1
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Calabretta MM, Michelini E. Current advances in the use of bioluminescence assays for drug discovery: an update of the last ten years. Expert Opin Drug Discov 2024; 19:85-95. [PMID: 37814480 DOI: 10.1080/17460441.2023.2266989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 10/02/2023] [Indexed: 10/11/2023]
Abstract
INTRODUCTION Bioluminescence is a well-established optical detection technique widely used in several bioanalytical applications, including high-throughput and high-content screenings. Thanks to advances in synthetic biology techniques and deep learning, a wide portfolio of luciferases is now available with tuned emission wavelengths, kinetics, and high stability. These luciferases can be implemented in the drug discovery and development pipeline, allowing high sensitivity and multiplexing capability. AREAS COVERED This review summarizes the latest advancements of bioluminescent systems as toolsets in drug discovery programs for in vitro applications. Particular attention is paid to the most advanced bioluminescence-based technologies for drug screening over the past 10 years (from 2013 to 2023) such as cell-free assays, cell-based assays based on genetically modified cells, bioluminescence resonance energy transfer, and protein complementation assays in 2D and 3D cell models. EXPERT OPINION The availability of tuned bioluminescent proteins with improved emission and stability properties is vital for the development of bioluminescence assays for drug discovery, spanning from reporter gene technology to protein-protein techniques. Further studies, combining machine learning with synthetic biology, will be necessary to obtain new tools for sustainable and highly predictive bioluminescent drug discovery platforms.
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Affiliation(s)
- Maria Maddalena Calabretta
- Department of Chemistry "Giacomo Ciamician", Alma Mater Studiorum-University of Bologna, Bologna, Italy
- Center for Applied Biomedical Research (CRBA), IRCCS St. Orsola Hospital, Bologna, Italy
| | - Elisa Michelini
- Department of Chemistry "Giacomo Ciamician", Alma Mater Studiorum-University of Bologna, Bologna, Italy
- Center for Applied Biomedical Research (CRBA), IRCCS St. Orsola Hospital, Bologna, Italy
- Health Sciences and Technologies Interdepartmental Center for Industrial Research (HSTICIR), University of Bologna, Bologna, Italy
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2
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Meyer C, McCoy M, Li L, Posner B, Westover KD. LIMS-Kinase provides sensitive and generalizable label-free in vitro measurement of kinase activity using mass spectrometry. CELL REPORTS. PHYSICAL SCIENCE 2023; 4:101599. [PMID: 38213501 PMCID: PMC10783653 DOI: 10.1016/j.xcrp.2023.101599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
Measurements of kinase activity are important for kinase-directed drug development, analysis of inhibitor structure and function, and understanding mechanisms of drug resistance. Sensitive, accurate, and miniaturized assay methods are crucial for these investigations. Here, we describe a label-free, high-throughput mass spectrometry-based assay for studying individual kinase enzymology and drug discovery in a purified system, with a focus on validated drug targets as benchmarks. We demonstrate that this approach can be adapted to many known kinase substrates and highlight the benefits of using mass spectrometry to measure kinase activity in vitro, including increased sensitivity. We speculate that this approach to measuring kinase activity will be generally applicable across most of the kinome, enabling research on understudied kinases and kinase drug discovery.
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Affiliation(s)
- Cynthia Meyer
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
- Department of Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
| | - Melissa McCoy
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
| | - Lianbo Li
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
- Department of Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
| | - Bruce Posner
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
| | - Kenneth D. Westover
- Department of Biochemistry, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
- Department of Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA
- X (formerly Twitter): @KENWESTOVER
- Lead contact
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3
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Chowdhury S, Zielinski DC, Dalldorf C, Rodrigues JV, Palsson BO, Shakhnovich EI. Empowering drug off-target discovery with metabolic and structural analysis. Nat Commun 2023; 14:3390. [PMID: 37296102 PMCID: PMC10256842 DOI: 10.1038/s41467-023-38859-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 05/15/2023] [Indexed: 06/12/2023] Open
Abstract
Elucidating intracellular drug targets is a difficult problem. While machine learning analysis of omics data has been a promising approach, going from large-scale trends to specific targets remains a challenge. Here, we develop a hierarchic workflow to focus on specific targets based on analysis of metabolomics data and growth rescue experiments. We deploy this framework to understand the intracellular molecular interactions of the multi-valent dihydrofolate reductase-targeting antibiotic compound CD15-3. We analyse global metabolomics data utilizing machine learning, metabolic modelling, and protein structural similarity to prioritize candidate drug targets. Overexpression and in vitro activity assays confirm one of the predicted candidates, HPPK (folK), as a CD15-3 off-target. This study demonstrates how established machine learning methods can be combined with mechanistic analyses to improve the resolution of drug target finding workflows for discovering off-targets of a metabolic inhibitor.
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Affiliation(s)
- Sourav Chowdhury
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Daniel C Zielinski
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Christopher Dalldorf
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Joao V Rodrigues
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800, Kongens Lyngby, Denmark
| | - Eugene I Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
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4
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Liu L, Song W, Zeng J, Peng Z. Evaluating a Specific Dual ROCK Inhibitor against Bleomycin-Induced Idiopathic Pulmonary Fibrosis in Rats. ACS Pharmacol Transl Sci 2022; 5:819-828. [PMID: 36110377 PMCID: PMC9469187 DOI: 10.1021/acsptsci.2c00149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Indexed: 11/29/2022]
Abstract
Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive, and fatal lung disease. Rho-associated protein kinases (ROCK) 1/2 are promising therapeutic targets for the treatment of IPF. However, a single inhibition of each of them is insufficient to prevent bleomycin-induced lung fibrosis. The current work reported that bleomycin-induced lung fibrosis can be reduced by dual inhibition of ROCK1/2 with compound 1. We evaluated the dual-selective ROCK1/2 inhibition activity of compound 1, its toxicity, and its preliminary efficacy on bleomycin-induced lung fibrosis. In vitro, compound 1 served as the ROCK1/2 inhibitor with half-maximal inhibitory concentration (IC50) values of 165 ±10.4 nM for ROCK1 and 16.1 ± 2.82 nM for ROCK2. In NIH/3T3 cells, compound 1 inhibited the mRNA expression of COL 1A1 and α-SMA. At therapeutic levels, compound 1 exhibited neither hepatic nor cardiac toxicity, also no CYP450 enzyme inhibition. In vivo, compound 1 had good pharmacokinetic properties, and its oral administration reduced bleomycin-induced pulmonary fibrosis in rats. All the outcomes prove the drug-like characteristics of compound 1 for the treatment of IPF.
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Affiliation(s)
- Li Liu
- Wuhan
Createrna Science and Technology Co.Ltd, Wuhan East Lake High-Tech
Development Zone, Biolake
C2-2, Wuhan 430073, China
| | - Wei Song
- School
of Life Science, Hubei University, Wuhan 430062, China
| | - Jing Zeng
- Wuhan
Createrna Science and Technology Co.Ltd, Wuhan East Lake High-Tech
Development Zone, Biolake
C2-2, Wuhan 430073, China
| | - Zhihong Peng
- School
of Life Science, Hubei University, Wuhan 430062, China
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5
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Arica-Sosa A, Alcántara R, Jiménez-Avalos G, Zimic M, Milón P, Quiliano M. Identifying RO9021 as a Potential Inhibitor of PknG from Mycobacterium tuberculosis: Combinative Computational and In Vitro Studies. ACS OMEGA 2022; 7:20204-20218. [PMID: 35721990 PMCID: PMC9201901 DOI: 10.1021/acsomega.2c02093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/12/2022] [Indexed: 06/07/2023]
Abstract
Tuberculosis (TB) is an infectious disease caused by Mycobacterium tuberculosis (Mtb). Despite being considered curable and preventable, the increase of antibiotic resistance is becoming a serious public health problem. Mtb is a pathogen capable of surviving in macrophages, causing long-term latent infection where the mycobacterial serine/threonine protein kinase G (PknG) plays a protective role. Therefore, PknG is an important inhibitory target to prevent Mtb from entering the latency stage. In this study, we use a pharmacophore-based virtual screening and biochemical assays to identify the compound RO9021 (CHEMBL3237561) as a PknG inhibitor. In detail, 1.5 million molecules were screened using a scalable cloud-based setup, identifying 689 candidates, which were further subjected to additional screening employing molecular docking. Molecular docking spotted 62 compounds with estimated binding affinities of -7.54 kcal/mol (s.d. = 0.77 kcal/mol). Finally, 14 compounds were selected for in vitro experiments considering previously reported biological activities and commercial availability. In vitro assays of PknG activity showed that RO9021 inhibits the kinase activity similarly to AX20017, a known inhibitor. The inhibitory effect was found to be dose dependent with a relative IC50 value of 4.4 ± 1.1 μM. Molecular dynamics simulations predicted that the PknG-RO9021 complex is stable along the tested timescale. Altogether, our study indicates that RO9021 is a noteworthy drug candidate for further developing new anti-TB drugs that hold excellent reported pharmacokinetic parameters.
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Affiliation(s)
- Alicia Arica-Sosa
- Drug
Development and Innovation Group, Biomolecules Laboratory, Faculty
of Health Sciences, Universidad Peruana
de Ciencias Aplicadas (UPC), 15023 Lima, Peru
| | - Roberto Alcántara
- Drug
Development and Innovation Group, Biomolecules Laboratory, Faculty
of Health Sciences, Universidad Peruana
de Ciencias Aplicadas (UPC), 15023 Lima, Peru
- Applied
Biophysics and Biochemistry Group, Biomolecules Laboratory, Faculty
of Health Sciences, Universidad Peruana
de Ciencias Aplicadas (UPC), 15023 Lima, Peru
| | - Gabriel Jiménez-Avalos
- Laboratorio
de Bioinformática, Biología Molecular y Desarrollos
Tecnológicos, Facultad de Ciencias y Filosofía, Departamento
de Ciencias Celulares y Moleculares, Universidad
Peruana Cayetano Heredia (UPCH), 15102 Lima, Peru
| | - Mirko Zimic
- Laboratorio
de Bioinformática, Biología Molecular y Desarrollos
Tecnológicos, Facultad de Ciencias y Filosofía, Departamento
de Ciencias Celulares y Moleculares, Universidad
Peruana Cayetano Heredia (UPCH), 15102 Lima, Peru
| | - Pohl Milón
- Applied
Biophysics and Biochemistry Group, Biomolecules Laboratory, Faculty
of Health Sciences, Universidad Peruana
de Ciencias Aplicadas (UPC), 15023 Lima, Peru
| | - Miguel Quiliano
- Drug
Development and Innovation Group, Biomolecules Laboratory, Faculty
of Health Sciences, Universidad Peruana
de Ciencias Aplicadas (UPC), 15023 Lima, Peru
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6
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Wang B, Wu H, Hu C, Wang H, Liu J, Wang W, Liu Q. An overview of kinase downregulators and recent advances in discovery approaches. Signal Transduct Target Ther 2021; 6:423. [PMID: 34924565 PMCID: PMC8685278 DOI: 10.1038/s41392-021-00826-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 10/28/2021] [Accepted: 11/05/2021] [Indexed: 12/17/2022] Open
Abstract
Since the clinical approval of imatinib, the discovery of protein kinase downregulators entered a prosperous age. However, challenges still exist in the discovery of kinase downregulator drugs, such as the high failure rate during development, side effects, and drug-resistance problems. With the progress made through multidisciplinary efforts, an increasing number of new approaches have been applied to solve the above problems during the discovery process of kinase downregulators. In terms of in vitro and in vivo drug evaluation, progress was also made in cellular and animal model platforms for better and more clinically relevant drug assessment. Here, we review the advances in drug design strategies, drug property evaluation technologies, and efficacy evaluation models and technologies. Finally, we discuss the challenges and perspectives in the development of kinase downregulator drugs.
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Affiliation(s)
- Beilei Wang
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
| | - Hong Wu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
| | - Chen Hu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
| | - Haizhen Wang
- Hefei PreceDo pharmaceuticals Co., Ltd, Hefei, Anhui, 230088, People's Republic of China
| | - Jing Liu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
| | - Wenchao Wang
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China
| | - Qingsong Liu
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China.
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, 230031, People's Republic of China.
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7
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Kwong AJ, Pham TND, Oelschlager HE, Munshi HG, Scheidt KA. Rational Design, Optimization, and Biological Evaluation of Novel MEK4 Inhibitors against Pancreatic Adenocarcinoma. ACS Med Chem Lett 2021; 12:1559-1567. [PMID: 34676038 DOI: 10.1021/acsmedchemlett.1c00376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Indexed: 01/05/2023] Open
Abstract
Growth, division, and development of healthy cells relies on efficient response to environmental survival cues. The conserved mitogen-activated protein kinase (MAPK) family of pathways interface extracellular stimuli to intracellular processes for this purpose. Within these pathways, the MEK family has been identified as a target of interest due to its clinical relevance. Particularly, MEK4 has drawn recent attention for its indications in pancreatic and prostate cancers. Here, we report two potent MEK4 inhibitors demonstrating significant reduction of phospho-JNK and antiproliferative properties against pancreatic cancer cell lines. Furthermore, molecular inhibition of MEK4 pathway activates the MEK1/2 pathway, with the combination of MEK1/2 and MEK4 inhibitors demonstrating synergistic effects against pancreatic cancer cells. Our inhibitors provided insight into the crosstalk between MAPK pathways and new tools for elucidating the roles of MEK4 in disease states, findings which will pave the way for better understanding of the MAPK pathways and development of additional probes.
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Affiliation(s)
- Ada J. Kwong
- Department of Chemistry, Department of Pharmacology, Feinberg School of Medicine, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Thao N. D. Pham
- Department of Medicine, Feinberg School of Medicine, Northwestern University, 303 E. Superior Street, Chicago, Illinois 60611, United States
| | - Hannah E. Oelschlager
- Department of Chemistry, Department of Pharmacology, Feinberg School of Medicine, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Hidayatullah G. Munshi
- Department of Medicine, Feinberg School of Medicine, Northwestern University, 303 E. Superior Street, Chicago, Illinois 60611, United States
| | - Karl A. Scheidt
- Department of Chemistry, Department of Pharmacology, Feinberg School of Medicine, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
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8
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Exploration of benzofuran-based compounds as potent and selective Plasmodium falciparum glycogen synthase kinase-3 (PfGSK-3) inhibitors. Bioorg Chem 2021; 112:104839. [PMID: 33813310 DOI: 10.1016/j.bioorg.2021.104839] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 02/12/2021] [Accepted: 03/17/2021] [Indexed: 12/30/2022]
Abstract
Plasmodium falciparum glycogen synthase kinase-3 (PfGSK-3) has been identified as a potential target for the development of novel drugs against multi-drug resistant malaria. A series of benzofuran-based compounds was synthesised and evaluated as inhibitors of recombinantly expressed and purified PfGSK-3 and human glycogen synthase kinase-3 beta (HsGSK-3β). Of this series, five compounds (5k, 5m, 5p, 5r, 5s) preferentially inhibited PfGSK-3, with four of these compounds exhibiting IC50 values in the sub-micromolar range (0.00048-0.440 µM). Evaluation of the structure-activity relationships required for PfGSK-3 selective inhibition indicated that a C6-OCH3 substitution on ring A is preferred, while the effect of the ring B substituent on activity, in decreasing order is: C4'-CN > C4'-F > C3'-OCH3 > C3',4'-diCl. To date, development of PfGSK-3 inhibitors has been limited to the 4-phenylthieno[2,3-b]pyridine class. Chalcone-based scaffolds, such as the benzofurans described herein, are promising new hits which can be explored for future design of PfGSK-3 selective inhibitors.
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9
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Suvarna K, Honda K, Muroi M, Kondoh Y, Osada H, Watanabe N. Measurement of ATPase Activity of Valosin-containing Protein/p97. Bio Protoc 2020; 10:e3516. [PMID: 33654741 DOI: 10.21769/bioprotoc.3516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/26/2019] [Accepted: 12/26/2019] [Indexed: 11/02/2022] Open
Abstract
Valosin-containing protein (VCP; also known as p97) is a type II ATPase regulating several cellular processes. Using proteomic techniques, we identified a chemical compound that binds to the D1 ATPase domain of VCP. The protocol described here was to study the effect of the compound on ATPase activity in vitro of purified VCP protein. ATPases are enzymes that hydrolyze ATP in a reaction resulting the release of an inorganic phosphate. This reaction can be measured using several methods, such as colorimetric, fluorescence, and radiometric assays, in addition to the bioluminescence assay mentioned here. Since the remaining ATP level after the reaction was detected using a luciferase assay, the luminescent signal indicates the ATPase activity inversely. This protocol is sensitive, rapid, and can be used for high-throughput screening assays to study the effect of compounds on ATPase function.
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Affiliation(s)
- Kruthi Suvarna
- Bio-Active Compounds Discovery Research Unit, RIKEN CSRS, Saitama, 351-0198, Japan.,Tokyo Medical Dental University, Yushima, Tokyo, 113-8510, Japan
| | - Kaori Honda
- Bio-Active Compounds Discovery Research Unit, RIKEN CSRS, Saitama, 351-0198, Japan.,Chemical Biology Research Group, RIKEN CSRS, Saitama, 351-0198, Japan
| | - Makoto Muroi
- Chemical Biology Research Group, RIKEN CSRS, Saitama, 351-0198, Japan
| | - Yasumitsu Kondoh
- Chemical Biology Research Group, RIKEN CSRS, Saitama, 351-0198, Japan
| | - Hiroyuki Osada
- Chemical Biology Research Group, RIKEN CSRS, Saitama, 351-0198, Japan.,RIKEN-Max Planck Joint Research Division, RIKEN CSRS, Saitama, 351-0198, Japan
| | - Nobumoto Watanabe
- Bio-Active Compounds Discovery Research Unit, RIKEN CSRS, Saitama, 351-0198, Japan.,Tokyo Medical Dental University, Yushima, Tokyo, 113-8510, Japan.,RIKEN-Max Planck Joint Research Division, RIKEN CSRS, Saitama, 351-0198, Japan
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10
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Royer L, Shangraw K, Herzog JJ, Pouvreau S, Marr MT, Paradis S. The Metastasis Suppressor Protein Nme1 Is a Concentration-Dependent Modulator of Ca 2+/Calmodulin-Dependent Protein Kinase II. Biochemistry 2019; 58:2710-2714. [PMID: 31141673 DOI: 10.1021/acs.biochem.9b00121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nucleoside diphosphate kinases (Nmes or NDPKs) have been implicated in a multitude of cellular processes, including an important role in metastasis suppression, and several enzymatic activities have been assigned to the Nme family. Nevertheless, for many of these processes, it has not been possible to establish a strong connection between Nme enzymatic activity and the relevant biological function. We hypothesized that, in addition to its known enzymatic functions, members of the Nme family might also regulate signaling cascades by acting on key signal transducers. Accordingly, here we show that Nme1 directly interacts with the calcium/calmodulin-dependent kinase II (CaMKII). Using purified proteins, we monitored the phosphorylation of a number of CaMKII substrates and determined that at nanomolar levels Nme1 enhances the phosphorylation of T-type substrates; this modulation shifts to inhibition at low micromolar concentrations. Specifically, the autophosphorylation of CaMKII at Thr286 is completely inhibited by 2 μM Nme1, a feature that distinguishes Nme1 from other known endogenous CaMKII inhibitors. Importantly, CaMKII inhibition does not require phosphotransfer activity by Nme1 because the kinase-dead Nme1 H118F mutant is as effective as the wild-type form of the enzyme. Our results provide a novel molecular mechanism whereby Nme1 could modulate diverse cellular processes in a manner that is independent of its known enzymatic activities.
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Affiliation(s)
- Leandro Royer
- Department of Biology , Brandeis University , Waltham , Massachusetts 02454 , United States
| | - Kathryn Shangraw
- Department of Biology , Brandeis University , Waltham , Massachusetts 02454 , United States
| | - Josiah J Herzog
- Department of Biology , Brandeis University , Waltham , Massachusetts 02454 , United States
| | - Sandrine Pouvreau
- Interdisciplinary Institute for Neuroscience , CNRS, UMR5297 , F-33000 Bordeaux , France.,University of Bordeaux , Interdisciplinary Institute for Neuroscience, UMR5297 , F-33000 Bordeaux , France
| | - Michael T Marr
- Department of Biology , Brandeis University , Waltham , Massachusetts 02454 , United States.,Rosenstiel Basic Medical Sciences Research Center , Brandeis University , Waltham , Massachusetts 02453 , United States
| | - Suzanne Paradis
- Department of Biology , Brandeis University , Waltham , Massachusetts 02454 , United States.,Volen Center for Complex Systems , Brandeis University , Waltham , Massachusetts 02454 , United States
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11
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Sinclair I, Davies G, Semple H. Acoustic mist ionization mass spectrometry (AMI-MS) as a drug discovery platform. Expert Opin Drug Discov 2019; 14:609-617. [DOI: 10.1080/17460441.2019.1613369] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Ian Sinclair
- Sample Management, Discovery Sciences, R&D BioPharmaceuticals, AstraZeneca, Macclesfield, UK
| | - Gareth Davies
- Hit Discovery, Discovery Sciences, R&D BioPharmaceuticals, AstraZeneca, Macclesfield, UK
| | - Hannah Semple
- Hit Discovery, Discovery Sciences, R&D BioPharmaceuticals, AstraZeneca, Macclesfield, UK
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12
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Coussens NP, Kales SC, Henderson MJ, Lee OW, Horiuchi KY, Wang Y, Chen Q, Kuznetsova E, Wu J, Chakka S, Cheff DM, Cheng KCC, Shinn P, Brimacombe KR, Shen M, Simeonov A, Lal-Nag M, Ma H, Jadhav A, Hall MD. High-throughput screening with nucleosome substrate identifies small-molecule inhibitors of the human histone lysine methyltransferase NSD2. J Biol Chem 2018; 293:13750-13765. [PMID: 29945974 DOI: 10.1074/jbc.ra118.004274] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Indexed: 12/15/2022] Open
Abstract
The histone lysine methyltransferase nuclear receptor-binding SET domain protein 2 (NSD2, also known as WHSC1/MMSET) is an epigenetic modifier and is thought to play a driving role in oncogenesis. Both NSD2 overexpression and point mutations that increase its catalytic activity are associated with several human cancers. Although NSD2 is an attractive therapeutic target, no potent, selective, and bioactive small molecule inhibitors of NSD2 have been reported to date, possibly due to the challenges of developing high-throughput assays for NSD2. Here, to establish a platform for the discovery and development of selective NSD2 inhibitors, we optimized and implemented multiple assays. We performed quantitative high-throughput screening with full-length WT NSD2 and a nucleosome substrate against a diverse collection of bioactive small molecules comprising 16,251 compounds. We further interrogated 174 inhibitory compounds identified in the primary screen with orthogonal and counter assays and with activity assays based on the clinically relevant NSD2 variants E1099K and T1150A. We selected five confirmed inhibitors for follow-up, which included a radiolabeled validation assay, surface plasmon resonance studies, methyltransferase profiling, and histone methylation in cells. We found that all five NSD2 inhibitors bind the catalytic SET domain and one exhibited apparent activity in cells, validating the workflow and providing a template for identifying selective NSD2 inhibitors. In summary, we have established a robust discovery pipeline for identifying potent NSD2 inhibitors from small-molecule libraries.
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Affiliation(s)
- Nathan P Coussens
- From the National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850 and
| | - Stephen C Kales
- From the National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850 and
| | - Mark J Henderson
- From the National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850 and
| | - Olivia W Lee
- From the National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850 and
| | | | - Yuren Wang
- the Reaction Biology Corporation, Malvern, Pennsylvania 19355
| | - Qing Chen
- the Reaction Biology Corporation, Malvern, Pennsylvania 19355
| | | | - Jianghong Wu
- the Reaction Biology Corporation, Malvern, Pennsylvania 19355
| | - Sirisha Chakka
- From the National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850 and
| | - Dorian M Cheff
- From the National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850 and
| | - Ken Chih-Chien Cheng
- From the National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850 and
| | - Paul Shinn
- From the National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850 and
| | - Kyle R Brimacombe
- From the National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850 and
| | - Min Shen
- From the National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850 and
| | - Anton Simeonov
- From the National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850 and
| | - Madhu Lal-Nag
- From the National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850 and
| | - Haiching Ma
- the Reaction Biology Corporation, Malvern, Pennsylvania 19355
| | - Ajit Jadhav
- From the National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850 and
| | - Matthew D Hall
- From the National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland 20850 and
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13
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Singh U, Chashoo G, Khan SU, Mahajan P, Nargotra A, Mahajan G, Singh A, Sharma A, Mintoo MJ, Guru SK, Aruri H, Thatikonda T, Sahu P, Chibber P, Kumar V, Mir SA, Bharate SS, Madishetti S, Nandi U, Singh G, Mondhe DM, Bhushan S, Malik F, Mignani S, Vishwakarma RA, Singh PP. Design of Novel 3-Pyrimidinylazaindole CDK2/9 Inhibitors with Potent In Vitro and In Vivo Antitumor Efficacy in a Triple-Negative Breast Cancer Model. J Med Chem 2017; 60:9470-9489. [DOI: 10.1021/acs.jmedchem.7b00663] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Umed Singh
- Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
| | - Gousia Chashoo
- Cancer Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
| | - Sameer U. Khan
- Cancer Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
| | - Priya Mahajan
- Discovery Informatics, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
| | - Amit Nargotra
- Discovery Informatics, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
| | - Girish Mahajan
- Cancer Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
| | - Amarinder Singh
- Pharmacokinetic & Pharmacodynamic Division, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
| | - Anjna Sharma
- Pharmacokinetic & Pharmacodynamic Division, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
| | - Mubashir J. Mintoo
- Cancer Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
| | - Santosh Kumar Guru
- Cancer Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
| | - Hariprasad Aruri
- Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
| | - Thanusha Thatikonda
- Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
| | - Promod Sahu
- Pharmacokinetic & Pharmacodynamic Division, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
| | - Pankaj Chibber
- Pharmacokinetic & Pharmacodynamic Division, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
| | - Vikas Kumar
- Preformulation Division, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
| | - Sameer A. Mir
- Cancer Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
| | - Sonali S. Bharate
- Preformulation Division, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
| | - Sreedhar Madishetti
- Pharmacokinetic & Pharmacodynamic Division, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
| | - Utpal Nandi
- Pharmacokinetic & Pharmacodynamic Division, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
| | - Gurdarshan Singh
- Pharmacokinetic & Pharmacodynamic Division, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
| | - Dilip Manikrao Mondhe
- Cancer Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
| | - Shashi Bhushan
- Cancer Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
- Indian Pharmacopoeia Commission, Sector-23, Raj Nagar, Ghaziabad-201002, India
| | - Fayaz Malik
- Cancer Pharmacology Division, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
| | - Serge Mignani
- Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
- PRES Sorbonne
Paris Cité, CNRS UMR 860, Laboratoire de Chimie et de Biochimie
Pharmacologiques et Toxicologique, Université Paris Descartes, 45,
rue des Saints Péres, 75006 Paris, France
| | - Ram A. Vishwakarma
- Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
| | - Parvinder Pal Singh
- Medicinal Chemistry Division, CSIR-Indian Institute of Integrative Medicine, Academy of Scientific and Innovative Research, Canal Road, Jammu, Jammu & Kashmir-180001, India
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14
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TRPA1-FGFR2 binding event is a regulatory oncogenic driver modulated by miRNA-142-3p. Nat Commun 2017; 8:947. [PMID: 29038531 PMCID: PMC5643494 DOI: 10.1038/s41467-017-00983-w] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 08/08/2017] [Indexed: 01/09/2023] Open
Abstract
Recent evidence suggests that the ion channel TRPA1 is implicated in lung adenocarcinoma (LUAD), where its role and mechanism of action remain unknown. We have previously established that the membrane receptor FGFR2 drives LUAD progression through aberrant protein–protein interactions mediated via its C-terminal proline-rich motif. Here we report that the N-terminal ankyrin repeats of TRPA1 directly bind to the C-terminal proline-rich motif of FGFR2 inducing the constitutive activation of the receptor, thereby prompting LUAD progression and metastasis. Furthermore, we show that upon metastasis to the brain, TRPA1 gets depleted, an effect triggered by the transfer of TRPA1-targeting exosomal microRNA (miRNA-142-3p) from brain astrocytes to cancer cells. This downregulation, in turn, inhibits TRPA1-mediated activation of FGFR2, hindering the metastatic process. Our study reveals a direct binding event and characterizes the role of TRPA1 ankyrin repeats in regulating FGFR2-driven oncogenic process; a mechanism that is hindered by miRNA-142-3p. TRPA1 has been reported to contribute lung cancer adenocarcinoma (LUAD), but the mechanisms are unclear. Here the authors propose that TRPA1/FGFR2 interaction is functional in LUAD and show that astrocytes oppose brain metastasis by mediating the downregulation of TRPA1 through exosome-delivered miRNA-142-3p.
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15
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Di Pisa F, Landi G, Dello Iacono L, Pozzi C, Borsari C, Ferrari S, Santucci M, Santarem N, Cordeiro-da-Silva A, Moraes CB, Alcantara LM, Fontana V, Freitas-Junior LH, Gul S, Kuzikov M, Behrens B, Pöhner I, Wade RC, Costi MP, Mangani S. Chroman-4-One Derivatives Targeting Pteridine Reductase 1 and Showing Anti-Parasitic Activity. Molecules 2017; 22:molecules22030426. [PMID: 28282886 PMCID: PMC6155272 DOI: 10.3390/molecules22030426] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/01/2017] [Accepted: 03/03/2017] [Indexed: 01/28/2023] Open
Abstract
Flavonoids have previously been identified as antiparasitic agents and pteridine reductase 1 (PTR1) inhibitors. Herein, we focus our attention on the chroman-4-one scaffold. Three chroman-4-one analogues (1–3) of previously published chromen-4-one derivatives were synthesized and biologically evaluated against parasitic enzymes (Trypanosoma brucei PTR1–TbPTR1 and Leishmania major–LmPTR1) and parasites (Trypanosoma brucei and Leishmania infantum). A crystal structure of TbPTR1 in complex with compound 1 and the first crystal structures of LmPTR1-flavanone complexes (compounds 1 and 3) were solved. The inhibitory activity of the chroman-4-one and chromen-4-one derivatives was explained by comparison of observed and predicted binding modes of the compounds. Compound 1 showed activity both against the targeted enzymes and the parasites with a selectivity index greater than 7 and a low toxicity. Our results provide a basis for further scaffold optimization and structure-based drug design aimed at the identification of potent anti-trypanosomatidic compounds targeting multiple PTR1 variants.
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Affiliation(s)
- Flavio Di Pisa
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy.
| | - Giacomo Landi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy.
| | - Lucia Dello Iacono
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy.
| | - Cecilia Pozzi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy.
| | - Chiara Borsari
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy.
| | - Stefania Ferrari
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy.
| | - Matteo Santucci
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy.
| | - Nuno Santarem
- Institute for Molecular and Cell Biology, 4150-180 Porto, Portugal and Instituto de Investigação e Inovação em Saúde, Universidade do Porto and Institute for Molecular and Cell Biology, 4150-180 Porto, Portugal.
| | - Anabela Cordeiro-da-Silva
- Institute for Molecular and Cell Biology, 4150-180 Porto, Portugal and Instituto de Investigação e Inovação em Saúde, Universidade do Porto and Institute for Molecular and Cell Biology, 4150-180 Porto, Portugal.
| | - Carolina B Moraes
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas SP13083-100, Brazil.
| | - Laura M Alcantara
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas SP13083-100, Brazil.
| | - Vanessa Fontana
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas SP13083-100, Brazil.
| | - Lucio H Freitas-Junior
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas SP13083-100, Brazil.
- GARDE, Instituto Butantan, São Paulo SP05503-900, Brazil.
| | - Sheraz Gul
- Fraunhofer Institute for Molecular Biology and Applied Ecology Screening Port, D-22525 Hamburg, Germany.
| | - Maria Kuzikov
- Fraunhofer Institute for Molecular Biology and Applied Ecology Screening Port, D-22525 Hamburg, Germany.
| | - Birte Behrens
- Fraunhofer Institute for Molecular Biology and Applied Ecology Screening Port, D-22525 Hamburg, Germany.
| | - Ina Pöhner
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany.
| | - Rebecca C Wade
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany.
- Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, 69120 Heidelberg, Germany.
- Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, 69120 Heidelberg, Germany.
| | - Maria Paola Costi
- Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, 41125 Modena, Italy.
| | - Stefano Mangani
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy.
- Magnetic Resonance Center CERM, University of Florence, 50019 Sesto Fiorentino (FI), Italy.
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16
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Identification of Novel Plasmodium falciparum Hexokinase Inhibitors with Antiparasitic Activity. Antimicrob Agents Chemother 2016; 60:6023-33. [PMID: 27458230 DOI: 10.1128/aac.00914-16] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 07/19/2016] [Indexed: 11/20/2022] Open
Abstract
Plasmodium falciparum, the deadliest species of malaria parasites, is dependent on glycolysis for the generation of ATP during the pathogenic red blood cell stage. Hexokinase (HK) catalyzes the first step in glycolysis, transferring the γ-phosphoryl group of ATP to glucose to yield glucose-6-phosphate. Here, we describe the validation of a high-throughput assay for screening small-molecule collections to identify inhibitors of the P. falciparum HK (PfHK). The assay, which employed an ADP-Glo reporter system in a 1,536-well-plate format, was robust with a signal-to-background ratio of 3.4 ± 1.2, a coefficient of variation of 6.8% ± 2.9%, and a Z'-factor of 0.75 ± 0.08. Using this assay, we screened 57,654 molecules from multiple small-molecule collections. Confirmed hits were resolved into four clusters on the basis of structural relatedness. Multiple singleton hits were also identified. The most potent inhibitors had 50% inhibitory concentrations as low as ∼1 μM, and several were found to have low-micromolar 50% effective concentrations against asexual intraerythrocytic-stage P. falciparum parasites. These molecules additionally demonstrated limited toxicity against a panel of mammalian cells. The identification of PfHK inhibitors with antiparasitic activity using this validated screening assay is encouraging, as it justifies additional HTS campaigns with more structurally amenable libraries for the identification of potential leads for future therapeutic development.
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17
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Davis MI, Auld DS, Inglese J. Bioluminescence Methods for Assaying Kinases in Quantitative High-Throughput Screening (qHTS) Format Applied to Yes1 Tyrosine Kinase, Glucokinase, and PI5P4Kα Lipid Kinase. Methods Mol Biol 2016; 1360:47-58. [PMID: 26501901 DOI: 10.1007/978-1-4939-3073-9_4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Assays in which the detection of a biological phenomenon is coupled to the production of bioluminescence by luciferase have gained widespread use. As firefly luciferases (FLuc) and kinases share a common substrate (ATP), coupling of a kinase to FLuc allows for the amount of ATP remaining following a kinase reaction to be assessed by quantitating the amount of luminescence produced. Alternatively, the amount of ADP produced by the kinase reaction can be coupled to FLuc through a two-step process. This chapter describes the bioluminescent assays that were developed for three classes of kinases (lipid, protein, and metabolic kinases) and miniaturized to 1536-well format, enabling their use for quantitative high-throughput (qHTS) of small-molecule libraries.
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Affiliation(s)
- Mindy I Davis
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Douglas S Auld
- Center for Proteomic Chemistry, Novartis Institutes for Biomedical Research, Cambridge, MA, USA
| | - James Inglese
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA.
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18
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Using Bioluminescent Kinase Profiling Strips to Identify Kinase Inhibitor Selectivity and Promiscuity. Methods Mol Biol 2016; 1360:59-73. [PMID: 26501902 DOI: 10.1007/978-1-4939-3073-9_5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The advancement of a kinase inhibitor throughout drug discovery and development is predicated upon its selectivity towards the target of interest. Thus, profiling the compound against a broad panel of kinases is important for providing a better understanding of its activity and for obviating any off-target activities that can result in undesirable consequences. To assess the selectivity and potency of an inhibitor against multiple kinases, it is desirable to use a universal assay that can monitor the activity of all classes of kinases regardless of the nature of their substrates. The luminescent ADP-Glo kinase assay is a universal platform that measures kinase activity by quantifying the amount of the common kinase reaction product ADP. Here we present a method using standardized kinase profiling systems for inhibitor profiling studies based on ADP detection by luminescence. The kinase profiling systems are sets of kinases organized by family, presented in multi-tube strips containing eight enzymes, each with corresponding substrate strips, and standardized for optimal kinase activity. We show that using the kinase profiling strips we could quickly and easily generate multiple selectivity profiles using small or large kinase panels, and identify compound promiscuity within the kinome.
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19
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Hsiao K, Zegzouti H, Goueli SA. Methyltransferase-Glo: a universal, bioluminescent and homogenous assay for monitoring all classes of methyltransferases. Epigenomics 2016; 8:321-39. [DOI: 10.2217/epi.15.113] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Aim: To develop a homogenous, nonradioactive, antibody-free and universal assay for diverse families of methyltransferases and monitor the activity of these enzymes in a high-throughput format. Materials & methods: The assay conditions are optimized for monitoring the enzymatic activity of a broad range of methyltransferases regardless of the chemical structure or nature of the enzyme substrate in a low- and high-throughput-formatted protocols. The assay detects S-adenosyl-l-homocysteine, the universal reaction products of all methyltransferases. Results: We demonstrate the utility of using this protocol to determine the activity of DNA, protein methyltransferases and also to determine kinetic parameters of several inhibitors using purified enzymes. The assay is sensitive (20–30 nM of S-adenosyl-l-homocysteine) and robust. Conclusion: The methyltransferase Glo is nonradioactive, antibody-free and homogenous, universal assay to determine enzyme activity of diverse families of methyltransferases. The assay is formatted to meet the requirements of high-throughput screening in drug discovery programs searching for modulators of methyltransferases.
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Affiliation(s)
- Kevin Hsiao
- Promega Corporation, R&D Department, 2800 Woods Hollow Road, Madison, WI 53711, USA
| | - Hicham Zegzouti
- Promega Corporation, R&D Department, 2800 Woods Hollow Road, Madison, WI 53711, USA
| | - Said A Goueli
- Promega Corporation, R&D Department, 2800 Woods Hollow Road, Madison, WI 53711, USA
- Department of Pathology & Laboratory Medicine, University of Wisconsin School of Medicine & Public Health, Madison, WI 53726, USA
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20
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Davis MI, Sasaki AT, Simeonov A. Method for Assaying the Lipid Kinase Phosphatidylinositol-5-phosphate 4-kinase α in Quantitative High-Throughput Screening (qHTS) Bioluminescent Format. Methods Mol Biol 2016; 1376:1-9. [PMID: 26552670 PMCID: PMC4696767 DOI: 10.1007/978-1-4939-3170-5_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Lipid kinases are important regulators of a variety of cellular processes and their dysregulation causes diseases such as cancer and metabolic diseases. Distinct lipid kinases regulate the seven different phosphorylated forms of phosphatidylinositol (PtdIns). Some lipid kinases utilize long-chain lipid substrates that have limited solubility in aqueous solutions, which can lead to difficulties in developing a robust and miniaturizable biochemical assay. The ability to prepare the lipid substrate and develop assays to identify modulators of lipid kinases is important and is the focus of this methods chapter. Herein, we describe a method to prepare a DMSO-based lipid mixture that enables the 1536-well screening of the lipid kinase phosphatidylinositol-5-phosphate 4-kinase α (PI5P4Kα) utilizing the D-myo-di16-PtIns(5)P substrate in quantitative high-throughput screening (qHTS) format using the ADP-Glo™ technology to couple the production of ADP to a bioluminescent readout.
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Affiliation(s)
- Mindy I Davis
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Atsuo T Sasaki
- Department of Internal Medicine, Division of Hematology Oncology, UC Cancer Institute, College of Medicine, University of Cincinnati, Cincinnati, OH, 45267, USA
- Department of Neurosurgery, Brain Tumor Center, UC Neuroscience Institute, College of Medicine, University of Cincinnati, Cincinnati, OH, 45267, USA
| | - Anton Simeonov
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA.
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21
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Hennek J, Alves J, Yao E, Goueli SA, Zegzouti H. Bioluminescent kinase strips: A novel approach to targeted and flexible kinase inhibitor profiling. Anal Biochem 2015; 495:9-20. [PMID: 26628096 DOI: 10.1016/j.ab.2015.11.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 11/11/2015] [Accepted: 11/16/2015] [Indexed: 11/19/2022]
Abstract
In addition to target efficacy, drug safety is a major requirement during the drug discovery process and is influenced by target specificity. Therefore, it is imperative that every new drug candidate be profiled against various liability panels that include protein kinases. Here, an effective methodology to streamline kinase inhibitor profiling is described. An accessible standardized profiling system for 112 protein kinases covering all branches of the kinome was developed. This approach consists of creating different sets of kinases and their corresponding substrates in multi-tube strips. The kinase stocks are pre-standardized for optimal kinase activity and used for inhibitor profiling using a bioluminescent ADP detection assay. We show that these strips can routinely generate inhibitor selectivity profiles for small or broad kinase family panels. Lipid kinases were also assembled in strip format and profiled together with protein kinases. We identified two specific PI3K inhibitors that have off-target effects on CK2 that were not reported before and would have been missed if compounds were not profiled against lipid and protein kinases simultaneously. To validate the accuracy of the data generated by this method, we confirmed that the inhibition potencies observed are consistent with published values produced by more complex technologies such as radioactivity assays.
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Affiliation(s)
- J Hennek
- R&D Department, Promega Corporation, Madison, WI 53711, USA
| | - J Alves
- R&D Department, Promega Corporation, Madison, WI 53711, USA
| | - E Yao
- SignalChem Pharmaceuticals, Richmond, British Columbia V6V 2J2, Canada
| | - S A Goueli
- R&D Department, Promega Corporation, Madison, WI 53711, USA; Department of Pathology and Laboratory Medicine, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - H Zegzouti
- R&D Department, Promega Corporation, Madison, WI 53711, USA.
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22
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Considerations for the design and reporting of enzyme assays in high-throughput screening applications. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.pisc.2013.12.001] [Citation(s) in RCA: 141] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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23
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Gode D, Schmitt C, Engel M, Volmer DA. Screening Dyrk1A inhibitors by MALDI-QqQ mass spectrometry: systematic comparison to established radiometric, luminescence, and LC-UV-MS assays. Anal Bioanal Chem 2014; 406:2841-52. [PMID: 24618988 DOI: 10.1007/s00216-014-7703-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Revised: 02/12/2014] [Accepted: 02/17/2014] [Indexed: 11/26/2022]
Abstract
Enzyme-catalyzed reactions play key roles in disease pathology, thus making them relevant subjects of therapeutic inhibitor screening experiments. Matrix-assisted laser desorption/ionization (MALDI) assays have been demonstrated to be able to replace established screening approaches. They offer increased sample throughput, but care must be taken to avoid instrumental bias from differences in ionization efficiencies. We compared a MALDI-triple-quadrupole (QqQ) method for the Dyrk1A peptide substrate woodtide to LC-MS, liquid chromatography with ultraviolet detection (LC-UV), luminescence, and radiometric assays. MALDI measurements were performed on a MALDI-QqQ instrument in the multiple-reaction monitoring mode. Different MALDI conditions were investigated to address whether matrix type, sample support, and MRM- or SIM-based detection conditions can be used to accommodate the molar responses of substrate peptide and its phosphorylated form. UV detection served as a reference method. The impact of MALDI matrix on IC50 values was small, even considering that matrix preparations were used that are known to alleviate response differences. IC50 values determined by MALDI were ca. 2-fold lower than those determined by LC-UV. Although MALDI generated lower ion yields for the phosphorylated peptide than for the peptide substrate, we found that a correction of compound potencies was readily possible using correction factors based on unbiased LC-UV results. A thorough method development delivered a robust assay with excellent performance (Z' > 0.91) that was close to that seen for LC-UV.
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Affiliation(s)
- David Gode
- Institute of Bioanalytical Chemistry, Saarland University, 66123, Saarbrücken, Germany
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24
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Coombs TC, Tanega C, Shen M, Wang JL, Auld DS, Gerritz SW, Schoenen FJ, Thomas CJ, Aubé J. Small-molecule pyrimidine inhibitors of the cdc2-like (Clk) and dual specificity tyrosine phosphorylation-regulated (Dyrk) kinases: development of chemical probe ML315. Bioorg Med Chem Lett 2013; 23:3654-61. [PMID: 23642479 PMCID: PMC3664191 DOI: 10.1016/j.bmcl.2013.02.096] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 02/21/2013] [Indexed: 01/17/2023]
Abstract
Substituted pyrimidine inhibitors of the Clk and Dyrk kinases have been developed, exploring structure-activity relationships around four different chemotypes. The most potent compounds have low-nanomolar inhibitory activity against Clk1, Clk2, Clk4, Dyrk1A and Dyrk1B. Kinome scans with 442 kinases using agents representing three of the chemotypes show these inhibitors to be highly selective for the Clk and Dyrk families. Further off-target pharmacological evaluation with ML315, the most selective agent, supports this conclusion.
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Affiliation(s)
- Thomas C Coombs
- University of Kansas Specialized Chemistry Center, University of Kansas, Lawrence, KS 66047, USA
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25
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Davis MI, Sasaki AT, Shen M, Emerling BM, Thorne N, Michael S, Pragani R, Boxer M, Sumita K, Takeuchi K, Auld DS, Li Z, Cantley LC, Simeonov A. A homogeneous, high-throughput assay for phosphatidylinositol 5-phosphate 4-kinase with a novel, rapid substrate preparation. PLoS One 2013; 8:e54127. [PMID: 23326584 PMCID: PMC3542272 DOI: 10.1371/journal.pone.0054127] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 12/05/2012] [Indexed: 12/20/2022] Open
Abstract
Phosphoinositide kinases regulate diverse cellular functions and are important targets for therapeutic development for diseases, such as diabetes and cancer. Preparation of the lipid substrate is crucial for the development of a robust and miniaturizable lipid kinase assay. Enzymatic assays for phosphoinositide kinases often use lipid substrates prepared from lyophilized lipid preparations by sonication, which result in variability in the liposome size from preparation to preparation. Herein, we report a homogeneous 1536-well luciferase-coupled bioluminescence assay for PI5P4Kα. The substrate preparation is novel and allows the rapid production of a DMSO-containing substrate solution without the need for lengthy liposome preparation protocols, thus enabling the scale-up of this traditionally difficult type of assay. The Z’-factor value was greater than 0.7 for the PI5P4Kα assay, indicating its suitability for high-throughput screening applications. Tyrphostin AG-82 had been identified as an inhibitor of PI5P4Kα by assessing the degree of phospho transfer of γ-32P-ATP to PI5P; its inhibitory activity against PI5P4Kα was confirmed in the present miniaturized assay. From a pilot screen of a library of bioactive compounds, another tyrphostin, I-OMe tyrphostin AG-538 (I-OMe-AG-538), was identified as an ATP-competitive inhibitor of PI5P4Kα with an IC50 of 1 µM, affirming the suitability of the assay for inhibitor discovery campaigns. This homogeneous assay may apply to other lipid kinases and should help in the identification of leads for this class of enzymes by enabling high-throughput screening efforts.
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Affiliation(s)
- Mindy I. Davis
- National Institutes of Health Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Atsuo T. Sasaki
- Beth Israel Deaconess Medical Center, Department of Medicine, Division of Signal Transduction; Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
- Division of Hematology and Oncology, Department of Internal Medicine, Neuroscience Institute: Brain Tumor Center, University of Cincinnati, College of Medicine, Cincinnati, Ohio, United States of America
| | - Min Shen
- National Institutes of Health Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Brooke M. Emerling
- Beth Israel Deaconess Medical Center, Department of Medicine, Division of Signal Transduction; Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Natasha Thorne
- National Institutes of Health Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Sam Michael
- National Institutes of Health Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Rajan Pragani
- National Institutes of Health Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Matthew Boxer
- National Institutes of Health Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Kazutaka Sumita
- Division of Hematology and Oncology, Department of Internal Medicine, Neuroscience Institute: Brain Tumor Center, University of Cincinnati, College of Medicine, Cincinnati, Ohio, United States of America
| | - Koh Takeuchi
- Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, Koto, Tokyo, Japan
| | - Douglas S. Auld
- National Institutes of Health Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
- Center for Proteomic Chemistry, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, United States of America
| | - Zhuyin Li
- National Institutes of Health Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
| | - Lewis C. Cantley
- Beth Israel Deaconess Medical Center, Department of Medicine, Division of Signal Transduction; Department of Systems Biology, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Anton Simeonov
- National Institutes of Health Chemical Genomics Center, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, United States of America
- * E-mail:
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26
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Abstract
Experimental approaches to detect, measure, and quantify protein-ligand binding, along with their theoretical bases, are described. A range of methods for detection of protein-ligand interactions is summarized. Specific protocols are provided for a nonequilibrium procedure pull-down assay, for an equilibrium direct binding method and its modification into a competition-based measurement and for steady-state measurements based on the effects of ligands on enzyme catalysis.
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Affiliation(s)
- Peter N Lowe
- Biomolecular Interactions Consultancy, Hertford, UK
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27
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Antczak C, Mahida JP, Bhinder B, Calder PA, Djaballah H. A high-content biosensor-based screen identifies cell-permeable activators and inhibitors of EGFR function: implications in drug discovery. ACTA ACUST UNITED AC 2012; 17:885-99. [PMID: 22573732 DOI: 10.1177/1087057112446174] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Early success of kinase inhibitors has validated their use as drugs. However, discovery efforts have also suffered from high attrition rates due to lack of cellular activity. We reasoned that screening for such candidates in live cells would identify novel cell-permeable modulators for development. For this purpose, we have used our recently optimized epidermal growth factor receptor (EGFR) biosensor assay to screen for modulators of EGFR activity. Here, we report on its validation under high-throughput screening (HTS) conditions displaying a signal-to-noise ratio of 21 and a Z' value of 0.56-attributes of a robust cell-based assay. We performed a pilot screen against a library of 6912 compounds demonstrating good reproducibility and identifying 82 inhibitors and 66 activators with initial hit rates of 1.2% and 0.95%, respectively. Follow-up dose-response studies revealed that 12 of the 13 known EGFR inhibitors in the library were confirmed as hits. ZM-306416, a vascular endothelial growth factor receptor (VEGFR) antagonist, was identified as a potent inhibitor of EGFR function. Flurandrenolide, beclomethasone, and ebastine were confirmed as activators of EGFR function. Taken together, our results validate this novel approach and demonstrate its utility in the discovery of novel kinase modulators with potential use in the clinic.
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28
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Takagi T, Shum D, Parisi M, Santos RE, Radu C, Calder P, Rizvi Z, Frattini MG, Djaballah H. Comparison of luminescence ADP production assay and radiometric scintillation proximity assay for Cdc7 kinase. Comb Chem High Throughput Screen 2012; 14:669-87. [PMID: 21564015 DOI: 10.2174/138620711796504442] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2010] [Revised: 03/19/2011] [Accepted: 04/26/2011] [Indexed: 12/20/2022]
Abstract
Several assay technologies have been successfully adapted and used in HTS to screen for protein kinase inhibitors; however, emerging comparative analysis studies report very low hit overlap between the different technologies, which challenges the working assumption that hit identification is not dependent on the assay method of choice. To help address this issue, we performed two screens on the cancer target, Cdc7-Dbf4 heterodimeric protein kinase, using a direct assay detection method measuring [(33)P]-phosphate incorporation into the substrate and an indirect method measuring residual ADP production using luminescence. We conducted the two screens under similar conditions, where in one, we measured [(33)P]-phosphate incorporation using scintillation proximity assay (SPA), and in the other, we detected luminescence signal of the ATP-dependent luciferase after regenerating ATP from residual ADP (LUM). Surprisingly, little or no correlation were observed between the positives identified by the two methods; at a threshold of 30% inhibition, 25 positives were identified in the LUM screen whereas the SPA screen only identified two positives, Tannic acid and Gentian violet, with Tannic acid being common to both. We tested 20 out of the 25 positive compounds in secondary confirmatory study and confirmed 12 compounds including Tannic acid as Cdc7-Dbf4 kinase inhibitors. Gentian violet, which was only positive in the SPA screen, inhibited luminescence detection and categorized as a false positive. This report demonstrates the strong impact in detection format on the success of a screening campaign and the importance of carefully designed confirmatory assays to eliminate those compounds that target the detection part of the assay.
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Affiliation(s)
- Toshimitsu Takagi
- HTS Core Facility, Molecular Pharmacology and Chemistry Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
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29
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Mezna M, Wong AC, Ainger M, Scott RW, Hammonds T, Olson MF. Development of a high-throughput screening method for LIM kinase 1 using a luciferase-based assay of ATP consumption. ACTA ACUST UNITED AC 2011; 17:460-8. [PMID: 22156225 DOI: 10.1177/1087057111430529] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Kinases are attractive drug targets because of the central roles they play in signal transduction pathways and human diseases. Their well-formed adenosine triphosphate (ATP)-binding pockets make ideal targets for small-molecule inhibitors. For drug discovery purposes, many peptide-based kinase assays have been developed that measure substrate phosphorylation using fluorescence-based readouts. However, for some kinases these assays may not be appropriate. In the case of the LIM kinases (LIMK), an inability to phosphorylate peptide substrates resulted in previous high-throughput screens (HTS) using radioactive labeling of recombinant cofilin protein as the readout. We describe the development of an HTS-compatible assay that measures relative ATP levels using luciferase-generated luminescence as a function of LIMK activity. The assay was inexpensive to perform, and proof-of-principle screening of kinase inhibitors demonstrated that compound potency against LIMK could be determined; ultimately, the assay was used for successful prosecution of automated HTS. Following HTS, the secondary assay format was changed to obtain more accurate measures of potency and mechanism of action using more complex (and expensive) assays. The luciferase assay nonetheless provides an inexpensive and reliable primary assay for HTS that allowed for the identification of LIMK inhibitors to initiate discovery programs for the eventual treatment of human diseases.
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Affiliation(s)
- Mokdad Mezna
- The Beatson Institute for Cancer Research, Glasgow Scotland, UK
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30
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Shapiro AB, Hajec L, Gao N. High-throughput, homogeneous, fluorescence intensity-based measurement of adenosine diphosphate and other ribonucleoside diphosphates with nanomolar sensitivity. Anal Biochem 2011; 415:190-6. [PMID: 21570943 DOI: 10.1016/j.ab.2011.04.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2011] [Revised: 04/15/2011] [Accepted: 04/18/2011] [Indexed: 10/18/2022]
Abstract
A new, homogeneous, high-throughput-compatible assay method is described for the fluorescence-based quantitation of nanomolar concentrations of ribonucleoside diphosphates (rNDPs). The principle of the method is the conversion of the rNDPs to RNA by the enzyme polynucleotide phosphorylase (EC 2.7.7.8) and detection of the RNA by the increased fluorescence of a commercial nucleic acid detection dye. A commercial RNA homopolymer complementary to the RNA product is included to increase the sensitivity for ADP and UDP. Standard curves for nanomolar concentrations of ADP, UDP, GDP, and CDP are shown. The assay detected 75 nM ADP produced by the pyruvate kinase-catalyzed phosphorylation of pyruvate with a signal-to-baseline ratio of 2.8. The assay may be used in either a continuous or a discontinuous mode.
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Affiliation(s)
- Adam B Shapiro
- Bioscience Department, Infection Innovative Medicines, AstraZeneca R&D Boston, Waltham, MA 02451, USA.
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31
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Illuminating insights into firefly luciferase and other bioluminescent reporters used in chemical biology. ACTA ACUST UNITED AC 2010; 17:646-57. [PMID: 20609414 DOI: 10.1016/j.chembiol.2010.05.012] [Citation(s) in RCA: 219] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Revised: 05/26/2010] [Accepted: 05/27/2010] [Indexed: 11/23/2022]
Abstract
Understanding luciferase enzymology and the structure of compounds that modulate luciferase activity can be used to improve the design of luminescence-based assays. This review provides an overview of these popular reporters with an emphasis on the commonly used firefly luciferase from Photinus pyralis (FLuc). Large-scale chemical profile studies have identified a variety of scaffolds that inhibit FLuc. In some cell-based assays, these inhibitors can act in a counterintuitive way, leading to a gain in luminescent signal. Although formerly attributed to transcriptional activation, intracellular stabilization of FLuc is the primary mechanism underlying this observation. FLuc inhibition and stabilization can be complex, as illustrated by the compound PTC124, which is converted by FLuc in the presence of ATP to a high affinity multisubstrate adduct inhibitor, PTC124-AMP. The potential influence these findings can have on drug discovery efforts is provided here.
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32
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Shukla SJ, Huang R, Austin CP, Xia M. The future of toxicity testing: a focus on in vitro methods using a quantitative high-throughput screening platform. Drug Discov Today 2010; 15:997-1007. [PMID: 20708096 DOI: 10.1016/j.drudis.2010.07.007] [Citation(s) in RCA: 172] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2010] [Revised: 06/08/2010] [Accepted: 07/30/2010] [Indexed: 01/16/2023]
Abstract
The US Tox21 collaborative program represents a paradigm shift in toxicity testing of chemical compounds from traditional in vivo tests to less expensive and higher throughput in vitro methods to prioritize compounds for further study, identify mechanisms of action and ultimately develop predictive models for adverse health effects in humans. The NIH Chemical Genomics Center (NCGC) is an integral component of the Tox21 collaboration owing to its quantitative high-throughput screening (qHTS) paradigm, in which titration-based screening is used to profile hundreds of thousands of compounds per week. Here, we describe the Tox21 collaboration, qHTS-based compound testing and the various Tox21 screening assays that have been validated and tested at the NCGC to date.
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Affiliation(s)
- Sunita J Shukla
- NIH Chemical Genomics Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892-3370, USA
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Zegzouti H, Zdanovskaia M, Hsiao K, Goueli SA. ADP-Glo: A Bioluminescent and homogeneous ADP monitoring assay for kinases. Assay Drug Dev Technol 2010; 7:560-72. [PMID: 20105026 DOI: 10.1089/adt.2009.0222] [Citation(s) in RCA: 188] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
ADP-Glo is a novel bioluminescent, homogeneous assay for monitoring ADP producing biochemical reactions and thus it is an ideal assay for detecting enzyme activity using a wide variety of substrates. It is a universal assay that can be used with protein kinases, lipid kinases, sugar kinases, and many more kinases as well as ATPases. Because of its high sensitivity, it is suitable for monitoring enzyme activities at very early substrate conversions requiring very low amount of enzymes. Furthermore, as the assay is applicable to a broad range of ATP and substrate concentrations, it is optimal for enzymes that require high ATP and substrate concentrations. This is critical since inhibitor potency has to be demonstrated at the cellular level where ATP is present at millimolar concentrations. ADP-Glo is performed in 2 steps upon completion of kinase reaction: a combined termination of kinase reaction and depletion of remaining ATP in the first step, and conversion of generated ADP to ATP and the newly produced ATP to light output using luciferase/luciferin reaction in the second step. The luminescent signal generated is proportional to the ADP concentration produced and is correlated with the kinase activity. Due to its high signal to background and luminescent readout, this assay is less susceptible to generation of false hits and thus it is applicable to not only primary and secondary screening but also kinase profiling.
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