1
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Krishna S, Borrel A, Huang R, Zhao J, Xia M, Kleinstreuer N. High-Throughput Chemical Screening and Structure-Based Models to Predict hERG Inhibition. BIOLOGY 2022; 11:209. [PMID: 35205076 PMCID: PMC8869358 DOI: 10.3390/biology11020209] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 01/18/2022] [Accepted: 01/21/2022] [Indexed: 12/23/2022]
Abstract
Chemical inhibition of the human ether-a -go-go-related gene (hERG) potassium channel leads to a prolonged QT interval that can contribute to severe cardiotoxicity. The adverse effects of hERG inhibition are one of the principal causes of drug attrition in clinical and pre-clinical development. Preliminary studies have demonstrated that a wide range of environmental chemicals and toxicants may also inhibit the hERG channel and contribute to the pathophysiology of cardiovascular (CV) diseases. As part of the US federal Tox21 program, the National Center for Advancing Translational Science (NCATS) applied a quantitative high throughput screening (qHTS) approach to screen the Tox21 library of 10,000 compounds (~7871 unique chemicals) at 14 concentrations in triplicate to identify chemicals perturbing hERG activity in the U2OS cell line thallium flux assay platform. The qHTS cell-based thallium influx assay provided a robust and reliable dataset to evaluate the ability of thousands of drugs and environmental chemicals to inhibit hERG channel protein, and the use of chemical structure-based clustering and chemotype enrichment analysis facilitated the identification of molecular features that are likely responsible for the observed hERG activity. We employed several machine-learning approaches to develop QSAR prediction models for the assessment of hERG liabilities for drug-like and environmental chemicals. The training set was compiled by integrating hERG bioactivity data from the ChEMBL database with the Tox21 qHTS thallium flux assay data. The best results were obtained with the random forest method (~92.6% balanced accuracy). The data and scripts used to generate hERG prediction models are provided in an open-access format as key in vitro and in silico tools that can be applied in a translational toxicology pipeline for drug development and environmental chemical screening.
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Affiliation(s)
- Shagun Krishna
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences (NIEHS), Research Triangle, NC 27560, USA;
| | | | - Ruili Huang
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), Bethesda, MD 20892-4874, USA; (R.H.); (J.Z.); (M.X.)
| | - Jinghua Zhao
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), Bethesda, MD 20892-4874, USA; (R.H.); (J.Z.); (M.X.)
| | - Menghang Xia
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences (NCATS), Bethesda, MD 20892-4874, USA; (R.H.); (J.Z.); (M.X.)
| | - Nicole Kleinstreuer
- Division of the National Toxicology Program, National Institute of Environmental Health Sciences (NIEHS), Research Triangle, NC 27560, USA;
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2
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Wilson C, Ray P, Zuccotto F, Hernandez J, Aggarwal A, Mackenzie C, Caldwell N, Taylor M, Huggett M, Mathieson M, Murugesan D, Smith A, Davis S, Cocco M, Parai MK, Acharya A, Tamaki F, Scullion P, Epemolu O, Riley J, Stojanovski L, Lopez-Román EM, Torres-Gómez PA, Toledo AM, Guijarro-Lopez L, Camino I, Engelhart CA, Schnappinger D, Massoudi LM, Lenaerts A, Robertson GT, Walpole C, Matthews D, Floyd D, Sacchettini JC, Read KD, Encinas L, Bates RH, Green SR, Wyatt PG. Optimization of TAM16, a Benzofuran That Inhibits the Thioesterase Activity of Pks13; Evaluation toward a Preclinical Candidate for a Novel Antituberculosis Clinical Target. J Med Chem 2022; 65:409-423. [PMID: 34910486 PMCID: PMC8762665 DOI: 10.1021/acs.jmedchem.1c01586] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Indexed: 11/28/2022]
Abstract
With increasing drug resistance in tuberculosis (TB) patient populations, there is an urgent need for new drugs. Ideally, new agents should work through novel targets so that they are unencumbered by preexisting clinical resistance to current treatments. Benzofuran 1 was identified as a potential lead for TB inhibiting a novel target, the thioesterase domain of Pks13. Although, having promising activity against Mycobacterium tuberculosis, its main liability was inhibition of the hERG cardiac ion channel. This article describes the optimization of the series toward a preclinical candidate. Despite improvements in the hERG liability in vitro, when new compounds were assessed in ex vivo cardiotoxicity models, they still induced cardiac irregularities. Further series development was stopped because of concerns around an insufficient safety window. However, the demonstration of in vivo activity for multiple series members further validates Pks13 as an attractive novel target for antitubercular drugs and supports development of alternative chemotypes.
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Affiliation(s)
- Caroline Wilson
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Peter Ray
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Fabio Zuccotto
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Jorge Hernandez
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Anup Aggarwal
- Department
of Biochemistry and Biophysics, Texas A&M
University, College
Station, Texas 77843, United States
| | - Claire Mackenzie
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Nicola Caldwell
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Malcolm Taylor
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Margaret Huggett
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Michael Mathieson
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Dinakaran Murugesan
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Alasdair Smith
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Susan Davis
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Mattia Cocco
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Maloy K. Parai
- Department
of Biochemistry and Biophysics, Texas A&M
University, College
Station, Texas 77843, United States
| | - Arjun Acharya
- Department
of Biochemistry and Biophysics, Texas A&M
University, College
Station, Texas 77843, United States
| | - Fabio Tamaki
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Paul Scullion
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Ola Epemolu
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Jennifer Riley
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Laste Stojanovski
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Eva Maria Lopez-Román
- Global
Health Pharma R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | | | - Ana Maria Toledo
- Global
Health Pharma R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Laura Guijarro-Lopez
- Global
Health Pharma R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Isabel Camino
- Global
Health Pharma R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Curtis A. Engelhart
- Department
of Microbiology and Immunology, Weill Cornell
Medical College, New York, New York 10065, United States
| | - Dirk Schnappinger
- Department
of Microbiology and Immunology, Weill Cornell
Medical College, New York, New York 10065, United States
| | - Lisa M. Massoudi
- Mycobacteria
Research Laboratories, Department of Microbiology, Immunology, and
Pathology, Colorado State University, 200 W. Lake Street, Fort Collins, Colorado 80523-1682, United States
| | - Anne Lenaerts
- Mycobacteria
Research Laboratories, Department of Microbiology, Immunology, and
Pathology, Colorado State University, 200 W. Lake Street, Fort Collins, Colorado 80523-1682, United States
| | - Gregory T. Robertson
- Mycobacteria
Research Laboratories, Department of Microbiology, Immunology, and
Pathology, Colorado State University, 200 W. Lake Street, Fort Collins, Colorado 80523-1682, United States
| | - Chris Walpole
- Structural
Genomics Consortium, Research Institute
of the McGill University Health Centre, 1001 Boulevard Décarie, Site Glen Block
E, ES1.1614, Montréal, Québec H4A 3J1, Canada
| | - David Matthews
- Structural
Genomics Consortium, Research Institute
of the McGill University Health Centre, 1001 Boulevard Décarie, Site Glen Block
E, ES1.1614, Montréal, Québec H4A 3J1, Canada
| | - David Floyd
- Structural
Genomics Consortium, Research Institute
of the McGill University Health Centre, 1001 Boulevard Décarie, Site Glen Block
E, ES1.1614, Montréal, Québec H4A 3J1, Canada
| | - James C. Sacchettini
- Department
of Biochemistry and Biophysics, Texas A&M
University, College
Station, Texas 77843, United States
| | - Kevin D. Read
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Lourdes Encinas
- Global
Health Pharma R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Robert H. Bates
- Global
Health Pharma R&D, GlaxoSmithKline, Severo Ochoa 2, Tres Cantos, Madrid 28760, Spain
| | - Simon R. Green
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Paul G. Wyatt
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
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3
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Ferreira RAA, Junior CDOR, Martinez PDG, Koovits PJ, Soares BM, Ferreira LLG, Michelan-Duarte S, Chelucci RC, Andricopulo AD, Galuppo MK, Uliana SRB, Matheeussen A, Caljon G, Maes L, Campbell S, Kratz JM, Mowbray CE, Dias LC. 2-aminobenzimidazoles for leishmaniasis: From initial hit discovery to in vivo profiling. PLoS Negl Trop Dis 2021; 15:e0009196. [PMID: 33617566 PMCID: PMC7932521 DOI: 10.1371/journal.pntd.0009196] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 03/04/2021] [Accepted: 02/02/2021] [Indexed: 12/30/2022] Open
Abstract
Leishmaniasis is a major infectious disease with hundreds of thousands of new cases and over 20,000 deaths each year. The current drugs to treat this life-threatening infection have several drawbacks such as toxicity and long treatment regimens. A library of 1.8 million compounds, from which the hits reported here are publicly available, was screened against Leishmania infantum as part of an optimization program; a compound was found with a 2-aminobenzimidazole functionality presenting moderate potency, low metabolic stability and high lipophilicity. Several rounds of synthesis were performed to incorporate chemical groups capable of reducing lipophilicity and clearance, leading to the identification of compounds that are active against different parasite strains and have improved in vitro properties. As a result of this optimization program, a group of compounds was further tested in anticipation of in vivo evaluation. In vivo tests were carried out with compounds 29 (L. infantum IC50: 4.1 μM) and 39 (L. infantum IC50: 0.5 μM) in an acute L. infantum VL mouse model, which showed problems of poor exposure and lack of efficacy, despite the good in vitro potency. Leishmaniasis is a neglected tropical disease affecting millions of people worldwide and, in the case of visceral leishmaniasis (VL), is potentially fatal if untreated. Protozoan parasites of the genus Leishmania spp. are the causative agents of leishmaniasis, which has different clinical manifestations, including the visceral form and a cutaneous form that causes disfiguring skin lesions. The current treatment options are limited either by the length of treatment or toxic side effects. Starting from a promising hit in an in vitro phenotypic screen, hundreds of analogues were synthesized with the aim of finding a molecule capable of killing the parasite whilst causing little or no harm to the patient. The program led to several active compounds with good in vitro activity against L. infantum intracellular amastigotes, however, in vivo data showed low parasiticidal efficacy.
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Affiliation(s)
| | | | | | - Paul John Koovits
- Institute of Chemistry, University of Campinas (UNICAMP), Campinas-SP, Brazil
| | | | - Leonardo L. G. Ferreira
- Laboratory of Medicinal and Computational Chemistry, Physics Institute of São Carlos, University of São Paulo (USP), São Carlos-SP, Brazil
| | - Simone Michelan-Duarte
- Laboratory of Medicinal and Computational Chemistry, Physics Institute of São Carlos, University of São Paulo (USP), São Carlos-SP, Brazil
| | - Rafael Consolin Chelucci
- Laboratory of Medicinal and Computational Chemistry, Physics Institute of São Carlos, University of São Paulo (USP), São Carlos-SP, Brazil
| | - Adriano D. Andricopulo
- Laboratory of Medicinal and Computational Chemistry, Physics Institute of São Carlos, University of São Paulo (USP), São Carlos-SP, Brazil
| | - Mariana K. Galuppo
- Department of Parasitology, Biomedical Sciences Institute, University of São Paulo (USP), São Paulo-SP, Brazil
| | - Silvia R. B. Uliana
- Department of Parasitology, Biomedical Sciences Institute, University of São Paulo (USP), São Paulo-SP, Brazil
| | - An Matheeussen
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), Antwerpen, Belgium
| | - Guy Caljon
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), Antwerpen, Belgium
| | - Louis Maes
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), Antwerpen, Belgium
| | - Simon Campbell
- Drugs for Neglected Diseases initiative (DNDi), Geneva, Switzerland
| | - Jadel M. Kratz
- Drugs for Neglected Diseases initiative (DNDi), Geneva, Switzerland
| | | | - Luiz Carlos Dias
- Institute of Chemistry, University of Campinas (UNICAMP), Campinas-SP, Brazil
- * E-mail:
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4
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Ray P, Huggett M, Turner PA, Taylor M, Cleghorn LAT, Early J, Kumar A, Bonnett SA, Flint L, Joerss D, Johnson J, Korkegian A, Mullen S, Moure AL, Davis SH, Murugesan D, Mathieson M, Caldwell N, Engelhart CA, Schnappinger D, Epemolu O, Zuccotto F, Riley J, Scullion P, Stojanovski L, Massoudi L, Robertson GT, Lenaerts AJ, Freiberg G, Kempf DJ, Masquelin T, Hipskind PA, Odingo J, Read KD, Green SR, Wyatt PG, Parish T. Spirocycle MmpL3 Inhibitors with Improved hERG and Cytotoxicity Profiles as Inhibitors of Mycobacterium tuberculosis Growth. ACS OMEGA 2021; 6:2284-2311. [PMID: 33521468 PMCID: PMC7841955 DOI: 10.1021/acsomega.0c05589] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 12/21/2020] [Indexed: 05/10/2023]
Abstract
With the emergence of multi-drug-resistant strains of Mycobacterium tuberculosis, there is a pressing need for new oral drugs with novel mechanisms of action. A number of scaffolds with potent anti-tubercular in vitro activity have been identified from phenotypic screening that appear to target MmpL3. However, the scaffolds are typically lipophilic, which facilitates partitioning into hydrophobic membranes, and several contain basic amine groups. Highly lipophilic basic amines are typically cytotoxic against mammalian cell lines and have associated off-target risks, such as inhibition of human ether-à-go-go related gene (hERG) and IKr potassium current modulation. The spirocycle compound 3 was reported to target MmpL3 and displayed promising efficacy in a murine model of acute tuberculosis (TB) infection. However, this highly lipophilic monobasic amine was cytotoxic and inhibited the hERG ion channel. Herein, the related spirocycles (1-2) are described, which were identified following phenotypic screening of the Eli Lilly corporate library against M. tuberculosis. The novel N-alkylated pyrazole portion offered improved physicochemical properties, and optimization led to identification of a zwitterion series, exemplified by lead 29, with decreased HepG2 cytotoxicity as well as limited hERG ion channel inhibition. Strains with mutations in MmpL3 were resistant to 29, and under replicating conditions, 29 demonstrated bactericidal activity against M. tuberculosis. Unfortunately, compound 29 had no efficacy in an acute model of TB infection; this was most likely due to the in vivo exposure remaining above the minimal inhibitory concentration for only a limited time.
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Affiliation(s)
- Peter
C. Ray
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Margaret Huggett
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Penelope A. Turner
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Malcolm Taylor
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Laura A. T. Cleghorn
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Julie Early
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
| | - Anuradha Kumar
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
| | - Shilah A. Bonnett
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
| | - Lindsay Flint
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
| | - Douglas Joerss
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
| | - James Johnson
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
| | - Aaron Korkegian
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
| | - Steven Mullen
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
| | - Abraham L. Moure
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Susan H. Davis
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Dinakaran Murugesan
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Michael Mathieson
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Nicola Caldwell
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Curtis A. Engelhart
- Department
of Microbiology and Immunology, Weill Cornell
Medical College, New York, New York 10065, United States
| | - Dirk Schnappinger
- Department
of Microbiology and Immunology, Weill Cornell
Medical College, New York, New York 10065, United States
| | - Ola Epemolu
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Fabio Zuccotto
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Jennifer Riley
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Paul Scullion
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Laste Stojanovski
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Lisa Massoudi
- Mycobacteria
Research Laboratories, Colorado State University, 200 W. Lake Street, Fort Collins, Colorado 80523-1682, United States
| | - Gregory T. Robertson
- Mycobacteria
Research Laboratories, Colorado State University, 200 W. Lake Street, Fort Collins, Colorado 80523-1682, United States
| | - Anne J. Lenaerts
- Mycobacteria
Research Laboratories, Colorado State University, 200 W. Lake Street, Fort Collins, Colorado 80523-1682, United States
| | - Gail Freiberg
- AbbVie, 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Dale J. Kempf
- AbbVie, 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Thierry Masquelin
- Discovery
Chemistry Research, Eli Lilly and Company, Lilly Corporate Centre, MC/87/02/203, G17, Indianapolis, Indiana 46285, United States
| | | | - Joshua Odingo
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
| | - Kevin D. Read
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Simon R. Green
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Paul G. Wyatt
- Drug
Discovery Unit, Division of Biological Chemistry and Drug Discovery,
College of Life Sciences, University of
Dundee, Dundee DD1 5EH, U.K.
| | - Tanya Parish
- TB
Discovery Research, Infectious Disease Research
Institute, 1616 Eastlake Avenue East, Suite 400, Seattle, Washington 98102, United States
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5
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Yang PC, DeMarco KR, Aghasafari P, Jeng MT, Dawson JRD, Bekker S, Noskov SY, Yarov-Yarovoy V, Vorobyov I, Clancy CE. A Computational Pipeline to Predict Cardiotoxicity: From the Atom to the Rhythm. Circ Res 2020; 126:947-964. [PMID: 32091972 DOI: 10.1161/circresaha.119.316404] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
RATIONALE Drug-induced proarrhythmia is so tightly associated with prolongation of the QT interval that QT prolongation is an accepted surrogate marker for arrhythmia. But QT interval is too sensitive a marker and not selective, resulting in many useful drugs eliminated in drug discovery. OBJECTIVE To predict the impact of a drug from the drug chemistry on the cardiac rhythm. METHODS AND RESULTS In a new linkage, we connected atomistic scale information to protein, cell, and tissue scales by predicting drug-binding affinities and rates from simulation of ion channel and drug structure interactions and then used these values to model drug effects on the hERG channel. Model components were integrated into predictive models at the cell and tissue scales to expose fundamental arrhythmia vulnerability mechanisms and complex interactions underlying emergent behaviors. Human clinical data were used for model framework validation and showed excellent agreement, demonstrating feasibility of a new approach for cardiotoxicity prediction. CONCLUSIONS We present a multiscale model framework to predict electrotoxicity in the heart from the atom to the rhythm. Novel mechanistic insights emerged at all scales of the system, from the specific nature of proarrhythmic drug interaction with the hERG channel, to the fundamental cellular and tissue-level arrhythmia mechanisms. Applications of machine learning indicate necessary and sufficient parameters that predict arrhythmia vulnerability. We expect that the model framework may be expanded to make an impact in drug discovery, drug safety screening for a variety of compounds and targets, and in a variety of regulatory processes.
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Affiliation(s)
- Pei-Chi Yang
- From the Department of Physiology and Membrane Biology (P.-C.Y., K.R.D., P.A., M.-T.J., J.R.D.D., V.Y.-Y., I.V., C.E.C.), University of California Davis
| | - Kevin R DeMarco
- From the Department of Physiology and Membrane Biology (P.-C.Y., K.R.D., P.A., M.-T.J., J.R.D.D., V.Y.-Y., I.V., C.E.C.), University of California Davis
| | - Parya Aghasafari
- From the Department of Physiology and Membrane Biology (P.-C.Y., K.R.D., P.A., M.-T.J., J.R.D.D., V.Y.-Y., I.V., C.E.C.), University of California Davis
| | - Mao-Tsuen Jeng
- From the Department of Physiology and Membrane Biology (P.-C.Y., K.R.D., P.A., M.-T.J., J.R.D.D., V.Y.-Y., I.V., C.E.C.), University of California Davis
| | - John R D Dawson
- From the Department of Physiology and Membrane Biology (P.-C.Y., K.R.D., P.A., M.-T.J., J.R.D.D., V.Y.-Y., I.V., C.E.C.), University of California Davis.,Biophysics Graduate Group (J.R.D.D.), University of California Davis
| | - Slava Bekker
- Department of Science and Engineering, American River College, Sacramento, CA (S.B.)
| | - Sergei Y Noskov
- Faculty of Science, Centre for Molecular Simulations and Department of Biological Sciences, University of Calgary, Alberta, Canada (S.Y.N.)
| | - Vladimir Yarov-Yarovoy
- From the Department of Physiology and Membrane Biology (P.-C.Y., K.R.D., P.A., M.-T.J., J.R.D.D., V.Y.-Y., I.V., C.E.C.), University of California Davis
| | - Igor Vorobyov
- From the Department of Physiology and Membrane Biology (P.-C.Y., K.R.D., P.A., M.-T.J., J.R.D.D., V.Y.-Y., I.V., C.E.C.), University of California Davis.,Department of Pharmacology (I.V., C.E.C.), University of California Davis
| | - Colleen E Clancy
- From the Department of Physiology and Membrane Biology (P.-C.Y., K.R.D., P.A., M.-T.J., J.R.D.D., V.Y.-Y., I.V., C.E.C.), University of California Davis.,Department of Pharmacology (I.V., C.E.C.), University of California Davis
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6
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In vitro growth inhibition of Theileria equi by bumped kinase inhibitors. Vet Parasitol 2018; 251:90-94. [PMID: 29426483 DOI: 10.1016/j.vetpar.2017.12.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 11/20/2017] [Accepted: 12/31/2017] [Indexed: 02/02/2023]
Abstract
INTRODUCTION Theileria equi, an etiologic agent of equine piroplasmosis, is a tick-transmitted hemoprotozoan of the phylum Apicomplexa. Recent outbreaks of piroplasmosis in the United States have renewed interest in safe and effective treatment options. Although imidocarb dipropionate (IMD) is the drug of choice for clearance of T. equi, adverse reactions and recently documented resistance support the need for alternative therapeutic strategies. The recently described bumped kinase inhibitors (BKIs) are a new class of compounds that could potentially be used as safe and effective alternatives to IMD. In an initial effort to evaluate this potential, herein we determined the T. equi growth inhibitory activity of 11 BKIs relative to that of IMD and the previously tested BKI 1294. Because some BKIs have known human ether-à-go-go related gene (hERG) channel activity, we also assessed the hERG activity of each compound with the goal to identify those with the highest potency against T. equi coupled with the lowest potential for cardiotoxicity. RESULTS Six BKIs inhibited T. equi growth in vitro, including the previously evaluated BKI 1294 which was used as a positive control. All six compounds were significantly less potent (higher 50% effective concentration (EC50)) than IMD. Two of those compounds were more potent than BKI 1294 control but had similar hERG activity. Although the remaining three compounds had similar to lower potency than BKI 1294, hERG EC50 was higher for three of them (BKI 1735, BKI 1369 and BKI 1318). CONCLUSIONS The BKI compounds evaluated in this study inhibited T. equi in vitro and had diverse hERG activity. Based on these considerations, three compounds would be suitable for further evaluation. While these results provide a foundation for future work, in vivo pharmacokinetic, pharmacodynamics, and safety studies are needed before BKI compounds can be recommended for clinical use in T. equi infected horses.
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7
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Hulverson MA, Vinayak S, Choi R, Schaefer DA, Castellanos-Gonzalez A, Vidadala RSR, Brooks CF, Herbert GT, Betzer DP, Whitman GR, Sparks HN, Arnold SLM, Rivas KL, Barrett LK, White AC, Maly DJ, Riggs MW, Striepen B, Van Voorhis WC, Ojo KK. Bumped-Kinase Inhibitors for Cryptosporidiosis Therapy. J Infect Dis 2017; 215:1275-1284. [PMID: 28329187 PMCID: PMC5853794 DOI: 10.1093/infdis/jix120] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 03/01/2017] [Indexed: 01/13/2023] Open
Abstract
Bumped kinase inhibitors (BKIs) of Cryptosporidium parvum calcium-dependent protein kinase 1 (CpCDPK1) are leading candidates for treatment of cryptosporidiosis-associated diarrhea. Potential cardiotoxicity related to anti-human ether-à-go-go potassium channel (hERG) activity of the first-generation anti-Cryptosporidium BKIs triggered further testing for efficacy. A luminescence assay adapted for high-throughput screening was used to measure inhibitory activities of BKIs against C. parvum in vitro. Furthermore, neonatal and interferon γ knockout mouse models of C. parvum infection identified BKIs with in vivo activity. Additional iterative experiments for optimum dosing and selecting BKIs with minimum levels of hERG activity and frequencies of other safety liabilities included those that investigated mammalian cell cytotoxicity, C. parvum proliferation inhibition in vitro, anti-human Src inhibition, hERG activity, in vivo pharmacokinetic data, and efficacy in other mouse models. Findings of this study suggest that fecal concentrations greater than parasite inhibitory concentrations correlate best with effective therapy in the mouse model of cryptosporidiosis, but a more refined model for efficacy is needed.
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Affiliation(s)
- Matthew A Hulverson
- Division of Allergy & Infectious Disease, Center for Emerging & Reemerging Infectious Disease (CERID), University of Washington, Seattle, Washington 98109, USA
| | - Sumiti Vinayak
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia 30602, USA
| | - Ryan Choi
- Division of Allergy & Infectious Disease, Center for Emerging & Reemerging Infectious Disease (CERID), University of Washington, Seattle, Washington 98109, USA
| | - Deborah A Schaefer
- School of Animal and Comparative Biomedical Sciences, College of Agriculture and Life Sciences, University of Arizona, Tucson
| | | | | | - Carrie F Brooks
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia 30602, USA
| | - Gillian T Herbert
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia 30602, USA
| | - Dana P Betzer
- School of Animal and Comparative Biomedical Sciences, College of Agriculture and Life Sciences, University of Arizona, Tucson
| | - Grant R Whitman
- Division of Allergy & Infectious Disease, Center for Emerging & Reemerging Infectious Disease (CERID), University of Washington, Seattle, Washington 98109, USA
| | | | - Samuel L M Arnold
- Division of Allergy & Infectious Disease, Center for Emerging & Reemerging Infectious Disease (CERID), University of Washington, Seattle, Washington 98109, USA
| | - Kasey L Rivas
- Division of Allergy & Infectious Disease, Center for Emerging & Reemerging Infectious Disease (CERID), University of Washington, Seattle, Washington 98109, USA
| | - Lynn K Barrett
- Division of Allergy & Infectious Disease, Center for Emerging & Reemerging Infectious Disease (CERID), University of Washington, Seattle, Washington 98109, USA
| | - A Clinton White
- Infectious Disease Division, Department of Internal Medicine, University of Texas Medical Branch, Galveston
| | - Dustin J Maly
- Chemistry & Biochemistry, University of Washington, Seattle
| | - Michael W Riggs
- School of Animal and Comparative Biomedical Sciences, College of Agriculture and Life Sciences, University of Arizona, Tucson
| | - Boris Striepen
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia 30602, USA
- Department of Cellular Biology, University of Georgia, Athens
| | - Wesley C Van Voorhis
- Division of Allergy & Infectious Disease, Center for Emerging & Reemerging Infectious Disease (CERID), University of Washington, Seattle, Washington 98109, USA
| | - Kayode K Ojo
- Division of Allergy & Infectious Disease, Center for Emerging & Reemerging Infectious Disease (CERID), University of Washington, Seattle, Washington 98109, USA
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8
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Wu WL, Burnett DA, Clader J, Greenlee WJ, Jiang Q, Hyde LA, Del Vecchio RA, Cohen-Williams ME, Song L, Lee J, Terracina G, Zhang Q, Nomeir A, Parker EM, Zhang L. Design and synthesis of water soluble β-aminosulfone analogues of SCH 900229 as γ-secretase inhibitors. Bioorg Med Chem Lett 2016; 26:5836-5841. [PMID: 27836402 DOI: 10.1016/j.bmcl.2016.04.095] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 04/27/2016] [Accepted: 04/28/2016] [Indexed: 11/16/2022]
Abstract
In this paper we describe our strategy to improve the aqueous solubility of SCH 900229, a potent PS1-selective γ-secretase inhibitor for the treatment of Alzheimer's disease. Incorporation of ionizable amino groups into the side chain terminal generates water soluble β-aminosulfone analogues of SCH 900229 that maintain robust in vitro potency and in vivo efficacy.
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Affiliation(s)
- Wen-Lian Wu
- Merck Research Laboratories, 2015 Galloping Hill Rd, Kenilworth, NJ 07033, USA
| | - Duane A Burnett
- Merck Research Laboratories, 2015 Galloping Hill Rd, Kenilworth, NJ 07033, USA
| | - John Clader
- Merck Research Laboratories, 2015 Galloping Hill Rd, Kenilworth, NJ 07033, USA
| | - William J Greenlee
- Merck Research Laboratories, 2015 Galloping Hill Rd, Kenilworth, NJ 07033, USA
| | - Qin Jiang
- Albany Molecular Research, Inc., 26 Corporate Cir, Albany, NY 12212, USA
| | - Lynn A Hyde
- Merck Research Laboratories, 2015 Galloping Hill Rd, Kenilworth, NJ 07033, USA
| | | | | | - Lixin Song
- Merck Research Laboratories, 2015 Galloping Hill Rd, Kenilworth, NJ 07033, USA
| | - Julie Lee
- Merck Research Laboratories, 2015 Galloping Hill Rd, Kenilworth, NJ 07033, USA
| | - Giuseppe Terracina
- Merck Research Laboratories, 2015 Galloping Hill Rd, Kenilworth, NJ 07033, USA
| | - Qi Zhang
- Merck Research Laboratories, 2015 Galloping Hill Rd, Kenilworth, NJ 07033, USA
| | - Amin Nomeir
- Merck Research Laboratories, 2015 Galloping Hill Rd, Kenilworth, NJ 07033, USA
| | - Eric M Parker
- Merck Research Laboratories, 2015 Galloping Hill Rd, Kenilworth, NJ 07033, USA
| | - Lili Zhang
- Merck Research Laboratories, 2015 Galloping Hill Rd, Kenilworth, NJ 07033, USA
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9
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Vidadala RSR, Rivas KL, Ojo KK, Hulverson MA, Zambriski JA, Bruzual I, Schultz TL, Huang W, Zhang Z, Scheele S, DeRocher AE, Choi R, Barrett LK, Siddaramaiah LK, Hol WGJ, Fan E, Merritt EA, Parsons M, Freiberg G, Marsh K, Kempf DJ, Carruthers VB, Isoherranen N, Doggett JS, Van Voorhis WC, Maly DJ. Development of an Orally Available and Central Nervous System (CNS) Penetrant Toxoplasma gondii Calcium-Dependent Protein Kinase 1 (TgCDPK1) Inhibitor with Minimal Human Ether-a-go-go-Related Gene (hERG) Activity for the Treatment of Toxoplasmosis. J Med Chem 2016; 59:6531-46. [PMID: 27309760 DOI: 10.1021/acs.jmedchem.6b00760] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
New therapies are needed for the treatment of toxoplasmosis, which is a disease caused by the protozoan parasite Toxoplasma gondii. To this end, we previously developed a potent and selective inhibitor (compound 1) of Toxoplasma gondii calcium-dependent protein kinase 1 (TgCDPK1) that possesses antitoxoplasmosis activity in vitro and in vivo. Unfortunately, 1 has potent human ether-a-go-go-related gene (hERG) inhibitory activity, associated with long Q-T syndrome, and consequently presents a cardiotoxicity risk. Here, we describe the identification of an optimized TgCDPK1 inhibitor 32, which does not have a hERG liability and possesses a favorable pharmacokinetic profile in small and large animals. 32 is CNS-penetrant and highly effective in acute and latent mouse models of T. gondii infection, significantly reducing the amount of parasite in the brain, spleen, and peritoneal fluid and reducing brain cysts by >85%. These properties make 32 a promising lead for the development of a new antitoxoplasmosis therapy.
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Affiliation(s)
- Rama Subba Rao Vidadala
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - Kasey L Rivas
- Department of Medicine, Division of Allergy and Infectious Diseases, and the Center for Emerging and Re-Emerging Infectious Diseases (CERID), University of Washington , Seattle, Washington 98109, United States
| | - Kayode K Ojo
- Department of Medicine, Division of Allergy and Infectious Diseases, and the Center for Emerging and Re-Emerging Infectious Diseases (CERID), University of Washington , Seattle, Washington 98109, United States
| | - Matthew A Hulverson
- Department of Medicine, Division of Allergy and Infectious Diseases, and the Center for Emerging and Re-Emerging Infectious Diseases (CERID), University of Washington , Seattle, Washington 98109, United States
| | - Jennifer A Zambriski
- Paul G. Allen School for Global Animal Health, College of Veterinary Medicine, Washington State University , Pullman, Washington 99164, United States
| | - Igor Bruzual
- Portland VA Medical Center , Portland, Oregon 97239, United States
| | - Tracey L Schultz
- Department of Microbiology and Immunology, University of Michigan Medical School , Ann Arbor, Michigan 48109, United States
| | - Wenlin Huang
- Department of Biochemistry, University of Washington , Seattle, Washington 98195, United States
| | - Zhongsheng Zhang
- Department of Biochemistry, University of Washington , Seattle, Washington 98195, United States
| | - Suzanne Scheele
- Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), Seattle, Washington 98109, United States
| | - Amy E DeRocher
- Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), Seattle, Washington 98109, United States
| | - Ryan Choi
- Department of Medicine, Division of Allergy and Infectious Diseases, and the Center for Emerging and Re-Emerging Infectious Diseases (CERID), University of Washington , Seattle, Washington 98109, United States
| | - Lynn K Barrett
- Department of Medicine, Division of Allergy and Infectious Diseases, and the Center for Emerging and Re-Emerging Infectious Diseases (CERID), University of Washington , Seattle, Washington 98109, United States
| | | | - Wim G J Hol
- Department of Biochemistry, University of Washington , Seattle, Washington 98195, United States
| | - Erkang Fan
- Department of Biochemistry, University of Washington , Seattle, Washington 98195, United States
| | - Ethan A Merritt
- Department of Biochemistry, University of Washington , Seattle, Washington 98195, United States
| | - Marilyn Parsons
- Center for Infectious Disease Research (formerly Seattle Biomedical Research Institute), Seattle, Washington 98109, United States.,Department of Global Health, University of Washington , Seattle, Washington 98195, United States
| | - Gail Freiberg
- AbbVie , North Chicago, Illinois 60064, United States
| | - Kennan Marsh
- AbbVie , North Chicago, Illinois 60064, United States
| | - Dale J Kempf
- AbbVie , North Chicago, Illinois 60064, United States
| | - Vern B Carruthers
- Department of Microbiology and Immunology, University of Michigan Medical School , Ann Arbor, Michigan 48109, United States
| | - Nina Isoherranen
- Department of Pharmaceutics, University of Washington , Seattle, Washington 98195, United States
| | - J Stone Doggett
- Portland VA Medical Center , Portland, Oregon 97239, United States
| | - Wesley C Van Voorhis
- Department of Medicine, Division of Allergy and Infectious Diseases, and the Center for Emerging and Re-Emerging Infectious Diseases (CERID), University of Washington , Seattle, Washington 98109, United States.,Department of Global Health, University of Washington , Seattle, Washington 98195, United States
| | - Dustin J Maly
- Department of Biochemistry, University of Washington , Seattle, Washington 98195, United States.,Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
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10
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Picones A, Loza-Huerta A, Segura-Chama P, Lara-Figueroa CO. Contribution of Automated Technologies to Ion Channel Drug Discovery. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2016; 104:357-378. [DOI: 10.1016/bs.apcsb.2016.01.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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11
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High throughput screening technologies for ion channels. Acta Pharmacol Sin 2016; 37:34-43. [PMID: 26657056 DOI: 10.1038/aps.2015.108] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 10/12/2015] [Indexed: 11/08/2022]
Abstract
Ion channels are involved in a variety of fundamental physiological processes, and their malfunction causes numerous human diseases. Therefore, ion channels represent a class of attractive drug targets and a class of important off-targets for in vitro pharmacological profiling. In the past decades, the rapid progress in developing functional assays and instrumentation has enabled high throughput screening (HTS) campaigns on an expanding list of channel types. Chronologically, HTS methods for ion channels include the ligand binding assay, flux-based assay, fluorescence-based assay, and automated electrophysiological assay. In this review we summarize the current HTS technologies for different ion channel classes and their applications.
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12
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Cardiotoxicity screening: a review of rapid-throughput in vitro approaches. Arch Toxicol 2015; 90:1803-16. [PMID: 26676948 DOI: 10.1007/s00204-015-1651-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 11/18/2015] [Indexed: 01/07/2023]
Abstract
Cardiac toxicity represents one of the leading causes of drug failure along different stages of drug development. Multiple very successful pharmaceuticals had to be pulled from the market or labeled with strict usage warnings due to adverse cardiac effects. In order to protect clinical trial participants and patients, the International Conference on Harmonization published guidelines to recommend that all new drugs to be tested preclinically for hERG (Kv11.1) channel sensitivity before submitting for regulatory reviews. However, extensive studies have demonstrated that measurement of hERG activity has limitations due to the multiple molecular targets of drug compound through which it may mitigate or abolish a potential arrhythmia, and therefore, a model measuring multiple ion channel effects is likely to be more predictive. Several phenotypic rapid-throughput methods have been developed to predict the potential cardiac toxic compounds in the early stages of drug development using embryonic stem cells- or human induced pluripotent stem cell-derived cardiomyocytes. These rapid-throughput methods include microelectrode array-based field potential assay, impedance-based or Ca(2+) dynamics-based cardiomyocytes contractility assays. This review aims to discuss advantages and limitations of these phenotypic assays for cardiac toxicity assessment.
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13
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Molinski SV, Ahmadi S, Hung M, Bear CE. Facilitating Structure-Function Studies of CFTR Modulator Sites with Efficiencies in Mutagenesis and Functional Screening. ACTA ACUST UNITED AC 2015; 20:1204-17. [PMID: 26385858 DOI: 10.1177/1087057115605834] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 08/23/2015] [Indexed: 12/20/2022]
Abstract
There are nearly 2000 mutations in the CFTR gene associated with cystic fibrosis disease, and to date, the only approved drug, Kalydeco, has been effective in rescuing the functional expression of a small subset of these mutant proteins with defects in channel activation. However, there is currently an urgent need to assess other mutations for possible rescue by Kalydeco, and further, definition of the binding site of such modulators on CFTR would enhance our understanding of the mechanism of action of such therapeutics. Here, we describe a simple and rapid one-step PCR-based site-directed mutagenesis method to generate mutations in the CFTR gene. This method was used to generate CFTR mutants bearing deletions (p.Gln2_Trp846del, p.Ser700_Asp835del, p.Ile1234_Arg1239del) and truncation with polyhistidine tag insertion (p.Glu1172-3Gly-6-His*), which either recapitulate a disease phenotype or render tools for modulator binding site identification, with subsequent evaluation of drug responses using a high-throughput (384-well) membrane potential-sensitive fluorescence assay of CFTR channel activity within a 1 wk time frame. This proof-of-concept study shows that these methods enable rapid and quantitative comparison of multiple CFTR mutants to emerging drugs, facilitating future large-scale efforts to stratify mutants according to their "theratype" or most promising targeted therapy.
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Affiliation(s)
- Steven V Molinski
- Molecular Structure and Function, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Saumel Ahmadi
- Molecular Structure and Function, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Maurita Hung
- Molecular Structure and Function, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Christine E Bear
- Molecular Structure and Function, Research Institute, Hospital for Sick Children, Toronto, Ontario, Canada Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada Department of Physiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
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14
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Du F, Babcock JJ, Yu H, Zou B, Li M. Global analysis reveals families of chemical motifs enriched for HERG inhibitors. PLoS One 2015; 10:e0118324. [PMID: 25700001 PMCID: PMC4336329 DOI: 10.1371/journal.pone.0118324] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 12/01/2014] [Indexed: 11/18/2022] Open
Abstract
Promiscuous inhibition of the human ether-à-go-go-related gene (hERG) potassium channel by drugs poses a major risk for life threatening arrhythmia and costly drug withdrawals. Current knowledge of this phenomenon is derived from a limited number of known drugs and tool compounds. However, in a diverse, naïve chemical library, it remains unclear which and to what degree chemical motifs or scaffolds might be enriched for hERG inhibition. Here we report electrophysiology measurements of hERG inhibition and computational analyses of >300,000 diverse small molecules. We identify chemical ‘communities’ with high hERG liability, containing both canonical scaffolds and structurally distinctive molecules. These data enable the development of more effective classifiers to computationally assess hERG risk. The resultant predictive models now accurately classify naïve compound libraries for tendency of hERG inhibition. Together these results provide a more complete reference map of characteristic chemical motifs for hERG liability and advance a systematic approach to rank chemical collections for cardiotoxicity risk.
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Affiliation(s)
- Fang Du
- The Solomon H. Snyder Department of Neuroscience, High Throughput Biology Center and Johns Hopkins Ion Channel Center (JHICC), Johns Hopkins University, 733 North Broadway, Baltimore, MD 21205, United States of America
| | - Joseph J. Babcock
- The Solomon H. Snyder Department of Neuroscience, High Throughput Biology Center and Johns Hopkins Ion Channel Center (JHICC), Johns Hopkins University, 733 North Broadway, Baltimore, MD 21205, United States of America
| | - Haibo Yu
- The Solomon H. Snyder Department of Neuroscience, High Throughput Biology Center and Johns Hopkins Ion Channel Center (JHICC), Johns Hopkins University, 733 North Broadway, Baltimore, MD 21205, United States of America
| | - Beiyan Zou
- The Solomon H. Snyder Department of Neuroscience, High Throughput Biology Center and Johns Hopkins Ion Channel Center (JHICC), Johns Hopkins University, 733 North Broadway, Baltimore, MD 21205, United States of America
| | - Min Li
- The Solomon H. Snyder Department of Neuroscience, High Throughput Biology Center and Johns Hopkins Ion Channel Center (JHICC), Johns Hopkins University, 733 North Broadway, Baltimore, MD 21205, United States of America
- * E-mail:
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15
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Abstract
INTRODUCTION Cardiac K(+) channels play a critical role in maintaining the normal electrical activity of the heart by setting the cell resting membrane potential and by determining the shape and duration of the action potential. Drugs that block the rapid (IKr) and slow (IKs) components of the delayed rectifier K(+) current have been widely used as class III antiarrhythmic agents. In addition, drugs that selectively target the ultra-rapid delayed rectifier current (IKur) and the acetylcholine-gated inward rectifier current (IKAch) have shown efficacy in the treatment of patients with atrial fibrillation. In order to meet the future demand for new antiarrhythmic agents, novel approaches for cardiac K(+) channel drug discovery will need to be developed. Further, K(+) channel screening assays utilizing primary and stem cell-derived cardiomyocytes will be essential for evaluating the cardiotoxicity of potential drug candidates. AREAS COVERED In this review, the author provides a brief background on the structure, function and pharmacology of cardiac voltage-gated and inward rectifier K(+) channels. He then focuses on describing and evaluating current technologies, such as ion flux and membrane potential-sensitive dye assays, used for cardiac K(+) channel drug discovery. EXPERT OPINION Cardiac K(+) channels will continue to represent significant clinical targets for drug discovery. Although fluorescent high-throughput screening (HTS) assays and automated patch clamp systems will remain the workhorse technologies for identifying lead compounds, innovations in the areas of microfluidics, micropatterning and biosensor fabrication will allow further growth of technologies using primary and stem cell-derived cardiomyocytes.
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Affiliation(s)
- Kenneth B Walsh
- University of South Carolina, School of Medicine, Department of Pharmacology, Physiology and Neuroscience , Columbia, SC 29209 , USA +1 803 216 3519 ; +1 803 216 3538 ;
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16
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Yarov-Yarovoy V, Allen TW, Clancy CE. Computational Models for Predictive Cardiac Ion Channel Pharmacology. ACTA ACUST UNITED AC 2014; 14:3-10. [PMID: 26635886 DOI: 10.1016/j.ddmod.2014.04.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A wealth of experimental data exists describing the elementary building blocks of complex physiological systems. However, it is increasingly apparent in the biomedical sciences that mechanisms of biological function cannot be observed or readily predicted via study of constituent elements alone. This is especially clear in the longstanding failures in prediction of effects of drug treatment for heart rhythm disturbances. These failures stem in part from classical assumptions that have been made in cardiac antiarrhythmic drug development - that a drug operates by one mechanism via one target receptor that arises from one gene.
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Affiliation(s)
| | - Toby W Allen
- Department of Chemistry, University of California, Davis
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17
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Ojo KK, Eastman RT, Vidadala R, Zhang Z, Rivas KL, Choi R, Lutz JD, Reid MC, Fox AMW, Hulverson MA, Kennedy M, Isoherranen N, Kim LM, Comess KM, Kempf DJ, Verlinde CLMJ, Su XZ, Kappe SHI, Maly DJ, Fan E, Van Voorhis WC. A specific inhibitor of PfCDPK4 blocks malaria transmission: chemical-genetic validation. J Infect Dis 2014; 209:275-84. [PMID: 24123773 PMCID: PMC3873787 DOI: 10.1093/infdis/jit522] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Accepted: 06/07/2013] [Indexed: 01/03/2023] Open
Abstract
Malaria parasites are transmitted by mosquitoes, and blocking parasite transmission is critical in reducing or eliminating malaria in endemic regions. Here, we report the pharmacological characterization of a new class of malaria transmission-blocking compounds that acts via the inhibition of Plasmodia CDPK4 enzyme. We demonstrate that these compounds achieved selectivity over mammalian kinases by capitalizing on a small serine gatekeeper residue in the active site of the Plasmodium CDPK4 enzyme. To directly confirm the mechanism of action of these compounds, we generated P. falciparum parasites that express a drug-resistant methionine gatekeeper (S147 M) CDPK4 mutant. Mutant parasites showed a shift in exflagellation EC50 relative to the wild-type strains in the presence of compound 1294, providing chemical-genetic evidence that CDPK4 is the target of the compound. Pharmacokinetic analyses suggest that coformulation of this transmission-blocking agent with asexual stage antimalarials such as artemisinin combination therapy (ACT) is a promising option for drug delivery that may reduce transmission of malaria including drug-resistant strains. Ongoing studies include refining the compounds to improve efficacy and toxicological properties for efficient blocking of malaria transmission.
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Affiliation(s)
- Kayode K. Ojo
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle
| | - Richard T. Eastman
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | | | | | - Kasey L. Rivas
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle
| | - Ryan Choi
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle
| | - Justin D. Lutz
- Department of Pharmaceutics, University of Washington, Seattle
| | - Molly C. Reid
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle
| | - Anna M. W. Fox
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle
| | - Matthew A. Hulverson
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle
| | - Mark Kennedy
- Seattle Biomedical Research Institute, Washington
| | | | - Laura M. Kim
- Global Pharmaceutical R&D, AbbVie, North Chicago, Illinois
| | | | - Dale J. Kempf
- Global Pharmaceutical R&D, AbbVie, North Chicago, Illinois
| | | | - Xin-zhuan Su
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland
| | | | | | | | - Wesley C. Van Voorhis
- Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington, Seattle
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18
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Townsend C, Brown BS. Predicting drug-induced QT prolongation and torsades de pointes: a review of preclinical endpoint measures. ACTA ACUST UNITED AC 2013; Chapter 10:Unit 10.16. [PMID: 23744708 DOI: 10.1002/0471141755.ph1016s61] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Compound-induced prolongation of the cardiac QT interval is a major concern in drug development and this unit discusses approaches that can predict QT effects prior to undertaking clinical trials. The majority of compounds that prolong the QT interval block the cardiac rapid delayed rectifier potassium current, IKr (hERG). Described in this overview are different ways to measure hERG, from recent advances in automated electrophysiology to the quantification of channel protein trafficking and binding. The contribution of other cardiac ion channels to hERG data interpretation is also discussed. In addition, endpoint measures of the integrated activity of cardiac ion channels at the single-cell, tissue, and whole-animal level, including for example the well-established action potential to the more recent beat-to-beat variability, transmural dispersion of repolarization, and field potential duration, are described in the context of their ability to predict QT prolongation and torsadogenicity in humans.
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Affiliation(s)
- Claire Townsend
- GlaxoSmithKline Biological Reagents and Assay Development, Research Triangle Park, NC, USA
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19
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Raphemot R, Kadakia RJ, Olsen ML, Banerjee S, Days E, Smith SS, Weaver CD, Denton JS. Development and validation of fluorescence-based and automated patch clamp-based functional assays for the inward rectifier potassium channel Kir4.1. Assay Drug Dev Technol 2013; 11:532-43. [PMID: 24266659 DOI: 10.1089/adt.2013.544] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The inward rectifier potassium (Kir) channel Kir4.1 plays essential roles in modulation of neurotransmission and renal sodium transport and may represent a novel drug target for temporal lobe epilepsy and hypertension. The molecular pharmacology of Kir4.1 is limited to neurological drugs, such as fluoxetine (Prozac(©)), exhibiting weak and nonspecific activity toward the channel. The development of potent and selective small-molecule probes would provide critically needed tools for exploring the integrative physiology and therapeutic potential of Kir4.1. A fluorescence-based thallium (Tl(+)) flux assay that utilizes a tetracycline-inducible T-Rex-HEK293-Kir4.1 cell line to enable high-throughput screening (HTS) of small-molecule libraries was developed. The assay is dimethyl sulfoxide tolerant and exhibits robust screening statistics (Z'=0.75±0.06). A pilot screen of 3,655 small molecules and lipids revealed 16 Kir4.1 inhibitors (0.4% hit rate). 3,3-Diphenyl-N-(1-phenylethyl)propan-1-amine, termed VU717, inhibits Kir4.1-mediated thallium flux with an IC50 of ∼6 μM. An automated patch clamp assay using the IonFlux HT workbench was developed to facilitate compound characterization. Leak-subtracted ensemble "loose patch" recordings revealed robust tetracycline-inducible and Kir4.1 currents that were inhibited by fluoxetine (IC50=10 μM), VU717 (IC50=6 μM), and structurally related calcium channel blocker prenylamine (IC50=6 μM). Finally, we demonstrate that VU717 inhibits Kir4.1 channel activity in cultured rat astrocytes, providing proof-of-concept that the Tl(+) flux and IonFlux HT assays can enable the discovery of antagonists that are active against native Kir4.1 channels.
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Affiliation(s)
- Rene Raphemot
- 1 Department of Anesthesiology, Vanderbilt University School of Medicine , Nashville, Tennessee
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20
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Babcock JJ, Du F, Xu K, Wheelan SJ, Li M. Integrated analysis of drug-induced gene expression profiles predicts novel hERG inhibitors. PLoS One 2013; 8:e69513. [PMID: 23936032 PMCID: PMC3720659 DOI: 10.1371/journal.pone.0069513] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 06/07/2013] [Indexed: 11/19/2022] Open
Abstract
Growing evidence suggests that drugs interact with diverse molecular targets mediating both therapeutic and toxic effects. Prediction of these complex interactions from chemical structures alone remains challenging, as compounds with different structures may possess similar toxicity profiles. In contrast, predictions based on systems-level measurements of drug effect may reveal pharmacologic similarities not evident from structure or known therapeutic indications. Here we utilized drug-induced transcriptional responses in the Connectivity Map (CMap) to discover such similarities among diverse antagonists of the human ether-à-go-go related (hERG) potassium channel, a common target of promiscuous inhibition by small molecules. Analysis of transcriptional profiles generated in three independent cell lines revealed clusters enriched for hERG inhibitors annotated using a database of experimental measurements (hERGcentral) and clinical indications. As a validation, we experimentally identified novel hERG inhibitors among the unannotated drugs in these enriched clusters, suggesting transcriptional responses may serve as predictive surrogates of cardiotoxicity complementing existing functional assays.
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Affiliation(s)
- Joseph J. Babcock
- The Solomon H. Snyder Department of Neuroscience and High Throughput Biology Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Fang Du
- The Solomon H. Snyder Department of Neuroscience and High Throughput Biology Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Kaiping Xu
- Johns Hopkins Ion Channel Center (JHICC), The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Sarah J. Wheelan
- Department of Oncology, Division of Biostatistics and Bioinformatics, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- * E-mail: (ML); (SJW)
| | - Min Li
- The Solomon H. Snyder Department of Neuroscience and High Throughput Biology Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Johns Hopkins Ion Channel Center (JHICC), The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- * E-mail: (ML); (SJW)
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21
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Vandenberg JI, Perry MD, Perrin MJ, Mann SA, Ke Y, Hill AP. hERG K+ Channels: Structure, Function, and Clinical Significance. Physiol Rev 2012; 92:1393-478. [DOI: 10.1152/physrev.00036.2011] [Citation(s) in RCA: 526] [Impact Index Per Article: 40.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The human ether-a-go-go related gene (hERG) encodes the pore-forming subunit of the rapid component of the delayed rectifier K+ channel, Kv11.1, which are expressed in the heart, various brain regions, smooth muscle cells, endocrine cells, and a wide range of tumor cell lines. However, it is the role that Kv11.1 channels play in the heart that has been best characterized, for two main reasons. First, it is the gene product involved in chromosome 7-associated long QT syndrome (LQTS), an inherited disorder associated with a markedly increased risk of ventricular arrhythmias and sudden cardiac death. Second, blockade of Kv11.1, by a wide range of prescription medications, causes drug-induced QT prolongation with an increase in risk of sudden cardiac arrest. In the first part of this review, the properties of Kv11.1 channels, including biogenesis, trafficking, gating, and pharmacology are discussed, while the second part focuses on the pathophysiology of Kv11.1 channels.
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Affiliation(s)
- Jamie I. Vandenberg
- Mark Cowley Lidwill Research Programme in Cardiac Electrophysiology, Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia; St Vincent's Clinical School, University of New South Wales, New South Wales, Australia; and University of Ottawa Heart Institute, Ottawa, Canada
| | - Matthew D. Perry
- Mark Cowley Lidwill Research Programme in Cardiac Electrophysiology, Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia; St Vincent's Clinical School, University of New South Wales, New South Wales, Australia; and University of Ottawa Heart Institute, Ottawa, Canada
| | - Mark J. Perrin
- Mark Cowley Lidwill Research Programme in Cardiac Electrophysiology, Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia; St Vincent's Clinical School, University of New South Wales, New South Wales, Australia; and University of Ottawa Heart Institute, Ottawa, Canada
| | - Stefan A. Mann
- Mark Cowley Lidwill Research Programme in Cardiac Electrophysiology, Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia; St Vincent's Clinical School, University of New South Wales, New South Wales, Australia; and University of Ottawa Heart Institute, Ottawa, Canada
| | - Ying Ke
- Mark Cowley Lidwill Research Programme in Cardiac Electrophysiology, Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia; St Vincent's Clinical School, University of New South Wales, New South Wales, Australia; and University of Ottawa Heart Institute, Ottawa, Canada
| | - Adam P. Hill
- Mark Cowley Lidwill Research Programme in Cardiac Electrophysiology, Victor Chang Cardiac Research Institute, Sydney, New South Wales, Australia; St Vincent's Clinical School, University of New South Wales, New South Wales, Australia; and University of Ottawa Heart Institute, Ottawa, Canada
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22
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Vazquez M, Dunn CA, Walsh KB. A fluorescent screening assay for identifying modulators of GIRK channels. J Vis Exp 2012:3850. [PMID: 22706581 DOI: 10.3791/3850] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
G protein-gated inward rectifier K+ (GIRK) channels function as cellular mediators of a wide range of hormones and neurotransmitters and are expressed in the brain, heart, skeletal muscle and endocrine tissue(1,2). GIRK channels become activated following the binding of ligands (neurotransmitters, hormones, drugs, etc.) to their plasma membrane-bound, G protein-coupled receptors (GPCRs). This binding causes the stimulation of G proteins (Gi and Go) which subsequently bind to and activate the GIRK channel. Once opened the GIRK channel allows the movement of K+ out of the cell causing the resting membrane potential to become more negative. As a consequence, GIRK channel activation in neurons decreases spontaneous action potential formation and inhibits the release of excitatory neurotransmitters. In the heart, activation of the GIRK channel inhibits pacemaker activity thereby slowing the heart rate. GIRK channels represent novel targets for the development of new therapeutic agents for the treatment neuropathic pain, drug addiction, cardiac arrhythmias and other disorders(3). However, the pharmacology of these channels remains largely unexplored. Although a number of drugs including anti-arrhythmic agents, antipsychotic drugs and antidepressants block the GIRK channel, this inhibition is not selective and occurs at relatively high drug concentrations(3). Here, we describe a real-time screening assay for identifying new modulators of GIRK channels. In this assay, neuronal AtT20 cells, expressing GIRK channels, are loaded with membrane potential-sensitive fluorescent dyes such as bis-(1,3-dibutylbarbituric acid) trimethine oxonol [DiBAC4(3)] or HLB 021-152 (Figure 1). The dye molecules become strongly fluorescent following uptake into the cells (Figure 1). Treatment of the cells with GPCR ligands stimulates the GIRK channels to open. The resulting K+ efflux out of the cell causes the membrane potential to become more negative and the fluorescent signal to decrease (Figure 1). Thus, drugs that modulate K+ efflux through the GIRK channel can be assayed using a fluorescent plate reader. Unlike other ion channel screening assays, such atomic absorption spectrometry(4) or radiotracer analysis(5), the GIRK channel fluorescent assay provides a fast, real-time and inexpensive screening procedure.
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Affiliation(s)
- Maribel Vazquez
- Department of Pharmacology, Physiology & Neuroscience, University of South Carolina, School of Medicine, SC, USA
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23
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Raphemot R, Lonergan DF, Nguyen TT, Utley T, Lewis LM, Kadakia R, Weaver CD, Gogliotti R, Hopkins C, Lindsley CW, Denton JS. Discovery, characterization, and structure-activity relationships of an inhibitor of inward rectifier potassium (Kir) channels with preference for Kir2.3, Kir3.x, and Kir7.1. Front Pharmacol 2011; 2:75. [PMID: 22275899 PMCID: PMC3254186 DOI: 10.3389/fphar.2011.00075] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Accepted: 11/07/2011] [Indexed: 12/03/2022] Open
Abstract
The inward rectifier family of potassium (Kir) channels is comprised of at least 16 family members exhibiting broad and often overlapping cellular, tissue, or organ distributions. The discovery of disease-causing mutations in humans and experiments on knockout mice has underscored the importance of Kir channels in physiology and in some cases raised questions about their potential as drug targets. However, the paucity of potent and selective small-molecule modulators targeting specific family members has with few exceptions mired efforts to understand their physiology and assess their therapeutic potential. A growing body of evidence suggests that G protein-coupled inward rectifier K (GIRK) channels of the Kir3.X subfamily may represent novel targets for the treatment of atrial fibrillation. In an effort to expand the molecular pharmacology of GIRK, we performed a thallium (Tl(+)) flux-based high-throughput screen of a Kir1.1 inhibitor library for modulators of GIRK. One compound, termed VU573, exhibited 10-fold selectivity for GIRK over Kir1.1 (IC(50) = 1.9 and 19 μM, respectively) and was therefore selected for further study. In electrophysiological experiments performed on Xenopus laevis oocytes and mammalian cells, VU573 inhibited Kir3.1/3.2 (neuronal GIRK) and Kir3.1/3.4 (cardiac GIRK) channels with equal potency and preferentially inhibited GIRK, Kir2.3, and Kir7.1 over Kir1.1 and Kir2.1.Tl(+) flux assays were established for Kir2.3 and the M125R pore mutant of Kir7.1 to support medicinal chemistry efforts to develop more potent and selective analogs for these channels. The structure-activity relationships of VU573 revealed few analogs with improved potency, however two compounds retained most of their activity toward GIRK and Kir2.3 and lost activity toward Kir7.1. We anticipate that the VU573 series will be useful for exploring the physiology and structure-function relationships of these Kir channels.
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Affiliation(s)
- Rene Raphemot
- Department of Anesthesiology, Vanderbilt University School of MedicineNashville, TN, USA
- Department of Pharmacology, Vanderbilt University School of MedicineNashville, TN, USA
| | - Daniel F. Lonergan
- Department of Anesthesiology, Vanderbilt University School of MedicineNashville, TN, USA
| | - Thuy T. Nguyen
- Department of Anesthesiology, Vanderbilt University School of MedicineNashville, TN, USA
- Department of Pharmacology, Vanderbilt University School of MedicineNashville, TN, USA
| | - Thomas Utley
- Department of Pharmacology, Vanderbilt University School of MedicineNashville, TN, USA
| | - L. Michelle Lewis
- Vanderbilt Institute of Chemical Biology, Vanderbilt UniversityNashville, TN, USA
| | - Rishin Kadakia
- Department of Anesthesiology, Vanderbilt University School of MedicineNashville, TN, USA
| | - C. David Weaver
- Department of Pharmacology, Vanderbilt University School of MedicineNashville, TN, USA
- Vanderbilt Institute of Chemical Biology, Vanderbilt UniversityNashville, TN, USA
| | - Rocco Gogliotti
- Department of Pharmacology, Vanderbilt University School of MedicineNashville, TN, USA
- Vanderbilt Center for Neuroscience Drug Discovery, Vanderbilt University School of MedicineNashville, TN, USA
| | - Corey Hopkins
- Department of Pharmacology, Vanderbilt University School of MedicineNashville, TN, USA
- Vanderbilt Institute of Chemical Biology, Vanderbilt UniversityNashville, TN, USA
- Vanderbilt Center for Neuroscience Drug Discovery, Vanderbilt University School of MedicineNashville, TN, USA
- Department of Chemistry, Vanderbilt UniversityNashville, TN, USA
- Vanderbilt Specialized Chemistry Center for Accelerated Probe Development, Molecular Libraries Probe Production Centers NetworkNashville, TN, USA
| | - Craig W. Lindsley
- Department of Pharmacology, Vanderbilt University School of MedicineNashville, TN, USA
- Vanderbilt Institute of Chemical Biology, Vanderbilt UniversityNashville, TN, USA
- Vanderbilt Center for Neuroscience Drug Discovery, Vanderbilt University School of MedicineNashville, TN, USA
- Department of Chemistry, Vanderbilt UniversityNashville, TN, USA
- Vanderbilt Specialized Chemistry Center for Accelerated Probe Development, Molecular Libraries Probe Production Centers NetworkNashville, TN, USA
| | - Jerod S. Denton
- Department of Anesthesiology, Vanderbilt University School of MedicineNashville, TN, USA
- Department of Pharmacology, Vanderbilt University School of MedicineNashville, TN, USA
- Vanderbilt Institute of Chemical Biology, Vanderbilt UniversityNashville, TN, USA
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24
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Zou B, Yu H, Babcock JJ, Chanda P, Bader JS, McManus OB, Li M. Profiling diverse compounds by flux- and electrophysiology-based primary screens for inhibition of human Ether-à-go-go related gene potassium channels. Assay Drug Dev Technol 2011; 8:743-54. [PMID: 21158688 DOI: 10.1089/adt.2010.0339] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Compound effects on cloned human Ether-à-go-go related gene (hERG) potassium channels have been used to assess the potential cardiac safety liabilities of drug development candidate compounds. In addition to radioactive ligand displacement tests, two other common approaches are surrogate ion-based flux assays and electrophysiological recordings. The former has much higher throughput, whereas the latter measures directly the effects on ionic currents. Careful characterization in earlier reports has been performed to compare the relative effectiveness of these approaches for known hERG blockers, which often yielded good overall correlation. However, cases were reported showing significant and reproducible differences in potency and/or sensitivity by the two methods. This raises a question concerning the rationale and criteria on which an assay should be selected for evaluating unknown compounds. To provide a general basis for considering assays to profile large compound libraries for hERG activity, we have conducted parallel flux and electrophysiological analyses of 2,000 diverse compounds, representative of the 300,000 compound collection of NIH Molecular Library Small Molecular Repository (MLSMR). Our results indicate that at the conventional testing concentration 1.0 μM, the overlap between the two assays ranges from 32% to 50% depending on the hit selection criteria. There was a noticeable rate of false negatives by the thallium-based assay relative to electrophysiological recording, which may be greatly reduced under modified comparative conditions. As these statistical results identify a preferred method for cardiac safety profiling of unknown compounds, they suggest an efficient method combining flux and electrophysiological assays to rapidly profile hERG liabilities of large collection of naive compounds.
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Affiliation(s)
- Beiyan Zou
- Department of Neuroscience, High Throughput Biology Center, Johns Hopkins University, Baltimore, Maryland 21205, USA
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25
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Schmalhofer WA, Swensen AM, Thomas BS, Felix JP, Haedo RJ, Solly K, Kiss L, Kaczorowski GJ, Garcia ML. A Pharmacologically Validated, High-Capacity, Functional Thallium Flux Assay for the Human Ether-à-go-go Related Gene Potassium Channel. Assay Drug Dev Technol 2010; 8:714-26. [DOI: 10.1089/adt.2010.0351] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
| | - Andrew M. Swensen
- Department of Ion Channels, Merck Research Laboratories, Rahway, New Jersey
| | - Brande S. Thomas
- Department of Ion Channels, Merck Research Laboratories, Rahway, New Jersey
| | - John P. Felix
- Department of Ion Channels, Merck Research Laboratories, Rahway, New Jersey
| | - Rodolfo J. Haedo
- Department of Ion Channels, Merck Research Laboratories, Rahway, New Jersey
| | - Kelli Solly
- Department of Automated Biotechnology, Merck Research Laboratories, North Wales, Pennsylvania
| | - Laszlo Kiss
- Department of Automated Biotechnology, Merck Research Laboratories, North Wales, Pennsylvania
| | | | - Maria L. Garcia
- Department of Ion Channels, Merck Research Laboratories, Rahway, New Jersey
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