1
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Lanne A, Bardelle C, Davies G, Turberville A, Semple H, Moore R, Holdgate GA. POLARISED views and FRETting about probe modulation assays: Learning from High Throughput Screening. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:100156. [PMID: 38642710 DOI: 10.1016/j.slasd.2024.100156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 03/28/2024] [Accepted: 04/14/2024] [Indexed: 04/22/2024]
Abstract
Fluorescent probe modulation assays are a widely used approach to monitor displacement or stabilisation of fluorescently labelled tool ligands by test compounds. These assays allow an optical read-out of probe-receptor binding and can be used to detect compounds that compete with the labelled ligand, either directly or indirectly. Probes for both orthosteric and allosteric sites are often employed. The method can also be used to identify test compounds that may stabilise the ternary complex, offering an opportunity to discover novel molecular glues. The utility of these fluorescence-based assays within high-throughput screening has been facilitated by the use of streptavidin labelled terbium as a donor and access to a range of different acceptor fluorophores. During 2023, the High-throughput Screening group at AstraZeneca carried out 8 high-throughput screens using these approaches. In this manuscript we will present the types of assays used, an overview of the timelines for assay development and screening, the application of orthogonal artefact methods to aid hit finding and the results of the screens in terms of hit rate and the number of compounds identified with IC50 values of better than 30 µM. Learning across the development, execution and analysis of these screens will be presented.
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Affiliation(s)
- Alice Lanne
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Catherine Bardelle
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, Macclesfield, UK
| | - Gareth Davies
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, Macclesfield, UK
| | | | - Hannah Semple
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Rachel Moore
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
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2
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Holdgate GA, Bardelle C, Berry SK, Lanne A, Cuomo ME. Screening for molecular glues - Challenges and opportunities. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:100136. [PMID: 38104659 DOI: 10.1016/j.slasd.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/03/2023] [Accepted: 12/14/2023] [Indexed: 12/19/2023]
Abstract
Molecular glues are small molecules, typically smaller than PROTACs, and usually with improved physicochemical properties that aim to stabilise the interaction between two proteins. Most often this approach is used to improve or induce an interaction between the target and an E3 ligase, but other interactions which stabilise interactions to increase activity or to inhibit binding to a natural effector have also been demonstrated. This review will describe the effects of induced proximity, discuss current methods used to identify molecular glues and introduce approaches that could be adapted for molecular glue screening.
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Affiliation(s)
| | - Catherine Bardelle
- High-throughput Screening, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
| | - Sophia K Berry
- High-throughput Screening, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
| | - Alice Lanne
- High-throughput Screening, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
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3
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Deng M, Zhang C, Yan W, Chen L, He B, Li Y. Development of Fluorescence-Based Assays for Key Viral Proteins in the SARS-CoV-2 Infection Process and Lifecycle. Int J Mol Sci 2024; 25:2850. [PMID: 38474097 DOI: 10.3390/ijms25052850] [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: 01/09/2024] [Revised: 02/09/2024] [Accepted: 02/25/2024] [Indexed: 03/14/2024] Open
Abstract
Since the appearance of SARS-CoV-2 in 2019, the ensuing COVID-19 (Corona Virus Disease 2019) pandemic has posed a significant threat to the global public health system, human health, life, and economic well-being. Researchers worldwide have devoted considerable efforts to curb its spread and development. The latest studies have identified five viral proteins, spike protein (Spike), viral main protease (3CLpro), papain-like protease (PLpro), RNA-dependent RNA polymerase (RdRp), and viral helicase (Helicase), which play crucial roles in the invasion of SARS-CoV-2 into the human body and its lifecycle. The development of novel anti-SARS-CoV-2 drugs targeting these five viral proteins holds immense promise. Therefore, the development of efficient, high-throughput screening methodologies specifically designed for these viral proteins is of utmost importance. Currently, a plethora of screening techniques exists, with fluorescence-based assays emerging as predominant contenders. In this review, we elucidate the foundational principles and methodologies underpinning fluorescence-based screening approaches directed at these pivotal viral targets, hoping to guide researchers in the judicious selection and refinement of screening strategies, thereby facilitating the discovery and development of lead compounds for anti-SARS-CoV-2 pharmaceuticals.
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Affiliation(s)
- Mingzhenlong Deng
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, Guizhou Medical University, Guiyang 550004, China
| | - Chuang Zhang
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, Guizhou Medical University, Guiyang 550004, China
| | - Wanli Yan
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, Guizhou Medical University, Guiyang 550004, China
| | - Lei Chen
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, Guizhou Medical University, Guiyang 550004, China
| | - Bin He
- State Key Laboratory of Functions and Applications of Medicinal Plants, Engineering Research Center for the Development and Application of Ethnic Medicine and TCM (Ministry of Education), Guizhou Provincial Key Laboratory of Pharmaceutics, School of Pharmacy, Guizhou Medical University, Guiyang 550004, China
| | - Yan Li
- School of Basic Medical Science, Guizhou Medical University, Guiyang 550004, China
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4
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Fessl T, Majellaro M, Bondar A. Microscopy and spectroscopy approaches to study GPCR structure and function. Br J Pharmacol 2023. [PMID: 38087925 DOI: 10.1111/bph.16297] [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: 06/30/2023] [Revised: 11/03/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024] Open
Abstract
The GPCR signalling cascade is a key pathway responsible for the signal transduction of a multitude of physical and chemical stimuli, including light, odorants, neurotransmitters and hormones. Understanding the structural and functional properties of the GPCR cascade requires direct observation of signalling processes in high spatial and temporal resolution, with minimal perturbation to endogenous systems. Optical microscopy and spectroscopy techniques are uniquely suited to this purpose because they excel at multiple spatial and temporal scales and can be used in living objects. Here, we review recent developments in microscopy and spectroscopy technologies which enable new insights into GPCR signalling. We focus on advanced techniques with high spatial and temporal resolution, single-molecule methods, labelling strategies and approaches suitable for endogenous systems and large living objects. This review aims to assist researchers in choosing appropriate microscopy and spectroscopy approaches for a variety of applications in the study of cellular signalling.
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Affiliation(s)
- Tomáš Fessl
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | | | - Alexey Bondar
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
- Laboratory of Microscopy and Histology, Institute of Entomology, Biology Centre of the Czech Academy of Sciences, České Budějovice, Czech Republic
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5
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Wang HY, Cecon E, Dam J, Pei Z, Jockers R, Burns LH. Simufilam Reverses Aberrant Receptor Interactions of Filamin A in Alzheimer's Disease. Int J Mol Sci 2023; 24:13927. [PMID: 37762230 PMCID: PMC10531384 DOI: 10.3390/ijms241813927] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 08/29/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023] Open
Abstract
Simufilam is a novel oral drug candidate in Phase 3 clinical trials for Alzheimer's disease (AD) dementia. This small molecule binds an altered form of filamin A (FLNA) that occurs in AD. This drug action disrupts FLNA's aberrant linkage to the α7 nicotinic acetylcholine receptor (α7nAChR), thereby blocking soluble amyloid beta1-42 (Aβ42)'s signaling via α7nAChR that hyperphosphorylates tau. Here, we aimed to clarify simufilam's mechanism. We now show that simufilam reduced Aβ42 binding to α7nAChR with a 10-picomolar IC50 using time-resolved fluorescence resonance energy transfer (TR-FRET), a robust technology to detect highly sensitive molecular interactions. We also show that FLNA links to multiple inflammatory receptors in addition to Toll-like receptor 4 (TLR4) in postmortem human AD brains and in AD transgenic mice: TLR2, C-X-C chemokine receptor type 4 (CXCR4), C-C chemokine receptor type 5 (CCR5), and T-cell co-receptor cluster of differentiation 4 (CD4). These aberrant FLNA linkages, which can be induced in a healthy control brain by Aβ42 incubation, were disrupted by simufilam. Simufilam reduced inflammatory cytokine release from Aβ42-stimulated human astrocytes. In the AD transgenic mice, CCR5-G protein coupling was elevated, indicating persistent activation. Oral simufilam reduced both the FLNA-CCR5 linkage and the CCR5-G protein coupling in these mice, while restoring CCR5's responsivity to C-C chemokine ligand 3 (CCL3). By disrupting aberrant FLNA-receptor interactions critical to AD pathogenic pathways, simufilam may promote brain health.
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Affiliation(s)
- Hoau-Yan Wang
- Department of Molecular, Cellular and Biomedical Sciences, City University of New York School of Medicine, New York, NY 10031, USA; (H.-Y.W.); (Z.P.)
- Department of Biology and Neuroscience, Graduate School, City University of New York, New York, NY 10016, USA
| | - Erika Cecon
- Institut Cochin, INSERM, CNRS, Université Paris Cité, 75014 Paris, France; (E.C.); (J.D.); (R.J.)
| | - Julie Dam
- Institut Cochin, INSERM, CNRS, Université Paris Cité, 75014 Paris, France; (E.C.); (J.D.); (R.J.)
| | - Zhe Pei
- Department of Molecular, Cellular and Biomedical Sciences, City University of New York School of Medicine, New York, NY 10031, USA; (H.-Y.W.); (Z.P.)
| | - Ralf Jockers
- Institut Cochin, INSERM, CNRS, Université Paris Cité, 75014 Paris, France; (E.C.); (J.D.); (R.J.)
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6
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Wakpal J, Pathiranage V, Walker AR, Nguyen HM. Rational Design and Expedient Synthesis of Heparan Sulfate Mimetics from Natural Aminoglycosides for Structure and Activity Relationship Studies. Angew Chem Int Ed Engl 2023; 62:e202304325. [PMID: 37285191 PMCID: PMC10527013 DOI: 10.1002/anie.202304325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 06/06/2023] [Accepted: 06/07/2023] [Indexed: 06/08/2023]
Abstract
Heparan sulfate (HS) contains variably repeating disaccharide units organized into high- and low-sulfated domains. This rich structural diversity enables HS to interact with many proteins and regulate key signaling pathways. Efforts to understand structure-function relationships and harness the therapeutic potential of HS are hindered by the inability to synthesize an extensive library of well-defined HS structures. We herein report a rational and expedient approach to access a library of 27 oligosaccharides from natural aminoglycosides as HS mimetics in 7-12 steps. This strategy significantly reduces the number of steps as compared to the traditional synthesis of HS oligosaccharides from monosaccharide building blocks. Combined with computational insight, we identify a new class of four trisaccharide compounds derived from the aminoglycoside tobramycin that mimic natural HS and have a strong binding to heparanase but a low affinity for off-target platelet factor-4 protein.
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Affiliation(s)
- Joseph Wakpal
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
| | | | - Alice R Walker
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
| | - Hien M Nguyen
- Department of Chemistry, Wayne State University, Detroit, MI 48202, USA
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7
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Kumar AP, P P, Mandal S, Kumar BRP, Raju RM, Dhanabal S, Rajagopal K, G R, X PN, Justin A. Computational studies, synthesis, in-vitro binding and transcription analysis of novel imidazolidine-2,4-dione and 2-thioxo thiazolidine-4-one based glitazones for central PPAR-γ agonism. J Mol Struct 2023. [DOI: 10.1016/j.molstruc.2023.135503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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8
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Liang Y, Jiang Q, Gong Y, Yu Y, Zou H, Zhao J, Zhang T, Zhang J. In vitro and in silico assessment of endocrine disrupting effects of food contaminants through pregnane X receptor. Food Chem Toxicol 2023; 175:113711. [PMID: 36893891 DOI: 10.1016/j.fct.2023.113711] [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: 02/14/2023] [Revised: 02/26/2023] [Accepted: 03/06/2023] [Indexed: 03/09/2023]
Abstract
As a promiscuous xenobiotic receptor, pregnane X receptor (PXR) has been confirmed to participate in numerous physiological process. In addition to the conventional estrogen/androgen receptor, PXR also serves as an alternative target for environmental chemical contaminants. In this work, the PXR-mediated endocrine disrupting effects of typical food contaminants were explored. Firstly, the time-resolved fluorescence resonance energy transfer assays confirmed the PXR binding affinities of 2,2',4,4',5,5'-hexachlorobiphenyl, bis(2-ethylhexyl) phthalate, dibutyl phthalate, chlorpyrifos, bisphenol A, and zearalenone, with IC50 values ranging from 1.88 to 4284.00 nM. Then their PXR agonist activities were assessed by PXR-mediated CYP3A4 reporter gene assays. Subsequently, the regulation of gene expressions of PXR and its targets CYP3A4, UGT1A1, and MDR1 by these compounds was further investigated. Intriguingly, all the tested compounds interfered with these gene expressions, confirming their endocrine disrupting effects via PXR-mediated signaling. The compound-PXR-LBD binding interactions were explored by molecular docking and molecular dynamics simulations to unravel the structural basis of their PXR binding capacities. The weak intermolecular interactions are key players in stabilizing these compound-PXR-LBD complexes. During the simulation process, 2,2',4,4',5,5'-hexachlorobiphenyl remained stable while the other 5 compounds underwent relatively severe disturbances. In conclusion, these food contaminants might exhibit endocrine disrupting effects via PXR.
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Affiliation(s)
- Yuan Liang
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Qiuyan Jiang
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Yiyao Gong
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Yifan Yu
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Haoyang Zou
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Jingqi Zhao
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Tiehua Zhang
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Jie Zhang
- College of Food Science and Engineering, Jilin University, Changchun, 130062, China.
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9
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Sarkar N, Singh A, Kumar P, Kaushik M. Protein kinases: Role of their dysregulation in carcinogenesis, identification and inhibition. Drug Res (Stuttg) 2023; 73:189-199. [PMID: 36822216 DOI: 10.1055/a-1989-1856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Protein kinases belong to the phosphor-transferases superfamily of enzymes, which "activate" enzymes via phosphorylation. The kinome of an organism is the total set of genes in the genome, which encode for all the protein kinases. Certain mutations in the kinome have been linked to dysregulation of protein kinases, which in turn can lead to several diseases and disorders including cancer. In this review, we have briefly discussed the role of protein kinases in various biochemical processes by categorizing cancer associated phenotypes and giving their protein kinase examples. Various techniques have also been discussed, which are being used to analyze the structure of protein kinases, and associate their roles in the oncogenesis. We have also discussed protein kinase inhibitors and United States Federal Drug Administration (USFDA) approved drugs, which target protein kinases and can serve as a counter to protein kinase dysregulation and mitigate the effects of oncogenesis. Overall, this review briefs about the importance of protein kinases, their roles in oncogenesis on dysregulation and how their inhibition via various drugs can be used to mitigate their effects.
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Affiliation(s)
- Niloy Sarkar
- Nano-Bioconjugate Chemistry Lab, Cluster Innovation Centre, University of Delhi, Delhi, India.,Department of Environmental Studies, University of Delhi, Delhi, India
| | - Amit Singh
- Nano-Bioconjugate Chemistry Lab, Cluster Innovation Centre, University of Delhi, Delhi, India.,Department of Chemistry, University of Delhi, Delhi, India
| | - Pankaj Kumar
- Nano-Bioconjugate Chemistry Lab, Cluster Innovation Centre, University of Delhi, Delhi, India.,Department of Chemistry, University of Delhi, Delhi, India
| | - Mahima Kaushik
- Nano-Bioconjugate Chemistry Lab, Cluster Innovation Centre, University of Delhi, Delhi, India
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10
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He S, Lim GE. The Application of High-Throughput Approaches in Identifying Novel Therapeutic Targets and Agents to Treat Diabetes. Adv Biol (Weinh) 2023; 7:e2200151. [PMID: 36398493 DOI: 10.1002/adbi.202200151] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 10/04/2022] [Indexed: 11/19/2022]
Abstract
During the past decades, unprecedented progress in technologies has revolutionized traditional research methodologies. Among these, advances in high-throughput drug screening approaches have permitted the rapid identification of potential therapeutic agents from drug libraries that contain thousands or millions of molecules. Moreover, high-throughput-based therapeutic target discovery strategies can comprehensively interrogate relationships between biomolecules (e.g., gene, RNA, and protein) and diseases and significantly increase the authors' knowledge of disease mechanisms. Diabetes is a chronic disease primarily characterized by the incapacity of the body to maintain normoglycemia. The prevalence of diabetes in modern society has become a severe public health issue that threatens the well-being of millions of patients. Although a number of pharmacological treatments are available, there is no permanent cure for diabetes, and discovering novel therapeutic targets and agents continues to be an urgent need. The present review discusses the technical details of high-throughput screening approaches in drug discovery, followed by introducing the applications of such approaches to diabetes research. This review aims to provide an example of the applicability of high-throughput technologies in facilitating different aspects of disease research.
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Affiliation(s)
- Siyi He
- Department of Medicine, Université de Montréal, Pavillon Roger-Gaudry, 2900 Edouard Montpetit Blvd, Montreal, Québec, H3T 1J4, Canada.,Cardiometabolic Axis, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), 900 rue St Denis, Montreal, Québec, H2X 0A9, Canada
| | - Gareth E Lim
- Department of Medicine, Université de Montréal, Pavillon Roger-Gaudry, 2900 Edouard Montpetit Blvd, Montreal, Québec, H3T 1J4, Canada.,Cardiometabolic Axis, Centre de Recherche du Centre Hospitalier de l'Université de Montréal (CRCHUM), 900 rue St Denis, Montreal, Québec, H2X 0A9, Canada
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11
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Thalhammer A, Bröker NK. Biophysical Approaches for the Characterization of Protein-Metabolite Interactions. Methods Mol Biol 2023; 2554:199-229. [PMID: 36178628 DOI: 10.1007/978-1-0716-2624-5_13] [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] [Indexed: 06/16/2023]
Abstract
With an estimate of hundred thousands of protein molecules per cell and the number of metabolites several orders of magnitude higher, protein-metabolite interactions are omnipresent. In vitro analyses are one of the main pillars on the way to establish a solid understanding of how these interactions contribute to maintaining cellular homeostasis. A repertoire of biophysical techniques is available by which protein-metabolite interactions can be quantitatively characterized in terms of affinity, specificity, and kinetics in a broad variety of solution environments. Several of those provide information on local or global conformational changes of the protein partner in response to ligand binding. This review chapter gives an overview of the state-of-the-art biophysical toolbox for the study of protein-metabolite interactions. It briefly introduces basic principles, highlights recent examples from the literature, and pinpoints promising future directions.
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Affiliation(s)
- Anja Thalhammer
- Physical Biochemistry, University of Potsdam, Potsdam, Germany.
| | - Nina K Bröker
- Physical Biochemistry, University of Potsdam, Potsdam, Germany
- Health and Medical University Potsdam, Potsdam, Germany
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12
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Rational design, molecular docking, dynamic simulation, synthesis, PPAR-γ competitive binding and transcription analysis of novel glitazones. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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13
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Tye MA, Payne NC, Johansson C, Singh K, Santos SA, Fagbami L, Pant A, Sylvester K, Luth MR, Marques S, Whitman M, Mota MM, Winzeler EA, Lukens AK, Derbyshire ER, Oppermann U, Wirth DF, Mazitschek R. Elucidating the path to Plasmodium prolyl-tRNA synthetase inhibitors that overcome halofuginone resistance. Nat Commun 2022; 13:4976. [PMID: 36008486 PMCID: PMC9403976 DOI: 10.1038/s41467-022-32630-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 08/10/2022] [Indexed: 02/07/2023] Open
Abstract
The development of next-generation antimalarials that are efficacious against the human liver and asexual blood stages is recognized as one of the world's most pressing public health challenges. In recent years, aminoacyl-tRNA synthetases, including prolyl-tRNA synthetase, have emerged as attractive targets for malaria chemotherapy. We describe the development of a single-step biochemical assay for Plasmodium and human prolyl-tRNA synthetases that overcomes critical limitations of existing technologies and enables quantitative inhibitor profiling with high sensitivity and flexibility. Supported by this assay platform and co-crystal structures of representative inhibitor-target complexes, we develop a set of high-affinity prolyl-tRNA synthetase inhibitors, including previously elusive aminoacyl-tRNA synthetase triple-site ligands that simultaneously engage all three substrate-binding pockets. Several compounds exhibit potent dual-stage activity against Plasmodium parasites and display good cellular host selectivity. Our data inform the inhibitor requirements to overcome existing resistance mechanisms and establish a path for rational development of prolyl-tRNA synthetase-targeted anti-malarial therapies.
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Affiliation(s)
- Mark A Tye
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Graduate School of Arts and Sciences, Cambridge, MA, USA
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - N Connor Payne
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Catrine Johansson
- Botnar Research Centre, NIHR Oxford Biomedical Research Unit, University of Oxford, Oxford, UK
- Centre for Medicines Discovery, University of Oxford, Oxford, UK
| | - Kritika Singh
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - Sofia A Santos
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Lọla Fagbami
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Graduate School of Arts and Sciences, Cambridge, MA, USA
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Akansha Pant
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | - Madeline R Luth
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | - Sofia Marques
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Malcolm Whitman
- Department of Developmental Biology, Harvard School of Dental Medicine, Boston, MA, USA
| | - Maria M Mota
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Elizabeth A Winzeler
- Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA
| | | | | | - Udo Oppermann
- Botnar Research Centre, NIHR Oxford Biomedical Research Unit, University of Oxford, Oxford, UK
- Centre for Medicines Discovery, University of Oxford, Oxford, UK
| | - Dyann F Wirth
- Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Ralph Mazitschek
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA.
- Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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14
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Kotulska AM, Pilch-Wróbel A, Lahtinen S, Soukka T, Bednarkiewicz A. Upconversion FRET quantitation: the role of donor photoexcitation mode and compositional architecture on the decay and intensity based responses. LIGHT, SCIENCE & APPLICATIONS 2022; 11:256. [PMID: 35986019 PMCID: PMC9391450 DOI: 10.1038/s41377-022-00946-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 07/03/2022] [Accepted: 07/25/2022] [Indexed: 05/15/2023]
Abstract
Lanthanide-doped colloidal nanoparticles capable of photon upconversion (UC) offer long luminescence lifetimes, narrowband absorption and emission spectra, and efficient anti-Stokes emission. These features are highly advantageous for Förster Resonance Energy Transfer (FRET) based detection. Upconverting nanoparticles (UCNPs) as donors may solve the existing problems of molecular FRET systems, such as photobleaching and limitations in quantitative analysis, but these new labels also bring new challenges. Here we have studied the impact of the core-shell compositional architecture of upconverting nanoparticle donors and the mode of photoexcitation on the performance of UC-FRET from UCNPs to Rose Bengal (RB) molecular acceptor. We have quantitatively compared luminescence rise and decay kinetics of Er3+ emission using core-only NaYF4: 20% Yb, 2% Er and core-shell NaYF4: 20% Yb @ NaYF4: 20% Yb, 5% Er donor UCNPs under three photoexcitation schemes: (1) direct short-pulse photoexcitation of Er3+ at 520 nm; indirect photoexcitation of Er3+ through Yb3+ sensitizer with (2) 980 nm short (5-7 ns) or (3) 980 nm long (4 ms) laser pulses. The donor luminescence kinetics and steady-state emission spectra differed between the UCNP architectures and excitation schemes. Aiming for highly sensitive kinetic upconversion FRET-based biomolecular assays, the experimental results underline the complexity of the excitation and energy-migration mechanisms affecting the Er3+ donor responses and suggest ways to optimize the photoexcitation scheme and the architecture of the UCNPs used as luminescent donors.
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Affiliation(s)
- Agata M Kotulska
- Division of Biomedical Physicochemistry, Institute of Low Temperature and Structure Research, PAN, ul. Okolna 2, Wrocław, 50-422, Poland
| | - Aleksandra Pilch-Wróbel
- Division of Biomedical Physicochemistry, Institute of Low Temperature and Structure Research, PAN, ul. Okolna 2, Wrocław, 50-422, Poland
| | - Satu Lahtinen
- Department of Life Technologies/Biotechnology, University of Turku, Kiinamyllynkatu 10, 20520, Turku, Finland
| | - Tero Soukka
- Department of Life Technologies/Biotechnology, University of Turku, Kiinamyllynkatu 10, 20520, Turku, Finland.
| | - Artur Bednarkiewicz
- Division of Biomedical Physicochemistry, Institute of Low Temperature and Structure Research, PAN, ul. Okolna 2, Wrocław, 50-422, Poland.
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15
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Loka RS, Song Z, Sletten ET, Kayal Y, Vlodavsky I, Zhang K, Nguyen HM. Heparan Sulfate Mimicking Glycopolymer Prevents Pancreatic β Cell Destruction and Suppresses Inflammatory Cytokine Expression in Islets under the Challenge of Upregulated Heparanase. ACS Chem Biol 2022; 17:1387-1400. [PMID: 35658404 PMCID: PMC9251817 DOI: 10.1021/acschembio.1c00908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Diabetes is a chronic disease in which the levels of blood glucose are too high because the body does not effectively produce insulin to meet its needs or is resistant to insulin. β Cells in human pancreatic islets produce insulin, which signals glucogen production by the liver and causes muscles and fat to uptake glucose. Progressive loss of insulin-producing β cells is the main cause of both type 1 and type 2 diabetes. Heparan sulfate (HS) is a ubiquitous polysaccharide found at the cell surface and in the extracellular matrix (ECM) of a variety of tissues. HS binds to and assembles proteins in ECM, thus playing important roles in the integrity of ECM (particularly basement membrane), barrier function, and ECM-cell interactions. Islet HS is highly expressed by the pancreatic β cells and critical for the survival of β cells. Heparanase is an endoglycosidase and cleaves islet HS in the pancreas, resulting in β-cell death and oxidative stress. Heparanase could also accelerate β-cell death by promoting cytokine release from ECM and secretion by activated inflammatory and endothelial cells. We demonstrate that HS-mimicking glycopolymer, a potent heparanase inhibitor, improves the survival of cultured mouse pancreatic β cells and protects HS contents under the challenge of heparanase in human pancreatic islets. Moreover, this HS-mimicking glycopolymer reduces the expression levels of cytokines (IL8, IL1β, and TNFα) and the gene encoding Toll-like Receptor 2 (TLR2) in human pancreatic islets.
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Affiliation(s)
- Ravi S Loka
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
| | - Zhenfeng Song
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan 48201, United States
| | - Eric T Sletten
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, United States
| | - Yasmin Kayal
- Cancer and Vascular Biology Research Center, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa 3525422, Israel
| | - Israel Vlodavsky
- Cancer and Vascular Biology Research Center, Rappaport Faculty of Medicine, Technion - Israel Institute of Technology, Haifa 3525422, Israel
| | - Kezhong Zhang
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, Michigan 48201, United States
| | - Hien M Nguyen
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, United States
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16
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A Practical and
High‐Affinity
Fluorescent Probe for Butyrylcholinesterase: A Good Strategy for Binding Affinity Characterization. CHINESE J CHEM 2022. [DOI: 10.1002/cjoc.202100910] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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17
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Gorshkov K, Morales Vasquez D, Chiem K, Ye C, Nguyen Tran B, Carlos de la Torre J, Moran T, Chen CZ, Martinez-Sobrido L, Zheng W. SARS-CoV-2 Nucleocapsid Protein TR-FRET Assay Amenable to High Throughput Screening. ACS Pharmacol Transl Sci 2022; 5:8-19. [PMID: 35036857 PMCID: PMC8751018 DOI: 10.1021/acsptsci.1c00182] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Indexed: 12/24/2022]
Abstract
![]()
Drug
development for specific antiviral agents against coronavirus
disease 2019 (COVID-19) is still an unmet medical need as the pandemic
continues to spread globally. Although huge efforts for drug repurposing
and compound screens have been put forth, only a few compounds are
in late-stage clinical trials. New approaches and assays are needed
to accelerate COVID-19 drug discovery and development. Here, we report
a time-resolved fluorescence resonance energy transfer-based assay
that detects the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
nucleocapsid protein (NP) produced in infected cells. It uses two
specific anti-NP monoclonal antibodies conjugated to donor and acceptor
fluorophores that produce a robust ratiometric signal for high throughput
screening of large compound collections. Using this assay, we measured
a half maximal inhibitory concentration (IC50) for remdesivir
of 9.3 μM against infection with SARS-CoV-2 USA/WA1/2020 (WA-1).
The assay also detected SARS-CoV-2 South African (Beta, β),
Brazilian/Japanese P.1 (Gamma, γ), and Californian (Epsilon,
ε) variants of concern (VoC). Therefore, this homogeneous SARS-CoV-2
NP detection assay can be used for accelerating lead compound discovery
for drug development and for evaluating drug efficacy against emerging
SARS-CoV-2 VoC.
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Affiliation(s)
- Kirill Gorshkov
- National Center for Advancing Translational Sciences, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Desarey Morales Vasquez
- Texas Biomedical Research Institute, 8715 West Military Drive, San Antonio, Texas 78227, United States
| | - Kevin Chiem
- Texas Biomedical Research Institute, 8715 West Military Drive, San Antonio, Texas 78227, United States
| | - Chengjin Ye
- Texas Biomedical Research Institute, 8715 West Military Drive, San Antonio, Texas 78227, United States
| | - Bruce Nguyen Tran
- National Center for Advancing Translational Sciences, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Juan Carlos de la Torre
- Department of Immunology and Microbiology, IMM6, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Thomas Moran
- Icahn School of Medicine, Mt. Sinai, 1 Gustave L. Levy Place, New York, New York 10029, United States
| | - Catherine Z Chen
- National Center for Advancing Translational Sciences, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
| | - Luis Martinez-Sobrido
- Texas Biomedical Research Institute, 8715 West Military Drive, San Antonio, Texas 78227, United States
| | - Wei Zheng
- National Center for Advancing Translational Sciences, 9800 Medical Center Drive, Rockville, Maryland 20850, United States
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18
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Unger MS, Blank M, Enzlein T, Hopf C. Label-free cell assays to determine compound uptake or drug action using MALDI-TOF mass spectrometry. Nat Protoc 2021; 16:5533-5558. [PMID: 34759382 DOI: 10.1038/s41596-021-00624-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 08/26/2021] [Indexed: 11/09/2022]
Abstract
Cell-based assays for compound screening and profiling are fundamentally important in life sciences, chemical biology and pharmaceutical research. Most cell assays measure the amount of a single reporter molecule or cellular endpoint, and require the use of fluorescence or other labeled materials. Consequently, there is high demand for label-free technologies that enable multiple biomolecules or endpoints to be measured simultaneously. Here, we describe how to develop, optimize and validate MALDI-TOF mass spectrometry (MS) cell assays that can be used to measure cellular uptake of transporter substrates, to monitor cellular drug target engagement or to discover cellular drug-response markers. In uptake assays, intracellular accumulation of a transporter substrate and its inhibition by test compounds is measured. In drug response assays, changes to multiple cellular metabolites or to abundant posttranslational protein modifications are monitored as reporters of drug activity. We detail a ten-part optimization protocol with every part taking 1-2 d that leads to a final 2 d optimized procedure, which includes cell treatment, transfer, MALDI MS-specific sample preparation, quantification using stable-isotope-labeled standards, MALDI-TOF MS data acquisition, data processing and analysis. Key considerations for validation and automation of MALDI-TOF MS cell assays are outlined. Overall, label-free MS cell-based assays offer speed, sensitivity, accuracy and versatility in drug research.
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Affiliation(s)
- Melissa S Unger
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Mannheim, Germany
| | - Martina Blank
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Mannheim, Germany.,Structural Molecular Biology Laboratory (LABIME), Department of Biochemistry, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Thomas Enzlein
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Mannheim, Germany
| | - Carsten Hopf
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim University of Applied Sciences, Mannheim, Germany.
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19
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Payne NC, Kalyakina AS, Singh K, Tye MA, Mazitschek R. Bright and stable luminescent probes for target engagement profiling in live cells. Nat Chem Biol 2021; 17:1168-1177. [PMID: 34675420 PMCID: PMC8555866 DOI: 10.1038/s41589-021-00877-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 08/11/2021] [Indexed: 01/18/2023]
Abstract
The pace of progress in biomedical research directly depends on techniques that enable the quantitative interrogation of interactions between proteins and other biopolymers, or with their small-molecule ligands. Time-resolved Förster resonance energy transfer (TR-FRET) assay platforms offer high sensitivity and specificity. However, the paucity of accessible and biocompatible luminescent lanthanide complexes, which are essential reagents for TR-FRET-based approaches, and their poor cellular permeability have limited broader adaptation of TR-FRET beyond homogeneous and extracellular assay applications. Here, we report the development of CoraFluors, a new class of macrotricyclic terbium complexes, which are synthetically readily accessible, stable in biological media and exhibit photophysical and physicochemical properties that are desirable for biological studies. We validate the performance of CoraFluors in cell-free systems, identify cell-permeable analogs and demonstrate their utility in the quantitative domain-selective characterization of Keap1 ligands, as well as in isoform-selective target engagement profiling of HDAC1 inhibitors in live cells.
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Affiliation(s)
- N Connor Payne
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Chemistry & Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Alena S Kalyakina
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
- Karlsruhe Institute of Technology, Institute of Organic Chemistry, Karlsruhe, Germany
| | - Kritika Singh
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Bioengineering, Northeastern University, Boston, MA, USA
| | - Mark A Tye
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA
- Harvard Graduate School of Arts and Sciences, Cambridge, MA, USA
| | - Ralph Mazitschek
- Center for Systems Biology, Massachusetts General Hospital, Boston, MA, USA.
- Harvard T.H. Chan School of Public Health, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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20
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Suchankova A, Harris M, Ladds G. Measuring the rapid kinetics of receptor-ligand interactions in live cells using NanoBRET. Methods Cell Biol 2021; 166:1-14. [PMID: 34752328 DOI: 10.1016/bs.mcb.2021.06.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The importance of receptor-ligand binding kinetics has often been overlooked during drug development, however, over the past decade it has become increasingly clear that a better understanding of the kinetic parameters is crucial for fully evaluating pharmacological effects of a drug. One technique enabling us to measure the real-time kinetics of receptor-ligand interactions in live cells is NanoBRET, which is a bioluminescence resonance energy transfer (BRET)-based assay that uses Nano luciferase. The assay described here allows the measurement of kinetic parameters of a fluorescent ligand and an unlabeled ligand binding to the same place at the receptor, as well as monitoring the effects of another compound like an allosteric modulator on the ligand binding.
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Affiliation(s)
- Anna Suchankova
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
| | - Matthew Harris
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom
| | - Graham Ladds
- Department of Pharmacology, University of Cambridge, Cambridge, United Kingdom.
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21
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Gorshkov K, Vasquez DM, Chiem K, Ye C, Tran BN, de la Torre JC, Moran T, Chen CZ, Martinez-Sobrido L, Zheng W. A SARS-CoV-2 nucleocapsid protein TR-FRET assay amenable to high-throughput screening. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 34268508 PMCID: PMC8282096 DOI: 10.1101/2021.07.03.450938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Drug development for specific antiviral agents against coronavirus disease 2019 (COVID-19) is still an unmet medical need as the pandemic continues to spread globally. Although huge efforts for drug repurposing and compound screens have put forth, only few compounds remain in late stage clinical trials. New approaches and assays are needed to accelerate COVID-19 drug discovery and development. Here we report a time-resolved fluorescence resonance energy transfer-based assay that detects the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleocapsid protein (NP) produced in infected cells. It uses two specific anti-NP monoclonal antibodies (MAbs) conjugated to donor and acceptor fluorophores that produces a robust ratiometric signal for high throughput screening of large compound collections. Using this assay, we measured a half maximal inhibitory concentration (IC50) for Remdesivir of 9.3 μM against infection with SARS-CoV-2 USA/WA1/2020 (WA-1). The assay also detected SARS-CoV-2 South African (Beta, β), Brazilian/Japanese variant P.1 (Gamma, γ), and Californian (Epsilon, ε), variants of concern or interest (VoC). Therefore, this homogeneous SARS-CoV-2 NP detection assay can be used for accelerating lead compound discovery for drug development and for evaluating drug efficacy against emerging SARS-CoV-2 VoC.
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22
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Sivinski J, Zhang DD, Chapman E. Targeting NRF2 to treat cancer. Semin Cancer Biol 2021; 76:61-73. [PMID: 34102289 DOI: 10.1016/j.semcancer.2021.06.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 12/17/2022]
Abstract
NRF2 is a basic leucine zipper (bZip) transcription factor that is the master regulator of redox homeostasis. Under basal conditions, the cellular level of NRF2 is low due to a posttranslational regulation by the ubiquitin proteasome system (UPS). But, when an organism is challenged with oxidative or xenobiotic stress, the NRF2 pathway is activated by inhibition of the E3 ubiquitin ligase complex that normally marks NRF2 for destruction. For several decades, researchers have searched for molecules that can intentionally activate NRF2, as this was shown to be a means to prevent certain diseases, at least in animal models. In the present era, there are many compounds known to activate the NRF2 pathway including natural products and synthetic compounds, covalent and non-covalent compounds, and others. However, it was also revealed that like many protective pathways, the NRF2 pathway has a dark side. Just as NRF2 can protect normal cells from damage, it can protect malignant cells from damage. As cells transform, they are exposed to many stressors and aberrant upregulation of NRF2 can facilitate transformation and it can help cancer cells to grow, to spread, and to resist treatment. For this reason, researchers are also interested in the discovery and development of NRF2 inhibitors. In the present review, we will begin with a general discussion of NRF2 structure and function, we will discuss the latest in NRF2 non-covalent activators, and we will discuss the current state of NRF2 inhibitors.
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Affiliation(s)
- Jared Sivinski
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ, 85721, USA
| | - Donna D Zhang
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ, 85721, USA
| | - Eli Chapman
- Department of Pharmacology and Toxicology, College of Pharmacy, University of Arizona, Tucson, AZ, 85721, USA.
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23
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Zhang XH, Hsiang J, Rosen ST. Flavopiridol (Alvocidib), a Cyclin-dependent Kinases (CDKs) Inhibitor, Found Synergy Effects with Niclosamide in Cutaneous T-cell Lymphoma. JOURNAL OF CLINICAL HAEMATOLOGY 2021; 2:48-61. [PMID: 34223559 PMCID: PMC8248901 DOI: 10.33696/haematology.2.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Flavopiridol (FVP; Alvocidib), a CDKs inhibitor, is currently undergoing clinical trials for treatment of leukemia and other blood cancers. Our studies demonstrated that FVP also inhibited p38 kinases activities with IC50 (μM) for p38α: 1.34; p38 β: 1.82; p38γ: 0.65, and p38δ: 0.45. FVP showed potent cytotoxicity in cutaneous T-cell lymphoma (CTCL) Hut78 cells, with IC50 <100 nM. NMR analysis revealed that FVP bound to p38γ in the ATP binding pocket, causing allosteric perturbation from sites surrounding the ATP binding pocket. Kinomic profiling with the PamGene platform in both cell-based and cell-free analysis further revealed dosage of FVP significantly affects downstream pathways in treated CTCL cells, which suggested a need for development of synergistic drugs with FVP to prevent its clinically adverse effects. It led us discover niclosamide as a synergistic drug of FVP for our future in vivo study.
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Affiliation(s)
- Xu Hannah Zhang
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope, Beckman Research Institute, National Medical Center, Duarte, CA 91010, USA
| | - Jack Hsiang
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope, Beckman Research Institute, National Medical Center, Duarte, CA 91010, USA
| | - Steven T Rosen
- Department of Hematology and Hematopoietic Cell Transplantation, City of Hope, Beckman Research Institute, National Medical Center, Duarte, CA 91010, USA
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24
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Wang SY, Liu X, Liu Y, Zhang HY, Zhang YB, Liu C, Song J, Niu JB, Zhang SY. Review of NEDDylation inhibition activity detection methods. Bioorg Med Chem 2021; 29:115875. [DOI: 10.1016/j.bmc.2020.115875] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 11/05/2020] [Accepted: 11/09/2020] [Indexed: 12/31/2022]
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25
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Platchek M, Lu Q, Tran H, Xie W. Comparative Analysis of Multiple Immunoassays for Cytokine Profiling in Drug Discovery. SLAS DISCOVERY 2020; 25:1197-1213. [PMID: 32924773 DOI: 10.1177/2472555220954389] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Cytokines and their receptors play critical roles in biological processes. Dysfunction or dysregulation of cytokines may cause a variety of pathophysiological conditions. Consequently, cytokine profiling and related technologies are essential for biological studies, disease diagnosis, and drug discovery. In this report, three cytokines, interleukin (IL)-1β, IL-6, and tumor necrosis factor alpha (TNF-α), from the same sets of samples were analyzed with several commonly used technologies (enzyme-linked immunosorbent assay [ELISA], Luminex, Meso Scale Discovery [MSD], time-resolved fluorescence resonance energy transfer [TR-FRET], cytometric bead array [CBA], AlphaLISA, and FirePlex). Through experimental data analysis, several assay features were compared, including sensitivity, dynamic range, and robustness. Our studies reveal that MSD has the best sensitivity in the low detection limit and the broadest dynamic range, while CBA and Luminex also demonstrate superior performance in the sensitivity and dynamic range. Additional aspects of these technologies, including assay principles, formats, throughputs, robustness, costs, and multiplexing capabilities, were also reviewed and compared. Combining all these features, our comparison highlights MSD as the most sensitive technology, while CBA is the most suitable one for cytokine high-throughput screening with multiplexing capability. Along with perspectives on new technology development in the field, this report aims to help readers understand these technologies and select the proper one for specific applications.
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Affiliation(s)
- Michael Platchek
- Novel Human Genetics Research Unit, GlaxoSmithKline, Collegeville, PA, USA
| | - Quinn Lu
- Novel Human Genetics Research Unit, GlaxoSmithKline, Collegeville, PA, USA
| | - Hoang Tran
- Research Statistics, GlaxoSmithKline, Collegeville, PA, USA
| | - Wensheng Xie
- Novel Human Genetics Research Unit, GlaxoSmithKline, Collegeville, PA, USA
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26
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Kopra K, Vuorinen E, Abreu-Blanco M, Wang Q, Eskonen V, Gillette W, Pulliainen AT, Holderfield M, Härmä H. Homogeneous Dual-Parametric-Coupled Assay for Simultaneous Nucleotide Exchange and KRAS/RAF-RBD Interaction Monitoring. Anal Chem 2020; 92:4971-4979. [PMID: 32106676 PMCID: PMC7143314 DOI: 10.1021/acs.analchem.9b05126] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We have developed a rapid and sensitive single-well dual-parametric method introduced in linked RAS nucleotide exchange and RAS/RAF-RBD interaction assays. RAS mutations are frequent drivers of multiple different human cancers, but the development of therapeutic strategies has been challenging. Traditionally, efforts to disrupt the RAS function have focused on nucleotide exchange inhibitors, GTP-RAS interaction inhibitors, and activators increasing GTPase activity of mutant RAS proteins. As the amount of biological knowledge grows, targeted biochemical assays enabling high-throughput screening have become increasingly interesting. We have previously introduced a homogeneous quenching resonance energy transfer (QRET) assay for nucleotide binding studies with RAS and heterotrimeric G proteins. Here, we introduce a novel homogeneous signaling technique called QTR-FRET, which combine QRET technology and time-resolved Förster resonance energy transfer (TR-FRET). The dual-parametric QTR-FRET technique enables the linking of guanine nucleotide exchange factor-induced Eu3+-GTP association to RAS, monitored at 615 nm, and subsequent Eu3+-GTP-loaded RAS interaction with RAF-RBD-Alexa680 monitored at 730 nm. Both reactions were monitored in a single-well assay applicable for inhibitor screening and real-time reaction monitoring. This homogeneous assay enables separable detection of both nucleotide exchange and RAS/RAF interaction inhibitors using low nanomolar protein concentrations. To demonstrate a wider applicability as a screening and real-time reaction monitoring method, the QTR-FRET technique was also applied for G(i)α GTP-loading and pertussis toxin-catalyzed ADP-ribosylation of G(i)α, for which we synthesized a novel γ-GTP-Eu3+ molecule. The study indicates that the QTR-FRET detection technique presented here can be readily applied to dual-parametric assays for various targets.
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Affiliation(s)
- Kari Kopra
- Materials Chemistry and Chemical Analysis, University of Turku, Vatselankatu 2, 20500 Turku, Finland
| | - Emmiliisa Vuorinen
- Materials Chemistry and Chemical Analysis, University of Turku, Vatselankatu 2, 20500 Turku, Finland
| | - Maria Abreu-Blanco
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, 8560 Progress Dr., Frederick, Maryland 21702, United States
| | - Qi Wang
- Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland
| | - Ville Eskonen
- Materials Chemistry and Chemical Analysis, University of Turku, Vatselankatu 2, 20500 Turku, Finland
| | - William Gillette
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, 8560 Progress Dr., Frederick, Maryland 21702, United States
| | - Arto T Pulliainen
- Institute of Biomedicine, University of Turku, Kiinamyllynkatu 10, 20520 Turku, Finland
| | - Matthew Holderfield
- Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, 8560 Progress Dr., Frederick, Maryland 21702, United States
| | - Harri Härmä
- Materials Chemistry and Chemical Analysis, University of Turku, Vatselankatu 2, 20500 Turku, Finland
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27
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Robers MB, Friedman-Ohana R, Huber KVM, Kilpatrick L, Vasta JD, Berger BT, Chaudhry C, Hill S, Müller S, Knapp S, Wood KV. Quantifying Target Occupancy of Small Molecules Within Living Cells. Annu Rev Biochem 2020; 89:557-581. [PMID: 32208767 DOI: 10.1146/annurev-biochem-011420-092302] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The binding affinity and kinetics of target engagement are fundamental to establishing structure-activity relationships (SARs) for prospective therapeutic agents. Enhancing these binding parameters for operative targets, while minimizing binding to off-target sites, can translate to improved drug efficacy and a widened therapeutic window. Compound activity is typically assessed through modulation of an observed phenotype in cultured cells. Quantifying the corresponding binding properties under common cellular conditions can provide more meaningful interpretation of the cellular SAR analysis. Consequently, methods for assessing drug binding in living cells have advanced and are now integral to medicinal chemistry workflows. In this review, we survey key technological advancements that support quantitative assessments of target occupancy in cultured cells, emphasizing generalizable methodologies able to deliver analytical precision that heretofore required reductionist biochemical approaches.
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Affiliation(s)
- M B Robers
- Promega Corporation, Madison, Wisconsin 53711, USA; , ,
| | | | - K V M Huber
- Target Discovery Institute and Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, United Kingdom; .,Structural Genomics Consortium, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - L Kilpatrick
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, United Kingdom; , .,Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands NG7 2UH, United Kingdom
| | - J D Vasta
- Promega Corporation, Madison, Wisconsin 53711, USA; , ,
| | - B-T Berger
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany; ,
| | - C Chaudhry
- Lead Discovery and Optimization, Bristol-Myers Squibb, Princeton, New Jersey 08648, USA;
| | - S Hill
- Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham NG7 2UH, United Kingdom; , .,Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands NG7 2UH, United Kingdom
| | - S Müller
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany; , .,Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe University Frankfurt, 60438 Frankfurt, Germany;
| | - S Knapp
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, 60438 Frankfurt, Germany; , .,Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe University Frankfurt, 60438 Frankfurt, Germany; .,German Cancer Network (DKTK), Frankfurt/Mainz, 60438 Frankfurt, Germany.,Frankfurt Cancer Institute (FCI), Goethe University, 60596 Frankfurt am Main, Germany
| | - K V Wood
- Promega Corporation, Madison, Wisconsin 53711, USA; , , .,Current affiliation: Light Bio, Inc., Mount Horeb, Wisconsin 53572, USA;
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28
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Lim S, Lee H, Kim E, Hur W. Identification of a Novel Oxadiazole Inhibitor of Mammalian Target of Rapamycin. B KOREAN CHEM SOC 2020. [DOI: 10.1002/bkcs.11965] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Sunwoo Lim
- Department of ChemistryKorea University Seoul 02841 South Korea
- Chemical Kinomics Research CenterKorea Institute of Science and Technology (KIST), 5 Hwarangro‐14‐gil Seoul 02792 South Korea
| | - Hyomin Lee
- Chemical Kinomics Research CenterKorea Institute of Science and Technology (KIST), 5 Hwarangro‐14‐gil Seoul 02792 South Korea
- University of Science and Technology (UST) Daejeon 34113 South Korea
| | - Euijung Kim
- Department of ChemistryKorea University Seoul 02841 South Korea
- Chemical Kinomics Research CenterKorea Institute of Science and Technology (KIST), 5 Hwarangro‐14‐gil Seoul 02792 South Korea
| | - Wooyoung Hur
- Chemical Kinomics Research CenterKorea Institute of Science and Technology (KIST), 5 Hwarangro‐14‐gil Seoul 02792 South Korea
- University of Science and Technology (UST) Daejeon 34113 South Korea
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29
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Vuorinen E, Valtonen S, Eskonen V, Kariniemi T, Jakovleva J, Kopra K, Härmä H. Sensitive Label-Free Thermal Stability Assay for Protein Denaturation and Protein-Ligand Interaction Studies. Anal Chem 2020; 92:3512-3516. [PMID: 32013400 PMCID: PMC7145280 DOI: 10.1021/acs.analchem.9b05712] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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In modern biochemistry,
protein stability and ligand interactions are of high interest. These
properties are often studied with methods requiring labeled biomolecules,
as the existing methods utilizing luminescent external probes suffer
from low sensitivity. Currently available label-free technologies,
e.g., thermal shift assays, circular dichroism, and differential scanning
calorimetry, enable studies on protein unfolding and protein–ligand
interactions (PLI). Unfortunately, the required micromolar protein
concentration increases the costs and predisposes these methods for
spontaneous protein aggregation. Here, we report a time-resolved luminescence
method for protein unfolding and PLI detection with nanomolar sensitivity.
The Protein-Probe method is based on highly luminescent europium chelate-conjugated
probe, which is the key component in sensing the hydrophobic regions
exposed to solution after protein unfolding. With the same Eu-probe,
we also demonstrate ligand-interaction induced thermal stabilization
with model proteins. The developed Protein-Probe method provides a
sensitive approach overcoming the problems of the current label-free
methodologies.
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Affiliation(s)
- Emmiliisa Vuorinen
- Department of Chemistry, University of Turku, Vatselankatu 2, 20500 Turku, Finland
| | - Salla Valtonen
- Department of Chemistry, University of Turku, Vatselankatu 2, 20500 Turku, Finland
| | - Ville Eskonen
- Department of Chemistry, University of Turku, Vatselankatu 2, 20500 Turku, Finland
| | - Taru Kariniemi
- Department of Chemistry, University of Turku, Vatselankatu 2, 20500 Turku, Finland
| | - Jelena Jakovleva
- Department of Chemistry, University of Turku, Vatselankatu 2, 20500 Turku, Finland
| | - Kari Kopra
- Department of Chemistry, University of Turku, Vatselankatu 2, 20500 Turku, Finland
| | - Harri Härmä
- Department of Chemistry, University of Turku, Vatselankatu 2, 20500 Turku, Finland
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30
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Liang K, Wang H, Li P, Zhu Y, Liu J, Tang B. Detection of microRNAs using toehold-initiated rolling circle amplification and fluorescence resonance energy transfer. Talanta 2020; 207:120285. [DOI: 10.1016/j.talanta.2019.120285] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Revised: 08/18/2019] [Accepted: 08/20/2019] [Indexed: 12/25/2022]
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31
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Syrjänpää M, Vuorinen E, Kulmala S, Wang Q, Härmä H, Kopra K. QTR-FRET: Efficient background reduction technology in time-resolved förster resonance energy transfer assays. Anal Chim Acta 2019; 1092:93-101. [PMID: 31708038 DOI: 10.1016/j.aca.2019.09.045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 09/16/2019] [Indexed: 12/18/2022]
Abstract
A novel homogeneous assay system QTR-FRET (Quencher modulated Time-Resolved Förster Resonance Energy Transfer) combining quenching resonance energy transfer (QRET) and time-resolved Förster resonance energy transfer (TR-FRET) was developed to reduce background signal in the conventional energy transfer applications. The TR-FRET functionality is often limited by the lanthanide donor background signal leading to the use of low donor concentration. QTR-FRET reduces this background by introducing soluble quencher molecule, and in this work the concept functionality was proven and compared to previously introduced QRET and TR-FRET technologies. Comparison was performed with three different Eu3+-chelates exhibiting different luminescent lifetime and stability. The side-by-side comparison of the three signaling systems and Eu3+-chelates was demonstrated in a model assay with Eu3+-chelate conjugated biotin and streptavidin (SA) or Cy5-SA conjugate. Comparison of the methodologies showed increased signal-to-background ratios when comparing QTR-FRET to TR-FRET, especially at high Eu3+-biotin concentrations. Quenching the non-bound Eu3+-biotin improved the assay performance, which suggests that an improved assay performance can be attained with the QTR-FRET method. QTR-FRET is expected to be especially useful for Eu3+-labeled ligands with low affinity or assays requiring high Eu3+-ligand concentration. The QTR-FRET indicated potential for multi-analyte approaches separately utilizing the direct QRET-type Eu3+-chelate signal and energy transfer signal readout in a single-well. This potential was hypothesized with Avi-KRAS nucleotide exchange assay as a second biologically relevant model system.
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Affiliation(s)
- Markku Syrjänpää
- Institute of Biomedicine, Department of Cell Biology and Anatomy, Laboratory of Biophysics, University of Turku, Tykistökatu 6A, FI-20520, Turku, Finland
| | - Emmiliisa Vuorinen
- Materials Chemistry and Chemical Analysis, Department of Chemistry, University of Turku, Vatselankatu 2, FI-20500, Turku, Finland
| | - Sakari Kulmala
- Laboratory of Analytical Chemistry, Department of Chemistry, Aalto University, P.O. Box 16100, FI-00076, Aalto, Finland
| | - Qi Wang
- Institute of Biomedicine, Department of Cell Biology and Anatomy, Laboratory of Biophysics, University of Turku, Tykistökatu 6A, FI-20520, Turku, Finland
| | - Harri Härmä
- Materials Chemistry and Chemical Analysis, Department of Chemistry, University of Turku, Vatselankatu 2, FI-20500, Turku, Finland
| | - Kari Kopra
- Materials Chemistry and Chemical Analysis, Department of Chemistry, University of Turku, Vatselankatu 2, FI-20500, Turku, Finland.
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32
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Todorović V, Su Z, Putman CB, Kakavas SJ, Salte KM, McDonald HA, Wetter JB, Paulsboe SE, Sun Q, Gerstein CE, Medina L, Sielaff B, Sadhukhan R, Stockmann H, Richardson PL, Qiu W, Argiriadi MA, Henry RF, Herold JM, Shotwell JB, McGaraughty SP, Honore P, Gopalakrishnan SM, Sun CC, Scott VE. Small Molecule IL-36γ Antagonist as a Novel Therapeutic Approach for Plaque Psoriasis. Sci Rep 2019; 9:9089. [PMID: 31235749 PMCID: PMC6591177 DOI: 10.1038/s41598-019-45626-w] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 06/07/2019] [Indexed: 12/26/2022] Open
Abstract
IL-36 cytokines are pro-inflammatory members of the IL-1 family that are upregulated in inflammatory disorders. Specifically, IL-36γ is highly expressed in active psoriatic lesions and can drive pro-inflammatory processes in 3D human skin equivalents supporting a role for this target in skin inflammation. Small molecule antagonists of interleukins have been historically challenging to generate. Nevertheless, we performed a small molecule high-throughput screen to identify IL-36 antagonists using a novel TR-FRET binding assay. Several compounds, including 2-oxypyrimidine containing structural analogs of the marketed endothelin receptor A antagonist Ambrisentan, were identified as hits from the screen. A-552 was identified as a the most potent antagonist of human IL-36γ, but not the closely related family member IL-36α, was capable of attenuating IL-36γ induced responses in mouse and human disease models. Additionally, x-ray crystallography studies identified key amino acid residues in the binding pocket present in human IL-36γ that are absent in human IL-36α. A-552 represents a first-in-class small molecule antagonist of IL-36 signaling that could be used as a chemical tool to further investigate the role of this pathway in inflammatory skin diseases such as psoriasis.
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Affiliation(s)
- Viktor Todorović
- AbbVie Inc., 1 North Waukegan Rd., North Chicago, IL, 60064, USA.
| | - Zhi Su
- AbbVie Inc., 1 North Waukegan Rd., North Chicago, IL, 60064, USA
| | - C Brent Putman
- AbbVie Inc., 1 North Waukegan Rd., North Chicago, IL, 60064, USA
| | - Stevan J Kakavas
- AbbVie Inc., 1 North Waukegan Rd., North Chicago, IL, 60064, USA
| | | | - Heath A McDonald
- AbbVie Inc., 1 North Waukegan Rd., North Chicago, IL, 60064, USA
| | - Joseph B Wetter
- AbbVie Inc., 1 North Waukegan Rd., North Chicago, IL, 60064, USA
| | | | - Qi Sun
- AbbVie Inc., 1 North Waukegan Rd., North Chicago, IL, 60064, USA
| | - Clare E Gerstein
- AbbVie Inc., 1 North Waukegan Rd., North Chicago, IL, 60064, USA
| | - Limary Medina
- AbbVie Bioresearch Center, 381 Plantation St., Worcester, MA, 01605, USA
| | - Bernhard Sielaff
- AbbVie Bioresearch Center, 381 Plantation St., Worcester, MA, 01605, USA
| | | | | | | | - Wei Qiu
- AbbVie Inc., 1 North Waukegan Rd., North Chicago, IL, 60064, USA
| | - Maria A Argiriadi
- AbbVie Bioresearch Center, 381 Plantation St., Worcester, MA, 01605, USA
| | - Rodger F Henry
- AbbVie Inc., 1 North Waukegan Rd., North Chicago, IL, 60064, USA
| | - J Martin Herold
- AbbVie Bioresearch Center, 381 Plantation St., Worcester, MA, 01605, USA
| | - J Brad Shotwell
- AbbVie Inc., 1 North Waukegan Rd., North Chicago, IL, 60064, USA
| | | | - Prisca Honore
- AbbVie Inc., 1 North Waukegan Rd., North Chicago, IL, 60064, USA
| | | | - Chaohong C Sun
- AbbVie Inc., 1 North Waukegan Rd., North Chicago, IL, 60064, USA
| | - Victoria E Scott
- AbbVie Inc., 1 North Waukegan Rd., North Chicago, IL, 60064, USA.
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33
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Zhang XH, Nam S, Wu J, Chen CH, Liu X, Li H, McKeithan T, Gong Q, Chan WC, Yin HH, Yuan YC, Pillai R, Querfeld C, Horne D, Chen Y, Rosen ST. Multi-Kinase Inhibitor with Anti-p38γ Activity in Cutaneous T-Cell Lymphoma. J Invest Dermatol 2018; 138:2377-2387. [PMID: 29758280 PMCID: PMC7269016 DOI: 10.1016/j.jid.2018.04.030] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 03/21/2018] [Accepted: 04/08/2018] [Indexed: 11/19/2022]
Abstract
Current cutaneous T-cell lymphoma (CTCL) therapies are marked by an abbreviated response, subsequent drug resistance, and poor prognosis for patients with advanced disease. An understanding of molecular regulators involved in CTCL is needed to develop effective targeted therapies. One candidate regulator is p38γ, a mitogen-activated protein kinase crucial for malignant T-cell activity and growth. p38γ gene expression is selectively increased in CTCL patient samples and cell lines but not in healthy T cells. In addition, gene silencing of p38γ reduced CTCL cell viability, showing a key role in CTCL pathogenesis. Screening p38γ inhibitors is critical for understanding the mechanism of CTCL tumorigenesis and developing therapeutic applications. We prioritized a potent p38γ inhibitor (F7, also known as PIK75) through a high-throughput kinase inhibitor screen. At nanomolar concentrations, PIK75, a multiple kinase inhibitor, selectively killed CD4+ malignant CTCL cells but spared healthy CD4+ cells; induced significant reduction of tumor size in mouse xenografts; and effectively inhibited p38γ enzymatic activity and phosphorylation of its substrate, DLGH1, in CTCL cells and mouse xenografts. Here, we report that PIK75 has a potential clinical application to serve as a scaffold molecule for the development of a more selective p38γ inhibitor.
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Affiliation(s)
- Xu Hannah Zhang
- Department of Hematology, City of Hope National Medical Center, Duarte, California, USA
| | - Sangkil Nam
- High-Throughput Screening Core, City of Hope National Medical Center, Duarte, California, USA
| | - Jun Wu
- Animal Tumor Models Core, City of Hope National Medical Center, Duarte, California, USA
| | - Chih-Hong Chen
- Department of Molecular Medicine, City of Hope National Medical Center, Duarte, California, USA
| | - Xuxiang Liu
- Department of Pathology, City of Hope National Medical Center, Duarte, California, USA; Computational Therapeutics Core, City of Hope National Medical Center, Duarte, California, USA
| | - Hongzhi Li
- Bioinformatics Core, City of Hope National Medical Center, Duarte, California, USA
| | - Timothy McKeithan
- Department of Pathology, City of Hope National Medical Center, Duarte, California, USA
| | - Qiang Gong
- Department of Pathology, City of Hope National Medical Center, Duarte, California, USA
| | - Wing C Chan
- Department of Pathology, City of Hope National Medical Center, Duarte, California, USA
| | - Hongwei Holly Yin
- Department of Pathology, City of Hope National Medical Center, Duarte, California, USA
| | - Yate-Ching Yuan
- Synthetic and Biopolymer Chemistry Core, City of Hope National Medical Center, Duarte, California, USA
| | - Raju Pillai
- Department of Pathology, City of Hope National Medical Center, Duarte, California, USA
| | - Christiane Querfeld
- Department of Pathology, City of Hope National Medical Center, Duarte, California, USA
| | - David Horne
- Irell & Manella Graduate School of Biological Sciences and Beckman Research Institute, City of Hope National Medical Center, Duarte, California, USA
| | - Yuan Chen
- Department of Molecular Medicine, City of Hope National Medical Center, Duarte, California, USA
| | - Steven T Rosen
- Department of Hematology, City of Hope National Medical Center, Duarte, California, USA.
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34
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Watari A, Kodaka M, Matsuhisa K, Sakamoto Y, Hisaie K, Kawashita N, Takagi T, Yamagishi Y, Suzuki H, Tsujino H, Yagi K, Kondoh M. Identification of claudin-4 binder that attenuates tight junction barrier function by TR-FRET-based screening assay. Sci Rep 2017; 7:14514. [PMID: 29109448 PMCID: PMC5674027 DOI: 10.1038/s41598-017-15108-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 10/20/2017] [Indexed: 12/14/2022] Open
Abstract
Claudins are key functional and structural components of tight junctions (TJs) in epithelial cell sheets. The C-terminal fragment of Clostridium perfringens enterotoxin (C-CPE) binds to claudin-4 and reversibly modulates intestinal TJ seals, thereby enhancing paracellular transport of solutes. However, the use of C-CPE as an absorption enhancer is limited by the molecule’s immunogenicity and manufacturing cost. Here, we developed a high-throughput screening system based on the Time-Resolved Fluorescence Resonance Energy Transfer (TR-FRET) method to identify claudin-4 binders in a library collection of 32,560 compounds. Thiostrepton, identified from the screen, decreased transepithelial electrical resistance and increased flux of 4-kDa fluorescein isothiocyanate–labelled dextran (FD-4) in Caco-2 cell monolayers, a model of intestinal epithelium. Thiostrepton changed the expression, but not the localisation, of TJ components. Treatment of rat jejunum with thiostrepton increased the absorption of FD-4 without tissue toxicity, indicating that thiostrepton is a novel claudin-4 binder that enhances intestinal permeability. The screening system may therefore be a useful tool for identifying claudin-4 binders to enhance drug absorption in mucosa.
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Affiliation(s)
- Akihiro Watari
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Miki Kodaka
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Koji Matsuhisa
- Department of Stress Protein Processing, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Yuta Sakamoto
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kota Hisaie
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Norihito Kawashita
- Faculty of Science and Engineering, Kindai University 3-4-1 Kowakae, Higashiosaka City, Osaka, 577-8502, Japan
| | - Tatsuya Takagi
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Research Institute for Microbial Diseases, Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yoshiaki Yamagishi
- Research Institute of Pharmaceutical Sciences, Musashino University, 1-1-20 Shinmachi, Nishi-Tokyo, 202-8585, Japan
| | - Hidehiko Suzuki
- Laboratory of Vaccine Materials and Laboratory of Gut Environmental System, National Institutes of Biomedical Innovation, Health and Nutrition (NIBIOHN), Osaka, 567-0085, Japan
| | - Hirofumi Tsujino
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kiyohito Yagi
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Masuo Kondoh
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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35
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A novel family of mammalian transmembrane proteins involved in cholesterol transport. Sci Rep 2017; 7:7450. [PMID: 28785058 PMCID: PMC5547113 DOI: 10.1038/s41598-017-07077-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 06/22/2017] [Indexed: 11/20/2022] Open
Abstract
Cholesterol is an essential compound in mammalian cells because it is involved in a wide range of functions, including as a key component of membranes, precursor of important molecules such as hormones, bile acids and vitamin D. The cholesterol transport across the circulatory system is a well-known process in contrast to the intracellular cholesterol transport, which is poorly understood. Recently in our laboratory, we identified a novel protein in C. elegans involved in dietary cholesterol uptake, which we have named ChUP-1. Insillicoanalysis identified two putative orthologue candidate proteins in mammals. The proteins SIDT1 and SIDT2 share identity and conserved cholesterol binding (CRAC) domains with C. elegans ChUP-1. Both mammalian proteins are annotated as RNA transporters in databases. In the present study, we show evidence indicating that SIDT1 and SIDT2 not only do not transport RNA, but they are involved in cholesterol transport. Furthermore, we show that single point mutations directed to disrupt the CRAC domains of both proteins prevent FRET between SIDT1 and SIDT2 and the cholesterol analogue dehydroergosterol (DHE) and alter cholesterol transport.
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36
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Gul S. Epigenetic assays for chemical biology and drug discovery. Clin Epigenetics 2017; 9:41. [PMID: 28439316 PMCID: PMC5399855 DOI: 10.1186/s13148-017-0342-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2016] [Accepted: 04/12/2017] [Indexed: 12/27/2022] Open
Abstract
The implication of epigenetic abnormalities in many diseases and the approval of a number of compounds that modulate specific epigenetic targets in a therapeutically relevant manner in cancer specifically confirms that some of these targets are druggable by small molecules. Furthermore, a number of compounds are currently in clinical trials for other diseases including cardiovascular, neurological and metabolic disorders. Despite these advances, the approved treatments for cancer only extend progression-free survival for a relatively short time and being associated with significant side effects. The current clinical trials involving the next generation of epigenetic drugs may address the disadvantages of the currently approved epigenetic drugs. The identification of chemical starting points of many drugs often makes use of screening in vitro assays against libraries of synthetic or natural products. These assays can be biochemical (using purified protein) or cell-based (using for example, genetically modified, cancer cell lines or primary cells) and performed in microtiter plates, thus enabling a large number of samples to be tested. A considerable number of such assays are available to monitor epigenetic target activity, and this review provides an overview of drug discovery and chemical biology and describes assays that monitor activities of histone deacetylase, lysine-specific demethylase, histone methyltransferase, histone acetyltransferase and bromodomain. It is of critical importance that an appropriate assay is developed and comprehensively validated for a given drug target prior to screening in order to improve the probability of the compound progressing in the drug discovery value chain.
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Affiliation(s)
- Sheraz Gul
- Fraunhofer Institute for Molecular Biology and Applied Ecology - ScreeningPort, Schnackenburgallee 114, 22525 Hamburg, Germany
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