1
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Al Khoury C, Thoumi S, Tokajian S, Sinno A, Nemer G, El Beyrouthy M, Rahy K. ABC transporter inhibition by beauvericin partially overcomes drug resistance in Leishmania tropica. Antimicrob Agents Chemother 2024; 68:e0136823. [PMID: 38572959 PMCID: PMC11064568 DOI: 10.1128/aac.01368-23] [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: 10/21/2023] [Accepted: 03/15/2024] [Indexed: 04/05/2024] Open
Abstract
Leishmaniasis is a neglected tropical disease infecting the world's poorest populations. Miltefosine (ML) remains the primary oral drug against the cutaneous form of leishmaniasis. The ATP-binding cassette (ABC) transporters are key players in the xenobiotic efflux, and their inhibition could enhance the therapeutic index. In this study, the ability of beauvericin (BEA) to overcome ABC transporter-mediated resistance of Leishmania tropica to ML was assessed. In addition, the transcription profile of genes involved in resistance acquisition to ML was inspected. Finally, we explored the efflux mechanism of the drug and inhibitor. The efficacy of ML against all developmental stages of L. tropica in the presence or absence of BEA was evaluated using an absolute quantification assay. The expression of resistance genes was evaluated, comparing susceptible and resistant strains. Finally, the mechanisms governing the interaction between the ABC transporter and its ligands were elucidated using molecular docking and dynamic simulation. Relative quantification showed that the expression of the ABCG sub-family is mostly modulated by ML. In this study, we used BEA to impede resistance of Leishmania tropica. The IC50 values, following BEA treatment, were significantly reduced from 30.83, 48.17, and 16.83 µM using ML to 8.14, 11.1, and 7.18 µM when using a combinatorial treatment (ML + BEA) against promastigotes, axenic amastigotes, and intracellular amastigotes, respectively. We also demonstrated a favorable BEA-binding enthalpy to L. tropica ABC transporter compared to ML. Our study revealed that BEA partially reverses the resistance development of L. tropica to ML by blocking the alternate ATP hydrolysis cycle.
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Affiliation(s)
- Charbel Al Khoury
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Beirut, Lebanon
| | - Sergio Thoumi
- Department of Computer Science and Mathematics, Lebanese American University, Beirut, Lebanon
| | - Sima Tokajian
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Byblos, Lebanon
| | - Aia Sinno
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Beirut, Lebanon
| | - Georges Nemer
- Division of Genomics and Translational Biomedicine, College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | - Mark El Beyrouthy
- Department of Agriculture and Food Engineering, Holy Spirit University of Kaslik, Jounieh, Lebanon
| | - Kelven Rahy
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Byblos, Lebanon
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2
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Moesgaard L, Pedersen ML, Uhd Nielsen C, Kongsted J. Structure-based discovery of novel P-glycoprotein inhibitors targeting the nucleotide binding domains. Sci Rep 2023; 13:21217. [PMID: 38040777 PMCID: PMC10692163 DOI: 10.1038/s41598-023-48281-4] [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: 09/22/2023] [Accepted: 11/24/2023] [Indexed: 12/03/2023] Open
Abstract
P-glycoprotein (P-gp), a membrane transport protein overexpressed in certain drug-resistant cancer cells, has been the target of numerous drug discovery projects aimed at overcoming drug resistance in cancer. Most characterized P-gp inhibitors bind at the large hydrophobic drug binding domain (DBD), but none have yet attained regulatory approval. In this study, we explored the potential of designing inhibitors that target the nucleotide binding domains (NBDs), by computationally screening a large library of 2.6 billion synthesizable molecules, using a combination of machine learning-guided molecular docking and molecular dynamics (MD). 14 of the computationally best-scoring molecules were subsequently tested for their ability to inhibit P-gp mediated calcein-AM efflux. In total, five diverse compounds exhibited inhibitory effects in the calcein-AM assay without displaying toxicity. The activity of these compounds was confirmed by their ability to decrease the verapamil-stimulated ATPase activity of P-gp in a subsequent assay. The discovery of these five novel P-gp inhibitors demonstrates the potential of in-silico screening in drug discovery and provides a new stepping point towards future potent P-gp inhibitors.
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Affiliation(s)
- Laust Moesgaard
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, 5230, Denmark.
| | - Maria L Pedersen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, 5230, Denmark
| | - Carsten Uhd Nielsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, 5230, Denmark
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, 5230, Denmark
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3
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Badiee SA, Isu UH, Khodadadi E, Moradi M. The Alternating Access Mechanism in Mammalian Multidrug Resistance Transporters and Their Bacterial Homologs. MEMBRANES 2023; 13:568. [PMID: 37367772 DOI: 10.3390/membranes13060568] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 05/23/2023] [Accepted: 05/27/2023] [Indexed: 06/28/2023]
Abstract
Multidrug resistance (MDR) proteins belonging to the ATP-Binding Cassette (ABC) transporter group play a crucial role in the export of cytotoxic drugs across cell membranes. These proteins are particularly fascinating due to their ability to confer drug resistance, which subsequently leads to the failure of therapeutic interventions and hinders successful treatments. One key mechanism by which multidrug resistance (MDR) proteins carry out their transport function is through alternating access. This mechanism involves intricate conformational changes that enable the binding and transport of substrates across cellular membranes. In this extensive review, we provide an overview of ABC transporters, including their classifications and structural similarities. We focus specifically on well-known mammalian multidrug resistance proteins such as MRP1 and Pgp (MDR1), as well as bacterial counterparts such as Sav1866 and lipid flippase MsbA. By exploring the structural and functional features of these MDR proteins, we shed light on the roles of their nucleotide-binding domains (NBDs) and transmembrane domains (TMDs) in the transport process. Notably, while the structures of NBDs in prokaryotic ABC proteins, such as Sav1866, MsbA, and mammalian Pgp, are identical, MRP1 exhibits distinct characteristics in its NBDs. Our review also emphasizes the importance of two ATP molecules for the formation of an interface between the two binding sites of NBD domains across all these transporters. ATP hydrolysis occurs following substrate transport and is vital for recycling the transporters in subsequent cycles of substrate transportation. Specifically, among the studied transporters, only NBD2 in MRP1 possesses the ability to hydrolyze ATP, while both NBDs of Pgp, Sav1866, and MsbA are capable of carrying out this reaction. Furthermore, we highlight recent advancements in the study of MDR proteins and the alternating access mechanism. We discuss the experimental and computational approaches utilized to investigate the structure and dynamics of MDR proteins, providing valuable insights into their conformational changes and substrate transport. This review not only contributes to an enhanced understanding of multidrug resistance proteins but also holds immense potential for guiding future research and facilitating the development of effective strategies to overcome multidrug resistance, thus improving therapeutic interventions.
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Affiliation(s)
- Shadi A Badiee
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Ugochi H Isu
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Ehsaneh Khodadadi
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
| | - Mahmoud Moradi
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, AR 72701, USA
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4
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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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Li H, Gong W. Study of Allosteric Transitions of Human P-Glycoprotein by Using the Two-State Anisotropic Network Model. Front Med (Lausanne) 2022; 9:815355. [PMID: 35223913 PMCID: PMC8863969 DOI: 10.3389/fmed.2022.815355] [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: 12/01/2021] [Accepted: 01/04/2022] [Indexed: 11/25/2022] Open
Abstract
Human P-glycoprotein (P-gp) is a kind of ATP-binding cassette (ABC) transporters. Once human P-gp is overexpressed in tumor cells, which can lead to tumor multidrug resistance (MDR). However, the present experimental methods are difficult to obtain the large-scale conformational transition process of human P-gp. In this work, we explored the allosteric pathway of human P-gp from the inward-facing (IF) to the outward-facing (OF) state in the substrate transport process with the two-state anisotropic network model (tANM). These results suggest that the allosteric transitions proceed in a coupled way. The conformational changes of nucleotide-binding domains (NBDs) finally make the transmembrane domains (TMDs) to the OF state via the role of the allosteric propagation of the intracellular helices IH1 and IH2. Additionally, this allosteric pathway is advantageous in energy compared with other methods. This study reveals the conformational transition of P-gp, which contributes to an understanding of the allosteric mechanism of ABC exporters.
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Affiliation(s)
- Hongwu Li
- School of Mathematics and Statistics, Nanyang Normal University, Nanyang, China
| | - Weikang Gong
- Faculty of Environmental and Life Sciences, Beijing University of Technology, Beijing, China
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6
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Zou W, Shi B, Zeng T, Zhang Y, Huang B, Ouyang B, Cai Z, Liu M. Drug Transporters in the Kidney: Perspectives on Species Differences, Disease Status, and Molecular Docking. Front Pharmacol 2021; 12:746208. [PMID: 34912216 PMCID: PMC8666590 DOI: 10.3389/fphar.2021.746208] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 10/27/2021] [Indexed: 01/09/2023] Open
Abstract
The kidneys are a pair of important organs that excretes endogenous waste and exogenous biological agents from the body. Numerous transporters are involved in the excretion process. The levels of these transporters could affect the pharmacokinetics of many drugs, such as organic anion drugs, organic cationic drugs, and peptide drugs. Eleven drug transporters in the kidney (OAT1, OAT3, OATP4C1, OCT2, MDR1, BCRP, MATE1, MATE2-K, OAT4, MRP2, and MRP4) have become necessary research items in the development of innovative drugs. However, the levels of these transporters vary between different species, sex-genders, ages, and disease statuses, which may lead to different pharmacokinetics of drugs. Here, we review the differences of the important transports in the mentioned conditions, in order to help clinicians to improve clinical prescriptions for patients. To predict drug-drug interactions (DDIs) caused by renal drug transporters, the molecular docking method is used for rapid screening of substrates or inhibitors of the drug transporters. Here, we review a large number of natural products that represent potential substrates and/or inhibitors of transporters by the molecular docking method.
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Affiliation(s)
- Wei Zou
- Changsha Research and Development Center on Obstetric and Gynecologic Traditional Chinese Medicine Preparation, NHC Key Laboratory of Birth Defects Research, Prevention and Treatment, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | - Birui Shi
- Biopharmaceutics, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Ting Zeng
- Changsha Research and Development Center on Obstetric and Gynecologic Traditional Chinese Medicine Preparation, NHC Key Laboratory of Birth Defects Research, Prevention and Treatment, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | - Yan Zhang
- Biopharmaceutics, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Baolin Huang
- Biopharmaceutics, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China
| | - Bo Ouyang
- Changsha Research and Development Center on Obstetric and Gynecologic Traditional Chinese Medicine Preparation, NHC Key Laboratory of Birth Defects Research, Prevention and Treatment, Hunan Provincial Maternal and Child Health Care Hospital, Changsha, China
| | - Zheng Cai
- Biopharmaceutics, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China.,TCM-Integrated Hospital, Southern Medical University, Guangzhou, China
| | - Menghua Liu
- Biopharmaceutics, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou, China.,TCM-Integrated Hospital, Southern Medical University, Guangzhou, China
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7
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Ammerman L, Mertz SB, Park C, Wise JG. Transport Dynamics of MtrD: An RND Multidrug Efflux Pump from Neisseria gonorrheae. Biochemistry 2021; 60:3098-3113. [PMID: 34609833 DOI: 10.1021/acs.biochem.1c00399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The MtrCDE system confers multidrug resistance to Neisseria gonorrheae, the causative agent of gonorrhea. Using free and directed molecular dynamics (MD) simulations, we analyzed the interactions between MtrD and azithromycin, a transport substrate of MtrD, and a last-resort clinical treatment for multidrug-resistant gonorrhea. We then simulated the interactions between MtrD and streptomycin, an apparent nonsubstrate of MtrD. Using known conformations of MtrD homologues, we simulated a potential dynamic transport cycle of MtrD using targeted MD techniques (TMD), and we noted that forces were not applied to ligands of interest. In these TMD simulations, we observed the transport of azithromycin and the rejection of streptomycin. In an unbiased, long-time scale simulation of AZY-bound MtrD, we observed the spontaneous diffusion of azithromycin through the periplasmic cleft. Our simulations show how the peristaltic motions of the periplasmic cleft facilitate the transport of substrates by MtrD. Our data also suggest that multiple transport pathways for macrolides may exist within the periplasmic cleft of MtrD.
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Affiliation(s)
- Lauren Ammerman
- Department of Biological Sciences, Southern Methodist University, Dallas, Texas 75275-0376, United States.,Center for Research Computing, Southern Methodist University, Dallas, Texas 75275-0376, United States.,Center for Drug Discovery, Design and Delivery, Southern Methodist University, Dallas, Texas 75275-0376, United States
| | - Sarah B Mertz
- Department of Biological Sciences, Southern Methodist University, Dallas, Texas 75275-0376, United States.,Center for Research Computing, Southern Methodist University, Dallas, Texas 75275-0376, United States.,Center for Drug Discovery, Design and Delivery, Southern Methodist University, Dallas, Texas 75275-0376, United States
| | - Chanyang Park
- Department of Biological Sciences, Southern Methodist University, Dallas, Texas 75275-0376, United States.,Center for Drug Discovery, Design and Delivery, Southern Methodist University, Dallas, Texas 75275-0376, United States
| | - John G Wise
- Department of Biological Sciences, Southern Methodist University, Dallas, Texas 75275-0376, United States.,Center for Research Computing, Southern Methodist University, Dallas, Texas 75275-0376, United States.,Center for Drug Discovery, Design and Delivery, Southern Methodist University, Dallas, Texas 75275-0376, United States
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8
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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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9
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Li YS, Mao S, Zhao DS, Wang CC, Zu D, Yang X, Liu GJ, Wang SJ, Zhang B, Bao XZ, Ye XY, Wei B, Cui ZN, Chen JW, Wang H. Rational design of phenyl thiophene (pyridine) derivatives that overcome P-glycoprotein mediated MDR in MCF-7/ADR cell. Bioorg Chem 2021; 114:105075. [PMID: 34217975 DOI: 10.1016/j.bioorg.2021.105075] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/04/2021] [Accepted: 06/06/2021] [Indexed: 01/04/2023]
Affiliation(s)
- Ya-Sheng Li
- College of Pharmaceutical Science & Green Pharmaceutical Collaborative Innovation Center of Yangtze River Del-ta Region, Zhejiang University of Technology, Hangzhou 310014, China
| | - Shen Mao
- College of Pharmaceutical Science & Green Pharmaceutical Collaborative Innovation Center of Yangtze River Del-ta Region, Zhejiang University of Technology, Hangzhou 310014, China
| | - Dong-Sheng Zhao
- Department of Pharmacy, Quanzhou Medical College, Quanzhou 362100, China
| | - Can-Can Wang
- College of Pharmaceutical Science & Green Pharmaceutical Collaborative Innovation Center of Yangtze River Del-ta Region, Zhejiang University of Technology, Hangzhou 310014, China
| | - Dan Zu
- College of Pharmaceutical Science & Green Pharmaceutical Collaborative Innovation Center of Yangtze River Del-ta Region, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xi Yang
- College of Pharmaceutical Science & Green Pharmaceutical Collaborative Innovation Center of Yangtze River Del-ta Region, Zhejiang University of Technology, Hangzhou 310014, China
| | - Gui-Jun Liu
- College of Pharmaceutical Science & Green Pharmaceutical Collaborative Innovation Center of Yangtze River Del-ta Region, Zhejiang University of Technology, Hangzhou 310014, China
| | - Si-Jia Wang
- College of Pharmaceutical Science & Green Pharmaceutical Collaborative Innovation Center of Yangtze River Del-ta Region, Zhejiang University of Technology, Hangzhou 310014, China; Center for Human Nutrition, David Geffen School of Medicine, University of California, Los Angeles, CA 90024, USA
| | - Bo Zhang
- College of Pharmaceutical Science & Green Pharmaceutical Collaborative Innovation Center of Yangtze River Del-ta Region, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xiao-Ze Bao
- College of Pharmaceutical Science & Green Pharmaceutical Collaborative Innovation Center of Yangtze River Del-ta Region, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xin-Yi Ye
- College of Pharmaceutical Science & Green Pharmaceutical Collaborative Innovation Center of Yangtze River Del-ta Region, Zhejiang University of Technology, Hangzhou 310014, China
| | - Bin Wei
- College of Pharmaceutical Science & Green Pharmaceutical Collaborative Innovation Center of Yangtze River Del-ta Region, Zhejiang University of Technology, Hangzhou 310014, China
| | - Zi-Ning Cui
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Integrative Microbiology Research Centre, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China.
| | - Jian-Wei Chen
- College of Pharmaceutical Science & Green Pharmaceutical Collaborative Innovation Center of Yangtze River Del-ta Region, Zhejiang University of Technology, Hangzhou 310014, China.
| | - Hong Wang
- College of Pharmaceutical Science & Green Pharmaceutical Collaborative Innovation Center of Yangtze River Del-ta Region, Zhejiang University of Technology, Hangzhou 310014, China.
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10
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McCormick JW, Ammerman L, Chen G, Vogel PD, Wise JG. Transport of Alzheimer's associated amyloid-β catalyzed by P-glycoprotein. PLoS One 2021; 16:e0250371. [PMID: 33901197 PMCID: PMC8075256 DOI: 10.1371/journal.pone.0250371] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 04/06/2021] [Indexed: 12/24/2022] Open
Abstract
P-glycoprotein (P-gp) is a critical membrane transporter in the blood brain barrier (BBB) and is implicated in Alzheimer’s disease (AD). However, previous studies on the ability of P-gp to directly transport the Alzheimer’s associated amyloid-β (Aβ) protein have produced contradictory results. Here we use molecular dynamics (MD) simulations, transport substrate accumulation studies in cell culture, and biochemical activity assays to show that P-gp actively transports Aβ. We observed transport of Aβ40 and Aβ42 monomers by P-gp in explicit MD simulations of a putative catalytic cycle. In in vitro assays with P-gp overexpressing cells, we observed enhanced accumulation of fluorescently labeled Aβ42 in the presence of Tariquidar, a potent P-gp inhibitor. We also showed that Aβ42 stimulated the ATP hydrolysis activity of isolated P-gp in nanodiscs. Our findings expand the substrate profile of P-gp, and suggest that P-gp may contribute to the onset and progression of AD.
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Affiliation(s)
- James W. McCormick
- Department of Biological Sciences, Southern Methodist University, Dallas, Texas, United States of America
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, Texas, United States of America
- * E-mail: (JGW); (JWM)
| | - Lauren Ammerman
- Department of Biological Sciences, Southern Methodist University, Dallas, Texas, United States of America
- The Center for Drug Discovery, Design and Delivery, Southern Methodist University, Dallas, Texas, United States of America
- The Center for Scientific Computation, Southern Methodist University, Dallas, Texas, United States of America
| | - Gang Chen
- Department of Biological Sciences, Southern Methodist University, Dallas, Texas, United States of America
- The Center for Drug Discovery, Design and Delivery, Southern Methodist University, Dallas, Texas, United States of America
| | - Pia D. Vogel
- Department of Biological Sciences, Southern Methodist University, Dallas, Texas, United States of America
- The Center for Drug Discovery, Design and Delivery, Southern Methodist University, Dallas, Texas, United States of America
| | - John G. Wise
- Department of Biological Sciences, Southern Methodist University, Dallas, Texas, United States of America
- The Center for Drug Discovery, Design and Delivery, Southern Methodist University, Dallas, Texas, United States of America
- The Center for Scientific Computation, Southern Methodist University, Dallas, Texas, United States of America
- * E-mail: (JGW); (JWM)
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11
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Singh A, Patel SK, Kumar P, Das KC, Verma D, Sharma R, Tripathi T, Giri R, Martins N, Garg N. Quercetin acts as a P-gp modulator via impeding signal transduction from nucleotide-binding domain to transmembrane domain. J Biomol Struct Dyn 2020; 40:4507-4515. [PMID: 33306006 DOI: 10.1080/07391102.2020.1858966] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The inherent ability of the cancer cells to resist chemotherapeutic agents is a major challenge in drug discovery. Chemotherapy is one of the most widely used treatment methods for cancer, but due to multidrug resistance (MDR) development in cancer cells, the healing procedure often fails. Various factors impart cancer resistance to cells; among them, P-glycoprotein (P-gp) overexpression is directly linked to MDR in cancer cells. P-gp leads to the efflux of drug molecules to the extracellular space. Several molecules have been reported to inhibit the P-gp activity. Among them, quercetin has revealed a great potential to modulate P-gp activity. However, the mechanistic understanding of quercetin induced modulation is not entirely elucidated. In the present work, we showed that quercetin binds in the interacting region between the transmembrane domain and nucleotide-binding domain out of the three plausible binding sites of P-gp and restrict the conformational change from inward- to outward-facing conformation of P-gp. Due to the absence of the inward-facing structure of human P-gp, we first modeled an inward-facing P-gp structure. Using molecular docking, the interacting residues of P-gp were identified, and the stability and interaction dynamics of the complex were studied using molecular dynamics simulation. Our work reveals the mechanistic understanding of quercetin induced modulation of P-gp and indicates its importance in cancer treatment.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ashutosh Singh
- School of Basic Sciences and BioX Center, Indian Institute of Technology Mandi, VPO Kamand, Mandi, Himachal Pradesh, India
| | - Sandesh Kumar Patel
- School of Basic Sciences and BioX Center, Indian Institute of Technology Mandi, VPO Kamand, Mandi, Himachal Pradesh, India
| | - Prateek Kumar
- School of Basic Sciences and BioX Center, Indian Institute of Technology Mandi, VPO Kamand, Mandi, Himachal Pradesh, India
| | - Kanhu Charan Das
- Department of Biochemistry, North-Eastern Hill University, Umshing, Shillong, Meghalaya, India
| | - Deepanshu Verma
- School of Basic Sciences and BioX Center, Indian Institute of Technology Mandi, VPO Kamand, Mandi, Himachal Pradesh, India
| | - Rohit Sharma
- Department of Rasashastra and Bhaishajya Kalpana, Faculty of Ayurveda, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Timir Tripathi
- Department of Biochemistry, North-Eastern Hill University, Umshing, Shillong, Meghalaya, India
| | - Rajanish Giri
- School of Basic Sciences and BioX Center, Indian Institute of Technology Mandi, VPO Kamand, Mandi, Himachal Pradesh, India
| | - Natália Martins
- Faculty of Medicine, University of Porto, Porto, Portugal.,Institute for Research and Innovation in Health (i3S), University of Porto, Porto, Portugal
| | - Neha Garg
- Department of Medicinal Chemistry, Faculty of Ayurveda, Institute of Medical Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India
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12
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Dehghani-Ghahnaviyeh S, Kapoor K, Tajkhorshid E. Conformational changes in the nucleotide-binding domains of P-glycoprotein induced by ATP hydrolysis. FEBS Lett 2020; 595:735-749. [PMID: 33159693 DOI: 10.1002/1873-3468.13992] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/19/2020] [Accepted: 10/30/2020] [Indexed: 12/16/2022]
Abstract
P-glycoprotein (Pgp) is a member of the ABC transporter superfamily with high physiological importance. Pgp nucleotide-binding domains (NBDs) drive the transport cycle through ATP binding and hydrolysis. We use molecular dynamics simulations to investigate the ATP hydrolysis-induced conformational changes in NBDs. Five systems, including all possible ATP/ADP combinations in the NBDs and the APO system, are simulated. ATP/ADP exchange induces conformational changes mostly within the conserved signature motif of the NBDs, resulting in relative orientational changes in the NBDs. Nucleotide removal leads to additional orientational changes in the NBDs, allowing their dissociation. Furthermore, we capture putative hydrolysis-competent configurations in which the conserved glutamate in the Walker-B motif acts as a catalytic base capturing a water molecule likely initiating ATP hydrolysis.
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Affiliation(s)
- Sepehr Dehghani-Ghahnaviyeh
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Center for Biophysics and Quantitative Biology, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, IL, USA
| | - Karan Kapoor
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Center for Biophysics and Quantitative Biology, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, IL, USA
| | - Emad Tajkhorshid
- Department of Biochemistry, NIH Center for Macromolecular Modeling and Bioinformatics, Center for Biophysics and Quantitative Biology, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, IL, USA
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13
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Fischer H, Senn C, Ullah M, Cantrill C, Schuler F, Yu L. Calculation of an Apical Efflux Ratio from P-Glycoprotein (P-gp) In Vitro Transport Experiments Shows an Improved Correlation with In Vivo Cerebrospinal Fluid Measurements in Rats: Impact on P-gp Screening and Compound Optimization. J Pharmacol Exp Ther 2020; 376:322-329. [PMID: 33288523 DOI: 10.1124/jpet.120.000158] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 12/02/2020] [Indexed: 11/22/2022] Open
Abstract
P-glycoprotein (P-gp) is a major blood-brain barrier (BBB) efflux transporter. In vitro approaches, including bidirectional efflux ratio (ER), are used to measure P-gp-mediated transport, but findings can be inconsistent across models. We propose a novel, more physiologically relevant, in vitro model: unidirectional apical efflux ratio (AP-ER)-a ratio of permeability rates at the apical side of the BBB with and without P-gp inhibitor. To test our approach, ER and AP-ER were calculated for 3227 structurally diverse compounds in porcine kidney epithelial cells (LLC-PK1) overexpressing human or mouse P-gp and classified based on their passive transcellular P-gp permeability or charged properties. In vivo rat infusion studies were performed for selected compounds with high ER but low AP-ER. One-third of the 3227 compounds had bidirectional ER that was much higher than AP-ER; very few had AP-ER higher than ER. Compounds with a large difference between AP-ER and ER were typically basic compounds with low-to-medium passive permeability and high lipophilicity and/or amphiphilicity, leading to strong membrane binding. Outcomes in the human model were similar to those in mice, suggesting AP-ER/ER ratios may be conserved for at least two species. AP-ER predicted measured cerebrospinal fluid (CSF) concentration better than ER for the five compounds tested in our in vivo rat infusion studies. We report superior estimations of the CSF concentrations of the compounds when based on less resource-intensive AP-ER versus classic ER. Better understanding of the properties leading to high P-gp-mediated efflux in vivo could support more efficient brain-penetrant compound screening and optimization. SIGNIFICANCE STATEMENT: To address inconsistencies associated with the historical, bidirectional efflux ratio (ER) calculation of P-glycoprotein-mediated transport, we propose to use the novel, more physiologically relevant, unidirectional apical efflux ratio (AP-ER) model. In vitro experiments suggested that compounds with strong membrane binding showed the largest difference between AP-ER and ER, and in vivo infusion studies showed that AP-ER predicted cerebrospinal fluid concentrations of compounds better than ER; outcomes in the human model were similar to those in mice.
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Affiliation(s)
- Holger Fischer
- Roche Pharmaceutical Research and Early Development, DMPK/PD project leader (H.F.), Comparative Pharmacology (C.S.), Investigative Safety, Pharmaceutical Sciences (M.U., C.C.), and Immunology, Infectious Disease and Ophthalmology (F.S.), Roche Innovation Center, Basel, Switzerland; and Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Translational and Clinical Research Center, Inc., and LIYU Pharmaceutical Consulting LCC, New Jersey, USA (L.Y.)
| | - Claudia Senn
- Roche Pharmaceutical Research and Early Development, DMPK/PD project leader (H.F.), Comparative Pharmacology (C.S.), Investigative Safety, Pharmaceutical Sciences (M.U., C.C.), and Immunology, Infectious Disease and Ophthalmology (F.S.), Roche Innovation Center, Basel, Switzerland; and Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Translational and Clinical Research Center, Inc., and LIYU Pharmaceutical Consulting LCC, New Jersey, USA (L.Y.)
| | - Mohammed Ullah
- Roche Pharmaceutical Research and Early Development, DMPK/PD project leader (H.F.), Comparative Pharmacology (C.S.), Investigative Safety, Pharmaceutical Sciences (M.U., C.C.), and Immunology, Infectious Disease and Ophthalmology (F.S.), Roche Innovation Center, Basel, Switzerland; and Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Translational and Clinical Research Center, Inc., and LIYU Pharmaceutical Consulting LCC, New Jersey, USA (L.Y.)
| | - Carina Cantrill
- Roche Pharmaceutical Research and Early Development, DMPK/PD project leader (H.F.), Comparative Pharmacology (C.S.), Investigative Safety, Pharmaceutical Sciences (M.U., C.C.), and Immunology, Infectious Disease and Ophthalmology (F.S.), Roche Innovation Center, Basel, Switzerland; and Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Translational and Clinical Research Center, Inc., and LIYU Pharmaceutical Consulting LCC, New Jersey, USA (L.Y.)
| | - Franz Schuler
- Roche Pharmaceutical Research and Early Development, DMPK/PD project leader (H.F.), Comparative Pharmacology (C.S.), Investigative Safety, Pharmaceutical Sciences (M.U., C.C.), and Immunology, Infectious Disease and Ophthalmology (F.S.), Roche Innovation Center, Basel, Switzerland; and Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Translational and Clinical Research Center, Inc., and LIYU Pharmaceutical Consulting LCC, New Jersey, USA (L.Y.)
| | - Li Yu
- Roche Pharmaceutical Research and Early Development, DMPK/PD project leader (H.F.), Comparative Pharmacology (C.S.), Investigative Safety, Pharmaceutical Sciences (M.U., C.C.), and Immunology, Infectious Disease and Ophthalmology (F.S.), Roche Innovation Center, Basel, Switzerland; and Roche Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Translational and Clinical Research Center, Inc., and LIYU Pharmaceutical Consulting LCC, New Jersey, USA (L.Y.)
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14
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Wang L, Sun Y. Efflux mechanism and pathway of verapamil pumping by human P-glycoprotein. Arch Biochem Biophys 2020; 696:108675. [PMID: 33197430 DOI: 10.1016/j.abb.2020.108675] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 09/23/2020] [Accepted: 11/08/2020] [Indexed: 11/28/2022]
Abstract
Multidrug resistance (MDR) caused by overexpressed permeability-glycoprotein (P-gp) in cancer cells is the main barrier for the cure of cancers. P-gp can pump many chemotherapeutic drugs, which is a viable target to overcome P-gp-mediated MDR by efficient inhibitors of P-gp. However, limited understanding of the efflux mechanism by human P-gp hinders the development of efficient inhibitors. Herein, the transport of a P-gp inhibitor, verapamil, by human P-gp has been investigated using targeted molecular dynamics simulations and energetics analysis based on our previous research on the transport of a drug (doxorubicin). The energetics analysis identifies that the driving forces for the transport of verapamil are electrostatic repulsions contributed by the positively charged residues in the initial stage and then hydrophobic interactions contributed by the important residues in the later stage. This scenario is generally consistent with that in the transport of doxorubicin. However, the positively charged residues and the important residues for the transport of verapamil are incompletely consistent with the relative residues for the transport of doxorubicin. Moreover, the binding free energy contributions of the positively charged residues for the transport of verapamil are generally higher than them for the transport of doxorubicin, while the important residues constitute significantly different binding free energy compositions in the transports of the two substrates. Consequently, the pathway for the transport of verapamil is identified, which shares only two residues (F336 and M986) with the pathway of doxorubicin. This may imply the weak competitiveness of verapamil with doxorubicin in the substrate efflux. Taken together, this work provided new insights into the efflux mechanisms by human P-gp and would be beneficial in the design of potent P-gp inhibitors.
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Affiliation(s)
- Lijie Wang
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China
| | - Yan Sun
- Department of Biochemical Engineering, School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China; Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300350, China.
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15
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Esposito C, Wang S, Lange UEW, Oellien F, Riniker S. Combining Machine Learning and Molecular Dynamics to Predict P-Glycoprotein Substrates. J Chem Inf Model 2020; 60:4730-4749. [DOI: 10.1021/acs.jcim.0c00525] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Carmen Esposito
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Shuzhe Wang
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Udo E. W. Lange
- Neuroscience Discovery, Medicinal Chemistry, AbbVie Deutschland GmbH & Co KG, Knollstrasse, 67061 Ludwigshafen, Germany
| | - Frank Oellien
- Neuroscience Discovery, Medicinal Chemistry, AbbVie Deutschland GmbH & Co KG, Knollstrasse, 67061 Ludwigshafen, Germany
| | - Sereina Riniker
- Laboratory of Physical Chemistry, ETH Zurich, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
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16
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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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17
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Bonito CA, Ferreira RJ, Ferreira MJU, Gillet JP, Cordeiro MNDS, Dos Santos DJVA. Theoretical insights on helix repacking as the origin of P-glycoprotein promiscuity. Sci Rep 2020; 10:9823. [PMID: 32555203 PMCID: PMC7300024 DOI: 10.1038/s41598-020-66587-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 04/27/2020] [Indexed: 12/14/2022] Open
Abstract
P-glycoprotein (P-gp, ABCB1) overexpression is, currently, one of the most important multidrug resistance (MDR) mechanisms in tumor cells. Thus, modulating drug efflux by P-gp has become one of the most promising approaches to overcome MDR in cancer. Yet, more insights on the molecular basis of drug specificity and efflux-related signal transmission mechanism between the transmembrane domains (TMDs) and the nucleotide binding domains (NBDs) are needed to develop molecules with higher selectivity and efficacy. Starting from a murine P-gp crystallographic structure at the inward-facing conformation (PDB ID: 4Q9H), we evaluated the structural quality of the herein generated human P-gp homology model. This initial human P-gp model, in the presence of the “linker” and inserted in a suitable lipid bilayer, was refined through molecular dynamics simulations and thoroughly validated. The best human P-gp model was further used to study the effect of four single-point mutations located at the TMDs, experimentally related with changes in substrate specificity and drug-stimulated ATPase activity. Remarkably, each P-gp mutation is able to induce transmembrane α-helices (TMHs) repacking, affecting the drug-binding pocket volume and the drug-binding sites properties (e.g. volume, shape and polarity) finally compromising drug binding at the substrate binding sites. Furthermore, intracellular coupling helices (ICH) also play an important role since changes in the TMHs rearrangement are shown to have an impact in residue interactions at the ICH-NBD interfaces, suggesting that identified TMHs repacking affect TMD-NBD contacts and interfere with signal transmission from the TMDs to the NBDs.
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Affiliation(s)
- Cátia A Bonito
- LAQV@REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal
| | - Ricardo J Ferreira
- Science for Life Laboratory, Department of Cell and Molecular Biology, Uppsala University, 75124, Uppsala, Sweden
| | - Maria-José U Ferreira
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal
| | - Jean-Pierre Gillet
- Laboratory of Molecular Cancer Biology, Molecular Physiology Research Unit-URPhyM, Namur Research Institute for Life Sciences (NARILIS), Faculty of Medicine, University of Namur, B-5000, Namur, Belgium
| | - M Natália D S Cordeiro
- LAQV@REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal
| | - Daniel J V A Dos Santos
- LAQV@REQUIMTE, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Rua do Campo Alegre, 4169-007, Porto, Portugal. .,Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisboa, Portugal.
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18
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Wise JG, Nanayakkara AK, Aljowni M, Chen G, De Oliveira MC, Ammerman L, Olengue K, Lippert AR, Vogel PD. Optimizing Targeted Inhibitors of P-Glycoprotein Using Computational and Structure-Guided Approaches. J Med Chem 2019; 62:10645-10663. [PMID: 31702922 DOI: 10.1021/acs.jmedchem.9b00966] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Overexpression of ABC transporters like P-glycoprotein (P-gp) has been correlated with resistances in cancer chemotherapy. Intensive efforts to identify P-gp inhibitors for use in combination therapy have not led to clinically approved inhibitors to date. Here, we describe computational approaches combined with structure-based design to improve the characteristics of a P-gp inhibitor previously identified by us. This hit compound represents a novel class of P-gp inhibitors that specifically targets and inhibits P-gp ATP hydrolysis while not being transported by the pump. We describe here a new program for virtual chemical synthesis and computational assessment, ChemGen, to produce hit compound variants with improved binding characteristics. The chemical syntheses of several variants, efficacy in reversing multidrug resistance in cell culture, and biochemical assessment of the inhibition mechanism are described. The usefulness of the computational predictions of binding characteristics of the inhibitor variants is discussed and compared to more traditional structure-based approaches.
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19
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Wang L, Zhang L, Liu F, Sun Y. Molecular Energetics of Doxorubicin Pumping by Human P-Glycoprotein. J Chem Inf Model 2019; 59:3889-3898. [DOI: 10.1021/acs.jcim.9b00429] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lijie Wang
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Lin Zhang
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Fufeng Liu
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
- Key Laboratory of Industrial Fermentation Microbiology of Ministry of Education, Tianjin Key Laboratory of Industrial Microbiology, National Engineering Laboratory for Industrial Enzymes, National and Local United Engineering Lab of Metabolic Control Fermentation Technology, College of Biotechnology, Tianjin University of Science & Technology, Tianjin 300457, China
| | - Yan Sun
- Department of Biochemical Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
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20
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Nanayakkara AK, Vogel PD, Wise JG. Prolonged inhibition of P-glycoprotein after exposure to chemotherapeutics increases cell mortality in multidrug resistant cultured cancer cells. PLoS One 2019; 14:e0217940. [PMID: 31173617 PMCID: PMC6555590 DOI: 10.1371/journal.pone.0217940] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 05/21/2019] [Indexed: 01/21/2023] Open
Abstract
One common reason for cancer chemotherapy failure is increased drug efflux catalyzed by membrane transporters with broad pump substrate specificities, which leads to resistances to a wide range of chemically unrelated drugs. This multidrug resistance (MDR) phenomenon results in failed therapies and poor patient prognoses. A common cause of MDR is over-expression of the P-glycoprotein (ABCB1/P-gp) transporter. We report here on an MDR modulator that is a small molecule inhibitor of P-glycoprotein, but is not a pump substrate for P-gp and we show for the first time that extended exposure of an MDR prostate cancer cell line to the inhibitor following treatment with chemotherapeutics and inhibitor resulted in trapping of the chemotherapeutics within the cancerous cells. This trapping led to decreased cell viability, survival, and motility, and increased indicators of apoptosis in the cancerous cells. In contrast, extended exposure of non-Pgp-overexpressing cells to the inhibitor during and after similar chemotherapy treatments did not lead to decreased cell viability and survival, indicating that toxicity of the chemotherapeutic was not increased by the inhibitor. Increases in efficacy in treating MDR cancer cells without increasing toxicity to normal cells by such extended inhibitor treatment might translate to increased clinical efficacy of chemotherapies if suitable inhibitors can be developed.
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Affiliation(s)
- Amila K. Nanayakkara
- Center for Drug Discovery, Design and Delivery, The Center for Scientific Computing, and The Department of Biological Sciences, Southern Methodist University, Dallas, Texas, United States of America
| | - Pia D. Vogel
- Center for Drug Discovery, Design and Delivery, The Center for Scientific Computing, and The Department of Biological Sciences, Southern Methodist University, Dallas, Texas, United States of America
- * E-mail: (JGW); (PDV)
| | - John G. Wise
- Center for Drug Discovery, Design and Delivery, The Center for Scientific Computing, and The Department of Biological Sciences, Southern Methodist University, Dallas, Texas, United States of America
- * E-mail: (JGW); (PDV)
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21
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Sachs J, Döhl K, Weber A, Bonus M, Ehlers F, Fleischer E, Klinger A, Gohlke H, Pietruszka J, Schmitt L, Teusch N. Novel 3,4-Dihydroisocoumarins Inhibit Human P-gp and BCRP in Multidrug Resistant Tumors and Demonstrate Substrate Inhibition of Yeast Pdr5. Front Pharmacol 2019; 10:400. [PMID: 31040786 PMCID: PMC6476959 DOI: 10.3389/fphar.2019.00400] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 04/01/2019] [Indexed: 12/15/2022] Open
Abstract
Multidrug resistance (MDR) in tumors and pathogens remains a major problem in the efficacious treatment of patients by reduction of therapy options and subsequent treatment failure. Various mechanisms are described to be involved in the development of MDR with overexpression of ATP-binding cassette (ABC) transporters reflecting the most extensively studied. These membrane transporters translocate a wide variety of substrates utilizing energy from ATP hydrolysis leading to decreased intracellular drug accumulation and impaired drug efficacy. One treatment strategy might be inhibition of transporter-mediated efflux by small molecules. Isocoumarins and 3,4-dihydroisocoumarins are a large group of natural products derived from various sources with great structural and functional variety, but have so far not been in the focus as potential MDR reversing agents. Thus, three natural products and nine novel 3,4-dihydroisocoumarins were designed and analyzed regarding cytotoxicity induction and inhibition of human ABC transporters P-glycoprotein (P-gp), multidrug resistance-associated protein 1 (MRP1) and breast cancer resistance protein (BCRP) in a variety of human cancer cell lines as well as the yeast ABC transporter Pdr5 in Saccharomyces cerevisiae. Dual inhibitors of P-gp and BCRP and inhibitors of Pdr5 were identified, and distinct structure-activity relationships for transporter inhibition were revealed. The strongest inhibitor of P-gp and BCRP, which inhibited the transporters up to 80 to 90% compared to the respective positive controls, demonstrated the ability to reverse chemotherapy resistance in resistant cancer cell lines up to 5.6-fold. In the case of Pdr5, inhibitors were identified that prevented substrate transport and/or ATPase activity with IC50 values in the low micromolar range. However, cell toxicity was not observed. Molecular docking of the test compounds to P-gp revealed that differences in inhibition capacity were based on different binding affinities to the transporter. Thus, these small molecules provide novel lead structures for further optimization.
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Affiliation(s)
- Julia Sachs
- Bio-Pharmaceutical Chemistry and Molecular Pharmacology, Faculty of Applied Natural Sciences, Technische Hochschule Köln, Leverkusen, Germany
| | - Katja Döhl
- Institute of Biochemistry, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Anja Weber
- Institute of Bioorganic Chemistry, Heinrich-Heine-Universität Düsseldorf im Forschungszentrum Jülich, Jülich, Germany
| | - Michele Bonus
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Ferdinand Ehlers
- Bio-Pharmaceutical Chemistry and Molecular Pharmacology, Faculty of Applied Natural Sciences, Technische Hochschule Köln, Leverkusen, Germany
| | | | | | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany.,John von Neumann Institute for Computing, Jülich Supercomputing Centre and Institute for Complex Systems - Structural Biochemistry, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Jörg Pietruszka
- Institute of Bioorganic Chemistry, Heinrich-Heine-Universität Düsseldorf im Forschungszentrum Jülich, Jülich, Germany.,IBG-1: Biotechnology, Forschungszentrum Jülich, Jülich, Germany
| | - Lutz Schmitt
- Institute of Biochemistry, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Nicole Teusch
- Bio-Pharmaceutical Chemistry and Molecular Pharmacology, Faculty of Applied Natural Sciences, Technische Hochschule Köln, Leverkusen, Germany
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22
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Rusli N, Amanah A, Kaur G, Adenan MI, Sulaiman SF, Wahab HA, Tan ML. The inhibitory effects of mitragynine on P-glycoprotein in vitro. Naunyn Schmiedebergs Arch Pharmacol 2019; 392:481-496. [DOI: 10.1007/s00210-018-01605-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 12/14/2018] [Indexed: 12/13/2022]
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23
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Zhang YT, Yu YQ, Yan XX, Wang WJ, Tian XT, Wang L, Zhu WL, Gong LK, Pan GY. Different structures of berberine and five other protoberberine alkaloids that affect P-glycoprotein-mediated efflux capacity. Acta Pharmacol Sin 2019; 40:133-142. [PMID: 30442987 DOI: 10.1038/s41401-018-0183-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Accepted: 10/10/2018] [Indexed: 11/09/2022] Open
Abstract
Berberine, berberrubine, thalifendine, demethyleneberberine, jatrorrhizine, and columbamine are six natural protoberberine alkaloid (PA) compounds that display extensive pharmacological properties and share the same protoberberine molecular skeleton with only slight substitution differences. The oral delivery of most PAs is hindered by their poor bioavailability, which is largely caused by P-glycoprotein (P-gp)-mediated drug efflux. Meanwhile, P-gp undergoes large-scale conformational changes (from an inward-facing to an outward-facing state) when transporting substrates, and these changes might strongly affect the P-gp-binding specificity. To confirm whether these six compounds are substrates of P-gp, to investigate the differences in efflux capacity caused by their trivial structural differences and to reveal the key to increasing their binding affinity to P-gp, we conducted a series of in vivo, in vitro, and in silico assays. Here, we first confirmed that all six compounds were substrates of P-gp by comparing the drug concentrations in wild-type and P-gp-knockout mice in vivo. The efflux capacity (net efflux) ranked as berberrubine > berberine > columbamine ~ jatrorrhizine > thalifendine > demethyleneberberine based on in vitro transport studies in Caco-2 monolayers. Using molecular dynamics simulation and molecular docking techniques, we determined the transport pathways of the six compounds and their binding affinities to P-gp. The results suggested that at the early binding stage, different hydrophobic and electrostatic interactions collectively differentiate the binding affinities of the compounds to P-gp, whereas electrostatic interactions are the main determinant at the late release stage. In addition to hydrophobic interactions, hydrogen bonds play an important role in discriminating the binding affinities.
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24
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Allosteric Role of Substrate Occupancy Toward the Alignment of P-glycoprotein Nucleotide Binding Domains. Sci Rep 2018; 8:14643. [PMID: 30279588 PMCID: PMC6168518 DOI: 10.1038/s41598-018-32815-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 09/15/2018] [Indexed: 01/16/2023] Open
Abstract
P-glycoprotein (Pgp) is an ATP-binding cassette transporter that eliminates toxins from the cell but causes multidrug resistance in chemotherapies. The crystal structures of Pgp revealed drug-like compounds bound to an inward-facing conformation in which the energy-harnessing nucleotide binding domains (NBDs) were widely separated with no interfacial interaction. Following drug binding, inward-facing Pgp must transition to an NBD dimer conformation to achieve ATP binding and hydrolysis at canonical sites defined by both halves of the interface. However, given the high degree of flexibility shown for this transporter, it is difficult to envision how NBDs overcome entropic considerations for achieving proper alignment in order to form the canonical ATP binding site. We explored the hypothesis that substrate occupancy of the polyspecific drug-binding cavity plays a role in the proper alignment of NBDs using computational approaches. We conducted twelve atomistic molecular dynamics (MD) simulations (100-300 ns) on inward-facing Pgp in a lipid bilayer with and without small molecule substrates to ascertain effects of drug occupancy on NBD dimerization. Both apo- and drug-occupied simulations showed NBDs approaching each other compared to the crystal structures. Apo-Pgp reached a pseudo-dimerization in which NBD signature motifs for ATP binding exhibited a significant misalignment during closure. In contrast, occupancy of three established substrates positioned by molecular docking achieved NBD alignment that was much more compatible with a canonical NBD dimerization trajectory. Additionally, aromatic amino acids, known to confer the polyspecific drug-binding characteristic of the internal pocket, may also govern polyspecific drug access to the cavity. The enrichment of aromatics comprising the TM4-TM6 portal suggested a preferential pathway over the aromatic-poor TM10-TM12 for lateral drug entry from the lipid bilayer. Our study also suggested that drug polyspecificity is enhanced due to a synergism between multiple drug-domain interactions involving 36 residues identified in TM1, 5, 6, 7, 11 and 12.
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Zhang Y, Gong W, Wang Y, Liu Y, Li C. Exploring movement and energy in human P-glycoprotein conformational rearrangement. J Biomol Struct Dyn 2018; 37:1104-1119. [PMID: 29620438 DOI: 10.1080/07391102.2018.1461133] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Human P-glycoprotein (P-gp), a kind of ATP-Binding Cassette transporter, can export a diverse variety of anti-cancer drugs out of the tumor cell. Its overexpression is one of the main reasons for the multidrug resistance (MDR) of tumor cells. It has been confirmed that during the substrate transport process, P-gp experiences a large-scale structural rearrangement from the inward- to outward-facing states. However, the mechanism of how the nucleotide-binding domains (NBDs) control the transmembrane domains (TMDs) to open towards the periplasm in the outward-facing state has not yet been fully characterized. Herein, targeted molecular dynamics simulations were performed to explore the conformational rearrangement of human P-gp. The results show that the allosteric process proceeds in a coupled way, and first the transition is driven by the NBDs, and then transmitted to the cytoplasmic parts of TMDs, finally to the periplasmic parts. The trajectories show that besides the translational motions, the NBDs undergo a rotation movement, which mainly occurs in xy plane and ensures the formation of the correct ATP-binding pockets. The analyses on the interaction energies between the six structure segments (cICLs) from the TMDs and NBDs reveal that their subtle energy differences play an important role in causing the periplasmic parts of the transmembrane helices to separate from each other in the established directions and in appropriate amplitudes. This conclusion can explain the two experimental phenomena about human P-gp in some extent. These studies have provided a detailed exploration into human P-gp rearrangement process and given an energy insight into the TMD reorientation during P-gp transition.
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Affiliation(s)
- Yue Zhang
- a College of Life Science and Bioengineering , Beijing University of Technology , Beijing , 100124 , China
| | - Weikang Gong
- a College of Life Science and Bioengineering , Beijing University of Technology , Beijing , 100124 , China
| | - Yan Wang
- b Key Laboratory of Molecular Biophysics of the Ministry of Education, School of Life Science and Technology , Huazhong University of Science and Technology , Wuhan , Hubei , 430074 , China
| | - Yang Liu
- a College of Life Science and Bioengineering , Beijing University of Technology , Beijing , 100124 , China
| | - Chunhua Li
- a College of Life Science and Bioengineering , Beijing University of Technology , Beijing , 100124 , China
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Szöllősi D, Szakács G, Chiba P, Stockner T. Dissecting the Forces that Dominate Dimerization of the Nucleotide Binding Domains of ABCB1. Biophys J 2018; 114:331-342. [PMID: 29401431 PMCID: PMC5984967 DOI: 10.1016/j.bpj.2017.11.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 10/11/2017] [Accepted: 11/14/2017] [Indexed: 01/10/2023] Open
Abstract
P-glycoprotein, also known as multidrug resistance protein 1 or ABCB1, can export a wide range of chemically unrelated compounds, including chemotherapeutic drugs. ABCB1 consists of two transmembrane domains that form the substrate binding and translocation domain, and of two cytoplasmic nucleotide binding domains (NBDs) that energize substrate transport by ATP binding and hydrolysis. ATP binding triggers dimerization of the NBDs, which switches the transporter from an inward facing to an outward facing transmembrane domain conformation. We performed MD simulations to study the dynamic behavior of the NBD dimer in the presence or absence of nucleotides. In the apo configuration, the NBDs were overall attractive to each other as shown in the potential of mean force profile, but the energy well was shallow and broad. In contrast, a sharp and deep energy minimum (∼-42 kJ/mol) was found in the presence of ATP, leading to a well-defined conformation. Motif interaction network analyses revealed that ATP stabilizes the NBD dimer by serving as the central hub for interdomain connections. Simulations showed that forces promoting dimerization are multilayered, dominated by electrostatic interactions between the nucleotide and conserved amino acids of the signature sequence and the Walker A motif. In addition, direct and water-bridged hydrogen bonds between NBDs provided conformation-defining interactions. Importantly, we characterized a largely unrecognized but essential contribution from hydrophobic interactions between the adenine moiety of the nucleotides and a hydrophobic surface of the X-loop to the stabilization of the nucleotide-bound NBD dimer. These hydrophobic interactions lead to a sharp energy minimum, thereby conformationally restricting the nucleotide-bound state.
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Affiliation(s)
- Dániel Szöllősi
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria
| | - Gergely Szakács
- Institute of Cancer Research, Medical University of Vienna, Vienna, Austria
| | - Peter Chiba
- Institute of Medical Chemistry, Center for Pathobiochemistry and Genetics, Medical University of Vienna, Vienna, Austria
| | - Thomas Stockner
- Institute of Pharmacology, Center for Physiology and Pharmacology, Medical University of Vienna, Vienna, Austria.
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Targeted inhibitors of P-glycoprotein increase chemotherapeutic-induced mortality of multidrug resistant tumor cells. Sci Rep 2018; 8:967. [PMID: 29343829 PMCID: PMC5772368 DOI: 10.1038/s41598-018-19325-x] [Citation(s) in RCA: 161] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Accepted: 12/27/2017] [Indexed: 12/17/2022] Open
Abstract
Overexpression of ATP-binding cassette (ABC) transporters is often linked to multidrug resistance (MDR) in cancer chemotherapies. P-glycoprotein (P-gp) is one of the best studied drug transporters associated with MDR. There are currently no approved drugs available for clinical use in cancer chemotherapies to reverse MDR by inhibiting P-glycoprotein. Using computational studies, we previously identified several compounds that inhibit P-gp by targeting its nucleotide binding domain and avoiding its drug binding domains. Several of these compounds showed successful MDR reversal when tested on a drug resistant prostate cancer cell line. Using conventional two-dimensional cell culture of MDR ovarian and prostate cancer cells and three dimensional prostate cancer microtumor spheroids, we demonstrated here that co-administration with chemotherapeutics significantly decreased cell viability and survival as well as cell motility. The P-gp inhibitors were not observed to be toxic on their own. The inhibitors increased cellular retention of chemotherapeutics and reporter compounds known to be transport substrates of P-gp. We also showed that these compounds are not transport substrates of P-gp and that two of the three inhibit P-gp, but not the closely related ABC transporter, ABCG2/BCRP. The results presented suggest that these P-gp inhibitors may be promising leads for future drug development.
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Ramos P, Schmitz M, Gama S, Portantiolo A, Durruthy MG, de Souza Votto AP, Cornetet LR, dos Santos Machado K, Werhli A, Tonel MZ, Fagan SB, Yunes JS, Monserrat JM. Cytoprotection of lipoic acid against toxicity induced by saxitoxin in hippocampal cell line HT-22 through in silico modeling and in vitro assays. Toxicology 2018; 393:171-184. [DOI: 10.1016/j.tox.2017.11.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 10/17/2017] [Accepted: 11/02/2017] [Indexed: 10/18/2022]
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29
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Szöllősi D, Rose-Sperling D, Hellmich UA, Stockner T. Comparison of mechanistic transport cycle models of ABC exporters. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1860:818-832. [PMID: 29097275 PMCID: PMC7610611 DOI: 10.1016/j.bbamem.2017.10.028] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 10/23/2017] [Accepted: 10/25/2017] [Indexed: 12/25/2022]
Abstract
ABC (ATP binding cassette) transporters, ubiquitous in all kingdoms of life, carry out essential substrate transport reactions across cell membranes. Their transmembrane domains bind and translocate substrates and are connected to a pair of nucleotide binding domains, which bind and hydrolyze ATP to energize import or export of substrates. Over four decades of investigations into ABC transporters have revealed numerous details from atomic-level structural insights to their functional and physiological roles. Despite all these advances, a comprehensive understanding of the mechanistic principles of ABC transporter function remains elusive. The human multidrug resistance transporter ABCB1, also referred to as P-glycoprotein (P-gp), is one of the most intensively studied ABC exporters. Using ABCB1 as the reference point, we aim to compare the dominating mechanistic models of substrate transport and ATP hydrolysis for ABC exporters and to highlight the experimental and computational evidence in their support. In particular, we point out in silico studies that enhance and complement available biochemical data. “This article is part of a Special Issue entitled: Beyond the Structure Function Horizon of Membrane Proteins edited by Ute Hellmich, Rupak Doshi and Benjamin McIlwain.”
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Affiliation(s)
- Dániel Szöllősi
- Medical University of Vienna, Institute of Pharmacology, Waehringerstr. 13A, Vienna 1090, Austria
| | - Dania Rose-Sperling
- Johannes Gutenberg-University, Department of Pharmacy and Biochemistry, Johann-Joachim-Becher-Weg 30, Mainz 55128, Germany; Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max von Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Ute A Hellmich
- Johannes Gutenberg-University, Department of Pharmacy and Biochemistry, Johann-Joachim-Becher-Weg 30, Mainz 55128, Germany; Centre for Biomolecular Magnetic Resonance (BMRZ), Goethe-University Frankfurt, Max von Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Thomas Stockner
- Medical University of Vienna, Institute of Pharmacology, Waehringerstr. 13A, Vienna 1090, Austria.
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30
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Loo TW, Clarke DM. A short cross-linker activates human P-glycoprotein missing a catalytic carboxylate. Biochem Pharmacol 2017; 145:27-33. [PMID: 28837794 DOI: 10.1016/j.bcp.2017.08.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 08/18/2017] [Indexed: 11/17/2022]
Abstract
P-glycoprotein (P-gp) is an ATP-dependent drug pump that protects us from toxic agents and confers multidrug resistance. It has a tweezer-like structure with each arm consisting of a transmembrane domain (TMD) and a nucleotide-binding domain (NBD). Drug substrates bind to sites within the TMDs to activate ATPase activity by promoting a tweezer-like closing of the gap between the NBDs. The catalytic carboxylates may be critical for NBD movements because the E556Q(NBD1) or E1201Q(NBD2) mutation inhibited drug-stimulated ATPase activity. If the catalytic carboxylates were components of the mechanism to bring the NBDs together, then we predicted that insertion of a flexible cross-linker between the arms would increase ATPase activity of the mutants. We found that cross-linking (between L175C(TMD1) and N820C(TMD2)) with a short flexible cross-linker (7.8Å maximum) restored high levels of drug-stimulated ATPase activity of the E556Q or E1201Q mutants. Cross-linking with a longer cross-linker (22Å maximum) however, did not restore activity. Cross-linking could not rescue all ATPase deficient mutants. For example, cross-linking L175C/N820C with short or long cross-linkers did not activate the H-loop mutants H587A or H1232A or the Walker A K433M or K1076M mutants. The results suggest that the E556 and E1201 catalytic carboxylates are part of a spring-like mechanism that is required to facilitate movements between the open and closed conformations of P-gp during ATP hydrolysis.
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Affiliation(s)
- Tip W Loo
- Department of Medicine and Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - David M Clarke
- Department of Medicine and Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
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31
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Ferreira RJ, Bonito CA, Ferreira MJU, dos Santos DJ. About P-glycoprotein: a new drugable domain is emerging from structural data. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1316] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Ricardo J. Ferreira
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy; Universidade de Lisboa; Lisboa Portugal
| | - Cátia A. Bonito
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy; Universidade de Lisboa; Lisboa Portugal
- LAQV@REQUIMTE/Department of Chemistry and Biochemistry, Faculty of Sciences; University of Porto; Porto Portugal
| | - Maria José U. Ferreira
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy; Universidade de Lisboa; Lisboa Portugal
| | - Daniel J.V.A. dos Santos
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy; Universidade de Lisboa; Lisboa Portugal
- LAQV@REQUIMTE/Department of Chemistry and Biochemistry, Faculty of Sciences; University of Porto; Porto Portugal
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32
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Computational modelling of efflux pumps and their inhibitors. Essays Biochem 2017; 61:141-156. [PMID: 28258237 DOI: 10.1042/ebc20160065] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 12/13/2016] [Accepted: 12/19/2016] [Indexed: 11/17/2022]
Abstract
Antimicrobial resistance is based on the multifarious strategies that bacteria adopt to face antibiotic therapies, making it a key public health concern of our era. Among these strategies, efflux pumps (EPs) contribute significantly to increase the levels and profiles of resistance by expelling a broad range of unrelated compounds - buying time for the organisms to develop specific resistance. In Gram-negative bacteria, many of these chromosomally encoded transporters form multicomponent 'pumps' that span both inner and outer membranes and are driven energetically by a primary or secondary transporter component.One of the strategies to reinvigorate the efficacy of antimicrobials is by joint administration with EP inhibitors (EPI), which either block the substrate binding and/or hinder any of the transport-dependent steps of the pump. In this review, we provide an overview of multidrug-resistance EPs, their inhibition strategies and the relevant findings from the various computational simulation studies reported to date with respect to deciphering the mechanism of action of inhibitors with the purpose of improving their rational design.
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Prachayasittikul V, Worachartcheewan A, Toropova AP, Toropov AA, Schaduangrat N, Prachayasittikul V, Nantasenamat C. Large-scale classification of P-glycoprotein inhibitors using SMILES-based descriptors. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2017; 28:1-16. [PMID: 28056566 DOI: 10.1080/1062936x.2016.1264468] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 11/21/2016] [Indexed: 06/06/2023]
Abstract
P-glycoprotein (Pgp) inhibition has been considered as an effective strategy towards combating multidrug-resistant cancers. Owing to the substrate promiscuity of Pgp, the classification of its interacting ligands is not an easy task and is an ongoing issue of debate. Chemical structures can be represented by the simplified molecular input line entry system (SMILES) in the form of linear string of symbols. In this study, the SMILES notations of 2254 Pgp inhibitors including 1341 active, and 913 inactive compounds were used for the construction of a SMILE-based classification model using CORrelation And Logic (CORAL) software. The model provided an acceptable predictive performance as observed from statistical parameters consisting of accuracy, sensitivity and specificity that afforded values greater than 70% and MCC value greater than 0.6 for training, calibration and validation sets. In addition, the CORAL method highlighted chemical features that may contribute to increased and decreased Pgp inhibitory activities. This study highlights the potential of CORAL software for rapid screening of prospective compounds from a large chemical space and provides information that could aid in the design and development of potential Pgp inhibitors.
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Affiliation(s)
- V Prachayasittikul
- a Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology , Mahidol University , Bangkok , Thailand
| | - A Worachartcheewan
- a Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology , Mahidol University , Bangkok , Thailand
- b Department of Community Medical Technology, Faculty of Medical Technology , Mahidol University , Bangkok , Thailand
- c Department of Clinical Chemistry, Faculty of Medical Technology , Mahidol University , Bangkok , Thailand
| | - A P Toropova
- d IRCCS , Istituto di Ricerche Farmacologiche Mario Negri , Milano , Italy
| | - A A Toropov
- d IRCCS , Istituto di Ricerche Farmacologiche Mario Negri , Milano , Italy
| | - N Schaduangrat
- a Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology , Mahidol University , Bangkok , Thailand
| | - V Prachayasittikul
- e Department of Clinical Microbiology and Applied Technology, Faculty of Medical Technology , Mahidol University , Bangkok , Thailand
| | - C Nantasenamat
- a Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology , Mahidol University , Bangkok , Thailand
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Loo TW, Clarke DM. Attachment of a 'molecular spring' restores drug-stimulated ATPase activity to P-glycoprotein lacking both Q loop glutamines. Biochem Biophys Res Commun 2016; 483:366-370. [PMID: 28025146 DOI: 10.1016/j.bbrc.2016.12.137] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 12/21/2016] [Indexed: 01/28/2023]
Abstract
P-glycoprotein (P-gp) is an ABC (ATP-Binding Cassette) drug pump that is clinically important because it confers multidrug resistance. Drugs bind at the interface between the transmembrane domains to activate ATPase activity at the two nucleotide-binding domains (NBDs). Drug transport involves ATP-dependent conformational changes between inward- (open, NBDs far apart) and outward-facing (closed, NBDs close together) conformations. Recently, it was reported that the conserved glutamines residues (Gln475 in NBD1 and Gln1118 in NBD2) in the Q loops of P-gp when mutated to alanine completely inhibited the drug-stimulated ATPase activity. It is unknown why the glutamine residues (Gln475 and Gln1118) in the Q loops of the NBDs of P-gp are required for drug-stimulated ATPase activity. Here we show that introduction of these mutations into the L175C/N820C mutant (L175C/N820C/Q475A/Q1118A) also abolished drug-stimulated ATPase activity. The ATPase activity was restored however, when the L175C/N820C/Q475A/Q1118A mutant was cross-linked with a flexible disulfide cross-linker. These results suggest that both Q-loop glutamines are not required for ATP hydrolysis and they might function as part of a spring-like mechanism in facilitating the open (inactive) to closed (active) conformational change during ATP hydrolysis. The molecular spring-like action of the Q-loop glutamines during drug-stimulated ATPase activity is likely mimicked by the attachment of the flexible cross-linker.
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Affiliation(s)
- Tip W Loo
- Department of Medicine and Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - David M Clarke
- Department of Medicine and Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.
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Furuta T, Sato Y, Sakurai M. Structural Dynamics of the Heterodimeric ABC Transporter TM287/288 Induced by ATP and Substrate Binding. Biochemistry 2016; 55:6730-6738. [PMID: 27933796 DOI: 10.1021/acs.biochem.6b00947] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
TM287/288 is a heterodimeric ATP-binding cassette (ABC) transporter, which harnesses the energy of ATP binding and hydrolysis at the nucleotide-binding domains (NBDs) to transport a wide variety of molecules through the transmembrane domains (TMDs) by alternating inward- and outward-facing conformations. Here, we conducted multiple 100 ns molecular dynamics simulations of TM287/288 in different ATP- and substrate-bound states to elucidate the effects of ATP and substrate binding. As a result, the binding of two ATP molecules to the NBDs induced the formation of the consensus ATP-binding pocket (ABP2) or the NBD dimerization, whereas these processes did not occur in the presence of a single ATP molecule or when the protein was in its apo state. Moreover, binding of the substrate to the TMDs enhanced the formation of ABP2 through allosteric TMD-NBD communication. Furthermore, in the apo state, α-helical subdomains of the NBDs approached each other, acquiring a conformation with core half-pockets exposed to the solvent, appropriate for ATP binding. We propose a "core-exposed" model for this novel conformation found in the apo state of ABC transporters. These findings provide important insights into the structural dynamics of ABC transporters.
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Affiliation(s)
- Tadaomi Furuta
- Center for Biological Resources and Informatics, Tokyo Institute of Technology , B-62 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Yukiko Sato
- Center for Biological Resources and Informatics, Tokyo Institute of Technology , B-62 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Minoru Sakurai
- Center for Biological Resources and Informatics, Tokyo Institute of Technology , B-62 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
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36
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Abstract
P-glycoprotein (P-gp) is an ATP-binding cassette transporter that exports a huge range of compounds out of cells and is thus one of the key proteins in conferring multi-drug resistance in cancer. Understanding how it achieves such a broad specificity and the series of conformational changes that allow export to occur form major, on-going, research objectives around the world. Much of our knowledge to date has been derived from mutagenesis and assay data. However, in recent years, there has also been great progress in structural biology and although the structure of human P-gp has not yet been solved, there are now a handful of related structures on which homology models can be built to aid in the interpretation of the vast amount of experimental data that currently exists. Many models for P-gp have been built with this aim, but the situation is complicated by the apparent flexibility of the system and by the fact that although many potential templates exist, there is large variation in the conformational state in which they have been crystallized. In this review, we summarize how homology modelling has been used in the past, how models are typically selected and finally illustrate how MD simulations can be used as a means to give more confidence about models that have been generated via this approach.
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Loo TW, Clarke DM. Drugs Modulate Interactions between the First Nucleotide-Binding Domain and the Fourth Cytoplasmic Loop of Human P-Glycoprotein. Biochemistry 2016; 55:2817-20. [DOI: 10.1021/acs.biochem.6b00233] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tip W. Loo
- Departments
of Medicine and
Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - David M. Clarke
- Departments
of Medicine and
Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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38
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Ferreira RJ, Ferreira MJU, dos Santos DJVA. Do adsorbed drugs onto P-glycoprotein influence its efflux capability? Phys Chem Chem Phys 2015; 17:22023-34. [PMID: 26235302 DOI: 10.1039/c5cp03216d] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The membrane biophysical aspects by which multidrug resistance (MDR) relate to the ABC transporter function still remain largely unknown. Notwithstanding the central role that efflux pumps like P-glycoprotein have in MDR onset, experimental studies classified additionally the lipid micro-environment where P-gp is inserted as a determinant for the increased efflux capability demonstrated in MDR cell lines. Recently, a nonlinear model for drug-membrane interactions showed that, upon drug adsorption, long-range mechanical alterations are predicted to affect the P-gp ATPase function at external drug concentrations of ∼10-100 μM. However, our results also show that drug adsorption may also occur at P-gp nucleotide-binding domains where conformational changes drive the efflux cycle. Thus, we assessed the effect of drug adsorption to both protein-water and lipid-water interfaces by means of molecular dynamics simulations. The results show that free energies of adsorption are lower for modulators in both lipid/water and protein/water interfaces. Important differences in drug-protein interactions, protein dynamics and membrane biophysical characteristics were observed between the different classes. Therefore, we hypothesize that drug adsorption to the protein and lipid-water interface accounts for a complex network of events that affect the ability of transporters to efflux drugs.
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Affiliation(s)
- Ricardo J Ferreira
- Research Institute for Medicines (iMed.Ulisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, Lisboa, Portugal.
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Xie XL, Li CH, Yang YX, Jin L, Tan JJ, Zhang XY, Su JG, Wang CX. Allosteric transitions of ATP-binding cassette transporter MsbA studied by the adaptive anisotropic network model. Proteins 2015; 83:1643-53. [DOI: 10.1002/prot.24850] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Revised: 06/02/2015] [Accepted: 06/24/2015] [Indexed: 01/04/2023]
Affiliation(s)
- Xiao Lu Xie
- College of Life Science and Bioengineering, Beijing University of Technology; Beijing 100124 China
| | - Chun Hua Li
- College of Life Science and Bioengineering, Beijing University of Technology; Beijing 100124 China
| | - Yong Xiao Yang
- College of Life Science and Bioengineering, Beijing University of Technology; Beijing 100124 China
| | - Lu Jin
- College of Life Science and Bioengineering, Beijing University of Technology; Beijing 100124 China
| | - Jian Jun Tan
- College of Life Science and Bioengineering, Beijing University of Technology; Beijing 100124 China
| | - Xiao Yi Zhang
- College of Life Science and Bioengineering, Beijing University of Technology; Beijing 100124 China
| | - Ji Guo Su
- College of Science, Yanshan University; Qinhuangdao 066004 China
| | - Cun Xin Wang
- College of Life Science and Bioengineering, Beijing University of Technology; Beijing 100124 China
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McCormick JW, Vogel PD, Wise JG. Multiple Drug Transport Pathways through Human P-Glycoprotein. Biochemistry 2015; 54:4374-90. [PMID: 26125482 DOI: 10.1021/acs.biochem.5b00018] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
P-Glycoprotein (P-gp) is a plasma membrane efflux pump that is commonly associated with therapy resistances in cancers and infectious diseases. P-gp can lower the intracellular concentrations of many drugs to subtherapeutic levels by translocating them out of the cell. Because of the broad range of substrates transported by P-gp, overexpression of P-gp causes multidrug resistance. We reported previously on dynamic transitions of P-gp as it moved through conformations based on crystal structures of homologous ABCB1 proteins using in silico targeted molecular dynamics techniques. We expanded these studies here by docking transport substrates to drug binding sites of P-gp in conformations open to the cytoplasm, followed by cycling the pump through conformations that opened to the extracellular space. We observed reproducible transport of two substrates, daunorubicin and verapamil, by an average of 11-12 Å through the plane of the membrane as P-gp progressed through a catalytic cycle. Methylpyrophosphate, a ligand that should not be transported by P-gp, did not show this movement through P-gp. Drug binding to either of two subsites on P-gp appeared to determine the initial pathway used for drug movement through the membrane. The specific side-chain interactions with drugs within each pathway seemed to be, at least in part, stochastic. The docking and transport properties of a P-gp inhibitor, tariquidar, were also studied. A mechanism of inhibition by tariquidar that involves stabilization of an outward open conformation with tariquidar bound in intracellular loops or at the drug binding domain of P-gp is presented.
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Affiliation(s)
- James W McCormick
- Center for Drug Discovery, Design and Delivery, Center for Scientific Computing, and Department of Biological Sciences, Southern Methodist University, Dallas, Texas 75275-0376, United States
| | - Pia D Vogel
- Center for Drug Discovery, Design and Delivery, Center for Scientific Computing, and Department of Biological Sciences, Southern Methodist University, Dallas, Texas 75275-0376, United States
| | - John G Wise
- Center for Drug Discovery, Design and Delivery, Center for Scientific Computing, and Department of Biological Sciences, Southern Methodist University, Dallas, Texas 75275-0376, United States
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41
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Zeino M, Brenk R, Gruber L, Zehl M, Urban E, Kopp B, Efferth T. Cytotoxicity of cardiotonic steroids in sensitive and multidrug-resistant leukemia cells and the link with Na(+)/K(+)-ATPase. J Steroid Biochem Mol Biol 2015; 150:97-111. [PMID: 25797029 DOI: 10.1016/j.jsbmb.2015.03.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 03/04/2015] [Accepted: 03/17/2015] [Indexed: 12/12/2022]
Abstract
Cardiotonic steroids have long been in clinical use for treatment of heart failure and are now emerging as promising agents in various diseases, especially cancer. Their main target is Na(+)/K(+)-ATPase, a membrane protein involved in cellular ion homeostasis. Na(+)/K(+)-ATPase has been implicated in cancer biology by affecting several cellular events and signaling pathways in both sensitive and drug-resistant cancer cells. Hence, we investigated the cytotoxic activities of 66 cardiotonic steroids and cardiotonic steroid derivatives in sensitive CCRF-CEM and multidrug-resistant CEM/ADR5000 leukemia cells. Data were then subjected to quantitative structure-activity relationship analysis (QSAR) and molecular docking into Na(+)/K(+)-ATPase, which both indicated a possible differential expression of the pump in the mentioned cell lines. This finding was confirmed by western blotting, intracellular potassium labeling and next generation sequencing which showed that Na(+)/K(+)-ATPase was less expressed in multidrug-resistant than in sensitive cells.
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Affiliation(s)
- Maen Zeino
- Department of Pharmaceutical Biology, Institute of Pharmacy and Biochemistry, Johannes Gutenberg University, Mainz, Germany
| | - Ruth Brenk
- Department of Pharmaceutical/Medicinal Chemistry, Institute of Pharmacy and Biochemistry, Johannes Gutenberg University, Mainz, Germany
| | - Lisa Gruber
- Department of Pharmaceutical Biology, Institute of Pharmacy and Biochemistry, Johannes Gutenberg University, Mainz, Germany
| | - Martin Zehl
- Department of Pharmacognosy, University of Vienna, Althanstraße 14, 1090 Vienna, Austria; Department of Pharmaceutical Chemistry, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Ernst Urban
- Department of Pharmaceutical Chemistry, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Brigitte Kopp
- Department of Pharmacognosy, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Thomas Efferth
- Department of Pharmaceutical Biology, Institute of Pharmacy and Biochemistry, Johannes Gutenberg University, Mainz, Germany.
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42
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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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43
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Loo TW, Clarke DM. The Transmission Interfaces Contribute Asymmetrically to the Assembly and Activity of Human P-glycoprotein. J Biol Chem 2015; 290:16954-63. [PMID: 25987565 PMCID: PMC4505440 DOI: 10.1074/jbc.m115.652602] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Indexed: 11/21/2022] Open
Abstract
P-glycoprotein (P-gp; ABCB1) is an ABC drug pump that protects us from toxic compounds. It is clinically important because it confers multidrug resistance. The homologous halves of P-gp each contain a transmembrane (TM) domain (TMD) with 6 TM segments followed by a nucleotide-binding domain (NBD). The drug- and ATP-binding sites reside at the interface between the TMDs and NBDs, respectively. Each NBD is connected to the TMDs by a transmission interface involving a pair of intracellular loops (ICLs) that form ball-and-socket joints. P-gp is different from CFTR (ABCC7) in that deleting NBD2 causes misprocessing of only P-gp. Therefore, NBD2 might be critical for stabilizing ICLs 2 and 3 that form a tetrahelix bundle at the NBD2 interface. Here we report that the NBD1 and NBD2 transmission interfaces in P-gp are asymmetric. Point mutations to 25 of 60 ICL2/ICL3 residues at the NBD2 transmission interface severely reduced P-gp assembly while changes to the equivalent residues in ICL1/ICL4 at the NBD1 interface had little effect. The hydrophobic nature at the transmission interfaces was also different. Mutation of Phe-1086 or Tyr-1087 to arginine at the NBD2 socket blocked activity or assembly while the equivalent mutations at the NBD1 socket had only modest effects. The results suggest that the NBD transmission interfaces are asymmetric. In contrast to the ICL2/3-NBD2 interface, the ICL1/4-NBD1 transmission interface is more hydrophilic and insensitive to mutations. Therefore the ICL2/3-NBD2 transmission interface forms a precise hydrophobic connection that acts as a linchpin for assembly and trafficking of P-gp.
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Affiliation(s)
- Tip W Loo
- From the Departments of Medicine and Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - David M Clarke
- From the Departments of Medicine and Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada
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44
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Li J, Wen PC, Moradi M, Tajkhorshid E. Computational characterization of structural dynamics underlying function in active membrane transporters. Curr Opin Struct Biol 2015; 31:96-105. [PMID: 25913536 PMCID: PMC4476910 DOI: 10.1016/j.sbi.2015.04.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Revised: 04/06/2015] [Accepted: 04/07/2015] [Indexed: 11/21/2022]
Abstract
Active transport of materials across the cellular membrane is one the most fundamental processes in biology. In order to accomplish this task, membrane transporters rely on a wide range of conformational changes spanning multiple time and size scales. These molecular events govern key functional aspects in membrane transporters, namely, coordinated gating motions underlying the alternating access mode of operation, and coupling of uphill transport of substrate to various sources of energy, for example, transmembrane electrochemical gradients and ATP binding and hydrolysis. Computational techniques such as molecular dynamics simulations and free energy calculations have equipped us with a powerful repertoire of biophysical tools offering unparalleled spatial and temporal resolutions that can effectively complement experimental methodologies, and therefore help fill the gap of knowledge in understanding the molecular basis of function in membrane transporters.
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Affiliation(s)
- Jing Li
- Department of Biochemistry, Center for Biophysics and Computational Biology, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Po-Chao Wen
- Department of Biochemistry, Center for Biophysics and Computational Biology, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Mahmoud Moradi
- Department of Biochemistry, Center for Biophysics and Computational Biology, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States
| | - Emad Tajkhorshid
- Department of Biochemistry, Center for Biophysics and Computational Biology, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, United States.
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45
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Jagodinsky JC, Akgun U. Characterizing the binding interactions between P-glycoprotein and eight known cardiovascular transport substrates. Pharmacol Res Perspect 2015; 3:e00114. [PMID: 25729581 PMCID: PMC4324688 DOI: 10.1002/prp2.114] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2014] [Revised: 10/21/2014] [Accepted: 10/26/2014] [Indexed: 02/02/2023] Open
Abstract
The multidrug efflux pump P-glycoprotein (Pgp) is upregulated in cardiomyocytes following chronic ischemia from infarction and hypoxia caused by sleep apnea. This report summarizes the molecular dynamic studies performed on eight cardiovascular drugs to determine their corresponding binding sites on mouse Pgp. Selected Pgp transport ligands include: Amiodarone, Bepridil, Diltiazem, Dipyridamole, Nicardipine, Nifedipine, Propranolol, and Quinidine. Extensive molecular dynamic equilibration simulations were performed to determine drug docking interactions. Distinct binding sites were not observed, but rather a binding belt was seen with multiple residues playing a role in each studied drug's stable docking. Three key drug–protein interactions were identified: hydrogen bonding, hydrophobic packing, and the formation of a “cage” of aromatic residues around the drug. After drug stabilization, water molecules were observed to leak into the binding belt and condense around the drug. Water influx into the binding domain of Pgp may play a role in catalytic transition and drug expulsion. The cytoplasmic recruitment theory was also tested, and the drugs were observed to interact with conserved loops of residues with a strong affinity. A free energy change of astronomical value is required to recruit the drug from the cytoplasm to the binding belt within the transmembrane domain of Pgp.
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Affiliation(s)
| | - Ugur Akgun
- Department of Physics, Coe College Cedar Rapids, IOWA
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Subhani S, Jayaraman A, Jamil K. Homology modelling and molecular docking of MDR1 with chemotherapeutic agents in non-small cell lung cancer. Biomed Pharmacother 2015; 71:37-45. [PMID: 25960213 DOI: 10.1016/j.biopha.2015.02.009] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 02/09/2015] [Indexed: 10/24/2022] Open
Abstract
MDR1, a protein commonly involved in drug transport, has been linked to multi drug resistance and disease progression in cancers such as non-small cell lung cancer. Hence, targeting this protein is essential for improving drug design and preventing adverse drug-drug interactions. The aim of the study was to examine chemotherapeutic drug binding to MDR1 and the interactions therein. We have used Schrödinger suite 2014, to perform homology modelling of human MDR1 based on Mouse MDR1, followed by Induced Fit Docking with Paclitaxel, Docetaxel, Gemcitabine, Carboplatin and Cisplatin drugs. Finally, we evaluated drug binding affinities using Prime/MMGBSA and using these scores we compared the affinities of combination therapies against MDR1. Analysis of the docking results showed Paclitaxel>Docetaxel>Gemcitabine>Carboplatin>Cisplatin as the order of binding affinities, with Paclitaxel having the best docking score. The combination drug binding affinity analysis showed Paclitaxel+Gemcitabine to have the best docking score and hence, efficacy. Through our investigation we have identified the residues Gln 195 and Gln 946 to be more frequently involved in drug binding interactions with MDR1. Our results suggest that, Paclitaxel or combination of Paclitaxel+Gemcitabine could serve as a suitable therapy against MDR1 in NSCLC patients. Thus, our study provides new insight into the possible repurposing of chemotherapeutic drugs in targeting elevated MDR1 levels in NSCLC patients, thereby ensuring better overall outcome. Further our study highlights the use of in silico methodologies in understanding drug binding to protein targets and its relevance to advancing lung cancer therapy.
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Affiliation(s)
- Syed Subhani
- Genetics Department, Bhagwan Mahavir Medical Research Centre, #10-1-1, Mahavir Marg, Masab Tank, Hyderabad 500004, Telangana, India.
| | - Archana Jayaraman
- Centre for Biotechnology and Bioinformatics, School of Life Sciences, Jawaharlal Nehru Institute of Advanced Studies (JNIAS), 6th Floor, Buddha Bhawan, M.G. Road, Secunderabad 500003, Telangana, India.
| | - Kaiser Jamil
- Genetics Department, Bhagwan Mahavir Medical Research Centre, #10-1-1, Mahavir Marg, Masab Tank, Hyderabad 500004, Telangana, India; Centre for Biotechnology and Bioinformatics, School of Life Sciences, Jawaharlal Nehru Institute of Advanced Studies (JNIAS), 6th Floor, Buddha Bhawan, M.G. Road, Secunderabad 500003, Telangana, India.
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47
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Equilibrated atomic models of outward-facing P-glycoprotein and effect of ATP binding on structural dynamics. Sci Rep 2015; 5:7880. [PMID: 25600711 PMCID: PMC4389535 DOI: 10.1038/srep07880] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 12/16/2014] [Indexed: 12/14/2022] Open
Abstract
P-glycoprotein (Pgp) is an ATP-binding cassette (ABC) transporter that alternates between inward- and outward-facing conformations to capture and force substrates out of cells like a peristaltic pump. The high degree of similarity in outward-facing structures across evolution of ABC transporters allowed construction of a high-confidence outward-facing Pgp atomic model based on crystal structures of outward-facing Sav1866 and inward-facing Pgp. The model adhered to previous experimentally determined secondary- and tertiary- configurations during all-atom molecular dynamics simulations in the presence or absence of MgATP. Three long lasting (>100 ns) meta-stable states were apparent in the presence of MgATP revealing new insights into alternating access. The two ATP-binding pockets are highly asymmetric resulting in differential control of overall structural dynamics and allosteric regulation of the drug-binding pocket. Equilibrated Pgp has a considerably different electrostatic profile compared to Sav1866 that implicates significant kinetic and thermodynamic differences in transport mechanisms.
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48
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Prajapati R, Sangamwar AT. Translocation mechanism of P-glycoprotein and conformational changes occurring at drug-binding site: Insights from multi-targeted molecular dynamics. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2014; 1838:2882-98. [DOI: 10.1016/j.bbamem.2014.07.018] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Revised: 07/03/2014] [Accepted: 07/08/2014] [Indexed: 11/29/2022]
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49
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Loo TW, Clarke DM. Tariquidar inhibits P-glycoprotein drug efflux but activates ATPase activity by blocking transition to an open conformation. Biochem Pharmacol 2014; 92:558-66. [PMID: 25456855 DOI: 10.1016/j.bcp.2014.10.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 10/06/2014] [Accepted: 10/07/2014] [Indexed: 12/21/2022]
Abstract
P-glycoprotein (P-gp, ABCB1) is a drug pump that confers multidrug resistance. Inhibition of P-gp would improve chemotherapy. Tariquidar is a potent P-gp inhibitor but its mechanism is unknown. Here, we tested our prediction that tariquidar inhibits P-gp cycling between the open and closed states during the catalytic cycle. Transition of P-gp to an open state can be monitored in intact cells using reporter cysteines introduced into extracellular loops 1 (A80C) and 4 (R741C). Residues A80C/R741C come close enough (<7Å) to spontaneously cross-link in the open conformation (<7Å) but are widely separated (>30Å) in the closed conformation. Cross-linking of A80C/R741C can be readily detected because it causes the mutant protein to migrate slower on SDS-PAGE gels. We tested whether drug substrates or inhibitors could inhibit cross-linking of the mutant. It was found that only tariquidar blocked A80C/R741C cross-linking. Tariquidar was also a more potent pharmacological chaperone than other P-gp substrates/modulators such as cyclosporine A. Only tariquidar promoted maturation of misprocessed mutant F804D to yield mature P-gp. Tariquidar interacted with the transmembrane domains because it could rescue a misprocessed truncation mutant lacking the nucleotide-binding domains. These results show that tariquidar is a potent pharmacological chaperone and inhibits P-gp drug efflux by blocking transition to the open state during the catalytic cycle.
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Affiliation(s)
- Tip W Loo
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Department of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - David M Clarke
- Department of Biochemistry, University of Toronto, Toronto, Ontario M5S 1A8, Canada; Department of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
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50
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Brewer FK, Follit CA, Vogel PD, Wise JG. In silico screening for inhibitors of p-glycoprotein that target the nucleotide binding domains. Mol Pharmacol 2014; 86:716-26. [PMID: 25270578 DOI: 10.1124/mol.114.095414] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Multidrug resistances and the failure of chemotherapies are often caused by the expression or overexpression of ATP-binding cassette transporter proteins such as the multidrug resistance protein, P-glycoprotein (P-gp). P-gp is expressed in the plasma membrane of many cell types and protects cells from accumulation of toxins. P-gp uses ATP hydrolysis to catalyze the transport of a broad range of mostly hydrophobic compounds across the plasma membrane and out of the cell. During cancer chemotherapy, the administration of therapeutics often selects for cells which overexpress P-gp, thereby creating populations of cancer cells resistant to a variety of chemically unrelated chemotherapeutics. The present study describes extremely high-throughput, massively parallel in silico ligand docking studies aimed at identifying reversible inhibitors of ATP hydrolysis that target the nucleotide-binding domains of P-gp. We used a structural model of human P-gp that we obtained from molecular dynamics experiments as the protein target for ligand docking. We employed a novel approach of subtractive docking experiments that identified ligands that bound predominantly to the nucleotide-binding domains but not the drug-binding domains of P-gp. Four compounds were found that inhibit ATP hydrolysis by P-gp. Using electron spin resonance spectroscopy, we showed that at least three of these compounds affected nucleotide binding to the transporter. These studies represent a successful proof of principle demonstrating the potential of targeted approaches for identifying specific inhibitors of P-gp.
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Affiliation(s)
- Frances K Brewer
- Department of Biological Sciences, the Center for Drug Discovery, Design and Delivery, and the Center for Scientific Computing, Southern Methodist University, Dallas, Texas
| | - Courtney A Follit
- Department of Biological Sciences, the Center for Drug Discovery, Design and Delivery, and the Center for Scientific Computing, Southern Methodist University, Dallas, Texas
| | - Pia D Vogel
- Department of Biological Sciences, the Center for Drug Discovery, Design and Delivery, and the Center for Scientific Computing, Southern Methodist University, Dallas, Texas
| | - John G Wise
- Department of Biological Sciences, the Center for Drug Discovery, Design and Delivery, and the Center for Scientific Computing, Southern Methodist University, Dallas, Texas
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