1
|
Gao Y, Wei C, Luo L, Tang Y, Yu Y, Li Y, Xing J, Pan X. Membrane-assisted tariquidar access and binding mechanisms of human ATP-binding cassette transporter P-glycoprotein. Front Mol Biosci 2024; 11:1364494. [PMID: 38560519 PMCID: PMC10979361 DOI: 10.3389/fmolb.2024.1364494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 02/20/2024] [Indexed: 04/04/2024] Open
Abstract
The human multidrug transporter P-glycoprotein (P-gp) is physiologically essential and of key relevance to biomedicine. Recent structural studies have shed light on the mode of inhibition of the third-generation inhibitors for human P-gp, but the molecular mechanism by which these inhibitors enter the transmembrane sites remains poorly understood. In this study, we utilized all-atom molecular dynamics (MD) simulations to characterize human P-gp dynamics under a potent inhibitor, tariquidar, bound condition, as well as the atomic-level binding pathways in an explicit membrane/water environment. Extensive unbiased simulations show that human P-gp remains relatively stable in tariquidar-free and bound states, while exhibiting a high dynamic binding mode at either the drug-binding pocket or the regulatory site. Free energy estimations by partial nudged elastic band (PNEB) simulations and Molecular Mechanics Generalized Born Surface Area (MM/GBSA) method identify two energetically favorable binding pathways originating from the cytoplasmic gate with an extended tariquidar conformation. Interestingly, free tariquidar in the lipid membrane predominantly adopts extended conformations similar to those observed at the regulatory site. These results suggest that membrane lipids may preconfigure tariquidar into an active ligand conformation for efficient binding to the regulatory site. However, due to its conformational plasticity, tariquidar ultimately moves toward the drug-binding pocket in both pathways, explaining how it acts as a substrate at low concentrations. Our molecular findings propose a membrane-assisted mechanism for the access and binding of the third-generation inhibitors to the binding sites of human P-gp, and offer deeper insights into the molecule design of more potent inhibitors against P-gp-mediated drug resistance.
Collapse
Affiliation(s)
- Yingjie Gao
- Department of Medicinal Chemistry, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
| | - Caiyan Wei
- Department of Medicinal Chemistry, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
| | - Lanxin Luo
- Department of Pathophysiology, School of Basic Medical Science, Southwest Medical University, Luzhou, Sichuan, China
| | - Yang Tang
- Department of Medicinal Chemistry, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
| | - Yongzhen Yu
- Department of Medicinal Chemistry, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
| | - Yaling Li
- Department of Pharmacy, The Affiliated Hospital, Southwest Medical University, Luzhou, Sichuan, China
| | - Juan Xing
- Department of Pathophysiology, School of Basic Medical Science, Southwest Medical University, Luzhou, Sichuan, China
| | - Xianchao Pan
- Department of Medicinal Chemistry, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China
| |
Collapse
|
2
|
Interaction of a Homologous Series of Amphiphiles with P-glycoprotein in a Membrane Environment-Contributions of Polar and Non-Polar Interactions. Pharmaceutics 2023; 15:pharmaceutics15010174. [PMID: 36678803 PMCID: PMC9862096 DOI: 10.3390/pharmaceutics15010174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/06/2022] [Accepted: 12/26/2022] [Indexed: 01/05/2023] Open
Abstract
The transport of drugs by efflux transporters in biomembranes limits their bioavailability and is a major determinant of drug resistance development by cancer cells and pathogens. A large number of chemically dissimilar drugs are transported, and despite extensive studies, the molecular determinants of substrate specificity are still not well understood. In this work, we explore the role of polar and non-polar interactions on the interaction of a homologous series of fluorescent amphiphiles with the efflux transporter P-glycoprotein. The interaction of the amphiphiles with P-glycoprotein is evaluated through effects on ATPase activity, efficiency in inhibition of [125I]-IAAP binding, and partition to the whole native membranes containing the transporter. The results were complemented with partition to model membranes with a representative lipid composition, and details on the interactions established were obtained from MD simulations. We show that when the total concentration of amphiphile is considered, the binding parameters obtained are apparent and do not reflect the affinity for P-gp. A new formalism is proposed that includes sequestration of the amphiphiles in the lipid bilayer and the possible binding of several molecules in P-gp's substrate-binding pocket. The intrinsic binding affinity thus obtained is essentially independent of amphiphile hydrophobicity, highlighting the importance of polar interactions. An increase in the lipophilicity and amphiphilicity led to a more efficient association with the lipid bilayer, which maintains the non-polar groups of the amphiphiles in the bilayer, while the polar groups interact with P-gp's binding pocket. The presence of several amphiphiles in this orientation is proposed as a mechanism for inhibition of P-pg function.
Collapse
|
3
|
Iqbal S, Flux C, Briggs DA, Deplazes E, Long J, Skrzypek R, Rothnie A, Kerr ID, Callaghan R. Vinca alkaloid binding to P-glycoprotein occurs in a processive manner. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:184005. [PMID: 35863425 DOI: 10.1016/j.bbamem.2022.184005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 07/08/2022] [Accepted: 07/12/2022] [Indexed: 06/15/2023]
Abstract
A mechanistic understanding of how P-glycoprotein (Pgp) is able to bind and transport its astonishing range of substrates remains elusive. Pharmacological data demonstrated the presence of at least four distinct binding sites, but their locations have not been fully elucidated. The combination of biochemical and structural data suggests that initial binding may occur in the central cavity or at the lipid-protein interface. Our objective was to define the binding sites for two transported substrates of Pgp; the anticancer drug vinblastine and the fluorescent probe rhodamine 123. A series of mutations was generated in positions proximal to previously defined drug-interacting residues on Pgp. The protein was purified and reconstituted into styrene-maleic acid lipid particles (SMALPs) to measure the apparent drug binding constant or into liposomes for assessment of drug-stimulated ATP hydrolysis. The biochemical data were reconciled with structural models of Pgp using molecular docking. The data indicated that the binding of rhodamine 123 occurred predominantly within the central cavity of Pgp. In contrast, the significantly more hydrophobic vinblastine bound to both the lipid-protein interface and within the central cavity. The data suggest that the initial interaction of vinca alkaloids with Pgp occurs at the lipid interface followed by internalisation into the central cavity, which also provides the transport conduit. This model is supported by recent structural observations with Pgp and early biophysical and cross-linking approaches. Moreover, the proposed model illustrates that the broad substrate profile for Pgp is underpinned by a combination of multiple initial interaction sites and an accommodating transport conduit.
Collapse
Affiliation(s)
- Shagufta Iqbal
- Division of Biomedical Science & Biochemistry, Research School of Biology, The Australian National University, Canberra, Australia
| | - Caitlin Flux
- Division of Biomedical Science & Biochemistry, Research School of Biology, The Australian National University, Canberra, Australia
| | - Deborah A Briggs
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, UK
| | - Evelyne Deplazes
- School of Chemistry and Molecular Biosciences, University of Queensland, St Lucia, Australia
| | - Jiansi Long
- Division of Biomedical Science & Biochemistry, Research School of Biology, The Australian National University, Canberra, Australia
| | - Ruth Skrzypek
- Division of Biomedical Science & Biochemistry, Research School of Biology, The Australian National University, Canberra, Australia
| | - Alice Rothnie
- Health & Life Sciences, Aston University, Aston Triangle, Birmingham, UK
| | - Ian D Kerr
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, UK
| | - Richard Callaghan
- Division of Biomedical Science & Biochemistry, Research School of Biology, The Australian National University, Canberra, Australia; School of Biomedical Sciences, Faculty of Biological Science, University of Leeds, Leeds, UK.
| |
Collapse
|
4
|
Behmard E, Barzegari E, Najafipour S, Kouhpayeh A, Ghasemi Y, Asadi-Pooya AA. Efflux dynamics of the antiseizure drug, levetiracetam, through the P-glycoprotein channel revealed by advanced comparative molecular simulations. Sci Rep 2022; 12:13674. [PMID: 35953704 PMCID: PMC9372152 DOI: 10.1038/s41598-022-17994-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 08/03/2022] [Indexed: 11/15/2022] Open
Abstract
Understanding the precise mechanistic details of the possible binding and transport of antiseizure medications (ASMs) through the P-glycoprotein (P-gp) efflux pump is essential to find strategies for the treatment of patients with epilepsy resistant to ASMs. In the present work, conventional molecular dynamics, binding free energy calculations, steered molecular dynamics and umbrella sampling were applied to study the interactions of levetiracetam and brivaracetam with P-gp and their possible egress path from the binding site. Comparative results for the control drugs, zosuquidar and verapamil, confirmed their established P-gp inhibitory activity. Brivaracetam, a non-substrate of P-gp, demonstrated stronger static and dynamic interactions with the exporter protein, than levetiracetam. The potential of mean force calculations indicated that the energy barriers through the ligand export were the lowest for levetiracetam, suggesting the drug as a P-gp substrate with facile passage through the transporter channel. Our findings also stressed the contribution of nonpolar interactions with P-gp channel lining as well as with membrane lipid molecules to hamper the ASM efflux by the transmembrane exporter. Appropriate structural engineering of the ASMs is thus recommended to address drug-resistant epilepsy.
Collapse
Affiliation(s)
- Esmaeil Behmard
- Epilepsy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran. .,School of Advanced Technologies in Medicine, Fasa University of Medical Sciences, Fasa, Iran.
| | - Ebrahim Barzegari
- Medical Biology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Sohrab Najafipour
- School of Advanced Technologies in Medicine, Fasa University of Medical Sciences, Fasa, Iran
| | - Amin Kouhpayeh
- Department of Pharmacology, Faculty of Medicine, Fasa University of Medical Sciences, Fasa, Iran
| | - Younes Ghasemi
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Ali A Asadi-Pooya
- Epilepsy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran. .,Shiraz University of Medical Sciences, Shiraz, Iran.
| |
Collapse
|
5
|
Fu T, Zheng Q, Zhang H. Investigation of the molecular and mechanistic basis for the regioselective metabolism of midazolam by cytochrome P450 3A4. Phys Chem Chem Phys 2022; 24:8104-8112. [PMID: 35319551 DOI: 10.1039/d2cp00232a] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Cytochrome P450 3A4 (CYP3A4) is the most important P450 enzyme for drug metabolism and drug-drug interaction, due to it being responsible for the biotransformation of approximately 50% of clinically used drugs. Advance knowledge of the molecular and mechanistic basis of CYP3A4 regioselective metabolism is beneficial for understanding the production of metabolites, and may allow personalized metabolic pathways or designing pathway-specific therapeutics. In this work, we focus on investigating the ligand-receptor interactions, substrate conformational transition, and key factors regulating the specificity of metabolic pathways using midazolam (MDZ) as a probe. Here, three types of substrate-binding conformations related to the diversity of MDZ metabolites are identified. The results also suggest that an allosteric site for MDZ is located near the F'-helix, A-anchor, and C-terminal loop of CYP3A4. The presence of an effector in the allosteric site can accelerate the conformational transition of the substrate via modulating a "sandwich" structure, and may affect the proportion of metabolites at high substrate concentration. We hope that the results can improve the understanding of the CYP3A4 structure and function, and provide a new perspective for drug development.
Collapse
Affiliation(s)
- Tingting Fu
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, 130023, China.
| | - Qingchuan Zheng
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, 130023, China. .,Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University, Changchun, 130023, China
| | - Hongxing Zhang
- Institute of Theoretical Chemistry, College of Chemistry, Jilin University, Changchun, 130023, China.
| |
Collapse
|
6
|
Kapoor K, Thangapandian S, Tajkhorshid E. Extended-ensemble docking to probe dynamic variation of ligand binding sites during large-scale structural changes of proteins. Chem Sci 2022; 13:4150-4169. [PMID: 35440993 PMCID: PMC8985516 DOI: 10.1039/d2sc00841f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 02/24/2022] [Indexed: 11/21/2022] Open
Abstract
Proteins can sample a broad landscape as they undergo conformational transition between different functional states. At the same time, as key players in almost all cellular processes, proteins are important drug targets. Considering the different conformational states of a protein is therefore central for a successful drug-design strategy. Here we introduce a novel docking protocol, termed extended-ensemble docking, pertaining to proteins that undergo large-scale (global) conformational changes during their function. In its application to multidrug ABC-transporter P-glycoprotein (Pgp), extensive non-equilibrium molecular dynamics simulations employing system-specific collective variables are first used to describe the transition cycle of the transporter. An extended set of conformations (extended ensemble) representing the full transition cycle between the inward- and the outward-facing states is then used to seed high-throughput docking calculations of known substrates, non-substrates, and modulators of the transporter. Large differences are predicted in the binding affinities to different conformations, with compounds showing stronger binding affinities to intermediate conformations compared to the starting crystal structure. Hierarchical clustering of the binding modes shows all ligands preferably bind to the large central cavity of the protein, formed at the apex of the transmembrane domain (TMD), whereas only small binding populations are observed in the previously described R and H sites present within the individual TMD leaflets. Based on the results, the central cavity is further divided into two major subsites, first preferably binding smaller substrates and high-affinity inhibitors, whereas the second one shows preference for larger substrates and low-affinity modulators. These central subsites along with the low-affinity interaction sites present within the individual TMD leaflets may respectively correspond to the proposed high- and low-affinity binding sites in Pgp. We propose further an optimization strategy for developing more potent inhibitors of Pgp, based on increasing its specificity to the extended ensemble of the protein, instead of using a single protein structure, as well as its selectivity for the high-affinity binding site. In contrast to earlier in silico studies using single static structures of Pgp, our results show better agreement with experimental studies, pointing to the importance of incorporating the global conformational flexibility of proteins in future drug-discovery endeavors.
Collapse
Affiliation(s)
- Karan Kapoor
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Sundar Thangapandian
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| | - Emad Tajkhorshid
- Theoretical and Computational Biophysics Group, NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, Department of Biochemistry, Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign Urbana IL 61801 USA
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Dai Y, Ma H, Wu M, Welsch TA, Vora SR, Ren D, Nangia S. Development of the computational antibiotic screening platform (CLASP) to aid in the discovery of new antibiotics. SOFT MATTER 2021; 17:2725-2736. [PMID: 33533373 DOI: 10.1039/d0sm02035d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Bacterial colonization of biotic and abiotic surfaces and antibiotic resistance are grand challenges with paramount societal impacts. However, in the face of increasing bacterial resistance to all known antibiotics, efforts to discover new classes of antibiotics have languished, creating an urgent need to accelerate the antibiotic discovery pipeline. A major deterrent in the discovering of new antibiotics is the limited permeability of molecules across the bacterial envelope. Notably, the Gram-negative bacteria have nutrient specific protein channels (or porins) that restrict the permeability of non-essential molecules, including antibiotics. Here, we have developed the Computational Antibiotic Screening Platform (CLASP) for screening of potential drug molecules through the porins. The CLASP takes advantage of coarse grain (CG) resolution, advanced sampling techniques, and a parallel computing environment to maximize its performance. The CLASP yields comprehensive thermodynamic and kinetic output data of a potential drug molecule within a few hours of wall-clock time. Its output includes the potential of mean force profile, energy barrier, the rate constant, and contact analysis of the molecule with the pore-lining residues, and the orientational analysis of the molecule in the porin channel. In our first CLASP application, we report the transport properties of six carbapenem antibiotics-biapenem, doripenem, ertapenem, imipenem, meropenem, and panipenem-through OccD3, a major channel for carbapenem uptake in Pseudomonas aeruginosa. The CLASP is designed to screen small molecule libraries with a fast turnaround time to yield structure-property relationships to discover antibiotics with high permeability. The CLASP will be freely distributed to enable accelerated antibiotic drug discovery.
Collapse
Affiliation(s)
- Yinghui Dai
- Department of Biomedical and Chemical Engineering, Syracuse University, 343 Link Hall, Syracuse, NY 13244, USA.
| | - Huilin Ma
- Department of Biomedical and Chemical Engineering, Syracuse University, 343 Link Hall, Syracuse, NY 13244, USA.
| | - Meishan Wu
- Department of Biomedical and Chemical Engineering, Syracuse University, 343 Link Hall, Syracuse, NY 13244, USA.
| | - Tory Alane Welsch
- Department of Biomedical and Chemical Engineering, Syracuse University, 343 Link Hall, Syracuse, NY 13244, USA.
| | - Soor Rajiv Vora
- Department of Biomedical and Chemical Engineering, Syracuse University, 343 Link Hall, Syracuse, NY 13244, USA.
| | - Dacheng Ren
- Department of Biomedical and Chemical Engineering, Syracuse University, 343 Link Hall, Syracuse, NY 13244, USA.
| | - Shikha Nangia
- Department of Biomedical and Chemical Engineering, Syracuse University, 343 Link Hall, Syracuse, NY 13244, USA.
| |
Collapse
|
9
|
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.
Collapse
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.
| |
Collapse
|
10
|
Zhang B, Zhang J, Kang Z, Liang L, Liu Y, Wang Q. On interactions of P-glycoprotein with various anti-tumor drugs by binding free energy calculations. J Biomol Struct Dyn 2020; 39:5335-5347. [PMID: 32608321 DOI: 10.1080/07391102.2020.1786456] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
P-glycoprotein (P-gp, MDR1), one of ATP-binding cassette transporters, may confer tumor cells cross-resistance to chemotherapeutics. A large amount of P-gp inhibitors were designed to inhibit the multidrug resistance (MDR) feature of P-gp. However, no sufficient researches were reported to explore the correlation between binding capacity and drug property by experiment. Without particular drug property found to inhibit the MDR feature of P-gp, the orientation of drug design is indefinite. In this work, 10 representative cancer drugs with various properties are used to bind with P-gp by molecular dynamics simulation. Binding free energy between P-gp and 10 drugs ranges -139 to -253 kJ/mol. It reveals that the promiscuity nature of P-gp is in light of the similar binding free energy in separate P-gp-ligand binding systems. The binding effect of P-gp and drugs correlates well with the size of drugs and has no apparent correlation with the polarity of each drug. The key reason is that van der Waal's interaction occupies most of the total binding free energy, and it is led by the number of atoms in the drugs. Two transmembrane segments (TM6 and TM12) and three types of amino acids (PHE, MET, and GLN) are vital in binding drugs with van der Waal's energy, which evident the influence between binding stability and size of drugs. This work provides the cause and theoretical basis for the promiscuity nature of P-gp.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Bo Zhang
- Department of Chemistry and Soft Matter Research Center, Zhejiang University, Hangzhou, People's Republic of China
| | - Junqiao Zhang
- Department of Chemistry and Soft Matter Research Center, Zhejiang University, Hangzhou, People's Republic of China
| | - Zhengzhong Kang
- Department of Chemistry and Soft Matter Research Center, Zhejiang University, Hangzhou, People's Republic of China
| | - Lijun Liang
- Department of Chemistry and Soft Matter Research Center, Zhejiang University, Hangzhou, People's Republic of China.,College of Life Information Science and Instrument Engineering, Hangzhou Dianzi University, Hangzhou, People's Republic of China
| | - Yingchun Liu
- Department of Chemistry and Soft Matter Research Center, Zhejiang University, Hangzhou, People's Republic of China
| | - Qi Wang
- Department of Chemistry and Soft Matter Research Center, Zhejiang University, Hangzhou, People's Republic of China
| |
Collapse
|
11
|
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
| |
Collapse
|
12
|
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
| |
Collapse
|
13
|
Pieńko T, Trylska J. Computational Methods Used to Explore Transport Events in Biological Systems. J Chem Inf Model 2019; 59:1772-1781. [DOI: 10.1021/acs.jcim.8b00974] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Tomasz Pieńko
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland
- Department of Drug Chemistry, Faculty of Pharmacy with the Laboratory Medicine Division, Medical University of Warsaw, S. Banacha 1a, 02-097 Warsaw, Poland
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, S. Banacha 2c, 02-097 Warsaw, Poland
| |
Collapse
|
14
|
Subramanian N, Schumann-Gillett A, Mark AE, O’Mara ML. Probing the Pharmacological Binding Sites of P-Glycoprotein Using Umbrella Sampling Simulations. J Chem Inf Model 2018; 59:2287-2298. [DOI: 10.1021/acs.jcim.8b00624] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Nandhitha Subramanian
- School of Chemistry and Molecular Biosciences (SCMB), University of Queensland, Brisbane, QLD 4072, Australia
- Research School of Chemistry (RSC), Australian National University, Canberra, ACT 2601, Australia
| | | | - Alan E. Mark
- School of Chemistry and Molecular Biosciences (SCMB), University of Queensland, Brisbane, QLD 4072, Australia
- The Institute for Molecular Biosciences (IMB), University of Queensland, Brisbane, QLD 4072, Australia
| | - Megan L. O’Mara
- School of Chemistry and Molecular Biosciences (SCMB), University of Queensland, Brisbane, QLD 4072, Australia
| |
Collapse
|
15
|
Abstract
This paper is the thirty-ninth consecutive installment of the annual review of research concerning the endogenous opioid system. It summarizes papers published during 2016 that studied the behavioral effects of molecular, pharmacological and genetic manipulation of opioid peptides, opioid receptors, opioid agonists and opioid antagonists. The particular topics that continue to be covered include the molecular-biochemical effects and neurochemical localization studies of endogenous opioids and their receptors related to behavior, and the roles of these opioid peptides and receptors in pain and analgesia, stress and social status, tolerance and dependence, learning and memory, eating and drinking, drug abuse and alcohol, sexual activity and hormones, pregnancy, development and endocrinology, mental illness and mood, seizures and neurologic disorders, electrical-related activity and neurophysiology, general activity and locomotion, gastrointestinal, renal and hepatic functions, cardiovascular responses, respiration and thermoregulation, and immunological responses.
Collapse
Affiliation(s)
- Richard J Bodnar
- Department of Psychology and CUNY Neuroscience Collaborative, Queens College, City University of New York, Flushing, NY 11367, United States.
| |
Collapse
|
16
|
Barreto-Ojeda E, Corradi V, Gu RX, Tieleman DP. Coarse-grained molecular dynamics simulations reveal lipid access pathways in P-glycoprotein. J Gen Physiol 2018; 150:417-429. [PMID: 29437858 PMCID: PMC5839720 DOI: 10.1085/jgp.201711907] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 01/17/2018] [Indexed: 12/13/2022] Open
Abstract
P-glycoprotein (P-gp) exports a broad range of dissimilar compounds, including drugs, lipids, and lipid-like molecules. Because of its substrate promiscuity, P-gp is a key player in the development of cancer multidrug resistance. Although P-gp is one of the most studied ABC transporters, the mechanism by which its substrates access the cavity remains unclear. In this study, we perform coarse-grained molecular dynamics simulations to explore possible lipid access pathways in the inward-facing conformation of P-gp embedded in bilayers of different lipid compositions. In the inward-facing orientation, only lipids from the lower leaflet access the cavity of the transporter. We identify positively charged residues at the portals of P-gp that favor lipid entrance to the cavity, as well as lipid-binding sites at the portals and within the cavity, which is in good agreement with previous experimental studies. This work includes several examples of lipid pathways for phosphatidylcholine and phosphatidylethanolamine lipids that help elucidate the molecular mechanism of lipid binding in P-gp.
Collapse
Affiliation(s)
- Estefania Barreto-Ojeda
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary, Calgary, Alberta, Canada
| | - Valentina Corradi
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary, Calgary, Alberta, Canada
| | - Ruo-Xu Gu
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary, Calgary, Alberta, Canada
| | - D Peter Tieleman
- Department of Biological Sciences and Centre for Molecular Simulation, University of Calgary, Calgary, Alberta, Canada
| |
Collapse
|
17
|
Condic-Jurkic K, Subramanian N, Mark AE, O’Mara ML. The reliability of molecular dynamics simulations of the multidrug transporter P-glycoprotein in a membrane environment. PLoS One 2018; 13:e0191882. [PMID: 29370310 PMCID: PMC5785007 DOI: 10.1371/journal.pone.0191882] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 01/13/2018] [Indexed: 11/19/2022] Open
Abstract
Despite decades of research, the mechanism of action of the ABC multidrug transporter P-glycoprotein (P-gp) remains elusive. Due to experimental limitations, many researchers have turned to molecular dynamics simulation studies in order to investigate different aspects of P-gp function. However, such studies are challenging and caution is required when interpreting the results. P-gp is highly flexible and the time scale on which it can be simulated is limited. There is also uncertainty regarding the accuracy of the various crystal structures available, let alone the structure of the protein in a physiologically relevant environment. In this study, three alternative structural models of mouse P-gp (3G5U, 4KSB, 4M1M), all resolved to 3.8 Å, were used to initiate sets of simulations of P-gp in a membrane environment in order to determine: a) the sensitivity of the results to differences in the starting configuration; and b) the extent to which converged results could be expected on the times scales commonly simulated for this system. The simulations suggest that the arrangement of the nucleotide binding domains (NBDs) observed in the crystal structures is not stable in a membrane environment. In all simulations, the NBDs rapidly associated (within 10 ns) and changes within the transmembrane helices were observed. The secondary structure within the transmembrane domain was best preserved in the 4M1M model under the simulation conditions used. However, the extent to which replicate simulations diverged on a 100 to 200 ns timescale meant that it was not possible to draw definitive conclusions as to which structure overall was most stable, or to obtain converged and reliable results for any of the properties examined. The work brings into question the reliability of conclusions made in regard to the nature of specific interactions inferred from previous simulation studies on this system involving similar sampling times. It also highlights the need to demonstrate the statistical significance of any results obtained in simulations of large flexible proteins, especially where the initial structure is uncertain.
Collapse
Affiliation(s)
- Karmen Condic-Jurkic
- Research School of Chemistry, The Australian National University, Canberra, ACT 2601, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, ACT 4072, Australia
| | - Nandhitha Subramanian
- Research School of Chemistry, The Australian National University, Canberra, ACT 2601, Australia
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, ACT 4072, Australia
| | - Alan E. Mark
- School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, ACT 4072, Australia
| | - Megan L. O’Mara
- Research School of Chemistry, The Australian National University, Canberra, ACT 2601, Australia
| |
Collapse
|
18
|
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.”
Collapse
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.
| |
Collapse
|
19
|
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
| |
Collapse
|
20
|
Mittra R, Pavy M, Subramanian N, George AM, O'Mara ML, Kerr ID, Callaghan R. Location of contact residues in pharmacologically distinct drug binding sites on P-glycoprotein. Biochem Pharmacol 2017; 123:19-28. [DOI: 10.1016/j.bcp.2016.10.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 10/06/2016] [Indexed: 10/20/2022]
|
21
|
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.
Collapse
|
22
|
Subramanian N, Condic-Jurkic K, O'Mara ML. Structural and dynamic perspectives on the promiscuous transport activity of P-glycoprotein. Neurochem Int 2016; 98:146-52. [PMID: 27180050 DOI: 10.1016/j.neuint.2016.05.005] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Revised: 04/28/2016] [Accepted: 05/03/2016] [Indexed: 11/25/2022]
Abstract
The multidrug transporter P-glycoprotein (P-gp) is expressed in the blood-brain barrier endothelium where it effluxes a range of drug substrates, preventing their accumulation within the brain. P-gp has been studied extensively for 40 years because of its crucial role in the absorption, distribution, metabolism and elimination of a range of pharmaceutical compounds. Despite this, many aspects of the structure-function mechanism of P-gp are unresolved. Here we review the emerging role of molecular dynamics simulation techniques in our understanding of the membrane-embedded conformation of P-gp. We discuss its conformational plasticity in the presence and absence of ATP, and recent efforts to characterize the drug binding sites and uptake pathways.
Collapse
Affiliation(s)
- Nandhitha Subramanian
- Research School of Chemistry (RSC), The Australian National University, Canberra, ACT, 2601, Australia
| | - Karmen Condic-Jurkic
- School of Chemistry and Molecular Biosciences (SCMB), University of Queensland, Brisbane, QLD, 4072, Australia
| | - Megan L O'Mara
- Research School of Chemistry (RSC), The Australian National University, Canberra, ACT, 2601, Australia. megan.o'
| |
Collapse
|
23
|
Liu H, Li D, Li Y, Hou T. Atomistic molecular dynamics simulations of ATP-binding cassette transporters. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2016. [DOI: 10.1002/wcms.1247] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Hui Liu
- College of Pharmaceutical Sciences; Zhejiang University; Hangzhou China
| | - Dan Li
- College of Pharmaceutical Sciences; Zhejiang University; Hangzhou China
| | - Youyong Li
- Institute of Functional Nano & Soft Materials (FUNSOM); Soochow University; Suzhou China
| | - Tingjun Hou
- College of Pharmaceutical Sciences; Zhejiang University; Hangzhou China
| |
Collapse
|
24
|
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.
Collapse
Affiliation(s)
- Ricardo J Ferreira
- Research Institute for Medicines (iMed.Ulisboa), Faculdade de Farmácia, Universidade de Lisboa, Av. Prof. Gama Pinto, Lisboa, Portugal.
| | | | | |
Collapse
|