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Veiga-Matos J, Morales AI, Prieto M, Remião F, Silva R. Study Models of Drug-Drug Interactions Involving P-Glycoprotein: The Potential Benefit of P-Glycoprotein Modulation at the Kidney and Intestinal Levels. Molecules 2023; 28:7532. [PMID: 38005253 PMCID: PMC10673607 DOI: 10.3390/molecules28227532] [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: 10/11/2023] [Revised: 11/03/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
P-glycoprotein (P-gp) is a crucial membrane transporter situated on the cell's apical surface, being responsible for eliminating xenobiotics and endobiotics. P-gp modulators are compounds that can directly or indirectly affect this protein, leading to changes in its expression and function. These modulators can act as inhibitors, inducers, or activators, potentially causing drug-drug interactions (DDIs). This comprehensive review explores diverse models and techniques used to assess drug-induced P-gp modulation. We cover several approaches, including in silico, in vitro, ex vivo, and in vivo methods, with their respective strengths and limitations. Additionally, we explore the therapeutic implications of DDIs involving P-gp, with a special focus on the renal and intestinal elimination of P-gp substrates. This involves enhancing the removal of toxic substances from proximal tubular epithelial cells into the urine or increasing the transport of compounds from enterocytes into the intestinal lumen, thereby facilitating their excretion in the feces. A better understanding of these interactions, and of the distinct techniques applied for their study, will be of utmost importance for optimizing drug therapy, consequently minimizing drug-induced adverse and toxic effects.
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Affiliation(s)
- Jéssica Veiga-Matos
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal;
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- Toxicology Unit (Universidad de Salamanca), Group of Translational Research on Renal and Cardiovascular Diseases (TRECARD), Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain; (A.I.M.); (M.P.)
| | - Ana I. Morales
- Toxicology Unit (Universidad de Salamanca), Group of Translational Research on Renal and Cardiovascular Diseases (TRECARD), Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain; (A.I.M.); (M.P.)
| | - Marta Prieto
- Toxicology Unit (Universidad de Salamanca), Group of Translational Research on Renal and Cardiovascular Diseases (TRECARD), Institute of Biomedical Research of Salamanca (IBSAL), 37007 Salamanca, Spain; (A.I.M.); (M.P.)
| | - Fernando Remião
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal;
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Renata Silva
- UCIBIO-Applied Molecular Biosciences Unit, Laboratory of Toxicology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal;
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
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2
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Gellen G, Klement E, Biwott K, Schlosser G, Kalló G, Csősz É, Medzihradszky KF, Bacso Z. Cross-Linking Mass Spectrometry on P-Glycoprotein. Int J Mol Sci 2023; 24:10627. [PMID: 37445813 DOI: 10.3390/ijms241310627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/21/2023] [Accepted: 06/22/2023] [Indexed: 07/15/2023] Open
Abstract
The ABC transporter P-glycoprotein (Pgp) has been found to be involved in multidrug resistance in tumor cells. Lipids and cholesterol have a pivotal role in Pgp's conformations; however, it is often difficult to investigate it with conventional structural biology techniques. Here, we applied robust approaches coupled with cross-linking mass spectrometry (XL-MS), where the natural lipid environment remains quasi-intact. Two experimental approaches were carried out using different cross-linkers (i) on living cells, followed by membrane preparation and immunoprecipitation enrichment of Pgp, and (ii) on-bead, subsequent to membrane preparation and immunoprecipitation. Pgp-containing complexes were enriched employing extracellular monoclonal anti-Pgp antibodies on magnetic beads, followed by on-bead enzymatic digestion. The LC-MS/MS results revealed mono-links on Pgp's solvent-accessible residues, while intraprotein cross-links confirmed a complex interplay between extracellular, transmembrane, and intracellular segments of the protein, of which several have been reported to be connected to cholesterol. Harnessing the MS results and those of molecular docking, we suggest an epitope for the 15D3 cholesterol-dependent mouse monoclonal antibody. Additionally, enriched neighbors of Pgp prove the strong connection of Pgp to the cytoskeleton and other cholesterol-regulated proteins. These findings suggest that XL-MS may be utilized for protein structure and network analyses in such convoluted systems as membrane proteins.
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Affiliation(s)
- Gabriella Gellen
- MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Department of Analytical Chemistry, Institute of Chemistry, ELTE Eötvös Loránd University, H-1117 Budapest, Hungary
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1., H-4032 Debrecen, Hungary
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, Egyetem tér 1., H-4032 Debrecen, Hungary
| | - Eva Klement
- Single Cell Omics Advanced Core Facility, HCEMM, H-6728 Szeged, Hungary
- Laboratory of Proteomics Research, BRC, H-6726 Szeged, Hungary
| | - Kipchumba Biwott
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1., H-4032 Debrecen, Hungary
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, Egyetem tér 1., H-4032 Debrecen, Hungary
| | - Gitta Schlosser
- MTA-ELTE Lendület Ion Mobility Mass Spectrometry Research Group, Department of Analytical Chemistry, Institute of Chemistry, ELTE Eötvös Loránd University, H-1117 Budapest, Hungary
| | - Gergő Kalló
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1., H-4032 Debrecen, Hungary
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1., H-4032 Debrecen, Hungary
| | - Éva Csősz
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1., H-4032 Debrecen, Hungary
- Proteomics Core Facility, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1., H-4032 Debrecen, Hungary
| | | | - Zsolt Bacso
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem tér 1., H-4032 Debrecen, Hungary
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, Egyetem tér 1., H-4032 Debrecen, Hungary
- Faculty of Pharmacology, University of Debrecen, Egyetem tér 1., H-4032 Debrecen, Hungary
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3
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Bonito C, Ferreira RJ, Ferreira MJ, Durães F, Sousa E, Gillet JP, Cordeiro MNS, dos Santos DJVA. Probing the Allosteric Modulation of P-Glycoprotein: A Medicinal Chemistry Approach Toward the Identification of Noncompetitive P-Gp Inhibitors. ACS OMEGA 2023; 8:11281-11287. [PMID: 37008154 PMCID: PMC10061618 DOI: 10.1021/acsomega.2c08273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 03/01/2023] [Indexed: 06/19/2023]
Abstract
A medicinal chemistry approach combining in silico and in vitro methodologies was performed aiming at identifying and characterizing putative allosteric drug-binding sites (aDBSs) at the interface of the transmembrane- and nucleotide-binding domains (TMD-NBD) of P-glycoprotein. Two aDBSs were identified, one in TMD1/NBD1 and another one in TMD2/NBD2, by means of in silico fragment-based molecular dynamics and characterized in terms of size, polarity, and lining residues. From a small library of thioxanthone and flavanone derivatives, experimentally described to bind at the TMD-NBD interfaces, several compounds were identified to be able to decrease the verapamil-stimulated ATPase activity. An IC50 of 81 ± 6.6 μM is reported for a flavanone derivative in the ATPase assays, providing evidence for an allosteric efflux modulation in P-glycoprotein. Molecular docking and molecular dynamics gave additional insights on the binding mode on how flavanone derivatives may act as allosteric inhibitors.
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Affiliation(s)
- Cátia
A. Bonito
- LAQV@REQUIMTE,
Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre, Porto 4169-007, Portugal
| | - Ricardo J. Ferreira
- Red
Glead Discovery AB, Medicon
Village, Scheelevägen 8, Lund 223 63, Sweden
| | - Maria-José.
U. Ferreira
- Research
Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, Lisbon 1649-003, Portugal
| | - Fernando Durães
- Interdisciplinary
Centre of Marine and Environmental Research (CIIMAR) & Laboratory
of Organic and Pharmaceutical Chemistry, Department of Chemical Sciences,
Faculty of Pharmacy, University of Porto, Rua Jorge Viterbo Ferreira 228, Porto 4050-313, Portugal
| | - Emília Sousa
- Interdisciplinary
Centre of Marine and Environmental Research (CIIMAR) & Laboratory
of Organic and Pharmaceutical Chemistry, Department of Chemical Sciences,
Faculty of Pharmacy, University of Porto, Rua Jorge Viterbo Ferreira 228, Porto 4050-313, Portugal
| | - Jean-Pierre Gillet
- Laboratory
of Molecular Cancer Biology, URPhyM, NARILIS, Faculty of Medicine, University of Namur, Namur 5000, Belgium
| | - M. Natália
D. S. Cordeiro
- LAQV@REQUIMTE,
Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre, Porto 4169-007, Portugal
| | - Daniel J. V. A. dos Santos
- CBIOS-Center
for Research in Biosciences & Health Technologies, Lusófona University, Campo Grande, 376, Lisboa 1749-024, Portugal
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Bonito CA, Ferreira RJ, Ferreira MJU, Gillet JP, Cordeiro MNDS, Dos Santos DJVA. Long-range communication between transmembrane- and nucleotide-binding domains does not depend on drug binding to mutant P-glycoprotein. J Biomol Struct Dyn 2023; 41:14428-14437. [PMID: 36858814 DOI: 10.1080/07391102.2023.2181633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Accepted: 02/12/2023] [Indexed: 03/03/2023]
Abstract
In this study, the impact of four P-gp mutations (G185V, G830V, F978A and ΔF335) on drug-binding and efflux-related signal-transmission mechanism was comprehensively evaluated in the presence of ligands within the drug-binding pocket (DBP), experimentally related with changes in their drug efflux profiles. The severe repacking of the transmembrane helices (TMH), induced by mutations and exacerbated by the presence of ligands, indicates that P-gp is sensitive to perturbations in the transmembrane region. Alterations on drug-binding were also observed as a consequence of the TMH repacking, but were not always correlated with alterations on ligands binding mode and/or binding affinity. Finally, and although all P-gp variants holo systems showed considerable changes in the intracellular coupling helices/nucleotide-binding domain (ICH-NBD) interactions, they seem to be primarily induced by the mutation itself rather than by the presence of ligands within the DBP. The data further suggest that the changes in drug efflux experimentally reported are mostly related with changes on drug specificity rather than effects on signal-transmission mechanism. We also hypothesize that an increase in the drug-binding affinity may also be related with the decreased drug efflux, while minor changes in binding affinities are possibly related with the increased drug efflux observed in transfected cells.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Cátia A Bonito
- LAQV@REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre, Porto, Portugal
| | - Ricardo J Ferreira
- Red Glead Discovery AB, Medicon Village, Lund, Sweden
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal
| | - Maria-José U Ferreira
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal
| | - Jean-Pierre Gillet
- Laboratory of Molecular Cancer Biology, URPhyM, NARILIS, Faculty of Medicine, University of Namur, Namur, Belgium
| | - M Natália D S Cordeiro
- LAQV@REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre, Porto, Portugal
| | - Daniel J V A Dos Santos
- LAQV@REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre, Porto, Portugal
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal
- CBIOS-Research Center for Biosciences & Health Technologies, Universidade Lusófona de Humanidades e Tecnologias, Lisbon, Portugal
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5
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A Structure-Based View on ABC-Transporter Linked to Multidrug Resistance. Molecules 2023; 28:molecules28020495. [PMID: 36677553 PMCID: PMC9862083 DOI: 10.3390/molecules28020495] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/29/2022] [Accepted: 12/16/2022] [Indexed: 01/06/2023] Open
Abstract
The discovery of the first ATP-binding cassette (ABC) transporter, whose overexpression in cancer cells is responsible for exporting anticancer drugs out of tumor cells, initiated enormous efforts to overcome tumor cell multidrug resistance (MDR) by inhibition of ABC-transporter. Because of its many physiological functions, diverse studies have been conducted on the mechanism, function and regulation of this important group of transmembrane transport proteins. In this review, we will focus on the structural aspects of this transporter superfamily. Since the resolution revolution of electron microscope, experimentally solved structures increased rapidly. A summary of the structures available and an overview of recent structure-based studies are provided. More specifically, the artificial intelligence (AI)-based predictions from AlphaFold-2 will be discussed.
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Interaction of a Homologous Series of Amphiphiles with P-glycoprotein in a Membrane Environment-Contributions of Polar and Non-Polar Interactions. Pharmaceutics 2023; 15:pharmaceutics15010174. [PMID: 36678803 PMCID: PMC9862096 DOI: 10.3390/pharmaceutics15010174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/06/2022] [Accepted: 12/26/2022] [Indexed: 01/05/2023] Open
Abstract
The transport of drugs by efflux transporters in biomembranes limits their bioavailability and is a major determinant of drug resistance development by cancer cells and pathogens. A large number of chemically dissimilar drugs are transported, and despite extensive studies, the molecular determinants of substrate specificity are still not well understood. In this work, we explore the role of polar and non-polar interactions on the interaction of a homologous series of fluorescent amphiphiles with the efflux transporter P-glycoprotein. The interaction of the amphiphiles with P-glycoprotein is evaluated through effects on ATPase activity, efficiency in inhibition of [125I]-IAAP binding, and partition to the whole native membranes containing the transporter. The results were complemented with partition to model membranes with a representative lipid composition, and details on the interactions established were obtained from MD simulations. We show that when the total concentration of amphiphile is considered, the binding parameters obtained are apparent and do not reflect the affinity for P-gp. A new formalism is proposed that includes sequestration of the amphiphiles in the lipid bilayer and the possible binding of several molecules in P-gp's substrate-binding pocket. The intrinsic binding affinity thus obtained is essentially independent of amphiphile hydrophobicity, highlighting the importance of polar interactions. An increase in the lipophilicity and amphiphilicity led to a more efficient association with the lipid bilayer, which maintains the non-polar groups of the amphiphiles in the bilayer, while the polar groups interact with P-gp's binding pocket. The presence of several amphiphiles in this orientation is proposed as a mechanism for inhibition of P-pg function.
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7
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Mora Lagares L, Novič M. Recent Advances on P-Glycoprotein (ABCB1) Transporter Modelling with In Silico Methods. Int J Mol Sci 2022; 23:ijms232314804. [PMID: 36499131 PMCID: PMC9740644 DOI: 10.3390/ijms232314804] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 11/14/2022] [Accepted: 11/24/2022] [Indexed: 12/02/2022] Open
Abstract
ABC transporters play a critical role in both drug bioavailability and toxicity, and with the discovery of the P-glycoprotein (P-gp), this became even more evident, as it plays an important role in preventing intracellular accumulation of toxic compounds. Over the past 30 years, intensive studies have been conducted to find new therapeutic molecules to reverse the phenomenon of multidrug resistance (MDR) ), that research has found is often associated with overexpression of P-gp, the most extensively studied drug efflux transporter; in MDR, therapeutic drugs are prevented from reaching their targets due to active efflux from the cell. The development of P-gp inhibitors is recognized as a good way to reverse this type of MDR, which has been the subject of extensive studies over the past few decades. Despite the progress made, no effective P-gp inhibitors to reverse multidrug resistance are yet on the market, mainly because of their toxic effects. Computational studies can accelerate this process, and in silico models such as QSAR models that predict the activity of compounds associated with P-gp (or analogous transporters) are of great value in the early stages of drug development, along with molecular modelling methods, which provide a way to explain how these molecules interact with the ABC transporter. This review highlights recent advances in computational P-gp research, spanning the last five years to 2022. Particular attention is given to the use of machine-learning approaches, drug-transporter interactions, and recent discoveries of potential P-gp inhibitors that could act as modulators of multidrug resistance.
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Affiliation(s)
- Liadys Mora Lagares
- Correspondence: (L.M.L.); (M.N.); Tel.: +386-1-4760-438 (L.M.L.); +386-1-4760-253 (M.N.)
| | - Marjana Novič
- Correspondence: (L.M.L.); (M.N.); Tel.: +386-1-4760-438 (L.M.L.); +386-1-4760-253 (M.N.)
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8
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Clouser AF, Atkins WM. Long Range Communication between the Drug-Binding Sites and Nucleotide Binding Domains of the Efflux Transporter ABCB1. Biochemistry 2022; 61:730-740. [PMID: 35384651 PMCID: PMC9022228 DOI: 10.1021/acs.biochem.2c00056] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
The ABC efflux pump
P-glycoprotein (P-gp) transports a wide variety
of drugs and is inhibited by others. Some drugs stimulate ATP hydrolysis
at the nucleotide binding domains (NBDs) and are transported, others
uncouple ATP hydrolysis and transport, and others inhibit ATP hydrolysis.
The molecular basis for the different behavior of these drugs is not
well understood despite the availability of several structural models
of P-gp complexes with ligands bound. Hypothetically, ligands differentially
alter the conformational dynamics of peptide segments that mediate
the coupling between the drug binding sites and the NBDs. Here, we
explore by hydrogen-deuterium exchange mass spectrometry the dynamic
consequences of a classic substrate and inhibitor, vinblastine and
zosuquidar, binding to mouse P-gp (mdr1a) in lipid nanodiscs. The
dynamics of P-gp in nucleotide-free, pre-hydrolysis, and post-hydrolysis
states in the presence of each drug reveal distinct mechanisms of
ATPase stimulation and implications for transport. For both drugs,
there are common regions affected in a similar manner, suggesting
that particular networks are the key to stimulating ATP hydrolysis.
However, drug binding effects diverge in the post-hydrolysis state,
particularly in the intracellular helices (ICHs 3 and 4) and neighboring
transmembrane helices. The local dynamics and conformational equilibria
in this region are critical for the coupling of drug binding and ATP
hydrolysis and are differentially modulated in the catalytic cycle.
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Affiliation(s)
- Amanda F Clouser
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195-7610, United States
| | - William M Atkins
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195-7610, United States
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Wang L, O'Mara ML. Effect of the Force Field on Molecular Dynamics Simulations of the Multidrug Efflux Protein P-Glycoprotein. J Chem Theory Comput 2021; 17:6491-6508. [PMID: 34506133 DOI: 10.1021/acs.jctc.1c00414] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Molecular dynamics (MD) simulations have been used extensively to study P-glycoprotein (P-gp), a flexible multidrug transporter that is a key player in the development of multidrug resistance to chemotherapeutics. A substantial body of literature has grown from simulation studies that have employed various simulation conditions and parameters, including AMBER, CHARMM, OPLS, GROMOS, and coarse-grained force fields, drawing conclusions from simulations spanning hundreds of nanoseconds. Each force field is typically parametrized and validated on different data and observables, usually of small molecules and peptides; there have been few comparisons of force field performance on large protein-membrane systems. Here we compare the conformational ensembles of P-gp embedded in a POPC/cholesterol bilayer generated over 500 ns of replicate simulation with five force fields from popular biomolecular families: AMBER 99SB-ILDN, CHARMM 36, OPLS-AA/L, GROMOS 54A7, and MARTINI. We find considerable differences among the ensembles with little conformational overlap, although they correspond to similar extents to structural data obtained from electron paramagnetic resonance and cross-linking studies. Moreover, each trajectory was still sampling new conformations at a high rate after 500 ns of simulation, suggesting the need for more sampling. This work highlights the need to consider known limitations of the force field used (e.g., biases toward certain secondary structures) and the simulation itself (e.g., whether sufficient sampling has been achieved) when interpreting accumulated results of simulation studies of P-gp and other transport proteins.
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Affiliation(s)
- Lily Wang
- Research School of Chemistry, College of Science, Australian National University, Canberra, ACT 2601, Australia
| | - Megan L O'Mara
- Research School of Chemistry, College of Science, Australian National University, Canberra, ACT 2601, Australia
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Structure activity relationships and the binding mode of quinolinone-pyrimidine hybrids as reversal agents of multidrug resistance mediated by P-gp. Sci Rep 2021; 11:16856. [PMID: 34413359 PMCID: PMC8376931 DOI: 10.1038/s41598-021-96226-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 08/06/2021] [Indexed: 02/07/2023] Open
Abstract
P-gp-associated multidrug resistance is a major impediment to the success of chemotherapy. With the aim of finding non-toxic and effective P-gp inhibitors, we investigated a panel of quinolin-2-one-pyrimidine hybrids. Among the active compounds, two of them significantly increased intracellular doxorubicin and rhodamine 123 accumulation by inhibiting the efflux mediated by P-gp and restored doxorubicin toxicity at nanomolar range. Structure-activity relationships showed that the number of methoxy groups, an optimal length of the molecule in its extended conformation, and at least one flexible methylene group bridging the quinolinone to the moiety bearing the pyrimidine favored the inhibitory potency of P-gp. The best compounds showed a similar binding pattern and interactions to those of doxorubicin and tariquidar, as revealed by MD and hybrid QM/MM simulations performed with the recent experimental structure of P-gp co-crystallized with paclitaxel. Analysis of the molecular interactions stabilizing the different molecular complexes determined by MD and QTAIM showed that binding to key residues from TMH 4-7 and 12 is required for inhibition.
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Marques SM, Šupolíková L, Molčanová L, Šmejkal K, Bednar D, Slaninová I. Screening of Natural Compounds as P-Glycoprotein Inhibitors against Multidrug Resistance. Biomedicines 2021; 9:biomedicines9040357. [PMID: 33808505 PMCID: PMC8066904 DOI: 10.3390/biomedicines9040357] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 03/25/2021] [Accepted: 03/26/2021] [Indexed: 12/25/2022] Open
Abstract
Multidrug resistance (MDR) is a common problem when fighting cancer with chemotherapy. P-glycoprotein (P-gp, or MDR1) is an active pump responsible for the efflux of xenobiotics out of the cell, including anti-cancer drugs. It is a validated target against MDR. No crystal structure of the human P-gp is available to date, and only recently several cryo-EM structures have been solved. In this paper, we present a comprehensive computational approach that includes constructing the full-length three-dimensional structure of the human P-gp and its refinement using molecular dynamics. We assessed its flexibility and conformational diversity, compiling a dynamical ensemble that was used to dock a set of lignan compounds, previously reported as active P-gp inhibitors, and disclose their binding modes. Based on the statistical analysis of the docking results, we selected a system for performing the structure-based virtual screening of new potential P-gp inhibitors. We tested the method on a library of 87 natural flavonoids described in the literature, and 10 of those were experimentally assayed. The results reproduced the theoretical predictions only partially due to various possible factors. However, at least two of the predicted natural flavonoids were demonstrated to be effective P-gp inhibitors. They were able to increase the accumulation of doxorubicin inside the human promyelocytic leukemia HL60/MDR cells overexpressing P-gp and potentiate the antiproliferative activity of this anti-cancer drug.
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Affiliation(s)
- Sérgio M. Marques
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/C13, 625-00 Brno, Czech Republic;
- International Clinical Research Center, St. Anne’s University Hospital Brno, Pekarska 53, 656-91 Brno, Czech Republic
| | - Lucie Šupolíková
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5/A6, 625-00 Brno, Czech Republic;
| | - Lenka Molčanová
- Department of Natural Drugs, Faculty of Pharmacy, Masaryk University, Palackého 1946/1, 612-00 Brno, Czech Republic; (L.M.); (K.Š.)
| | - Karel Šmejkal
- Department of Natural Drugs, Faculty of Pharmacy, Masaryk University, Palackého 1946/1, 612-00 Brno, Czech Republic; (L.M.); (K.Š.)
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Faculty of Science, Masaryk University, Kamenice 5/C13, 625-00 Brno, Czech Republic;
- International Clinical Research Center, St. Anne’s University Hospital Brno, Pekarska 53, 656-91 Brno, Czech Republic
- Correspondence: (D.B.); (I.S.); Tel.: +420-549492616 (D.B.); +420-549496985 (I.S.)
| | - Iva Slaninová
- Department of Biology, Faculty of Medicine, Masaryk University, Kamenice 5/A6, 625-00 Brno, Czech Republic;
- Correspondence: (D.B.); (I.S.); Tel.: +420-549492616 (D.B.); +420-549496985 (I.S.)
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Demmer A, Thole H, Raida M, Tümmler B. Lysine 268 adjacent to transmembrane helix 5 of hamster P-glycoprotein is the major photobinding site of iodomycin in CHO B30 cells. FEBS Open Bio 2021; 11:1084-1092. [PMID: 33565718 PMCID: PMC8016128 DOI: 10.1002/2211-5463.13112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 01/31/2021] [Accepted: 02/08/2021] [Indexed: 12/05/2022] Open
Abstract
P‐glycoprotein (Pgp) detoxifies cells by exporting hundreds of chemically dissimilar hydrophobic and amphipathic compounds and is implicated in multidrug resistance (MDR) in the treatment of cancers. Photoaffinity labeling of plasma membrane vesicles of MDR CHO B30 cells with the anthracycline [125I]‐iodomycin, subsequent sequential cleavage with BNPS‐skatol and endoproteinase Lys‐C, and the Edman sequencing of the purified photoaffinity‐labeled peptide identified the lysine residue at position 268 in the hamster Pgp primary sequence as the major photobinding site of iodomycin in CHO B30 cells. Lysine 268 is located adjacent to the cytosolic terminus of transmembrane 5. According to thermodynamic and kinetic analyses, this location should present the equilibrium binding site of ATP‐free Pgp for daunomycin and iodomycin in B30 cells.
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Affiliation(s)
- Annette Demmer
- Klinische Forschergruppe, Klinik für Pädiatrische Pneumologie, Allergologie und Neonatologie, Medizinische Hochschule Hannover, Germany
| | - Hubert Thole
- Klinische Forschergruppe, Klinik für Pädiatrische Pneumologie, Allergologie und Neonatologie, Medizinische Hochschule Hannover, Germany
| | - Manfred Raida
- Singapore Lipidomics Incubator (SLING), Life Sciences Institute, National University of Singapore, Singapore
| | - Burkhard Tümmler
- Klinische Forschergruppe, Klinik für Pädiatrische Pneumologie, Allergologie und Neonatologie, Medizinische Hochschule Hannover, Germany.,Biomedical Research in Endstage and Obstructive Lung Disease Hannover, Deutsches Zentrum für Lungenforschung (DZL), Medizinische Hochschule Hannover, Germany
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Clouser AF, Alam YH, Atkins WM. Cholesterol Asymmetrically Modulates the Conformational Ensemble of the Nucleotide-Binding Domains of P-Glycoprotein in Lipid Nanodiscs. Biochemistry 2020; 60:85-94. [PMID: 33350827 DOI: 10.1021/acs.biochem.0c00824] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
P-Glycoprotein (P-gp) is an ATP-dependent efflux pump that clears a wide variety of drugs and toxins from cells. P-gp undergoes large-scale structural changes and demonstrates conformational heterogeneity even within a single catalytic or drug-bound state, although the role of heterogeneity remains unclear. P-gp is found in a variety of cell types that vary in lipid composition, which modulates its activity. An understanding of structural or dynamic changes due to the lipid environment is lacking. We aimed to determine the effects of cholesterol in a membrane on the conformational behavior of P-gp in lipid nanodiscs. The presence of cholesterol stimulates ATP hydrolysis and alters lipid order and fluidity. Hydrogen/deuterium exchange mass spectrometry demonstrates that cholesterol in the membrane induces asymmetric, long-range changes in the distributions and exchange kinetics of conformations of the nucleotide-binding domains, correlating the effects of lipid composition on activity with specific changes in the P-gp conformational landscape.
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Affiliation(s)
- Amanda F Clouser
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195-7610, United States
| | - Yasmine H Alam
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195-7610, United States.,Department of Biological Sciences, MARC Program, California State University, Fullerton, California 92834-6850, United States
| | - William M Atkins
- Department of Medicinal Chemistry, University of Washington, Seattle, Washington 98195-7610, United States
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Mollazadeh S, Hadizadeh F, Ferreira RJ. Theoretical studies on 1,4-dihydropyridine derivatives as P-glycoprotein allosteric inhibitors: insights on symmetry and stereochemistry. J Biomol Struct Dyn 2020; 39:4752-4763. [DOI: 10.1080/07391102.2020.1780942] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Shirin Mollazadeh
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Farzin Hadizadeh
- Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ricardo J. Ferreira
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
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