1
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Wang Z, Thakare RP, Chitale S, Mishra AK, Goldstein SI, Fan AC, Li R, Zhu LJ, Brown LE, Cencic R, Huang S, Green MR, Pelletier J, Malonia SK, Porco JA. Identification of Rocaglate Acyl Sulfamides as Selective Inhibitors of Glioblastoma Stem Cells. ACS CENTRAL SCIENCE 2024; 10:1640-1656. [PMID: 39220711 PMCID: PMC11363328 DOI: 10.1021/acscentsci.4c01073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2024] [Revised: 07/22/2024] [Accepted: 07/23/2024] [Indexed: 09/04/2024]
Abstract
Glioblastoma (GBM) is the most aggressive and frequently occurring type of malignant brain tumor in adults. The initiation, progression, and recurrence of malignant tumors are known to be driven by a small subpopulation of cells known as tumor-initiating cells or cancer stem cells (CSCs). GBM CSCs play a pivotal role in orchestrating drug resistance and tumor relapse. As a prospective avenue for GBM intervention, the targeted suppression of GBM CSCs holds considerable promise. In this study, we found that rocaglates, compounds which are known to inhibit translation via targeting of the DEAD-box helicase eIF4A, exert a robust, dose-dependent cytotoxic impact on GBM CSCs with minimal killing of nonstem GBM cells. Subsequent optimization identified novel rocaglate derivatives (rocaglate acyl sulfamides or Roc ASFs) that selectively inhibit GBM CSCs with nanomolar EC50 values. Furthermore, comparative evaluation of a lead CSC-optimized Roc ASF across diverse mechanistic and target profiling assays revealed suppressed translation inhibition relative to that of other CSC-selective rocaglates, with enhanced targeting of the DEAD-box helicase DDX3X, a recently identified secondary target of rocaglates. Overall, these findings suggest a promising therapeutic strategy for targeting GBM CSCs.
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Affiliation(s)
- Zihao Wang
- Department
of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Ritesh P. Thakare
- Department
of Molecular, Cell and Cancer Biology, University
of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States
| | - Shalaka Chitale
- Department
of Molecular, Cell and Cancer Biology, University
of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States
| | - Alok K. Mishra
- Department
of Molecular, Cell and Cancer Biology, University
of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States
| | - Stanley I. Goldstein
- Boston
University Target Discovery Laboratory (BU-TDL), Boston, Massachusetts 02215, United States
- Department
of Pharmacology, Physiology, and Biophysics, Boston University, Boston, Massachusetts 02118, United States
| | - Alice C. Fan
- Department
of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Boston
University Target Discovery Laboratory (BU-TDL), Boston, Massachusetts 02215, United States
| | - Rui Li
- Department
of Molecular, Cell and Cancer Biology, University
of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States
- Department
of Molecular Medicine and Program in Bioinformatics and Integrative
Biology, University of Massachusetts Chan
Medical School, Worcester, Massachusetts 01605, United States
| | - Lihua Julie Zhu
- Department
of Molecular, Cell and Cancer Biology, University
of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States
- Department
of Molecular Medicine and Program in Bioinformatics and Integrative
Biology, University of Massachusetts Chan
Medical School, Worcester, Massachusetts 01605, United States
| | - Lauren E. Brown
- Department
of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
| | - Regina Cencic
- Department
of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Sidong Huang
- Department
of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Michael R. Green
- Department
of Molecular, Cell and Cancer Biology, University
of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States
| | - Jerry Pelletier
- Department
of Biochemistry, McGill University, Montreal, QC H3G 1Y6, Canada
| | - Sunil K. Malonia
- Department
of Molecular, Cell and Cancer Biology, University
of Massachusetts Chan Medical School, Worcester, Massachusetts 01605, United States
| | - John A. Porco
- Department
of Chemistry and Center for Molecular Discovery (BU-CMD), Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
- Boston
University Target Discovery Laboratory (BU-TDL), Boston, Massachusetts 02215, United States
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2
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Capener JL, Vasta JD, Katis VL, Michaud A, Beck MT, Daglish SCD, Cohen-Kedar S, Barda ES, Howell S, Dotan I, Robers MB, Axtman AD, Bashore FM. Development of SYK NanoBRET Cellular Target Engagement Assays for Gain-of-Function Variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.12.598544. [PMID: 38915605 PMCID: PMC11195201 DOI: 10.1101/2024.06.12.598544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Spleen tyrosine kinase (SYK) is a non-receptor tyrosine kinase that is activated by phosphorylation events downstream of FcR, B-cell and T-cell receptors, integrins, and C-type lectin receptors. When the tandem Src homology 2 (SH2) domains of SYK bind to phosphorylated immunoreceptor tyrosine-based activation motifs (pITAMs) contained within these immunoreceptors, or when SYK is phosphorylated in interdomain regions A and B, SYK is activated. SYK gain-of-function (GoF) variants were previously identified in six patients that had higher levels of phosphorylated SYK and phosphorylated downstream proteins JNK and ERK. Furthermore, the increased SYK activation resulted in the clinical manifestation of immune dysregulation, organ inflammation, and a predisposition for lymphoma. The knowledge that the SYK GoF variants have enhanced activity was leveraged to develop a SYK NanoBRET cellular target engagement assay in intact live cells with constructs for the SYK GoF variants. Herein, we developed a potent SYK-targeted NanoBRET tracer using a SYK donated chemical probe, MRL-SYKi, that enabled a NanoBRET cellular target engagement assay for SYK GoF variants, SYK(S550Y), SYK(S550F), and SYK(P342T). We determined that ATP-competitive SYK inhibitors bind potently to these SYK variants in intact live cells. Additionally, we demonstrated that MRL-SYKi can effectively reduce the catalytic activity of SYK variants, and the phosphorylation levels of SYK(S550Y) in an epithelial cell line (SW480) stably expressing SYK(S550Y).
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Affiliation(s)
- Jacob L. Capener
- Structural Genomics Consortium, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - James D. Vasta
- Promega Corporation, 2800 Woods Hollow Road, Madison, WI 53711, USA
| | - Vittorio L. Katis
- ARUK Oxford Drug Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, UK
| | - Ani Michaud
- Promega Corporation, 2800 Woods Hollow Road, Madison, WI 53711, USA
| | - Michael T. Beck
- Promega Corporation, 2800 Woods Hollow Road, Madison, WI 53711, USA
| | - Sabrina C. D. Daglish
- Structural Genomics Consortium, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Sarit Cohen-Kedar
- Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, Israel
- Felsenstein Medical Research Center, Faculty of Medical & Health Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Efrat Shaham Barda
- Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, Israel
- Felsenstein Medical Research Center, Faculty of Medical & Health Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | - Stefanie Howell
- Structural Genomics Consortium, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Iris Dotan
- Division of Gastroenterology, Rabin Medical Center, Petah-Tikva, Israel
- Felsenstein Medical Research Center, Faculty of Medical & Health Sciences, Tel-Aviv University, Tel-Aviv, Israel
| | | | - Alison D. Axtman
- Structural Genomics Consortium, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Frances M. Bashore
- Structural Genomics Consortium, Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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3
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Hoare BL, Tippett DN, Kaur A, Cullum SA, Miljuš T, Koers EJ, Harwood CR, Dijon N, Holliday ND, Sykes DA, Veprintsev DB. ThermoBRET: A Ligand-Engagement Nanoscale Thermostability Assay Applied to GPCRs. Chembiochem 2024; 25:e202300459. [PMID: 37872746 DOI: 10.1002/cbic.202300459] [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: 06/22/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 10/25/2023]
Abstract
Measurements of membrane protein thermostability reflect ligand binding. Current thermostability assays often require protein purification or rely on pre-existing radiolabelled or fluorescent ligands, limiting their application to established targets. Alternative methods, such as fluorescence-detection size exclusion chromatography thermal shift, detect protein aggregation but are not amenable to high-throughput screening. Here, we present a ThermoBRET method to quantify the relative thermostability of G protein coupled receptors (GPCRs), using cannabinoid receptors (CB1 and CB2 ) and the β2 -adrenoceptor (β2 AR) as model systems. ThermoBRET reports receptor unfolding, does not need labelled ligands and can be used with non-purified proteins. It uses Bioluminescence Resonance Energy Transfer (BRET) between Nanoluciferase (Nluc) and a thiol-reactive fluorescent dye that binds cysteines exposed by unfolding. We demonstrate that the melting point (Tm ) of Nluc-fused GPCRs can be determined in non-purified detergent solubilised membrane preparations or solubilised whole cells, revealing differences in thermostability for different solubilising conditions and in the presence of stabilising ligands. We extended the range of the assay by developing the thermostable tsNLuc by incorporating mutations from the fragments of split-Nluc (Tm of 87 °C versus 59 °C). ThermoBRET allows the determination of GPCR thermostability, which is useful for protein purification optimisation and drug discovery screening.
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Affiliation(s)
- Bradley L Hoare
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
- Current address, Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC 3052, Australia
| | - David N Tippett
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
- Current address, Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Amandeep Kaur
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Sean A Cullum
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Tamara Miljuš
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
- Institute of Metabolism and Systems Research, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Eline J Koers
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Clare R Harwood
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Nicola Dijon
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Nicholas D Holliday
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - David A Sykes
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
| | - Dmitry B Veprintsev
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, Midlands, UK
- Division of Physiology, Pharmacology & Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, NG7 2UH, UK
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4
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Mahran R, Vello N, Komulainen A, Malakoutikhah M, Härmä H, Kopra K. Isothermal chemical denaturation assay for monitoring protein stability and inhibitor interactions. Sci Rep 2023; 13:20066. [PMID: 37973851 PMCID: PMC10654576 DOI: 10.1038/s41598-023-46720-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 11/03/2023] [Indexed: 11/19/2023] Open
Abstract
Thermal shift assay (TSA) with altered temperature has been the most widely used method for monitoring protein stability for drug research. However, there is a pressing need for isothermal techniques as alternatives. This urgent demand arises from the limitations of TSA, which can sometimes provide misleading ranking of protein stability and fail to accurately reflect protein stability under physiological conditions. Although differential scanning fluorimetry has significantly improved throughput in comparison to differential scanning calorimetry and differential static light scattering throughput, all these methods exhibit moderate sensitivity. In contrast, current isothermal chemical denaturation (ICD) techniques may not offer the same throughput capabilities as TSA, but it provides more precise information about protein stability and interactions. Unfortunately, ICD also suffers from limited sensitivity, typically in micromolar range. We have developed a novel method to overcome these challenges, namely throughput and sensitivity. The novel Förster Resonance Energy Transfer (FRET)-Probe as an external probe is highly applicable to isothermal protein stability monitoring but also to conventional TSA. We have investigated ICD for multiple proteins with focus on KRASG12C with covalent inhibitors and three chemical denaturants performed at nanomolar protein concentration. Data showed corresponding inhibitor-induced stabilization of KRASG12C to those reported by nucleotide exchange assay.
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Affiliation(s)
- Randa Mahran
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland.
| | - Niklas Vello
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
| | - Anita Komulainen
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
| | | | - Harri Härmä
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
| | - Kari Kopra
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500, Turku, Finland
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5
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Ramachandran S, Makukhin N, Haubrich K, Nagala M, Forrester B, Lynch DM, Casement R, Testa A, Bruno E, Gitto R, Ciulli A. Structure-based design of a phosphotyrosine-masked covalent ligand targeting the E3 ligase SOCS2. Nat Commun 2023; 14:6345. [PMID: 37816714 PMCID: PMC10564737 DOI: 10.1038/s41467-023-41894-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 09/14/2023] [Indexed: 10/12/2023] Open
Abstract
The Src homology 2 (SH2) domain recognizes phosphotyrosine (pY) post translational modifications in partner proteins to trigger downstream signaling. Drug discovery efforts targeting the SH2 domains have long been stymied by the poor drug-like properties of phosphate and its mimetics. Here, we use structure-based design to target the SH2 domain of the E3 ligase suppressor of cytokine signaling 2 (SOCS2). Starting from the highly ligand-efficient pY amino acid, a fragment growing approach reveals covalent modification of Cys111 in a co-crystal structure, which we leverage to rationally design a cysteine-directed electrophilic covalent inhibitor MN551. We report the prodrug MN714 containing a pivaloyloxymethyl (POM) protecting group and evidence its cell permeability and capping group unmasking using cellular target engagement and in-cell 19F NMR spectroscopy. Covalent engagement at Cys111 competitively blocks recruitment of cellular SOCS2 protein to its native substrate. The qualified inhibitors of SOCS2 could find attractive applications as chemical probes to understand the biology of SOCS2 and its CRL5 complex, and as E3 ligase handles in proteolysis targeting chimera (PROTACs) to induce targeted protein degradation.
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Affiliation(s)
- Sarath Ramachandran
- Centre for Targeted Protein Degradation, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee, DD1 5JJ, United Kingdom
| | - Nikolai Makukhin
- Centre for Targeted Protein Degradation, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee, DD1 5JJ, United Kingdom
- Amphista Therapeutics Ltd, Cory Building, Granta Park, Great Abington, Cambridge, CB21 6GQ, United Kingdom
| | - Kevin Haubrich
- Centre for Targeted Protein Degradation, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee, DD1 5JJ, United Kingdom
| | - Manjula Nagala
- Centre for Targeted Protein Degradation, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee, DD1 5JJ, United Kingdom
| | - Beth Forrester
- Centre for Targeted Protein Degradation, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee, DD1 5JJ, United Kingdom
| | - Dylan M Lynch
- Centre for Targeted Protein Degradation, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee, DD1 5JJ, United Kingdom
| | - Ryan Casement
- Centre for Targeted Protein Degradation, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee, DD1 5JJ, United Kingdom
| | - Andrea Testa
- Centre for Targeted Protein Degradation, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee, DD1 5JJ, United Kingdom
- Amphista Therapeutics Ltd, Cory Building, Granta Park, Great Abington, Cambridge, CB21 6GQ, United Kingdom
| | - Elvira Bruno
- Centre for Targeted Protein Degradation, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee, DD1 5JJ, United Kingdom
| | - Rosaria Gitto
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, Viale Stagno D'Alcontres 31, Pole Papardo, 98166, Messina, Italy
| | - Alessio Ciulli
- Centre for Targeted Protein Degradation, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee, DD1 5JJ, United Kingdom.
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6
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Llowarch P, Usselmann L, Ivanov D, Holdgate GA. Thermal unfolding methods in drug discovery. BIOPHYSICS REVIEWS 2023; 4:021305. [PMID: 38510342 PMCID: PMC10903397 DOI: 10.1063/5.0144141] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 04/13/2023] [Indexed: 03/22/2024]
Abstract
Thermal unfolding methods, applied in both isolated protein and cell-based settings, are increasingly used to identify and characterize hits during early drug discovery. Technical developments over recent years have facilitated their application in high-throughput approaches, and they now are used more frequently for primary screening. Widespread access to instrumentation and automation, the ability to miniaturize, as well as the capability and capacity to generate the appropriate scale and quality of protein and cell reagents have all played a part in these advances. As the nature of drug targets and approaches to their modulation have evolved, these methods have broadened our ability to provide useful chemical start points. Target proteins without catalytic function, or those that may be difficult to express and purify, are amenable to these methods. Here, we provide a review of the applications of thermal unfolding methods applied in hit finding during early drug discovery.
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Affiliation(s)
- Poppy Llowarch
- High Throughput Screening, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, United Kingdom
| | - Laura Usselmann
- High Throughput Screening, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, United Kingdom
| | - Delyan Ivanov
- High Throughput Screening, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, United Kingdom
| | - Geoffrey A. Holdgate
- High Throughput Screening, Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Alderley Park, United Kingdom
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7
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Tu Y, Tan L, Tao H, Li Y, Liu H. CETSA and thermal proteome profiling strategies for target identification and drug discovery of natural products. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 116:154862. [PMID: 37216761 DOI: 10.1016/j.phymed.2023.154862] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/21/2023] [Accepted: 05/04/2023] [Indexed: 05/24/2023]
Abstract
BACKGROUND Monitoring target engagement at various stages of drug development is essential for natural product (NP)-based drug discovery and development. The cellular thermal shift assay (CETSA) developed in 2013 is a novel, broadly applicable, label-free biophysical assay based on the principle of ligand-induced thermal stabilization of target proteins, which enables direct assessment of drug-target engagement in physiologically relevant contexts, including intact cells, cell lysates and tissues. This review aims to provide an overview of the work principles of CETSA and its derivative strategies and their recent progress in protein target validation, target identification and drug lead discovery of NPs. METHODS A literature-based survey was conducted using the Web of Science and PubMed databases. The required information was reviewed and discussed to highlight the important role of CETSA-derived strategies in NP studies. RESULTS After nearly ten years of upgrading and evolution, CETSA has been mainly developed into three formats: classic Western blotting (WB)-CETSA for target validation, thermal proteome profiling (TPP, also known as MS-CETSA) for unbiased proteome-wide target identification, and high-throughput (HT)-CETSA for drug hit discovery and lead optimization. Importantly, the application possibilities of a variety of TPP approaches for the target discovery of bioactive NPs are highlighted and discussed, including TPP-temperature range (TPP-TR), TPP-compound concentration range (TPP-CCR), two-dimensional TPP (2D-TPP), cell surface-TPP (CS-TPP), simplified TPP (STPP), thermal stability shift-based fluorescence difference in 2D gel electrophoresis (TS-FITGE) and precipitate supported TPP (PSTPP). In addition, the key advantages, limitations and future outlook of CETSA strategies for NP studies are discussed. CONCLUSION The accumulation of CETSA-based data can significantly accelerate the elucidation of the mechanism of action and drug lead discovery of NPs, and provide strong evidence for NP treatment against certain diseases. The CETSA strategy will certainly bring a great return far beyond the initial investment and open up more possibilities for future NP-based drug research and development.
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Affiliation(s)
- Yanbei Tu
- School of Pharmacy, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Lihua Tan
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Taipa, Macao SAR 999078, China
| | - Hongxun Tao
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, Jiangsu 212013, China
| | - Yanfang Li
- School of Chemical Engineering, Sichuan University, Chengdu, Sichuan 610065, China.
| | - Hanqing Liu
- School of Pharmacy, Jiangsu University, Zhenjiang, Jiangsu 212013, China.
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8
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Gricajeva A, Kalėdienė L. Investigation of amino acids related to Staphylococcus saprophyticus AG1 EstAG1 carboxylesterase catalytic function revealed a new family of bacterial lipolytic enzymes. Int J Biol Macromol 2023; 235:123791. [PMID: 36828093 DOI: 10.1016/j.ijbiomac.2023.123791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/07/2023] [Accepted: 02/17/2023] [Indexed: 02/24/2023]
Abstract
Most of the lipolytic enzymes (carboxylesterases, EC 3.1.1.1 and triacylglycerol acylhydrolases, EC 3.1.1.3) originate from bacteria and form a large group of functionally important enzymes that are also well known for their use in multiple biotechnology sectors. Rapid and increasing amount of bacterial lipolytic enzymes being discovered and characterized led to a necessity to classify them. More than twenty years ago bacterial lipolytic enzymes were originally classified into eight families and six true lipase sub-families based on the differences in their amino acid sequences and biochemical properties. Later, this classification was comprehensively updated to 19 families with eight subfamilies, and more recently, employing deeper comparative analysis methods, classification expanded to 35 families and 11 subfamilies. Bacterial lipolytic enzymes that cannot be classified into currently existing families are still being discovered. This work provides site-directed mutagenesis and differential scanning fluorimetry based investigation of catalytic function-related amino acids of previously discovered and characterized EstAG1 carboxylesterase from Staphylococcus saprophyticus AG1. Experimental results obtained in this work revealed that EstAG1 carboxylesterase can be placed into a new family of bacterial lipolytic enzymes.
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Affiliation(s)
- Alisa Gricajeva
- Department of Microbiology and Biotechnology, Institute of Biosciences, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257 Vilnius, Lithuania.
| | - Lilija Kalėdienė
- Department of Microbiology and Biotechnology, Institute of Biosciences, Life Sciences Center, Vilnius University, Sauletekio av. 7, LT-10257 Vilnius, Lithuania
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9
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Han YN, Lambert LJ, De Backer LJS, Wu J, Cosford NDP, Tautz L. Detection of Cellular Target Engagement for Small-Molecule Modulators of Striatal-Enriched Protein Tyrosine Phosphatase (STEP). Methods Mol Biol 2023; 2706:167-175. [PMID: 37558948 PMCID: PMC10956569 DOI: 10.1007/978-1-0716-3397-7_12] [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: 08/11/2023]
Abstract
Striatal-enriched protein tyrosine phosphatase (STEP) is a brain-specific enzyme that regulates the signaling molecules that control synaptic plasticity and neuronal function. Dysregulation of STEP is linked to the pathophysiology of Alzheimer's disease and other neuropsychiatric disorders. Experimental results from neurological deficit disease models suggest that the modulation of STEP could be beneficial in a number of these disorders. This prompted our work to identify small-molecule modulators of STEP to provide the foundation of a drug discovery program. As a component of our testing funnel to identify small-molecule STEP inhibitors, we have developed a cellular target engagement assay that can identify compounds that interact with STEP46. We provide a comprehensive protocol to enable the use of this miniaturized assay, and we demonstrate its utility to benchmark the binding of newly discovered compounds.
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Affiliation(s)
- Ye Na Han
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Lester J Lambert
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Laurent J S De Backer
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Jiaqian Wu
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Nicholas D P Cosford
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Lutz Tautz
- NCI-Designated Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
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10
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Sabatier P, Beusch CM, Meng Z, Zubarev RA. System-Wide Profiling by Proteome Integral Solubility Alteration Assay of Drug Residence Times for Target Characterization. Anal Chem 2022; 94:15772-15780. [DOI: 10.1021/acs.analchem.2c03506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Pierre Sabatier
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm17177, Sweden
- Department of Surgical Sciences, Uppsala University, Uppsala751 85, Sweden
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Copenhagen2200, Denmark
| | - Christian M. Beusch
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm17177, Sweden
| | - Zhaowei Meng
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm17177, Sweden
| | - Roman A. Zubarev
- Division of Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm17177, Sweden
- Department of Pharmacological & Technological Chemistry, I.M. Sechenov First Moscow State Medical University, Moscow119146, Russia
- The National Medical Research Center for Endocrinology, Moscow115478, Russia
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11
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Ding Y, Xing D, Fei Y, Lu B. Emerging degrader technologies engaging lysosomal pathways. Chem Soc Rev 2022; 51:8832-8876. [PMID: 36218065 PMCID: PMC9620493 DOI: 10.1039/d2cs00624c] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Indexed: 08/24/2023]
Abstract
Targeted protein degradation (TPD) provides unprecedented opportunities for drug discovery. While the proteolysis-targeting chimera (PROTAC) technology has already entered clinical trials and changed the landscape of small-molecule drugs, new degrader technologies harnessing alternative degradation machineries, especially lysosomal pathways, have emerged and broadened the spectrum of degradable targets. We have recently proposed the concept of autophagy-tethering compounds (ATTECs) that hijack the autophagy protein microtubule-associated protein 1A/1B light chain 3 (LC3) for targeted degradation. Other groups also reported degrader technologies engaging lysosomal pathways through different mechanisms including AUTACs, AUTOTACs, LYTACs and MoDE-As. In this review, we analyse and discuss ATTECs along with other lysosomal-relevant degrader technologies. Finally, we will briefly summarize the current status of these degrader technologies and envision possible future studies.
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Affiliation(s)
- Yu Ding
- Neurology Department at Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, School of Life Sciences, Fudan University, Shanghai, China.
| | - Dong Xing
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai, China.
| | - Yiyan Fei
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Fudan University, Shanghai, China.
| | - Boxun Lu
- Neurology Department at Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, School of Life Sciences, Fudan University, Shanghai, China.
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12
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Sanchez TW, Ronzetti MH, Owens AE, Antony M, Voss T, Wallgren E, Talley D, Balakrishnan K, Leyes Porello SE, Rai G, Marugan JJ, Michael SG, Baljinnyam B, Southall N, Simeonov A, Henderson MJ. Real-Time Cellular Thermal Shift Assay to Monitor Target Engagement. ACS Chem Biol 2022; 17:2471-2482. [PMID: 36049119 PMCID: PMC9486815 DOI: 10.1021/acschembio.2c00334] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Determining a molecule's mechanism of action is paramount during chemical probe development and drug discovery. The cellular thermal shift assay (CETSA) is a valuable tool to confirm target engagement in cells for a small molecule that demonstrates a pharmacological effect. CETSA directly detects biophysical interactions between ligands and protein targets, which can alter a protein's unfolding and aggregation properties in response to thermal challenge. In traditional CETSA experiments, each temperature requires an individual sample, which restricts throughput and requires substantial optimization. To capture the full aggregation profile of a protein from a single sample, we developed a prototype real-time CETSA (RT-CETSA) platform by coupling a real-time PCR instrument with a CCD camera to detect luminescence. A thermally stable Nanoluciferase variant (ThermLuc) was bioengineered to withstand unfolding at temperatures greater than 90 °C and was compatible with monitoring target engagement events when fused to diverse targets. Utilizing well-characterized inhibitors of lactate dehydrogenase alpha, RT-CETSA showed significant correlation with enzymatic, biophysical, and other cell-based assays. A data analysis pipeline was developed to enhance the sensitivity of RT-CETSA to detect on-target binding. RT-CETSA technology advances capabilities of the CETSA method and facilitates the identification of ligand-target engagement in cells, a critical step in assessing the mechanism of action of a small molecule.
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13
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Vu V, Szewczyk MM, Nie DY, Arrowsmith CH, Barsyte-Lovejoy D. Validating Small Molecule Chemical Probes for Biological Discovery. Annu Rev Biochem 2022; 91:61-87. [PMID: 35363509 DOI: 10.1146/annurev-biochem-032620-105344] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Small molecule chemical probes are valuable tools for interrogating protein biological functions and relevance as a therapeutic target. Rigorous validation of chemical probe parameters such as cellular potency and selectivity is critical to unequivocally linking biological and phenotypic data resulting from treatment with a chemical probe to the function of a specific target protein. A variety of modern technologies are available to evaluate cellular potency and selectivity, target engagement, and functional response biomarkers of chemical probe compounds. Here, we review these technologies and the rationales behind using them for the characterization and validation of chemical probes. In addition, large-scale phenotypic characterization of chemical probes through chemical genetic screening is increasingly leading to a wealth of information on the cellular pharmacology and disease involvement of potential therapeutic targets. Extensive compound validation approaches and integration of phenotypic information will lay foundations for further use of chemical probes in biological discovery. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Victoria Vu
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada; .,Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Magdalena M Szewczyk
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada;
| | - David Y Nie
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada; .,Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada; .,Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Dalia Barsyte-Lovejoy
- Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada; .,Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
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14
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Owens AE, Iannotti MJ, Sanchez TW, Voss T, Kapoor A, Hall MD, Marugan JJ, Michael S, Southall N, Henderson MJ. High-Throughput Cellular Thermal Shift Assay Using Acoustic Transfer of Protein Lysates. ACS Chem Biol 2022; 17:322-330. [PMID: 35119255 PMCID: PMC10026039 DOI: 10.1021/acschembio.1c00760] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Cellular thermal shift assay (CETSA) is a valuable method to confirm target engagement within a complex cellular environment, by detecting changes in a protein's thermal stability upon ligand binding. The classical CETSA method measures changes in the thermal stability of endogenous proteins using immunoblotting, which is low-throughput and laborious. Reverse-phase protein arrays (RPPAs) have been demonstrated as a detection modality for CETSA; however, the reported procedure requires manual processing steps that limit throughput and preclude screening applications. We developed a high-throughput CETSA using an acoustic RPPA (HT-CETSA-aRPPA) protocol that is compatible with 96- and 384-well microplates from start-to-finish, using low speed centrifugation to remove thermally destabilized proteins. The utility of HT-CETSA-aRPPA for guiding structure-activity relationship studies was demonstrated for inhibitors of lactate dehydrogenase A. Additionally, a collection of kinase inhibitors was screened to identify compounds that engage MEK1, a clinically relevant kinase target.
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Affiliation(s)
- Ashley E. Owens
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, 20850, USA
| | - Michael J. Iannotti
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, 20850, USA
| | - Tino W. Sanchez
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, 20850, USA
| | - Ty Voss
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, 20850, USA
| | - Abhijeet Kapoor
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, 20850, USA
| | - Matthew D. Hall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, 20850, USA
| | - Juan J. Marugan
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, 20850, USA
| | - Sam Michael
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, 20850, USA
| | - Noel Southall
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, 20850, USA
| | - Mark J. Henderson
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, Maryland, 20850, USA
- Corresponding Author: Mark Henderson;
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15
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Mortison JD, Cornella-Taracido I, Venkatchalam G, Partridge AW, Siriwardana N, Bushell SM. Rapid Evaluation of Small Molecule Cellular Target Engagement with a Luminescent Thermal Shift Assay. ACS Med Chem Lett 2021; 12:1288-1294. [PMID: 34413958 DOI: 10.1021/acsmedchemlett.1c00276] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/07/2021] [Indexed: 12/13/2022] Open
Abstract
Determination of target engagement for candidate drug molecules in the native cellular environment is a significant challenge for drug discovery programs. The cellular thermal shift assay (CETSA) has emerged as a powerful tool for determining compound target engagement through measurement of changes to a protein's thermal stability upon ligand binding. Here, we present a HiBiT thermal shift assay (BiTSA) that deploys a quantitative peptide tag for determination of compound target engagement in the native cellular environment using a high throughput, plate-based luminescence readout. We demonstrate that BiTSA can rapidly assess cellular target engagement of small molecule ligands against their cognate targets and highlight two applications of BiTSA for differentiating small molecules targeting mutant KRAS and TP53.
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Affiliation(s)
| | | | | | | | | | - Simon M. Bushell
- Chemical Biology, Merck & Co., Inc., Boston, Massachusetts 02115, United States
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16
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Receptor tyrosine kinases and cancer: oncogenic mechanisms and therapeutic approaches. Oncogene 2021; 40:4079-4093. [PMID: 34079087 DOI: 10.1038/s41388-021-01841-2] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/29/2021] [Accepted: 05/13/2021] [Indexed: 02/05/2023]
Abstract
Receptor tyrosine kinases (RTKs) are transmembrane receptors of great clinical interest due to their role in disease, notably cancer. Since their discovery, several mechanisms of RTK dysregulation have been identified, resulting in multiple cancer types displaying 'oncogenic addiction' to RTKs. As a result, RTKs have represented a major class for targeted therapeutics over the past two decades, with numerous small molecule-based tyrosine kinase inhibitor (TKI) therapeutics having been developed and clinically approved for several cancers. However, many of the current RTK inhibitor treatments eventually result in the rapid development of acquired resistance and subsequent tumor relapse. Recent technological advances and tools are being generated for the identification of novel RTK small molecule therapeutics. These newer technologies will be important for the identification of diverse types of RTK inhibitors, targeting both the receptors themselves as well as key cellular factors that play important roles in the RTK signaling cascade.
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17
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Casement R, Bond A, Craigon C, Ciulli A. Mechanistic and Structural Features of PROTAC Ternary Complexes. Methods Mol Biol 2021; 2365:79-113. [PMID: 34432240 DOI: 10.1007/978-1-0716-1665-9_5] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The rapid and ever-growing advancements from within the field of proteolysis-targeting chimeras (PROTAC)-induced protein degradation have driven considerable development to gain a deeper understanding of their mode of action. The ternary complex formed by PROTACs with their target protein and E3 ubiquitin ligase is the key species in their substoichiometric catalytic mechanism. Here, we describe the theoretical framework that underpins ternary complexes, including a current understanding of the three-component binding model, cooperativity, hook effect and structural considerations. We discuss in detail the biophysical methods used to interrogate ternary complex formation in vitro, including X-ray crystallography, AlphaLISA, FRET, FP, ITC and SPR. Finally, we provide detailed ITC methods and discuss approaches to assess binary and ternary target engagement, target ubiquitination and degradation that can be used to obtain a more holistic understanding of the mode of action within a cellular environment.
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Affiliation(s)
- Ryan Casement
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, Scotland, UK
| | - Adam Bond
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, Scotland, UK
| | - Conner Craigon
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, Scotland, UK
| | - Alessio Ciulli
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, Scotland, UK.
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18
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Schirle M, Jenkins JL. Contemporary Techniques for Target Deconvolution and Mode of Action Elucidation. PHENOTYPIC DRUG DISCOVERY 2020. [DOI: 10.1039/9781839160721-00083] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The elucidation of the cellular efficacy target and mechanism of action of a screening hit remain key steps in phenotypic drug discovery. A large number of experimental and in silico approaches have been introduced to address these questions and are being discussed in this chapter with a focus on recent developments. In addition to practical considerations such as throughput and technological requirements, these approaches differ conceptually in the specific compound characteristic that they are focusing on, including physical and functional interactions, cellular response patterns as well as structural features. As a result, different approaches often provide complementary information and we describe a multipronged strategy that is frequently key to successful identification of the efficacy target but also other epistatic nodes and off-targets that together shape the overall cellular effect of a bioactive compound.
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Affiliation(s)
- Markus Schirle
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research Cambridge MA 02139 USA
| | - Jeremy L. Jenkins
- Chemical Biology and Therapeutics, Novartis Institutes for BioMedical Research Cambridge MA 02139 USA
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19
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Huang H, Howard CA, Zari S, Cho HJ, Shukla S, Li H, Ndoj J, González-Alonso P, Nikolaidis C, Abbott J, Rogawski DS, Potopnyk MA, Kempinska K, Miao H, Purohit T, Henderson A, Mapp A, Sulis ML, Ferrando A, Grembecka J, Cierpicki T. Covalent inhibition of NSD1 histone methyltransferase. Nat Chem Biol 2020; 16:1403-1410. [PMID: 32868895 PMCID: PMC7669657 DOI: 10.1038/s41589-020-0626-6] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 06/29/2020] [Indexed: 11/09/2022]
Abstract
The nuclear receptor-binding SET domain (NSD) family of histone methyltransferases is associated with various malignancies, including aggressive acute leukemia with NUP98-NSD1 translocation. While NSD proteins represent attractive drug targets, their catalytic SET domains exist in autoinhibited conformation, presenting notable challenges for inhibitor development. Here, we employed a fragment-based screening strategy followed by chemical optimization, which resulted in the development of the first-in-class irreversible small-molecule inhibitors of the nuclear receptor-binding SET domain protein 1 (NSD1) SET domain. The crystal structure of NSD1 in complex with covalently bound ligand reveals a conformational change in the autoinhibitory loop of the SET domain and formation of a channel-like pocket suitable for targeting with small molecules. Our covalent lead-compound BT5-demonstrates on-target activity in NUP98-NSD1 leukemia cells, including inhibition of histone H3 lysine 36 dimethylation and downregulation of target genes, and impaired colony formation in an NUP98-NSD1 patient sample. This study will facilitate the development of the next generation of potent and selective inhibitors of the NSD histone methyltransferases.
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Affiliation(s)
- Huang Huang
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Christina A Howard
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA
| | - Sergei Zari
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Hyo Je Cho
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Shirish Shukla
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Hao Li
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA
| | - Juliano Ndoj
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | | | | | - Joshua Abbott
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - David S Rogawski
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | | | | | - Hongzhi Miao
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Trupta Purohit
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Andrew Henderson
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Anna Mapp
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Maria Luisa Sulis
- Department of Pediatric Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Adolfo Ferrando
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
- Department of Systems Biology, Columbia University, New York, NY, USA
- Department of Pathology & Cell Biology, Columbia University, New York, NY, USA
- Department of Pediatrics, Columbia University, New York, NY, USA
| | - Jolanta Grembecka
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA.
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA.
| | - Tomasz Cierpicki
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA.
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI, USA.
- Department of Biophysics, University of Michigan, Ann Arbor, MI, USA.
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20
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Ding Y, Ball KA, Webb KJ, Gao Y, D'Alessandro A, Old WM, Stowell MHB, Ding X. On-Chip Acousto Thermal Shift Assay for Rapid and Sensitive Assessment of Protein Thermodynamic Stability. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e2003506. [PMID: 32893496 DOI: 10.1002/smll.202003506] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 08/12/2020] [Indexed: 06/11/2023]
Abstract
Thermal shift assays (TSAs) have been extensively used to study thermodynamics of proteins and provide an efficient means to assess protein-ligand binding or protein-protein interactions. However, existing TSAs have limitations, such as being time consuming, labor intensive, or having low sensitivity. Herein, an acousto thermal shift assay (ATSA), the first ultrasound enabled TSA, is reported for real-time analysis of protein thermodynamic stability. It capitalizes the coupling of unique acoustic mechanisms to achieve protein unfolding, concentration, and measurement on a single microfluidic chip within minutes. Compared to conventional TSA methods, the ATSA technique enables ultrafast (at least 30 times faster), highly sensitive (7-34 folds higher), and label-free monitoring of protein-ligand interactions and protein stability. ATSA paves new avenues for protein analysis in biology, medicine, and fast diagnosis.
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Affiliation(s)
- Yonghui Ding
- Paul M. Rady Department of Mechanical Engineering, University of Colorado, Boulder, CO, 80309, USA
| | - Kerri A Ball
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, 80309, USA
| | - Kristofor J Webb
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, 80309, USA
| | - Yu Gao
- Paul M. Rady Department of Mechanical Engineering, University of Colorado, Boulder, CO, 80309, USA
| | - Angelo D'Alessandro
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - William M Old
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, 80309, USA
| | - Michael H B Stowell
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, 80309, USA
| | - Xiaoyun Ding
- Paul M. Rady Department of Mechanical Engineering, University of Colorado, Boulder, CO, 80309, USA
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21
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Ansar S, Vetrivel U. KinomeRun: An interactive utility for kinome target screening and interaction fingerprint analysis towards holistic visualization on kinome tree. Chem Biol Drug Des 2020; 96:1162-1175. [PMID: 32418310 DOI: 10.1111/cbdd.13705] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/15/2020] [Accepted: 05/06/2020] [Indexed: 12/27/2022]
Abstract
Kinases are key targets for many of the pathological conditions. Inverse screening of ligands serves as an essential mode to identify potential kinase targets in modern drug discovery research. Hence, we intend to develop KinomeRun, a robust pipeline for inverse screening and kinome tree visualization through the seamless integration of kinome structures, docking and kinome-drug interaction fingerprint analysis. In this pipeline, the hurdle of residue numbering in kinome is also resolved by creating a common index file with the conserved kinase pocket residues for comparative interaction analysis. KinomeRun can be used to screen the ligands of interest docked against multiple kinase structures in parallel around the kinase binding site and also to filter out the targets with unique interaction patterns. This automation is essential for prioritization of kinase targets that show specificity for a given drug and will also serve as a crucial tool kit for holistic approaches in kinase drug discovery. KinomeRun is developed using python and bash programming language and is distributed freely under the GNU GPL licence-3.0 and can be downloaded at https://github.com/inpacdb/KinomeRun. The tutorial videos for installation, target screening and customized filtration are available at https://www.youtube.com/playlist?list=PLuIaEFtMVgQ7v__WigQH9ilGVxrfI1LKs and also be downloaded for offline viewing from the github link.
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Affiliation(s)
- Samdani Ansar
- Centre for Bioinformatics, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Sankara Nethralaya, Chennai, India.,School of Chemical and Biotechnology, SASTRA Deemed University, Thanjavur, India
| | - Umashankar Vetrivel
- Centre for Bioinformatics, Kamalnayan Bajaj Institute for Research in Vision and Ophthalmology, Vision Research Foundation, Sankara Nethralaya, Chennai, India.,National Institute of Traditional Medicine, Indian Council of Medical Research, Department of Health Research (Govt. of India), Belagavi, India
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22
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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: 32] [Impact Index Per Article: 8.0] [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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23
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Henderson MJ, Holbert MA, Simeonov A, Kallal LA. High-Throughput Cellular Thermal Shift Assays in Research and Drug Discovery. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2020; 25:137-147. [PMID: 31566060 PMCID: PMC10915787 DOI: 10.1177/2472555219877183] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Thermal shift assays (TSAs) can reveal changes in protein structure, due to a resultant change in protein thermal stability. Since proteins are often stabilized upon binding of ligand molecules, these assays can provide a readout for protein target engagement. TSA has traditionally been applied using purified proteins and more recently has been extended to study target engagement in cellular environments with the emergence of cellular thermal shift assays (CETSAs). The utility of CETSA in confirming molecular interaction with targets in a more native context, and the desire to apply this technique more broadly, has fueled the emergence of higher-throughput techniques for CETSA (HT-CETSA). Recent studies have demonstrated that HT-CETSA can be performed in standard 96-, 384-, and 1536-well microtiter plate formats using methods such as beta-galactosidase and NanoLuciferase reporters and AlphaLISA assays. HT-CETSA methods can be used to select and characterize compounds from high-throughput screens and to prioritize compounds in lead optimization by facilitating dose-response experiments. In conjunction with cellular and biochemical activity assays for targets, HT-CETSA can be a valuable addition to the suite of assays available to characterize molecules of interest. Despite the successes in implementing HT-CETSA for a diverse set of targets, caveats and challenges must also be recognized to avoid overinterpretation of results. Here, we review the current landscape of HT-CETSA and discuss the methodologies, practical considerations, challenges, and applications of this approach in research and drug discovery. Additionally, a perspective on potential future directions for the technology is presented.
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Affiliation(s)
- Mark J Henderson
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Marc A Holbert
- Protein, Cellular, & Structural Sciences, GlaxoSmithKline, Collegeville, PA, USA
| | - Anton Simeonov
- National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, USA
| | - Lorena A Kallal
- Screening, Profiling, and Mechanistic Biology, GlaxoSmithKline, Collegeville, PA, USA
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24
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Allali-Hassani A, Szewczyk MM, Ivanochko D, Organ SL, Bok J, Ho JSY, Gay FPH, Li F, Blazer L, Eram MS, Halabelian L, Dilworth D, Luciani GM, Lima-Fernandes E, Wu Q, Loppnau P, Palmer N, Talib SZA, Brown PJ, Schapira M, Kaldis P, O'Hagan RC, Guccione E, Barsyte-Lovejoy D, Arrowsmith CH, Sanders JM, Kattar SD, Bennett DJ, Nicholson B, Vedadi M. Discovery of a chemical probe for PRDM9. Nat Commun 2019; 10:5759. [PMID: 31848333 PMCID: PMC6917776 DOI: 10.1038/s41467-019-13652-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 11/15/2019] [Indexed: 12/14/2022] Open
Abstract
PRDM9 is a PR domain containing protein which trimethylates histone 3 on lysine 4 and 36. Its normal expression is restricted to germ cells and attenuation of its activity results in altered meiotic gene transcription, impairment of double-stranded breaks and pairing between homologous chromosomes. There is growing evidence for a role of aberrant expression of PRDM9 in oncogenesis and genome instability. Here we report the discovery of MRK-740, a potent (IC50: 80 ± 16 nM), selective and cell-active PRDM9 inhibitor (Chemical Probe). MRK-740 binds in the substrate-binding pocket, with unusually extensive interactions with the cofactor S-adenosylmethionine (SAM), conferring SAM-dependent substrate-competitive inhibition. In cells, MRK-740 specifically and directly inhibits H3K4 methylation at endogenous PRDM9 target loci, whereas the closely related inactive control compound, MRK-740-NC, does not. The discovery of MRK-740 as a chemical probe for the PRDM subfamily of methyltransferases highlights the potential for exploiting SAM in targeting SAM-dependent methyltransferases.
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Affiliation(s)
| | - Magdalena M Szewczyk
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Danton Ivanochko
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada.,Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 2M9, Canada
| | - Shawna L Organ
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Jabez Bok
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Jessica Sook Yuin Ho
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Florence P H Gay
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Fengling Li
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Levi Blazer
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Mohammad S Eram
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Levon Halabelian
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - David Dilworth
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Genna M Luciani
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | | | - Qin Wu
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Peter Loppnau
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Nathan Palmer
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - S Zakiah A Talib
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Peter J Brown
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada
| | - Matthieu Schapira
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, M5S 1A8, Canada
| | - Philipp Kaldis
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,National University of Singapore (NUS), Department of Biochemistry, 117597, Singapore, Singapore
| | - Ronan C O'Hagan
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033, USA
| | - Ernesto Guccione
- Institute of Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.,Department of Oncological Sciences and Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Department of Pharmacological Sciences and Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Dalia Barsyte-Lovejoy
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada.,Nature Research Center, Vilnius, Akademijos, 2, Lithuania
| | - Cheryl H Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada.,Princess Margaret Cancer Centre and Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 2M9, Canada
| | - John M Sanders
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033, USA
| | - Solomon D Kattar
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033, USA
| | | | - Benjamin Nicholson
- Merck & Co., Inc., 2000 Galloping Hill Road, Kenilworth, NJ, 07033, USA.
| | - Masoud Vedadi
- Structural Genomics Consortium, University of Toronto, Toronto, ON, M5G 1L7, Canada. .,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, M5S 1A8, Canada.
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25
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Seashore-Ludlow B, Axelsson H, Lundbäck T. Perspective on CETSA Literature: Toward More Quantitative Data Interpretation. SLAS DISCOVERY 2019; 25:118-126. [PMID: 31665966 DOI: 10.1177/2472555219884524] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The cellular thermal shift assay (CETSA) was introduced in 2013 to investigate drug-target engagement inside live cells and tissues. As with all thermal shift assays, the response measured by CETSA is not simply governed by ligand affinity to the investigated target protein, but the thermodynamics and kinetics of ligand binding and protein unfolding also contribute to the observed protein stabilization. This limitation is commonly neglected in current applications of the method to validate the target of small-molecule probes. Instead, there is an eagerness to make direct comparisons of CETSA measurements with functional and phenotypic readouts from cells at 37 °C. Here, we present a perspective of the early CETSA literature and put the accumulated data into a quantitative context. The analysis includes annotation of ~270 peer-reviewed papers, the majority of which do not consider the underlying biophysical basis of CETSA. We also detail what future technology developments are needed to enable CETSA-based optimization of structure-activity relationships and more appropriate comparisons of these data with functional or phenotypic responses. Finally, we describe ongoing developments in assay formats that allow for CETSA measurements at single-cell resolution, with the aspiration to allow differentiation in cellular target engagement between cells in co-cultures and more complex models, such as organoids and potentially even tissue.
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Affiliation(s)
- Brinton Seashore-Ludlow
- Department of Oncology and Pathology, Science for Life Laboratories, Karolinska Institutet, Solna, Sweden
| | - Hanna Axelsson
- Chemical Biology Consortium Sweden, Science for Life Laboratories, Karolinska Institutet, Solna, Sweden
| | - Thomas Lundbäck
- Chemical Biology Consortium Sweden, Science for Life Laboratories, Karolinska Institutet, Solna, Sweden.,Mechanistic Biology & Profiling, Discovery Sciences, R&D, AstraZeneca, Mölndal, Sweden
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26
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Gaetani M, Sabatier P, Saei AA, Beusch CM, Yang Z, Lundström SL, Zubarev RA. Proteome Integral Solubility Alteration: A High-Throughput Proteomics Assay for Target Deconvolution. J Proteome Res 2019; 18:4027-4037. [DOI: 10.1021/acs.jproteome.9b00500] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Massimiliano Gaetani
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17 177 Stockholm, Sweden
- SciLifeLab, SE-17 177 Stockholm, Sweden
| | - Pierre Sabatier
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17 177 Stockholm, Sweden
| | - Amir A. Saei
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17 177 Stockholm, Sweden
| | - Christian M. Beusch
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17 177 Stockholm, Sweden
| | - Zhe Yang
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17 177 Stockholm, Sweden
| | - Susanna L. Lundström
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17 177 Stockholm, Sweden
- SciLifeLab, SE-17 177 Stockholm, Sweden
| | - Roman A. Zubarev
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-17 177 Stockholm, Sweden
- SciLifeLab, SE-17 177 Stockholm, Sweden
- Department of Pharmacological & Technological Chemistry, I.M. Sechenov First Moscow State Medical University, Moscow, 119146, Russia
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27
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Fragment-based discovery of a chemical probe for the PWWP1 domain of NSD3. Nat Chem Biol 2019; 15:822-829. [PMID: 31285596 DOI: 10.1038/s41589-019-0310-x] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Accepted: 05/19/2019] [Indexed: 01/10/2023]
Abstract
Here, we report the fragment-based discovery of BI-9321, a potent, selective and cellular active antagonist of the NSD3-PWWP1 domain. The human NSD3 protein is encoded by the WHSC1L1 gene located in the 8p11-p12 amplicon, frequently amplified in breast and squamous lung cancer. Recently, it was demonstrated that the PWWP1 domain of NSD3 is required for the viability of acute myeloid leukemia cells. To further elucidate the relevance of NSD3 in cancer biology, we developed a chemical probe, BI-9321, targeting the methyl-lysine binding site of the PWWP1 domain with sub-micromolar in vitro activity and cellular target engagement at 1 µM. As a single agent, BI-9321 downregulates Myc messenger RNA expression and reduces proliferation in MOLM-13 cells. This first-in-class chemical probe BI-9321, together with the negative control BI-9466, will greatly facilitate the elucidation of the underexplored biological function of PWWP domains.
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28
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Weigt D, Parrish CA, Krueger JA, Oleykowski CA, Rendina AR, Hopf C. Mechanistic MALDI-TOF Cell-Based Assay for the Discovery of Potent and Specific Fatty Acid Synthase Inhibitors. Cell Chem Biol 2019; 26:1322-1331.e4. [PMID: 31279605 DOI: 10.1016/j.chembiol.2019.06.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 05/24/2019] [Accepted: 06/14/2019] [Indexed: 12/25/2022]
Abstract
Human cancers require fatty acid synthase (FASN)-dependent de novo long-chain fatty acid synthesis for proliferation. FASN is therefore an attractive drug target, but fast technologies for reliable label-free cellular compound profiling are lacking. Recently, MALDI-mass spectrometry (MALDI-MS) has emerged as an effective technology for discovery of recombinant protein target inhibitors. Here we present an automated, mechanistic MALDI-MS cell assay, which monitors accumulation of the FASN substrate, malonyl-coenzyme A (CoA), in whole cells with limited sample preparation. Profiling of inhibitors, including unpublished compounds, identified compound 1 as the most potent FASN inhibitor (1 nM in A549 cells) discovered to date. Moreover, cellular MALDI-MS assays enable parallel profiling of additional pathway metabolites. Surprisingly, several compounds triggered cytidine 5'-diphosphocholine (CDP-choline) but not malonyl-CoA accumulation indicating that they inhibit diacylglycerol generation but not FASN activity. Taken together, our study suggests that MALDI-MS cell assays may become important tools in drug profiling that provide additional mechanistic insights concerning compound action on metabolic pathways.
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Affiliation(s)
- David Weigt
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim Technical University, Paul-Wittsack-Strasse 10, 68163 Mannheim, Germany
| | - Cynthia A Parrish
- Medicinal Chemistry, GlaxoSmithKline, 1250 S Collegeville Road, Collegeville, PA 19426, USA
| | - Julie A Krueger
- Immuno-Oncology and Combinations Research Unit, GlaxoSmithKline, 1250 S Collegeville Road, Collegeville, PA 19426, USA
| | - Catherine A Oleykowski
- Immuno-Oncology and Combinations Research Unit, GlaxoSmithKline, 1250 S Collegeville Road, Collegeville, PA 19426, USA
| | - Alan R Rendina
- Screening, Profiling and Mechanistic Biology, GlaxoSmithKline, 1250 S Collegeville Road, Collegeville, PA 19426, USA
| | - Carsten Hopf
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), Mannheim Technical University, Paul-Wittsack-Strasse 10, 68163 Mannheim, Germany.
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29
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Shaw J, Dale I, Hemsley P, Leach L, Dekki N, Orme JP, Talbot V, Narvaez AJ, Bista M, Martinez Molina D, Dabrowski M, Main MJ, Gianni D. Positioning High-Throughput CETSA in Early Drug Discovery through Screening against B-Raf and PARP1. SLAS DISCOVERY 2018; 24:121-132. [PMID: 30543471 PMCID: PMC6484527 DOI: 10.1177/2472555218813332] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Methods to measure cellular target engagement are increasingly being used in early drug discovery. The Cellular Thermal Shift Assay (CETSA) is one such method. CETSA can investigate target engagement by measuring changes in protein thermal stability upon compound binding within the intracellular environment. It can be performed in high-throughput, microplate-based formats to enable broader application to early drug discovery campaigns, though high-throughput forms of CETSA have only been reported for a limited number of targets. CETSA offers the advantage of investigating the target of interest in its physiological environment and native state, but it is not clear yet how well this technology correlates to more established and conventional cellular and biochemical approaches widely used in drug discovery. We report two novel high-throughput CETSA (CETSA HT) assays for B-Raf and PARP1, demonstrating the application of this technology to additional targets. By performing comparative analyses with other assays, we show that CETSA HT correlates well with other screening technologies and can be applied throughout various stages of hit identification and lead optimization. Our results support the use of CETSA HT as a broadly applicable and valuable methodology to help drive drug discovery campaigns to molecules that engage the intended target in cells.
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Affiliation(s)
- Joseph Shaw
- 1 Discovery Biology, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - Ian Dale
- 1 Discovery Biology, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - Paul Hemsley
- 1 Discovery Biology, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - Lindsey Leach
- 2 Hit Discovery, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Alderley Park, UK
| | | | - Jonathan P Orme
- 1 Discovery Biology, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - Verity Talbot
- 4 Mechanistic Biology & Profiling, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - Ana J Narvaez
- 4 Mechanistic Biology & Profiling, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - Michal Bista
- 5 Structure, Biophysics & Fragment Based Lead Generation, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | | | | | - Martin J Main
- 1 Discovery Biology, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Cambridge, UK.,6 Medicines Discovery Catapult, Mereside, Alderley Park, UK
| | - Davide Gianni
- 1 Discovery Biology, Discovery Sciences, IMED Biotech Unit, AstraZeneca, Cambridge, UK
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30
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Seashore-Ludlow B, Axelsson H, Almqvist H, Dahlgren B, Jonsson M, Lundbäck T. Quantitative Interpretation of Intracellular Drug Binding and Kinetics Using the Cellular Thermal Shift Assay. Biochemistry 2018; 57:6715-6725. [PMID: 30418016 DOI: 10.1021/acs.biochem.8b01057] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Evidence of physical interaction with the target protein is essential in the development of chemical probes and drugs. The cellular thermal shift assay (CETSA) allows evaluation of drug binding in live cells but lacks a framework to support quantitative interpretations and comparisons with functional data. We outline an experimental platform for such analysis using human kinase p38α. Systematic variations to the assay's characteristic heat challenge demonstrate an apparent loss of compound potency with an increase in duration or temperature, in line with expectations from the literature for thermal shift assays. Importantly, data for five structurally diverse inhibitors can be quantitatively explained using a simple model of linked equilibria and published binding parameters. The platform further distinguishes between ligand mechanisms and allows for quantitative comparisons of drug binding affinities and kinetics in live cells and lysates. We believe this work has broad implications in the appropriate use of the CETSA for target and compound validation.
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Affiliation(s)
- Brinton Seashore-Ludlow
- Chemical Biology Consortium Sweden, Science for Life Laboratories , Karolinska Institutet , SE-171 65 Solna , Sweden.,Department of Medical Biochemistry and Biophysics , Karolinska Institutet , SE-171 65 Solna , Sweden
| | - Hanna Axelsson
- Chemical Biology Consortium Sweden, Science for Life Laboratories , Karolinska Institutet , SE-171 65 Solna , Sweden.,Department of Medical Biochemistry and Biophysics , Karolinska Institutet , SE-171 65 Solna , Sweden
| | - Helena Almqvist
- Chemical Biology Consortium Sweden, Science for Life Laboratories , Karolinska Institutet , SE-171 65 Solna , Sweden.,Department of Medical Biochemistry and Biophysics , Karolinska Institutet , SE-171 65 Solna , Sweden
| | - Björn Dahlgren
- Department of Chemistry , KTH Royal Institute of Technology , SE-100 44 Stockholm , Sweden
| | - Mats Jonsson
- Department of Chemistry , KTH Royal Institute of Technology , SE-100 44 Stockholm , Sweden
| | - Thomas Lundbäck
- Chemical Biology Consortium Sweden, Science for Life Laboratories , Karolinska Institutet , SE-171 65 Solna , Sweden.,Department of Medical Biochemistry and Biophysics , Karolinska Institutet , SE-171 65 Solna , Sweden.,Mechanistic Biology & Profiling, Discovery Sciences, IMED Biotech Unit , AstraZeneca , Gothenburg, SE-431 83 Mölndal , Sweden
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