1
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Figueroa-Navedo AM, Ivanov AR. Experimental and data analysis advances in thermal proteome profiling. CELL REPORTS METHODS 2024; 4:100717. [PMID: 38412830 PMCID: PMC10921035 DOI: 10.1016/j.crmeth.2024.100717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 12/17/2023] [Accepted: 02/05/2024] [Indexed: 02/29/2024]
Abstract
Method development for mass spectrometry (MS)-based thermal shift proteomic assays have advanced to probe small molecules with known and unknown protein-ligand interaction mechanisms and specificity, which is predominantly used in characterization of drug-protein interactions. In the discovery of target and off-target protein-ligand interactions, a thorough investigation of method development and their impact on the sensitivity and accuracy of protein-small molecule and protein-protein interactions is warranted. In this review, we discuss areas of improvement at each stage of thermal proteome profiling data analysis that includes processing of MS-based data, method development, and their effect on the overall quality of thermal proteome profiles. We also overview the optimization of experimental strategies and prioritization of an increased number of independent biological replicates over the number of evaluated temperatures.
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Affiliation(s)
- Amanda M Figueroa-Navedo
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA
| | - Alexander R Ivanov
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA 02115, USA.
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2
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Johnson FD, Hughes CS, Liu A, Lockwood WW, Morin GB. Tandem mass tag-based thermal proteome profiling for the discovery of drug-protein interactions in cancer cells. STAR Protoc 2023; 4:102012. [PMID: 36856765 PMCID: PMC9860163 DOI: 10.1016/j.xpro.2022.102012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 11/21/2022] [Accepted: 12/21/2022] [Indexed: 01/15/2023] Open
Abstract
Identification of effector targets is imperative to the characterization of the mechanisms of action of novel small molecules. Here, we describe steps to identify effector drug-protein interactions in lysates derived from cancer cell lines using a thermal proteome profiling (TPP) protocol. Building on existing TTP approaches, we detail the use of an in-solution trypsin digestion technique to streamline sample preparation, a nonparametric analysis to rank proteins for prioritization, and a follow-up strategy for identifying effector interactors. For complete details on the use and execution of this protocol, please refer to Johnson et al. (2022).1.
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Affiliation(s)
- Fraser D Johnson
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada; Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Christopher S Hughes
- Department of Molecular Oncology, University of British Columbia, Vancouver, BC, Canada; Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Alvin Liu
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
| | - William W Lockwood
- Department of Integrative Oncology, BC Cancer Research Institute, Vancouver, BC, Canada; Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.
| | - Gregg B Morin
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada.
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3
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Osman S, Bendtsen C, Peel S, Yrlid L, Muthas D, Simpson J, Willison KR, Klug DR. Evaluation of FOXO1 Target Engagement Using a Single-Cell Microfluidic Platform. Anal Chem 2021; 93:14659-14666. [PMID: 34694778 DOI: 10.1021/acs.analchem.1c02808] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The cellular thermal shift assay (CETSA) has been used extensively since its introduction to study drug-target engagement within both live cells and cellular lysate. This has proven to be a useful tool in early stage drug discovery and is used to study a wide range of protein classes. We describe the application of a single-cell CETSA workflow within a microfluidic affinity capture (MAC) chip. This has enabled us to quantitatively determine the active FOXO1 single-molecule count and observe FOXO1 stabilization and destabilization in the presence of three small molecule inhibitors, including demonstrating the determination of EC50. The successful use of the MAC chip for single-cell CETSA paves the way for the study of precious clinical samples owing to the low number of cells needed by the chip. It also provides a useful tool for studying any underlying population heterogeneity that exists within a cellular system, a feature that is usually masked when conducting ensemble measurements.
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Affiliation(s)
- Suhuur Osman
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, 80 Wood Lane, London, W12 0BZ, United Kingdom
| | - Claus Bendtsen
- Discovery Sciences, R&D, AstraZeneca, 310 Milton Road, Cambridge, CB4 0WG, United Kingdom
| | - Samantha Peel
- Discovery Sciences, R&D, AstraZeneca, 310 Milton Road, Cambridge, CB4 0WG, United Kingdom
| | - Linda Yrlid
- Early Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43150 Gothenburg, Sweden
| | - Daniel Muthas
- Early Respiratory & Immunology, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, 43150 Gothenburg, Sweden
| | - John Simpson
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, 80 Wood Lane, London, W12 0BZ, United Kingdom
| | - Keith R Willison
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, 80 Wood Lane, London, W12 0BZ, United Kingdom
| | - David R Klug
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, 80 Wood Lane, London, W12 0BZ, United Kingdom
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4
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Holdgate GA, Bergsdorf C. Applications of Biophysics in Early Drug Discovery. SLAS DISCOVERY 2021; 26:945-946. [PMID: 34415216 DOI: 10.1177/24725552211035123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
| | - Christian Bergsdorf
- Chemical Biology and Therapeutics, Novartis Institutes for Biomedical Research, Basel, Switzerland
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5
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Al-Amin RA, Gallant CJ, Muthelo PM, Landegren U. Sensitive Measurement of Drug-Target Engagement by a Cellular Thermal Shift Assay with Multiplex Proximity Extension Readout. Anal Chem 2021; 93:10999-11009. [PMID: 34319715 PMCID: PMC8358919 DOI: 10.1021/acs.analchem.1c02225] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
The ability to monitor
target engagement in cellular contexts is
a key for successful drug discovery and also valuable in clinical
routine. A cellular thermal shift assay (CETSA) provides realistic
information about drug binding in cells and tissues, revealing drug-target
engagement in clinically relevant samples. The CETSA combined with
mass spectrometry (MS) detection can be applied in the early hit identification
phase to generate target engagement data for large sets of proteins.
However, the analysis is slow, requires substantial amounts of the
sample material, and often misses proteins of specific interest. Here,
we combined the CETSA and the multiplex proximity extension assay
(PEA) for analysis of target engagement of a set of 67 proteins from
small amounts of the sample material treated with kinase inhibitors.
The results were concordant with the corresponding analyses read out
via MS. Our approach allows analyses of large numbers of specific
target proteins at high sensitivity in limited sample aliquots. Highly
sensitive multiplex CETSA-PEA assays are therefore promising for monitoring
drug-target engagement in small sample aliquots in the course of drug
development and potentially in clinical settings.
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Affiliation(s)
- Rasel A Al-Amin
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala SE-751 08, Sweden
| | - Caroline J Gallant
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala SE-751 08, Sweden
| | - Phathutshedzo M Muthelo
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala SE-751 08, Sweden
| | - Ulf Landegren
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala SE-751 08, Sweden
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6
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Dai L, Li Z, Chen D, Jia L, Guo J, Zhao T, Nordlund P. Target identification and validation of natural products with label-free methodology: A critical review from 2005 to 2020. Pharmacol Ther 2020; 216:107690. [PMID: 32980441 DOI: 10.1016/j.pharmthera.2020.107690] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 09/22/2020] [Accepted: 09/22/2020] [Indexed: 02/08/2023]
Abstract
Natural products (NPs) have been an important source of therapeutic drugs in clinic use and contributed many chemical probes for research. The usefulness of NPs is however often marred by the incomplete understanding of their direct cellular targets. A number of experimental methods for drug target identification have been developed over the years. One class of methods, termed "label-free" methodology, exploits the energetic and biophysical features accompanying the association of macromolecules with drugs and other compounds in their native forms. Herein we review the working principles, assay implementations, and key applications of the most important approaches, and also give examples where they have been applied to NPs. We also assess the key advantages and limitations of each method. Furthermore, we address when and how the label-free methodology can be particularly useful considering some of the unique features of NP chemistry and bioactivation.
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Affiliation(s)
- Lingyun Dai
- Department of Urology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Urology Minimally Invasive Engineering Center, Shenzhen 518020, Guangdong, China; Department of Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, Guangdong, China; Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore.
| | - Zhijie Li
- Department of Urology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Urology Minimally Invasive Engineering Center, Shenzhen 518020, Guangdong, China; Department of Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, Guangdong, China
| | - Dan Chen
- Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore
| | - Lin Jia
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China
| | - Jinan Guo
- Department of Urology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Urology Minimally Invasive Engineering Center, Shenzhen 518020, Guangdong, China
| | - Tianyun Zhao
- Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore
| | - Pär Nordlund
- Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore; Department of Oncology and Pathology, Karolinska Institutet, 171 77 Stockholm, Sweden.
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7
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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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8
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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: 19] [Impact Index Per Article: 3.8] [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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9
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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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10
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Liu YK, Chen HY, Chueh PJ, Liu PF. A one-pot analysis approach to simplify measurements of protein stability and folding kinetics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1867:184-193. [PMID: 30578861 DOI: 10.1016/j.bbapap.2018.12.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/16/2018] [Accepted: 12/17/2018] [Indexed: 10/27/2022]
Abstract
To achieve a good understanding of the characteristics of a protein, it is important to study its stability and folding kinetics. Investigations of protein stability have been recently applied to drug-target identification, drug screening, and proteomic studies. The efficiency of the experiments performed to study protein stability and folding kinetics is now a crucial factor that needs to be optimized for these potential applications. However, the standard procedures used to carry out these experiments are usually complicated and time consuming. Large number of measurements is the bottleneck that limits the application of protein folding to large-scale experiments. To overcome this limitation, we developed a method denoted as "one-pot analysis" which is based on taking a single measurement from a mixture of samples rather than from every sample. We combined one-pot analysis with pulse proteolysis to determine the effects of the binding of maltose to maltose-binding protein on the protein folding properties. After carrying out a simple optimization, we demonstrated that protein stability or unfolding kinetics could be measured accurately with just one detection measurement. We then further applied the optimized conditions to cellular thermal shift assay (CETSA). Combining one-pot analysis with CETSA led to a successful determination of the effects of the binding of methotrexate to dihydrofolate reductase in HCT116 cancer cells. Our results demonstrated the applicability of one-pot analysis to energetics-based methods for studying protein folding. We expect the combination of one-pot analysis and energetics-based methods to significantly benefit studies such as drug-target identification, proteomic investigations, and drug screening.
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Affiliation(s)
- Yi-Kai Liu
- Department of Food Science and Biotechnology, National Chung Hsing University, 145 Xingda Rd., South Dist., Taichung City 402, Taiwan, ROC
| | - Huei-Yu Chen
- Institute of Biomedical Science, National Chung Hsing University, 145 Xingda Rd., South Dist., Taichung City 402, Taiwan, ROC
| | - Pin Ju Chueh
- Institute of Biomedical Science, National Chung Hsing University, 145 Xingda Rd., South Dist., Taichung City 402, Taiwan, ROC
| | - Pei-Fen Liu
- Department of Food Science and Biotechnology, National Chung Hsing University, 145 Xingda Rd., South Dist., Taichung City 402, Taiwan, ROC.
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11
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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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12
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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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13
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Wang J, Wu J, Li X, Liu H, Qin J, Bai Z, Chi B, Chen X. Identification and validation nucleolin as a target of curcumol in nasopharyngeal carcinoma cells. J Proteomics 2018; 182:1-11. [PMID: 29684682 DOI: 10.1016/j.jprot.2018.04.025] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 03/22/2018] [Accepted: 04/19/2018] [Indexed: 11/16/2022]
Abstract
Identification of the specific protein target(s) of a drug is a critical step in unraveling its mechanisms of action (MOA) in many natural products. Curcumol, isolated from well known Chinese medicinal plant Curcuma zedoary, has been shown to possess multiple biological activities. It can inhibit nasopharyngeal carcinoma (NPC) proliferation and induce apoptosis, but its target protein(s) in NPC cells remains unclear. In this study, we employed a mass spectrometry-based chemical proteomics approach reveal the possible protein targets of curcumol in NPC cells. Cellular thermal shift assay (CETSA), molecular docking and cell-based assay was used to validate the binding interactions. Chemical proteomics capturing uncovered that NCL is a target of curcumol in NPC cells, Molecular docking showed that curcumol bound to NCL with an -7.8 kcal/mol binding free energy. Cell function analysis found that curcumol's treatment leads to a degradation of NCL in NPC cells, and it showed slight effects on NP69 cells. In conclusion, our results providing evidences that NCL is a target protein of curcumol. We revealed that the anti-cancer effects of curcumol in NPC cells are mediated, at least in part, by NCL inhibition. SIGNIFICANCE Many natural products showed high bioactivity, while their mechanisms of action (MOA) are very poor or completely missed. Understanding the MOA of natural drugs can thoroughly exploit their therapeutic potential and minimize their adverse side effects. Identification of the specific protein target(s) of a drug is a critical step in unraveling its MOA. Compound-centric chemical proteomics is a classic chemical proteomics approach which integrates chemical synthesis with cell biology and mass spectrometry (MS) to identify protein targets of natural products determine the drug mechanism of action, describe its toxicity, and figure out the possible cause of off-target. It is an affinity-based chemical proteomics method to identify small molecule-protein interactions through affinity chromatography approach coupled with mass spectrometry, has been conventionally used to identify target proteins and has yielded good results. Curcumol, has shown effective inhibition on Nasopharyngeal Carcinoma (NPC) Cells, interacted with NCL and then initiated the anti-tumor biological effect. This research demonstrated the effectiveness of chemical proteomics approaches in natural drugs molecular target identification, revealing and understanding of the novel mechanism of actions of curcumol is crucial for cancer prevention and treatment in nasopharynx cancer.
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Affiliation(s)
- Juan Wang
- Xiangya Hospital, Central South University, Changsha 410008, China; College of Pharmacy, Guilin Medical University, Guilin 541004, China
| | - Jiacai Wu
- Research Center for Science, Guilin Medical University, Guilin 541004, China
| | - Xumei Li
- College of Pharmacy, Guilin Medical University, Guilin 541004, China
| | - Haowei Liu
- College of Pharmacy, Guilin Medical University, Guilin 541004, China
| | - Jianli Qin
- College of Pharmacy, Guilin Medical University, Guilin 541004, China
| | - Zhun Bai
- Intensive Care Unit, The Affiliated Zhuzhou Hospital XiangYa Medical College CSU, Zhuzhou 412007, China
| | - Bixia Chi
- Department of Gastroenterology, The First People's Hospital of Yueyang, Yueyang 414000, China
| | - Xu Chen
- College of Pharmacy, Guilin Medical University, Guilin 541004, China.
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14
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Dart ML, Machleidt T, Jost E, Schwinn MK, Robers MB, Shi C, Kirkland TA, Killoran MP, Wilkinson JM, Hartnett JR, Zimmerman K, Wood KV. Homogeneous Assay for Target Engagement Utilizing Bioluminescent Thermal Shift. ACS Med Chem Lett 2018; 9:546-551. [PMID: 29937980 PMCID: PMC6004564 DOI: 10.1021/acsmedchemlett.8b00081] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 04/16/2018] [Indexed: 12/16/2022] Open
Abstract
Protein thermal shift assays (TSAs) provide a means for characterizing target engagement through ligand-induced thermal stabilization. Although these assays are widely utilized for screening libraries and validating hits in drug discovery programs, they can impose encumbering operational requirements, such as the availability of purified proteins or selective antibodies. Appending the target protein with a small luciferase (NanoLuc) allows coupling of thermal denaturation with luminescent output, providing a rapid and sensitive means for assessing target engagement in compositionally complex environments such as permeabilized cells. The intrinsic thermal stability of NanoLuc is greater than mammalian proteins, and our results indicate that the appended luciferase does not alter thermal denaturation of the target protein. We have successfully applied the NanoLuc luciferase thermal shift assay (NaLTSA) to several clinically relevant protein families, including kinases, bromodomains, and histone deacetylases. We have also demonstrated the suitability of this assay method for library screening and compound profiling.
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Affiliation(s)
- Melanie L. Dart
- Promega
Corporation, 2800 Woods Hollow Road, Madison, Wisconsin 53711, United States
| | - Thomas Machleidt
- Promega
Corporation, 2800 Woods Hollow Road, Madison, Wisconsin 53711, United States
| | - Emily Jost
- Promega
Corporation, 2800 Woods Hollow Road, Madison, Wisconsin 53711, United States
| | - Marie K. Schwinn
- Promega
Corporation, 2800 Woods Hollow Road, Madison, Wisconsin 53711, United States
| | - Matthew B. Robers
- Promega
Corporation, 2800 Woods Hollow Road, Madison, Wisconsin 53711, United States
| | - Ce Shi
- Promega
Biosciences Incorporated, 277 Granada Drive, San Luis Obispo, California 93401, United States
| | - Thomas A. Kirkland
- Promega
Biosciences Incorporated, 277 Granada Drive, San Luis Obispo, California 93401, United States
| | - Michael P. Killoran
- Promega
Corporation, 2800 Woods Hollow Road, Madison, Wisconsin 53711, United States
| | - Jennifer M. Wilkinson
- Promega
Corporation, 2800 Woods Hollow Road, Madison, Wisconsin 53711, United States
| | - James R. Hartnett
- Promega
Corporation, 2800 Woods Hollow Road, Madison, Wisconsin 53711, United States
| | - Kristopher Zimmerman
- Promega
Corporation, 2800 Woods Hollow Road, Madison, Wisconsin 53711, United States
| | - Keith V. Wood
- Promega
Corporation, 2800 Woods Hollow Road, Madison, Wisconsin 53711, United States
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15
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Axelsson H, Almqvist H, Otrocka M, Vallin M, Lundqvist S, Hansson P, Karlsson U, Lundbäck T, Seashore-Ludlow B. In Situ Target Engagement Studies in Adherent Cells. ACS Chem Biol 2018; 13:942-950. [PMID: 29433316 DOI: 10.1021/acschembio.7b01079] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A prerequisite for successful drugs is effective binding of the desired target protein in the complex environment of a living system. Drug-target engagement has typically been difficult to monitor in physiologically relevant models, and with current methods, especially, while maintaining spatial information. One recent technique for quantifying drug-target engagement is the cellular thermal shift assay (CETSA), in which ligand-induced protein stabilization is measured after a heat challenge. Here, we describe a CETSA protocol in live A431 cells for p38α (MAPK14), where remaining soluble protein is detected in situ, using high-content imaging in 384-well, microtiter plates. We validate this assay concept using a number of known p38α inhibitors and further demonstrate the potential of this technology for chemical probe and drug discovery purposes by performing a small pilot screen for novel p38α binders. Importantly, this protocol creates a workflow that is amenable to adherent cells in their native state and yields spatially resolved target engagement information measurable at the single-cell level.
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Affiliation(s)
- Hanna Axelsson
- Chemical Biology Consortium Sweden, Science for Life Laboratory, 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 Laboratory, Karolinska Institutet, SE-171 65 Solna, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 65 Solna, Sweden
| | - Magdalena Otrocka
- Chemical Biology Consortium Sweden, Science for Life Laboratory, Karolinska Institutet, SE-171 65 Solna, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 65 Solna, Sweden
| | - Michaela Vallin
- Chemical Biology Consortium Sweden, Science for Life Laboratory, Karolinska Institutet, SE-171 65 Solna, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 65 Solna, Sweden
| | - Sara Lundqvist
- Discovery
Sciences,
IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Pia Hansson
- Discovery
Sciences,
IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Ulla Karlsson
- Discovery
Sciences,
IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Thomas Lundbäck
- Chemical Biology Consortium Sweden, Science for Life Laboratory, Karolinska Institutet, SE-171 65 Solna, Sweden
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, SE-171 65 Solna, Sweden
- Discovery
Sciences,
IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Brinton Seashore-Ludlow
- Chemical Biology Consortium Sweden, Science for Life Laboratory, Karolinska Institutet, SE-171 65 Solna, Sweden
- Science for Life Laboratory, Department of Oncology-Pathology, Karolinska Institutet, SE-171 76 Stockholm, Sweden
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16
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Massey AJ. A high content, high throughput cellular thermal stability assay for measuring drug-target engagement in living cells. PLoS One 2018; 13:e0195050. [PMID: 29617433 PMCID: PMC5884524 DOI: 10.1371/journal.pone.0195050] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 03/15/2018] [Indexed: 01/08/2023] Open
Abstract
Determining and understanding drug target engagement is critical for drug discovery. This can be challenging within living cells as selective readouts are often unavailable. Here we describe a novel method for measuring target engagement in living cells based on the principle of altered protein thermal stabilization / destabilization in response to ligand binding. This assay (HCIF-CETSA) utilizes high content, high throughput single cell immunofluorescent detection to determine target protein levels following heating of adherent cells in a 96 well plate format. We have used target engagement of Chk1 by potent small molecule inhibitors to validate the assay. Target engagement measured by this method was subsequently compared to target engagement measured by two alternative methods (autophosphorylation and CETSA). The HCIF-CETSA method appeared robust and a good correlation in target engagement measured by this method and CETSA for the selective Chk1 inhibitor V158411 was observed. However, these EC50 values were 23- and 12-fold greater than the autophosphorylation IC50. The described method is therefore a valuable advance in the CETSA method allowing the high throughput determination of target engagement in adherent cells.
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17
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Geneste CC, Massey AJ. Cell Density Affects the Detection of Chk1 Target Engagement by the Selective Inhibitor V158411. SLAS DISCOVERY 2017; 23:144-153. [PMID: 29048945 DOI: 10.1177/2472555217738534] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Understanding drug target engagement and the relationship to downstream pharmacology is critical for drug discovery. Here we have evaluated target engagement of Chk1 by the small-molecule inhibitor V158411 using two different target engagement methods (autophosphorylation and cellular thermal shift assay [CETSA]). Target engagement measured by these methods was subsequently related to Chk1 inhibitor-dependent pharmacology. Inhibition of autophosphorylation was a robust method for measuring V158411 Chk1 target engagement. In comparison, while target engagement determined using CETSA appeared robust, the V158411 CETSA target engagement EC50 values were 43- and 19-fold greater than the autophosphorylation IC50 values. This difference was attributed to the higher cell density in the CETSA assay configuration. pChk1 (S296) IC50 values determined using the CETSA assay conditions were 54- and 33-fold greater than those determined under standard conditions and were equivalent to the CETSA EC50 values. Cellular conditions, especially cell density, influenced the target engagement of V158411 for Chk1. The effects of high cell density on apparent compound target engagement potency should be evaluated when using target engagement assays that necessitate high cell densities (such as the CETSA conditions used in this study). In such cases, the subsequent relation of these data to downstream pharmacological changes should therefore be interpreted with care.
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18
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McNulty DE, Bonnette WG, Qi H, Wang L, Ho TF, Waszkiewicz A, Kallal LA, Nagarajan RP, Stern M, Quinn AM, Creasy CL, Su DS, Graves AP, Annan RS, Sweitzer SM, Holbert MA. A High-Throughput Dose-Response Cellular Thermal Shift Assay for Rapid Screening of Drug Target Engagement in Living Cells, Exemplified Using SMYD3 and IDO1. SLAS DISCOVERY 2017; 23:34-46. [DOI: 10.1177/2472555217732014] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A persistent problem in early small-molecule drug discovery is the frequent lack of rank-order correlation between biochemical potencies derived from initial screens using purified proteins and the diminished potency and efficacy observed in subsequent disease-relevant cellular phenotypic assays. The introduction of the cellular thermal shift assay (CETSA) has bridged this gap by enabling assessment of drug target engagement directly in live cells based on ligand-induced changes in protein thermal stability. Initial success in applying CETSA across multiple drug target classes motivated our investigation into replacing the low-throughput, manually intensive Western blot readout with a quantitative, automated higher-throughput assay that would provide sufficient capacity to use CETSA as a primary hit qualification strategy. We introduce a high-throughput dose-response cellular thermal shift assay (HTDR-CETSA), a single-pot homogenous assay adapted for high-density microtiter plate format. The assay features titratable BacMam expression of full-length target proteins fused to the DiscoverX 42 amino acid ePL tag in HeLa suspension cells, facilitating enzyme fragment complementation–based chemiluminescent quantification of ligand-stabilized soluble protein. This simplified format can accommodate determination of full-dose CETSA curves for hundreds of individual compounds/analyst/day in replicates. HTDR-CETSA data generated for substrate site and alternate binding mode inhibitors of the histone-lysine N-methyltransferase SMYD3 in HeLa suspension cells demonstrate excellent correlation with rank-order potencies observed in cellular mechanistic assays and direct translation to target engagement of endogenous Smyd3 in cancer-relevant cell lines. We envision this workflow to be generically applicable to HTDR-CETSA screening spanning a wide variety of soluble intracellular protein target classes.
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19
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Prediction of intracellular exposure bridges the gap between target- and cell-based drug discovery. Proc Natl Acad Sci U S A 2017; 114:E6231-E6239. [PMID: 28701380 DOI: 10.1073/pnas.1701848114] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Inadequate target exposure is a major cause of high attrition in drug discovery. Here, we show that a label-free method for quantifying the intracellular bioavailability (Fic) of drug molecules predicts drug access to intracellular targets and hence, pharmacological effect. We determined Fic in multiple cellular assays and cell types representing different targets from a number of therapeutic areas, including cancer, inflammation, and dementia. Both cytosolic targets and targets localized in subcellular compartments were investigated. Fic gives insights on membrane-permeable compounds in terms of cellular potency and intracellular target engagement, compared with biochemical potency measurements alone. Knowledge of the amount of drug that is locally available to bind intracellular targets provides a powerful tool for compound selection in early drug discovery.
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20
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Jain V, Sharma A, Singh G, Yogavel M, Sharma A. Structure-Based Targeting of Orthologous Pathogen Proteins Accelerates Antiparasitic Drug Discovery. ACS Infect Dis 2017; 3:281-292. [PMID: 28195698 DOI: 10.1021/acsinfecdis.6b00181] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Parasitic diseases caused by eukaryotic pathogens impose significant health and economic burden worldwide. The level of research funding available for many parasitic diseases is insufficient in relation to their adverse social and economic impact. In this article, we discuss that extant 3D structural data on protein-inhibitor complexes can be harnessed to accelerate drug discovery against many related pathogens. Assessment of sequence conservation within drug/inhibitor-binding residues in enzyme-inhibitor complexes can be leveraged to predict and validate both new lead compounds and their molecular targets in multiple parasitic diseases. Hence, structure-based targeting of orthologous pathogen proteins accelerates the discovery of new antiparasitic drugs. This approach offers significant benefits for jumpstarting the discovery of new lead compounds and their molecular targets in diverse human, livestock, and plant pathogens.
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Affiliation(s)
- Vitul Jain
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Road, New Delhi 110067, India
| | - Arvind Sharma
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Road, New Delhi 110067, India
| | - Gajinder Singh
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Road, New Delhi 110067, India
| | - Manickam Yogavel
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Road, New Delhi 110067, India
| | - Amit Sharma
- Molecular Medicine Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Road, New Delhi 110067, India
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21
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A rhodium(III)-based inhibitor of autotaxin with antiproliferative activity. Biochim Biophys Acta Gen Subj 2017; 1861:256-263. [DOI: 10.1016/j.bbagen.2016.11.032] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 11/09/2016] [Accepted: 11/21/2016] [Indexed: 12/17/2022]
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