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Xiao Y, Yuan Y, Liu Y, Lin Z, Zheng G, Zhou D, Lv D. Targeted Protein Degradation: Current and Emerging Approaches for E3 Ligase Deconvolution. J Med Chem 2024; 67:11580-11596. [PMID: 38981094 DOI: 10.1021/acs.jmedchem.4c00723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
Targeted protein degradation (TPD), including the use of proteolysis-targeting chimeras (PROTACs) and molecular glue degraders (MGDs) to degrade proteins, is an emerging strategy to develop novel therapies for cancer and beyond. PROTACs or MGDs function by inducing the proximity between an E3 ligase and a protein of interest (POI), leading to ubiquitination and consequent proteasomal degradation of the POI. Notably, one major issue in TPD is the lack of ligandable E3 ligases, as current studies predominantly use CUL4CRBN and CUL2VHL. The TPD community is seeking to expand the landscape of ligandable E3 ligases, but most discoveries rely on phenotypic screens or serendipity, necessitating systematic target deconvolution. Here, we examine and discuss both current and emerging E3 ligase deconvolution approaches for degraders discovered from phenotypic screens or monovalent glue chemistry campaigns, highlighting future prospects for identifying more ligandable E3 ligases.
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Affiliation(s)
- Yufeng Xiao
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, Florida 32610, United States
| | - Yaxia Yuan
- Department of Biochemistry and Structural Biology and Center for Innovative Drug Discovery, School of Medicine, University of Texas Health San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
- Mays Cancer Center, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
| | - Yi Liu
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, Florida 32610, United States
| | - Zongtao Lin
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, Missouri 63110, United States
| | - Guangrong Zheng
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, Florida 32610, United States
| | - Daohong Zhou
- Department of Biochemistry and Structural Biology and Center for Innovative Drug Discovery, School of Medicine, University of Texas Health San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
- Mays Cancer Center, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
| | - Dongwen Lv
- Department of Biochemistry and Structural Biology and Center for Innovative Drug Discovery, School of Medicine, University of Texas Health San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
- Mays Cancer Center, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
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2
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Federspiel JD, Catlin NR, Nowland WS, Stethem CM, Mathialagan N, Fernandez Ocaña M, Bowman CJ. Differential Analysis of Cereblon Neosubstrates in Rabbit Embryos Using Targeted Proteomics. Mol Cell Proteomics 2024; 23:100797. [PMID: 38866076 PMCID: PMC11263748 DOI: 10.1016/j.mcpro.2024.100797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/31/2024] [Accepted: 06/06/2024] [Indexed: 06/14/2024] Open
Abstract
Targeted protein degradation is the selective removal of a protein of interest through hijacking intracellular protein cleanup machinery. This rapidly growing field currently relies heavily on the use of the E3 ligase cereblon (CRBN) to target proteins for degradation, including the immunomodulatory drugs (IMiDs) thalidomide, lenalidomide, and pomalidomide which work through a molecular glue mechanism of action with CRBN. While CRBN recruitment can result in degradation of a specific protein of interest (e.g., efficacy), degradation of other proteins (called CRBN neosubstrates) also occurs. Degradation of one or more of these CRBN neosubstrates is believed to play an important role in thalidomide-related developmental toxicity observed in rabbits and primates. We identified a set of 25 proteins of interest associated with CRBN-related protein homeostasis and/or embryo/fetal development. We developed a targeted assay for these proteins combining peptide immunoaffinity enrichment and high-resolution mass spectrometry and successfully applied this assay to rabbit embryo samples from pregnant rabbits dosed with three IMiDs. We confirmed previously reported in vivo decreases in neosubstrates like SALL4, as well as provided evidence of neosubstrate changes for proteins only examined in vitro previously. While there were many proteins that were similarly decreased by all three IMiDs, no compound had the exact same neosubstrate degradation profile as another. We compared our data to previous literature reports of IMiD-induced degradation and known developmental biology associations. Based on our observations, we recommend monitoring at least a major subset of these neosubstrates in a developmental test system to improve CRBN-binding compound-specific risk assessment. A strength of our assay is that it is configurable, and the target list can be readily adapted to focus on only a subset of proteins of interest or expanded to incorporate new findings as additional information about CRBN biology is discovered.
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Affiliation(s)
- Joel D Federspiel
- Drug Safety Research & Development, Pfizer, Inc, Andover, Massachusetts, USA
| | - Natasha R Catlin
- Drug Safety Research & Development, Pfizer, Inc, Groton, Connecticut, USA
| | - William S Nowland
- Drug Safety Research & Development, Pfizer, Inc, Groton, Connecticut, USA
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3
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Holdgate GA, Bardelle C, Berry SK, Lanne A, Cuomo ME. Screening for molecular glues - Challenges and opportunities. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:100136. [PMID: 38104659 DOI: 10.1016/j.slasd.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/03/2023] [Accepted: 12/14/2023] [Indexed: 12/19/2023]
Abstract
Molecular glues are small molecules, typically smaller than PROTACs, and usually with improved physicochemical properties that aim to stabilise the interaction between two proteins. Most often this approach is used to improve or induce an interaction between the target and an E3 ligase, but other interactions which stabilise interactions to increase activity or to inhibit binding to a natural effector have also been demonstrated. This review will describe the effects of induced proximity, discuss current methods used to identify molecular glues and introduce approaches that could be adapted for molecular glue screening.
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Affiliation(s)
| | - Catherine Bardelle
- High-throughput Screening, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
| | - Sophia K Berry
- High-throughput Screening, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
| | - Alice Lanne
- High-throughput Screening, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
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4
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Patel S, Karlsson M, Klahn JT, Gambino F, Costa H, McGuire KA, Baumgartner CK, Williams J, Sandoz S, Kath JE. Quantitative target engagement of RIPK1 in human whole blood via the cellular thermal shift assay for potential pre-clinical and clinical applications. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:100135. [PMID: 38101572 DOI: 10.1016/j.slasd.2023.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 11/29/2023] [Accepted: 12/12/2023] [Indexed: 12/17/2023]
Abstract
The cellular thermal shift assay (CETSA®) is a target engagement method widely used for preclinical characterization of small molecule compounds. CETSA® has been used for semi-quantitative readouts in whole blood with PBMC isolation, and quantitative, plate-based readouts using cell lines. However, there has been no quantitative evaluation of CETSA® in unprocessed human whole blood, which is preferred for clinical applications. Here we report two separate assay formats - Alpha CETSA® and MSD CETSA® - that require less than 100 μL of whole blood per sample without PBMC isolation. We chose RIPK1 as a proof-of-concept target and, by measuring engagement of seven different inhibitors, demonstrate high assay sensitivity and robustness. These quantitative CETSA® platforms enable possible applications in preclinical pharmacokinetic-pharmacodynamic studies, and direct target engagement with small molecules in clinical trials.
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5
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Wu Q, Zheng J, Sui X, Fu C, Cui X, Liao B, Ji H, Luo Y, He A, Lu X, Xue X, Tan CSH, Tian R. High-throughput drug target discovery using a fully automated proteomics sample preparation platform. Chem Sci 2024; 15:2833-2847. [PMID: 38404368 PMCID: PMC10882491 DOI: 10.1039/d3sc05937e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 12/19/2023] [Indexed: 02/27/2024] Open
Abstract
Drug development is plagued by inefficiency and high costs due to issues such as inadequate drug efficacy and unexpected toxicity. Mass spectrometry (MS)-based proteomics, particularly isobaric quantitative proteomics, offers a solution to unveil resistance mechanisms and unforeseen side effects related to off-targeting pathways. Thermal proteome profiling (TPP) has gained popularity for drug target identification at the proteome scale. However, it involves experiments with multiple temperature points, resulting in numerous samples and considerable variability in large-scale TPP analysis. We propose a high-throughput drug target discovery workflow that integrates single-temperature TPP, a fully automated proteomics sample preparation platform (autoSISPROT), and data independent acquisition (DIA) quantification. The autoSISPROT platform enables the simultaneous processing of 96 samples in less than 2.5 hours, achieving protein digestion, desalting, and optional TMT labeling (requires an additional 1 hour) with 96-channel all-in-tip operations. The results demonstrated excellent sample preparation performance with >94% digestion efficiency, >98% TMT labeling efficiency, and >0.9 intra- and inter-batch Pearson correlation coefficients. By automatically processing 87 samples, we identified both known targets and potential off-targets of 20 kinase inhibitors, affording over a 10-fold improvement in throughput compared to classical TPP. This fully automated workflow offers a high-throughput solution for proteomics sample preparation and drug target/off-target identification.
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Affiliation(s)
- Qiong Wu
- Department of Chemistry, School of Science, Southern University of Science and Technology Shenzhen 518055 China
| | - Jiangnan Zheng
- Department of Chemistry, School of Science, Southern University of Science and Technology Shenzhen 518055 China
- Southern University of Science and Technology, Guangming Advanced Research Institute Shenzhen 518055 China
| | - Xintong Sui
- Department of Chemistry, School of Science, Southern University of Science and Technology Shenzhen 518055 China
| | - Changying Fu
- Department of Chemistry, School of Science, Southern University of Science and Technology Shenzhen 518055 China
| | - Xiaozhen Cui
- Department of Chemistry, School of Science, Southern University of Science and Technology Shenzhen 518055 China
| | - Bin Liao
- Department of Chemistry, School of Science, Southern University of Science and Technology Shenzhen 518055 China
| | - Hongchao Ji
- Department of Chemistry, School of Science, Southern University of Science and Technology Shenzhen 518055 China
| | - Yang Luo
- Department of Chemistry, School of Science, Southern University of Science and Technology Shenzhen 518055 China
| | - An He
- Department of Chemistry, School of Science, Southern University of Science and Technology Shenzhen 518055 China
| | - Xue Lu
- Department of Chemistry, School of Science, Southern University of Science and Technology Shenzhen 518055 China
| | - Xinyue Xue
- Department of Chemistry, School of Science, Southern University of Science and Technology Shenzhen 518055 China
| | - Chris Soon Heng Tan
- Department of Chemistry, School of Science, Southern University of Science and Technology Shenzhen 518055 China
- Research Center for Chemical Biology and Omics Analysis, School of Science, Southern University of Science and Technology 1088 Xueyuan Road Shenzhen 518055 China
- Southern University of Science and Technology, Guangming Advanced Research Institute Shenzhen 518055 China
| | - Ruijun Tian
- Department of Chemistry, School of Science, Southern University of Science and Technology Shenzhen 518055 China
- Research Center for Chemical Biology and Omics Analysis, School of Science, Southern University of Science and Technology 1088 Xueyuan Road Shenzhen 518055 China
- Southern University of Science and Technology, Guangming Advanced Research Institute Shenzhen 518055 China
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6
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Sathe G, Sapkota GP. Proteomic approaches advancing targeted protein degradation. Trends Pharmacol Sci 2023; 44:786-801. [PMID: 37778939 DOI: 10.1016/j.tips.2023.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/18/2023] [Accepted: 08/25/2023] [Indexed: 10/03/2023]
Abstract
Targeted protein degradation (TPD) is an emerging modality for research and therapeutics. Most TPD approaches harness cellular ubiquitin-dependent proteolytic pathways. Proteolysis-targeting chimeras (PROTACs) and molecular glue (MG) degraders (MGDs) represent the most advanced TPD approaches, with some already used in clinical settings. Despite these advances, TPD still faces many challenges, pertaining to both the development of effective, selective, and tissue-penetrant degraders and understanding their mode of action. In this review, we focus on progress made in addressing these challenges. In particular, we discuss the utility and application of recent proteomic approaches as indispensable tools to enable insights into degrader development, including target engagement, degradation selectivity, efficacy, safety, and mode of action.
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Affiliation(s)
- Gajanan Sathe
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
| | - Gopal P Sapkota
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
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7
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Ruwolt M, Piazza I, Liu F. The potential of cross-linking mass spectrometry in the development of protein-protein interaction modulators. Curr Opin Struct Biol 2023; 82:102648. [PMID: 37423038 DOI: 10.1016/j.sbi.2023.102648] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 06/03/2023] [Accepted: 06/08/2023] [Indexed: 07/11/2023]
Abstract
Cross-linking mass spectrometry (XL-MS) can provide a wealth of information on endogenous protein-protein interaction (PPI) networks and protein binding interfaces. These features make XL-MS an attractive tool to support the development of PPI-targeting drugs. Though not yet widely used, applications of XL-MS to drug characterization are beginning to emerge. Here, we compare XL-MS to established structural proteomics methods in drug research, discuss the current state and remaining challenges of XL-MS technology, and provide a perspective on the future role XL-MS can play in drug development, with a particular emphasis on PPI modulators.
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Affiliation(s)
- Max Ruwolt
- Department of Structural Biology, Leibniz, Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, 13125 Berlin, Germany. https://twitter.com/@MRuwolt
| | - Ilaria Piazza
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC Berlin), Berlin, Germany.
| | - Fan Liu
- Department of Structural Biology, Leibniz, Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, 13125 Berlin, Germany; Charité - Universitätsmedizin Berlin, Charitépl. 1, 10117 Berlin, Germany.
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8
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Caballero I, Lundgren S. A Shift in Thinking: Cellular Thermal Shift Assay-Enabled Drug Discovery. ACS Med Chem Lett 2023; 14:369-375. [PMID: 37077396 PMCID: PMC10108388 DOI: 10.1021/acsmedchemlett.2c00545] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 03/06/2023] [Indexed: 03/19/2023] Open
Abstract
A decade has passed since the cellular thermal shift assay (CETSA) was introduced to the drug discovery community. Over the years, the method has guided numerous projects by providing insights about, for example, target engagement, lead generation, target identification, lead optimization, and preclinical profiling. With this Microperspective, we intend to highlight recently published applications of CETSA and how the data generated can enable efficient decision-making and prioritization throughout the drug discovery and development value chain.
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9
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Amrhein JA, Berger LM, Tjaden A, Krämer A, Elson L, Tolvanen T, Martinez-Molina D, Kaiser A, Schubert-Zsilavecz M, Müller S, Knapp S, Hanke T. Discovery of 3-Amino-1 H-pyrazole-Based Kinase Inhibitors to Illuminate the Understudied PCTAIRE Family. Int J Mol Sci 2022; 23:ijms232314834. [PMID: 36499165 PMCID: PMC9736855 DOI: 10.3390/ijms232314834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 11/29/2022] Open
Abstract
The PCTAIRE subfamily belongs to the CDK (cyclin-dependent kinase) family and represents an understudied class of kinases of the dark kinome. They exhibit a highly conserved binding pocket and are activated by cyclin Y binding. CDK16 is targeted to the plasma membrane after binding to N-myristoylated cyclin Y and is highly expressed in post-mitotic tissues, such as the brain and testis. Dysregulation is associated with several diseases, including breast, prostate, and cervical cancer. Here, we used the N-(1H-pyrazol-3-yl)pyrimidin-4-amine moiety from the promiscuous inhibitor 1 to target CDK16, by varying different residues. Further optimization steps led to 43d, which exhibited high cellular potency for CDK16 (EC50 = 33 nM) and the other members of the PCTAIRE and PFTAIRE family with 20-120 nM and 50-180 nM, respectively. A DSF screen against a representative panel of approximately 100 kinases exhibited a selective inhibition over the other kinases. In a viability assessment, 43d decreased the cell count in a dose-dependent manner. A FUCCI cell cycle assay revealed a G2/M phase cell cycle arrest at all tested concentrations for 43d, caused by inhibition of CDK16.
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Affiliation(s)
- Jennifer Alisa Amrhein
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Lena Marie Berger
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Amelie Tjaden
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Andreas Krämer
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), DKTK Site Frankfurt-Mainz, 69120 Heidelberg, Germany
| | - Lewis Elson
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Tuomas Tolvanen
- Division of Rheumatology, Department of Medicine Solna, Karolinska University Hospital and Karolinska Institute, Solnavägen 1, 17177 Solna, Sweden
| | | | - Astrid Kaiser
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Manfred Schubert-Zsilavecz
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
| | - Susanne Müller
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), DKTK Site Frankfurt-Mainz, 69120 Heidelberg, Germany
- Correspondence: (S.K.); (T.H.)
| | - Thomas Hanke
- Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt am Main, Germany
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt am Main, Germany
- Correspondence: (S.K.); (T.H.)
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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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11
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Lin Z, Woo CM. Methods to characterize and discover molecular degraders in cells. Chem Soc Rev 2022; 51:7115-7137. [PMID: 35899832 DOI: 10.1039/d2cs00261b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cells use many post-translational modifications (PTMs) to tailor proteins and transduce cellular signals. Recent years have witnessed the rapid growth of small molecule and enzymatic strategies to purposely manipulate one particular PTM, ubiquitination, on desired target proteins in cells. These approaches typically act by induced proximity between an E3 ligase and a target protein resulting in ubiquitination and degradation of the substrate in cells. In this review, we cover recent approaches to study molecular degraders and discover their induced substrates in vitro and in live cells. Methods that have been adapted and applied to the development of molecular degraders are described, including global proteomics, affinity-purification, chemical proteomics and enzymatic strategies. Extension of these strategies to edit additional PTMs in cells is also discussed. This review is intended to assist researchers who are interested in editing PTMs with new modalities to select suitable method(s) and guide their studies.
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Affiliation(s)
- Zhi Lin
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
| | - Christina M Woo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
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12
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Abstract
Knowing that the drug candidate binds to its intended target is a vital part of drug discovery. Thus, several labeled and label-free methods have been developed to study target engagement. In recent years, the cellular thermal shift assay (CETSA) with its variations has been widely adapted to drug discovery workflows. Western blot–based CETSA is used primarily to validate the target binding of a molecule to its target protein whereas CETSA based on bead chemistry detection methods (CETSA HT) has been used to screen molecular libraries to find novel molecules binding to a pre-determined target. Mass spectrometry–based CETSA also known as thermal proteome profiling (TPP) has emerged as a powerful tool for target deconvolution and finding novel binding partners for old and novel molecules. With this technology, it is possible to probe thermal shifts among over 7,000 proteins from one sample and to identify the wanted target binding but also binding to unwanted off-targets known to cause adverse effects. In addition, this proteome-wide method can provide information on the biological process initiated by the ligand binding. The continued development of mass spectrometry labeling reagents, such as isobaric tandem mass tag technology (TMT) continues to increase the throughput of CETSA MS, allowing its use for structure–activity relationship (SAR) studies with a limited number of molecules. In this review, we discussed the differences between different label-free methods to study target engagement, but our focus was on CETSA and recent advances in the CETSA method.
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Affiliation(s)
- Tuomas Aleksi Tolvanen
- Division of Rheumatology, Department of Medicine Solna, Karolinska University Hospital and Karolinska Institute, Stockholm, Sweden.,Pelago Bioscience AB, Solna, Sweden
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13
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Dayalan Naidu S, Dikovskaya D, Moore TW, Dinkova-Kostova AT. Detection of thermal shift in cellular Keap1 by protein-protein interaction inhibitors using immunoblot- and fluorescence microplate-based assays. STAR Protoc 2022; 3:101265. [PMID: 35391936 PMCID: PMC8980889 DOI: 10.1016/j.xpro.2022.101265] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Pharmacologic inhibition of the protein-protein interaction (PPI) interface of the Keap1:Nrf2 complex, which leads to Nrf2 activation and cytoprotective gene expression, offers a promising strategy for disease prevention and treatment. To facilitate identification and validation of small-molecule Keap1:Nrf2 PPI inhibitors in the cellular environment in a low- and medium-throughput manner, we detail two adapted cellular thermal shift assay (CETSA) protocols, Keap1-CETSA, an immunoblotting-based methodology for detecting endogenous Keap1, and Keap1-Glow CETSA, a microtiter plate assay of overexpressed fluorescently-tagged Keap1. For an example of the use and execution of this protocol, please refer to Dayalan Naidu et al. (2021).
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Affiliation(s)
- Sharadha Dayalan Naidu
- Division of Cellular Medicine, School of Medicine, University of Dundee, Dundee DD1 9SY, UK
| | - Dina Dikovskaya
- Division of Cellular Medicine, School of Medicine, University of Dundee, Dundee DD1 9SY, UK
| | - Terry W. Moore
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Albena T. Dinkova-Kostova
- Division of Cellular Medicine, School of Medicine, University of Dundee, Dundee DD1 9SY, UK
- Department of Pharmacology and Molecular Sciences and Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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14
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Campbell RM. The SLAS Discovery Editor's Top 10 for 2021. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2022; 27:77-78. [PMID: 35104635 DOI: 10.1016/j.slasd.2022.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
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Hendricks JA, Beaton N, Chernobrovkin A, Miele E, Hamza GM, Ricchiuto P, Tomlinson RC, Friman T, Borenstain C, Barlaam B, Hande S, Lamb ML, De Savi C, Davies R, Main M, Hellner J, Beeler K, Feng Y, Bruderer R, Reiter L, Molina DM, Castaldi MP. Mechanistic Insights into a CDK9 Inhibitor Via Orthogonal Proteomics Methods. ACS Chem Biol 2022; 17:54-67. [PMID: 34955012 DOI: 10.1021/acschembio.1c00488] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cyclin-dependent-kinases (CDKs) are members of the serine/threonine kinase family and are highly regulated by cyclins, a family of regulatory subunits that bind to CDKs. CDK9 represents one of the most studied examples of these transcriptional CDKs. CDK9 forms a heterodimeric complex with its regulatory subunit cyclins T1, T2 and K to form the positive transcription elongation factor b (P-TEFb). This complex regulates transcription via the phosphorylation of RNA polymerase II (RNAPolII) on Ser-2, facilitating promoter clearance and transcription elongation and thus remains an attractive therapeutic target. Herein, we have utilized classical affinity purification chemical proteomics, kinobeads assay, compressed CEllular Thermal Shift Assay (CETSA)-MS and Limited Proteolysis (LiP) to study the selectivity, target engagement and downstream mechanistic insights of a CDK9 tool compound. The above experiments highlight the value of quantitative mass spectrometry approaches to drug discovery, specifically proteome wide target identification and selectivity profiling. The approaches utilized in this study unanimously indicated that the CDK family of kinases are the main target of the compound of interest, with CDK9, showing the highest target affinity with remarkable consistency across approaches. We aim to provide guidance to the scientific community on the available chemical biology/proteomic tools to study advanced lead molecules and to highlight pros and cons of each technology while describing our findings in the context of the CDKs biology.
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Affiliation(s)
- J. Adam Hendricks
- Discovery Sciences, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Nigel Beaton
- Biognosys AG, Wagistrasse 21, Schlieren 8952, Switzerland
| | | | - Eric Miele
- Discovery Sciences, AstraZeneca, Boston, Massachusetts 02451, United States
| | - Ghaith M. Hamza
- Discovery Sciences, AstraZeneca, Boston, Massachusetts 02451, United States
- Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire 03824, United States
| | | | | | - Tomas Friman
- Pelago Bioscience AB, Banvaktsvägen 20, Solna 17148, Sweden
| | | | | | - Sudhir Hande
- Oncology R&D, Boston, Massachusetts 02451, United States
| | | | - Chris De Savi
- Oncology R&D, Boston, Massachusetts 02451, United States
| | - Rick Davies
- Discovery Sciences, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Martin Main
- Discovery Sciences, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Joakim Hellner
- Pelago Bioscience AB, Banvaktsvägen 20, Solna 17148, Sweden
| | | | - Yuehan Feng
- Biognosys AG, Wagistrasse 21, Schlieren 8952, Switzerland
| | | | - Lukas Reiter
- Biognosys AG, Wagistrasse 21, Schlieren 8952, Switzerland
| | | | - M. Paola Castaldi
- Discovery Sciences, AstraZeneca, Boston, Massachusetts 02451, United States
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Chen L, Zhang J, Wang X, Li Y, Zhou L, Lu X, Dong G, Sheng C. Discovery of novel KRAS‒PDE δ inhibitors with potent activity in patient-derived human pancreatic tumor xenograft models. Acta Pharm Sin B 2022; 12:274-290. [PMID: 35127385 PMCID: PMC8799878 DOI: 10.1016/j.apsb.2021.07.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/03/2021] [Accepted: 07/05/2021] [Indexed: 11/15/2022] Open
Abstract
KRAS‒PDEδ interaction is revealed as a promising target for suppressing the function of mutant KRAS. The bottleneck in clinical development of PDEδ inhibitors is the poor antitumor activity of known chemotypes. Here, we identified novel spiro-cyclic PDEδ inhibitors with potent antitumor activity both in vitro and in vivo. In particular, compound 36l (K D = 127 ± 16 nmol/L) effectively bound to PDEδ and interfered with KRAS-PDEδ interaction. It influenced the distribution of KRAS in Mia PaCa-2 cells, downregulated the phosphorylation of t-ERK and t-AKT and promoted apoptosis of the cells. The novel inhibitor 36l exhibited significant in vivo antitumor potency in pancreatic cancer patient-derived xenograft (PDX) models. It represents a promising lead compound for investigating the druggability of KRAS‒PDEδ interaction.
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Affiliation(s)
- Long Chen
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Jing Zhang
- Department of Pathology, Changzheng Hospital, Second Military Medical University, Shanghai 200003, China
| | - Xinjing Wang
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University, Shanghai 200025, China
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yu Li
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Lu Zhou
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Xiongxiong Lu
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University, Shanghai 200025, China
- Research Institute of Pancreatic Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Corresponding authors. Tel./fax: +86 21 64370045 671003 (Xiongxiong Lu), +86 21 81871242 (Guoqiang Dong), +86 21 81871239 (Chunquan Sheng).
| | - Guoqiang Dong
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China
- Corresponding authors. Tel./fax: +86 21 64370045 671003 (Xiongxiong Lu), +86 21 81871242 (Guoqiang Dong), +86 21 81871239 (Chunquan Sheng).
| | - Chunquan Sheng
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China
- Corresponding authors. Tel./fax: +86 21 64370045 671003 (Xiongxiong Lu), +86 21 81871242 (Guoqiang Dong), +86 21 81871239 (Chunquan Sheng).
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Kannt A, Đikić I. Expanding the arsenal of E3 ubiquitin ligases for proximity-induced protein degradation. Cell Chem Biol 2021; 28:1014-1031. [PMID: 33945791 DOI: 10.1016/j.chembiol.2021.04.007] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/09/2021] [Accepted: 04/05/2021] [Indexed: 12/13/2022]
Abstract
Efficacy and selectivity of molecules inducing protein degradation depend on their affinity to the target protein but also on the type of E3 ubiquitin ligase that is recruited to trigger proteasomal degradation. While tremendous progress has been made on the former, the latter-the arsenal of E3 ligases that can be hijacked for targeted protein degradation-is still largely unexplored. Only about 2% of the more than 600 E3 ligases have been utilized to date. Exploiting additional E3 ligases that are, for example, selectively expressed in specific tissues or cells, or regulated under certain conditions, can considerably broaden the applicability of molecular degraders as a therapeutic modality. Here, we provide an overview of major classes of E3 ligases, review the enzymes that have been exploited for induced protein degradation and approaches used to identify or design E3 ligands, and highlight challenges and opportunities for targeting new E3 ligases.
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Affiliation(s)
- Aimo Kannt
- Fraunhofer Institute of Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany; Fraunhofer Cluster of Excellence for Immune-Mediated Diseases CIMD, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany; Institute of Clinical Pharmacology, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany.
| | - Ivan Đikić
- Fraunhofer Institute of Translational Medicine and Pharmacology ITMP, Theodor-Stern-Kai 7, 60596 Frankfurt am Main, Germany; Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany; Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Max-von-Laue-Straße 15, 60438 Frankfurt am Main, Germany; Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Max-von-Laue Straße 3, 60438 Frankfurt am Main, Germany.
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Castaldi MP, Fisher SL. Advances in Protein Degradation. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2021; 26:471-473. [PMID: 33780295 DOI: 10.1177/24725552211001823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
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