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Wagner A, Zhang J, Liu C, Covey TR, Olah TV, Weller H(BN, Shou WZ. Ultrahigh-Throughput and Chromatography-Free Bioanalysis of Polar Analytes with Acoustic Ejection Mass Spectrometry. Anal Chem 2020; 92:13525-13531. [DOI: 10.1021/acs.analchem.0c03006] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Andrew Wagner
- Bristol-Myers Squibb, 3551 Lawrenceville Princeton Road, Princeton, New Jersey 08648, United States
| | - Jun Zhang
- Bristol-Myers Squibb, 3551 Lawrenceville Princeton Road, Princeton, New Jersey 08648, United States
| | - Chang Liu
- Sciex, 71 Four Valley Drive, Concord, Ontario L4K 4 V8, Canada
| | - Thomas R. Covey
- Sciex, 71 Four Valley Drive, Concord, Ontario L4K 4 V8, Canada
| | - Timothy V. Olah
- Bristol-Myers Squibb, 3551 Lawrenceville Princeton Road, Princeton, New Jersey 08648, United States
| | - Harold (Bud) N. Weller
- Bristol-Myers Squibb, 3551 Lawrenceville Princeton Road, Princeton, New Jersey 08648, United States
| | - Wilson Z. Shou
- Bristol-Myers Squibb, 3551 Lawrenceville Princeton Road, Princeton, New Jersey 08648, United States
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2
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Türková A, Zdrazil B. Current Advances in Studying Clinically Relevant Transporters of the Solute Carrier (SLC) Family by Connecting Computational Modeling and Data Science. Comput Struct Biotechnol J 2019; 17:390-405. [PMID: 30976382 PMCID: PMC6438991 DOI: 10.1016/j.csbj.2019.03.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 02/28/2019] [Accepted: 03/01/2019] [Indexed: 01/18/2023] Open
Abstract
Organic anion and cation transporting proteins (OATs, OATPs, and OCTs), as well as the Multidrug and Toxin Extrusion (MATE) transporters of the Solute Carrier (SLC) family are playing a pivotal role in the discovery and development of new drugs due to their involvement in drug disposition, drug-drug interactions, adverse drug effects and related toxicity. Computational methods to understand and predict clinically relevant transporter interactions can provide useful guidance at early stages in drug discovery and design, especially if they include contemporary data science approaches. In this review, we summarize the current state-of-the-art of computational approaches for exploring ligand interactions and selectivity for these drug (uptake) transporters. The computational methods discussed here by highlighting interesting examples from the current literature are ranging from semiautomatic data mining and integration, to ligand-based methods (such as quantitative structure-activity relationships, and combinatorial pharmacophore modeling), and finally structure-based methods (such as comparative modeling, molecular docking, and molecular dynamics simulations). We are focusing on promising computational techniques such as fold-recognition methods, proteochemometric modeling or techniques for enhanced sampling of protein conformations used in the context of these ADMET-relevant SLC transporters with a special focus on methods useful for studying ligand selectivity.
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Affiliation(s)
- Alžběta Türková
- Department of Pharmaceutical Chemistry, Divison of Drug Design and Medicinal Chemistry, University of Vienna, Althanstraße 14, A-1090 Vienna, Austria
| | - Barbara Zdrazil
- Department of Pharmaceutical Chemistry, Divison of Drug Design and Medicinal Chemistry, University of Vienna, Althanstraße 14, A-1090 Vienna, Austria
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3
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Edmonds DJ, Kung DW, Kalgutkar AS, Filipski KJ, Ebner DC, Cabral S, Smith AC, Aspnes GE, Bhattacharya SK, Borzilleri KA, Brown JA, Calabrese MF, Caspers NL, Cokorinos EC, Conn EL, Dowling MS, Eng H, Feng B, Fernando DP, Genung NE, Herr M, Kurumbail RG, Lavergne SY, Lee ECY, Li Q, Mathialagan S, Miller RA, Panteleev J, Polivkova J, Rajamohan F, Reyes AR, Salatto CT, Shavnya A, Thuma BA, Tu M, Ward J, Withka JM, Xiao J, Cameron KO. Optimization of Metabolic and Renal Clearance in a Series of Indole Acid Direct Activators of 5′-Adenosine Monophosphate-Activated Protein Kinase (AMPK). J Med Chem 2018; 61:2372-2383. [DOI: 10.1021/acs.jmedchem.7b01641] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- David J. Edmonds
- Pfizer Worldwide Research and Development, 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Daniel W. Kung
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Amit S. Kalgutkar
- Pfizer Worldwide Research and Development, 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Kevin J. Filipski
- Pfizer Worldwide Research and Development, 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - David C. Ebner
- Pfizer Worldwide Research and Development, 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Shawn Cabral
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Aaron C. Smith
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Gary E. Aspnes
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Samit K. Bhattacharya
- Pfizer Worldwide Research and Development, 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Kris A. Borzilleri
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Janice A. Brown
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Matthew F. Calabrese
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Nicole L. Caspers
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Emily C. Cokorinos
- Pfizer Worldwide Research and Development, 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Edward L. Conn
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Matthew S. Dowling
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Heather Eng
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Bo Feng
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Dilinie P. Fernando
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Nathan E. Genung
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Michael Herr
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Ravi G. Kurumbail
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Sophie Y. Lavergne
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Esther C.-Y. Lee
- Pfizer Worldwide Research and Development, 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Qifang Li
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Sumathy Mathialagan
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Russell A. Miller
- Pfizer Worldwide Research and Development, 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Jane Panteleev
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Jana Polivkova
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Francis Rajamohan
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Allan R. Reyes
- Pfizer Worldwide Research and Development, 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Christopher T. Salatto
- Pfizer Worldwide Research and Development, 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Andre Shavnya
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Benjamin A. Thuma
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Meihua Tu
- Pfizer Worldwide Research and Development, 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Jessica Ward
- Pfizer Worldwide Research and Development, 610 Main Street, Cambridge, Massachusetts 02139, United States
| | - Jane M. Withka
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Jun Xiao
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Kimberly O. Cameron
- Pfizer Worldwide Research and Development, 610 Main Street, Cambridge, Massachusetts 02139, United States
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Abstract
1. Biliary excretion of compounds is dependant on several transporter proteins for the active uptake of compounds from the blood into the hepatocytes. Organic anion-transporting polypeptides (OATPs) are some of the most abundant transporter proteins in the sinusoidal membrane and have been shown to have substrate specificity similar to the structural characteristics of cholephilic compounds. 2. In this study, we sought to use measures of OATP binding as predictors of biliary excretion in conjunction with molecular descriptors in a quantitative structure-activity relationship (QSAR) study. Percentage inhibitions of three subtypes of OATPs were used as surrogate indicators of OATP substrates. Several statistical modelling techniques were incorporated including classification and regression trees, boosted trees, random forest and multivariate adaptive regression splines (MARS) in order to first develop QSARs for the prediction of OATP inhibition of compounds. The predicted OATP percentage inhibition using selected models were then used as features of the QSAR models for the prediction of biliary excretion of compounds in rat. 3. The results indicated that incorporation of predicted OATP inhibition improves accuracy of biliary excretion models. The best result was obtained from a simple regression tree that used predicted OATP1B1 percentage inhibition at the root node of the tree.
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Affiliation(s)
- Mohsen Sharifi
- a Medway School of Pharmacy, Universities of Kent and Greenwich , Chatham , Kent , UK.,b Division of Systems Biology , National Center for Toxicological Research, US Food and Drug Administration , Jefferson , AR , USA , and
| | - Taravat Ghafourian
- a Medway School of Pharmacy, Universities of Kent and Greenwich , Chatham , Kent , UK.,c School of Life Sciences, University of Sussex , Falmer , Brighton , UK
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Riley RJ, Foley SA, Barton P, Soars MG, Williamson B. Hepatic drug transporters: the journey so far. Expert Opin Drug Metab Toxicol 2016; 12:201-16. [PMID: 26670591 DOI: 10.1517/17425255.2016.1132308] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
INTRODUCTION The key role of transporter biology in both the manifestation and treatment of disease is now firmly established. Experiences of sub-optimal drug exposure due to drug-transporter interplay have supported incorporation of studies aimed at understanding the interactions between compounds and drug transporters much earlier in drug discovery. While drug transporters can impact the most pivotal pharmacokinetic parameter with respect to human dose and exposure projections, clearance, at a renal or hepatobiliary level, the latter will form the focus of this perspective. AREAS COVERED A synopsis of guidelines on which transporters to study together with an overview of the currently available toolkit is presented. A perspective on when to conduct studies with various hepatic transporters is also provided together with structural "alerts" which should prompt early investigation. EXPERT OPINION Great progress has been made in individual laboratories and via consortia to understand the role of drug transporters in disease, drug disposition, drug-drug interactions and toxicity. A systematic analysis of the value posed by the available approaches and an inter-lab comparison now seems warranted. The emerging ability to use physico-chemical properties to guide future screening cascades promises to revolutionise the efficiency of early drug discovery.
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Affiliation(s)
| | | | - P Barton
- b School of Life Sciences , University of Nottingham , Nottingham , UK
| | - M G Soars
- c Drug Metabolism and Pharmacokinetics , Bristol-Myers Squibb , Wallingford , CT , USA
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Wang M, Qi H, Li J, Xu Y, Zhang H. Transmembrane transport of steviol glucuronide and its potential interaction with selected drugs and natural compounds. Food Chem Toxicol 2015; 86:217-24. [PMID: 26525112 DOI: 10.1016/j.fct.2015.10.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 10/17/2015] [Accepted: 10/20/2015] [Indexed: 02/05/2023]
Abstract
Steviol glucuronide (SVG) is the major metabolite derived from steviol, the aglycone of stevioside and rebaudioside A. After the ingestion of stevioside and rebaudioside A, SVG is formed and excreted into the urine in humans. In the present study, transporter mediated efflux and uptake of SVG was investigated in order to understand molecular mechanisms underlying its renal clearance. Results showed that SVG was not a substrate of efflux transporters BCRP, MRP2, MATE1 or P-gp. In contrast, OAT3 played a predominant role in the uptake of SVG in comparison to OATP1B1, OATP1B3, or OATP2B1. Quercetin, telmisartan, diclofenac, and mulberrin displayed a relatively strong inhibition against OAT3 mediated uptake of SVG with IC50 values of 1.8, 2.9, 8.0, and 10.0 μM, respectively. Because OAT3 is a major uptake transporter in the kidney, inhibition of OAT3 activity may alter SVG's renal clearance by drugs and natural compounds that are used concomitantly with stevia leaf extracts.
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Affiliation(s)
- Meiyu Wang
- College of Pharmaceutical Sciences, Soochow University, Suzhou, China
| | - Huixin Qi
- College of Pharmaceutical Sciences, Soochow University, Suzhou, China
| | - Jiajun Li
- College of Pharmaceutical Sciences, Soochow University, Suzhou, China
| | - Yunting Xu
- College of Pharmaceutical Sciences, Soochow University, Suzhou, China
| | - Hongjian Zhang
- College of Pharmaceutical Sciences, Soochow University, Suzhou, China.
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Matsson P, Bergström CAS. Computational modeling to predict the functions and impact of drug transporters. In Silico Pharmacol 2015; 3:8. [PMID: 26820893 PMCID: PMC4559557 DOI: 10.1186/s40203-015-0012-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 08/14/2015] [Indexed: 02/04/2023] Open
Abstract
Transport proteins are important mediators of cellular drug influx and efflux and play crucial roles in drug distribution, disposition and clearance. Drug-drug interactions have increasingly been found to occur at the transporter level and, hence, computational tools for studying drug-transporter interactions have gained in interest. In this short review, we present the most important transport proteins for drug influx and efflux. Computational tools for predicting and understanding the substrate and inhibitor interactions with these membrane-bound proteins are discussed. We have primarily focused on ligand-based and structure-based modeling, for which the state-of-the-art and future challenges are also discussed.
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Affiliation(s)
- Pär Matsson
- Department of Pharmacy, Uppsala University, Box 580, SE-751 23, Uppsala, Sweden. .,Uppsala University Drug Optimization and Pharmaceutical Profiling Platform (UDOPP) - a node of the Chemical Biology Consortium Sweden, Uppsala, Sweden.
| | - Christel A S Bergström
- Department of Pharmacy, Uppsala University, Box 580, SE-751 23, Uppsala, Sweden. .,Uppsala University Drug Optimization and Pharmaceutical Profiling Platform (UDOPP) - a node of the Chemical Biology Consortium Sweden, Uppsala, Sweden.
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