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Shen H, Yang Z, Rodrigues AD. Cynomolgus Monkey as an Emerging Animal Model to Study Drug Transporters: In Vitro, In Vivo, In Vitro-To-In Vivo Translation. Drug Metab Dispos 2021; 50:299-319. [PMID: 34893475 DOI: 10.1124/dmd.121.000695] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/06/2021] [Indexed: 11/22/2022] Open
Abstract
Membrane transporters have been recognized as one of the key determinants of pharmacokinetics and are also known to affect the efficacy and toxicity of drugs. Both qualitatively and quantitatively, however, transporter studies conducted using human in vitro systems have not always been predictive. Consequently, researchers have utilized cynomolgus monkeys as a model to study drug transporters and anticipate their effects in humans. Burgeoning reports of data in the last few years necessitates a comprehensive review on the topic of drug transporters in cynomolgus monkeys that includes cell-based tools, sequence homology, tissue expression, in vitro studies, in vivo studies, and in vitro-to-in vivo extrapolation (IVIVE). This review highlights the state-of-the-art applications of monkey transporter models to support the evaluation of transporter-mediated drug-drug interactions, clearance predictions, and endogenous transporter biomarker identification and validation. The data demonstrate that cynomolgus monkey transporter models, when used appropriately, can be an invaluable tool to support drug discovery and development processes. Most importantly, they provide an early IVIVE assessment which provides additional context to human in vitro data. Additionally, comprehending species similarities and differences in transporter tissue expression and activity is crucial when translating monkey data to humans. The challenges and limitations when applying such models to inform decision-making must also be considered. Significance Statement This paper presents a comprehensive review of currently available published reports describing cynomolgus monkey transporter models. The data indicate that cynomolgus monkeys provide mechanistic insight regarding the role of intestinal, hepatic, and renal transporters in drug and biomarker disposition and drug interactions. It is concluded that the data generated with cynomolgus monkey models provide mechanistic insight regarding transporter-mediated absorption and disposition, as well as human clearance prediction, drug-drug interaction assessment, and endogenous biomarker development related to drug transporters.
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Affiliation(s)
- Hong Shen
- Drug Metabolism and Pharmacokinetics, Bristol Myers Squibb, United States
| | - Zheng Yang
- Metabolism and Pharmacokinetics, Bristol-Myers Squibb Co., United States
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2
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Deshmukh R, Rana N, Liu Y, Zeng S, Agarwal G, Sonah H, Varshney R, Joshi T, Patil GB, Nguyen HT. Soybean transporter database: A comprehensive database for identification and exploration of natural variants in soybean transporter genes. PHYSIOLOGIA PLANTARUM 2021; 171:756-770. [PMID: 33231322 DOI: 10.1111/ppl.13287] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 10/05/2020] [Accepted: 11/17/2020] [Indexed: 06/11/2023]
Abstract
Transporters, a class of membrane proteins that facilitate exchange of solutes including diverse molecules and ions across the cellular membrane, are vital component for the survival of all organisms. Understanding plant transporters is important to get insight of the basic cellular processes, physiology, and molecular mechanisms including nutrient uptake, signaling, response to external stress, and many more. In this regard, extensive analysis of transporters predicted in soybean and other plant species was performed. In addition, an integrated database for soybean transporter protein, SoyTD, was developed that will facilitate the identification, classification, and extensive characterization of transporter proteins by integrating expression, gene ontology, conserved domain and motifs, gene structure organization, and chromosomal distribution features. A comprehensive analysis was performed to identify highly confident transporters by integrating various prediction tools. Initially, 7541 transmembrane (TM) proteins were predicted in the soybean genome; out of these, 3306 non-redundant transporter genes carrying two or more transmembrane domains were selected for further analysis. The identified transporter genes were classified according to a standard transporter classification (TC) system. Comparative analysis of transporter genes among 47 plant genomes provided insights into expansion and duplication of transporter genes in land plants. The whole genome resequencing (WGRS) and tissue-specific transcriptome datasets of soybean were integrated to investigate the natural variants and expression profile associated with transporter(s) of interest. Overall, SoyTD provides a comprehensive interface to study genetic and molecular function of soybean transporters. SoyTD is publicly available at http://artemis.cyverse.org/soykb_dev/SoyTD/.
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Affiliation(s)
- Rupesh Deshmukh
- Agriculture Biotechnology Department, National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Nitika Rana
- Agriculture Biotechnology Department, National Agri-Food Biotechnology Institute (NABI), Mohali, India
- Department of Biotechnology, Panjab University, Chandigarh, India
| | - Yang Liu
- Christopher S. Bond Life Science Center, University of Missouri, Columbia, Missouri, USA
| | - Shuai Zeng
- Christopher S. Bond Life Science Center, University of Missouri, Columbia, Missouri, USA
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA
| | - Gaurav Agarwal
- Department of Plant Pathology, University of Georgia, Tifton, Georgia, USA
| | - Humira Sonah
- Agriculture Biotechnology Department, National Agri-Food Biotechnology Institute (NABI), Mohali, India
| | - Rajeev Varshney
- Center of Excellence in Genomics and System Biology, International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Trupti Joshi
- Christopher S. Bond Life Science Center, University of Missouri, Columbia, Missouri, USA
- Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, Missouri, USA
| | - Gunvant B Patil
- Department of Plant and Soil Sciences, Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, Texas, USA
| | - Henry T Nguyen
- Division of Plant Science, National Center for Soybean Biotechnology, University of Missouri, Columbia, Missouri, USA
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3
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Liu QR, Canseco-Alba A, Liang Y, Ishiguro H, Onaivi ES. Low Basal CB2R in Dopamine Neurons and Microglia Influences Cannabinoid Tetrad Effects. Int J Mol Sci 2020; 21:E9763. [PMID: 33371336 PMCID: PMC7767340 DOI: 10.3390/ijms21249763] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 12/04/2020] [Accepted: 12/17/2020] [Indexed: 12/13/2022] Open
Abstract
There are two well-characterized cannabinoid receptors (CB1R and CB2R and other candidates): the central nervous system (CNS) enriched CB1R and peripheral tissue enriched CB2R with a wide dynamic range of expression levels in different cell types of human tissues. Hepatocytes and neurons express low baseline CB1R and CB2R, respectively, and their cell-type-specific functions are not well defined. Here we report inducible expression of CB1R in the liver by high-fat and high sugar diet and CB2R in cortical neurons by methamphetamine. While there is less controversy about hepatocyte CB1R, the presence of functional neuronal CB2R is still debated to date. We found that neuron CB2R basal expression was higher than that of hepatocyte CB1R by measuring mRNA levels of specific isoform CB2A in neurons isolated by fluorescence-activated cell sorting (FACS) and CB1A in hepatocytes isolated by collagenase perfusion of liver. For in vivo studies, we generated hepatocyte, dopaminergic neuron, and microglia-specific conditional knockout mice (Abl-Cnr1Δ, Dat-Cnr2Δ, and Cx3cr1-Cnr2Δ) of CB1R and CB2R by crossing Cnr1f/f and Cnr2f/f strains to Abl-Cre, Dat-Cre, and Cx3cr1-Cre deleter mouse strains, respectively. Our data reveals that neuron and microglia CB2Rs are involved in the "tetrad" effects of the mixed agonist WIN 55212-2, CB1R selective agonist arachidonyl-2'-chloroethylamide (ACEA), and CB2R selective agonist JWH133. Dat-Cnr2Δ and Cx3cr1-Cnr2Δ mice showed genotypic differences in hypomobility, hypothermia, analgesia, and catalepsy induced by the synthetic cannabinoids. Alcohol conditioned place preference was abolished in DAT-Cnr2Δ mice and remained intact in Cx3cr1-Cnr2Δ mice in comparison to WT mice. These Cre-loxP recombinant mouse lines provide unique approaches in cannabinoid research for dissecting the complex endocannabinoid system that is implicated in many chronic disorders.
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MESH Headings
- Animals
- Behavior, Animal/drug effects
- Cannabinoids/pharmacology
- Dopaminergic Neurons/drug effects
- Dopaminergic Neurons/metabolism
- Male
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Microglia/drug effects
- Microglia/metabolism
- Rats
- Rats, Sprague-Dawley
- Receptor, Cannabinoid, CB1/genetics
- Receptor, Cannabinoid, CB1/metabolism
- Receptor, Cannabinoid, CB1/physiology
- Receptor, Cannabinoid, CB2/genetics
- Receptor, Cannabinoid, CB2/metabolism
- Receptor, Cannabinoid, CB2/physiology
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Affiliation(s)
- Qing-Rong Liu
- Laboratory of Clinical Investigation, National Institute on Aging, Baltimore, MD 21224, USA
| | - Ana Canseco-Alba
- Department of Biology, William Paterson University, Wayne, NJ 07470, USA;
| | - Ying Liang
- College of Food Science and Engineering, Central South University of Forestry and Technology, Changsha 410004, Hunan, China;
| | - Hiroki Ishiguro
- Department of Neuropsychiatry, Graduate School of Medical Science, University of Yamanashi, Chuo, Yamanashi 409-3898, Japan;
| | - Emmanuel S. Onaivi
- Department of Biology, William Paterson University, Wayne, NJ 07470, USA;
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4
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Generating therapeutic monoclonal antibodies to complex multi-spanning membrane targets: Overcoming the antigen challenge and enabling discovery strategies. Methods 2020; 180:111-126. [PMID: 32422249 DOI: 10.1016/j.ymeth.2020.05.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/21/2020] [Accepted: 05/13/2020] [Indexed: 12/17/2022] Open
Abstract
Complex integral membrane proteins, which are embedded in the cell surface lipid bilayer by multiple transmembrane spanning helices, encompass families of proteins which are important target classes for drug discovery. These protein families include G protein-coupled receptors, ion channels and transporters. Although these proteins have typically been targeted by small molecule drugs and peptides, the high specificity of monoclonal antibodies offers a significant opportunity to selectively modulate these target proteins. However, it remains the case that isolation of antibodies with desired pharmacological function(s) has proven difficult due to technical challenges in preparing membrane protein antigens suitable to support antibody drug discovery. In this review recent progress in defining strategies for generation of membrane protein antigens is outlined. We also highlight antibody isolation strategies which have generated antibodies which bind the membrane protein and modulate the protein function.
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5
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dbEMT 2.0: An updated database for epithelial-mesenchymal transition genes with experimentally verified information and precalculated regulation information for cancer metastasis. J Genet Genomics 2019; 46:595-597. [PMID: 31941584 DOI: 10.1016/j.jgg.2019.11.010] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 10/29/2019] [Accepted: 11/10/2019] [Indexed: 12/11/2022]
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6
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Lee CC, Huang PJ, Yeh YM, Chen SY, Chiu CH, Cheng WH, Tang P. Pathogenic Protist Transmembranome database (PPTdb): a web-based platform for searching and analysis of protist transmembrane proteins. BMC Bioinformatics 2019; 20:382. [PMID: 31337335 PMCID: PMC6651900 DOI: 10.1186/s12859-019-2857-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Pathogenic protist membrane transporter proteins play important roles not only in exchanging molecules into and out of cells but also in acquiring nutrients and biosynthetic compounds from their hosts. Currently, there is no centralized protist membrane transporter database published, which makes system-wide comparisons and studies of host-pathogen membranomes difficult to achieve. RESULTS We analyzed over one million protein sequences from 139 protists with full or partial genome sequences. Putative transmembrane proteins were annotated by primary sequence alignments, conserved secondary structural elements, and functional domains. We have constructed the PPTdb (Pathogenic Protist Transmembranome database), a comprehensive membrane transporter protein portal for pathogenic protists and their human hosts. The PPTdb is a web-based database with a user-friendly searching and data querying interface, including hierarchical transporter classification (TC) numbers, protein sequences, functional annotations, conserved functional domains, batch sequence retrieving and downloads. The PPTdb also serves as an analytical platform to provide useful comparison/mining tools, including transmembrane ability evaluation, annotation of unknown proteins, informative visualization charts, and iterative functional mining of host-pathogen transporter proteins. CONCLUSIONS The PPTdb collected putative protist transporter proteins and offers a user-friendly data retrieving interface. Moreover, a pairwise functional comparison ability can provide useful information for identifying functional uniqueness of each protist. Finally, the host and non-host protein similarity search can fulfill the needs of comprehensive studies of protists and their hosts. The PPTdb is freely accessible at http://pptdb.cgu.edu.tw .
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Affiliation(s)
- Chi-Ching Lee
- Department and Graduate Institute of Computer Science and Information Engineering, Chang Gung University, Taoyuan, Taiwan.,Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Po-Jung Huang
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan.,Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
| | - Yuan-Ming Yeh
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Sin-You Chen
- Department and Graduate Institute of Computer Science and Information Engineering, Chang Gung University, Taoyuan, Taiwan
| | - Cheng-Hsun Chiu
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan.,Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Wei-Hung Cheng
- Department of Parasitology, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
| | - Petrus Tang
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan. .,Department of Parasitology, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
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7
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Balik-Meisner MR, Mav D, Phadke DP, Everett LJ, Shah RR, Tal T, Shepard PJ, Merrick BA, Paules RS. Development of a Zebrafish S1500+ Sentinel Gene Set for High-Throughput Transcriptomics. Zebrafish 2019; 16:331-347. [PMID: 31188086 PMCID: PMC6685209 DOI: 10.1089/zeb.2018.1720] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Sentinel gene sets have been developed with the purpose of maximizing the information from targeted transcriptomic platforms. We recently described the development of an S1500+ sentinel gene set, which was built for the human transcriptome, utilizing a data- and knowledge-driven hybrid approach to select a small subset of genes that optimally capture transcriptional diversity, correlation with other genes based on large-scale expression profiling, and known pathway annotation within the human genome. While this detailed bioinformatics approach for gene selection can in principle be applied to other species, the reliability of the resulting gene set depends on availability of a large body of transcriptomics data. For the model organism zebrafish, we aimed to create a similar sentinel gene set (Zf S1500+ gene set); however, there is insufficient standardized expression data in the public domain to train the gene correlation model. Therefore, our strategy was to use human-zebrafish ortholog mapping of the human S1500+ genes and nominations from experts in the zebrafish scientific community. In this study, we present the bioinformatics curation and refinement process to produce the final Zf S1500+ gene set, explore whole transcriptome extrapolation using this gene set, and assess pathway-level inference. This gene set will add value to targeted high-throughput transcriptomics in zebrafish for toxicogenomic screening and other research domains.
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Affiliation(s)
| | - Deepak Mav
- 1Sciome, LLC, Research Triangle Park, North Carolina
| | | | | | - Ruchir R Shah
- 1Sciome, LLC, Research Triangle Park, North Carolina
| | - Tamara Tal
- 2National Health and Environmental Effects Research Laboratory, Office of Research and Development, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina
| | | | - B Alex Merrick
- 4Division of the National Toxicology Program, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina
| | - Richard S Paules
- 4Division of the National Toxicology Program, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina
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8
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Pharmacokinetic principles in the inner ear: Influence of drug properties on intratympanic applications. Hear Res 2018; 368:28-40. [PMID: 29551306 DOI: 10.1016/j.heares.2018.03.002] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 02/06/2018] [Accepted: 03/02/2018] [Indexed: 01/12/2023]
Abstract
Local drug delivery to the ear has gained wide clinical acceptance, with the choice of drug and application protocol in humans largely empirically-derived. Here, we review the pharmacokinetics underlying local therapy of the ear using the drugs commonly used in clinical practice as examples. Based on molecular properties and perilymph measurements interpreted through computer simulations we now better understand the principles underlying entry and distribution of these and other drugs in the ear. From our analysis, we have determined that dexamethasone-phosphate, a pro-drug widely-used clinically, has molecular and pharmacokinetic properties that make it ill-suited for use as a local therapy for hearing disorders. This polar form of dexamethasone, used as a more soluble agent in intravenous preparations, passes less readily through lipid membranes, such as those of the epithelia restricting entry at the round window membrane and stapes. Once within the inner ear, dexamethasone-phosphate is cleaved to the active form, dexamethasone, which is less polar, passes more readily through lipid membranes of the blood-perilymph barrier and is rapidly eliminated from perilymph without distributing to apical cochlear regions. Dexamethasone-phosphate therefore provides only a brief exposure of the basal regions of the cochlea to active drug. Other steroids, such as triamcinolone-acetonide, exhibit pharmacokinetic properties more appropriate to the ear and merit more detailed consideration.
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9
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Lepist EI, Ray AS. Beyond drug-drug interactions: effects of transporter inhibition on endobiotics, nutrients and toxins. Expert Opin Drug Metab Toxicol 2017; 13:1075-1087. [PMID: 28847160 DOI: 10.1080/17425255.2017.1372425] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
INTRODUCTION Membrane transport proteins play a central role in regulating the disposition of endobiotics, dietary nutrients and environmental toxins. The inhibition of transporters by drugs has potential physiologic consequences. The full extent of the effect of drugs on the function of transporters is poorly understood because only a small subset of the hundreds of transporters expressed in humans - primarily those mediating the rate-determining step in the elimination of specific drugs - are assessed during clinical development. Areas covered: We provide a comprehensive overview of literature reports implicating the inhibition of transporters as the mechanism for off-target effects of drugs. Expert opinion: Transporter inhibition, the mechanism of action of many marketed drugs, appears to play an underappreciated role in a number of side effects including vitamin deficiency, edema, dyslipidemia, cholestasis and gout. Cell systems more broadly expressing transporter networks and methods like unbiased metabolomics should be incorporated into the screening paradigm to expand our understanding of the impact of drugs on the physiologic function of transporters and to allow for these effects to be taken into account in drug discovery and clinical practice.
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Affiliation(s)
- Eve-Irene Lepist
- a Departments of Drug Metabolism , Gilead Sciences, Inc ., Foster City , CA , USA
| | - Adrian S Ray
- b Clinical Research , Gilead Sciences, Inc ., Foster City , CA , USA
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10
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Lacerda R, Menezes J, Romão L. More than just scanning: the importance of cap-independent mRNA translation initiation for cellular stress response and cancer. Cell Mol Life Sci 2017; 74:1659-1680. [PMID: 27913822 PMCID: PMC11107732 DOI: 10.1007/s00018-016-2428-2] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 11/24/2016] [Accepted: 11/29/2016] [Indexed: 12/11/2022]
Abstract
The scanning model for eukaryotic mRNA translation initiation states that the small ribosomal subunit, along with initiation factors, binds at the cap structure at the 5' end of the mRNA and scans the 5' untranslated region (5'UTR) until an initiation codon is found. However, under conditions that impair canonical cap-dependent translation, the synthesis of some proteins is kept by alternative mechanisms that are required for cell survival and stress recovery. Alternative modes of translation initiation include cap- and/or scanning-independent mechanisms of ribosomal recruitment. In most cap-independent translation initiation events there is a direct recruitment of the 40S ribosome into a position upstream, or directly at, the initiation codon via a specific internal ribosome entry site (IRES) element in the 5'UTR. Yet, in some cellular mRNAs, a different translation initiation mechanism that is neither cap- nor IRES-dependent seems to occur through a special RNA structure called cap-independent translational enhancer (CITE). Recent evidence uncovered a distinct mechanism through which mRNAs containing N 6-methyladenosine (m6A) residues in their 5'UTR directly bind eukaryotic initiation factor 3 (eIF3) and the 40S ribosomal subunit in order to initiate translation in the absence of the cap-binding proteins. This review focuses on the important role of cap-independent translation mechanisms in human cells and how these alternative mechanisms can either act individually or cooperate with other cis-acting RNA regulons to orchestrate specific translational responses triggered upon several cellular stress states, and diseases such as cancer. Elucidation of these non-canonical mechanisms reveals the complexity of translational control and points out their potential as prospective novel therapeutic targets.
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Affiliation(s)
- Rafaela Lacerda
- Department of Human Genetics, Instituto Nacional de Saúde Doutor Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal
- Biosystems and Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Juliane Menezes
- Department of Human Genetics, Instituto Nacional de Saúde Doutor Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal
- Biosystems and Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Luísa Romão
- Department of Human Genetics, Instituto Nacional de Saúde Doutor Ricardo Jorge, Av. Padre Cruz, 1649-016, Lisbon, Portugal.
- Biosystems and Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal.
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Del Amo EM, Rimpelä AK, Heikkinen E, Kari OK, Ramsay E, Lajunen T, Schmitt M, Pelkonen L, Bhattacharya M, Richardson D, Subrizi A, Turunen T, Reinisalo M, Itkonen J, Toropainen E, Casteleijn M, Kidron H, Antopolsky M, Vellonen KS, Ruponen M, Urtti A. Pharmacokinetic aspects of retinal drug delivery. Prog Retin Eye Res 2016; 57:134-185. [PMID: 28028001 DOI: 10.1016/j.preteyeres.2016.12.001] [Citation(s) in RCA: 398] [Impact Index Per Article: 49.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 11/25/2016] [Accepted: 12/01/2016] [Indexed: 12/14/2022]
Abstract
Drug delivery to the posterior eye segment is an important challenge in ophthalmology, because many diseases affect the retina and choroid leading to impaired vision or blindness. Currently, intravitreal injections are the method of choice to administer drugs to the retina, but this approach is applicable only in selected cases (e.g. anti-VEGF antibodies and soluble receptors). There are two basic approaches that can be adopted to improve retinal drug delivery: prolonged and/or retina targeted delivery of intravitreal drugs and use of other routes of drug administration, such as periocular, suprachoroidal, sub-retinal, systemic, or topical. Properties of the administration route, drug and delivery system determine the efficacy and safety of these approaches. Pharmacokinetic and pharmacodynamic factors determine the required dosing rates and doses that are needed for drug action. In addition, tolerability factors limit the use of many materials in ocular drug delivery. This review article provides a critical discussion of retinal drug delivery, particularly from the pharmacokinetic point of view. This article does not include an extensive review of drug delivery technologies, because they have already been reviewed several times recently. Instead, we aim to provide a systematic and quantitative view on the pharmacokinetic factors in drug delivery to the posterior eye segment. This review is based on the literature and unpublished data from the authors' laboratory.
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Affiliation(s)
- Eva M Del Amo
- School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Anna-Kaisa Rimpelä
- Centre for Drug Research, Division of Pharmaceutical Biosciences, University of Helsinki, Helsinki, Finland
| | - Emma Heikkinen
- School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Otto K Kari
- Centre for Drug Research, Division of Pharmaceutical Biosciences, University of Helsinki, Helsinki, Finland
| | - Eva Ramsay
- School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Tatu Lajunen
- Centre for Drug Research, Division of Pharmaceutical Biosciences, University of Helsinki, Helsinki, Finland
| | - Mechthild Schmitt
- Centre for Drug Research, Division of Pharmaceutical Biosciences, University of Helsinki, Helsinki, Finland
| | - Laura Pelkonen
- School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Madhushree Bhattacharya
- Centre for Drug Research, Division of Pharmaceutical Biosciences, University of Helsinki, Helsinki, Finland
| | - Dominique Richardson
- Centre for Drug Research, Division of Pharmaceutical Biosciences, University of Helsinki, Helsinki, Finland
| | - Astrid Subrizi
- School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Tiina Turunen
- Centre for Drug Research, Division of Pharmaceutical Biosciences, University of Helsinki, Helsinki, Finland
| | - Mika Reinisalo
- School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Jaakko Itkonen
- Centre for Drug Research, Division of Pharmaceutical Biosciences, University of Helsinki, Helsinki, Finland
| | - Elisa Toropainen
- School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Marco Casteleijn
- Centre for Drug Research, Division of Pharmaceutical Biosciences, University of Helsinki, Helsinki, Finland
| | - Heidi Kidron
- Centre for Drug Research, Division of Pharmaceutical Biosciences, University of Helsinki, Helsinki, Finland
| | - Maxim Antopolsky
- Centre for Drug Research, Division of Pharmaceutical Biosciences, University of Helsinki, Helsinki, Finland
| | | | - Marika Ruponen
- School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Arto Urtti
- Centre for Drug Research, Division of Pharmaceutical Biosciences, University of Helsinki, Helsinki, Finland; School of Pharmacy, University of Eastern Finland, Kuopio, Finland.
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12
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Elbourne LDH, Tetu SG, Hassan KA, Paulsen IT. TransportDB 2.0: a database for exploring membrane transporters in sequenced genomes from all domains of life. Nucleic Acids Res 2016; 45:D320-D324. [PMID: 27899676 PMCID: PMC5210551 DOI: 10.1093/nar/gkw1068] [Citation(s) in RCA: 203] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 10/20/2016] [Accepted: 10/25/2016] [Indexed: 01/24/2023] Open
Abstract
All cellular life contains an extensive array of membrane transport proteins. The vast majority of these transporters have not been experimentally characterized. We have developed a bioinformatic pipeline to identify and annotate complete sets of transporters in any sequenced genome. This pipeline is now fully automated enabling it to better keep pace with the accelerating rate of genome sequencing. This manuscript describes TransportDB 2.0 (http://www.membranetransport.org/transportDB2/), a completely updated version of TransportDB, which provides access to the large volumes of data generated by our automated transporter annotation pipeline. The TransportDB 2.0 web portal has been rebuilt to utilize contemporary JavaScript libraries, providing a highly interactive interface to the annotation information, and incorporates analysis tools that enable users to query the database on a number of levels. For example, TransportDB 2.0 includes tools that allow users to select annotated genomes of interest from the thousands of species held in the database and compare their complete transporter complements.
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Affiliation(s)
- Liam D H Elbourne
- Department of Chemistry and Biomolecular Sciences, Macquarie University, NSW 2109, Australia
| | - Sasha G Tetu
- Department of Chemistry and Biomolecular Sciences, Macquarie University, NSW 2109, Australia
| | - Karl A Hassan
- Department of Chemistry and Biomolecular Sciences, Macquarie University, NSW 2109, Australia
| | - Ian T Paulsen
- Department of Chemistry and Biomolecular Sciences, Macquarie University, NSW 2109, Australia
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13
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Qosa H, Mohamed LA, Alqahtani S, Abuasal BS, Hill RA, Kaddoumi A. Transporters as Drug Targets in Neurological Diseases. Clin Pharmacol Ther 2016; 100:441-453. [PMID: 27447939 DOI: 10.1002/cpt.435] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 07/13/2016] [Accepted: 07/15/2016] [Indexed: 12/13/2022]
Abstract
Membrane transport proteins have central physiological function in maintaining cerebral homeostasis. These transporters are expressed in almost all cerebral cells in which they regulate the movement of a wide range of solutes, including endogenous substrates, xenobiotic, and therapeutic drugs. Altered activity/expression of central nervous system (CNS) transporters has been implicated in the onset and progression of multiple neurological diseases. Neurological diseases are heterogeneous diseases that involve complex pathological alterations with only a few treatment options; therefore, there is a great need for the development of novel therapeutic treatments. To that end, transporters have emerged recently to be promising therapeutic targets to halt or slow the course of neurological diseases. The objective of this review is to discuss implications of transporters in neurological diseases and summarize available evidence for targeting transporters as decent therapeutic approach in the treatment of neurological diseases.
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Affiliation(s)
- H Qosa
- Department of Basic Pharmaceutical Sciences, School of Pharmacy, University of Louisiana at Monroe, Monroe, Louisiana, USA
| | - L A Mohamed
- Department of Basic Pharmaceutical Sciences, School of Pharmacy, University of Louisiana at Monroe, Monroe, Louisiana, USA
| | - S Alqahtani
- Department of Basic Pharmaceutical Sciences, School of Pharmacy, University of Louisiana at Monroe, Monroe, Louisiana, USA
| | - B S Abuasal
- Department of Basic Pharmaceutical Sciences, School of Pharmacy, University of Louisiana at Monroe, Monroe, Louisiana, USA
| | - R A Hill
- Department of Basic Pharmaceutical Sciences, School of Pharmacy, University of Louisiana at Monroe, Monroe, Louisiana, USA
| | - A Kaddoumi
- Department of Basic Pharmaceutical Sciences, School of Pharmacy, University of Louisiana at Monroe, Monroe, Louisiana, USA.
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14
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Hwang JU, Song WY, Hong D, Ko D, Yamaoka Y, Jang S, Yim S, Lee E, Khare D, Kim K, Palmgren M, Yoon HS, Martinoia E, Lee Y. Plant ABC Transporters Enable Many Unique Aspects of a Terrestrial Plant's Lifestyle. MOLECULAR PLANT 2016; 9:338-355. [PMID: 26902186 DOI: 10.1016/j.molp.2016.02.003] [Citation(s) in RCA: 201] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 02/11/2016] [Accepted: 02/14/2016] [Indexed: 05/17/2023]
Abstract
Terrestrial plants have two to four times more ATP-binding cassette (ABC) transporter genes than other organisms, including their ancestral microalgae. Recent studies found that plants harboring mutations in these transporters exhibit dramatic phenotypes, many of which are related to developmental processes and functions necessary for life on dry land. These results suggest that ABC transporters multiplied during evolution and assumed novel functions that allowed plants to adapt to terrestrial environmental conditions. Examining the literature on plant ABC transporters from this viewpoint led us to propose that diverse ABC transporters enabled many unique and essential aspects of a terrestrial plant's lifestyle, by transporting various compounds across specific membranes of the plant.
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Affiliation(s)
- Jae-Ung Hwang
- Department of Life Science, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Korea
| | - Won-Yong Song
- Division of Integrative Bioscience and Biotechnology, POSTECH, Pohang, 37673, Korea
| | - Daewoong Hong
- Department of Life Science, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Korea
| | - Donghwi Ko
- Department of Life Science, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Korea
| | - Yasuyo Yamaoka
- Department of Life Science, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Korea
| | - Sunghoon Jang
- Department of Life Science, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Korea
| | - Sojeong Yim
- Department of Life Science, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Korea
| | - Eunjung Lee
- Department of Life Science, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Korea
| | - Deepa Khare
- Department of Life Science, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Korea
| | - Kyungyoon Kim
- Department of Life Science, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Korea
| | - Michael Palmgren
- Center for Membrane Pumps in Cells and Disease - PUMPKIN, Danish National Research Foundation, Department of Plant and Environmental Science, University of Copenhagen, 1871 Frederiksberg, Denmark
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon, 16419, Korea
| | - Enrico Martinoia
- Department of Plant and Microbial Biology, University Zurich, Zurich, 8008 Zurich, Switzerland
| | - Youngsook Lee
- Department of Life Science, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Korea; Division of Integrative Bioscience and Biotechnology, POSTECH, Pohang, 37673, Korea.
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15
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Zhao M, Wang T, Adamson KJ, Storey KB, Cummins SF. Multi-tissue transcriptomics for construction of a comprehensive gene resource for the terrestrial snail Theba pisana. Sci Rep 2016; 6:20685. [PMID: 26852673 PMCID: PMC4745086 DOI: 10.1038/srep20685] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 01/04/2016] [Indexed: 11/18/2022] Open
Abstract
The land snail Theba pisana is native to the Mediterranean region but has become one of the most abundant invasive species worldwide. Here, we present three transcriptomes of this agriculture pest derived from three tissues: the central nervous system, hepatopancreas (digestive gland), and foot muscle. Sequencing of the three tissues produced 339,479,092 high quality reads and a global de novo assembly generated a total of 250,848 unique transcripts (unigenes). BLAST analysis mapped 52,590 unigenes to NCBI non-redundant protein databases and further functional analysis annotated 21,849 unigenes with gene ontology. We report that T. pisana transcripts have representatives in all functional classes and a comparison of differentially expressed transcripts amongst all three tissues demonstrates enormous differences in their potential metabolic activities. The genes differentially expressed include those with sequence similarity to those genes associated with multiple bacterial diseases and neurological diseases. To provide a valuable resource that will assist functional genomics study, we have implemented a user-friendly web interface, ThebaDB (http://thebadb.bioinfo-minzhao.org/). This online database allows for complex text queries, sequence searches, and data browsing by enriched functional terms and KEGG mapping.
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Affiliation(s)
- M Zhao
- School of Engineering, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore DC, Queensland, 4558, Australia
| | - T Wang
- School of Engineering, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore DC, Queensland, 4558, Australia
| | - K J Adamson
- School of Engineering, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore DC, Queensland, 4558, Australia
| | - K B Storey
- Institute of Biochemistry &Department of Biology, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - S F Cummins
- School of Engineering, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore DC, Queensland, 4558, Australia
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16
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Zhao M, Chen Y, Qu D, Qu H. METSP: a maximum-entropy classifier based text mining tool for transporter-substrate identification with semistructured text. BIOMED RESEARCH INTERNATIONAL 2015; 2015:254838. [PMID: 26495291 PMCID: PMC4606149 DOI: 10.1155/2015/254838] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 06/21/2015] [Indexed: 01/16/2023]
Abstract
The substrates of a transporter are not only useful for inferring function of the transporter, but also important to discover compound-compound interaction and to reconstruct metabolic pathway. Though plenty of data has been accumulated with the developing of new technologies such as in vitro transporter assays, the search for substrates of transporters is far from complete. In this article, we introduce METSP, a maximum-entropy classifier devoted to retrieve transporter-substrate pairs (TSPs) from semistructured text. Based on the high quality annotation from UniProt, METSP achieves high precision and recall in cross-validation experiments. When METSP is applied to 182,829 human transporter annotation sentences in UniProt, it identifies 3942 sentences with transporter and compound information. Finally, 1547 confidential human TSPs are identified for further manual curation, among which 58.37% pairs with novel substrates not annotated in public transporter databases. METSP is the first efficient tool to extract TSPs from semistructured annotation text in UniProt. This tool can help to determine the precise substrates and drugs of transporters, thus facilitating drug-target prediction, metabolic network reconstruction, and literature classification.
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Affiliation(s)
- Min Zhao
- School of Engineering, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore DC, QLD 4558, Australia
| | - Yanming Chen
- School of Computer Science & Technology, Beijing Institute of Technology, Beijing 100081, China
| | - Dacheng Qu
- School of Computer Science & Technology, Beijing Institute of Technology, Beijing 100081, China
| | - Hong Qu
- Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
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17
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Mak L, Marcus D, Howlett A, Yarova G, Duchateau G, Klaffke W, Bender A, Glen RC. Metrabase: a cheminformatics and bioinformatics database for small molecule transporter data analysis and (Q)SAR modeling. J Cheminform 2015; 7:31. [PMID: 26106450 PMCID: PMC4477067 DOI: 10.1186/s13321-015-0083-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2015] [Accepted: 06/10/2015] [Indexed: 11/17/2022] Open
Abstract
ABSTRACT Both metabolism and transport are key elements defining the bioavailability and biological activity of molecules, i.e. their adverse and therapeutic effects. Structured and high quality experimental data stored in a suitable container, such as a relational database, facilitates easy computational processing and thus allows for high quality information/knowledge to be efficiently inferred by computational analyses. Our aim was to create a freely accessible database that would provide easy access to data describing interactions between proteins involved in transport and xenobiotic metabolism and their small molecule substrates and modulators. We present Metrabase, an integrated cheminformatics and bioinformatics resource containing curated data related to human transport and metabolism of chemical compounds. Its primary content includes over 11,500 interaction records involving nearly 3,500 small molecule substrates and modulators of transport proteins and, currently to a much smaller extent, cytochrome P450 enzymes. Data was manually extracted from the published literature and supplemented with data integrated from other available resources. Metrabase version 1.0 is freely available under a CC BY-SA 4.0 license at http://www-metrabase.ch.cam.ac.uk.
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Affiliation(s)
- Lora Mak
- />The Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
- />European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - David Marcus
- />The Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
- />European Molecular Biology Laboratory - European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD UK
| | - Andrew Howlett
- />The Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
| | - Galina Yarova
- />Unilever Research & Development, 40 Merritt Blvd, Trumbull, CT 06611 USA
| | - Guus Duchateau
- />Unilever Research & Development, Olivier van Noortlaan, 3133 AT Vlaardingen, The Netherlands
| | - Werner Klaffke
- />Unilever Research & Development, Olivier van Noortlaan, 3133 AT Vlaardingen, The Netherlands
- />Haus der Technik e.V., Hollestrasse 1, 45127 Essen, Germany
| | - Andreas Bender
- />The Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
| | - Robert C Glen
- />The Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW UK
- />Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, SW7 2AZ London, UK
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