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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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Postiglione AE, Adams LL, Ekhator ES, Odelade AE, Patwardhan S, Chaudhari M, Pardue AS, Kumari A, LeFever WA, Tornow OP, Kaoud TS, Neiswinger J, Jeong JS, Parsonage D, Nelson KJ, Kc DB, Furdui CM, Zhu H, Wommack AJ, Dalby KN, Dong M, Poole LB, Keyes JD, Newman RH. Hydrogen peroxide-dependent oxidation of ERK2 within its D-recruitment site alters its substrate selection. iScience 2023; 26:107817. [PMID: 37744034 PMCID: PMC10514464 DOI: 10.1016/j.isci.2023.107817] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 07/11/2023] [Accepted: 08/30/2023] [Indexed: 09/26/2023] Open
Abstract
Extracellular signal-regulated kinases 1 and 2 (ERK1/2) are dysregulated in many pervasive diseases. Recently, we discovered that ERK1/2 is oxidized by signal-generated hydrogen peroxide in various cell types. Since the putative sites of oxidation lie within or near ERK1/2's ligand-binding surfaces, we investigated how oxidation of ERK2 regulates interactions with the model substrates Sub-D and Sub-F. These studies revealed that ERK2 undergoes sulfenylation at C159 on its D-recruitment site surface and that this modification modulates ERK2 activity differentially between substrates. Integrated biochemical, computational, and mutational analyses suggest a plausible mechanism for peroxide-dependent changes in ERK2-substrate interactions. Interestingly, oxidation decreased ERK2's affinity for some D-site ligands while increasing its affinity for others. Finally, oxidation by signal-generated peroxide enhanced ERK1/2's ability to phosphorylate ribosomal S6 kinase A1 (RSK1) in HeLa cells. Together, these studies lay the foundation for examining crosstalk between redox- and phosphorylation-dependent signaling at the level of kinase-substrate selection.
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Affiliation(s)
- Anthony E. Postiglione
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, USA
- Department of Biology, Wake Forest University, Winston-Salem, NC 27101, USA
| | - Laquaundra L. Adams
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, USA
| | - Ese S. Ekhator
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, USA
| | - Anuoluwapo E. Odelade
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, USA
| | - Supriya Patwardhan
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, USA
| | - Meenal Chaudhari
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, USA
- Department of Computational Data Science and Engineering, North Carolina A&T State University, Greensboro, NC 27411, USA
- Department of Mathematics and Computer Science, University of Virginia at Wise, Wise, VA 24293, USA
| | - Avery S. Pardue
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, USA
| | - Anjali Kumari
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, USA
| | - William A. LeFever
- Department of Chemistry, High Point University, High Point, NC 27268, USA
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Olivia P. Tornow
- Department of Chemistry, High Point University, High Point, NC 27268, USA
| | - Tamer S. Kaoud
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
| | - Johnathan Neiswinger
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
- Department of Biology, Belhaven University, Jackson, MS 39202, USA
| | - Jun Seop Jeong
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, USA
| | - Derek Parsonage
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Kimberly J. Nelson
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Dukka B. Kc
- Department of Computer Science, Michigan Technological University, Houghton, MI 49931, USA
| | - Cristina M. Furdui
- Department of Internal Medicine, Section on Molecular Medicine, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Heng Zhu
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Andrew J. Wommack
- Department of Chemistry, High Point University, High Point, NC 27268, USA
| | - Kevin N. Dalby
- Division of Chemical Biology and Medicinal Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
| | - Ming Dong
- Department of Chemistry, North Carolina A&T State University, Greensboro, NC 27411, USA
- Department of Chemistry and Biochemistry, University of North Carolina Wilmington, Wilmington, NC 28403, USA
| | - Leslie B. Poole
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
| | - Jeremiah D. Keyes
- Department of Biochemistry, Wake Forest University School of Medicine, Winston-Salem, NC 27157, USA
- Department of Biology, Penn State University Behrend, Erie, PA 16563, USA
- Magee-Womens Research Institute, Pittsburgh, PA 15213, USA
| | - Robert H. Newman
- Department of Biology, North Carolina A&T State University, Greensboro, NC 27411, USA
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Shafei MA, Forshaw T, Davis J, Flemban A, Qualtrough D, Dean S, Perks C, Dong M, Newman R, Conway ME. BCATc modulates crosstalk between the PI3K/Akt and the Ras/ERK pathway regulating proliferation in triple negative breast cancer. Oncotarget 2020; 11:1971-1987. [PMID: 32523652 PMCID: PMC7260123 DOI: 10.18632/oncotarget.27607] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 04/14/2020] [Indexed: 12/12/2022] Open
Abstract
The cytosolic branched chain aminotransferase (BCATc) protein has been found to be highly expressed in breast cancer subtypes, including triple negative breast cancer (TNBC), compared with normal breast tissue. The catabolism of branched-chain amino acids (BCAAs) by BCATc leads to the production of glutamate and key metabolites which further drive the TCA cycle, important for cellular metabolism and growth. Upregulation of BCATc has been associated with increased cell proliferation, cell cycle progression and metastasis in several malignancies including breast, gliomas, ovarian and colorectal cancer but the underlying mechanisms are unclear. As nutrient levels of BCAAs, substrates of BCATc, regulate the PI3K/Akt pathway we hypothesized that increased expression of BCATc would contribute to tumour cell growth through upregulation of the insulin/IGF-1 signalling pathway. This pathway is known to potentiate proliferation and metastasis of malignant cells through the activation of PI3K/Akt and the RAS/ERK signalling cascades. Here we show that knockdown of BCATc significantly reduced insulin and IGF-1-mediated proliferation, migration and invasion of TNBC cells. An analysis of this pathway showed that when overexpressed BCATc regulates proliferation through the PI3K/Akt axis, whilst simultaneously attenuating the Ras/Erk pathway indicating that BCATc acts as a conduit between these two pathways. This ultimately led to an increase in FOXO3a, a key regulator of cell proliferation and Nrf2, which mediates redox homeostasis. Together this data indicates that BCATc regulates TNBC cell proliferation, migration and invasion through the IGF-1/insulin PI3K/Akt pathway, culminating in the upregulation of FOXO3a and Nrf2, pointing to a novel therapeutic target for breast cancer treatment.
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Affiliation(s)
- Mai Ahmed Shafei
- Faculty of Health and Applied Sciences, University of the West of England, Coldharbor Lane, Bristol, UK
| | - Thomas Forshaw
- Faculty of Health and Applied Sciences, University of the West of England, Coldharbor Lane, Bristol, UK
| | - Jasmine Davis
- Faculty of Health and Applied Sciences, University of the West of England, Coldharbor Lane, Bristol, UK
| | - Arwa Flemban
- Faculty of Health and Applied Sciences, University of the West of England, Coldharbor Lane, Bristol, UK
| | - David Qualtrough
- Faculty of Health and Applied Sciences, University of the West of England, Coldharbor Lane, Bristol, UK
| | - Sarah Dean
- Faculty of Health and Applied Sciences, University of the West of England, Coldharbor Lane, Bristol, UK
| | - Claire Perks
- IGFs and Metabolic Endocrinology Group, University of Bristol, Bristol Medical School, Bristol, UK
| | - Ming Dong
- Department of Chemistry, North Carolina Agricultural and Technical State University, Greensboro, NC, USA
| | - Robert Newman
- Department of Biology, North Carolina Agricultural and Technical State University, Greensboro, NC, USA
| | - Myra Elizabeth Conway
- Faculty of Health and Applied Sciences, University of the West of England, Coldharbor Lane, Bristol, UK
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Li C, Zhang X, Zhang N, Zhou Y, Sun G, Zhao L, Zhong R. Identification and Biological Evaluation of CK2 Allosteric Fragments through Structure-Based Virtual Screening. Molecules 2020; 25:molecules25010237. [PMID: 31935979 PMCID: PMC6983002 DOI: 10.3390/molecules25010237] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/30/2019] [Accepted: 01/01/2020] [Indexed: 12/19/2022] Open
Abstract
Casein kinase II (CK2) is considered as an attractive cancer therapeutic target, and recent efforts have been made to develop its ATP-competitive inhibitors. However, achieving selectivity with respect to related kinases remains challenging due to the highly conserved ATP-binding pocket of kinases. Allosteric inhibitors, by targeting the much more diversified allosteric site relative to the highly conserved ATP-binding pocket, might be a promising strategy with the enhanced selectivity and reduced toxicity than ATP-competitive inhibitors. The previous studies have highlighted the traditional serendipitousity of discovering allosteric inhibitors owing to the complicate allosteric modulation. In this current study, we identified the novel allosteric inhibitors of CK2α by combing structure-based virtual screening and biological evaluation methods. The structure-based pharmacophore model was built based on the crystal structure of CK2α-compound 15 complex. The ChemBridge fragment library was searched by evaluating the fit values of these molecules with the optimized pharmacophore model, as well as the binding affinity of the CK2α-ligand complexes predicted by Alloscore web server. Six hits forming the holistic interaction mechanism with the αD pocket were retained after pharmacophore- and Alloscore-based screening for biological test. Compound 3 was found to be the most potent non-ATP competitive CK2α inhibitor (IC50 = 13.0 μM) with the anti-proliferative activity on A549 cancer cells (IC50 = 23.1 μM). Our results provide new clues for further development of CK2 allosteric inhibitors as anti-cancer hits.
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Affiliation(s)
- Chunqiong Li
- Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China; (C.L.); (X.Z.); (G.S.); (L.Z.); (R.Z.)
| | - Xuewen Zhang
- Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China; (C.L.); (X.Z.); (G.S.); (L.Z.); (R.Z.)
| | - Na Zhang
- Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China; (C.L.); (X.Z.); (G.S.); (L.Z.); (R.Z.)
- Correspondence: ; Tel.: +86-10-67392001
| | - Yue Zhou
- State Key Laboratory of Bioactive Substances and Functions of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China;
| | - Guohui Sun
- Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China; (C.L.); (X.Z.); (G.S.); (L.Z.); (R.Z.)
| | - Lijiao Zhao
- Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China; (C.L.); (X.Z.); (G.S.); (L.Z.); (R.Z.)
| | - Rugang Zhong
- Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, China; (C.L.); (X.Z.); (G.S.); (L.Z.); (R.Z.)
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Guo X, Yang D, Fan Z, Zhang N, Zhao B, Huang C, Wang F, Ma R, Meng M, Deng Y. Discovery and structure-activity relationship of novel diphenylthiazole derivatives as BTK inhibitor with potent activity against B cell lymphoma cell lines. Eur J Med Chem 2019; 178:767-781. [DOI: 10.1016/j.ejmech.2019.06.035] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Revised: 06/09/2019] [Accepted: 06/10/2019] [Indexed: 10/26/2022]
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Imamura RM, Kumagai K, Nakano H, Okabe T, Nagano T, Kojima H. Inexpensive High-Throughput Screening of Kinase Inhibitors Using One-Step Enzyme-Coupled Fluorescence Assay for ADP Detection. SLAS DISCOVERY 2018; 24:284-294. [PMID: 30418800 DOI: 10.1177/2472555218810139] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Protein kinases are attractive targets for both biological research and drug development. Several assay kits, especially for the detection of adenosine diphosphate (ADP), which is universally produced by kinases, are commercially available for high-throughput screening (HTS) of kinase inhibitors, but their cost is quite high for large-scale screening. Here, we report a new enzyme-coupled fluorescence assay for ADP detection, which uses just 10 inexpensive, commercially available components. The assay protocol is very simple, requiring only the mixing of test solutions with ADP detection solution and reading the fluorescence intensity of resorufin produced by coupling reaction. To validate the assay, we focused on CDC2-like kinase 1 (CLK1), a dual-specificity kinase that plays an important role in alternative splicing, and we used the optimized assay to screen an in-house chemical library of about 215,000 compounds for CLK1 inhibitors. We identified and validated 12 potent inhibitors of CLK1, including a novel inhibitory scaffold. The results demonstrate that this assay platform is not only simple and cost-effective, but also sufficiently robust, showing good reproducibility and giving similar results to those obtained with the widely used ADP-Glo bioluminescent assay.
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Affiliation(s)
| | - Kazuo Kumagai
- 1 Drug Discovery Initiative, The University of Tokyo, Tokyo, Japan.,2 Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, Kobe, Japan
| | - Hirofumi Nakano
- 1 Drug Discovery Initiative, The University of Tokyo, Tokyo, Japan
| | - Takayoshi Okabe
- 1 Drug Discovery Initiative, The University of Tokyo, Tokyo, Japan
| | - Tetsuo Nagano
- 1 Drug Discovery Initiative, The University of Tokyo, Tokyo, Japan
| | - Hirotatsu Kojima
- 1 Drug Discovery Initiative, The University of Tokyo, Tokyo, Japan
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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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