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Abstract
Spontaneous solute and solvent permeation through membranes is of vital importance to human life, be it gas exchange in red blood cells, metabolite excretion, drug/toxin uptake, or water homeostasis. Knowledge of the underlying molecular mechanisms is the sine qua non of every functional assignment to membrane transporters. The basis of our current solubility diffusion model was laid by Meyer and Overton. It correlates the solubility of a substance in an organic phase with its membrane permeability. Since then, a wide range of studies challenging this rule have appeared. Commonly, the discrepancies have their origin in ill-used measurement approaches, as we demonstrate on the example of membrane CO2 transport. On the basis of the insight that scanning electrochemical microscopy offered into solute concentration distributions in immediate membrane vicinity of planar membranes, we analyzed the interplay between chemical reactions and diffusion for solvent transport, weak acid permeation, and enzymatic reactions adjacent to membranes. We conclude that buffer reactions must also be considered in spectroscopic investigations of weak acid transport in vesicular suspensions. The evaluation of energetic contributions to membrane translocation of charged species demonstrates the compatibility of the resulting membrane current with the solubility diffusion model. A local partition coefficient that depends on membrane penetration depth governs spontaneous membrane translocation of both charged and uncharged molecules. It is determined not only by the solubility in an organic phase but also by other factors like cholesterol concentration and intrinsic electric membrane potentials.
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Affiliation(s)
- Christof Hannesschlaeger
- From the Institute of Biophysics , Johannes Kepler University Linz , Gruberstrasse 40 , 4020 Linz , Austria
| | - Andreas Horner
- From the Institute of Biophysics , Johannes Kepler University Linz , Gruberstrasse 40 , 4020 Linz , Austria
| | - Peter Pohl
- From the Institute of Biophysics , Johannes Kepler University Linz , Gruberstrasse 40 , 4020 Linz , Austria
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52
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Borodina I. Understanding metabolite transport gives an upper hand in strain development. Microb Biotechnol 2019; 12:69-70. [PMID: 30508284 PMCID: PMC6302705 DOI: 10.1111/1751-7915.13347] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 11/12/2018] [Indexed: 01/02/2023] Open
Abstract
Cell factories can be engineered for more efficient product secretion through modulation of membrane transporters.
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Affiliation(s)
- Irina Borodina
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKongens LyngbyDenmark
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53
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Lu H, Marti J. Binding free energies of small-molecules in phospholipid membranes: Aminoacids, serotonin and melatonin. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.10.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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54
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Lauersen KJ, Wichmann J, Baier T, Kampranis SC, Pateraki I, Møller BL, Kruse O. Phototrophic production of heterologous diterpenoids and a hydroxy-functionalized derivative from Chlamydomonas reinhardtii. Metab Eng 2018; 49:116-127. [DOI: 10.1016/j.ymben.2018.07.005] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Revised: 07/09/2018] [Accepted: 07/10/2018] [Indexed: 12/14/2022]
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55
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Kimoto E, Mathialagan S, Tylaska L, Niosi M, Lin J, Carlo AA, Tess DA, Varma MVS. Organic Anion Transporter 2–Mediated Hepatic Uptake Contributes to the Clearance of High-Permeability–Low-Molecular-Weight Acid and Zwitterion Drugs: Evaluation Using 25 Drugs. J Pharmacol Exp Ther 2018; 367:322-334. [DOI: 10.1124/jpet.118.252049] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 08/15/2018] [Indexed: 01/16/2023] Open
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56
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Ehrl B, Mogusu EO, Kim K, Hofstetter H, Pedersen JA, Elsner M. High Permeation Rates in Liposome Systems Explain Rapid Glyphosate Biodegradation Associated with Strong Isotope Fractionation. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:7259-7268. [PMID: 29790342 PMCID: PMC7193547 DOI: 10.1021/acs.est.8b01004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 05/17/2018] [Accepted: 05/23/2018] [Indexed: 05/22/2023]
Abstract
Bacterial uptake of charged organic pollutants such as the widely used herbicide glyphosate is typically attributed to active transporters, whereas passive membrane permeation as an uptake pathway is usually neglected. For 1-palmitoyl-2-oleoyl- sn-glycero-3-phosphocholine (POPC) liposomes, the pH-dependent apparent membrane permeation coefficients ( Papp) of glyphosate, determined by nuclear magnetic resonance (NMR) spectroscopy, varied from Papp (pH 7.0) = 3.7 (±0.3) × 10-7 m·s-1 to Papp (pH 4.1) = 4.2 (±0.1) × 10-6 m·s-1. The magnitude of this surprisingly rapid membrane permeation depended on glyphosate speciation and was, at circumneutral pH, in the range of polar, noncharged molecules. These findings point to passive membrane permeation as a potential uptake pathway during glyphosate biodegradation. To test this hypothesis, a Gram-negative glyphosate degrader, Ochrobactrum sp. FrEM, was isolated from glyphosate-treated soil and glyphosate permeation rates inferred from the liposome model system were compared to bacterial degradation rates. Estimated maximum permeation rates were, indeed, 2 orders of magnitude higher than degradation rates of glyphosate. In addition, biodegradation of millimolar glyphosate concentrations gave rise to pronounced carbon isotope fractionation with an apparent kinetic isotope effect, AKIEcarbon, of 1.014 ± 0.003. This value lies in the range typical of non-masked enzymatic isotope fractionation demonstrating that glyphosate biodegradation was not subject to mass transfer limitations and glyphosate exchange across the cell membrane was rapid relative to enzymatic turnover.
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Affiliation(s)
- Benno
N. Ehrl
- Institute
of Groundwater Ecology, Helmholtz Zentrum
München, Ingolstädter
Landstrasse 1, 85764 Neuherberg, Germany
| | - Emmanuel O. Mogusu
- Institute
of Groundwater Ecology, Helmholtz Zentrum
München, Ingolstädter
Landstrasse 1, 85764 Neuherberg, Germany
- Department
of Chemistry, Mwenge Catholic University, P.O. Box 1226, Moshi, Tanzania
| | - Kyoungtea Kim
- Molecular
and Environmental Toxicology Center, University
of Wisconsin, Madison, Wisconsin 53706, United States
| | - Heike Hofstetter
- Department
of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Joel A. Pedersen
- Molecular
and Environmental Toxicology Center, University
of Wisconsin, Madison, Wisconsin 53706, United States
- Department
of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
- Departments
of Soil Science and Civil & Environmental Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Martin Elsner
- Institute
of Groundwater Ecology, Helmholtz Zentrum
München, Ingolstädter
Landstrasse 1, 85764 Neuherberg, Germany
- Institute
of Hydrochemistry, Chair for Analytical Chemistry and Water Chemistry, Technical University of Munich, Marchioninistrasse 17, 81377 Munich, Germany
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57
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Darbani B, Kell DB, Borodina I. Energetic evolution of cellular Transportomes. BMC Genomics 2018; 19:418. [PMID: 29848286 PMCID: PMC5977736 DOI: 10.1186/s12864-018-4816-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Accepted: 05/22/2018] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Transporter proteins mediate the translocation of substances across the membranes of living cells. Many transport processes are energetically expensive and the cells use 20 to 60% of their energy to power the transportomes. We hypothesized that there may be an evolutionary selection pressure for lower energy transporters. RESULTS We performed a genome-wide analysis of the compositional reshaping of the transportomes across the kingdoms of bacteria, archaea, and eukarya. We found that the share of ABC transporters is much higher in bacteria and archaea (ca. 27% of the transportome) than in primitive eukaryotes (13%), algae and plants (10%) and in fungi and animals (5-6%). This decrease is compensated by an increased occurrence of secondary transporters and ion channels. The share of ion channels is particularly high in animals (ca. 30% of the transportome) and algae and plants with (ca. 13%), when compared to bacteria and archaea with only 6-7%. Therefore, our results show a move to a preference for the low-energy-demanding transporters (ion channels and carriers) over the more energy-costly transporter classes (ATP-dependent families, and ABCs in particular) as part of the transition from prokaryotes to eukaryotes. The transportome analysis also indicated seven bacterial species, including Neorickettsia risticii and Neorickettsia sennetsu, as likely origins of the mitochondrion in eukaryotes, based on the phylogenetically restricted presence therein of clear homologues of modern mitochondrial solute carriers. CONCLUSIONS The results indicate that the transportomes of eukaryotes evolved strongly towards a higher energetic efficiency, as ATP-dependent transporters diminished and secondary transporters and ion channels proliferated. These changes have likely been important in the development of tissues performing energetically costly cellular functions.
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Affiliation(s)
- Behrooz Darbani
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
| | - Douglas B. Kell
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
- School of Chemistry & Manchester Institute of Biotechnology, The University of Manchester, 131 Princess St, Manchester, M1 7DN UK
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark
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58
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Zhang Q, Cong D, An D, Fan A, Liu Q, Yi Y, Song Z, Chen X, Lu Y, Zhao D, He L. Determination of oroxylin A and oroxylin A 7-O-d-glucuronide in HepG2 cell lysate and subcellular fractions with SPE-UPLC–MS/MS: Cellular pharmacokinetic study to indicate anti-cancer mechanisms. J Pharm Biomed Anal 2018; 154:364-372. [DOI: 10.1016/j.jpba.2018.03.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 03/07/2018] [Accepted: 03/10/2018] [Indexed: 11/30/2022]
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59
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Kerley RN, McCarthy C, Kell DB, Kenny LC. The potential therapeutic effects of ergothioneine in pre-eclampsia. Free Radic Biol Med 2018; 117:145-157. [PMID: 29284116 DOI: 10.1016/j.freeradbiomed.2017.12.030] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Revised: 12/21/2017] [Accepted: 12/22/2017] [Indexed: 12/21/2022]
Abstract
Ergothioneine (ERG), is a water-soluble amino acid that is derived entirely from dietary sources. It has received much attention as a therapeutic agent due to its anti-oxidant properties, and there are claims of preferential accumulation within high oxidative stress organs. Pre-eclampsia, a condition accompanied by increased oxidative stress, is one of the leading causes of maternal morbidity and mortality. Despite intense research efforts, its aetiologies remain somewhat unclear and there are still no effective treatment options. Clinical trials of the anti-oxidants vitamin C and vitamin E have proven largely ineffective with little improvement in clinical outcome or even a negative response. This could be explained in part by their inability to permeate the plasma and mitochondrial membranes and scavenge mitochondria-derived superoxide species, and for the former by the fact that it is actually a pro-oxidant in the presence of unliganded iron. ERG accumulates within tissues through the action of a specific organic cation transporter, SLC22A4 (previously referred to as OCTN1), which is possibly also expressed in mammalian mitochondria. Mitochondrial dysfunction has been implicated in a variety of vascular diseases including pre-eclampsia. This review discusses the use of ERG as a possibly mitochondrial-targeted anti-oxidant, focusing on its physical properties, potential mechanisms of action, safety profile and administration in relation to pregnancies complicated by pre-eclampsia.
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Affiliation(s)
- Robert N Kerley
- Irish Centre for Fetal and Neonatal Translational Research (INFANT), Cork University Maternity Hospital, Cork, Ireland.
| | - Cathal McCarthy
- Irish Centre for Fetal and Neonatal Translational Research (INFANT), Cork University Maternity Hospital, Cork, Ireland
| | - Douglas B Kell
- School of Chemistry and The Manchester Institute of Biotechnology, The University of Manchester, 131 Princess St, Manchester M1 7DN, UK.
| | - Louise C Kenny
- Irish Centre for Fetal and Neonatal Translational Research (INFANT), Cork University Maternity Hospital, Cork, Ireland.
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60
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O'Hagan S, Wright Muelas M, Day PJ, Lundberg E, Kell DB. GeneGini: Assessment via the Gini Coefficient of Reference "Housekeeping" Genes and Diverse Human Transporter Expression Profiles. Cell Syst 2018; 6:230-244.e1. [PMID: 29428416 PMCID: PMC5840522 DOI: 10.1016/j.cels.2018.01.003] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 09/26/2017] [Accepted: 12/30/2017] [Indexed: 01/13/2023]
Abstract
The expression levels of SLC or ABC membrane transporter transcripts typically differ 100- to 10,000-fold between different tissues. The Gini coefficient characterizes such inequalities and here is used to describe the distribution of the expression of each transporter among different human tissues and cell lines. Many transporters exhibit extremely high Gini coefficients even for common substrates, indicating considerable specialization consistent with divergent evolution. The expression profiles of SLC transporters in different cell lines behave similarly, although Gini coefficients for ABC transporters tend to be larger in cell lines than in tissues, implying selection. Transporter genes are significantly more heterogeneously expressed than the members of most non-transporter gene classes. Transcripts with the stablest expression have a low Gini index and often differ significantly from the "housekeeping" genes commonly used for normalization in transcriptomics/qPCR studies. PCBP1 has a low Gini coefficient, is reasonably expressed, and is an excellent novel reference gene. The approach, referred to as GeneGini, provides rapid and simple characterization of expression-profile distributions and improved normalization of genome-wide expression-profiling data.
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Affiliation(s)
- Steve O'Hagan
- School of Chemistry, 131, Princess Street, Manchester M1 7DN, UK; The Manchester Institute of Biotechnology, 131, Princess Street, Manchester M1 7DN, UK
| | - Marina Wright Muelas
- School of Chemistry, 131, Princess Street, Manchester M1 7DN, UK; The Manchester Institute of Biotechnology, 131, Princess Street, Manchester M1 7DN, UK
| | - Philip J Day
- The Manchester Institute of Biotechnology, 131, Princess Street, Manchester M1 7DN, UK; Faculty of Biology, Medicine and Health, The University of Manchester, Oxford Road, Manchester M13 9PL, UK
| | - Emma Lundberg
- Science for Life Laboratory, Royal Institute of Technology (KTH), SE-17121 Solna, Sweden.
| | - Douglas B Kell
- School of Chemistry, 131, Princess Street, Manchester M1 7DN, UK; The Manchester Institute of Biotechnology, 131, Princess Street, Manchester M1 7DN, UK.
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61
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O'Hagan S, Kell DB. Analysing and Navigating Natural Products Space for Generating Small, Diverse, But Representative Chemical Libraries. Biotechnol J 2017; 13. [PMID: 29168302 DOI: 10.1002/biot.201700503] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 11/09/2017] [Indexed: 01/01/2023]
Abstract
Armed with the digital availability of two natural products libraries, amounting to some 195 885 molecular entities, we ask the question of how we can best sample from them to maximize their "representativeness" in smaller and more usable libraries of 96, 384, 1152, and 1920 molecules. The term "representativeness" is intended to include diversity, but for numerical reasons (and the likelihood of being able to perform a QSAR) it is necessary to focus on areas of chemical space that are more highly populated. Encoding chemical structures as fingerprints using the RDKit "patterned" algorithm, we first assess the granularity of the natural products space using a simple clustering algorithm, showing that there are major regions of "denseness" but also a great many very sparsely populated areas. We then apply a "hybrid" hierarchical K-means clustering algorithm to the data to produce more statistically robust clusters from which representative and appropriate numbers of samples may be chosen. There is necessarily again a trade-off between cluster size and cluster number, but within these constraints, libraries containing 384 or 1152 molecules can be found that come from clusters that represent some 18 and 30% of the whole chemical space, with cluster sizes of, respectively, 50 and 27 or above, just about sufficient to perform a QSAR. By using the online availability of molecules via the Molport system (www.molport.com), we are also able to construct (and, for the first time, provide the contents of) a small virtual library of available molecules that provided effective coverage of the chemical space described. Consistent with this, the average molecular similarities of the contents of the libraries developed is considerably smaller than is that of the original libraries. The suggested libraries may have use in molecular or phenotypic screening, including for determining possible transporter substrates.
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Affiliation(s)
- Steve O'Hagan
- Dr. S. O'Hagan, Prof. D. B. Kell, School of Chemistry, The University of Manchester, 131 Princess St, Manchester M1 7DN, UK.,Dr. S. O'Hagan, Prof. D. B. Kell, The Manchester Institute of Biotechnology, The University of Manchester, 131 Princess St, Manchester M1 7DN, UK
| | - Douglas B Kell
- Dr. S. O'Hagan, Prof. D. B. Kell, School of Chemistry, The University of Manchester, 131 Princess St, Manchester M1 7DN, UK.,Dr. S. O'Hagan, Prof. D. B. Kell, The Manchester Institute of Biotechnology, The University of Manchester, 131 Princess St, Manchester M1 7DN, UK.,Prof. D. B. Kell, Centre for the Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), The University of Manchester, 131 Princess St, Manchester M1 7DN, UK
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62
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Karbanova S, Cerveny L, Ceckova M, Ptackova Z, Jiraskova L, Greenwood S, Staud F. Role of nucleoside transporters in transplacental pharmacokinetics of nucleoside reverse transcriptase inhibitors zidovudine and emtricitabine. Placenta 2017; 60:86-92. [PMID: 29208244 DOI: 10.1016/j.placenta.2017.10.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Revised: 10/29/2017] [Accepted: 10/30/2017] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Zidovudine (AZT) and emtricitabine (FTC) are effective and well tolerated antiretroviral drugs, routinely used in the prevention of perinatal HIV transmission. However, precise mechanism(s) involved in their transfer from mother to fetus are not fully elucidated. Since both drugs are nucleoside analogues, we hypothesized that the mechanisms of their transplacental passage might include equilibrative nucleoside transporters, ENT1 and/or ENT2. METHODS To address this issue, we performed in vitro accumulation assays in the BeWo placental trophoblast cell line, ex vivo uptake studies in fresh villous fragments isolated from human placenta and in situ dually perfused rat term placenta experiments. RESULTS Applying this complex array of methods, we did not prove that ENTs play a significant role in transfer of AZT or FTC across the placenta. DISCUSSION We conclude that the transplacental passage of AZT and FTC is independent of ENTs. Disposition of either compound into the fetal circulation should thus not be affected by ENT-mediated drug-drug interactions or placental expression of the transporters.
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Affiliation(s)
- S Karbanova
- Department of Pharmacology and Toxicology, Charles University, Faculty of Pharmacy in Hradec Kralove, Akademika Heyrovskeho 1203, 50005 Hradec Kralove, Czech Republic
| | - L Cerveny
- Department of Pharmacology and Toxicology, Charles University, Faculty of Pharmacy in Hradec Kralove, Akademika Heyrovskeho 1203, 50005 Hradec Kralove, Czech Republic
| | - M Ceckova
- Department of Pharmacology and Toxicology, Charles University, Faculty of Pharmacy in Hradec Kralove, Akademika Heyrovskeho 1203, 50005 Hradec Kralove, Czech Republic
| | - Z Ptackova
- Department of Pharmacology and Toxicology, Charles University, Faculty of Pharmacy in Hradec Kralove, Akademika Heyrovskeho 1203, 50005 Hradec Kralove, Czech Republic
| | - L Jiraskova
- Department of Pharmacology and Toxicology, Charles University, Faculty of Pharmacy in Hradec Kralove, Akademika Heyrovskeho 1203, 50005 Hradec Kralove, Czech Republic
| | - S Greenwood
- Maternal and Fetal Health Research Centre, Institute of Human Development, University of Manchester, St. Mary's Hospital, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester M13 9WL, UK
| | - F Staud
- Department of Pharmacology and Toxicology, Charles University, Faculty of Pharmacy in Hradec Kralove, Akademika Heyrovskeho 1203, 50005 Hradec Kralove, Czech Republic.
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63
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Grixti JM, O'Hagan S, Day PJ, Kell DB. Enhancing Drug Efficacy and Therapeutic Index through Cheminformatics-Based Selection of Small Molecule Binary Weapons That Improve Transporter-Mediated Targeting: A Cytotoxicity System Based on Gemcitabine. Front Pharmacol 2017; 8:155. [PMID: 28396636 PMCID: PMC5366350 DOI: 10.3389/fphar.2017.00155] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 03/10/2017] [Indexed: 12/23/2022] Open
Abstract
The transport of drug molecules is mainly determined by the distribution of influx and efflux transporters for which they are substrates. To enable tissue targeting, we sought to develop the idea that we might affect the transporter-mediated disposition of small-molecule drugs via the addition of a second small molecule that of itself had no inhibitory pharmacological effect but that influenced the expression of transporters for the primary drug. We refer to this as a “binary weapon” strategy. The experimental system tested the ability of a molecule that on its own had no cytotoxic effect to increase the toxicity of the nucleoside analog gemcitabine to Panc1 pancreatic cancer cells. An initial phenotypic screen of a 500-member polar drug (fragment) library yielded three “hits.” The structures of 20 of the other 2,000 members of this library suite had a Tanimoto similarity greater than 0.7 to those of the initial hits, and each was itself a hit (the cheminformatics thus providing for a massive enrichment). We chose the top six representatives for further study. They fell into three clusters whose members bore reasonable structural similarities to each other (two were in fact isomers), lending strength to the self-consistency of both our conceptual and experimental strategies. Existing literature had suggested that indole-3-carbinol might play a similar role to that of our fragments, but in our hands it was without effect; nor was it structurally similar to any of our hits. As there was no evidence that the fragments could affect toxicity directly, we looked for effects on transporter transcript levels. In our hands, only the ENT1-3 uptake and ABCC2,3,4,5, and 10 efflux transporters displayed measurable transcripts in Panc1 cultures, along with a ribonucleoside reductase RRM1 known to affect gemcitabine toxicity. Very strikingly, the addition of gemcitabine alone increased the expression of the transcript for ABCC2 (MRP2) by more than 12-fold, and that of RRM1 by more than fourfold, and each of the fragment “hits” served to reverse this. However, an inhibitor of ABCC2 was without significant effect, implying that RRM1 was possibly the more significant player. These effects were somewhat selective for Panc cells. It seems, therefore, that while the effects we measured were here mediated more by efflux than influx transporters, and potentially by other means, the binary weapon idea is hereby fully confirmed: it is indeed possible to find molecules that manipulate the expression of transporters that are involved in the bioactivity of a pharmaceutical drug. This opens up an entirely new area, that of chemical genomics-based drug targeting.
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Affiliation(s)
- Justine M Grixti
- Faculty of Biology, Medicine and Health, University of ManchesterManchester, UK; Manchester Institute of Biotechnology, University of ManchesterManchester, UK
| | - Steve O'Hagan
- Manchester Institute of Biotechnology, University of ManchesterManchester, UK; School of Chemistry, University of ManchesterManchester, UK; Centre for Synthetic Biology of Fine and Speciality Chemicals, University of ManchesterManchester, UK
| | - Philip J Day
- Faculty of Biology, Medicine and Health, University of ManchesterManchester, UK; Manchester Institute of Biotechnology, University of ManchesterManchester, UK
| | - Douglas B Kell
- Manchester Institute of Biotechnology, University of ManchesterManchester, UK; School of Chemistry, University of ManchesterManchester, UK; Centre for Synthetic Biology of Fine and Speciality Chemicals, University of ManchesterManchester, UK
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64
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O'Hagan S, Kell DB. Analysis of drug-endogenous human metabolite similarities in terms of their maximum common substructures. J Cheminform 2017; 9:18. [PMID: 28316656 PMCID: PMC5344883 DOI: 10.1186/s13321-017-0198-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 02/09/2017] [Indexed: 12/21/2022] Open
Abstract
In previous work, we have assessed the structural similarities between marketed drugs (‘drugs’) and endogenous natural human metabolites (‘metabolites’ or ‘endogenites’), using ‘fingerprint’ methods in common use, and the Tanimoto and Tversky similarity metrics, finding that the fingerprint encoding used had a dramatic effect on the apparent similarities observed. By contrast, the maximal common substructure (MCS), when the means of determining it is fixed, is a means of determining similarities that is largely independent of the fingerprints, and also has a clear chemical meaning. We here explored the utility of the MCS and metrics derived therefrom. In many cases, a shared scaffold helps cluster drugs and endogenites, and gives insight into enzymes (in particular transporters) that they both share. Tanimoto and Tversky similarities based on the MCS tend to be smaller than those based on the MACCS fingerprint-type encoding, though the converse is also true for a significant fraction of the comparisons. While no single molecular descriptor can account for these differences, a machine learning-based analysis of the nature of the differences (MACCS_Tanimoto vs MCS_Tversky) shows that they are indeed deterministic, although the features that are used in the model to account for this vary greatly with each individual drug. The extent of its utility and interpretability vary with the drug of interest, implying that while MCS is neither ‘better’ nor ‘worse’ for every drug–endogenite comparison, it is sufficiently different to be of value. The overall conclusion is thus that the use of the MCS provides an additional and valuable strategy for understanding the structural basis for similarities between synthetic, marketed drugs and natural intermediary metabolites.
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Affiliation(s)
- Steve O'Hagan
- School of Chemistry, The University of Manchester, 131 Princess St, Manchester, M1 7DN UK.,Manchester Institute of Biotechnology, The University of Manchester, 131 Princess St, Manchester, M1 7DN UK
| | - Douglas B Kell
- School of Chemistry, The University of Manchester, 131 Princess St, Manchester, M1 7DN UK.,Manchester Institute of Biotechnology, The University of Manchester, 131 Princess St, Manchester, M1 7DN UK.,Centre for the Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), The University of Manchester, 131 Princess St, Manchester, M1 7DN UK
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65
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Scott D, Ghosh A, Di L, Maurer T. Passive drug permeation through membranes and cellular distribution. Pharmacol Res 2017; 117:94-102. [DOI: 10.1016/j.phrs.2016.11.028] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 11/22/2016] [Indexed: 12/24/2022]
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66
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Proteins behaving badly. Substoichiometric molecular control and amplification of the initiation and nature of amyloid fibril formation: lessons from and for blood clotting. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017; 123:16-41. [DOI: 10.1016/j.pbiomolbio.2016.08.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Revised: 08/14/2016] [Accepted: 08/19/2016] [Indexed: 02/08/2023]
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Mooij MG, Nies AT, Knibbe CAJ, Schaeffeler E, Tibboel D, Schwab M, de Wildt SN. Development of Human Membrane Transporters: Drug Disposition and Pharmacogenetics. Clin Pharmacokinet 2016; 55:507-24. [PMID: 26410689 PMCID: PMC4823323 DOI: 10.1007/s40262-015-0328-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Membrane transporters play an essential role in the transport of endogenous and exogenous compounds, and consequently they mediate the uptake, distribution, and excretion of many drugs. The clinical relevance of transporters in drug disposition and their effect in adults have been shown in drug–drug interaction and pharmacogenomic studies. Little is known, however, about the ontogeny of human membrane transporters and their roles in pediatric pharmacotherapy. As they are involved in the transport of endogenous substrates, growth and development may be important determinants of their expression and activity. This review presents an overview of our current knowledge on human membrane transporters in pediatric drug disposition and effect. Existing pharmacokinetic and pharmacogenetic data on membrane substrate drugs frequently used in children are presented and related, where possible, to existing ex vivo data, providing a basis for developmental patterns for individual human membrane transporters. As data for individual transporters are currently still scarce, there is a striking information gap regarding the role of human membrane transporters in drug therapy in children.
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Affiliation(s)
- Miriam G Mooij
- Intensive Care and Department of Pediatric Surgery, Erasmus MC-Sophia Children's Hospital, Room Sp-3458, Wytemaweg 80, PO-box 2060, 3000 CB, Rotterdam, The Netherlands
| | - Anne T Nies
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany
| | - Catherijne A J Knibbe
- Faculty of Science, Leiden Academic Centre for Research, Pharmacology, Leiden, The Netherlands.,Hospital Pharmacy and Clinical Pharmacology, St. Antonius Hospital, Nieuwegein, The Netherlands
| | - Elke Schaeffeler
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,University of Tuebingen, Tuebingen, Germany
| | - Dick Tibboel
- Intensive Care and Department of Pediatric Surgery, Erasmus MC-Sophia Children's Hospital, Room Sp-3458, Wytemaweg 80, PO-box 2060, 3000 CB, Rotterdam, The Netherlands
| | - Matthias Schwab
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany.,Department of Clinical Pharmacology, University Hospital Tuebingen, Tuebingen, Germany
| | - Saskia N de Wildt
- Intensive Care and Department of Pediatric Surgery, Erasmus MC-Sophia Children's Hospital, Room Sp-3458, Wytemaweg 80, PO-box 2060, 3000 CB, Rotterdam, The Netherlands.
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68
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Silver LL. A Gestalt approach to Gram-negative entry. Bioorg Med Chem 2016; 24:6379-6389. [DOI: 10.1016/j.bmc.2016.06.044] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 06/12/2016] [Accepted: 06/22/2016] [Indexed: 01/01/2023]
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Pretorius E, Akeredolu OO, Soma P, Kell DB. Major involvement of bacterial components in rheumatoid arthritis and its accompanying oxidative stress, systemic inflammation and hypercoagulability. Exp Biol Med (Maywood) 2016; 242:355-373. [PMID: 27889698 PMCID: PMC5298544 DOI: 10.1177/1535370216681549] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
We review the evidence that infectious agents, including those that become dormant within the host, have a major role to play in much of the etiology of rheumatoid arthritis and the inflammation that is its hallmark. This occurs in particular because they can produce cross-reactive (auto-)antigens, as well as potent inflammagens such as lipopolysaccharide that can themselves catalyze further inflammagenesis, including via β-amyloid formation. A series of observables coexist in many chronic, inflammatory diseases as well as rheumatoid arthritis. They include iron dysregulation, hypercoagulability, anomalous morphologies of host erythrocytes, and microparticle formation. Iron dysregulation may be responsible for the periodic regrowth and resuscitation of the dormant bacteria, with concomitant inflammagen production. The present systems biology analysis benefits from the philosophical idea of "coherence," that reflects the principle that if a series of ostensibly unrelated findings are brought together into a self-consistent narrative, that narrative is thereby strengthened. As such, we provide a coherent and testable narrative for the major involvement of (often dormant) bacteria in rheumatoid arthritis.
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Affiliation(s)
- Etheresia Pretorius
- 1 Department of Physiology, Faculty of Health Sciences, University of Pretoria, Arcadia, Pretoria 0007, South Africa
| | - Oore-Ofe Akeredolu
- 1 Department of Physiology, Faculty of Health Sciences, University of Pretoria, Arcadia, Pretoria 0007, South Africa
| | - Prashilla Soma
- 1 Department of Physiology, Faculty of Health Sciences, University of Pretoria, Arcadia, Pretoria 0007, South Africa
| | - Douglas B Kell
- 2 School of Chemistry, The University of Manchester, Manchester, M13 9PL, UK.,3 The Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN, UK.,4 Centre for Synthetic Biology of Fine and Speciality Chemicals, The University of Manchester, Manchester, M1 7DN, UK
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Abstract
Cells need to strictly control their internal milieu, a function which is performed by the plasma membrane. Selective passage of molecules across the plasma membrane is controlled by transport proteins. As the liver is the central organ for drug metabolism, hepatocytes are equipped with numerous drug transporters expressed at the plasma membrane. Drug disposition includes absorption, distribution, metabolism, and elimination of a drug and hence multiple passages of drugs and their metabolites across membranes. Consequently, understanding the exact mechanisms of drug transporters is essential both in drug development and in drug therapy. While many drug transporters are expressed in hepatocytes, and some of them are well characterized, several transporters have only recently been identified as new drug transporters. Novel powerful tools to deorphanize (drug) transporters are being applied and show promising results. Although a large set of tools are available for studying transport in vitro and in isolated cells, tools for studying transport in living organisms, including humans, are evolving now and rely predominantly on imaging techniques, e.g. positron emission tomography. Imaging is an area which, certainly in the near future, will provide important insights into "transporters at work" in vivo.
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Affiliation(s)
- Bruno Stieger
- Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, University of Zurich, Zurich, 8091, Switzerland
| | - Bruno Hagenbuch
- Department of Pharmacology, Toxicology and Therapeutics, The University of Kansas Medical Center, Kansas City, KS, 66160, USA
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71
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Kell DB, Pretorius E. On the translocation of bacteria and their lipopolysaccharides between blood and peripheral locations in chronic, inflammatory diseases: the central roles of LPS and LPS-induced cell death. Integr Biol (Camb) 2016; 7:1339-77. [PMID: 26345428 DOI: 10.1039/c5ib00158g] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We have recently highlighted (and added to) the considerable evidence that blood can contain dormant bacteria. By definition, such bacteria may be resuscitated (and thus proliferate). This may occur under conditions that lead to or exacerbate chronic, inflammatory diseases that are normally considered to lack a microbial component. Bacterial cell wall components, such as the endotoxin lipopolysaccharide (LPS) of Gram-negative strains, are well known as potent inflammatory agents, but should normally be cleared. Thus, their continuing production and replenishment from dormant bacterial reservoirs provides an easy explanation for the continuing, low-grade inflammation (and inflammatory cytokine production) that is characteristic of many such diseases. Although experimental conditions and determinants have varied considerably between investigators, we summarise the evidence that in a great many circumstances LPS can play a central role in all of these processes, including in particular cell death processes that permit translocation between the gut, blood and other tissues. Such localised cell death processes might also contribute strongly to the specific diseases of interest. The bacterial requirement for free iron explains the strong co-existence in these diseases of iron dysregulation, LPS production, and inflammation. Overall this analysis provides an integrative picture, with significant predictive power, that is able to link these processes via the centrality of a dormant blood microbiome that can resuscitate and shed cell wall components.
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Affiliation(s)
- Douglas B Kell
- School of Chemistry and The Manchester Institute of Biotechnology, The University of Manchester, 131, Princess St, Manchester M1 7DN, Lancs, UK.
| | - Etheresia Pretorius
- Department of Physiology, Faculty of Health Sciences, University of Pretoria, Arcadia 0007, South Africa.
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Abstract
BACKGROUND The term 'metabolome' was introduced to the scientific literature in September 1998. AIM AND KEY SCIENTIFIC CONCEPTS OF THE REVIEW To mark its 18-year-old 'coming of age', two of the co-authors of that paper review the genesis of metabolomics, whence it has come and where it may be going.
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Affiliation(s)
- Douglas B. Kell
- School of Chemistry, The University of Manchester, 131 Princess St, Manchester, M1 7DN UK
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess St, Manchester, M1 7DN UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), The University of Manchester, 131, Princess St, Manchester, M1 7DN UK
| | - Stephen G. Oliver
- Cambridge Systems Biology Centre, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge, CB2 1GA UK
- Department of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge, CB2 1GA UK
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73
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O'Hagan S, Kell DB. MetMaxStruct: A Tversky-Similarity-Based Strategy for Analysing the (Sub)Structural Similarities of Drugs and Endogenous Metabolites. Front Pharmacol 2016; 7:266. [PMID: 27597830 PMCID: PMC4992690 DOI: 10.3389/fphar.2016.00266] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 08/08/2016] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Previous studies compared the molecular similarity of marketed drugs and endogenous human metabolites (endogenites), using a series of fingerprint-type encodings, variously ranked and clustered using the Tanimoto (Jaccard) similarity coefficient (TS). Because this gives equal weight to all parts of the encoding (thence to different substructures in the molecule) it may not be optimal, since in many cases not all parts of the molecule will bind to their macromolecular targets. Unsupervised methods cannot alone uncover this. We here explore the kinds of differences that may be observed when the TS is replaced-in a manner more equivalent to semi-supervised learning-by variants of the asymmetric Tversky (TV) similarity, that includes α and β parameters. RESULTS Dramatic differences are observed in (i) the drug-endogenite similarity heatmaps, (ii) the cumulative "greatest similarity" curves, and (iii) the fraction of drugs with a Tversky similarity to a metabolite exceeding a given value when the Tversky α and β parameters are varied from their Tanimoto values. The same is true when the sum of the α and β parameters is varied. A clear trend toward increased endogenite-likeness of marketed drugs is observed when α or β adopt values nearer the extremes of their range, and when their sum is smaller. The kinds of molecules exhibiting the greatest similarity to two interrogating drug molecules (chlorpromazine and clozapine) also vary in both nature and the values of their similarity as α and β are varied. The same is true for the converse, when drugs are interrogated with an endogenite. The fraction of drugs with a Tversky similarity to a molecule in a library exceeding a given value depends on the contents of that library, and α and β may be "tuned" accordingly, in a semi-supervised manner. At some values of α and β drug discovery library candidates or natural products can "look" much more like (i.e., have a numerical similarity much closer to) drugs than do even endogenites. CONCLUSIONS Overall, the Tversky similarity metrics provide a more useful range of examples of molecular similarity than does the simpler Tanimoto similarity, and help to draw attention to molecular similarities that would not be recognized if Tanimoto alone were used. Hence, the Tversky similarity metrics are likely to be of significant value in many general problems in cheminformatics.
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Affiliation(s)
- Steve O'Hagan
- School of Chemistry, The University of ManchesterManchester, UK
- The Manchester Institute of Biotechnology, The University of ManchesterManchester, UK
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals, The University of ManchesterManchester, UK
| | - Douglas B. Kell
- School of Chemistry, The University of ManchesterManchester, UK
- The Manchester Institute of Biotechnology, The University of ManchesterManchester, UK
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals, The University of ManchesterManchester, UK
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74
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Elder DP, Kuentz M, Holm R. Pharmaceutical excipients — quality, regulatory and biopharmaceutical considerations. Eur J Pharm Sci 2016; 87:88-99. [DOI: 10.1016/j.ejps.2015.12.018] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 11/25/2015] [Accepted: 12/11/2015] [Indexed: 12/27/2022]
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75
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Fouché M, Schäfer M, Blatter M, Berghausen J, Desrayaud S, Roth HJ. Pharmacokinetic Studies around the Mono- and Difunctionalization of a Bioavailable Cyclic Decapeptide Scaffold. ChemMedChem 2016; 11:1060-8. [DOI: 10.1002/cmdc.201600083] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Indexed: 12/15/2022]
Affiliation(s)
- Marianne Fouché
- Global Discovery Chemistry/Macrocycles; Novartis Institute for BioMedical Research; Basel 4002 Switzerland
| | - Michael Schäfer
- Global Discovery Chemistry/CADD; Novartis Institute for BioMedical Research; Basel 4002 Switzerland
| | - Markus Blatter
- Global Discovery Chemistry/Analytics (NMR); Novartis Institute for BioMedical Research; Basel 4002 Switzerland
| | - Jörg Berghausen
- Metabolism and Pharmacokinetics; Novartis Institute for BioMedical Research; Basel 4002 Switzerland
| | - Sandrine Desrayaud
- Metabolism and Pharmacokinetics; Novartis Institute for BioMedical Research; Basel 4002 Switzerland
| | - Hans-Jörg Roth
- Global Discovery Chemistry/Macrocycles; Novartis Institute for BioMedical Research; Basel 4002 Switzerland
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76
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Mendes P, Oliver SG, Kell DB. Response to ‘The Need for Speed’, by Matsson et al . Trends Pharmacol Sci 2016; 37:245-246. [DOI: 10.1016/j.tips.2016.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 02/02/2016] [Indexed: 12/22/2022]
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77
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Kell DB, Kenny LC. A Dormant Microbial Component in the Development of Preeclampsia. Front Med (Lausanne) 2016; 3:60. [PMID: 27965958 PMCID: PMC5126693 DOI: 10.3389/fmed.2016.00060] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 11/04/2016] [Indexed: 12/12/2022] Open
Abstract
Preeclampsia (PE) is a complex, multisystem disorder that remains a leading cause of morbidity and mortality in pregnancy. Four main classes of dysregulation accompany PE and are widely considered to contribute to its severity. These are abnormal trophoblast invasion of the placenta, anti-angiogenic responses, oxidative stress, and inflammation. What is lacking, however, is an explanation of how these themselves are caused. We here develop the unifying idea, and the considerable evidence for it, that the originating cause of PE (and of the four classes of dysregulation) is, in fact, microbial infection, that most such microbes are dormant and hence resist detection by conventional (replication-dependent) microbiology, and that by occasional resuscitation and growth it is they that are responsible for all the observable sequelae, including the continuing, chronic inflammation. In particular, bacterial products such as lipopolysaccharide (LPS), also known as endotoxin, are well known as highly inflammagenic and stimulate an innate (and possibly trained) immune response that exacerbates the inflammation further. The known need of microbes for free iron can explain the iron dysregulation that accompanies PE. We describe the main routes of infection (gut, oral, and urinary tract infection) and the regularly observed presence of microbes in placental and other tissues in PE. Every known proteomic biomarker of "preeclampsia" that we assessed has, in fact, also been shown to be raised in response to infection. An infectious component to PE fulfills the Bradford Hill criteria for ascribing a disease to an environmental cause and suggests a number of treatments, some of which have, in fact, been shown to be successful. PE was classically referred to as endotoxemia or toxemia of pregnancy, and it is ironic that it seems that LPS and other microbial endotoxins really are involved. Overall, the recognition of an infectious component in the etiology of PE mirrors that for ulcers and other diseases that were previously considered to lack one.
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Affiliation(s)
- Douglas B. Kell
- School of Chemistry, The University of Manchester, Manchester, UK
- The Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals, The University of Manchester, Manchester, UK
- *Correspondence: Douglas B. Kell,
| | - Louise C. Kenny
- The Irish Centre for Fetal and Neonatal Translational Research (INFANT), University College Cork, Cork, Ireland
- Department of Obstetrics and Gynecology, University College Cork, Cork, Ireland
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78
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Johnston AJ, Busch S, Pardo LC, Callear SK, Biggin PC, McLain SE. On the atomic structure of cocaine in solution. Phys Chem Chem Phys 2016; 18:991-9. [DOI: 10.1039/c5cp06090g] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
A combination of neutron diffraction and computation has been used to investigate the atomic scale structure of cocaine in aqueous solutions.
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Affiliation(s)
| | - Sebastian Busch
- German Engineering Materials Science Centre (GEMS) at Heinz Maier-Leibnitz Zentrum (MLZ)
- Helmholtz-Zentrum Geesthacht GmbH
- 85747 Garching bei München
- Germany
| | - Luis Carlos Pardo
- Departament de Física i Enginyeria Nuclear
- Escola Tècnica Superior d'Enginyeria Industrial de Barcelona (ETSEIB)
- Universitat Politècnica de Catalunya
- 08028 Barcelona
- Spain
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79
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Kell DB. The transporter-mediated cellular uptake of pharmaceutical drugs is based on their metabolite-likeness and not on their bulk biophysical properties: Towards a systems pharmacology. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.pisc.2015.06.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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80
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Karlgren M, Bergström CAS. How Physicochemical Properties of Drugs Affect Their Metabolism and Clearance. NEW HORIZONS IN PREDICTIVE DRUG METABOLISM AND PHARMACOKINETICS 2015. [DOI: 10.1039/9781782622376-00001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
In this chapter the transport proteins and enzymes of importance for drug clearance are discussed. The primary organ for drug metabolism is the liver and to reach the intracellular compartment of hepatocytes, orally administered drugs must cross both the intestinal wall and the cell membrane of the liver cells. Transport proteins present in the cellular membrane may facilitate or hinder the compounds crossing these cellular barriers and hence will influence to what extent compounds will reach the enzymes. Here, the enzymes and transport proteins of importance for drug clearance are discussed. The molecular features of importance for drug interactions with transport proteins and enzymes are analyzed and the possibility to predict molecular features vulnerable to enzymatic degradation is discussed. From detailed analysis of the current literature it is concluded that for interaction, both with transport proteins and enzymes, lipophilicity plays a major role. In addition to this property, molecular properties such as hydrogen bond acceptors and donors, charge, aromaticity and molecular size can be used to distinguish between routes of clearance.
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Affiliation(s)
- Maria Karlgren
- Department of Pharmacy, Uppsala University Biomedical Centre P.O. Box 580, Husargatan 3 SE-75123 Uppsala Sweden
| | - Christel A. S. Bergström
- Department of Pharmacy, Uppsala University Biomedical Centre P.O. Box 580, Husargatan 3 SE-75123 Uppsala Sweden
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81
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O’Hagan S, Kell DB. The apparent permeabilities of Caco-2 cells to marketed drugs: magnitude, and independence from both biophysical properties and endogenite similarities. PeerJ 2015; 3:e1405. [PMID: 26618081 PMCID: PMC4655101 DOI: 10.7717/peerj.1405] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 10/25/2015] [Indexed: 12/25/2022] Open
Abstract
We bring together fifteen, nonredundant, tabulated collections (amounting to 696 separate measurements) of the apparent permeability (P app) of Caco-2 cells to marketed drugs. While in some cases there are some significant interlaboratory disparities, most are quite minor. Most drugs are not especially permeable through Caco-2 cells, with the median P app value being some 16 ⋅ 10(-6) cm s(-1). This value is considerably lower than those (1,310 and 230 ⋅ 10(-6) cm s(-1)) recently used in some simulations that purported to show that P app values were too great to be transporter-mediated only. While these values are outliers, all values, and especially the comparatively low values normally observed, are entirely consistent with transporter-only mediated uptake, with no need to invoke phospholipid bilayer diffusion. The apparent permeability of Caco-2 cells to marketed drugs is poorly correlated with either simple biophysical properties, the extent of molecular similarity to endogenous metabolites (endogenites), or any specific substructural properties. In particular, the octanol:water partition coefficient, logP, shows negligible correlation with Caco-2 permeability. The data are best explained on the basis that most drugs enter (and exit) Caco-2 cells via a multiplicity of transporters of comparatively weak specificity.
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Affiliation(s)
- Steve O’Hagan
- School of Chemistry & The Manchester Institute of Biotechnology and Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), The University of Manchester, Manchester, Lancs, United Kingdom
| | - Douglas B. Kell
- School of Chemistry & The Manchester Institute of Biotechnology and Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), The University of Manchester, Manchester, Lancs, United Kingdom
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82
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Mendes P, Oliver SG, Kell DB. Fitting Transporter Activities to Cellular Drug Concentrations and Fluxes: Why the Bumblebee Can Fly. Trends Pharmacol Sci 2015; 36:710-723. [PMID: 26538313 PMCID: PMC4642801 DOI: 10.1016/j.tips.2015.07.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Revised: 07/23/2015] [Accepted: 07/23/2015] [Indexed: 12/18/2022]
Abstract
A recent paper in this journal argued that reported expression levels, kcat and Km for drug transporters could be used to estimate the likelihood that drug fluxes through Caco-2 cells could be accounted for solely by protein transporters. It was in fact concluded that if five such transporters contributed ‘randomly’ they could account for the flux of the most permeable drug tested (verapamil) 35% of the time. However, the values of permeability cited for verapamil were unusually high; this and other drugs have much lower permeabilities. Even for the claimed permeabilities, we found that a single ‘random’ transporter could account for the flux 42% of the time, and that two transporters can achieve 10 · 10−6 cm·s−1 90% of the time. Parameter optimisation methods show that even a single transporter can account for Caco-2 drug uptake of the most permeable drug. Overall, the proposal that ‘phospholipid bilayer diffusion (of drugs) is negligible’ is not disproved by the calculations of ‘likely’ transporter-based fluxes. There has been recent debate as to the relative extents to which cellular transmembrane drug transports occur through any phospholipid bilayer region or is transporter-mediated only. Much recent evidence suggests (perhaps surprisingly) that phospholipid bilayer diffusion is negligible. A recent article in this journal suggested that the expression profile and kinetics of known transporters might not be adequate to explain the most active drug fluxes (of verapamil and propranolol) in Caco-2 cells via transporters only. We show with our own simulations that this is not in fact the case, especially when evolutionary selection is taken into account, and that the Haldane relation accounts straightforwardly for directional differences, even for equilibrative transporters. Typical protein transporters alone can easily account for measured drug fluxes in Caco-2 cells.
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Affiliation(s)
- Pedro Mendes
- School of Computer Science; Manchester Institute of Biotechnology, The University of Manchester, 131 Princess St, Manchester M1 7DN, UK; Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), The University of Manchester, 131, Princess St, Manchester M1 7DN, United Kingdom; Center for Quantitative Medicine, University of Connecticut, UConn Health, 263 Farmington Avenue, Farmington, CT 06030-6033, USA
| | - Stephen G Oliver
- Cambridge Systems Biology Centre; Dept of Biochemistry, University of Cambridge, Sanger Building, 80 Tennis Court Road, Cambridge CB2 1GA, UK
| | - Douglas B Kell
- Manchester Institute of Biotechnology, The University of Manchester, 131 Princess St, Manchester M1 7DN, UK; Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), The University of Manchester, 131, Princess St, Manchester M1 7DN, United Kingdom; School of Chemistry, The University of Manchester, Manchester M13 9PL, United Kingdom.
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83
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César-Razquin A, Snijder B, Frappier-Brinton T, Isserlin R, Gyimesi G, Bai X, Reithmeier RA, Hepworth D, Hediger MA, Edwards AM, Superti-Furga G. A Call for Systematic Research on Solute Carriers. Cell 2015; 162:478-87. [PMID: 26232220 DOI: 10.1016/j.cell.2015.07.022] [Citation(s) in RCA: 388] [Impact Index Per Article: 43.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Indexed: 01/10/2023]
Abstract
Solute carrier (SLC) membrane transport proteins control essential physiological functions, including nutrient uptake, ion transport, and waste removal. SLCs interact with several important drugs, and a quarter of the more than 400 SLC genes are associated with human diseases. Yet, compared to other gene families of similar stature, SLCs are relatively understudied. The time is right for a systematic attack on SLC structure, specificity, and function, taking into account kinship and expression, as well as the dependencies that arise from the common metabolic space.
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Affiliation(s)
- Adrián César-Razquin
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Berend Snijder
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | | | - Ruth Isserlin
- The Donnelly Centre, University of Toronto, Toronto, Ontario, M5S 3E1, Canada
| | - Gergely Gyimesi
- Institute of Biochemistry and Molecular Medicine and Swiss National Center of Competence in Research, NCCR TransCure, University of Bern, 3012 Bern, Switzerland
| | - Xiaoyun Bai
- Department of Biochemistry, University of Toronto, Toronto, Ontario, M5S 1A8 Canada
| | | | - David Hepworth
- Worldwide Medicinal Chemistry, Pfizer Worldwide Research and Development, Cambridge, MA 02139, USA
| | - Matthias A Hediger
- Institute of Biochemistry and Molecular Medicine and Swiss National Center of Competence in Research, NCCR TransCure, University of Bern, 3012 Bern, Switzerland.
| | - Aled M Edwards
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada.
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria; Center for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria.
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84
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Marelli UK, Ovadia O, Frank AO, Chatterjee J, Gilon C, Hoffman A, Kessler H. cis-Peptide Bonds: A Key for Intestinal Permeability of Peptides? Chemistry 2015; 21:15148-52. [DOI: 10.1002/chem.201501600] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Indexed: 12/12/2022]
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85
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Abstract
Nearly 30years ago, certain small, relatively nontoxic peptides were discovered to be capable of traversing the cell membrane. These cell-penetrating peptides, as they are now called, have been shown to not only be capable of crossing the cell membrane themselves but can also carry many different therapeutic agents into cells, including small molecules, plasmid DNA, siRNA, therapeutic proteins, viruses, imaging agents, and other various nanoparticles. Many cell-penetrating peptides have been derived from natural proteins, but several other cell-penetrating peptides have been developed that are either chimeric or completely synthetic. How cell-penetrating peptides are internalized into cells has been a topic of debate, with some peptides seemingly entering cells through an endocytic mechanism and others by directly penetrating the cell membrane. Although the entry mechanism is still not entirely understood, it seems to be dependent on the peptide type, the peptide concentration, the cargo the peptide transports, and the cell type tested. With new intracellular disease targets being discovered, cell-penetrating peptides offer an exciting approach for delivering drugs to these intracellular targets. There are hundreds of cell-penetrating peptides being studied for drug delivery, and ongoing studies are demonstrating their success both in vitro and in vivo.
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Affiliation(s)
- Joshua D Ramsey
- School of Chemical Engineering, Oklahoma State University, Stillwater, OK 74078, United States.
| | - Nicholas H Flynn
- School of Chemical Engineering, Oklahoma State University, Stillwater, OK 74078, United States
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86
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Camp D, Garavelas A, Campitelli M. Analysis of Physicochemical Properties for Drugs of Natural Origin. JOURNAL OF NATURAL PRODUCTS 2015; 78:1370-1382. [PMID: 26039921 DOI: 10.1021/acs.jnatprod.5b00255] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The impact of time, therapy area, and route of administration on 13 physicochemical properties calculated for 664 drugs developed from a natural prototype was investigated. The mean values for the majority of properties sampled over five periods from pre-1900 to 2013 were found to change in a statistically significant manner. In contrast, lipophilicity and aromatic ring count remained relatively constant, suggesting that these parameters are the most important for successful prosecution of a natural product drug discovery program if the route of administration is not focused exclusively on oral availability. An examination by therapy area revealed that anti-infective agents had the most differences in physicochemical property profiles compared with other areas, particularly with respect to lipophilicity. However, when this group was removed, the variation between the mean values for lipophilicity and aromatic ring count across the remaining therapy areas was again found not to change in a meaningful manner, further highlighting the importance of these two parameters. The vast majority of drugs with a natural progenitor were formulated for either oral and/or injectable administration. Injectables were, on average, larger and more polar than drugs developed for oral, topical, and inhalation routes.
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Affiliation(s)
| | | | - Marc Campitelli
- §QIMR Berghofer Medical Research Institute, Herston, QLD 4006, Australia
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87
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Marcondes MC, Fernandes ACS, Itabaiana I, de Souza ROMA, Sola-Penna M, Zancan P. Nanomicellar Formulation of Clotrimazole Improves Its Antitumor Action toward Human Breast Cancer Cells. PLoS One 2015; 10:e0130555. [PMID: 26098874 PMCID: PMC4476588 DOI: 10.1371/journal.pone.0130555] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 05/21/2015] [Indexed: 02/04/2023] Open
Abstract
Background Although demonstrated as a selective anticancer drug, the clinical use of clotrimazole (CTZ) is limited due to its low solubility in hydrophilic fluids. Thus, we prepared a water-soluble nanomicellar formulation of CTZ (nCTZ) and tested on the human breast cancer cell line MCF-7 biology. Methodology/Principal Findings CTZ was nanoencapsulated in tween 80 micelles, which generated nanomicelles of, approximately, 17 nm of diameter. MCF-7 cells were treated with nCTZ and unencapsulated DMSO-solubilized drug (sCTZ) was used for comparison. After treatment, the cells were evaluated in terms of metabolism, proliferation, survival and structure. We found that nCTZ was more efficient than sCTZ at inhibiting glycolytic and other cytosolic and mitochondrial enzymes. Moreover, this increased activity was also observed for lactate production, intracellular ATP content, ROS production and antioxidant potential. As a consequence, nCTZ-treated MCF-7 cells displayed alterations to the plasma membrane, mitochondria and the nucleus. Finally, nCTZ induced both apoptosis and necrosis in MCF-7 cells. Conclusions/Significance MCF-7 cells are more sensible to nCTZ than to sCTZ. This was especially evident on regard to antioxidant potential, which is an important cell defense against drugs that affect cell metabolism. Moreover, this water-soluble formulation of CTZ strengths its potential use as an anticancer medicine.
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Affiliation(s)
- Mariah C. Marcondes
- Laboratório de Oncobiologia Molecular (LabOMol), Departamento de Biotecnologia Farmacêutica (BioTecFar), Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - Anne C. S. Fernandes
- Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - Ivaldo Itabaiana
- Laboratório de Biocatálise e Síntese Orgânica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - Rodrigo O. M. A. de Souza
- Laboratório de Biocatálise e Síntese Orgânica, Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - Mauro Sola-Penna
- Laboratório de Enzimologia e Controle do Metabolismo (LabECoM), Departamento de Biotecnologia Farmacêutica (BioTecFar), Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
| | - Patricia Zancan
- Laboratório de Oncobiologia Molecular (LabOMol), Departamento de Biotecnologia Farmacêutica (BioTecFar), Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brasil
- * E-mail:
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88
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Oja M, Maran U. The Permeability of an Artificial Membrane for Wide Range of pH in Human Gastrointestinal Tract: Experimental Measurements and Quantitative StructureActivity Relationship. Mol Inform 2015; 34:493-506. [PMID: 27490393 DOI: 10.1002/minf.201400147] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2014] [Accepted: 05/06/2015] [Indexed: 11/08/2022]
Abstract
In silico models for membrane permeability have been based on values measured for single pH. Depending on the diet (fasted/fed state) and part of human intestine the range of pH varies approximately from 2.4 to 8.0. This motivated to study and model the membrane permeability of chemicals considering the whole range of pH in the human intestine. For this, effective membrane permeability values were measured for 65 drugs and drug-like compounds using PAMPA method at four pHs (3, 5, 7.4, 9) over 48 h, introducing technological innovations for the time-dependence measurement. The highest permeability value of a compound from four pHs was used to derive QSAR analyzing a large pool of molecular descriptors and introducing new descriptor. Using stepwise forward selection approach a significant QSAR model was derived that included only two mechanistically relevant descriptors, the logarithmic octanol-water partition coefficient and hydrogen bonding surface area. Prediction confidence of the model was blind tested with a true external validation set of 15 compounds. The resulting QSAR model shows potential to combine permeability values from various pH-s into one descriptive and predictive model for estimating maximum permeability in human gastrointestinal tract. The QSAR model and data are available through the QsarDB repository (http://dx.doi.org/10.15152/QDB.137).
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Affiliation(s)
- Mare Oja
- Institute of Chemistry, University of Tartu, Ravila 14A, Tartu 50411, Estonia phone +372 7 375 254, fax +372 7 375 264
| | - Uko Maran
- Institute of Chemistry, University of Tartu, Ravila 14A, Tartu 50411, Estonia phone +372 7 375 254, fax +372 7 375 264.
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89
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O'Hagan S, Kell DB. Understanding the foundations of the structural similarities between marketed drugs and endogenous human metabolites. Front Pharmacol 2015; 6:105. [PMID: 26029108 PMCID: PMC4429554 DOI: 10.3389/fphar.2015.00105] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 04/29/2015] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND A recent comparison showed the extensive similarities between the structural properties of metabolites in the reconstructed human metabolic network ("endogenites") and those of successful, marketed drugs ("drugs"). RESULTS Clustering indicated the related but differential population of chemical space by endogenites and drugs. Differences between the drug-endogenite similarities resulting from various encodings and judged by Tanimoto similarity could be related simply to the fraction of the bitstrings set to 1. By extracting drug/endogenite substructures, we develop a novel family of fingerprints, the Drug Endogenite Substructure (DES) encodings, based on the ranked frequency of the various substructures. These provide a natural assessment of drug-endogenite likeness, and may be used as descriptors with which to derive quantitative structure-activity relationships (QSARs). CONCLUSIONS "Drug-endogenite likeness" seems to have utility, and leads to a simple, novel and interpretable substructure-based molecular encoding for cheminformatics.
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Affiliation(s)
- Steve O'Hagan
- School of Chemistry, The University of Manchester Manchester, UK ; The Manchester Institute of Biotechnology, The University of Manchester Manchester, UK
| | - Douglas B Kell
- School of Chemistry, The University of Manchester Manchester, UK ; The Manchester Institute of Biotechnology, The University of Manchester Manchester, UK
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90
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Marelli UK, Bezençon J, Puig E, Ernst B, Kessler H. Enantiomeric Cyclic Peptides with Different Caco-2 Permeability Suggest Carrier-Mediated Transport. Chemistry 2015; 21:8023-7. [DOI: 10.1002/chem.201501270] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Indexed: 12/23/2022]
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91
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Membrane transporter engineering in industrial biotechnology and whole cell biocatalysis. Trends Biotechnol 2015; 33:237-46. [DOI: 10.1016/j.tibtech.2015.02.001] [Citation(s) in RCA: 145] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Revised: 01/15/2015] [Accepted: 02/02/2015] [Indexed: 02/06/2023]
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92
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Currin A, Swainston N, Day PJ, Kell DB. Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. Chem Soc Rev 2015; 44:1172-239. [PMID: 25503938 PMCID: PMC4349129 DOI: 10.1039/c4cs00351a] [Citation(s) in RCA: 251] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Indexed: 12/21/2022]
Abstract
The amino acid sequence of a protein affects both its structure and its function. Thus, the ability to modify the sequence, and hence the structure and activity, of individual proteins in a systematic way, opens up many opportunities, both scientifically and (as we focus on here) for exploitation in biocatalysis. Modern methods of synthetic biology, whereby increasingly large sequences of DNA can be synthesised de novo, allow an unprecedented ability to engineer proteins with novel functions. However, the number of possible proteins is far too large to test individually, so we need means for navigating the 'search space' of possible protein sequences efficiently and reliably in order to find desirable activities and other properties. Enzymologists distinguish binding (Kd) and catalytic (kcat) steps. In a similar way, judicious strategies have blended design (for binding, specificity and active site modelling) with the more empirical methods of classical directed evolution (DE) for improving kcat (where natural evolution rarely seeks the highest values), especially with regard to residues distant from the active site and where the functional linkages underpinning enzyme dynamics are both unknown and hard to predict. Epistasis (where the 'best' amino acid at one site depends on that or those at others) is a notable feature of directed evolution. The aim of this review is to highlight some of the approaches that are being developed to allow us to use directed evolution to improve enzyme properties, often dramatically. We note that directed evolution differs in a number of ways from natural evolution, including in particular the available mechanisms and the likely selection pressures. Thus, we stress the opportunities afforded by techniques that enable one to map sequence to (structure and) activity in silico, as an effective means of modelling and exploring protein landscapes. Because known landscapes may be assessed and reasoned about as a whole, simultaneously, this offers opportunities for protein improvement not readily available to natural evolution on rapid timescales. Intelligent landscape navigation, informed by sequence-activity relationships and coupled to the emerging methods of synthetic biology, offers scope for the development of novel biocatalysts that are both highly active and robust.
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Affiliation(s)
- Andrew Currin
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
| | - Neil Swainston
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- School of Computer Science , The University of Manchester , Manchester M13 9PL , UK
| | - Philip J. Day
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
- Faculty of Medical and Human Sciences , The University of Manchester , Manchester M13 9PT , UK
| | - Douglas B. Kell
- Manchester Institute of Biotechnology , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK . ; http://dbkgroup.org/; @dbkell ; Tel: +44 (0)161 306 4492
- School of Chemistry , The University of Manchester , Manchester M13 9PL , UK
- Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM) , The University of Manchester , 131, Princess St , Manchester M1 7DN , UK
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93
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Kucinska M, Skupin-Mrugalska P, Szczolko W, Sobotta L, Sciepura M, Tykarska E, Wierzchowski M, Teubert A, Fedoruk-Wyszomirska A, Wyszko E, Gdaniec M, Kaczmarek M, Goslinski T, Mielcarek J, Murias M. Phthalocyanine derivatives possessing 2-(morpholin-4-yl)ethoxy groups as potential agents for photodynamic therapy. J Med Chem 2015; 58:2240-55. [PMID: 25700089 DOI: 10.1021/acs.jmedchem.5b00052] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Three 2-(morpholin-4-yl)ethoxy substituted phthalocyanines were synthesized and characterized. Phthalocyanine derivatives revealed moderate to high quantum yields of singlet oxygen production depending on the solvent applied (e.g., in DMF ranging from 0.25 to 0.53). Their photosensitizing potential for photodynamic therapy was investigated in an in vitro model using cancer cell lines. Biological test results were found particularly encouraging for the zinc(II) phthalocyanine derivative possessing two 2-(morpholin-4-yl)ethoxy substituents in nonperipheral positions. Cells irradiated for 20 min at 2 mW/cm(2) revealed the lowest IC50 value at 0.25 μM for prostate cell line (PC3), whereas 1.47 μM was observed for human malignant melanoma (A375) cells. The cytotoxic activity in nonirradiated cells of novel phthalocyanine was found to be very low. Moreover, the cellular uptake, localization, cell cycle, apoptosis through an ELISA assay, and immunochemistry method were investigated in LNCaP cells. Our results showed that the tested photosensitizer possesses very interesting biological activity, depending on experimental conditions.
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Affiliation(s)
- Malgorzata Kucinska
- Department of Toxicology, Poznan University of Medical Sciences , Dojazd 30, 60-631 Poznan, Poland
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94
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Zheng Y, Benet LZ, Okochi H, Chen X. pH Dependent but not P-gp Dependent Bidirectional Transport Study of S-propranolol: The Importance of Passive Diffusion. Pharm Res 2015; 32:2516-26. [PMID: 25690341 DOI: 10.1007/s11095-015-1640-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Accepted: 01/26/2015] [Indexed: 01/06/2023]
Abstract
PURPOSE Recent controversial publications, citing studies purporting to show that P-gp mediates the transport of propranolol, proposed that passive biological membrane transport is negligible. Based on the BDDCS, the extensively metabolized-highly permeable-highly soluble BDDCS class 1 drug, propranolol, shows a high passive permeability at concentrations unrestricted by solubility that can overwhelm any potential transporter effects. Here we reinvestigate the effects of passive diffusion and carrier-mediated transport on S-propranolol. METHODS Bidirectional permeability and inhibition of efflux transport studies were carried out in MDCK, MDCK-MDR1 and Caco-2 cell lines at different concentrations. Transcellular permeability studies were conducted at different apical pHs in the rat jejunum Ussing chamber model and PAMPA system. RESULTS S-propranolol exhibited efflux ratios lower than 1 in MDCK, MDCK-MDR1 and Caco-2 cells. No significant differences of Papp, B->A in the presence and absence of the efflux inhibitor GG918 were observed. However, an efflux ratio of 3.63 was found at apical pH 6.5 with significant decrease in Papp, A->B and increase in Papp, B->A compared to apical pH 7.4 in Caco-2 cell lines. The pH dependent permeability was confirmed in the Ussing chamber model. S-propranolol flux was unchanged during inhibition by verapamil and rifampin. Furthermore, pH dependent permeability was also observed in the PAMPA system. CONCLUSIONS S-propranolol does not exhibit active transport as proposed previously. The "false" positive efflux ratio can be explained by the pH partition theory. As expected, passive diffusion, but not active transport, plays the primary role in the permeability of the BDDCS class 1 drug propranolol.
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Affiliation(s)
- Yi Zheng
- Center of Drug Metabolism and Pharmacokinetics, China Pharmaceutical University, #24 Tongjiaxiang, Mailbox 210, Nanjing, 210009, Jiangsu, China
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95
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96
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Mécanismes des interactions pharmacocinétiques impliquant les agents anticancéreux oraux. Bull Cancer 2015; 102:65-72. [DOI: 10.1016/j.bulcan.2014.11.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2014] [Accepted: 11/20/2014] [Indexed: 11/21/2022]
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97
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Dahlgren D, Roos C, Sjögren E, Lennernäs H. Direct In Vivo Human Intestinal Permeability (Peff ) Determined with Different Clinical Perfusion and Intubation Methods. J Pharm Sci 2014; 104:2702-26. [PMID: 25410736 DOI: 10.1002/jps.24258] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 10/17/2014] [Accepted: 10/17/2014] [Indexed: 12/21/2022]
Abstract
Regional in vivo human intestinal effective permeability (Peff ) is calculated by measuring the disappearance rate of substances during intestinal perfusion. Peff is the most relevant parameter in the prediction of rate and extent of drug absorption from all parts of the intestine. Today, human intestinal perfusions are not performed on a routine basis in drug development. Therefore, it would be beneficial to increase the accuracy of the in vitro and in silico tools used to evaluate the intestinal Peff of novel drugs. This review compiles historical Peff data from 273 individual measurements of 80 substances from 61 studies performed in all parts of the human intestinal tract. These substances include: drugs, monosaccharaides, amino acids, dipeptides, vitamins, steroids, bile acids, ions, fatty acids, and water. The review also discusses the determination and prediction of Peff using in vitro and in silico methods such as quantitative structure-activity relationship, Caco-2, Ussing chamber, animal intestinal perfusion, and physiologically based pharmacokinetic (PBPK) modeling. Finally, we briefly outline how to acquire accurate human intestinal Peff data by deconvolution of plasma concentration-time profiles following regional intestinal bolus dosing.
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Affiliation(s)
- David Dahlgren
- Department of Pharmacy, Uppsala University, Uppsala, Sweden
| | - Carl Roos
- Department of Pharmacy, Uppsala University, Uppsala, Sweden
| | - Erik Sjögren
- Department of Pharmacy, Uppsala University, Uppsala, Sweden
| | - Hans Lennernäs
- Department of Pharmacy, Uppsala University, Uppsala, Sweden
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98
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Kell DB. What would be the observable consequences if phospholipid bilayer diffusion of drugs into cells is negligible? Trends Pharmacol Sci 2014; 36:15-21. [PMID: 25458537 DOI: 10.1016/j.tips.2014.10.005] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Revised: 10/11/2014] [Accepted: 10/14/2014] [Indexed: 12/27/2022]
Abstract
For drug transport across (i.e., through) an intact biological membrane, two main routes are possible: drugs may cross (i) through the phospholipid bilayer portion of the membrane, and/or (ii) via proteinaceous pores or transporters. Perhaps surprisingly, there is in fact no direct scientific evidence that the first of these takes place at any significant rate because, in the experiments performed to date, it has neither been varied as an independent variable nor measured directly as a dependent variable. Using a standard hypothetico-deductive framework, I assess the intellectual and observable consequences of assuming that, for drugs, phospholipid bilayer diffusion is negligible - 'PBIN' - (i.e., may be neglected, relative to transporter-mediated transmembrane fluxes). Predictions and postdictions of the PBIN hypothesis are not refuted by available experimental evidence.
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Affiliation(s)
- Douglas B Kell
- School of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
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99
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O'Connor IA, Veltman K, Huijbregts MAJ, Ragas AMJ, Russel FGM, Hendriks AJ. Including carrier-mediated transport in oral uptake prediction of nutrients and pharmaceuticals in humans. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2014; 38:938-947. [PMID: 25461554 DOI: 10.1016/j.etap.2014.10.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2014] [Revised: 09/28/2014] [Accepted: 10/10/2014] [Indexed: 06/04/2023]
Abstract
Most toxicokinetic models consider passive diffusion as the only mechanism when modeling the oral uptake of chemicals. However, the overall uptake of nutrients and xenobiotics, such as pharmaceuticals and environmental pollutants, can be increased by influx transport proteins. We incorporated carrier-mediated transport into a one-compartment toxicokinetic model originally developed for passive diffusion only. The predictions were compared with measured oral uptake efficiencies of nutrients and pharmaceuticals, i.e. the fraction of the chemical reaching systemic circulation. Including carrier-mediated uptake improved model predictions for hydrophilic nutrients (RMSE=10% vs. 56%, Coefficient of Efficiency CoE=0.5 vs. -9.6) and for pharmaceuticals (RMSE=21% vs. 28% and CoE=-0.4 vs. -1.1). However, the negative CoE for pharmaceuticals indicates that further improvements are needed. Most important in this respect is a more accurate estimation of vMAX and KM as well as the determination of the amount of expressed and functional transport proteins both in vivo and in vitro.
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Affiliation(s)
- Isabel A O'Connor
- Radboud University Nijmegen, Institute for Water and Wetland Research, Department of Environmental Science, PO Box 9010, NL-6500 GL Nijmegen, The Netherlands.
| | - Karin Veltman
- Radboud University Nijmegen, Institute for Water and Wetland Research, Department of Environmental Science, PO Box 9010, NL-6500 GL Nijmegen, The Netherlands
| | - Mark A J Huijbregts
- Radboud University Nijmegen, Institute for Water and Wetland Research, Department of Environmental Science, PO Box 9010, NL-6500 GL Nijmegen, The Netherlands
| | - Ad M J Ragas
- Radboud University Nijmegen, Institute for Water and Wetland Research, Department of Environmental Science, PO Box 9010, NL-6500 GL Nijmegen, The Netherlands; Open University, School of Science, PO Box 2960, NL-6401 DL Heerlen, The Netherlands
| | - Frans G M Russel
- Radboud University Medical Center, Radboud Institute for Molecular Life Sciences, Department of Pharmacology and Toxicology (149), PO Box 9101, NL-6500 HB Nijmegen, The Netherlands
| | - A Jan Hendriks
- Radboud University Nijmegen, Institute for Water and Wetland Research, Department of Environmental Science, PO Box 9010, NL-6500 GL Nijmegen, The Netherlands
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100
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Pisco AO, Jackson DA, Huang S. Reduced Intracellular Drug Accumulation in Drug-Resistant Leukemia Cells is Not Only Solely Due to MDR-Mediated Efflux but also to Decreased Uptake. Front Oncol 2014; 4:306. [PMID: 25401091 PMCID: PMC4215691 DOI: 10.3389/fonc.2014.00306] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 10/15/2014] [Indexed: 12/18/2022] Open
Abstract
Expression of ABC family transporter proteins that promote drug efflux from cancer cells is a widely observed mechanism of multi-drug resistance of cancer cells. Cell adaptation in long-term culture of HL60 leukemic cells in the presence of chemotherapy leads to induction and maintenance of the ABC transporters expression, preventing further accumulation of drugs. However, we found that decreased accumulation of drugs and fluorescent dyes also contributed by a reduced uptake by the resistant cells. Confocal time-lapse microscopy and flow cytometry revealed that fluid-phase endocytosis was diminished in drug-resistant cells compared to drug-sensitive cells. Drug uptake was increased by insulin co-treatment when cells were grown in methylcellulose and monitored under the microscope, but not when cultured in suspension. We propose that multi-drug resistance is not only solely achieved by enhanced efflux capacity but also by supressed intake of the drug, offering an alternative target to overcome drug resistance or potentiate chemotherapy.
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Affiliation(s)
- Angela Oliveira Pisco
- Institute for Systems Biology , Seattle, WA , USA ; Faculty of Life Sciences, University of Manchester , Manchester , UK
| | | | - Sui Huang
- Institute for Systems Biology , Seattle, WA , USA ; Department of Biological Sciences, University of Calgary , Calgary, AB , Canada
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