1
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Novischi SYP, Karoly-Lakatos A, Chok K, Bonifer C, Becker-Baldus J, Glaubitz C. Probing the allosteric NBD-TMD crosstalk in the ABC transporter MsbA by solid-state NMR. Commun Biol 2024; 7:43. [PMID: 38182790 PMCID: PMC10770068 DOI: 10.1038/s42003-023-05617-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 11/21/2023] [Indexed: 01/07/2024] Open
Abstract
The ABC transporter MsbA plays a critical role in Gram-negative bacteria in the regulation of the outer membrane by translocating core-LPS across the inner membrane. Additionally, a broad substrate specificity for lipophilic drugs has been shown. The allosteric interplay between substrate binding in the transmembrane domains and ATP binding and turnover in the nucleotide-binding domains must be mediated via the NBD/TMD interface. Previous studies suggested the involvement of two intracellular loops called coupling helix 1 and 2 (CH1, CH2). Here, we demonstrate by solid-state NMR spectroscopy that substantial chemical shift changes within both CH1 and CH2 occur upon substrate binding, in the ATP hydrolysis transition state, and upon inhibitor binding. CH2 is domain-swapped within the MsbA structure, and it is noteworthy that substrate binding induces a larger response in CH2 compared to CH1. Our data demonstrate that CH1 and CH2 undergo structural changes as part of the TMD-NBD cross-talk.
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Affiliation(s)
- S Y Phoebe Novischi
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max von Laue Str. 9, 60438, Frankfurt, Germany
| | - Andrea Karoly-Lakatos
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max von Laue Str. 9, 60438, Frankfurt, Germany
| | - Kerby Chok
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max von Laue Str. 9, 60438, Frankfurt, Germany
| | - Christian Bonifer
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max von Laue Str. 9, 60438, Frankfurt, Germany
| | - Johanna Becker-Baldus
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max von Laue Str. 9, 60438, Frankfurt, Germany
| | - Clemens Glaubitz
- Institute for Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max von Laue Str. 9, 60438, Frankfurt, Germany.
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2
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Theuretzbacher U, Blasco B, Duffey M, Piddock LJV. Unrealized targets in the discovery of antibiotics for Gram-negative bacterial infections. Nat Rev Drug Discov 2023; 22:957-975. [PMID: 37833553 DOI: 10.1038/s41573-023-00791-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2023] [Indexed: 10/15/2023]
Abstract
Advances in areas that include genomics, systems biology, protein structure determination and artificial intelligence provide new opportunities for target-based antibacterial drug discovery. The selection of a 'good' new target for direct-acting antibacterial compounds is the first decision, for which multiple criteria must be explored, integrated and re-evaluated as drug discovery programmes progress. Criteria include essentiality of the target for bacterial survival, its conservation across different strains of the same species, bacterial species and growth conditions (which determines the spectrum of activity of a potential antibiotic) and the level of homology with human genes (which influences the potential for selective inhibition). Additionally, a bacterial target should have the potential to bind to drug-like molecules, and its subcellular location will govern the need for inhibitors to penetrate one or two bacterial membranes, which is a key challenge in targeting Gram-negative bacteria. The risk of the emergence of target-based drug resistance for drugs with single targets also requires consideration. This Review describes promising but as-yet-unrealized targets for antibacterial drugs against Gram-negative bacteria and examples of cognate inhibitors, and highlights lessons learned from past drug discovery programmes.
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Affiliation(s)
| | - Benjamin Blasco
- Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland
| | - Maëlle Duffey
- Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland
| | - Laura J V Piddock
- Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland.
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3
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Bonito CA, Ferreira RJ, Ferreira MJU, Gillet JP, Cordeiro MNDS, Dos Santos DJVA. Long-range communication between transmembrane- and nucleotide-binding domains does not depend on drug binding to mutant P-glycoprotein. J Biomol Struct Dyn 2023; 41:14428-14437. [PMID: 36858814 DOI: 10.1080/07391102.2023.2181633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 02/12/2023] [Indexed: 03/03/2023]
Abstract
In this study, the impact of four P-gp mutations (G185V, G830V, F978A and ΔF335) on drug-binding and efflux-related signal-transmission mechanism was comprehensively evaluated in the presence of ligands within the drug-binding pocket (DBP), experimentally related with changes in their drug efflux profiles. The severe repacking of the transmembrane helices (TMH), induced by mutations and exacerbated by the presence of ligands, indicates that P-gp is sensitive to perturbations in the transmembrane region. Alterations on drug-binding were also observed as a consequence of the TMH repacking, but were not always correlated with alterations on ligands binding mode and/or binding affinity. Finally, and although all P-gp variants holo systems showed considerable changes in the intracellular coupling helices/nucleotide-binding domain (ICH-NBD) interactions, they seem to be primarily induced by the mutation itself rather than by the presence of ligands within the DBP. The data further suggest that the changes in drug efflux experimentally reported are mostly related with changes on drug specificity rather than effects on signal-transmission mechanism. We also hypothesize that an increase in the drug-binding affinity may also be related with the decreased drug efflux, while minor changes in binding affinities are possibly related with the increased drug efflux observed in transfected cells.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Cátia A Bonito
- LAQV@REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre, Porto, Portugal
| | - Ricardo J Ferreira
- Red Glead Discovery AB, Medicon Village, Lund, Sweden
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal
| | - Maria-José U Ferreira
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal
| | - Jean-Pierre Gillet
- Laboratory of Molecular Cancer Biology, URPhyM, NARILIS, Faculty of Medicine, University of Namur, Namur, Belgium
| | - M Natália D S Cordeiro
- LAQV@REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre, Porto, Portugal
| | - Daniel J V A Dos Santos
- LAQV@REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre, Porto, Portugal
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal
- CBIOS-Research Center for Biosciences & Health Technologies, Universidade Lusófona de Humanidades e Tecnologias, Lisbon, Portugal
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4
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Sergent JA, Mathouet H, Hulen C, Lameiras P, Feuilloley M, Elomri A, Lomri NE. Effects of Two Natural Bisbenzylisoquinolines, Curine and Guattegaumerine, Extracted from Isolona hexaloba on Rhodamine Efflux by Abcb1b from Rat Glycocholic-Acid-Resistant Hepatocarcinoma Cells. Molecules 2022; 27:molecules27093030. [PMID: 35566380 PMCID: PMC9099951 DOI: 10.3390/molecules27093030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 04/29/2022] [Accepted: 05/05/2022] [Indexed: 02/06/2023] Open
Abstract
To develop new therapeutic molecules, it is essential to understand the biological effects and targets of clinically relevant compounds. In this article, we describe the extraction and characterization of two alkaloids from the roots of Isolona hexaloba—curine and guattegaumerine. The effect of these alkaloids on the multidrug efflux pump ABCB1 (MDR1/P-Glycoprotein) and their antiproliferative properties were studied. Compared to verapamil, a widely used inhibitor of P-gp, curine and guattegaumerine were found to be weak inhibitors of MDR1/P-Glycoprotein. The highest inhibition of efflux produced by verapamil disappeared in the presence of curine or guattegaumerine as competitors, and the most pronounced effect was achieved with curine. Altogether, this work has provided new insights into the biological effects of these alkaloids on the rat Mdr1b P-gp efflux mechanism and would be beneficial in the design of potent P-gp inhibitors.
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Affiliation(s)
- Jacques-Aurélien Sergent
- Department of Biology, UFR Sciences and Techniques, University of Cergy-Pontoise, 2 Ave A. Chauvin, 95302 Cergy-Pontoise, France;
| | - Hilarion Mathouet
- UNIROUEN, INSA Rouen, CNRS, COBRA (UMR 6014), Normandie University, 76000 Rouen, France; (H.M.); (P.L.)
| | - Christian Hulen
- Bacterial Communication and Antimicrobial Strategies Research Unit, University of Rouen Normandy, 55 rue Saint Germain, 2700 Evreux, France; (C.H.); (M.F.)
| | - Pedro Lameiras
- UNIROUEN, INSA Rouen, CNRS, COBRA (UMR 6014), Normandie University, 76000 Rouen, France; (H.M.); (P.L.)
| | - Marc Feuilloley
- Bacterial Communication and Antimicrobial Strategies Research Unit, University of Rouen Normandy, 55 rue Saint Germain, 2700 Evreux, France; (C.H.); (M.F.)
| | - Abdelhakim Elomri
- UNIROUEN, INSA Rouen, CNRS, COBRA (UMR 6014), Normandie University, 76000 Rouen, France; (H.M.); (P.L.)
- Correspondence: (A.E.); (N.-E.L.); Tel.: +33-235-148-591 (A.E.); +33-134-256-555 (N.-E.L.)
| | - Nour-Eddine Lomri
- Department of Biology, UFR Sciences and Techniques, University of Cergy-Pontoise, 2 Ave A. Chauvin, 95302 Cergy-Pontoise, France;
- Bacterial Communication and Antimicrobial Strategies Research Unit, University of Rouen Normandy, 55 rue Saint Germain, 2700 Evreux, France; (C.H.); (M.F.)
- Correspondence: (A.E.); (N.-E.L.); Tel.: +33-235-148-591 (A.E.); +33-134-256-555 (N.-E.L.)
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5
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Fang Y, Cao W, Xia M, Pan S, Xu X. Transport and Interactions of Co-incubated Bi-functional Flavonoids through Inhibiting the Function of P-Glycoprotein (P-gp) Using KB/Multidrug-Resistant (MDR) Cells and Rat Everted Gut Sacs. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:1923-1933. [PMID: 35112564 DOI: 10.1021/acs.jafc.1c07694] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
This study aims to evaluate the interaction of flavonoid-flavonoid by inhibiting the function of P-glycoprotein (P-gp). The cellular uptake of seven substrates and eleven co-incubated inhibitors was measured in KB/MDR cells. The effect of galangin or morin on the absorption of silibinin or wogonin was carried out in the rat everted gut sacs. Docking was performed to evaluate the interactions between inhibitors and P-gp. Most substrates were greatly enhanced by at least five co-incubated inhibitors. Conversely, the increased uptake of substrates coincided with a decrease or without affecting the uptake of inhibitors, implying a competitive/non-competitive inhibition on P-gp. The enhancement effect by galangin or morin on the transport of silibinin or wogonin was verified in everted gut sacs. Docking explained the inhibition of flavonoids on P-gp by competitively binding to the ATP site. These results provide a strategy for increasing the absorption of flavonoids by co-administration.
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Affiliation(s)
- Yajing Fang
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, P. R. China
- Department of Food Science, Faculty of Science, University of Copenhagen, Frederiksberg C DK-1958, Denmark
| | - Weiwei Cao
- College of Food and Bioengineering, Henan University of Science and Technology, Luoyang 471023, P. R. China
| | - Mengmeng Xia
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Siyi Pan
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Xiaoyun Xu
- Key Laboratory of Environment Correlative Dietology, Ministry of Education, Huazhong Agricultural University, Wuhan 430070, P. R. China
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6
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Abstract
A variety of environmental toxicants such as heavy metals, pesticides, organic
chemicals, etc produce harmful effects in our living systems. In the literature, various reports have
indicated the detrimental effects of toxicants such as immunotoxicity, cardiotoxicity,
nephrotoxicity, etc. Experimental animals are generally used to investigate the safety profile of
environmental chemicals, but research on animals has some limitations. Thus, there is a need for
alternative approaches. Docking study is one of the alternate techniques which predict the binding
affinity of molecules in the active site of a particular receptor without using animals. These
techniques can also be used to check the interactions of environmental toxicants towards biological
targets. Varieties of user-friendly software are available in the market for molecular docking, but
very few toxicologists use these techniques in the field of toxicology. To increase the use of these
techniques in the field of toxicology, understanding of basic concepts of these techniques is
required among toxicological scientists. This article has summarized the fundamental concepts of
docking in the context of its role in toxicology. Furthermore, these promising techniques are also
discussed in this study.
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Affiliation(s)
- Meenakshi Gupta
- Department of Pharmacology, Indo-Soviet Friendship Pharmacy College (ISFCP), Moga, Punjab, India
| | - Ruchika Sharma
- Department of Biotechnology, Indo-Soviet Friendship College of Professional Studies (ISFCPS), Moga, Punjab, India
| | - Anoop Kumar
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER)-Raebareli, Lucknow (UP), India
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7
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Syed SB, Lin SY, Arya H, Fu IH, Yeh TK, Charles MRC, Periyasamy L, Hsieh HP, Coumar MS. Overcoming vincristine resistance in cancer: Computational design and discovery of piperine-inspired P-glycoprotein inhibitors. Chem Biol Drug Des 2020; 97:51-66. [PMID: 32633857 DOI: 10.1111/cbdd.13758] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 06/05/2020] [Accepted: 06/28/2020] [Indexed: 01/03/2023]
Abstract
P-glycoprotein (P-gp)/MDR-1 plays a major role in the development of multidrug resistance (MDR) by pumping the chemotherapeutic drugs out of the cancer cells and reducing their efficacy. A number of P-gp inhibitors were reported to reverse the MDR when co-administered with chemotherapeutic drugs. Unfortunately, none has approved for clinical use due to toxicity issues. Some of the P-gp inhibitors tested in the clinics are reported to have cross-reactivity with CYP450 drug-metabolizing enzymes, resulting in unpredictable pharmacokinetics and toxicity of co-administered chemotherapeutic drugs. In this study, two piperine analogs (3 and 4) having lower cross-reactivity with CYP3A4 drug-metabolizing enzyme are identified as P-glycoprotein (P-gp) inhibitors through computational design, followed by synthesis and testing in MDR cancer cell lines over-expressing P-gp (KB ChR 8-5, SW480-VCR, and HCT-15). Both the analogs significantly increased the vincristine efficacy in MDR cancer cell lines at low micromole concentrations. Specifically, 3 caused complete reversal of vincristine resistance in KB ChR 8-5 cells and found to act as competitive inhibitor of P-gp as well as potentiated the vincristine-induced NF-KB-mediated apoptosis. Therefore, 3 ((2E,4E)-1-(6,7-dimethoxy-3,4-dihydroisoquinolin-2(1H)-yl)-5-(4-hydroxy-3-methoxyphenyl)penta-2,4-dien-1-one) can serve as a potential P-gp inhibitor for in vivo investigations, to reverse multidrug resistance in cancer.
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Affiliation(s)
- Safiulla Basha Syed
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, India.,DBT-Interdisciplinary Program in Life Sciences, Pondicherry University, Kalapet, India
| | - Shu-Yu Lin
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan
| | - Hemant Arya
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, India
| | - I-Hsuan Fu
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan
| | - Teng-Kuang Yeh
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan
| | | | - Latha Periyasamy
- Department of Biochemistry & Molecular Biology, School of Life Sciences, Pondicherry University, Kalapet, India
| | - Hsing-Pang Hsieh
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Zhunan, Taiwan.,Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan
| | - Mohane Selvaraj Coumar
- Centre for Bioinformatics, School of Life Sciences, Pondicherry University, Kalapet, India
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8
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Bonito CA, Ferreira RJ, Ferreira MJU, Gillet JP, Cordeiro MNDS, Dos Santos DJVA. Theoretical insights on helix repacking as the origin of P-glycoprotein promiscuity. Sci Rep 2020; 10:9823. [PMID: 32555203 PMCID: PMC7300024 DOI: 10.1038/s41598-020-66587-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 04/27/2020] [Indexed: 12/14/2022] Open
Abstract
P-glycoprotein (P-gp, ABCB1) overexpression is, currently, one of the most important multidrug resistance (MDR) mechanisms in tumor cells. Thus, modulating drug efflux by P-gp has become one of the most promising approaches to overcome MDR in cancer. Yet, more insights on the molecular basis of drug specificity and efflux-related signal transmission mechanism between the transmembrane domains (TMDs) and the nucleotide binding domains (NBDs) are needed to develop molecules with higher selectivity and efficacy. Starting from a murine P-gp crystallographic structure at the inward-facing conformation (PDB ID: 4Q9H), we evaluated the structural quality of the herein generated human P-gp homology model. This initial human P-gp model, in the presence of the “linker” and inserted in a suitable lipid bilayer, was refined through molecular dynamics simulations and thoroughly validated. The best human P-gp model was further used to study the effect of four single-point mutations located at the TMDs, experimentally related with changes in substrate specificity and drug-stimulated ATPase activity. Remarkably, each P-gp mutation is able to induce transmembrane α-helices (TMHs) repacking, affecting the drug-binding pocket volume and the drug-binding sites properties (e.g. volume, shape and polarity) finally compromising drug binding at the substrate binding sites. Furthermore, intracellular coupling helices (ICH) also play an important role since changes in the TMHs rearrangement are shown to have an impact in residue interactions at the ICH-NBD interfaces, suggesting that identified TMHs repacking affect TMD-NBD contacts and interfere with signal transmission from the TMDs to the NBDs.
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Affiliation(s)
- Cátia A Bonito
- LAQV@REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal
| | - Ricardo J Ferreira
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, 75124, Uppsala, Sweden
| | - Maria-José U Ferreira
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
| | - Jean-Pierre Gillet
- Laboratory of Molecular Cancer Biology, Molecular Physiology Research Unit-URPhyM, Namur Research Institute for Life Sciences (NARILIS), Faculty of Medicine, University of Namur, B-5000, Namur, Belgium
| | - M Natália D S Cordeiro
- LAQV@REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal
| | - Daniel J V A Dos Santos
- LAQV@REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal. .,Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal.
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9
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Mora Lagares L, Minovski N, Caballero Alfonso AY, Benfenati E, Wellens S, Culot M, Gosselet F, Novič M. Homology Modeling of the Human P-glycoprotein (ABCB1) and Insights into Ligand Binding through Molecular Docking Studies. Int J Mol Sci 2020; 21:ijms21114058. [PMID: 32517082 PMCID: PMC7312539 DOI: 10.3390/ijms21114058] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Revised: 05/28/2020] [Accepted: 06/02/2020] [Indexed: 12/12/2022] Open
Abstract
The ABCB1 transporter also known as P-glycoprotein (P-gp) is a transmembrane protein belonging to the ATP binding cassette super-family of transporters; it is a xenobiotic efflux pump that limits intracellular drug accumulation by pumping the compounds out of cells. P-gp contributes to a decrease of toxicity and possesses broad substrate specificity. It is involved in the failure of numerous anticancer and antiviral chemotherapies due to the multidrug resistance (MDR) phenomenon, where it removes the chemotherapeutics out of the targeted cells. Understanding the details of the ligand–P-gp interaction is therefore crucial for the development of drugs that might overcome the MRD phenomenon and for obtaining a more effective prediction of the toxicity of certain compounds. In this work, an in silico modeling was performed using homology modeling and molecular docking methods with the aim of better understanding the ligand–P-gp interactions. Based on different mouse P-gp structural templates from the PDB repository, a 3D model of the human P-gp (hP-gp) was constructed by means of protein homology modeling. The homology model was then used to perform molecular docking calculations on a set of thirteen compounds, including some well-known compounds that interact with P-gp as substrates, inhibitors, or both. The sum of ranking differences (SRD) was employed for the comparison of the different scoring functions used in the docking calculations. A consensus-ranking scheme was employed for the selection of the top-ranked pose for each docked ligand. The docking results showed that a high number of π interactions, mainly π–sigma, π–alkyl, and π–π type of interactions, together with the simultaneous presence of hydrogen bond interactions contribute to the stability of the ligand–protein complex in the binding site. It was also observed that some interacting residues in hP-gp are the same when compared to those observed in a co-crystallized ligand (PBDE-100) with mouse P-gp (PDB ID: 4XWK). Our in silico approach is consistent with available experimental results regarding P-gp efflux transport assay; therefore it could be useful in the prediction of the role of new compounds in systemic toxicity.
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Affiliation(s)
- Liadys Mora Lagares
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, 1000 Ljubljana, Slovenia;
- Jožef Stefan International Postgraduate School, 1000 Ljubljana, Slovenia;
- Correspondence: (L.M.L.); (M.N.); Tel.: +386-01-476-0253 (L.M.L. & M.N.)
| | - Nikola Minovski
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, 1000 Ljubljana, Slovenia;
| | - Ana Yisel Caballero Alfonso
- Jožef Stefan International Postgraduate School, 1000 Ljubljana, Slovenia;
- Laboratory of Environmental Chemistry and Toxicology, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche “Mario Negri”—IRCCS, 20156 Milano, Italy;
| | - Emilio Benfenati
- Laboratory of Environmental Chemistry and Toxicology, Department of Environmental Health Sciences, Istituto di Ricerche Farmacologiche “Mario Negri”—IRCCS, 20156 Milano, Italy;
| | - Sara Wellens
- Laboratoire de la Barrière Hémato-Encéphalique (LBHE), University Artois, UR 2465, F-62300 Lens, France; (S.W.); (M.C.); (F.G.)
| | - Maxime Culot
- Laboratoire de la Barrière Hémato-Encéphalique (LBHE), University Artois, UR 2465, F-62300 Lens, France; (S.W.); (M.C.); (F.G.)
| | - Fabien Gosselet
- Laboratoire de la Barrière Hémato-Encéphalique (LBHE), University Artois, UR 2465, F-62300 Lens, France; (S.W.); (M.C.); (F.G.)
| | - Marjana Novič
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, 1000 Ljubljana, Slovenia;
- Correspondence: (L.M.L.); (M.N.); Tel.: +386-01-476-0253 (L.M.L. & M.N.)
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10
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Vilar S, Sobarzo-Sánchez E, Uriarte E. In Silico Prediction of P-glycoprotein Binding: Insights from Molecular Docking Studies. Curr Med Chem 2019; 26:1746-1760. [DOI: 10.2174/0929867325666171129121924] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 11/10/2017] [Accepted: 11/21/2017] [Indexed: 12/21/2022]
Abstract
The P-glycoprotein is an efflux transporter that expels substances out of the
cells and has an important impact on the pharmacokinetic and pharmacodynamic properties
of drugs. The study of the interactions between ligands and the P-glycoprotein has
implications in the design of Central Nervous System drugs and their transport across the
blood-brain barrier. Moreover, since the P-glycoprotein is overexpressed in some types of
cancers, the protein is responsible for expelling the drug therapies from the cells, and
hence, for drug resistance. In this review, we describe different P-glycoprotein binding
sites reported for substrates, inhibitors and modulators, and focus on molecular docking
studies that provide useful information about drugs and P-glycoprotein interactions.
Docking in crystallized structures and homology models showed potential in the detection
of the binding site and key residues responsible for ligand recognition. Moreover, virtual
screening through molecular docking discriminates P-glycoprotein ligands from decoys.
We also discuss challenges and limitations of molecular docking simulations applied to
this particular protein. Computational structure-based approaches are very helpful in the
study of novel ligands that interact with the P-glycoprotein and provide insights to understand
the P-glycoprotein molecular mechanism of action.
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Affiliation(s)
- Santiago Vilar
- Departamento de Quimica Organica, Facultad de Farmacia, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Eduardo Sobarzo-Sánchez
- Departamento de Quimica Organica, Facultad de Farmacia, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Eugenio Uriarte
- Departamento de Quimica Organica, Facultad de Farmacia, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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11
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Yakusheva EN, Titov DS. Structure and Function of Multidrug Resistance Protein 1. BIOCHEMISTRY (MOSCOW) 2018; 83:907-929. [DOI: 10.1134/s0006297918080047] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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12
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Gade DR, Makkapati A, Yarlagadda RB, Peters GJ, Sastry B, Rajendra Prasad V. Elucidation of chemosensitization effect of acridones in cancer cell lines: Combined pharmacophore modeling, 3D QSAR, and molecular dynamics studies. Comput Biol Chem 2018; 74:63-75. [PMID: 29547875 DOI: 10.1016/j.compbiolchem.2018.02.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 02/05/2018] [Accepted: 02/15/2018] [Indexed: 02/07/2023]
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13
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Jeremić S, Amić A, Stanojević-Pirković M, Marković Z. Selected anthraquinones as potential free radical scavengers and P-glycoprotein inhibitors. Org Biomol Chem 2018; 16:1890-1902. [DOI: 10.1039/c8ob00060c] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this article, we estimated the scavenger capacity of six selected anthraquinones toward free radicals and their efficacy as inhibitors of P-glycoproteins.
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Affiliation(s)
- S. Jeremić
- Department of Chemical-Technological Sciences
- State University of Novi Pazar
- 36300 Novi Pazar
- Serbia
| | - A. Amić
- Department of Chemistry
- Josip Juraj Strossmayer University of Osijek
- 31000 Osijek
- Croatia
| | | | - Z. Marković
- Department of Chemical-Technological Sciences
- State University of Novi Pazar
- 36300 Novi Pazar
- Serbia
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14
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Ferreira RJ, Bonito CA, Ferreira MJU, dos Santos DJ. About P-glycoprotein: a new drugable domain is emerging from structural data. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1316] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Ricardo J. Ferreira
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy; Universidade de Lisboa; Lisboa Portugal
| | - Cátia A. Bonito
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy; Universidade de Lisboa; Lisboa Portugal
- LAQV@REQUIMTE/Department of Chemistry and Biochemistry, Faculty of Sciences; University of Porto; Porto Portugal
| | - Maria José U. Ferreira
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy; Universidade de Lisboa; Lisboa Portugal
| | - Daniel J.V.A. dos Santos
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy; Universidade de Lisboa; Lisboa Portugal
- LAQV@REQUIMTE/Department of Chemistry and Biochemistry, Faculty of Sciences; University of Porto; Porto Portugal
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15
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Prachayasittikul V, Worachartcheewan A, Toropova AP, Toropov AA, Schaduangrat N, Prachayasittikul V, Nantasenamat C. Large-scale classification of P-glycoprotein inhibitors using SMILES-based descriptors. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2017; 28:1-16. [PMID: 28056566 DOI: 10.1080/1062936x.2016.1264468] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 11/21/2016] [Indexed: 06/06/2023]
Abstract
P-glycoprotein (Pgp) inhibition has been considered as an effective strategy towards combating multidrug-resistant cancers. Owing to the substrate promiscuity of Pgp, the classification of its interacting ligands is not an easy task and is an ongoing issue of debate. Chemical structures can be represented by the simplified molecular input line entry system (SMILES) in the form of linear string of symbols. In this study, the SMILES notations of 2254 Pgp inhibitors including 1341 active, and 913 inactive compounds were used for the construction of a SMILE-based classification model using CORrelation And Logic (CORAL) software. The model provided an acceptable predictive performance as observed from statistical parameters consisting of accuracy, sensitivity and specificity that afforded values greater than 70% and MCC value greater than 0.6 for training, calibration and validation sets. In addition, the CORAL method highlighted chemical features that may contribute to increased and decreased Pgp inhibitory activities. This study highlights the potential of CORAL software for rapid screening of prospective compounds from a large chemical space and provides information that could aid in the design and development of potential Pgp inhibitors.
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Affiliation(s)
- V Prachayasittikul
- a Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology , Mahidol University , Bangkok , Thailand
| | - A Worachartcheewan
- a Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology , Mahidol University , Bangkok , Thailand
- b Department of Community Medical Technology, Faculty of Medical Technology , Mahidol University , Bangkok , Thailand
- c Department of Clinical Chemistry, Faculty of Medical Technology , Mahidol University , Bangkok , Thailand
| | - A P Toropova
- d IRCCS , Istituto di Ricerche Farmacologiche Mario Negri , Milano , Italy
| | - A A Toropov
- d IRCCS , Istituto di Ricerche Farmacologiche Mario Negri , Milano , Italy
| | - N Schaduangrat
- a Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology , Mahidol University , Bangkok , Thailand
| | - V Prachayasittikul
- e Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology , Mahidol University , Bangkok , Thailand
| | - C Nantasenamat
- a Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology , Mahidol University , Bangkok , Thailand
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16
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Ledwitch KV, Gibbs ME, Barnes RW, Roberts AG. Cooperativity between verapamil and ATP bound to the efflux transporter P-glycoprotein. Biochem Pharmacol 2016; 118:96-108. [PMID: 27531061 DOI: 10.1016/j.bcp.2016.08.013] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 08/12/2016] [Indexed: 12/21/2022]
Abstract
The P-glycoprotein (Pgp) transporter plays a central role in drug disposition by effluxing a chemically diverse range of drugs from cells through conformational changes and ATP hydrolysis. A number of drugs are known to activate ATP hydrolysis of Pgp, but coupling between ATP and drug binding is not well understood. The cardiovascular drug verapamil is one of the most widely studied Pgp substrates and therefore, represents an ideal drug to investigate the drug-induced ATPase activation of Pgp. As previously noted, verapamil-induced Pgp-mediated ATP hydrolysis kinetics was biphasic at saturating ATP concentrations. However, at subsaturating ATP concentrations, verapamil-induced ATPase activation kinetics became monophasic. To further understand this switch in kinetic behavior, the Pgp-coupled ATPase activity kinetics was checked with a panel of verapamil and ATP concentrations and fit with the substrate inhibition equation and the kinetic fitting software COPASI. The fits suggested that cooperativity between ATP and verapamil switched between low and high verapamil concentration. Fluorescence spectroscopy of Pgp revealed that cooperativity between verapamil and a non-hydrolyzable ATP analog leads to distinct global conformational changes of Pgp. NMR of Pgp reconstituted in liposomes showed that cooperativity between verapamil and the non-hydrolyzable ATP analog modulate each other's interactions. This information was used to produce a conformationally-gated model of drug-induced activation of Pgp-mediated ATP hydrolysis.
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Affiliation(s)
- Kaitlyn V Ledwitch
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA 30602, United States
| | - Morgan E Gibbs
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA 30602, United States
| | - Robert W Barnes
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA 30602, United States
| | - Arthur G Roberts
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, GA 30602, United States.
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17
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Mohana S, Ganesan M, Agilan B, Karthikeyan R, Srithar G, Beaulah Mary R, Ananthakrishnan D, Velmurugan D, Rajendra Prasad N, Ambudkar SV. Screening dietary flavonoids for the reversal of P-glycoprotein-mediated multidrug resistance in cancer. MOLECULAR BIOSYSTEMS 2016; 12:2458-70. [PMID: 27216424 PMCID: PMC4955727 DOI: 10.1039/c6mb00187d] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
P-Glycoprotein (P-gp) serves as a therapeutic target for the development of inhibitors to overcome multidrug resistance in cancer cells. Although various screening procedures have been practiced so far to develop first three generations of P-gp inhibitors, their toxicity and drug interaction profiles are still a matter of concern. To address the above important problem of developing safe and effective P-gp inhibitors, we have made systematic computational and experimental studies on the interaction of natural phytochemicals with human P-gp. Molecular docking and QSAR studies were carried out for 40 dietary phytochemicals in the drug-binding site of the transmembrane domains (TMDs) of P-gp. Dietary flavonoids exhibit better interactions with homology modeled human P-gp. Based on the computational analysis, selected flavonoids were tested for their inhibitory potential against P-gp transport function in drug resistant cell lines using calcein-AM and rhodamine 123 efflux assays. It has been found that quercetin and rutin were the highly desirable flavonoids for the inhibition of P-gp transport function and they significantly reduced resistance in cytotoxicity assays to paclitaxel in P-gp overexpressing MDR cell lines. Hence, quercetin and rutin may be considered as potential chemosensitizing agents to overcome multidrug resistance in cancer.
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MESH Headings
- ATP Binding Cassette Transporter, Subfamily B, Member 1/antagonists & inhibitors
- ATP Binding Cassette Transporter, Subfamily B, Member 1/chemistry
- ATP Binding Cassette Transporter, Subfamily B, Member 1/genetics
- ATP Binding Cassette Transporter, Subfamily B, Member 1/metabolism
- Antineoplastic Agents/chemistry
- Antineoplastic Agents/pharmacology
- Binding Sites
- Catalytic Domain
- Cell Line, Tumor
- Computer Simulation
- Dietary Supplements
- Dose-Response Relationship, Drug
- Drug Resistance, Neoplasm/genetics
- Drug Screening Assays, Antitumor
- Flavonoids/chemistry
- Flavonoids/pharmacology
- Humans
- Ligands
- Models, Molecular
- Molecular Docking Simulation
- Protein Binding
- Protein Conformation
- Structure-Activity Relationship
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Affiliation(s)
- S Mohana
- Department of Biochemistry and Biotechnology, Annamalai University, Annamalai Nagar-608 002, Tamilnadu, India.
| | - M Ganesan
- Department of Biochemistry and Biotechnology, Annamalai University, Annamalai Nagar-608 002, Tamilnadu, India.
| | - B Agilan
- Department of Biochemistry and Biotechnology, Annamalai University, Annamalai Nagar-608 002, Tamilnadu, India.
| | - R Karthikeyan
- Department of Biochemistry and Biotechnology, Annamalai University, Annamalai Nagar-608 002, Tamilnadu, India.
| | - G Srithar
- Department of Biochemistry and Biotechnology, Annamalai University, Annamalai Nagar-608 002, Tamilnadu, India.
| | - R Beaulah Mary
- Department of Biochemistry and Biotechnology, Annamalai University, Annamalai Nagar-608 002, Tamilnadu, India.
| | - D Ananthakrishnan
- Bioinformatics Infrastructure Facility (BIF), University of Madras, Guindy Campus, Chennai, Tamil Nadu, India
| | - D Velmurugan
- Bioinformatics Infrastructure Facility (BIF), University of Madras, Guindy Campus, Chennai, Tamil Nadu, India and CAS in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai, Tamil Nadu, India
| | - N Rajendra Prasad
- Department of Biochemistry and Biotechnology, Annamalai University, Annamalai Nagar-608 002, Tamilnadu, India.
| | - Suresh V Ambudkar
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive, Bethesda, Maryland 20892-4256, USA.
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18
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Verebova V, Belej D, Joniova J, Jurasekova Z, Miskovsky P, Kozar T, Horvath D, Stanicova J, Huntosova V. Deeper insights into the drug defense of glioma cells against hydrophobic molecules. Int J Pharm 2016; 503:56-67. [PMID: 26940808 DOI: 10.1016/j.ijpharm.2016.02.042] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 02/24/2016] [Accepted: 02/26/2016] [Indexed: 12/28/2022]
Abstract
By means of fluorescence microscopy the intracellular distribution of fluorescent drugs with different hydrophobicity (quinizarin, emodin and hypericin) was studied. Selective photoactivation of these drugs in precisely defined position (nuclear envelope) allowed moderately hydrophobic emodin enter the nucleus. Highly hydrophobic hypericin was predominantly kept in the membranes with no fluorescence observed in the nucleus. The redistribution of quinizarin, emodin and hypericin between lipids, proteins and DNA was studied in solutions and cells. Based on these results was proposed theoretical model of hydrophobic drugs' nuclear internalization after photo-activation. Molecular docking models showed that hypericin has the strongest affinity to P-glycoprotein involved in the cell detoxification. Presence of 10 μM quinizarin, emodin or hypericin increased P-glycoprotein function in U87 MG cells. Moreover, emodin pretreatment allowed quinizarin nuclear internalization without photo-activation, which was not the case for hypericin. The synergy of such pretreatment and photo-activation should lessen the drug doses with simultaneous increase of drug efficacy triggering cell apoptosis/necrosis.
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Affiliation(s)
- Valeria Verebova
- Institute of Biophysics, University of Veterinary Medicine and Pharmacy, Komenskeho 73, 041 81 Kosice, Slovakia.
| | - Dominik Belej
- Department of Biophysics, Faculty of Science, P. J. Safarik University in Kosice, Jesenna 5, 041 54 Kosice, Slovakia.
| | - Jaroslava Joniova
- Department of Biophysics, Faculty of Science, P. J. Safarik University in Kosice, Jesenna 5, 041 54 Kosice, Slovakia.
| | - Zuzana Jurasekova
- Department of Biophysics, Faculty of Science, P. J. Safarik University in Kosice, Jesenna 5, 041 54 Kosice, Slovakia; Center for Interdisciplinary Biosciences, Faculty of Science, P. J. Safarik University in Kosice, Jesenna 5, 041 54 Kosice, Slovakia.
| | - Pavol Miskovsky
- Department of Biophysics, Faculty of Science, P. J. Safarik University in Kosice, Jesenna 5, 041 54 Kosice, Slovakia; Center for Interdisciplinary Biosciences, Faculty of Science, P. J. Safarik University in Kosice, Jesenna 5, 041 54 Kosice, Slovakia.
| | - Tibor Kozar
- Center for Interdisciplinary Biosciences, Faculty of Science, P. J. Safarik University in Kosice, Jesenna 5, 041 54 Kosice, Slovakia.
| | - Denis Horvath
- Center for Interdisciplinary Biosciences, Faculty of Science, P. J. Safarik University in Kosice, Jesenna 5, 041 54 Kosice, Slovakia.
| | - Jana Stanicova
- Institute of Biophysics, University of Veterinary Medicine and Pharmacy, Komenskeho 73, 041 81 Kosice, Slovakia; Institute of Biophysics and Informatics, First Faculty of Medicine, Charles University in Prague, Salmovska 1, 120 00 Prague 2, Czech Republic.
| | - Veronika Huntosova
- Center for Interdisciplinary Biosciences, Faculty of Science, P. J. Safarik University in Kosice, Jesenna 5, 041 54 Kosice, Slovakia.
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19
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Subramanian N, Condic-Jurkic K, Mark AE, O'Mara ML. Identification of Possible Binding Sites for Morphine and Nicardipine on the Multidrug Transporter P-Glycoprotein Using Umbrella Sampling Techniques. J Chem Inf Model 2015; 55:1202-17. [PMID: 25938863 DOI: 10.1021/ci5007382] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The multidrug transporter P-glycoprotein (P-gp) is central to the development of multidrug resistance in cancer. While residues essential for transport and binding have been identified, the location, composition, and specificity of potential drug binding sites are uncertain. Here molecular dynamics simulations are used to calculate the free energy profile for the binding of morphine and nicardipine to P-gp. We show that morphine and nicardipine primarily interact with key residues implicated in binding and transport from mutational studies, binding at different but overlapping sites within the transmembrane pore. Their permeation pathways were distinct but involved overlapping sets of residues. The results indicate that the binding location and permeation pathways of morphine and nicardipine are not well separated and cannot be considered as unique. This has important implications for our understanding of substrate uptake and transport by P-gp. Our results are independent of the choice of starting structure and consistent with a range of experimental studies.
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Affiliation(s)
- Nandhitha Subramanian
- †School of Chemistry and Molecular Biosciences, §The Institute for Molecular Biosciences, and ‡School of Mathematics and Physics, University of Queensland, Brisbane, QLD 4072, Australia
| | - Karmen Condic-Jurkic
- †School of Chemistry and Molecular Biosciences, §The Institute for Molecular Biosciences, and ‡School of Mathematics and Physics, University of Queensland, Brisbane, QLD 4072, Australia
| | - Alan E Mark
- †School of Chemistry and Molecular Biosciences, §The Institute for Molecular Biosciences, and ‡School of Mathematics and Physics, University of Queensland, Brisbane, QLD 4072, Australia
| | - Megan L O'Mara
- †School of Chemistry and Molecular Biosciences, §The Institute for Molecular Biosciences, and ‡School of Mathematics and Physics, University of Queensland, Brisbane, QLD 4072, Australia
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20
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Loo TW, Clarke DM. The Transmission Interfaces Contribute Asymmetrically to the Assembly and Activity of Human P-glycoprotein. J Biol Chem 2015; 290:16954-63. [PMID: 25987565 PMCID: PMC4505440 DOI: 10.1074/jbc.m115.652602] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Indexed: 11/21/2022] Open
Abstract
P-glycoprotein (P-gp; ABCB1) is an ABC drug pump that protects us from toxic compounds. It is clinically important because it confers multidrug resistance. The homologous halves of P-gp each contain a transmembrane (TM) domain (TMD) with 6 TM segments followed by a nucleotide-binding domain (NBD). The drug- and ATP-binding sites reside at the interface between the TMDs and NBDs, respectively. Each NBD is connected to the TMDs by a transmission interface involving a pair of intracellular loops (ICLs) that form ball-and-socket joints. P-gp is different from CFTR (ABCC7) in that deleting NBD2 causes misprocessing of only P-gp. Therefore, NBD2 might be critical for stabilizing ICLs 2 and 3 that form a tetrahelix bundle at the NBD2 interface. Here we report that the NBD1 and NBD2 transmission interfaces in P-gp are asymmetric. Point mutations to 25 of 60 ICL2/ICL3 residues at the NBD2 transmission interface severely reduced P-gp assembly while changes to the equivalent residues in ICL1/ICL4 at the NBD1 interface had little effect. The hydrophobic nature at the transmission interfaces was also different. Mutation of Phe-1086 or Tyr-1087 to arginine at the NBD2 socket blocked activity or assembly while the equivalent mutations at the NBD1 socket had only modest effects. The results suggest that the NBD transmission interfaces are asymmetric. In contrast to the ICL2/3-NBD2 interface, the ICL1/4-NBD1 transmission interface is more hydrophilic and insensitive to mutations. Therefore the ICL2/3-NBD2 transmission interface forms a precise hydrophobic connection that acts as a linchpin for assembly and trafficking of P-gp.
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Affiliation(s)
- Tip W Loo
- From the Departments of Medicine and Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - David M Clarke
- From the Departments of Medicine and Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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21
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Singh B, Kumar A, Joshi P, Guru SK, Kumar S, Wani ZA, Mahajan G, Hussain A, Qazi AK, Kumar A, Bharate SS, Gupta BD, Sharma PR, Hamid A, Saxena AK, Mondhe DM, Bhushan S, Bharate SB, Vishwakarma RA. Colchicine derivatives with potent anticancer activity and reduced P-glycoprotein induction liability. Org Biomol Chem 2015; 13:5674-89. [PMID: 25895604 DOI: 10.1039/c5ob00406c] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Colchicine (1), a nature-derived microtubule polymerization inhibitor, develops multi-drug resistance in tumor cells due to its P-gp substrate and induction activity, which in turn leads to its rapid efflux from tumor cells. This auto-induction of the efflux of colchicine remains a major challenge to medicinal chemists. Based on structure-based molecular modeling, a series of new colchicine derivatives were designed and synthesized with a potential for reduced P-gp induction liability. Screening of the prepared derivatives for P-gp induction activity revealed that a number of derivatives possess remarkably lower P-gp-induction activity (>90% intracellular accumulation of rhodamine 123 in LS-180 cells) compared to the parent natural product colchicine (62% Rh123 accumulation in LS-180 cells). The reduced P-gp-induction activity of new derivatives may be due to their reduced ability to interact and change the conformation of P-gp. The synthesized derivatives were then screened for antiproliferative activity against two colon cancer cell lines including HCT-116 and Colo-205. The derivative 4o showed potent cytotoxicity in HCT-116 cells with IC50 of 0.04 μM with significantly reduced P-gp induction liability. Compound 4o also inhibited microtubule assembly and induced expression of pro-apoptotic protein p21. In an Ehrlich solid tumor mice model, compound 4o showed 38% TGI with no mortality at 2 mg kg(-1) dose (oral). Compound 4o, with potent in vitro and in vivo anticancer activity, significantly reduced P-gp induction activity and its excellent physicochemical and pharmacokinetic properties open up new opportunities for the colchicine scaffold.
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Affiliation(s)
- Baljinder Singh
- Natural Product Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu 180001, India
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22
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Prajapati R, Sangamwar AT. Translocation mechanism of P-glycoprotein and conformational changes occurring at drug-binding site: Insights from multi-targeted molecular dynamics. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:2882-98. [DOI: 10.1016/j.bbamem.2014.07.018] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 07/03/2014] [Accepted: 07/08/2014] [Indexed: 11/29/2022]
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23
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Daddam JR, Dowlathabad MR, Panthangi S, Jasti P. Molecular docking and P-glycoprotein inhibitory activity of Flavonoids. Interdiscip Sci 2014; 6:167-75. [DOI: 10.1007/s12539-012-0197-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2012] [Revised: 03/19/2012] [Accepted: 09/11/2012] [Indexed: 12/18/2022]
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24
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Structure and function of BCRP, a broad specificity transporter of xenobiotics and endobiotics. Arch Toxicol 2014; 88:1205-48. [DOI: 10.1007/s00204-014-1224-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2014] [Accepted: 03/06/2014] [Indexed: 12/20/2022]
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25
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Chae SW, Han AR, Park JH, Rhie JY, Lim HJ, Seo EK, Lee HJ. In vitro and in vivo evaluation of phenylbutenoid dimers as inhibitors of P-glycoprotein. JOURNAL OF NATURAL PRODUCTS 2013; 76:2277-2281. [PMID: 24266329 DOI: 10.1021/np4004917] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
The expression of P-glycoprotein (P-gp), an ATP-dependent efflux transporter, is closely associated with the failure of chemotherapy and drug absorption. Two synthesized optically active phenylbutenoid dimers, 3S-(3,4-dimethoxyphenyl)-4R-{(E)-3,4-dimethoxystyryl}cyclohex-1-ene (1) and 3R-(3,4-dimethoxyphenyl)-4S-{(E)-3,4-dimethoxystyryl}cyclohex-1-ene (2), were tested for their P-gp inhibitory effects by measuring cellular accumulation and efflux of daunomycin in P-gp-overexpressed human breast cancer cells (MCF-7/ADR). Compound 2 significantly increased the accumulation of daunomycin (539%) and decreased the efflux of this compound (55.4%), and similar results were observed for 1. ATPase assays and Western blot analysis were performed to identify the mechanisms by which compounds 1 and 2 inhibit P-gp. In addition, changes in the pharmacokinetic profile of paclitaxel coadministered with 2 in rats were evaluated. Paclitaxel (25 mg/kg) when orally administered with 2 (5 mg/kg) improved its relative bioavailability by 185%. Compound 2 effectively improved cellular accumulation by reducing the efflux of daunomycin and significantly enhanced oral exposure to paclitaxel. Therefore, compound 2 may be useful for improving oral exposure and cellular availability of drugs that are also substrates of P-gp.
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Affiliation(s)
- Song Wha Chae
- College of Pharmacy, Graduate School of Pharmaceutical Sciences (Ewha Global Top 5 Program), Ewha Womans University , Seoul 120-750, Korea
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26
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Tan W, Mei H, Chao L, Liu T, Pan X, Shu M, Yang L. Combined QSAR and molecule docking studies on predicting P-glycoprotein inhibitors. J Comput Aided Mol Des 2013; 27:1067-73. [DOI: 10.1007/s10822-013-9697-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 12/02/2013] [Indexed: 12/27/2022]
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27
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Saneja A, Khare V, Alam N, Dubey RD, Gupta PN. Advances in P-glycoprotein-based approaches for delivering anticancer drugs: pharmacokinetic perspective and clinical relevance. Expert Opin Drug Deliv 2013; 11:121-38. [DOI: 10.1517/17425247.2014.865014] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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28
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Kapoor K, Bhatnagar J, Chufan EE, Ambudkar SV. Mutations in intracellular loops 1 and 3 lead to misfolding of human P-glycoprotein (ABCB1) that can be rescued by cyclosporine A, which reduces its association with chaperone Hsp70. J Biol Chem 2013; 288:32622-32636. [PMID: 24064216 DOI: 10.1074/jbc.m113.498980] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
P-glycoprotein (P-gp) is an ATP binding cassette transporter that effluxes a variety of structurally diverse compounds including anticancer drugs. Computational models of human P-gp in the apo- and nucleotide-bound conformation show that the adenine group of ATP forms hydrogen bonds with the conserved Asp-164 and Asp-805 in intracellular loops 1 and 3, respectively, which are located at the interface between the nucleotide binding domains and transmembrane domains. We investigated the role of Asp-164 and Asp-805 residues by substituting them with cysteine in a cysteine-less background. It was observed that the D164C/D805C mutant, when expressed in HeLa cells, led to misprocessing of P-gp, which thus failed to transport the drug substrates. The misfolded protein could be rescued to the cell surface by growing the cells at a lower temperature (27 °C) or by treatment with substrates (cyclosporine A, FK506), modulators (tariquidar), or small corrector molecules. We also show that short term (4-6 h) treatment with 15 μM cyclosporine A or FK506 rescues the pre-formed immature protein trapped in the endoplasmic reticulum in an immunophilin-independent pathway. The intracellularly trapped misprocessed protein associates more with chaperone Hsp70, and the treatment with cyclosporine A reduces the association of mutant P-gp, thus allowing it to be trafficked to the cell surface. The function of rescued cell surface mutant P-gp is similar to that of wild-type protein. These data demonstrate that the Asp-164 and Asp-805 residues are not important for ATP binding, as proposed earlier, but are critical for proper folding and maturation of a functional transporter.
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Affiliation(s)
- Khyati Kapoor
- From the Laboratory of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892-4256
| | - Jaya Bhatnagar
- From the Laboratory of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892-4256
| | - Eduardo E Chufan
- From the Laboratory of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892-4256
| | - Suresh V Ambudkar
- From the Laboratory of Cell Biology, Center for Cancer Research, NCI, National Institutes of Health, Bethesda, Maryland 20892-4256.
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Yang T, Xu F, Xu J, Fang D, Yu Y, Chen Y. Comparison of liquid chromatography-tandem mass spectrometry-based targeted proteomics and conventional analytical methods for the determination of P-glycoprotein in human breast cancer cells. J Chromatogr B Analyt Technol Biomed Life Sci 2013; 936:18-24. [PMID: 23968647 DOI: 10.1016/j.jchromb.2013.07.023] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 07/05/2013] [Accepted: 07/23/2013] [Indexed: 10/26/2022]
Abstract
P-glycoprotein (P-gp) is the most frequently proposed factor for multi-drug resistance. It is traditionally measured using antibody-based methods. While these techniques can provide relative quantification values for P-gp levels, the important information that is usually missing is its amount in the biological system. In this study, a novel and advanced liquid chromatography-tandem mass spectrometry (LC/MS/MS)-based targeted proteomics assay was developed and validated for the determination of P-gp in the breast cancer drug sensitive cell line MCF-7/WT and the drug resistant cell line MCF-7/ADR. Three tryptic peptides (434STTVQLMQR442, 674GSQAQDR680 and 368IIDNKPSIDSYSK380) can specifically represent P-gp. Among these peptides, 434STTVQLMQR442 was selected as the surrogate analyte for quantification, and a stable isotope-labeled synthetic peptide with the same sequence was used as an internal standard. The calibration range was validated from 10 to 1000ng/mL. The intra- and inter-day precisions were within 5.9% and 3.7%, respectively. The accuracy for the quality control (QC) samples was within 8.0%. Using this assay, the amounts of P-gp were accurately quantified as 3.53fg/cell (∼2.08×10(-2)amol/cell) in the MCF-7/WT cells and 34.5fg/cell (∼2.02×10(-1)amol/cell) in the MCF-7/ADR cells. This outcome was then compared with those obtained by conventional analytical methods including confocal microscopy, western blotting and flow cytometry. The comparative results show that not only is the LC/MS/MS-based targeted proteomics assay able to monitor the protein levels in a more accurate manner, but the large discrepancy observed between the other methods was most likely due to the lack of specificity and the semi-quantitative nature of the conventional assays.
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Affiliation(s)
- Ting Yang
- School of Pharmacy, Nanjing Medical University, 818 Tian Yuan East Road, Nanjing 211166, China
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Wen PC, Verhalen B, Wilkens S, Mchaourab HS, Tajkhorshid E. On the origin of large flexibility of P-glycoprotein in the inward-facing state. J Biol Chem 2013; 288:19211-20. [PMID: 23658020 PMCID: PMC3696692 DOI: 10.1074/jbc.m113.450114] [Citation(s) in RCA: 103] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
P-glycoprotein (Pgp) is one of the most biomedically relevant transporters in the ATP binding
cassette (ABC) superfamily due to its involvement in developing multidrug resistance in cancer
cells. Employing molecular dynamics simulations and double electron-electron resonance spectroscopy,
we have investigated the structural dynamics of membrane-bound Pgp in the inward-facing state and
found that Pgp adopts an unexpectedly wide range of conformations, highlighted by the degree of
separation between the two nucleotide-binding domains (NBDs). The distance between the two NBDs in
the equilibrium simulations covers a range of at least 20 Å, including, both, more open and
more closed NBD configurations than the crystal structure. The double electron-electron resonance
measurements on spin-labeled Pgp mutants also show wide distributions covering both longer and
shorter distances than those observed in the crystal structure. Based on structural and sequence
analyses, we propose that the transmembrane domains of Pgp might be more flexible than other
structurally known ABC exporters. The structural flexibility of Pgp demonstrated here is not only in
close agreement with, but also helps rationalize, the reported high NBD fluctuations in several ABC
exporters and possibly represents a fundamental difference in the transport mechanism between ABC
exporters and ABC importers. In addition, during the simulations we have captured partial entrance
of a lipid molecule from the bilayer into the lumen of Pgp, reaching the putative drug binding site.
The location of the protruding lipid suggests a putative pathway for direct drug recruitment from
the membrane.
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Affiliation(s)
- Po-Chao Wen
- Center for Biophysics and Computational Biology, Department of Biochemistry, College of Medicine, and The Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illnois 61801, USA
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In silico model for P-glycoprotein substrate prediction: insights from molecular dynamics and in vitro studies. J Comput Aided Mol Des 2013; 27:347-63. [DOI: 10.1007/s10822-013-9650-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Accepted: 04/16/2013] [Indexed: 11/25/2022]
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Orlandi F, Coronnello M, Bellucci C, Dei S, Guandalini L, Manetti D, Martelli C, Romanelli MN, Scapecchi S, Salerno M, Menif H, Bello I, Mini E, Teodori E. New structure-activity relationship studies in a series of N,N-bis(cyclohexanol)amine aryl esters as potent reversers of P-glycoprotein-mediated multidrug resistance (MDR). Bioorg Med Chem 2012; 21:456-65. [PMID: 23245571 DOI: 10.1016/j.bmc.2012.11.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Revised: 11/07/2012] [Accepted: 11/12/2012] [Indexed: 10/27/2022]
Abstract
As a continuation of previous research on a new series of potent and efficacious P-gp-dependent multidrug resistant (MDR) reversers with a N,N-bis(cyclohexanol)amine scaffold, we have designed and synthesized several analogs by modulation of the two aromatic moieties linked through ester functions to the N,N-bis(cyclohexanol)amine, aiming to optimize activity and to extend structure-activity relationships (SAR) within the series. This scaffold, when esterified with two different aromatic carboxylic acids, gives origin to four geometric isomers (cis/trans, trans/trans, cis/cis and trans/cis). The new compounds were tested on doxorubicin-resistant erythroleukemia K562 cells (K562/DOX) in the pirarubicin uptake assay. Most of them resulted in being potent modulators of the extrusion pump P-gp, showing potency values ([I](0.5)) in the submicromolar and nanomolar range. Of these, compounds 2b, 2c, 3d, 5a-d and 6d, showed excellent efficacy with a α(max) close to 1. Selected compounds (2d, 3a, 3b, 5a-d) were further studied to evaluate their doxorubicin cytotoxicity potentiation (RF) on doxorubicin-resistant erythroleukemia K562 cells and were found able to enhance significantly doxorubicin cytotoxicity on K562/DOX cells. The results of both pirarubicin uptake and the cytotoxicity assay, indicate that the new compounds of the series are potent P-gp-mediated MDR reversers. They present a structure with a mix of flexible and rigid moieties, a property that seems critical to allow the molecules to choose the most productive of the several binding modes possible in the transporter recognition site. In particular, compounds 5c and 5d, similar to the already reported analogous isomers 1c and 1d,(29) are potent and efficacious modulators of P-gp-dependent MDR and may be promising leads for the development of MDR-reversal drugs.
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Affiliation(s)
- Francesca Orlandi
- Dipartimento di Scienze Farmaceutiche, Università di Firenze, via Ugo Schiff 6, 50019 Sesto Fiorentino, FI, Italy
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34
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Abstract
Multidrug resistance proteins that belong to the ATP-binding cassette family like the human P-glycoprotein (ABCB1 or Pgp) are responsible for many failed cancer and antiviral chemotherapies because these membrane transporters remove the chemotherapeutics from the targeted cells. Understanding the details of the catalytic mechanism of Pgp is therefore critical to the development of inhibitors that might overcome these resistances. In this work, targeted molecular dynamics techniques were used to elucidate catalytically relevant structures of Pgp. Crystal structures of homologues in four different conformations were used as intermediate targets in the dynamics simulations. Transitions from conformations that were wide open to the cytoplasm to transition state conformations that were wide open to the extracellular space were studied. Twenty-six nonredundant transitional protein structures were identified from these targeted molecular dynamics simulations using evolutionary structure analyses. Coupled movement of nucleotide binding domains (NBDs) and transmembrane domains (TMDs) that form the drug binding cavities were observed. Pronounced twisting of the NBDs as they approached each other as well as the quantification of a dramatic opening of the TMDs to the extracellular space as the ATP hydrolysis transition state was reached were observed. Docking interactions of 21 known transport ligands or inhibitors were analyzed with each of the 26 transitional structures. Many of the docking results obtained here were validated by previously published biochemical determinations. As the ATP hydrolysis transition state was approached, drug docking in the extracellular half of the transmembrane domains seemed to be destabilized as transport ligand exit gates opened to the extracellular space.
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Affiliation(s)
- John G Wise
- Department of Biological Sciences, Center for Drug Discovery, Design and Delivery at Dedman College, and Center for Scientific Computation, Southern Methodist University, Dallas, Texas 75275-0376, USA.
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35
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Chen L, Li Y, Yu H, Zhang L, Hou T. Computational models for predicting substrates or inhibitors of P-glycoprotein. Drug Discov Today 2012; 17:343-51. [DOI: 10.1016/j.drudis.2011.11.003] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2011] [Revised: 10/24/2011] [Accepted: 11/10/2011] [Indexed: 01/11/2023]
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36
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Moroy G, Martiny VY, Vayer P, Villoutreix BO, Miteva MA. Toward in silico structure-based ADMET prediction in drug discovery. Drug Discov Today 2011; 17:44-55. [PMID: 22056716 DOI: 10.1016/j.drudis.2011.10.023] [Citation(s) in RCA: 164] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Revised: 10/07/2011] [Accepted: 10/21/2011] [Indexed: 12/12/2022]
Abstract
Quantitative structure-activity relationship (QSAR) methods and related approaches have been used to investigate the molecular features that influence the absorption, distribution, metabolism, excretion and toxicity (ADMET) of drugs. As the three-dimensional structures of several major ADMET proteins become available, structure-based (docking-scoring) computations can be carried out to complement or to go beyond QSAR studies. Applying docking-scoring methods to ADMET proteins is a challenging process because they usually have a large and flexible binding cavity; however, promising results relating to metabolizing enzymes have been reported. After reviewing current trends in the field we applied structure-based methods in the context of receptor flexibility in a case study involving the phase II metabolizing sulfotransferases. Overall, the explored concepts and results suggested that structure-based ADMET profiling will probably join the mainstream during the coming years.
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Affiliation(s)
- Gautier Moroy
- Inserm UMR-S 973, Molécules Thérapeutiques In Silico, Université Paris Diderot, Sorbonne Paris Cité, 35 Rue Helene Brion, 75013 Paris, France
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37
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Stoll F, Göller AH, Hillisch A. Utility of protein structures in overcoming ADMET-related issues of drug-like compounds. Drug Discov Today 2011; 16:530-8. [PMID: 21554979 DOI: 10.1016/j.drudis.2011.04.008] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Revised: 03/01/2011] [Accepted: 04/08/2011] [Indexed: 01/28/2023]
Abstract
The number of solved X-ray structures of proteins relevant for ADMET processes of drug molecules has increased remarkably over recent years. In principle, this development offers the possibility to complement the quantitative structure-property relationship (QSPR)-dominated repertoire of in silico ADMET methods with protein-structure-based approaches. However, the complex nature and the weak nonspecific ligand-binding properties of ADMET proteins take structural biology methods and current docking programs to the limit. In this review we discuss the utility of protein-structure-based design and docking approaches aimed at overcoming issues related to plasma protein binding, active transport via P-glycoprotein, hERG channel mediated cardiotoxicity and cytochrome P450 inhibition, metabolism and induction.
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Affiliation(s)
- Friederike Stoll
- Bayer HealthCare AG, Global Drug Discovery, Medicinal Chemistry, Wuppertal, Germany.
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38
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Homology modeling and binding site assessment of the human P-glycoprotein. Future Med Chem 2011; 3:297-307. [DOI: 10.4155/fmc.10.276] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Background: Due to its impact on multidrug resistance and pharmacokinetics P-glycoprotein (P-gp) has been identified as an important anti-target in pharmaceutical research. Recent publication of the mouse P-gp structure prompted us to build a new model for human P-gp and investigate its binding-site characteristics. Results: We developed and validated the human P-gp model that was used for induced-fit docking of experimentally characterized P-gp substrates. Residues located in the binding pocket are in good correlation with the results of side-directed mutagenesis studies. However, enrichment studies aimed at discriminating inhibitors and substrates from decoys resulted in only limited enrichments. Conclusion: A mouse P-gp-based homology model might be useful when analyzing protein–ligand interactions of known human P-gp substrates if induced-fit effects are considered.
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39
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Loo TW, Bartlett MC, Clarke DM. The W232R suppressor mutation promotes maturation of a truncation mutant lacking both nucleotide-binding domains and restores interdomain assembly and activity of P-glycoprotein processing mutants. Biochemistry 2011; 50:672-85. [PMID: 21182301 DOI: 10.1021/bi1016809] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
ATP-binding cassette (ABC) proteins contain two nucleotide-binding domains (NBDs) and two transmembrane (TM) domains (TMDs). Interdomain interactions and packing of the TM segments are critical for function, and disruption by genetic mutations contributes to disease. P-glycoprotein (P-gp) is a useful model to identify mechanisms that repair processing defects because numerous arginine suppressor mutations have been identified in the TM segments. Here, we tested the prediction that a mechanism of arginine rescue was to promote intradomain interactions between TM segments and restore interdomain assembly. We found that suppressor W232R(TM4/TMD1) rescued mutants with processing mutations in any domain and restored defective NBD1-NBD2, NBD1-TMD2, and TMD1-TMD2 interactions. W232R also promoted packing of the TM segments because it rescued a truncation mutant lacking both NBDs. The mechanism of W232R rescue likely involved intradomain hydrogen bond interactions with Asn296(TM5) since only N296A abolished rescue by W232R and rescue was only observed when Trp232 was replaced with hydrogen-bonding residues. In TMD2, suppressor T945R(TM11) also promoted packing of the TM segments because it rescued the truncation mutant lacking the NBDs and suppressed formation of alternative topologies. We propose that T945R rescue was mediated by interactions with Glu875(TM10) since T945E/E875R promoted maturation while T945R/E875A did not.
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Affiliation(s)
- Tip W Loo
- Department of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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40
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Crouthamel MH, Wu D, Yang Z, Ho RJY. A novel MDR1 GT1292-3TG (Cys431Leu) genetic variation and its effect on P-glycoprotein biologic functions. AAPS JOURNAL 2010; 12:548-55. [PMID: 20623213 DOI: 10.1208/s12248-010-9216-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Accepted: 06/18/2010] [Indexed: 01/08/2023]
Abstract
P-glycoprotein (P-gp) is a membrane-bound transporter protein that is encoded by the human multidrug resistance gene MDR1 (ABCB1). P-gp recognizes a wide range of xenobiotics, is pivotal in mediating cancer drug resistance, and plays an important role in limiting drug penetration across the blood-brain barrier. MDR1 genetic variation can lead to changes in P-gp function and may have implications on drug pharmacokinetics. We have identified a novel MDR1 (GT1292-3TG) (Cys431Leu) genetic variation through systematic profiling of subjects with leukemia. The cellular and transport function of this variation was investigated with recombinant human embryonic kidney cells expressing MDR1. Compared with the wild type, MDR1 (GT1292-3TG) recombinant cells exhibited a lower drug resistance phenotype for a panel of chemotherapeutic agents. When compared with wild type, MDR1 (GT1292-3TG) recombinant cells exposed exhibited a 75% decrease in IC₅₀ for doxorubicin (162.6 ± 17.4 to 37.9 ± 2.6 nM) and a 50% decrease in IC(50) for paclitaxel (155.7 ± 27.5 to 87.7 ± 9.2 nM), vinblastine (128.0 ± 15.9 to 65.9 ± 5.1 nM), and vincristine (593.7 ± 61.8 to 307.3 ± 17.0 nM). The effects of the Cys431Leu variation, due to MDR1 (GT1292-3TG) nucleotide transition, on P-gp-dependent intracellular substrate accumulation appeared to be substrate dependent where doxorubicin, vinblastine, and paclitaxel exhibit an increased accumulation (p < 0.05), while verapamil and Hoechst33342 exhibit a decreased intracellular concentration compared with wild type (p < 0.05). Collectively, these data suggest MDR1 (GT1292-3TG) variation of P-gp may reduce drug resistance and that subjects with this genotype undergoing chemotherapy with drugs that are transported by P-gp could potentially be more responsive to therapy than those with MDR1 wild-type genotype.
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41
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Klepsch F, Ecker GF. Impact of the Recent Mouse P-Glycoprotein Structure for Structure-Based Ligand Design. Mol Inform 2010; 29:276-86. [PMID: 27463054 DOI: 10.1002/minf.201000017] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2010] [Accepted: 04/08/2010] [Indexed: 01/20/2023]
Abstract
P-Glycoprotein (P-gp), a transmembrane, ATP-dependent drug efflux transporter, has attracted considerable interest both with respect to its role in tumour cell multidrug resistance and in absorption-distribution and elimination of drugs. Although known since more than 30 years, the understanding of the molecular basis of drug/transporter interaction is still limited, which is mainly due to the lack of structural information available. However, within the past decade X-ray structures of several bacterial homologues as well as very recently also of mouse P-gp have become available. Within this review we give an overview on the current status of structural information available and on its impact for structure-based drug design.
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Affiliation(s)
- Freya Klepsch
- University of Vienna, Department of Medicinal Chemistry, Althanstraße 14, 1090 Wien, Austria phone: +43-1-4277-55110; fax: +43-1-4277-9551
| | - Gerhard F Ecker
- University of Vienna, Department of Medicinal Chemistry, Althanstraße 14, 1090 Wien, Austria phone: +43-1-4277-55110; fax: +43-1-4277-9551.
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42
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Loo TW, Bartlett MC, Clarke DM. Human P-glycoprotein is active when the two halves are clamped together in the closed conformation. Biochem Biophys Res Commun 2010; 395:436-40. [PMID: 20394729 DOI: 10.1016/j.bbrc.2010.04.057] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Accepted: 04/09/2010] [Indexed: 10/19/2022]
Abstract
The P-glycoprotein (P-gp, ABCB1) drug pump protects us from toxic compounds and confers multidrug resistance. Each of the two homologous halves of P-gp is composed of a transmembrane domain (TMD) with six TM segments followed by a nucleotide-binding domain (NBD). The drug- and ATP-binding sites reside at the interface between the TMDs and NBDs, respectively. Crystal structures show drug pumps in the open and closed conformations, where the drug-binding pocket and NBDs are open or closed at the cytoplasmic side, respectively. Although it has been postulated that drug substrates enter the drug-binding pocket in the open conformation, it is unknown if they can enter in the closed conformation. To determine this, we introduced cysteines into regions of TM3 (residues 175-178) and TM9 (residues 820-822) that extend into the cytoplasm and are 4 A and 20 A apart in the closed and open conformations, respectively. The 12 double cysteine mutants were then cross-linked with a short cross-linker, M1M (4 A) at 0 degrees C to reduce thermal motion in the protein. Only mutant L175C/N820C was cross-linked. Cross-linking was not increased in the presence of ATP or drug substrates. Cross-linking increased its basal ATPase activity about 3-fold. Activity could be increased further by drug substrates such as verapamil and rhodamine B. These results suggest that P-gp in the membrane is in the closed conformation that has a high affinity for drug substrates.
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Affiliation(s)
- Tip W Loo
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
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43
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Zazímalová E, Murphy AS, Yang H, Hoyerová K, Hosek P. Auxin transporters--why so many? Cold Spring Harb Perspect Biol 2010; 2:a001552. [PMID: 20300209 PMCID: PMC2829953 DOI: 10.1101/cshperspect.a001552] [Citation(s) in RCA: 300] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Interacting and coordinated auxin transporter actions in plants underlie a flexible network that mobilizes auxin in response to many developmental and environmental changes encountered by these sessile organisms. The independent but synergistic activity of individual transporters can be differentially regulated at various levels. This invests auxin transport mechanisms with robust functional redundancy and added auxin flow capacity when needed. An evolutionary perspective clarifies the roles of the different transporter groups in plant development. Mathematical and functional analysis of elements of auxin transport makes it possible to rationalize the relative contributions of members of the respective transporter classes to the localized auxin transport streams that then underlie both preprogrammed developmental changes and reactions to environmental stimuli.
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Affiliation(s)
- Eva Zazímalová
- Institute of Experimental Botany AS CR, Rozvojová 263, CZ-165 02 Prague 6, Czech Republic.
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44
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Demel MA, Krämer O, Ettmayer P, Haaksma EEJ, Ecker GF. Predicting ligand interactions with ABC transporters in ADME. Chem Biodivers 2010; 6:1960-9. [PMID: 19937827 DOI: 10.1002/cbdv.200900138] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
ABC-type drug efflux pumps, e.g., ABCB1 (=P-glycoprotein, =MDR1), ABCC1 (=MRP1), and ABCG2 (=MXR, =BCRP), confer a multi-drug resistance (MDR) phenotype to cancer cells. Furthermore, the important contribution of ABC transporters for bioavailability, distribution, elimination, and blood-brain barrier permeation of drug candidates is increasingly recognized. This review presents an overview on the different computational methods and models pursued to predict ABC transporter substrate properties of drug-like compounds. They encompass ligand-based approaches ranging from 'simple rule'-based efforts to sophisticated machine learning methods. Many of these models show excellent performance for the data sets used. However, due to the complex nature of the applied methods, useful interpretation of the models that can be directly translated into chemical structures by the medicinal chemist is rather difficult. Additionally, very recent and promising attempts in the field of structure-based modeling of ABC transporters, which embody homology modeling as well as recently published X-ray structures of murine ABCB1, will be discussed.
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Affiliation(s)
- Michael A Demel
- University of Vienna, Department of Medicinal Chemistry, Emerging Field Pharmacoinformatics, Althanstrasse 14, AT-1090 Vienna
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45
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Abstract
The role of the ATP-binding cassette ABCB1 in mediating the resistance to chemotherapy in many forms of cancer has been well established. The protein is also endogenously expressed in numerous barrier and excretory tissues, thereby regulating or impacting on drug pharmacokinetic profiles. Given these prominent roles in health and disease, a great deal of biochemical, structural and pharmacological research has been directed towards modulating its activity. Despite the effort, only a small handful of compounds have reached the later stages of clinical trials. What is responsible for this poor return on the heavy research investment? Perhaps the most significant factor is the lack of information on the location, physical features and chemical properties of the drug-binding site(s) in ABCB1. This minireview outlines the various strategies and outcomes of research efforts to pin-point the sites of interaction. The data may be assimilated into two working hypotheses to describe drug binding to ABCB1; (a) the central cavity and the (b) domain interface models.
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Affiliation(s)
- Emily Crowley
- Nuffield Department of Clinical Laboratory Sciences, University of Oxford, Oxford, UK
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46
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Pajeva IK, Globisch C, Wiese M. Comparison of the inward- and outward-open homology models and ligand binding of human P-glycoprotein. FEBS J 2009; 276:7016-26. [PMID: 19878299 DOI: 10.1111/j.1742-4658.2009.07415.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An homology model of human P-glycoprotein, based on the X-ray structure of the recently resolved mouse P-glycoprotein, is presented. The model corresponds to the inward-facing conformation competent for drug binding. From the model, the residues involved in the protein-binding cavity are identified and compared with those in the outward-facing conformation of human P-glycoprotein developed previously based on the Sav1866 structure. A detailed analysis of the interactions of the cyclic peptides QZ59-RRR and QZ59-SSS is presented in both the X-ray structures of mouse P-glycoprotein and the human P-glycoprotein model generated by ligand docking. The results confirm the functional role of transmembrane domains TM4, TM6, TM10 and TM12 as entrance gates to the protein cavity, and also imply differences in their functions. The analysis of the cavities in both models suggests that the ligands remain bound to the same residues during the transition from the inward- to the outward-facing conformations. The analysis of the ligand-protein interactions in the X-ray complexes shows differences in the residues involved, as well as in the specific interactions performed by the same ligand within the same protein. This observation is supported by docking of the QZ59 ligands into human P-glycoprotein, thus aiding in the understanding of the complex behavior of P-glycoprotein substrates and inhibitors. The results confirm the possibility for multispecific drug interactions of the protein, and are important for elucidating the P-glycoprotein function and ligand interactions.
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Affiliation(s)
- Ilza K Pajeva
- Pharmaceutical Institute, University of Bonn, Germany
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Ravna AW, Sylte I, Sager G. Binding site of ABC transporter homology models confirmed by ABCB1 crystal structure. Theor Biol Med Model 2009; 6:20. [PMID: 19732422 PMCID: PMC2747915 DOI: 10.1186/1742-4682-6-20] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2009] [Accepted: 09/04/2009] [Indexed: 01/12/2023] Open
Abstract
The human ATP-binding cassette (ABC) transporters ABCB1, ABCC4 and ABCC5 are involved in resistance to chemotherapeutic agents. Here we present molecular models of ABCB1, ABCC4 and ABCC5 by homology based on a wide open inward-facing conformation of Escherichia coli MsbA, which were constructed in order to elucidate differences in the electrostatic and molecular features of their drug recognition conformations. As a quality assurance of the methodology, the ABCB1 model was compared to an ABCB1 X-ray crystal structure, and with published cross-linking and site directed mutagenesis data of ABCB1. Amino acids Ile306 (TMH5), Ile340 (TMH6), Phe343 (TMH6), Phe728 (TMH7), and Val982 (TMH12), form a putative substrate recognition site in the ABCB1 model, which is confirmed by both the ABCB1 X-ray crystal structure and the site-directed mutagenesis studies. The ABCB1, ABCC4 and ABCC5 models display distinct differences in the electrostatic properties of their drug recognition sites.
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Affiliation(s)
- Aina W Ravna
- Department of Medical Pharmacology and Toxicology, Institute of Medical Biology, Faculty of Health Sciences, University of Tromsø, N-9037 Tromsø, Norway.
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Gannon MK, Holt JJ, Bennett SM, Wetzel BR, Loo TW, Bartlett MC, Clarke DM, Sawada GA, Higgins JW, Tombline G, Raub TJ, Detty MR. Rhodamine inhibitors of P-glycoprotein: an amide/thioamide "switch" for ATPase activity. J Med Chem 2009; 52:3328-41. [PMID: 19402665 DOI: 10.1021/jm900253g] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We have examined 46 tetramethylrosamine/rhodamine derivatives with structural diversity in the heteroatom of the xanthylium core, the amino substituents of the 3- and 6-positions, and the alkyl, aryl, or heteroaryl group at the 9-substituent. These compounds were examined for affinity and ATPase stimulation in isolated MDR3 CL P-gp and human P-gp-His(10), for their ability to promote uptake of calcein AM and vinblastine in multidrug-resistant MDCKII-MDR1 cells, and for transport in monolayers of MDCKII-MDR1 cells. Thioamide 31-S gave K(M) of 0.087 microM in human P-gp. Small changes in structure among this set of compounds affected affinity as well as transport rate (or flux) even though all derivatives examined were substrates for P-gp. With isolated protein, tertiary amide groups dictate high affinity and high stimulation while tertiary thioamide groups give high affinity and inhibition of ATPase activity. In MDCKII-MDR1 cells, the tertiary thioamide-containing derivatives promote uptake of calcein AM and have very slow passive, absorptive, and secretory rates of transport relative to transport rates for tertiary amide-containing derivatives. Thioamide 31-S promoted uptake of calcein AM and inhibited efflux of vinblastine with IC(50)'s of approximately 2 microM in MDCKII-MDR1 cells.
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Affiliation(s)
- Michael K Gannon
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260-3000, USA
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Loo TW, Bartlett MC, Clarke DM. Identification of residues in the drug translocation pathway of the human multidrug resistance P-glycoprotein by arginine mutagenesis. J Biol Chem 2009; 284:24074-87. [PMID: 19581304 DOI: 10.1074/jbc.m109.023267] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
P-glycoprotein (P-gp, ATP-binding cassette B1) is a drug pump that extracts toxic drug substrates from the plasma membrane and catalyzes their ATP-dependent efflux. To map the residues in the drug translocation pathway, we performed arginine-scanning mutagenesis on all transmembrane (TM) segments (total = 237 residues) of a P-gp processing mutant (G251V) defective in folding (15% maturation efficiency) (glycosylation state used to monitor folding). The rationale was that arginines introduced into the drug-binding sites would mimic drug rescue and enhance maturation of wild-type or processing mutants of P-gp. It was found that 38 of the 89 mutants that matured had enhanced maturation. Enhancer mutations were found in 11 of the 12 TM segments with the largest number found in TMs 6 and 12 (seven in each), TMs that are critical for P-gp-drug substrate interactions. Modeling of the TM segments showed that the enhancer arginines were found on the hydrophilic face, whereas inhibitory arginines were located on a hydrophobic face that may be in contact with the lipid bilayer. It was found that many of the enhancer arginines caused large alterations in P-gp-drug interactions in ATPase assays. For example, mutants A302R (TM5), L339R (TM6), G872R (TM10), F942R (TM11), Q946R (TM11), V982R (TM12), and S993R (TM12) reduced the apparent affinity for verapamil by approximately 10-fold, whereas the F336R (TM6) and M986R (TM12) mutations caused at least a 10-fold increase in apparent affinity for rhodamine B. The results suggest that P-gp contains a large aqueous-filled drug translocation pathway with multiple drug-binding sites that can accommodate the bulky arginine side chains to promote folding of the protein.
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Affiliation(s)
- Tip W Loo
- Department of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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