry, School of Pharmacy , University of Athens , Athens , Greece
| | - Nikolaos Kavantzas
- d First Department of Pathology, Medical School , University of Athens , Athens , Greece
| | - Stamatios Theocharis
- d First Department of Pathology, Medical School , University of Athens , Athens , Greece
| | - Constantinos Giaginis
- a Department of Food Science and Nutrition, School of Environment , University of the Aegean , Lemnos , Greece
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22
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Montanari F, Zdrazil B, Digles D, Ecker GF. Selectivity profiling of BCRP versus P-gp inhibition: from automated collection of polypharmacology data to multi-label learning. J Cheminform 2016; 8:7. [PMID: 26855674 PMCID: PMC4743411 DOI: 10.1186/s13321-016-0121-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 01/27/2016] [Indexed: 12/20/2022] Open
Abstract
Background The human ATP binding cassette transporters Breast Cancer Resistance Protein (BCRP) and Multidrug Resistance Protein 1 (P-gp) are co-expressed in many tissues and barriers, especially at the blood–brain barrier and at the hepatocyte canalicular membrane. Understanding their interplay in affecting the pharmacokinetics of drugs is of prime interest. In silico tools to predict inhibition and substrate profiles towards BCRP and P-gp might serve as early filters in the drug discovery and development process. However, to build such models, pharmacological data must be collected for both targets, which is a tedious task, often involving manual and poorly reproducible steps. Results Compounds with inhibitory activity measured against BCRP and/or P-gp were retrieved by combining Open Data and manually curated data from literature using a KNIME workflow. After determination of compound overlap, machine learning approaches were used to establish multi-label classification models for BCRP/P-gp. Different ways of addressing multi-label problems are explored and compared: label-powerset, binary relevance and classifiers chain. Label-powerset revealed important molecular features for selective or polyspecific inhibitory activity. In our dataset, only two descriptors (the numbers of hydrophobic and aromatic atoms) were sufficient to separate selective BCRP inhibitors from selective P-gp inhibitors. Also, dual inhibitors share properties with both groups of selective inhibitors. Binary relevance and classifiers chain allow improving the predictivity of the models. Conclusions The KNIME workflow proved a useful tool to merge data from diverse sources. It could be used for building multi-label datasets of any set of pharmacological targets for which there is data available either in the open domain or in-house. By applying various multi-label learning algorithms, important molecular features driving transporter selectivity could be retrieved. Finally, using the dataset with missing annotations, predictive models can be derived in cases where no accurate dense dataset is available (not enough data overlap or no well balanced class distribution).. ![]() Electronic supplementary material The online version of this article (doi:10.1186/s13321-016-0121-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Floriane Montanari
- Pharmacoinformatics Research Group, Department of Pharmaceutical Chemistry, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Barbara Zdrazil
- Pharmacoinformatics Research Group, Department of Pharmaceutical Chemistry, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Daniela Digles
- Pharmacoinformatics Research Group, Department of Pharmaceutical Chemistry, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Gerhard F Ecker
- Pharmacoinformatics Research Group, Department of Pharmaceutical Chemistry, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
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23
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Egido E, Müller R, Li-Blatter X, Merino G, Seelig A. Predicting Activators and Inhibitors of the Breast Cancer Resistance Protein (ABCG2) and P-Glycoprotein (ABCB1) Based on Mechanistic Considerations. Mol Pharm 2015; 12:4026-37. [DOI: 10.1021/acs.molpharmaceut.5b00463] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Estefanía Egido
- University of Basel, Biozentrum, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
- INDEGSAL,
Campus Vegazana s/n, University of Leon, 24071 Leon, Spain
- Department
of Biomedical Sciences—Physiology, Veterinary Faculty, Campus
Vegazana s/n, University of Leon, 24071 Leon, Spain
| | - Rita Müller
- University of Basel, Biozentrum, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Xiaochun Li-Blatter
- University of Basel, Biozentrum, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
| | - Gracia Merino
- INDEGSAL,
Campus Vegazana s/n, University of Leon, 24071 Leon, Spain
- Department
of Biomedical Sciences—Physiology, Veterinary Faculty, Campus
Vegazana s/n, University of Leon, 24071 Leon, Spain
| | - Anna Seelig
- University of Basel, Biozentrum, Klingelbergstrasse 50/70, CH-4056 Basel, Switzerland
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