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Barbosa F, Araújo J, Gonçalves VMF, Palmeira A, Cunha A, Silva PMA, Fernandes C, Pinto M, Bousbaa H, Queirós O, Tiritan ME. Evaluation of Antitumor Activity of Xanthones Conjugated with Amino Acids. Int J Mol Sci 2024; 25:2121. [PMID: 38396802 PMCID: PMC10889492 DOI: 10.3390/ijms25042121] [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: 12/24/2023] [Revised: 02/04/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Cancer is a complex disease characterized by several alterations, which confer, to the cells, the capacity to proliferate uncontrollably and to resist cellular death. Multiresistance to conventional chemotherapy drugs is often the cause of treatment failure; thus, the search for natural products or their derivatives with therapeutic action is essential. Chiral derivatives of xanthones (CDXs) have shown potential inhibitory activity against the growth of some human tumor cell lines. This work reports the screening of a library of CDXs, through viability assays, in different cancer cell lines: A375-C5, MCF-7, NCI-H460, and HCT-15. CDXs' effect was analyzed based on several parameters of cancer cells, and it was also verified if these compounds were substrates of glycoprotein-P (Pgp), one of the main mechanisms of resistance in cancer therapy. Pgp expression was evaluated in all cell lines, but no expression was observed, except for HCT-15. Also, when a humanized yeast expressing the human gene MDR1 was used, no conclusions could be drawn about CDXs as Pgp substrates. The selected CDXs did not induce significant differences in the metabolic parameters analyzed. These results show that some CDXs present promising antitumor activity, but other mechanisms should be triggered by these compounds.
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Affiliation(s)
- Flávia Barbosa
- UNIPRO—Oral Pathology and Rehabilitation Research Unit, University Institute of Health Sciences (IUCS-CESPU), 4585-116 Gandra, Portugal; (F.B.); (V.M.F.G.); (A.C.); (P.M.A.S.); (H.B.); (O.Q.)
| | - Joana Araújo
- Laboratory of Organic and Pharmaceutical Chemistry, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; (J.A.); (A.P.); (C.F.); (M.P.)
| | - Virgínia M. F. Gonçalves
- UNIPRO—Oral Pathology and Rehabilitation Research Unit, University Institute of Health Sciences (IUCS-CESPU), 4585-116 Gandra, Portugal; (F.B.); (V.M.F.G.); (A.C.); (P.M.A.S.); (H.B.); (O.Q.)
- 1H-TOXRUN—One Health Toxicology Research Unit, University Institute of Health Sciences (IUCS), University Institute of Health Sciences-CESPU (IUCS-CESPU), 4585-116 Gandra, Portugal
| | - Andreia Palmeira
- Laboratory of Organic and Pharmaceutical Chemistry, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; (J.A.); (A.P.); (C.F.); (M.P.)
- CIIMAR-Interdisciplinary Center for Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, 4450-208 Matosinhos, Portugal
| | - Andrea Cunha
- UNIPRO—Oral Pathology and Rehabilitation Research Unit, University Institute of Health Sciences (IUCS-CESPU), 4585-116 Gandra, Portugal; (F.B.); (V.M.F.G.); (A.C.); (P.M.A.S.); (H.B.); (O.Q.)
| | - Patrícia M. A. Silva
- UNIPRO—Oral Pathology and Rehabilitation Research Unit, University Institute of Health Sciences (IUCS-CESPU), 4585-116 Gandra, Portugal; (F.B.); (V.M.F.G.); (A.C.); (P.M.A.S.); (H.B.); (O.Q.)
- 1H-TOXRUN—One Health Toxicology Research Unit, University Institute of Health Sciences (IUCS), University Institute of Health Sciences-CESPU (IUCS-CESPU), 4585-116 Gandra, Portugal
| | - Carla Fernandes
- Laboratory of Organic and Pharmaceutical Chemistry, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; (J.A.); (A.P.); (C.F.); (M.P.)
- CIIMAR-Interdisciplinary Center for Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, 4450-208 Matosinhos, Portugal
| | - Madalena Pinto
- Laboratory of Organic and Pharmaceutical Chemistry, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; (J.A.); (A.P.); (C.F.); (M.P.)
- CIIMAR-Interdisciplinary Center for Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, 4450-208 Matosinhos, Portugal
| | - Hassan Bousbaa
- UNIPRO—Oral Pathology and Rehabilitation Research Unit, University Institute of Health Sciences (IUCS-CESPU), 4585-116 Gandra, Portugal; (F.B.); (V.M.F.G.); (A.C.); (P.M.A.S.); (H.B.); (O.Q.)
| | - Odília Queirós
- UNIPRO—Oral Pathology and Rehabilitation Research Unit, University Institute of Health Sciences (IUCS-CESPU), 4585-116 Gandra, Portugal; (F.B.); (V.M.F.G.); (A.C.); (P.M.A.S.); (H.B.); (O.Q.)
| | - Maria Elizabeth Tiritan
- UNIPRO—Oral Pathology and Rehabilitation Research Unit, University Institute of Health Sciences (IUCS-CESPU), 4585-116 Gandra, Portugal; (F.B.); (V.M.F.G.); (A.C.); (P.M.A.S.); (H.B.); (O.Q.)
- Laboratory of Organic and Pharmaceutical Chemistry, Department of Chemical Sciences, Faculty of Pharmacy, University of Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal; (J.A.); (A.P.); (C.F.); (M.P.)
- 1H-TOXRUN—One Health Toxicology Research Unit, University Institute of Health Sciences (IUCS), University Institute of Health Sciences-CESPU (IUCS-CESPU), 4585-116 Gandra, Portugal
- CIIMAR-Interdisciplinary Center for Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, 4450-208 Matosinhos, Portugal
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2
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Kapoor K, Thangapandian S, Tajkhorshid E. Extended-ensemble docking to probe dynamic variation of ligand binding sites during large-scale structural changes of proteins. Chem Sci 2022; 13:4150-4169. [PMID: 35440993 PMCID: PMC8985516 DOI: 10.1039/d2sc00841f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 02/24/2022] [Indexed: 11/21/2022] Open
Abstract
Proteins can sample a broad landscape as they undergo conformational transition between different functional states. At the same time, as key players in almost all cellular processes, proteins are important drug targets. Considering the different conformational states of a protein is therefore central for a successful drug-design strategy. Here we introduce a novel docking protocol, termed extended-ensemble docking, pertaining to proteins that undergo large-scale (global) conformational changes during their function. In its application to multidrug ABC-transporter P-glycoprotein (Pgp), extensive non-equilibrium molecular dynamics simulations employing system-specific collective variables are first used to describe the transition cycle of the transporter. An extended set of conformations (extended ensemble) representing the full transition cycle between the inward- and the outward-facing states is then used to seed high-throughput docking calculations of known substrates, non-substrates, and modulators of the transporter. Large differences are predicted in the binding affinities to different conformations, with compounds showing stronger binding affinities to intermediate conformations compared to the starting crystal structure. Hierarchical clustering of the binding modes shows all ligands preferably bind to the large central cavity of the protein, formed at the apex of the transmembrane domain (TMD), whereas only small binding populations are observed in the previously described R and H sites present within the individual TMD leaflets. Based on the results, the central cavity is further divided into two major subsites, first preferably binding smaller substrates and high-affinity inhibitors, whereas the second one shows preference for larger substrates and low-affinity modulators. These central subsites along with the low-affinity interaction sites present within the individual TMD leaflets may respectively correspond to the proposed high- and low-affinity binding sites in Pgp. We propose further an optimization strategy for developing more potent inhibitors of Pgp, based on increasing its specificity to the extended ensemble of the protein, instead of using a single protein structure, as well as its selectivity for the high-affinity binding site. In contrast to earlier in silico studies using single static structures of Pgp, our results show better agreement with experimental studies, pointing to the importance of incorporating the global conformational flexibility of proteins in future drug-discovery endeavors.
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Affiliation(s)
- Karan Kapoor
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Sundar Thangapandian
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
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3
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Martins E, Silva V, Lemos A, Palmeira A, Puthongking P, Sousa E, Rocha-Pereira C, Ghanem CI, Carmo H, Remião F, Silva R. Newly Synthesized Oxygenated Xanthones as Potential P-Glycoprotein Activators: In Vitro, Ex Vivo, and In Silico Studies. Molecules 2019; 24:molecules24040707. [PMID: 30781374 PMCID: PMC6412186 DOI: 10.3390/molecules24040707] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 02/01/2019] [Accepted: 02/09/2019] [Indexed: 12/03/2022] Open
Abstract
P-glycoprotein (P-gp) plays a crucial role in the protection of susceptible organs, by significantly decreasing the absorption/distribution of harmful xenobiotics and, consequently, their toxicity. Therefore, P-gp has been proposed as a potential antidotal pathway, when activated and/or induced. Knowing that xanthones are known to interact with P-gp, the main goal was to study P-gp induction or/and activation by six new oxygenated xanthones (OX 1-6). Furthermore, the potential protection of Caco-2 cells against paraquat cytotoxicity was also assessed. The most promising compound was further tested for its ability to increase P-gp activity ex vivo, using everted intestinal sacs from adult Wistar-Han rats. The oxygenated xanthones interacted with P-gp in vitro, increasing P-gp expression and/or activity 24 h after exposure. Additionally, after a short-incubation period, several xanthones were identified as P-gp activators, as they immediately increased P-gp activity. Moreover, some xanthones decreased PQ cytotoxicity towards Caco-2 cells, an effect prevented under P-gp inhibition. Ex vivo, a significant increase in P-gp activity was observed in the presence of OX6, which was selectively blocked by a model P-gp inhibitor, zosuquidar, confirming the in vitro results. Docking simulations between a validated P-gp model and the tested xanthones predicted these interactions, and these compounds also fitted onto previously described P-gp induction and activation pharmacophores. In conclusion, the in vitro, ex vivo, and in silico results suggest the potential of some of the oxygenated xanthones in the modulation of P-gp, disclosing new perspectives in the therapeutics of intoxications by P-gp substrates.
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Affiliation(s)
- Eva Martins
- UCIBIO-REQUIMTE, Laboratório de Toxicologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal.
| | - Vera Silva
- UCIBIO-REQUIMTE, Laboratório de Toxicologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal.
| | - Agostinho Lemos
- Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal.
| | - Andreia Palmeira
- Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal.
| | - Ploenthip Puthongking
- Faculty of Pharmaceutical Sciences, Khon Kaen University, Khon Kaen 40002, Thailand.
| | - Emília Sousa
- Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal.
- Centro Interdisciplinar de Investigação Marinha e Ambiental (CIIMAR/CIMAR), Universidade do Porto, Rua dos Bragas 289, 4050-123 Porto, Portugal.
| | - Carolina Rocha-Pereira
- UCIBIO-REQUIMTE, Laboratório de Toxicologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal.
| | - Carolina I Ghanem
- Universidad de Buenos Aires, CONICET, Facultad de Farmacia y Bioquímica, Instituto de Investigaciones Farmacológicas (ININFA), Buenos Aires C1053, Argentina.
| | - Helena Carmo
- UCIBIO-REQUIMTE, Laboratório de Toxicologia, Departamento de Ciências Biológicas, Faculdade de Farmácia, Universidade do Porto, Rua de 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 de 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 de Jorge Viterbo Ferreira 228, 4050-313 Porto, Portugal.
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4
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Subramanian N, Schumann-Gillett A, Mark AE, O’Mara ML. Probing the Pharmacological Binding Sites of P-Glycoprotein Using Umbrella Sampling Simulations. J Chem Inf Model 2018; 59:2287-2298. [DOI: 10.1021/acs.jcim.8b00624] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Nandhitha Subramanian
- School of Chemistry and Molecular Biosciences (SCMB), University of Queensland, Brisbane, QLD 4072, Australia
- Research School of Chemistry (RSC), Australian National University, Canberra, ACT 2601, Australia
| | | | - Alan E. Mark
- School of Chemistry and Molecular Biosciences (SCMB), University of Queensland, Brisbane, QLD 4072, Australia
- The Institute for Molecular Biosciences (IMB), University of Queensland, Brisbane, QLD 4072, Australia
| | - Megan L. O’Mara
- School of Chemistry and Molecular Biosciences (SCMB), University of Queensland, Brisbane, QLD 4072, Australia
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5
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Subramanian N, Condic-Jurkic K, O'Mara ML. Structural and dynamic perspectives on the promiscuous transport activity of P-glycoprotein. Neurochem Int 2016; 98:146-52. [PMID: 27180050 DOI: 10.1016/j.neuint.2016.05.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 04/28/2016] [Accepted: 05/03/2016] [Indexed: 11/25/2022]
Abstract
The multidrug transporter P-glycoprotein (P-gp) is expressed in the blood-brain barrier endothelium where it effluxes a range of drug substrates, preventing their accumulation within the brain. P-gp has been studied extensively for 40 years because of its crucial role in the absorption, distribution, metabolism and elimination of a range of pharmaceutical compounds. Despite this, many aspects of the structure-function mechanism of P-gp are unresolved. Here we review the emerging role of molecular dynamics simulation techniques in our understanding of the membrane-embedded conformation of P-gp. We discuss its conformational plasticity in the presence and absence of ATP, and recent efforts to characterize the drug binding sites and uptake pathways.
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Affiliation(s)
- Nandhitha Subramanian
- Research School of Chemistry (RSC), The Australian National University, Canberra, ACT, 2601, Australia
| | - Karmen Condic-Jurkic
- School of Chemistry and Molecular Biosciences (SCMB), University of Queensland, Brisbane, QLD, 4072, Australia
| | - Megan L O'Mara
- Research School of Chemistry (RSC), The Australian National University, Canberra, ACT, 2601, Australia. megan.o'
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6
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Subramanian N, Condic-Jurkic K, Mark AE, O'Mara ML. Identification of Possible Binding Sites for Morphine and Nicardipine on the Multidrug Transporter P-Glycoprotein Using Umbrella Sampling Techniques. J Chem Inf Model 2015; 55:1202-17. [PMID: 25938863 DOI: 10.1021/ci5007382] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The multidrug transporter P-glycoprotein (P-gp) is central to the development of multidrug resistance in cancer. While residues essential for transport and binding have been identified, the location, composition, and specificity of potential drug binding sites are uncertain. Here molecular dynamics simulations are used to calculate the free energy profile for the binding of morphine and nicardipine to P-gp. We show that morphine and nicardipine primarily interact with key residues implicated in binding and transport from mutational studies, binding at different but overlapping sites within the transmembrane pore. Their permeation pathways were distinct but involved overlapping sets of residues. The results indicate that the binding location and permeation pathways of morphine and nicardipine are not well separated and cannot be considered as unique. This has important implications for our understanding of substrate uptake and transport by P-gp. Our results are independent of the choice of starting structure and consistent with a range of experimental studies.
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Affiliation(s)
- Nandhitha Subramanian
- †School of Chemistry and Molecular Biosciences, §The Institute for Molecular Biosciences, and ‡School of Mathematics and Physics, University of Queensland, Brisbane, QLD 4072, Australia
| | - Karmen Condic-Jurkic
- †School of Chemistry and Molecular Biosciences, §The Institute for Molecular Biosciences, and ‡School of Mathematics and Physics, University of Queensland, Brisbane, QLD 4072, Australia
| | - Alan E Mark
- †School of Chemistry and Molecular Biosciences, §The Institute for Molecular Biosciences, and ‡School of Mathematics and Physics, University of Queensland, Brisbane, QLD 4072, Australia
| | - Megan L O'Mara
- †School of Chemistry and Molecular Biosciences, §The Institute for Molecular Biosciences, and ‡School of Mathematics and Physics, University of Queensland, Brisbane, QLD 4072, Australia
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7
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Dei S, Coronnello M, Floriddia E, Bartolucci G, Bellucci C, Guandalini L, Manetti D, Romanelli MN, Salerno M, Bello I, Mini E, Teodori E. Multidrug resistance (MDR) reversers: High activity and efficacy in a series of asymmetrical N,N-bis(alkanol)amine aryl esters. Eur J Med Chem 2014; 87:398-412. [PMID: 25282263 DOI: 10.1016/j.ejmech.2014.09.084] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 09/12/2014] [Accepted: 09/26/2014] [Indexed: 11/16/2022]
Abstract
As a continuation of our research on potent and efficacious P-gp-dependent multidrug resistance (MDR) reversers, several new N,N-bis(alkanol)amine aryl esters were designed and synthesized, varying the aromatic moieties or the length of the methylenic chain. The new compounds were tested on doxorubicin-resistant erythroleukemia K562 cells (K562/DOX) in the pirarubicin uptake assay, where most of the new compounds were shown to be active. In particular the asymmetrical compounds, characterized by two linkers of different length, generally showed fairly high activities as MDR reversers. Some selected compounds (isomers 15-17) were further studied by evaluating their doxorubicin cytotoxicity enhancement (reversal fold, RF) on the K562/DOX cell line. The results of both pharmacological assays indicate that compounds 16 (GDE6) and 17 (GDE19) could be interesting leads for the development of new P-gp dependent MDR modulators.
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Affiliation(s)
- Silvia Dei
- Dipartimento NEUROFARBA-Sezione di Farmaceutica e Nutraceutica, Università di Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino, FI, Italy.
| | - Marcella Coronnello
- Dipartimento di Scienze della Salute, Università di Firenze, Viale Pieraccini 6, 50139 Firenze, Italy
| | - Elisa Floriddia
- Dipartimento NEUROFARBA-Sezione di Farmaceutica e Nutraceutica, Università di Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino, FI, Italy
| | - Gianluca Bartolucci
- Dipartimento NEUROFARBA-Sezione di Farmaceutica e Nutraceutica, Università di Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino, FI, Italy
| | - Cristina Bellucci
- Dipartimento NEUROFARBA-Sezione di Farmaceutica e Nutraceutica, Università di Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino, FI, Italy
| | - Luca Guandalini
- Dipartimento NEUROFARBA-Sezione di Farmaceutica e Nutraceutica, Università di Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino, FI, Italy
| | - Dina Manetti
- Dipartimento NEUROFARBA-Sezione di Farmaceutica e Nutraceutica, Università di Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino, FI, Italy
| | - Maria Novella Romanelli
- Dipartimento NEUROFARBA-Sezione di Farmaceutica e Nutraceutica, Università di Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino, FI, Italy
| | - Milena Salerno
- Université Paris 13, Sorbonne Paris Cité, Laboratoire CSPBAT, CNRS (UMR 7244), UFR-SMBH, 74 Rue Marcel Cachin, 93017 Bobigny, France
| | - Ivan Bello
- Université Paris 13, Sorbonne Paris Cité, Laboratoire CSPBAT, CNRS (UMR 7244), UFR-SMBH, 74 Rue Marcel Cachin, 93017 Bobigny, France
| | - Enrico Mini
- Dipartimento di Scienze della Salute, Università di Firenze, Viale Pieraccini 6, 50139 Firenze, Italy
| | - Elisabetta Teodori
- Dipartimento NEUROFARBA-Sezione di Farmaceutica e Nutraceutica, Università di Firenze, Via Ugo Schiff 6, 50019 Sesto Fiorentino, FI, Italy
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8
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Pregnane X Receptor and P-glycoprotein: a connexion for Alzheimer’s disease management. Mol Divers 2014; 18:895-909. [DOI: 10.1007/s11030-014-9550-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 08/28/2014] [Indexed: 12/01/2022]
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9
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Tan W, Mei H, Chao L, Liu T, Pan X, Shu M, Yang L. Combined QSAR and molecule docking studies on predicting P-glycoprotein inhibitors. J Comput Aided Mol Des 2013; 27:1067-73. [DOI: 10.1007/s10822-013-9697-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2013] [Accepted: 12/02/2013] [Indexed: 12/27/2022]
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10
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Jara GE, Vera DMA, Pierini AB. Binding of modulators to mouse and human multidrug resistance P-glycoprotein. A computational study. J Mol Graph Model 2013; 46:10-21. [DOI: 10.1016/j.jmgm.2013.09.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 08/08/2013] [Accepted: 09/02/2013] [Indexed: 02/02/2023]
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11
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Liu M, Hou T, Feng Z, Li Y. The flexibility of P-glycoprotein for its poly-specific drug binding from molecular dynamics simulations. J Biomol Struct Dyn 2013; 31:612-29. [DOI: 10.1080/07391102.2012.706079] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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12
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Orlandi F, Coronnello M, Bellucci C, Dei S, Guandalini L, Manetti D, Martelli C, Romanelli MN, Scapecchi S, Salerno M, Menif H, Bello I, Mini E, Teodori E. New structure-activity relationship studies in a series of N,N-bis(cyclohexanol)amine aryl esters as potent reversers of P-glycoprotein-mediated multidrug resistance (MDR). Bioorg Med Chem 2012; 21:456-65. [PMID: 23245571 DOI: 10.1016/j.bmc.2012.11.019] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Revised: 11/07/2012] [Accepted: 11/12/2012] [Indexed: 10/27/2022]
Abstract
As a continuation of previous research on a new series of potent and efficacious P-gp-dependent multidrug resistant (MDR) reversers with a N,N-bis(cyclohexanol)amine scaffold, we have designed and synthesized several analogs by modulation of the two aromatic moieties linked through ester functions to the N,N-bis(cyclohexanol)amine, aiming to optimize activity and to extend structure-activity relationships (SAR) within the series. This scaffold, when esterified with two different aromatic carboxylic acids, gives origin to four geometric isomers (cis/trans, trans/trans, cis/cis and trans/cis). The new compounds were tested on doxorubicin-resistant erythroleukemia K562 cells (K562/DOX) in the pirarubicin uptake assay. Most of them resulted in being potent modulators of the extrusion pump P-gp, showing potency values ([I](0.5)) in the submicromolar and nanomolar range. Of these, compounds 2b, 2c, 3d, 5a-d and 6d, showed excellent efficacy with a α(max) close to 1. Selected compounds (2d, 3a, 3b, 5a-d) were further studied to evaluate their doxorubicin cytotoxicity potentiation (RF) on doxorubicin-resistant erythroleukemia K562 cells and were found able to enhance significantly doxorubicin cytotoxicity on K562/DOX cells. The results of both pirarubicin uptake and the cytotoxicity assay, indicate that the new compounds of the series are potent P-gp-mediated MDR reversers. They present a structure with a mix of flexible and rigid moieties, a property that seems critical to allow the molecules to choose the most productive of the several binding modes possible in the transporter recognition site. In particular, compounds 5c and 5d, similar to the already reported analogous isomers 1c and 1d,(29) are potent and efficacious modulators of P-gp-dependent MDR and may be promising leads for the development of MDR-reversal drugs.
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Affiliation(s)
- Francesca Orlandi
- Dipartimento di Scienze Farmaceutiche, Università di Firenze, via Ugo Schiff 6, 50019 Sesto Fiorentino, FI, Italy
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13
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Abstract
Multidrug resistance proteins that belong to the ATP-binding cassette family like the human P-glycoprotein (ABCB1 or Pgp) are responsible for many failed cancer and antiviral chemotherapies because these membrane transporters remove the chemotherapeutics from the targeted cells. Understanding the details of the catalytic mechanism of Pgp is therefore critical to the development of inhibitors that might overcome these resistances. In this work, targeted molecular dynamics techniques were used to elucidate catalytically relevant structures of Pgp. Crystal structures of homologues in four different conformations were used as intermediate targets in the dynamics simulations. Transitions from conformations that were wide open to the cytoplasm to transition state conformations that were wide open to the extracellular space were studied. Twenty-six nonredundant transitional protein structures were identified from these targeted molecular dynamics simulations using evolutionary structure analyses. Coupled movement of nucleotide binding domains (NBDs) and transmembrane domains (TMDs) that form the drug binding cavities were observed. Pronounced twisting of the NBDs as they approached each other as well as the quantification of a dramatic opening of the TMDs to the extracellular space as the ATP hydrolysis transition state was reached were observed. Docking interactions of 21 known transport ligands or inhibitors were analyzed with each of the 26 transitional structures. Many of the docking results obtained here were validated by previously published biochemical determinations. As the ATP hydrolysis transition state was approached, drug docking in the extracellular half of the transmembrane domains seemed to be destabilized as transport ligand exit gates opened to the extracellular space.
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Affiliation(s)
- John G Wise
- Department of Biological Sciences, Center for Drug Discovery, Design and Delivery at Dedman College, and Center for Scientific Computation, Southern Methodist University, Dallas, Texas 75275-0376, USA.
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Predicting P-glycoprotein-mediated drug transport based on support vector machine and three-dimensional crystal structure of P-glycoprotein. PLoS One 2011; 6:e25815. [PMID: 21991360 PMCID: PMC3186768 DOI: 10.1371/journal.pone.0025815] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Accepted: 09/11/2011] [Indexed: 01/16/2023] Open
Abstract
Human P-glycoprotein (P-gp) is an ATP-binding cassette multidrug transporter that confers resistance to a wide range of chemotherapeutic agents in cancer cells by active efflux of the drugs from cells. P-gp also plays a key role in limiting oral absorption and brain penetration and in facilitating biliary and renal elimination of structurally diverse drugs. Thus, identification of drugs or new molecular entities to be P-gp substrates is of vital importance for predicting the pharmacokinetics, efficacy, safety, or tissue levels of drugs or drug candidates. At present, publicly available, reliable in silico models predicting P-gp substrates are scarce. In this study, a support vector machine (SVM) method was developed to predict P-gp substrates and P-gp-substrate interactions, based on a training data set of 197 known P-gp substrates and non-substrates collected from the literature. We showed that the SVM method had a prediction accuracy of approximately 80% on an independent external validation data set of 32 compounds. A homology model of human P-gp based on the X-ray structure of mouse P-gp as a template has been constructed. We showed that molecular docking to the P-gp structures successfully predicted the geometry of P-gp-ligand complexes. Our SVM prediction and the molecular docking methods have been integrated into a free web server (http://pgp.althotas.com), which allows the users to predict whether a given compound is a P-gp substrate and how it binds to and interacts with P-gp. Utilization of such a web server may prove valuable for both rational drug design and screening.
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