1
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Glocker UM, Braun F, Eberl HC, Bantscheff M. A Probe-Based Target Engagement Assay for Kinases in Live Cells. Mol Cell Proteomics 2025; 24:100963. [PMID: 40187494 PMCID: PMC12076712 DOI: 10.1016/j.mcpro.2025.100963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2024] [Accepted: 02/27/2025] [Indexed: 04/07/2025] Open
Abstract
The efficacy and safety of kinase inhibitor drugs are largely influenced by their selectivity. Available profiling technologies are primarily based on overexpressed or endogenously expressed kinases in cell extracts. We compared kinase capture with the cell penetrant covalent probe XO44 to three derivatives and found that replacing the alkyne handle with a trans-cyclooctene group allowed the development of a more robust kinase capture and enrichment protocol. An intracellular chemoproteomics target profiling and engagement assay was devised by optimizing probe concentration and incubation time and using an isobaric mass tag-based strategy for relative quantification. Comparing intracellular kinase profiles of the marketed drug dasatinib and the tool compound dinaciclib with the lysate-based kinobeads assay revealed excellent agreement in rank-order of binding. Dinaciclib showed a systematic shift to higher IC50s, suggesting that intracellular cosubstrate concentrations, cell penetration of the compound, as well as kinase localization and complexes in live cells influence target profiles. Further, we show that sepiapterin reductase SPR and multidrug resistance protein 1 ABCC1 are off-targets of kinase inhibitor scaffolds with potential implications on efficacy and safety.
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Affiliation(s)
| | - Florian Braun
- Chemical Synthesis Core Facility, European Molecular Biology Laboratory, Heidelberg, Germany
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2
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Crispim Tropéia N, Paccielli Freire P, Willian de Alencar Pereira E, Ferraz Sampaio M, Bassani Borges J, Bastos GM, Strelow Thurow H, Reinel Castro L, Nakazone MA, Carmo TS, Hirata MH, Monteiro Ferreira G. Structural and functional implications of ABCC1 variants on clinical statin response. J Biomol Struct Dyn 2025:1-14. [PMID: 40057820 DOI: 10.1080/07391102.2025.2475225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 02/02/2025] [Indexed: 03/20/2025]
Abstract
ATP-binding cassette (ABC) proteins are membrane transporters responsible for metabolites and active substances removal from cells. Their genes' variations have been associated with protein function and expression defects. Familial Hypercholesterolemia (FH) patients hosting those alterations might compromise the efficacy of high-dose statin treatment, a primary therapeutic strategy. ABCC1 is a member of the ABC-transporter superfamily, potentially relevant to pharmacological therapy responses and toxicity risks in hypercholesterolemic patients. Here, we evaluated specific non-synonymous (SNV) missense variants in the ABCC1 gene from a FH patient cohort, assessing potential impacts on protein structure, molecular dynamics and interactions with rosuvastatin, atorvastatin, pravastatin, pitavastatin, and lovastatin. Molecular docking, complemented by motion, visual and binding affinity analysis using the PLANNET model, suggested that these mutations had minimal impact on drug interactions. These findings prompted further analysis of two other efflux pumps, ABCG2 and P-gp, and their statin interactions. Interestingly, diminished binding affinities hinted at a compensatory mechanism wherein other transporters might mitigate potential ABCC1 mutation effects, ensuring effective drug efflux. Clinical profiles from the patient cohort did not show a correlation between these variants and clinical outcomes, potentially pointing to the role of alternate drug transporters in statin interaction.
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Affiliation(s)
- Naomí Crispim Tropéia
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, São Paulo, Brazil
| | - Paula Paccielli Freire
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, São Paulo, Brazil
| | | | - Marcelo Ferraz Sampaio
- Department of Research, Hospital Beneficência Portuguesa de São Paulo, São Paulo, Brazil
| | - Jéssica Bassani Borges
- Department of Research, Hospital Beneficência Portuguesa de São Paulo, São Paulo, Brazil
| | - Gisele Medeiros Bastos
- Department of Research, Hospital Beneficência Portuguesa de São Paulo, São Paulo, Brazil
| | - Helena Strelow Thurow
- Department of Research, Hospital Beneficência Portuguesa de São Paulo, São Paulo, Brazil
| | - Lara Reinel Castro
- Department of Research, Hospital Beneficência Portuguesa de São Paulo, São Paulo, Brazil
| | | | | | - Mario Hiroyuki Hirata
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, São Paulo, Brazil
| | - Glaucio Monteiro Ferreira
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of Sao Paulo, São Paulo, Brazil
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3
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Shinde O, Boyer JA, Cambier S, VanPortfliet JJ, Sui X, Yadav GP, Viverette EG, Borgnia MJ, West AP, Zhang Q, Stetson DB, Li P. Structures of ATP-binding cassette transporter ABCC1 reveal the molecular basis of cyclic dinucleotide cGAMP export. Immunity 2025; 58:59-73.e5. [PMID: 39765229 PMCID: PMC11735300 DOI: 10.1016/j.immuni.2024.12.002] [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: 03/28/2024] [Revised: 09/20/2024] [Accepted: 12/04/2024] [Indexed: 01/11/2025]
Abstract
Cyclic nucleotide GMP-AMP (cGAMP) plays a critical role in mediating the innate immune response through the cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) pathway. Recent studies showed that ATP-binding cassette subfamily C member 1 (ABCC1) is a cGAMP exporter. The exported cGAMP can be imported into uninfected cells to stimulate a STING-mediated innate immune response. However, the molecular basis of cGAMP export mediated by ABCC1 remains unclear. Here, we report the cryoelectron microscopy (cryo-EM) structures of human ABCC1 in a ligand-free state and a cGAMP-bound state. These structures reveal that ABCC1 forms a homodimer via its N-terminal transmembrane domain. The ligand-bound structure shows that cGAMP is recognized by a positively charged pocket. Mutagenesis and functional studies confirmed the roles of the ligand-binding pocket in cGAMP recognition and export. This study provides insights into the structure and function of ABCC1 as a cGAMP exporter and lays a foundation for future research targeting ABCC1 in infection and anti-cancer immunity.
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Affiliation(s)
- Omkar Shinde
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Joshua A Boyer
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA; RNA Discovery Center, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Stephanie Cambier
- Department of Immunology, University of Washington School of Medicine, Seattle, WA 98109, USA
| | | | - Xuewu Sui
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Gaya P Yadav
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Elizabeth G Viverette
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | - Mario J Borgnia
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA
| | | | - Qi Zhang
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA; RNA Discovery Center, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Daniel B Stetson
- Department of Immunology, University of Washington School of Medicine, Seattle, WA 98109, USA
| | - Pingwei Li
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA.
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4
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Shahpouri P, Mehralitabar H, Kheirabadi M, Kazemi Noureini S. Potential suppression of multidrug-resistance-associated protein 1 by coumarin derivatives: an insight from molecular docking and MD simulation studies. J Biomol Struct Dyn 2024; 42:9184-9200. [PMID: 37667877 DOI: 10.1080/07391102.2023.2250456] [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: 04/24/2023] [Accepted: 08/15/2023] [Indexed: 09/06/2023]
Abstract
Human MRP1 protein plays a vital role in cancer multidrug resistance. Coumarins show promising pharmacological properties. Virtual screening, ADMET, molecular docking and molecular dynamics (MD) simulations were utilized as pharmacoinformatic tools to identify potential MRP1 inhibitors among coumarin derivatives. Using in silico ADMET, 50 hits were further investigated for their selectivity toward the nucleotide-binding domains (NBDs) of MRP1 using molecular docking. Accordingly, coumarin, its symmetrical ketone derivative Lig. No. 4, and Reversan were candidates for focused docking study with the NBDs domains compared with ATP. The result indicates that Lig. No. 4, with the best binding score, interacts with NBDs via hydrogen bonds with residues: GLN713, LYS684, GLY683, CYS682 in NBD1, and GLY1432, GLY771, SER769 and GLN1374 in NBD2, which mostly overlap with ATP binding residues. Moreover, doxorubicin (Doxo) was docked to the transmembrane domains (TMDs) active site of MRP1. Doxo interaction with TMDs was subjected to MD simulation in the NBDs free and occupied with Lig. No. 4 states. The results showed that Doxo interacts more strongly with TMD residues in inward facing feature of TMDs helices. However, when Lig. No. 4 exists in NBDs, Doxo interactions are different, and TMD helices show more outward-facing conformation. This result may suggest a partial competitive inhibition mechanism for the Lig. No. 4 on MRP1 compared with ATP. So, it may inhibit active complex formation by interfering with ATP entrance to NBDs and locking MRP1 conformation in outward-facing mode. This study suggests a valuable coumarin derivative that can be further investigated for potent MRP1 inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Parisa Shahpouri
- Department of Biology, Faculty of Science, Hakim Sabzevari University, Sabzevar, Iran
| | - Havva Mehralitabar
- Department of Biology, Faculty of Science, Hakim Sabzevari University, Sabzevar, Iran
| | - Mitra Kheirabadi
- Department of Biology, Faculty of Science, Hakim Sabzevari University, Sabzevar, Iran
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Sizun C. Biophysical Reviews' "Meet the Editors Series": a profile of Christina Sizun. Biophys Rev 2023; 15:301-304. [PMID: 37396447 PMCID: PMC10310629 DOI: 10.1007/s12551-023-01071-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2023] [Indexed: 07/04/2023] Open
Abstract
This edition of the continuing "Biophysical Reviews Meet the Editors Series" introduces Dr. Christina Sizun, physical chemist, member of the Biophysical Reviews editorial board and current Treasurer of the International Union for Pure and Applied Biophysics (IUPAB).
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Affiliation(s)
- Christina Sizun
- Institut de Chimie des Substances Naturelles, Centre National de la Recherche Scientifique, Université Paris-Saclay, Gif-sur-Yvette, France
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6
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Murugaiyaa Pandiyan S, Shanmugaraj P, Manoharan JP, Vidyalakshmi S. A network pharmacological approach to reveal the multidrug resistance reversal and associated mechanisms of acetogenins against colorectal cancer. J Biomol Struct Dyn 2022; 40:13527-13546. [PMID: 34669561 DOI: 10.1080/07391102.2021.1990130] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Multidrug Resistance (MDR) in tumors is caused by the over-expression of ATP Binding Cassette transporter proteins such as Multidrug Resistance Protein 1 and Breast Cancer Resistance Protein 1. This in silico study focuses on identifying a MDR inhibitor among acetogenins (AGEs) of Annona muricata and also aims at predicting colorectal cancer (CRC) core targets of AGEs through a network pharmacological approach. Twenty-four AGEs were initially screened for their ADME properties. Molecular interaction studies were performed with the two proteins MRP1 and BCRP1. As the structure of MRP1 was not available, an inward-facing conformation of MRP1 was modeled. A Protein-protein interaction network was constructed for the correlating targets of CRC. KEGG pathway and Gene Ontology analysis were performed for the predicted CRC targets. We identified four lead AGEs: Muricatocin B, Annonacinone, Annonacin A and Annomuricin E having a higher binding affinity towards MDR proteins. MD simulation studies performed with the three lead AGEs and the MDR proteins showed that MRP1(DBD): Annomuricin E complex was stable throughout the simulation. Our analysis revealed ABCG2, ERBB2, STAT3, AR, SRC and ABCC1 as CRC targets of the lead molecules. The top 10 signaling pathways and functions of correlative CRC targets were also predicted. We conclude that the identified lead molecules might act as competitive inhibitors for reversing MDR in CRC. Additionally, network pharmacological studies established the correlative CRC targets and their mechanisms of action. Further experimental studies are needed to validate our findings. Communicated by Ramaswamy H. Sarma.
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Bickers SC, Benlekbir S, Rubinstein JL, Kanelis V. Structure of Ycf1p reveals the transmembrane domain TMD0 and the regulatory region of ABCC transporters. Proc Natl Acad Sci U S A 2021; 118:e2025853118. [PMID: 34021087 PMCID: PMC8166025 DOI: 10.1073/pnas.2025853118] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
ATP binding cassette (ABC) proteins typically function in active transport of solutes across membranes. The ABC core structure is composed of two transmembrane domains (TMD1 and TMD2) and two cytosolic nucleotide binding domains (NBD1 and NBD2). Some members of the C-subfamily of ABC (ABCC) proteins, including human multidrug resistance proteins (MRPs), also possess an N-terminal transmembrane domain (TMD0) that contains five transmembrane α-helices and is connected to the ABC core by the L0 linker. While TMD0 was resolved in SUR1, the atypical ABCC protein that is part of the hetero-octameric ATP-sensitive K+ channel, little is known about the structure of TMD0 in monomeric ABC transporters. Here, we present the structure of yeast cadmium factor 1 protein (Ycf1p), a homolog of human MRP1, determined by electron cryo-microscopy (cryo-EM). A comparison of Ycf1p, SUR1, and a structure of MRP1 that showed TMD0 at low resolution demonstrates that TMD0 can adopt different orientations relative to the ABC core, including a ∼145° rotation between Ycf1p and SUR1. The cryo-EM map also reveals that segments of the regulatory (R) region, which links NBD1 to TMD2 and was poorly resolved in earlier ABCC structures, interacts with the L0 linker, NBD1, and TMD2. These interactions, combined with fluorescence quenching experiments of isolated NBD1 with and without the R region, suggest how posttranslational modifications of the R region modulate ABC protein activity. Mapping known mutations from MRP2 and MRP6 onto the Ycf1p structure explains how mutations involving TMD0 and the R region of these proteins lead to disease.
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Affiliation(s)
- Sarah C Bickers
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada
- Department of Chemical and Physical Sciences, University of Toronto, Mississauga, ON L5L 1C6, Canada
| | - Samir Benlekbir
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada
| | - John L Rubinstein
- Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada;
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Voula Kanelis
- Department of Chemistry, University of Toronto, Toronto, ON M5S 3H6, Canada;
- Department of Chemical and Physical Sciences, University of Toronto, Mississauga, ON L5L 1C6, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, ON M5S 3G5, Canada
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8
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Mary YS, Mary YS, Rad AS, Yadav R, Celik I, Sarala S. Theoretical investigation on the reactive and interaction properties of sorafenib – DFT, AIM, spectroscopic and Hirshfeld analysis, docking and dynamics simulation. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115652] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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9
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Abstract
Drug transporters are integral membrane proteins that play a critical role in drug disposition by affecting absorption, distribution, and excretion. They translocate drugs, as well as endogenous molecules and toxins, across membranes using ATP hydrolysis, or ion/concentration gradients. In general, drug transporters are expressed ubiquitously, but they function in drug disposition by being concentrated in tissues such as the intestine, the kidneys, the liver, and the brain. Based on their primary sequence and their mechanism, transporters can be divided into the ATP-binding cassette (ABC), solute-linked carrier (SLC), and the solute carrier organic anion (SLCO) superfamilies. Many X-ray crystallography and cryo-electron microscopy (cryo-EM) structures have been solved in the ABC and SLC transporter superfamilies or of their bacterial homologs. The structures have provided valuable insight into the structural basis of transport. This chapter will provide particular focus on the promiscuous drug transporters because of their effect on drug disposition and the challenges associated with them.
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Affiliation(s)
- Arthur G Roberts
- Pharmaceutical and Biomedical Sciences Department, University of Georgia, Athens, GA, USA.
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10
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Characterization of the nucleotide-binding domain NsrF from the BceAB-type ABC-transporter NsrFP from the human pathogen Streptococcus agalactiae. Sci Rep 2020; 10:15208. [PMID: 32938989 PMCID: PMC7494861 DOI: 10.1038/s41598-020-72237-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Accepted: 08/27/2020] [Indexed: 01/14/2023] Open
Abstract
Treatment of bacterial infections is a great challenge of our era due to the various resistance mechanisms against antibiotics. Antimicrobial peptides are considered to be potential novel compound as antibiotic treatment. However, some bacteria, especially many human pathogens, are inherently resistant to these compounds, due to the expression of BceAB-type ABC transporters. This rather new transporter family is not very well studied. Here, we report the first full characterization of the nucleotide binding domain of a BceAB type transporter from Streptococcus agalactiae, namely SaNsrF of the transporter SaNsrFP, which confers resistance against nisin and gallidermin. We determined the NTP hydrolysis kinetics and used molecular modeling and simulations in combination with small angle X-ray scattering to obtain structural models of the SaNsrF monomer and dimer. The fact that the SaNsrFH202A variant displayed no ATPase activity was rationalized in terms of changes of the structural dynamics of the dimeric interface. Kinetic data show a clear preference for ATP as a substrate, and the prediction of binding modes allowed us to explain this selectivity over other NTPs.
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11
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Nair B, Anto RJ, M S, Nath LR. Kaempferol-Mediated Sensitization Enhances Chemotherapeutic Efficacy of Sorafenib Against Hepatocellular Carcinoma: An In Silico and In Vitro Approach. Adv Pharm Bull 2020; 10:472-476. [PMID: 32665908 PMCID: PMC7335979 DOI: 10.34172/apb.2020.058] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 02/02/2020] [Accepted: 02/03/2020] [Indexed: 02/05/2023] Open
Abstract
Purpose: Sorafenib is the sole FDA approved drug conventionally used for the treatment of advanced hepatocellular carcinoma (HCC). Despite of the beneficial use of sorafenib in the treatment of HCC, multidrug resistance still remains a challenge. HCC is inherently known as chemotherapy resistant tumor due to P-glycoprotein (P-gp)-mediated multidrug resistance. Methods: We studied the interaction energy of kaempferol with human multidrug resistance protein-1 (RCSB PDB ID: 2CBZ) using in silico method with the help of BIOVIA Discovery Studio. HepG2 and N1S1 liver cancer cell lines were treated in suitable cell culture media to evaluate the efficacy of kaempferol in chemo-sensitizing liver cancer cells towards the effect of sorafenib. Cell viability study was performed by MTT assay. Results: In silico analysis of kaempferol showed best docking score of 23.14 with Human Multi Drug Resistant Protein-1 (RCSB PDB ID: 2CBZ) compared with positive control verapamil. Inin-vitro condition, combination of sub-toxic concentrations of both kaempferol and sorafenib produced 50% cytotoxicity with concentration of 2.5 µM each which indicates that kaempferol has the ability to reverse the MDR by decreasing the over-expression of P-gp. Conclusion: Kaempferol is able to sensitize the HepG2 and N1S1 against the sub-toxic concentration of sorafenib. Hence, we consider that the efficacy of sorafenib chemotherapy can be enhanced by the significant approach of combining the sub-toxic concentrations of sorafenib with kaempferol. Thus, kaempferol can be used as a better candidate molecule along with sorafenib for enhancing its efficacy, if validated through preclinical studies.
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Affiliation(s)
- Bhagyalakshmi Nair
- Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Science Campus, Ponekkara P.O., Kochi, Kerala 682041, India
| | - Ruby John Anto
- Division of Cancer Research, Rajiv Gandhi Center for Biotechnology, Thycaud, Thiruvananthapuram, Kerala- 695014, India. Introduction
| | - Sabitha M
- Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Science Campus, Ponekkara P.O., Kochi, Kerala 682041, India
| | - Lekshmi R. Nath
- Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Science Campus, Ponekkara P.O., Kochi, Kerala 682041, India
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12
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Lusvarghi S, Robey RW, Gottesman MM, Ambudkar SV. Multidrug transporters: recent insights from cryo-electron microscopy-derived atomic structures and animal models. F1000Res 2020; 9. [PMID: 32055397 PMCID: PMC6961416 DOI: 10.12688/f1000research.21295.1] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/06/2020] [Indexed: 12/12/2022] Open
Abstract
P-glycoprotein, ABCG2, and MRP1 are members of the ATP-binding cassette (ABC) transporter superfamily that utilize energy from ATP-binding and hydrolysis to efflux a broad range of chemically dissimilar substrates including anticancer drugs. As a consequence, they play an important role in the pharmacokinetics and bioavailability of many drugs; in particular, their role in multidrug resistance in cancer cells as well as at the blood-brain barrier has been the subject of studies for decades. However, the atomic structures of these transporters in the presence of substrates or modulators and at different stages of the ATP-hydrolysis cycle have only recently been resolved by using cryo-electron microscopy. In addition, new animal models have shed new light on our understanding of the role of these transporters at the blood-brain barrier. This new information should open doors for the design of novel chemotherapeutics and treatments to bypass recognition by ABC drug pumps to overcome clinical drug resistance. In this review, we discuss the most recent advances in our understanding of ligand interactions and mechanistic aspects of drug transport based on atomic structures of these transporters as well as the development of new in vivo models to study their role in clinical drug resistance in cancer.
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Affiliation(s)
- Sabrina Lusvarghi
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Dr., Bethesda, MD, 20892, USA
| | - Robert W Robey
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Dr., Bethesda, MD, 20892, USA
| | - Michael M Gottesman
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Dr., Bethesda, MD, 20892, USA
| | - Suresh V Ambudkar
- Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Dr., Bethesda, MD, 20892, USA
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13
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Rodríguez-Chávez JL, Méndez-Cuesta CA, Ramírez-Apan T, Egas V, Ávila JL, Neira-González A, Hernández T, Espinosa-García FJ, Delgado G. Chemo-sensitizing activity of natural cadinanes from Heterotheca inuloides in human uterine sarcoma cells and their in silico interaction with ABC transporters. Bioorg Chem 2019; 91:103091. [PMID: 31319298 DOI: 10.1016/j.bioorg.2019.103091] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 06/20/2019] [Accepted: 06/25/2019] [Indexed: 12/20/2022]
Abstract
Sensitizing activities exerted by 3,4-dihydro-7-hydroxycadalene (1), rac-3,7-dihydroxy-3(4H)-isocadalen-4-one (4) and (1R,4R)-4H-1,2,3,4-tetrahydro-1-hydroxycadalen-15-oic acid (9), the major cadinanes isolated from Heterotheca inuloides, towards multidrug-resistant MES-SA/MX2 and parental MES-SA epithelial human uterine sarcoma cell lines were evaluated. We also evaluated the in silico interactions (expressed as ΔGbinding in kcal/mol) of cadinanes 1, 4 and 9 in an in vitro assay, and also tested several structurally related natural compounds with the multidrug resistance protein (MDR1, P-glycoprotein), human multidrug resistance protein 1 (MRP1), and breast cancer resistance protein (BCRP) structures as pharmacological targets using AutoDock and AutoDock Vina. Compound 1 potentiated the cytotoxicity of doxorubicin and mitoxantrone drugs in resistant MES-SA/MX2 cells, compared to cells treated with each drug alone. Compound 1 could reverse the resistance to doxorubicin 12.44 fold at a concentration of 5 μM. It also re-sensitized cells to mitoxantrone 3.94 fold. Hence, compound 1 may be considered as a potential chemosensitizing agent to overcome multidrug resistance in cancer. The docking analysis suggested that there are interactions between cadinanes from H. inuloides and MDR1, MRP1, and BCRP proteins mainly through π-π interactions and hydrogen bonds.
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Affiliation(s)
- José Luis Rodríguez-Chávez
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510 Ciudad de México, Mexico
| | - Carlos A Méndez-Cuesta
- Departamento de Sistemas Biológicos, Universidad Autónoma Metropolitana-Xochimilco, Calzada del Hueso 1100, Ciudad de México 04960, Mexico
| | - Teresa Ramírez-Apan
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510 Ciudad de México, Mexico
| | - Verónica Egas
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510 Ciudad de México, Mexico
| | - José Luis Ávila
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510 Ciudad de México, Mexico
| | - Adriana Neira-González
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510 Ciudad de México, Mexico
| | - Tzasna Hernández
- FES-Iztacala, Universidad Nacional Autónoma de México, Av. de los Barrios No. 1, Tlalnepantla 54090, Estado de México, Mexico
| | - Francisco J Espinosa-García
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, Ex Hacienda de San José de la Huerta 58190, Morelia, Michoacán, Mexico
| | - Guillermo Delgado
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510 Ciudad de México, Mexico.
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14
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Ran Y, Zheng A, Thibodeau PH. Structural analysis reveals pathomechanisms associated with pseudoxanthoma elasticum-causing mutations in the ABCC6 transporter. J Biol Chem 2018; 293:15855-15866. [PMID: 30154241 DOI: 10.1074/jbc.ra118.004806] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 08/23/2018] [Indexed: 11/06/2022] Open
Abstract
Mutations in ABC subfamily C member 6 (ABCC6) transporter are associated with pseudoxanthoma elasticum (PXE), a disease resulting in ectopic mineralization and affecting multiple tissues. A growing number of mutations have been identified in individuals with PXE. For most of these variants, no mechanistic information is available regarding their role in normal and pathophysiologies. To assess how PXE-associated mutations alter ABCC6 biosynthesis and structure, we biophysically and biochemically evaluated the N-terminal nucleotide-binding domain. A high-resolution X-ray structure of nucleotide-binding domain 1 (NBD1) of human ABCC6 was obtained at 2.3 Å that provided a template on which to evaluate PXE-causing mutations. Biochemical analysis of mutations in this domain indicated that multiple PXE-causing mutations altered its structural properties. Analyses of the full-length protein revealed a strong correlation between the alterations in NBD properties and the processing and expression of ABCC6. These results suggest that a significant fraction of PXE-associated mutations located in NBD1 causes changes in its structural properties and that these mutation-induced alterations directly affect the maturation of the full-length ABCC6 protein.
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Affiliation(s)
- Yanchao Ran
- From the Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15219
| | - Aiping Zheng
- From the Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15219
| | - Patrick H Thibodeau
- From the Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15219
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15
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Johnson ZL, Chen J. ATP Binding Enables Substrate Release from Multidrug Resistance Protein 1. Cell 2017; 172:81-89.e10. [PMID: 29290467 DOI: 10.1016/j.cell.2017.12.005] [Citation(s) in RCA: 141] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Revised: 10/02/2017] [Accepted: 11/30/2017] [Indexed: 10/18/2022]
Abstract
The multidrug resistance protein MRP1 is an ATP-driven pump that confers resistance to chemotherapy. Previously, we have shown that intracellular substrates are recruited to a bipartite binding site when the transporter rests in an inward-facing conformation. A key question remains: how are high-affinity substrates transferred across the membrane and released outside the cell? Using electron cryomicroscopy, we show here that ATP binding opens the transport pathway to the extracellular space and reconfigures the substrate-binding site such that it relinquishes its affinity for substrate. Thus, substrate is released prior to ATP hydrolysis. With this result, we now have a complete description of the conformational cycle that enables substrate transfer in a eukaryotic ABC exporter.
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Affiliation(s)
- Zachary Lee Johnson
- Laboratory of Membrane Biology and Biophysics, The Rockefeller University and Howard Hughes Medical Institute, New York, NY 10065, USA
| | - Jue Chen
- Laboratory of Membrane Biology and Biophysics, The Rockefeller University and Howard Hughes Medical Institute, New York, NY 10065, USA.
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16
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Pan X, Zhang Q, Qu S, Huang S, Wang H, Mei H. Allosteric effects of ATP binding on the nucleotide-binding domain of a heterodimeric ATP-binding cassette transporter. Integr Biol (Camb) 2017; 8:1158-1169. [PMID: 27731447 DOI: 10.1039/c6ib00136j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
ATP-binding cassette (ABC) exporters mediate vital transport of a variety of molecules across the lipid bilayer in all organisms. To explore the allosteric effect of ATP binding at the asymmetric ATPase sites, molecular dynamics simulations were performed on the nucleotide-binding domains (NBDs) of a heterodimeric exporter TM287/288 in 4 different ATP-bound states. The results showed that ATP bound at the degenerate site can maintain a semi-open conformation of NBD1-NBD2, which may be defective in ATP hydrolysis. By contrast, when bound at the consensus site, ATP can induce an intra-domain rotation of the α-helical subdomain towards the RecA-like subdomain of NBD2 at the degenerate site. The rotation of the α-helical subdomain rearranged the hydrogen bond networks at the NBD1-NBD2 interface, induced a significant conformational change in the D-loop at the degenerate site and inter- and intra-domain communications at both sites, and eventually elicited dimerization of NBD1-NBD2. These findings indicate that the asymmetric ATPase sites of the heterodimeric exporter are structurally and functionally distinct.
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Affiliation(s)
- Xianchao Pan
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Chongqing University, Chongqing 400044, China. and College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Qiaoxia Zhang
- Chongqing Research Institute of Chemical Industry, Chongqing 400021, China
| | - Sujun Qu
- College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Shuheng Huang
- College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Huicong Wang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Chongqing University, Chongqing 400044, China. and College of Bioengineering, Chongqing University, Chongqing 400044, China
| | - Hu Mei
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, Chongqing University, Chongqing 400044, China. and College of Bioengineering, Chongqing University, Chongqing 400044, China
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17
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Dai F, Yoo WG, Lee JY, Lu Y, Pak JH, Sohn WM, Hong SJ. Multidrug resistance-associated protein 4 is a bile transporter of Clonorchis sinensis simulated by in silico docking. Parasit Vectors 2017; 10:578. [PMID: 29157307 PMCID: PMC5697364 DOI: 10.1186/s13071-017-2523-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 11/05/2017] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Multidrug resistance-associated protein 4 (MRP4) is a member of the C subfamily of the ABC family of ATP-binding cassette (ABC) transporters. MRP4 regulates ATP-dependent efflux of various organic anionic substrates and bile acids out of cells. Since Clonorchis sinensis lives in host's bile duct, accumulation of bile juice can be toxic to the worm's tissues and cells. Therefore, C. sinensis needs bile transporters to reduce accumulation of bile acids within its body. RESULTS We cloned MRP4 (CsMRP4) from C. sinensis and obtained a cDNA encoding an open reading frame of 1469 amino acids. Phylogenetic analysis revealed that CsMRP4 belonged to the MRP/SUR/CFTR subfamily. A tertiary structure of CsMRP4 was generated by homology modeling based on multiple structures of MRP1 and P-glycoprotein. CsMRP4 had two membrane-spanning domains (MSD1 & 2) and two nucleotide-binding domains (NBD1 & 2) as common structural folds. Docking simulation with nine bile acids showed that CsMRP4 transports bile acids through the inner cavity. Moreover, it was found that CsMRP4 mRNA was more abundant in the metacercariae than in the adults. Mouse immune serum, generated against the CsMRP4-NBD1 (24.9 kDa) fragment, localized CsMRP4 mainly in mesenchymal tissues and oral and ventral suckers of the metacercariae and the adults. CONCLUSIONS Our findings shed new light on MRPs and their homologs and provide a platform for further structural and functional investigations on the bile transporters and parasites' survival.
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Affiliation(s)
- Fuhong Dai
- Department of Medical Environmental Biology, Chung-Ang University College of Medicine, Seoul, 06974, South Korea
| | - Won Gi Yoo
- Department of Medical Environmental Biology, Chung-Ang University College of Medicine, Seoul, 06974, South Korea
| | - Ji-Yun Lee
- Department of Medical Environmental Biology, Chung-Ang University College of Medicine, Seoul, 06974, South Korea
| | - Yanyan Lu
- Department of Medical Environmental Biology, Chung-Ang University College of Medicine, Seoul, 06974, South Korea
| | - Jhang Ho Pak
- Department of Convergence Medicine, University of Ulsan College of Medicine and Asan Institute for Life Sciences, Asan Medical Center, Seoul, 05505, South Korea
| | - Woon-Mok Sohn
- Department of Parasitology and Institute of Health Sciences, Gyeongsang National University School of Medicine, Jinju, 52828, South Korea
| | - Sung-Jong Hong
- Department of Medical Environmental Biology, Chung-Ang University College of Medicine, Seoul, 06974, South Korea.
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18
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Vernon RM, Chong PA, Lin H, Yang Z, Zhou Q, Aleksandrov AA, Dawson JE, Riordan JR, Brouillette CG, Thibodeau PH, Forman-Kay JD. Stabilization of a nucleotide-binding domain of the cystic fibrosis transmembrane conductance regulator yields insight into disease-causing mutations. J Biol Chem 2017; 292:14147-14164. [PMID: 28655774 PMCID: PMC5572908 DOI: 10.1074/jbc.m116.772335] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 06/16/2017] [Indexed: 11/06/2022] Open
Abstract
Characterization of the second nucleotide-binding domain (NBD2) of the cystic fibrosis transmembrane conductance regulator (CFTR) has lagged behind research into the NBD1 domain, in part because NBD1 contains the F508del mutation, which is the dominant cause of cystic fibrosis. Research on NBD2 has also been hampered by the overall instability of the domain and the difficulty of producing reagents. Nonetheless, multiple disease-causing mutations reside in NBD2, and the domain is critical for CFTR function, because channel gating involves NBD1/NBD2 dimerization, and NBD2 contains the catalytically active ATPase site in CFTR. Recognizing the paucity of structural and biophysical data on NBD2, here we have defined a bioinformatics-based method for manually identifying stabilizing substitutions in NBD2, and we used an iterative process of screening single substitutions against thermal melting points to both produce minimally mutated stable constructs and individually characterize mutations. We present a range of stable constructs with minimal mutations to help inform further research on NBD2. We have used this stabilized background to study the effects of NBD2 mutations identified in cystic fibrosis (CF) patients, demonstrating that mutants such as N1303K and G1349D are characterized by lower stability, as shown previously for some NBD1 mutations, suggesting a potential role for NBD2 instability in the pathology of CF.
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Affiliation(s)
- Robert M Vernon
- From the Program in Molecular Medicine, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - P Andrew Chong
- From the Program in Molecular Medicine, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Hong Lin
- From the Program in Molecular Medicine, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - Zhengrong Yang
- Center for Structural Biology and Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Qingxian Zhou
- Center for Structural Biology and Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Andrei A Aleksandrov
- Department of Biochemistry and Biophysics, Cystic Fibrosis Treatment and Research Center, University of North Carolina, Chapel Hill, North Carolina 27599, and
| | - Jennifer E Dawson
- From the Program in Molecular Medicine, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada
| | - John R Riordan
- Department of Biochemistry and Biophysics, Cystic Fibrosis Treatment and Research Center, University of North Carolina, Chapel Hill, North Carolina 27599, and
| | - Christie G Brouillette
- Center for Structural Biology and Department of Chemistry, University of Alabama at Birmingham, Birmingham, Alabama 35294
| | - Patrick H Thibodeau
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15219
| | - Julie D Forman-Kay
- From the Program in Molecular Medicine, Hospital for Sick Children, Toronto, Ontario M5G 0A4, Canada,; Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
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19
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Alvarez CP, Stagljar M, Muhandiram DR, Kanelis V. Hyperinsulinism-Causing Mutations Cause Multiple Molecular Defects in SUR1 NBD1. Biochemistry 2017; 56:2400-2416. [PMID: 28346775 DOI: 10.1021/acs.biochem.6b00681] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The sulfonylurea receptor 1 (SUR1) protein forms the regulatory subunit in ATP sensitive K+ (KATP) channels in the pancreas. SUR proteins are members of the ATP binding cassette (ABC) superfamily of proteins. Binding and hydrolysis of MgATP at the SUR nucleotide binding domains (NBDs) lead to channel opening. Pancreatic KATP channels play an important role in insulin secretion. SUR1 mutations that result in increased levels of channel opening ultimately inhibit insulin secretion and lead to neonatal diabetes. In contrast, SUR1 mutations that disrupt trafficking and/or decrease gating of KATP channels cause congenital hyperinsulinism, where oversecretion of insulin occurs even in the presence of low glucose levels. Here, we present data on the effects of specific congenital hyperinsulinism-causing mutations (G716V, R842G, and K890T) located in different regions of the first nucleotide binding domain (NBD1). Nuclear magnetic resonance (NMR) and fluorescence data indicate that the K890T mutation affects residues throughout NBD1, including residues that bind MgATP, NBD2, and coupling helices. The mutations also decrease the MgATP binding affinity of NBD1. Size exclusion and NMR data indicate that the G716V and R842G mutations cause aggregation of NBD1 in vitro, possibly because of destabilization of the domain. These data describe structural characterization of SUR1 NBD1 and shed light on the underlying molecular basis of mutations that cause congenital hyperinsulinism.
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Affiliation(s)
- Claudia P Alvarez
- Department of Chemical and Physical Sciences, University of Toronto Mississauga , 3359 Mississauga Road, Mississauga, Ontario, Canada L5L 1C6.,Department of Chemistry, University of Toronto , 80 St. George Street, Toronto, Ontario, Canada M5S 3H6
| | - Marijana Stagljar
- Department of Chemical and Physical Sciences, University of Toronto Mississauga , 3359 Mississauga Road, Mississauga, Ontario, Canada L5L 1C6.,Department of Chemistry, University of Toronto , 80 St. George Street, Toronto, Ontario, Canada M5S 3H6.,Department of Cell and Systems Biology, University of Toronto , 25 Harbord Street, Toronto, Ontario, Canada M5S 3G5
| | - D Ranjith Muhandiram
- Department of Molecular Genetics, University of Toronto , 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8
| | - Voula Kanelis
- Department of Chemical and Physical Sciences, University of Toronto Mississauga , 3359 Mississauga Road, Mississauga, Ontario, Canada L5L 1C6.,Department of Chemistry, University of Toronto , 80 St. George Street, Toronto, Ontario, Canada M5S 3H6.,Department of Cell and Systems Biology, University of Toronto , 25 Harbord Street, Toronto, Ontario, Canada M5S 3G5
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20
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Gameiro M, Silva R, Rocha-Pereira C, Carmo H, Carvalho F, Bastos MDL, Remião F. Cellular Models and In Vitro Assays for the Screening of modulators of P-gp, MRP1 and BCRP. Molecules 2017; 22:600. [PMID: 28397762 PMCID: PMC6153761 DOI: 10.3390/molecules22040600] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 03/24/2017] [Accepted: 03/28/2017] [Indexed: 12/12/2022] Open
Abstract
Adenosine triphosphate (ATP)-binding cassette (ABC) transporters are highly expressed in tumor cells, as well as in organs involved in absorption and secretion processes, mediating the ATP-dependent efflux of compounds, both endogenous substances and xenobiotics, including drugs. Their expression and activity levels are modulated by the presence of inhibitors, inducers and/or activators. In vitro, ex vivo and in vivo studies with both known and newly synthesized P-glycoprotein (P-gp) inducers and/or activators have shown the usefulness of these transport mechanisms in reducing the systemic exposure and specific tissue access of potentially harmful compounds. This article focuses on the main ABC transporters involved in multidrug resistance [P-gp, multidrug resistance-associated protein 1 (MRP1) and breast cancer resistance protein (BCRP)] expressed in tissues of toxicological relevance, such as the blood-brain barrier, cardiovascular system, liver, kidney and intestine. Moreover, it provides a review of the available cellular models, in vitro and ex vivo assays for the screening and selection of safe and specific inducers and activators of these membrane transporters. The available cellular models and in vitro assays have been proposed as high throughput and low-cost alternatives to excessive animal testing, allowing the evaluation of a large number of compounds.
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MESH Headings
- ATP Binding Cassette Transporter, Subfamily B, Member 1/chemistry
- ATP Binding Cassette Transporter, Subfamily B, Member 1/metabolism
- ATP Binding Cassette Transporter, Subfamily G, Member 2/chemistry
- ATP Binding Cassette Transporter, Subfamily G, Member 2/metabolism
- Animals
- Drug Discovery
- Drug Evaluation, Preclinical/methods
- Drug Resistance/drug effects
- Humans
- Models, Biological
- Multidrug Resistance-Associated Proteins/chemistry
- Multidrug Resistance-Associated Proteins/metabolism
- Organ Specificity
- Structure-Activity Relationship
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Affiliation(s)
- Mariline Gameiro
- UCIBIO/REQUIMTE, Laboratório de Toxicologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal.
| | - Renata Silva
- UCIBIO/REQUIMTE, Laboratório de Toxicologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal.
| | - Carolina Rocha-Pereira
- UCIBIO/REQUIMTE, Laboratório de Toxicologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal.
| | - Helena Carmo
- UCIBIO/REQUIMTE, Laboratório de Toxicologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal.
| | - Félix Carvalho
- UCIBIO/REQUIMTE, Laboratório de Toxicologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal.
| | - Maria de Lourdes Bastos
- UCIBIO/REQUIMTE, Laboratório de Toxicologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal.
| | - Fernando Remião
- UCIBIO/REQUIMTE, Laboratório de Toxicologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal.
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21
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Kakarla P, Inupakutika M, Devireddy AR, Gunda SK, Willmon TM, Ranjana KC, Shrestha U, Ranaweera I, Hernandez AJ, Barr S, Varela MF. 3D-QSAR AND CONTOUR MAP ANALYSIS OF TARIQUIDAR ANALOGUES AS MULTIDRUG RESISTANCE PROTEIN-1 (MRP1) INHIBITORS. INTERNATIONAL JOURNAL OF PHARMACEUTICAL SCIENCES AND RESEARCH 2016; 7:554-572. [PMID: 26913287 PMCID: PMC4762489 DOI: 10.13040/ijpsr.0975-8232.7(2).554-72] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
One of the major obstacles to the successful chemotherapy towards several cancers is multidrug resistance of human cancer cells to anti-cancer drugs. An important contributor to multidrug resistance is the human multidrug resistance protein-1 transporter (MRP1), which is an efflux pump of the ABC (ATP binding cassette) superfamily. Thus, highly efficacious, third generation MRP1 inhibitors, like tariquidar analogues, are promising inhibitors of multidrug resistance and are under clinical trials. To maximize the efficacy of MRP1 inhibitors and to reduce systemic toxicity, it is important to limit the exposure of MRP1 inhibitors and anticancer drugs to normal tissues and to increase their co-localization with tumor cells. Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Similarity Indices Analysis (CoMSIA) associated with 3D-Quantitiative structure-activity relationship (3D-QSAR) studies were performed on a series of tariquidar analogues, as selective MDR modulators. Best predictability was obtained with CoMFA model r2 (non-cross-validated square of correlation coefficient) = 0.968, F value = 151.768 with five components, standard error of estimate = 0.107 while the CoMSIA yielded r2 = 0.982, F value = 60.628 with six components, and standard error of estimate = 0.154. These results indicate that steric, electrostatic, hydrophobic (lipophilic), and hydrogen bond donor substituents play significant roles in multidrug resistance modulation of tariquidar analogues upon MRP1. The tariquidar analogue and MRP1 binding and stability data generated from CoMFA and CoMSIA based 3D-contour maps may further aid in study and design of tariquidar analogues as novel, potent and selective MDR modulator drug candidates.
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Affiliation(s)
- Prathusha Kakarla
- Department of Biology, Eastern New Mexico University, Station 33, Portales, NM, 88130, USA
| | - Madhuri Inupakutika
- Department of Biological Sciences, College of Arts and Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX 76203, USA
| | - Amith R. Devireddy
- Department of Biological Sciences, College of Arts and Sciences, University of North Texas, 1155 Union Circle #305220, Denton, TX 76203, USA
| | - Shravan Kumar Gunda
- Bioinformatics Division, Osmania University, Hyderabad-500007, Andhra Pradesh, India
| | - Thomas Mark Willmon
- Department of Biology, Eastern New Mexico University, Station 33, Portales, NM, 88130, USA
| | - KC Ranjana
- Department of Biology, Eastern New Mexico University, Station 33, Portales, NM, 88130, USA
| | - Ugina Shrestha
- Department of Biology, Eastern New Mexico University, Station 33, Portales, NM, 88130, USA
| | - Indrika Ranaweera
- Department of Biology, Eastern New Mexico University, Station 33, Portales, NM, 88130, USA
| | - Alberto J. Hernandez
- Department of Biology, Eastern New Mexico University, Station 33, Portales, NM, 88130, USA
| | - Sharla Barr
- Department of Biology, Eastern New Mexico University, Station 33, Portales, NM, 88130, USA
| | - Manuel F. Varela
- Department of Biology, Eastern New Mexico University, Station 33, Portales, NM, 88130, USA
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22
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de Araujo ED, Alvarez CP, López-Alonso JP, Sooklal CR, Stagljar M, Kanelis V. Phosphorylation-dependent changes in nucleotide binding, conformation, and dynamics of the first nucleotide binding domain (NBD1) of the sulfonylurea receptor 2B (SUR2B). J Biol Chem 2015. [PMID: 26198630 DOI: 10.1074/jbc.m114.636233] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
The sulfonylurea receptor 2B (SUR2B) forms the regulatory subunit of ATP-sensitive potassium (KATP) channels in vascular smooth muscle. Phosphorylation of the SUR2B nucleotide binding domains (NBD1 and NBD2) by protein kinase A results in increased channel open probability. Here, we investigate the effects of phosphorylation on the structure and nucleotide binding properties of NBD1. Phosphorylation sites in SUR2B NBD1 are located in an N-terminal tail that is disordered. Nuclear magnetic resonance (NMR) data indicate that phosphorylation of the N-terminal tail affects multiple residues in NBD1, including residues in the NBD2-binding site, and results in altered conformation and dynamics of NBD1. NMR spectra of NBD1 lacking the N-terminal tail, NBD1-ΔN, suggest that phosphorylation disrupts interactions of the N-terminal tail with the core of NBD1, a model supported by dynamic light scattering. Increased nucleotide binding of phosphorylated NBD1 and NBD1-ΔN, compared with non-phosphorylated NBD1, suggests that by disrupting the interaction of the NBD core with the N-terminal tail, phosphorylation also exposes the MgATP-binding site on NBD1. These data provide insights into the molecular basis by which phosphorylation of SUR2B NBD1 activates KATP channels.
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Affiliation(s)
- Elvin D de Araujo
- From the Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, the Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, and
| | - Claudia P Alvarez
- From the Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, the Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, and
| | - Jorge P López-Alonso
- From the Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, the Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, and the Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada
| | - Clarissa R Sooklal
- From the Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, the Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, and
| | - Marijana Stagljar
- From the Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, the Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, and the Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada
| | - Voula Kanelis
- From the Department of Chemical and Physical Sciences, University of Toronto Mississauga, Mississauga, Ontario L5L 1C6, the Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, and the Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario M5S 3G5, Canada
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23
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Iram SH, Gruber SJ, Raguimova ON, Thomas DD, Robia SL. ATP-Binding Cassette Transporter Structure Changes Detected by Intramolecular Fluorescence Energy Transfer for High-Throughput Screening. Mol Pharmacol 2015; 88:84-94. [PMID: 25924616 PMCID: PMC4468642 DOI: 10.1124/mol.114.096792] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 04/29/2015] [Indexed: 11/22/2022] Open
Abstract
Multidrug resistance protein 1 (MRP1) actively transports a wide variety of drugs out of cells. To quantify MRP1 structural dynamics, we engineered a "two-color MRP1" construct by fusing green fluorescent protein (GFP) and TagRFP to MRP1 nucleotide-binding domains NBD1 and NBD2, respectively. The recombinant MRP1 protein expressed and trafficked normally to the plasma membrane. Two-color MRP1 transport activity was normal, as shown by vesicular transport of [(3)H]17β-estradiol-17-β-(D-glucuronide) and doxorubicin efflux in AAV-293 cells. We quantified fluorescence resonance energy transfer (FRET) from GFP to TagRFP as an index of NBD conformational changes. Our results show that ATP binding induces a large-amplitude conformational change that brings the NBDs into closer proximity. FRET was further increased by substrate in the presence of ATP but not by substrate alone. The data suggest that substrate binding is required to achieve a fully closed and compact structure. ATP analogs bind MRP1 with reduced apparent affinity, inducing a partially closed conformation. The results demonstrate the utility of the two-color MRP1 construct for investigating ATP-binding cassette transporter structural dynamics, and it holds great promise for high-throughput screening of chemical libraries for unknown activators, inhibitors, or transportable substrates of MRP1.
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Affiliation(s)
- Surtaj H Iram
- Department of Cell and Molecular Physiology (S.H.I., O.N.R., S.L.R.), Cardiovascular Research Institute (O.N.R., S.L.R.), Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois; and Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota (S.J.G., D.D.T); and Department of Chemistry and Biochemistry, South Dakota State University, Brookings, South Dakota (S.H.I.)
| | - Simon J Gruber
- Department of Cell and Molecular Physiology (S.H.I., O.N.R., S.L.R.), Cardiovascular Research Institute (O.N.R., S.L.R.), Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois; and Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota (S.J.G., D.D.T); and Department of Chemistry and Biochemistry, South Dakota State University, Brookings, South Dakota (S.H.I.)
| | - Olga N Raguimova
- Department of Cell and Molecular Physiology (S.H.I., O.N.R., S.L.R.), Cardiovascular Research Institute (O.N.R., S.L.R.), Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois; and Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota (S.J.G., D.D.T); and Department of Chemistry and Biochemistry, South Dakota State University, Brookings, South Dakota (S.H.I.)
| | - David D Thomas
- Department of Cell and Molecular Physiology (S.H.I., O.N.R., S.L.R.), Cardiovascular Research Institute (O.N.R., S.L.R.), Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois; and Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota (S.J.G., D.D.T); and Department of Chemistry and Biochemistry, South Dakota State University, Brookings, South Dakota (S.H.I.)
| | - Seth L Robia
- Department of Cell and Molecular Physiology (S.H.I., O.N.R., S.L.R.), Cardiovascular Research Institute (O.N.R., S.L.R.), Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois; and Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota (S.J.G., D.D.T); and Department of Chemistry and Biochemistry, South Dakota State University, Brookings, South Dakota (S.H.I.)
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24
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Bukowska MA, Hohl M, Geertsma ER, Hürlimann LM, Grütter MG, Seeger MA. A Transporter Motor Taken Apart: Flexibility in the Nucleotide Binding Domains of a Heterodimeric ABC Exporter. Biochemistry 2015; 54:3086-99. [PMID: 25947941 DOI: 10.1021/acs.biochem.5b00188] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
ABC exporters are ubiquitous multidomain transport proteins that couple ATP hydrolysis at a pair of nucleotide binding domains to substrate transport across the lipid bilayer mediated by two transmembrane domains. Recently, the crystal structure of the heterodimeric ABC exporter TM287/288 was determined. One of its asymmetric ATP binding sites is called the degenerate site; it binds nucleotides tightly but is impaired in terms of ATP hydrolysis. Here we report the crystal structures of both isolated motor domains of TM287/288. Unexpectedly, structural elements constituting the degenerate ATP binding site are disordered in these crystals and become structured only in the context of the full-length transporter. In addition, hydrogen bonding patterns of key residues, including those of the catalytically important Walker B and the switch loop motifs, are fundamentally different in the solitary NBDs compared to those in the intact transport protein. The structures reveal crucial interdomain contacts that need to be established for the proper assembly of the functional transporter complex.
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Affiliation(s)
- Magdalena A Bukowska
- †Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Michael Hohl
- †Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.,‡Institute of Medical Microbiology, University of Zurich, Gloriastrasse 30/32, 8006 Zurich, Switzerland
| | - Eric R Geertsma
- †Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Lea M Hürlimann
- †Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.,‡Institute of Medical Microbiology, University of Zurich, Gloriastrasse 30/32, 8006 Zurich, Switzerland
| | - Markus G Grütter
- †Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Markus A Seeger
- †Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland.,‡Institute of Medical Microbiology, University of Zurich, Gloriastrasse 30/32, 8006 Zurich, Switzerland
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25
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Spinelli D, Budriesi R, Cosimelli B, Severi E, Micucci M, Baroni M, Fusi F, Ioan P, Cross S, Frosini M, Saponara S, Matucci R, Rosano C, Viale M, Chiarini A, Carosati E. Playing with opening and closing of heterocycles: using the cusmano-ruccia reaction to develop a novel class of oxadiazolothiazinones, active as calcium channel modulators and P-glycoprotein inhibitors. Molecules 2014; 19:16543-72. [PMID: 25317581 PMCID: PMC6271282 DOI: 10.3390/molecules191016543] [Citation(s) in RCA: 5] [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: 06/20/2014] [Revised: 08/15/2014] [Accepted: 09/04/2014] [Indexed: 11/23/2022] Open
Abstract
As a result of the ring-into-ring conversion of nitrosoimidazole derivatives, we obtained a molecular scaffold that, when properly decorated, is able to decrease inotropy by blocking L-type calcium channels. Previously, we used this scaffold to develop a quantitative structure-activity relationship (QSAR) model, and we used the most potent oxadiazolothiazinone as a template for ligand-based virtual screening. Here, we enlarge the diversity of chemical decorations, present the synthesis and in vitro data for 11 new derivatives, and develop a new 3D-QSAR model with recent in silico techniques. We observed a key role played by the oxadiazolone moiety: given the presence of positively charged calcium ions in the transmembrane channel protein, we hypothesize the formation of a ternary complex between the oxadiazolothiazinone, the Ca2+ ion and the protein. We have supported this hypothesis by means of pharmacophore generation and through the docking of the pharmacophore into a homology model of the protein. We also studied with docking experiments the interaction with a homology model of P-glycoprotein, which is inhibited by this series of molecules, and provided further evidence toward the relevance of this scaffold in biological interactions.
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Affiliation(s)
- Domenico Spinelli
- Dipartimento di Chimica "G. Ciamician", Alma Mater Studiorum-Università di Bologna, Via F. Selmi 2, Bologna 40126, Italy.
| | - Roberta Budriesi
- Dipartimento di Farmacia e Biotecnologie, Alma Mater Studiorum-Università di Bologna, Via Belmeloro 6, Bologna 40126, Italy.
| | - Barbara Cosimelli
- Dipartimento di Farmacia, Università di Napoli "Federico II", Via D. Montesano 49, Napoli 80131, Italy.
| | - Elda Severi
- Dipartimento di Farmacia, Università di Napoli "Federico II", Via D. Montesano 49, Napoli 80131, Italy.
| | - Matteo Micucci
- Dipartimento di Farmacia e Biotecnologie, Alma Mater Studiorum-Università di Bologna, Via Belmeloro 6, Bologna 40126, Italy.
| | - Massimo Baroni
- Molecular Discovery Ltd., 215 Marsh Road, Pinner, Middlesex HA5 5NE, UK.
| | - Fabio Fusi
- Dipartimento di Scienze della Vita, Università degli Studi di Siena, Via A. Moro 2, Siena 53100, Italy.
| | - Pierfranco Ioan
- Dipartimento di Farmacia e Biotecnologie, Alma Mater Studiorum-Università di Bologna, Via Belmeloro 6, Bologna 40126, Italy.
| | - Simon Cross
- Molecular Discovery Ltd., 215 Marsh Road, Pinner, Middlesex HA5 5NE, UK.
| | - Maria Frosini
- Dipartimento di Scienze della Vita, Università degli Studi di Siena, Via A. Moro 2, Siena 53100, Italy.
| | - Simona Saponara
- Dipartimento di Scienze della Vita, Università degli Studi di Siena, Via A. Moro 2, Siena 53100, Italy.
| | - Rosanna Matucci
- Dipartimento di Neuroscienze, Area del Farmaco e Salute del Bambino (NEUROFARBA) Viale Pieraccini 6, Firenze 50139, Italy.
| | - Camillo Rosano
- IRCCS Azienda Ospedaliera Universitaria San Martino-IST Istituto Nazionale per la Ricerca sul Cancro, U.O.S. Biopolimeri e Proteomica, L.go R. Benzi, 10, Genova 16132, Italy.
| | - Maurizio Viale
- IRCCS Azienda Ospedaliera Universitaria San Martino-IST Istituto Nazionale per la Ricerca sul Cancro, U.O.C. Bioterapie, L.go R. Benzi, 10, Genova 16132, Italy.
| | - Alberto Chiarini
- Dipartimento di Farmacia e Biotecnologie, Alma Mater Studiorum-Università di Bologna, Via Belmeloro 6, Bologna 40126, Italy.
| | - Emanuele Carosati
- Dipartimento di Chimica, Biologia e Biotecnologie, Università di Perugia, Via Elce di Sotto 10, Perugia 06123, Italy.
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Abstract
INTRODUCTION Cancer remains the leading cause of death worldwide. Numerous therapeutic strategies that include smart biological treatments toward specific cellular pathways are being developed. Yet, inherent and acquired multidrug resistance (MDR) to chemotherapeutic drugs remains the major obstacle in effective cancer treatments. AREAS COVERED Herein, we focused on an implementation of nanoscale drug delivery strategies (nanomedicines) to treat tumors that resist MDR. Specifically, we briefly discuss the MDR phenomenon and provide structural and functional characterization of key proteins that account for MDR. We next describe the strategies to target tumors using nanoparticles and provide a mechanistic overview of how changes in the influx:efflux ratio result in overcoming MDR. EXPERT OPINION Various strategies have been applied in preclinical and clinical settings to overcome cancer MDR. Among them are the use of chemosensitizers that aim to sensitize the cancer cells to chemotherapeutic treatment and the use of nanomedicines as delivery vehicles that can increase the influx of drugs into cancer cells. These strategies can enhance the therapeutic response in resistant tumors by bypassing efflux pumps or by increasing the nominal amounts of therapeutic payloads into the cancer cells at a given time point.
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Affiliation(s)
- Assaf Ganoth
- The Interdisciplinary Center (IDC) , P.O. Box 167, Herzliya 46150 , Israel
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27
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de Araujo ED, Kanelis V. Successful development and use of a thermodynamic stability screen for optimizing the yield of nucleotide binding domains. Protein Expr Purif 2014; 103:38-47. [PMID: 25153533 DOI: 10.1016/j.pep.2014.08.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 08/08/2014] [Accepted: 08/09/2014] [Indexed: 01/09/2023]
Abstract
ATP sensitive potassium (KATP) channels consist of four copies of a pore-forming inward rectifying potassium channel (Kir6.1 or Kir6.2) and four copies of a sulfonylurea receptor (SUR1, SUR2A, or SUR2B). SUR proteins are members of the ATP-binding cassette superfamily of proteins. Binding of ATP to the Kir6.x subunit mediates channel inhibition, whereas MgATP binding and hydrolysis at the SUR NBDs results in channel opening. Mutations in SUR1 and SUR2A NBDs cause diseases of insulin secretion and cardiac disorders, respectively, underlying the importance of studying the NBDs. Although purification of SUR2A NBD1 in a soluble form is possible, the lack of long-term sample stability of the protein in a concentrated form has precluded detailed studies of the protein aimed at gaining a molecular-level understanding of how SUR mutations cause disease. Here we use a convenient and cost-effective thermodynamic screening method to probe stabilizing conditions for SUR2A NBD1. Results from the screen are used to alter the purification protocol to allow for significantly increased yields of the purified protein. In addition, the screen provides strategies for long-term storage of NBD1 and generating NBD1 samples at high concentrations suitable for NMR studies. NMR spectra of NBD1 with MgAMP-PNP are of higher quality compared to using MgATP, indicating that MgAMP-PNP be used as the ligand in future NMR studies. The screen presented here can be expanded to using different additives and can be employed to enhance purification yields, sample life times, and storage of other low stability nucleotide binding domains, such as GTPases.
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Affiliation(s)
- Elvin D de Araujo
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada; Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Rd., Mississauga, Ontario L5L 1C6, Canada
| | - Voula Kanelis
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada; Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Rd., Mississauga, Ontario L5L 1C6, Canada; Department of Cell and Systems Biology, University of Toronto, 25 Harbord St., Toronto, Ontario M5S 3G5, Canada.
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28
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Kunická T, Václavíková R, Hlaváč V, Vrána D, Pecha V, Rauš K, Trnková M, Kubáčková K, Ambruš M, Vodičková L, Vodička P, Souček P. Non-coding polymorphisms in nucleotide binding domain 1 in ABCC1 gene associate with transcript level and survival of patients with breast cancer. PLoS One 2014; 9:e101740. [PMID: 25078270 PMCID: PMC4117604 DOI: 10.1371/journal.pone.0101740] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Accepted: 06/10/2014] [Indexed: 12/21/2022] Open
Abstract
OBJECTIVES ATP-Binding Cassette (ABC) transporters may cause treatment failure by transporting of anticancer drugs outside of the tumor cells. Multidrug resistance-associated protein 1 coded by the ABCC1 gene has recently been suggested as a potential prognostic marker in breast cancer patients. This study aimed to explore tagged haplotype covering nucleotide binding domain 1 of ABCC1 in relation with corresponding transcript levels in tissues and clinical phenotype of breast cancer patients. METHODS The distribution of twelve ABCC1 polymorphisms was assessed by direct sequencing in peripheral blood DNA (n = 540). RESULTS Tumors from carriers of the wild type genotype in rs35623 or rs35628 exhibited significantly lower levels of ABCC1 transcript than those from carriers of the minor allele (p = 0.003 and p = 0.004, respectively). The ABCC1 transcript levels significantly increased in the order CT-GT>CC-GT>CC-GG for the predicted rs35626-rs4148351 diplotype. Chemotherapy-treated patients carrying the T allele in rs4148353 had longer disease-free survival than those with the GG genotype (p = 0.043). On the other hand, hormonal therapy-treated patients with the AA genotype in rs35628 had significantly longer disease-free survival than carriers of the G allele (p = 0.012). CONCLUSIONS Taken together, our study shows that genetic variability in the nucleotide binding domain 1 has a significant impact on the ABCC1 transcript level in the target tissue and may modify survival of breast cancer patients.
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Affiliation(s)
- Tereza Kunická
- Department of Toxicogenomics, National Institute of Public Health, Prague, Czech Republic
- 3rd Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Radka Václavíková
- Department of Toxicogenomics, National Institute of Public Health, Prague, Czech Republic
| | - Viktor Hlaváč
- Department of Toxicogenomics, National Institute of Public Health, Prague, Czech Republic
- 3rd Faculty of Medicine, Charles University, Prague, Czech Republic
| | - David Vrána
- Department of Toxicogenomics, National Institute of Public Health, Prague, Czech Republic
- Department of Oncology, Palacky University Medical School and Teaching Hospital, Olomouc, Czech Republic
| | - Václav Pecha
- Institute for the Care for Mother and Child, Prague, Czech Republic
| | - Karel Rauš
- Institute for the Care for Mother and Child, Prague, Czech Republic
| | | | - Kateřina Kubáčková
- Department of Oncology, Motol University Hospital, Prague, Czech Republic
| | - Miloslav Ambruš
- Department of Radiotherapy and Oncology, Faculty Hospital Kralovske Vinohrady, Prague, Czech Republic
| | - Ludmila Vodičková
- Department of Toxicogenomics, National Institute of Public Health, Prague, Czech Republic
- Institute of Experimental Medicine, Czech Academy of Sciences, Prague, Czech Republic
| | - Pavel Vodička
- Institute of Experimental Medicine, Czech Academy of Sciences, Prague, Czech Republic
- Institute of Biology and Medical Genetics, 1st Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Pavel Souček
- Department of Toxicogenomics, National Institute of Public Health, Prague, Czech Republic
- * E-mail:
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29
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Abstract
Multidrug resistance presents one of the most important causes of cancer treatment failure. Numerous in vitro and in vivo data have made it clear that multidrug resistance is frequently caused by enhanced expression of ATP-binding cassette (ABC) transporters. ABC transporters are membrane-bound proteins involved in cellular defense mechanisms, namely, in outward transport of xenobiotics and physiological substrates. Their function thus prevents toxicity as carcinogenesis on one hand but may contribute to the resistance of tumor cells to a number of drugs including chemotherapeutics on the other. Within 48 members of the human ABC superfamily there are several multidrug resistance-associated transporters. Due to the well documented susceptibility of numerous drugs to efflux via ABC transporters it is highly desirable to assess the status of ABC transporters for individualization of treatment by their substrates. The multidrug resistance associated protein 1 (MRP1) encoded by ABCC1 gene is one of the most studied ABC transporters. Despite the fact that its structure and functions have already been explored in detail, there are significant gaps in knowledge which preclude clinical applications. Tissue-specific patterns of expression and broad genetic variability make ABCC1/MRP1 an optimal candidate for use as a marker or member of multi-marker panel for prediction of chemotherapy resistance. The purpose of this review was to summarize investigations about associations of gene and protein expression and genetic variability with prognosis and therapy outcome of major cancers. Major advances in the knowledge have been identified and future research directions are highlighted.
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Affiliation(s)
- Tereza Kunická
- Department of Toxicogenomics, National Institute of Public Health , Prague , Czech Republic
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30
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Rosano C, Viale M, Cosimelli B, Severi E, Gangemi R, Ciogli A, De Totero D, Spinelli D. ABCB1 Structural Models, Molecular Docking, and Synthesis of New Oxadiazolothiazin-3-one Inhibitors. ACS Med Chem Lett 2013; 4:694-8. [PMID: 24900735 DOI: 10.1021/ml300436x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Accepted: 05/13/2013] [Indexed: 01/13/2023] Open
Abstract
Docking methods are powerful tools for in silico screening and drug lead generation and optimization. Here, we describe the synthesis of new inhibitors of ABCB1 whose design was based on construction and preliminary confirmation of a model for this membrane transporter of the ATP-binding cassette family. We chose the strategy to build our three-dimensional model of the ABCB1 transporter by homology. Atomic coordinates were then assayed for their reliability using the measured activity of some oxadiazolothiazin-3-one compounds. Once established their performance by docking analysis, we synthesized new compounds whose forecasted activity was tested by MTT and cytofluorimetric assays. Our docking model of MDR1, MONBD1, seems to reliably satisfy our need to design and forecast, on the basis of their LTCC blockers ability, the inhibitory activity of new molecules on the ABCB1 transporter.
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Affiliation(s)
- Camillo Rosano
- IRCCS SM-IST, U.O.S. Biopolimeri e Proteomica, Largo R. Benzi 10, 16132 Genova,
Italy
| | - Maurizio Viale
- IRCCS SM-IST, U.O.C. Terapia Immunologica, Largo R. Benzi 10, 16132 Genova,
Italy
| | - Barbara Cosimelli
- Dip. di Farmacia, Università degli Studi di Napoli “Federico II”, Via D. Montesano 49, 80131 Napoli, Italy
| | - Elda Severi
- Dip. di Farmacia, Università degli Studi di Napoli “Federico II”, Via D. Montesano 49, 80131 Napoli, Italy
| | - Rosaria Gangemi
- IRCCS SM-IST, U.O.C. Terapia Immunologica, Largo R. Benzi 10, 16132 Genova,
Italy
| | - Alessia Ciogli
- Dip. di Chimica e Tecnologie
del Farmaco, Sapienza Università di Roma, Piazzale A. Moro 5, 00185 Roma, Italy
| | - Daniela De Totero
- IRCCS SM-IST, U.O.C. Trasferimento Genico, Largo R. Benzi 10, 16132 Genova,
Italy
| | - Domenico Spinelli
- Dip. di Chimica “G.
Ciamician”, Università degli Studi di Bologna, Via F. Selmi
2, 40126 Bologna, Italy
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31
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López-Alonso JP, de Araujo ED, Kanelis V. NMR and fluorescence studies of drug binding to the first nucleotide binding domain of SUR2A. Biochemistry 2012; 51:9211-22. [PMID: 23078514 DOI: 10.1021/bi301019e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
ATP sensitive potassium (K(ATP)) channels are composed of four copies of a pore-forming inward rectifying potassium channel (Kir6.1 or Kir6.2) and four copies of a sulfonylurea receptor (SUR1, SUR2A, or SUR2B) that surround the pore. SUR proteins are members of the ATP-binding cassette (ABC) superfamily of proteins. Binding of MgATP at the SUR nucleotide binding domains (NBDs) results in NBD dimerization, and hydrolysis of MgATP at the NBDs leads to channel opening. The SUR proteins also mediate interactions with K(ATP) channel openers (KCOs) that activate the channel, with KCO binding and/or activation involving residues in the transmembrane helices and cytoplasmic loops of the SUR proteins. Because the cytoplasmic loops make extensive interactions with the NBDs, we hypothesized that the NBDs may also be involved in KCO binding. Here, we report nuclear magnetic resonance (NMR) spectroscopy studies that demonstrate a specific interaction of the KCO pinacidil with the first nucleotide binding domain (NBD1) from SUR2A, the regulatory SUR protein in cardiac K(ATP) channels. Intrinsic tryptophan fluorescence titrations also demonstrate binding of pinacidil to SUR2A NBD1, and fluorescent nucleotide binding studies show that pinacidil binding increases the affinity of SUR2A NBD1 for ATP. In contrast, the KCO diazoxide does not interact with SUR2A NBD1 under the same conditions. NMR relaxation experiments and size exclusion chromatography indicate that SUR2A NBD1 is monomeric under the conditions used in drug binding studies. These studies identify additional binding sites for commonly used KCOs and provide a foundation for testing binding of drugs to the SUR NBDs.
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Affiliation(s)
- Jorge P López-Alonso
- Department of Chemical and Physical Sciences, University of Toronto Mississauga, 3359 Mississauga Road, Mississauga, Ontario, Canada L5L 1C6
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32
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Rungsardthong K, Mares- Sámano S, Penny J. Virtual screening of ABCC1 transporter nucleotidebinding domains as a therapeutic target in multidrug resistant cancer. Bioinformation 2012; 8:907-11. [PMID: 23144549 PMCID: PMC3488831 DOI: 10.6026/97320630008907] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Accepted: 09/20/2012] [Indexed: 11/23/2022] Open
Abstract
UNLABELLED ABCC1 is a member of the ATP-binding Cassette super family of transporters, actively effluxes xenobiotics from cells. Clinically, ABCC1 expression is linked to cancer multidrug resistance. Substrate efflux is energised by ATP binding and hydrolysis at the nucleotide-binding domains (NBDs) and inhibition of these events may help combat drug resistance. The aim of this study is to identify potential inhibitors of ABCC1 through virtual screening of National Cancer Institute (NCI) compounds. A threedimensional model of ABCC1 NBD2 was generated using MODELLER whilst the X-ray crystal structure of ABCC1 NBD1 was retrieved from the Protein Data Bank. A pharmacophore hypothesis was generated based on flavonoids known to bind at the NBDs using PHASE, and used to screen the NCI database. GLIDE was employed in molecular docking studies for all hit compounds identified by pharmacophore screening. The best potential inhibitors were identified as compounds possessing predicted binding affinities greater than ATP. Approximately 5% (13/265) of the hit compounds possessed lower docking scores than ATP in ABCC1 NBD1 (NSC93033, NSC662377, NSC319661, NSC333748, NSC683893, NSC226639, NSC94231, NSC55979, NSC169121, NSC166574, NSC73380, NSC127738, NSC115534), whereas approximately 7% (7/104) of docked NCI compounds were predicted to possess lower docking scores than ATP in ABCC1 NBD2 (NSC91789, NSC529483, NSC211168, NSC318214, NSC116519, NSC372332, NSC526974). Analyses of docking orientations revealed P-loop residues of each NBD and the aromatic amino acids Trp653 (NBD1) and Tyr1302 (NBD2) were key in interacting with high-affinity compounds. On the basis of docked orientation and docking score the compounds identified may be potential inhibitors of ABCC1 and require further pharmacological analysis. ABBREVIATIONS ABC - ATP-binding cassette, DHS - dehydrosilybin, MDR - multidrug resistance, NBD - nucleotide-binding domain, PDB - protein data bank.
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Affiliation(s)
- Kanin Rungsardthong
- University of Manchester, School of Pharmacy & Pharmaceutical Sciences, Stopford Building, M13 9PT, UK
| | - Sergio Mares- Sámano
- University of Manchester, School of Pharmacy & Pharmaceutical Sciences, Stopford Building, M13 9PT, UK
| | - Jeffrey Penny
- University of Manchester, School of Pharmacy & Pharmaceutical Sciences, Stopford Building, M13 9PT, UK
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33
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A plausible explanation for enhanced bioavailability of P-gp substrates in presence of piperine: simulation for next generation of P-gp inhibitors. J Mol Model 2012; 19:227-38. [PMID: 22864626 DOI: 10.1007/s00894-012-1535-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2012] [Accepted: 07/10/2012] [Indexed: 10/28/2022]
Abstract
P-glycoprotein (P-gp) has a major role to play in drug pharmacokinetics and pharmacodynamics, since it effluxes many cytotoxic hydrophobic anticancer drugs from gastrointestinal tract, brain, liver and kidney. Piperine is known to enhance the bioavailability of curcumin, as a substrate of P-gp by at least 2000%. Besides these at least 50 other substrates and inhibitors of P-gp have been reported so far. All P-gp inhibitors have diverse structures. Although little is known about binding of some flavonoids and steroids at the NBD (nucleotide binding domain) of P-gp in the vicinity of ATP binding site inhibiting its hydrolysis, a valid explanation of how P-gp accommodates such a diverse set of inhibitors is still awaited. In the present study, piperine up to 100 μM has not shown observable cytotoxic effect on MDCK cell line, and it has been shown to accumulate rhodamine by fluorescence microscopy and fluorescent activated cell sorter in MDCK cells. Computational simulation for piperine and some first and second generation P-gp inhibitors has shown that these dock at the NBD site of P-gp. A comparative simulation study has been carried out regarding their docking and binding energies. Binding conformation of P-gp co-crystallized complexes with ADP, AMP-PNP (Adenylyl-imidodiphosphate), and ATP were compared with piperine. The receptor based E-pharmacophore of docked piperine has been simulated to find common features amongst P-gp inhibitors. Finally it has been concluded that piperine could be utilized as base molecule for design and development of safe non-toxic inhibitor of P-gp in order to enhance the bioavailability of most of its substrates.
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34
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de Wet H, Shimomura K, Aittoniemi J, Ahmad N, Lafond M, Sansom MSP, Ashcroft FM. A universally conserved residue in the SUR1 subunit of the KATP channel is essential for translating nucleotide binding at SUR1 into channel opening. J Physiol 2012; 590:5025-36. [PMID: 22802590 PMCID: PMC3495298 DOI: 10.1113/jphysiol.2012.236075] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The sulphonylurea receptor (SUR1) subunit of the ATP-sensitive potassium (KATP) channel is a member of the ATP-binding cassette (ABC) protein family. Binding of MgADP to nucleotide-binding domain 2 (NBD2) is critical for channel activation.We identified a residue in NBD2 (G1401) that is fully conserved among ABC proteins and whose functional importance is unknown. Homology modelling places G1401 on the outer surface of the protein, distant from the nucleotide-binding site. The ATPase activity of purified SUR1-NBD2-G1410R (bound to maltose-binding protein) was slightly inhibited when compared to the wild-type protein, but its inhibition by MgADP was unchanged, indicating that MgADP binding is not altered. However, MgADP activation of channel activity was abolished. This implies that the G1401R mutation impairs the mechanism by which MgADP binding to NBD2 is translated into opening of the KATP channel pore. The location of G1401 would be consistent with interaction of this residue with the pore-forming Kir6.2 subunit. Channel activity in the presence of MgATP reflects the balance between the stimulatory (at SUR1) and inhibitory (at Kir6.2) effects of nucleotides. Mutant channels were 2.5-fold less sensitive to MgATP inhibition and not activated by MgATP. This suggests that ATP block of the channel is reduced by the SUR1 mutation. Interestingly, this effect was dependent on the functional integrity of the NBDs. These results therefore suggest that SUR1 modulates both nucleotide inhibition and activation of the KATP channel.
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Affiliation(s)
- Heidi de Wet
- Henry Wellcome Centre for Gene Function, Department of Physiology, Anatomy and Genetics, University of Oxford, Parks Road, Oxford OX1 3PT, UK
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Crystal structure of a heterodimeric ABC transporter in its inward-facing conformation. Nat Struct Mol Biol 2012; 19:395-402. [PMID: 22447242 DOI: 10.1038/nsmb.2267] [Citation(s) in RCA: 195] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Accepted: 02/17/2012] [Indexed: 11/08/2022]
Abstract
ATP-binding cassette (ABC) transporters shuttle a wide variety of molecules across cell membranes by alternating between inward- and outward-facing conformations, harnessing the energy of ATP binding and hydrolysis at their nucleotide binding domains (NBDs). Here we present the 2.9-Å crystal structure of the heterodimeric ABC transporter TM287-TM288 (TM287/288) from Thermotoga maritima in its inward-facing state. In contrast to previous studies, we found that the NBDs only partially separate, remaining in contact through an interface involving conserved motifs that connect the two ATP hydrolysis sites. We observed AMP-PNP binding to the degenerate catalytic site, which deviates from the consensus sequence in the same positions as the eukaryotic homologs CFTR and TAP1-TAP2 (TAP1/2). The TM287/288 structure provides unprecedented insights into the mechanism of heterodimeric ABC exporters and will enable future studies on this large transporter superfamily.
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Balamurugan R, Stalin A, Ignacimuthu S. Molecular docking of γ-sitosterol with some targets related to diabetes. Eur J Med Chem 2011; 47:38-43. [PMID: 22078765 DOI: 10.1016/j.ejmech.2011.10.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Revised: 09/22/2011] [Accepted: 10/04/2011] [Indexed: 11/26/2022]
Abstract
γ-sitosterol isolated from Lippia nodiflora was taken as ligand for molecular docking. The molecular targets, glucokinase, Fructose 1, 6- bisphosphatase 1, Human multidrug resistance protein 1 and Cytochromes P450 whose crystallographic structures are available on the PDB database as 1V4S, 2JJK, 3LC4, 2CBZ respectively, were used for the docking analysis using the Autodock tool v 4.2 and ADT v1.5.4 programs. The docking studies of the ligand γ- sitosterol with four different target proteins showed that this is a good molecule which docks well with various targets related to diabetes mellitus. Hence γ-sitosterol can be considered for developing into a potent antidiabetic drug.
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Affiliation(s)
- Rangachari Balamurugan
- Division of Ethnopharmacology, Entomology Research Institute, Loyola College, Nungambakkam, Chennai 600 034, Tamil Nadu, India
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de Araujo ED, Ikeda LK, Tzvetkova S, Kanelis V. The first nucleotide binding domain of the sulfonylurea receptor 2A contains regulatory elements and is folded and functions as an independent module. Biochemistry 2011; 50:6655-66. [PMID: 21714514 DOI: 10.1021/bi200434d] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The sulfonylurea receptor 2A (SUR2A) is an ATP-binding cassette (ABC) protein that forms the regulatory subunit of ATP-sensitive potassium (K(ATP)) channels in the heart. ATP binding and hydrolysis at the SUR2A nucleotide binding domains (NBDs) control gating of K(ATP) channels, and mutations in the NBDs that affect ATP hydrolysis and cellular trafficking cause cardiovascular disorders. To date, there is limited information on the SUR2A NBDs and the effects of disease-causing mutations on their structure and interactions. Structural and biophysical studies of NBDs, especially from eukaryotic ABC proteins like SUR2A, have been hindered by low solubility of the isolated domains. We hypothesized that the solubility of heterologously expressed SUR2A NBDs depends on the precise definition of the domain boundaries. Putative boundaries of SUR2A NBD1 were identified by structure-based sequence alignments and subsequently tested by exploring the solubility of SUR2A NBD1 constructs with different N and C termini. We have determined boundaries of SUR2A NBD1 that allow for soluble heterologous expression of the protein, producing a folded domain with ATP binding activity. Surprisingly, our alignment and screening data indicate that SUR2A NBD1 contains two putative, previously unidentified, regulatory elements: a large insert within the β-sheet subdomain and a C-terminal extension. Our approach, which combines the use of structure-based sequence alignments and predictions of disordered regions combined with biochemical and biophysical studies, may be applied as a general method for developing suitable constructs of other NBDs of ABC proteins.
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Affiliation(s)
- Elvin D de Araujo
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, Ontario M5S 3H6, Canada
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Ostuni A, Miglionico R, Monné M, Castiglione Morelli MA, Bisaccia F. The nucleotide-binding domain 2 of the human transporter protein MRP6. J Bioenerg Biomembr 2011; 43:465-71. [PMID: 21748403 DOI: 10.1007/s10863-011-9372-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2011] [Accepted: 06/13/2011] [Indexed: 02/03/2023]
Abstract
Multidrug-resistance-associated protein 6 (MRP6/ABCC6) belongs to the ABC transporter family, whose members share many characteristic features including membrane domains and two nucleotide-binding domains (NBD1 and NBD2). These function cooperatively to bind and hydrolyze ATP for the transport of substrates across biological membranes. In this study, MRP6-NBD2 (residues 1252-1503) was expressed in Escherichia coli, purified and structurally and functionally characterized. CD spectra suggested that the protein is folded. Furthermore, NBD2 is shown to be biologically active as it binds ATP and presents ATPase activity although significantly lower compared with isolated NBD1. The mixture of NBD2 and NBD1 exhibited an activity similar to the NBD2 alone, indicating that NBD1 and NBD2 form a heterodimer with the latter limiting ATP hydrolysis. These findings suggest that NBD1 has a higher tendency to form an active homodimer, which is also supported by in silico analysis of energy-minimized dimers of the homology models of the two domains.
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Affiliation(s)
- Angela Ostuni
- Department of Chemistry "Antonio Mario Tamburro", University of Basilicata, viale Ateneo Lucano 10, 85100 Potenza, Italy.
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Yang R, Hou YX, Campbell CA, Palaniyandi K, Zhao Q, Bordner AJ, Chang XB. Glutamine residues in Q-loops of multidrug resistance protein MRP1 contribute to ATP binding via interaction with metal cofactor. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2011; 1808:1790-6. [PMID: 21315686 DOI: 10.1016/j.bbamem.2011.02.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2010] [Revised: 01/07/2011] [Accepted: 02/03/2011] [Indexed: 10/18/2022]
Abstract
Structural analyses of bacterial ATP-binding-cassette transporters revealed that the glutamine residue in Q-loop plays roles in interacting with: 1) a metal cofactor to participate in ATP binding; 2) a putative catalytic water molecule to participate in ATP hydrolysis; 3) other residues to transmit the conformational changes between nucleotide-binding-domains and transmembrane-domains, in ATP-dependent solute transport. We have mutated the glutamines at 713 and 1375 to asparagine, methionine or leucine to determine the functional roles of these residues in Q-loops of MRP1. All these single mutants significantly decreased Mg·ATP binding and increased the K(m) (Mg·ATP) and V(max) values in Mg·ATP-dependent leukotriene-C4 transport. However, the V(max) values of the double mutants Q713N/Q1375N, Q713M/Q1375M and Q713L/Q1375L were lower than that of wtMRP1, implying that the double mutants cannot efficiently bind Mg·ATP. Interestingly, MRP1 has higher affinity for Mn·ATP than for Mg·ATP and the Mn·ATP-dependent leukotriene-C4 transport activities of Q713N/Q1375N and Q713M/Q1375M are significantly higher than that of wtMRP1. All these results suggest that: 1) the glutamine residues in Q-loops contribute to ATP-binding via interaction with a metal cofactor; 2) it is most unlikely that these glutamine residues would play crucial roles in ATP hydrolysis and in transmitting the conformational changes between nucleotide-binding-domains and transmembrane-domains.
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Affiliation(s)
- Runying Yang
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Mayo Clinic, Scottsdale, AZ, USA
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40
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Kelly L, Fukushima H, Karchin R, Gow JM, Chinn LW, Pieper U, Segal MR, Kroetz DL, Sali A. Functional hot spots in human ATP-binding cassette transporter nucleotide binding domains. Protein Sci 2011; 19:2110-21. [PMID: 20799350 DOI: 10.1002/pro.491] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The human ATP-binding cassette (ABC) transporter superfamily consists of 48 integral membrane proteins that couple the action of ATP binding and hydrolysis to the transport of diverse substrates across cellular membranes. Defects in 18 transporters have been implicated in human disease. In hundreds of cases, disease phenotypes and defects in function can be traced to nonsynonymous single nucleotide polymorphisms (nsSNPs). The functional impact of the majority of ABC transporter nsSNPs has yet to be experimentally characterized. Here, we combine experimental mutational studies with sequence and structural analysis to describe the impact of nsSNPs in human ABC transporters. First, the disease associations of 39 nsSNPs in 10 transporters were rationalized by identifying two conserved loops and a small α-helical region that may be involved in interdomain communication necessary for transport of substrates. Second, an approach to discriminate between disease-associated and neutral nsSNPs was developed and tailored to this superfamily. Finally, the functional impact of 40 unannotated nsSNPs in seven ABC transporters identified in 247 ethnically diverse individuals studied by the Pharmacogenetics of Membrane Transporters consortium was predicted. Three predictions were experimentally tested using human embryonic kidney epithelial (HEK) 293 cells stably transfected with the reference multidrug resistance transporter 4 and its variants to examine functional differences in transport of the antiviral drug, tenofovir. The experimental results confirmed two predictions. Our analysis provides a structural and evolutionary framework for rationalizing and predicting the functional effects of nsSNPs in this clinically important membrane transporter superfamily.
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Affiliation(s)
- Libusha Kelly
- Graduate Group in Bioinformatics, University of California at San Francisco, San Francisco, California, USA
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41
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Milane L, Duan Z, Amiji M. Development of EGFR-targeted polymer blend nanocarriers for combination paclitaxel/lonidamine delivery to treat multi-drug resistance in human breast and ovarian tumor cells. Mol Pharm 2010; 8:185-203. [PMID: 20942457 DOI: 10.1021/mp1002653] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Multi-drug resistant (MDR) cancer is a significant clinical obstacle and is often implicated in cases of recurrent, nonresponsive disease. Targeted nanoparticles were made by synthesizing a poly(D,L-lactide-co-glycolide)/poly(ethylene glycol)/epidermal growth factor receptor targeting peptide (PLGA/PEG/EGFR-peptide) construct for incorporation in poly(epsilon-caprolactone) (PCL) nanoparticles. MDR was induced in a panel of nine human breast and ovarian cancer cell lines using hypoxia. EGFR-targeted polymer blend nanoparticles were shown to actively target EGFR overexpressing cell lines, especially upon induction of hypoxia. The nanoparticles were capable of sustained drug release. Combination therapy with lonidamine and paclitaxel significantly improved the therapeutic index of both drugs. Treatment with a nanoparticle dose of 1 μM paclitaxel/10 μM lonidamine resulted in less than 10% cell viability for all hypoxic/MDR cell lines and less than 5% cell viability for all normoxic cell lines. Comparatively, treatment with 1 μM paclitaxel alone was the approximate IC₅₀ value of the MDR cells while treatment with lonidamine alone had very little effect. The PLGA/PEG/EGFR-peptide delivery system actively targets a MDR cell by exploiting the expression of EGFR. This system treats MDR by inhibiting the Warburg effect and promoting mitochondrial binding of pro-apoptotic Bcl-2 proteins (lonidamine), while hyperstabilizing microtubules (paclitaxel). This nanocarrier system actively targets a MDR associated phenotype (EGFR receptor overexpression), further enhancing the therapeutic index of both drugs and potentiating the use of lonidamine/paclitaxel combination therapy in the treatment of MDR cancer.
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Affiliation(s)
- Lara Milane
- Department of Pharmaceutical Sciences, School of Pharmacy, Northeastern University, Boston, Massachusetts 02115, USA
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42
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Doppelt-Azeroual O, Delfaud F, Moriaud F, de Brevern AG. Fast and automated functional classification with MED-SuMo: an application on purine-binding proteins. Protein Sci 2010; 19:847-67. [PMID: 20162627 DOI: 10.1002/pro.364] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Ligand-protein interactions are essential for biological processes, and precise characterization of protein binding sites is crucial to understand protein functions. MED-SuMo is a powerful technology to localize similar local regions on protein surfaces. Its heuristic is based on a 3D representation of macromolecules using specific surface chemical features associating chemical characteristics with geometrical properties. MED-SMA is an automated and fast method to classify binding sites. It is based on MED-SuMo technology, which builds a similarity graph, and it uses the Markov Clustering algorithm. Purine binding sites are well studied as drug targets. Here, purine binding sites of the Protein DataBank (PDB) are classified. Proteins potentially inhibited or activated through the same mechanism are gathered. Results are analyzed according to PROSITE annotations and to carefully refined functional annotations extracted from the PDB. As expected, binding sites associated with related mechanisms are gathered, for example, the Small GTPases. Nevertheless, protein kinases from different Kinome families are also found together, for example, Aurora-A and CDK2 proteins which are inhibited by the same drugs. Representative examples of different clusters are presented. The effectiveness of the MED-SMA approach is demonstrated as it gathers binding sites of proteins with similar structure-activity relationships. Moreover, an efficient new protocol associates structures absent of cocrystallized ligands to the purine clusters enabling those structures to be associated with a specific binding mechanism. Applications of this classification by binding mode similarity include target-based drug design and prediction of cross-reactivity and therefore potential toxic side effects.
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Affiliation(s)
- Olivia Doppelt-Azeroual
- INSERM UMR-S 665, Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB), Université Paris Diderot-Paris 7, Institut National de la Transfusion Sanguine (INTS), 6, rue Alexandre Cabanel, 75739 Paris cedex 15, France.
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Haffke M, Menzel A, Carius Y, Jahn D, Heinz DW. Structures of the nucleotide-binding domain of the human ABCB6 transporter and its complexes with nucleotides. ACTA CRYSTALLOGRAPHICA SECTION D: BIOLOGICAL CRYSTALLOGRAPHY 2010; 66:979-87. [PMID: 20823549 DOI: 10.1107/s0907444910028593] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2010] [Accepted: 07/17/2010] [Indexed: 02/01/2023]
Abstract
The human ATP-binding cassette (ABC) transporter ABCB6 is involved in haem-precursor transport across the mitochondrial membrane. The crystal structure of its nucleotide-binding domain (NBD) has been determined in the apo form and in complexes with ADP, with ADP and Mg(2+) and with ATP at high resolution. The overall structure is L-shaped and consists of two lobes, consistent with other reported NBD structures. Nucleotide binding is mediated by the highly conserved Tyr599 and the Walker A motif, and induces notable structural changes. Structural comparison with other structurally characterized NBDs and full-length ABC transporters gives the first insight into the possible catalytic mechanism of ABCB6 and the role of the N-terminal helix alpha(1) in full-length ABCB6.
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Affiliation(s)
- Matthias Haffke
- Helmholtz Zentrum für Infektionsforschung, Braunschweig, Germany
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Chang XB. Molecular mechanism of ATP-dependent solute transport by multidrug resistance-associated protein 1. Methods Mol Biol 2010; 596:223-49. [PMID: 19949927 DOI: 10.1007/978-1-60761-416-6_11] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Millions of new cancer patients are diagnosed each year and over half of these patients die from this devastating disease. Thus, cancer causes a major public health problem worldwide. Chemotherapy remains the principal mode to treat many metastatic cancers. However, occurrence of cellular multidrug resistance (MDR) prevents efficient killing of cancer cells, leading to chemotherapeutic treatment failure. Over-expression of ATP-binding cassette transporters, such as P-glycoprotein, breast cancer resistance protein and/or multidrug resistance-associated protein 1 (MRP1), confers an acquired MDR due to their capabilities of transporting a broad range of chemically diverse anticancer drugs across the cell membrane barrier. In this review, the molecular mechanism of ATP-dependent solute transport by MRP1 will be addressed.
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Affiliation(s)
- Xiu-bao Chang
- Mayo Clinic College of Medicine, Mayo Clinic Arizona, Scottsdale, AZ, USA.
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Hou YX, Li CZ, Palaniyandi K, Magtibay PM, Homolya L, Sarkadi B, Chang XB. Effects of putative catalytic base mutation E211Q on ABCG2-mediated methotrexate transport. Biochemistry 2009; 48:9122-31. [PMID: 19691360 DOI: 10.1021/bi900675v] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
ABCG2 is a half-ATP binding cassette (ABC) drug transporter that consists of a nucleotide binding domain (NBD) followed by a transmembrane domain. This half-ABC transporter is thought to form a homodimer in the plasma membrane where it transports anticancer drugs across the biological membranes in an ATP-dependent manner. Substitution of the putative catalytic residue E211 with a nonacidic amino acid glutamine (E211Q) completely abolished its ATPase activity and ATP-dependent methotrexate transport, suggesting that ATP hydrolysis is required for the ATP-dependent solute transport. However, whether one ATP hydrolysis or two ATP hydrolyses in the homodimer of ABCG2 with the NBD.ATP.ATP.NBD sandwich structure is/are required for the ATP-dependent solute transport is not known yet. To address this question, we have made an YFP/ABCG2 fusion protein and expressed this 99 kDa fusion protein alone or along with the 70 kDa E211Q-mutated ABCG2 in BHK cells. Although membrane vesicles prepared from BHK cells expressing YFP/ABCG2 exert higher ATPase activity than that of wt ABCG2, the dATP-dependent methotrexate transport activities of these two proteins are the same. Interestingly, membrane vesicles prepared from BHK cells expressing both YFP/ABCG2 and E211Q-mutated ABCG2 (with a ratio of 1:1) form homodimers and heterodimer and exert 55% of wt ABCG2 ATPase activity that can be further enhanced by anticancer drugs, suggesting that the wt NBD in the heterodimer of YFP/ABCG2 and E211Q may be able to hydrolyze ATP. Furthermore, the membrane vesicles containing both YFP/ABCG2 and E211Q exert approximately 79% of wt ABCG2-mediated methotrexate transport activity, implying that the heterodimer harboring YFP/ABCG2 and E211Q may be able to transport the anticancer drug methotrexate across the biological membranes.
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Affiliation(s)
- Yue-xian Hou
- Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, 13400 East Shea Boulevard, Scottsdale, Arizona 85259, USA
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Kos V, Ford RC. The ATP-binding cassette family: a structural perspective. Cell Mol Life Sci 2009; 66:3111-26. [PMID: 19544044 PMCID: PMC11115812 DOI: 10.1007/s00018-009-0064-9] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2009] [Revised: 05/27/2009] [Accepted: 06/03/2009] [Indexed: 10/20/2022]
Abstract
The ATP-binding cassette family is one of the largest groupings of membrane proteins, moving allocrites across lipid membranes, using energy from ATP. In bacteria, they reside in the inner membrane and are involved in both uptake and export. In eukaryotes, these transporters reside in the cell's internal membranes as well as in the plasma membrane and are unidirectional-out of the cytoplasm. The range of substances that these proteins can transport is huge, which makes them interesting for structure-function studies. Moreover, their abundance in nature has made them targets for structural proteomics consortia. There are eight independent structures for ATP-binding cassette transporters, making this one of the best characterised membrane protein families. Our understanding of the mechanism of transport across membranes and membrane protein structure in general has been enhanced by recent developments for this family.
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Affiliation(s)
- Veronica Kos
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of Guelph, Guelph, ON N1G 2W1 Canada
| | - Robert Curtis Ford
- Faculty of Life Sciences, Manchester Interdisplinary Biocentre, The University of Manchester, Manchester, M1 7DN UK
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Eckford PDW, Sharom FJ. ABC efflux pump-based resistance to chemotherapy drugs. Chem Rev 2009; 109:2989-3011. [PMID: 19583429 DOI: 10.1021/cr9000226] [Citation(s) in RCA: 480] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Paul D W Eckford
- Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
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Abstract
AbstractIn order to fulfill their function, membrane transport proteins have to cycle through a number of conformational and/or energetic states. Thus, understanding the role of conformational dynamics seems to be the key for elucidation of the functional mechanism of these proteins. However, membrane proteins in general are often difficult to express heterologously and in sufficient amounts for structural studies. It is especially challenging to trap a stable energy minimum, e.g., for crystallographic analysis. Furthermore, crystallization is often only possible by subjecting the protein to conditions that do not resemble its native environment and crystals can only be snapshots of selected conformational states. Nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR) spectroscopy are complementary methods that offer unique possibilities for studying membrane proteins in their natural membrane environment and for investigating functional conformational changes, lipid interactions, substrate-lipid and substrate-protein interactions, oligomerization states and overall dynamics of membrane transporters. Here, we review recent progress in the field including studies from primary and secondary active transporters.
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49
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Cancer-relevant biochemical targets of cytotoxic Lonchocarpus flavonoids: A molecular docking analysis. J Mol Model 2009; 16:311-26. [DOI: 10.1007/s00894-009-0547-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2009] [Accepted: 06/11/2009] [Indexed: 11/25/2022]
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50
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Identification of novel specific and general inhibitors of the three major human ATP-binding cassette transporters P-gp, BCRP and MRP2 among registered drugs. Pharm Res 2009; 26:1816-31. [PMID: 19421845 DOI: 10.1007/s11095-009-9896-0] [Citation(s) in RCA: 245] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2009] [Accepted: 04/11/2009] [Indexed: 01/16/2023]
Abstract
PURPOSE To study the inhibition patterns of the three major human ABC transporters P-gp (ABCB1), BCRP (ABCG2) and MRP2 (ABCC2), using a dataset of 122 structurally diverse drugs. METHODS Inhibition was investigated in cellular and vesicular systems over-expressing single transporters. Computational models discriminating either single or general inhibitors from non-inhibitors were developed using multivariate statistics. RESULTS Specific (n = 23) and overlapping (n = 19) inhibitors of the three ABC transporters were identified. GF120918 and Ko143 were verified to specifically inhibit P-gp/BCRP and BCRP in defined concentration intervals, whereas the MRP inhibitor MK571 was revealed to inhibit all three transporters within one log unit of concentration. Virtual docking experiments showed that MK571 binds to the ATP catalytic site, which could contribute to its multi-specific inhibition profile. A computational model predicting general ABC inhibition correctly classified 80% of both ABC transporter inhibitors and non-inhibitors in an external test set. CONCLUSIONS The inhibitor specificities of P-gp, BCRP and MRP2 were shown to be highly overlapping. General ABC inhibitors were more lipophilic and aromatic than specific inhibitors and non-inhibitors. The identified specific inhibitors can be used to delineate transport processes in complex experimental systems, whereas the multi-specific inhibitors are useful in primary ABC transporter screening in drug discovery settings.
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