1
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Greco FA, Krämer A, Wahl L, Elson L, Ehret TAL, Gerninghaus J, Möckel J, Müller S, Hanke T, Knapp S. Synthesis and evaluation of chemical linchpins for highly selective CK2α targeting. Eur J Med Chem 2024; 276:116672. [PMID: 39067440 DOI: 10.1016/j.ejmech.2024.116672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 07/08/2024] [Accepted: 07/09/2024] [Indexed: 07/30/2024]
Abstract
Casein kinase-2 (CK2) are serine/threonine kinases with dual co-factor (ATP and GTP) specificity, that are involved in the regulation of a wide variety of cellular functions. Small molecules targeting CK2 have been described in the literature targeting different binding pockets of the kinase with a focus on type I inhibitors such as the recently published chemical probe SGC-CK2-1. In this study, we investigated whether known allosteric inhibitors binding to a pocket adjacent to helix αD could be combined with ATP mimetic moieties defining a novel class of ATP competitive compounds with a unique binding mode. Linking both binding sites requires a chemical linking moiety that would introduce a 90-degree angle between the ATP mimetic ring system and the αD targeting moiety, which was realized using a sulfonamide. The synthesized inhibitors were highly selective for CK2 with binding constants in the nM range and low micromolar activity. While these inhibitors need to be further improved, the present work provides a structure-based design strategy for highly selective CK2 inhibitors.
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Affiliation(s)
- Francesco A Greco
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt Am Main, Germany; Structural Genomics Consortium, Buchmann Institute for Molecular 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 Molecular 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
| | - Laurenz Wahl
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt Am Main, Germany; Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt Am Main, 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 Molecular Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt Am Main, Germany
| | - Theresa A L Ehret
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt Am Main, Germany; Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt Am Main, Germany
| | - Joshua Gerninghaus
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt Am Main, Germany; Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt Am Main, Germany
| | - Janina Möckel
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438 Frankfurt Am Main, Germany; Structural Genomics Consortium, Buchmann Institute for Molecular Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 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 Molecular Life Sciences, Goethe-University Frankfurt, Max-von-Laue-Str. 15, 60438 Frankfurt Am Main, Germany
| | - 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 Molecular 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 Molecular 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.
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2
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Rovers E, Schapira M. Benchmarking Methods for PROTAC Ternary Complex Structure Prediction. J Chem Inf Model 2024; 64:6162-6173. [PMID: 39087481 DOI: 10.1021/acs.jcim.4c00426] [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: 08/02/2024]
Abstract
Proteolysis targeting chimeras (PROTACs) are bifunctional compounds that recruit an E3 ligase to a target protein to induce ubiquitination and degradation of the target. Rational optimization of PROTAC requires a structural model of the ternary complex. In the absence of an experimental structure, computational tools have emerged that attempt to predict PROTAC ternary complexes. Here, we systematically benchmark three commonly used tools: PRosettaC, MOE, and ICM. We find that these PROTAC-focused methods produce an array of ternary complex structures, including some that are observed experimentally, but also many that significantly deviate from the crystal structure. Molecular dynamics simulations show that PROTAC complexes may exist in a multiplicity of configurational states and question the use of experimentally observed structures as a reference for accurate predictions. The pioneering computational tools benchmarked here highlight the promises and challenges in the field and may be more valuable when guided by clear structural and biophysical data. The benchmarking data set that we provide may also be valuable for evaluating other and future computational tools for ternary complex modeling.
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Affiliation(s)
- Evianne Rovers
- Structural Genomics Consortium, Toronto M5G 1L7, Canada
- Department of Pharmacology, University of Toronto, Toronto M5G 1L7, Canada
| | - Matthieu Schapira
- Structural Genomics Consortium, Toronto M5G 1L7, Canada
- Department of Pharmacology, University of Toronto, Toronto M5G 1L7, Canada
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3
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Kumar H, Sobhia ME. Interplay of PROTAC Complex Dynamics for Undruggable Targets: Insights into Ternary Complex Behavior and Linker Design. ACS Med Chem Lett 2024; 15:1306-1318. [PMID: 39140051 PMCID: PMC11317996 DOI: 10.1021/acsmedchemlett.4c00189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 07/25/2024] [Accepted: 07/25/2024] [Indexed: 08/15/2024] Open
Abstract
Protein degraders, such as bifunctional proteolysis-targeting chimeras (PROTACs), selectively eliminate target proteins by leveraging the natural protein degradation machinery. PROTACs bridge the target protein with an E3 ligase, which induces ubiquitination and degradation. Investigating ternary complex structures elucidates the molecular mechanisms of their formation and degradation. This study examines the binding dynamics of E3 ligases (VHL, CRBN, and cIAP) with proteins of interest, focusing on dynamics, cooperativity, selectivity, linker length, and PROTAC conformations. The influence of interface residues and linker lengths on specific conformations for target proteins and E3 ligases is highlighted. Utilizing molecular dynamics and steered molecular dynamics simulations, the study provides comprehensive parameters on the behavior and stability of diverse ternary complexes. These insights are crucial for designing PROTACs targeting disease-causing proteins and advancing the development of degradable ternary complexes for therapeutic applications.
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Affiliation(s)
- Harish Kumar
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and
Research (NIPER), Sector 67, S.A.S. Nagar (Mohali), 160062 Punjab, India
| | - Masilamani Elizabeth Sobhia
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and
Research (NIPER), Sector 67, S.A.S. Nagar (Mohali), 160062 Punjab, India
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4
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Schwalm MP, Saxena K, Müller S, Knapp S. Luciferase- and HaloTag-based reporter assays to measure small-molecule-induced degradation pathway in living cells. Nat Protoc 2024; 19:2317-2357. [PMID: 38637703 DOI: 10.1038/s41596-024-00979-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 01/31/2024] [Indexed: 04/20/2024]
Abstract
The rational development of small-molecule degraders (e.g., proteolysis targeting chimeras) remains a challenge as the rate-limiting steps that determine degrader efficiency are largely unknown. Standard methods in the field of targeted protein degradation mostly rely on classical, low-throughput endpoint assays such as western blots or quantitative proteomics. Here we applied NanoLuciferase- and HaloTag-based screening technologies to determine the kinetics and stability of small-molecule-induced ternary complex formation between a protein of interest and a selected E3 ligase. A collection of live-cell assays were designed to probe the most critical steps of the degradation process while minimizing the number of required expression constructs, making the proposed assay pipeline flexible and adaptable to the requirements of the users. This approach evaluates the underlying mechanism of selective target degraders and reveals the exact characteristics of the developed degrader molecules in living cells. The protocol allows scientists trained in basic cell culture and molecular biology to carry out small-molecule proximity-inducer screening via tracking of the ternary complex formation within 2 weeks of establishment, while degrader screening using the HiBiT system requires a CRISPR-Cas9 engineered cell line whose generation can take up to 3 months. After cell-line generation, degrader screening and validation can be carried out in high-throughput manner within days.
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Affiliation(s)
- Martin P Schwalm
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany.
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Frankfurt am Main, Germany.
- German Cancer Consortium (DKTK)/German Cancer Research Center (DKFZ), DTKT Site Frankfurt-Mainz, Heidelberg, Germany.
| | - Krishna Saxena
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Frankfurt am Main, Germany
| | - Susanne Müller
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Frankfurt am Main, Germany
| | - Stefan Knapp
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany.
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Frankfurt am Main, Germany.
- German Cancer Consortium (DKTK)/German Cancer Research Center (DKFZ), DTKT Site Frankfurt-Mainz, Heidelberg, Germany.
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5
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Zhao H. Structural Basis of Conformational Dynamics in the PROTAC-Induced Protein Degradation. ChemMedChem 2024; 19:e202400171. [PMID: 38655701 DOI: 10.1002/cmdc.202400171] [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: 03/04/2024] [Revised: 04/19/2024] [Accepted: 04/23/2024] [Indexed: 04/26/2024]
Abstract
Pronounced conformational dynamics is unveiled upon analyzing multiple crystal structures of the same proteins recruited to the same E3 ligases by PROTACs, and yet, is largely permissive for targeted protein degradation due to the intrinsic mobility of E3 assemblies creating a large ubiquitylation zone. Mathematical modelling of ternary dynamics on ubiquitylation probability confirms the experimental finding that ternary complex rigidification need not correlate with enhanced protein degradation. Salt bridges are found to prevail in the PROTAC-induced ternary complexes, and may contribute to a positive cooperativity and prolonged half-life. The analysis highlights the importance of presenting lysines close to the active site of the E2 enzyme while constraining ternary dynamics in PROTAC design to achieve high degradation efficiency.
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Affiliation(s)
- Hongtao Zhao
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
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6
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Dopfer J, Vasta JD, Müller S, Knapp S, Robers MB, Schwalm MP. tracerDB: a crowdsourced fluorescent tracer database for target engagement analysis. Nat Commun 2024; 15:5646. [PMID: 38969708 PMCID: PMC11226670 DOI: 10.1038/s41467-024-49896-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 06/20/2024] [Indexed: 07/07/2024] Open
Abstract
Investigating ligand-protein complexes is essential in the areas of chemical biology and drug discovery. However, detailed information on key reagents such as fluorescent tracers and associated data for the development of widely used bioluminescence resonance energy transfer (BRET) assays including NanoBRET, time-resolved Förster resonance energy transfer (TR-FRET) and fluorescence polarization (FP) assays are not easily accessible to the research community. We created tracerDB, a curated database of validated tracers. This resource provides an open access knowledge base and a unified system for tracer and assay validation. The database is freely available at https://www.tracerdb.org/ .
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Grants
- 424228829 Deutsche Forschungsgemeinschaft (German Research Foundation)
- M.P.S., J.D., S.M.K. and S.K. are grateful for support by the Structural Genomics Consortium (SGC), a registered charity (no: 1097737) that receives funds from Bayer AG, Boehringer Ingelheim, Bristol Myers Squibb, Genentech, Genome Canada through Ontario Genomics Institute, EU/EFPIA/OICR/McGill/KTH/Diamond Innovative Medicines Initiative 2 Joint Undertaking [EUbOPEN grant 875510], Janssen, Merck KGaA, Pfizer and Takeda, and by the German Cancer Research Center DKTK, and the Frankfurt Cancer Institute (FCI). M.P.S. is funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation), CRC1430 (Project-ID 424228829).
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Affiliation(s)
- Johannes Dopfer
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
- Structural Genomics Consortium, Goethe University Frankfurt, Buchmann Institute for Life Sciences, Max-von-Laue-Str. 15, 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, Goethe University Frankfurt, Buchmann Institute for Life Sciences, 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, Goethe University Frankfurt, Buchmann Institute for Life Sciences, 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
| | | | - Martin P Schwalm
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany.
- Structural Genomics Consortium, Goethe University Frankfurt, Buchmann Institute for Life Sciences, 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.
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7
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Tian Y, Seifermann M, Bauer L, Luchena C, Wiedmann JJ, Schmidt S, Geisel A, Afonin S, Höpfner J, Brehm M, Liu X, Hopf C, Popova AA, Levkin PA. High-Throughput Miniaturized Synthesis of PROTAC-Like Molecules. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2307215. [PMID: 38258390 DOI: 10.1002/smll.202307215] [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: 08/21/2023] [Revised: 01/03/2024] [Indexed: 01/24/2024]
Abstract
The development of miniaturized high-throughput in situ screening platforms capable of handling the entire process of drug synthesis to final screening is essential for advancing drug discovery in the future. In this study, an approach based on combinatorial solid-phase synthesis, enabling the efficient synthesis of libraries of proteolysis targeting chimeras (PROTACs) in an array format is presented. This on-chip platform allows direct biological screening without the need for transfer steps. UV-induced release of target molecules into individual droplets facilitates further on-chip experimentation. Utilizing a mitogen-activated protein kinase kinases (MEK1/2) degrader as a template, a series of 132 novel PROTAC-like molecules is synthesized using solid-phase Ugi reaction. These compounds are further characterized using various methods, including matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) imaging, while consuming only a few milligrams of starting materials in total. Furthermore, the feasibility of culturing cancer cells on the modified spots and quantifying the effect of MEK suppression is demonstrated. The miniaturized synthesis platform lays a foundation for high-throughput in situ biological screening of potent PROTACs for potential anticancer activity and offers the potential for accelerating the drug discovery process by integrating miniaturized synthesis and biological steps on the same array.
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Affiliation(s)
- Ye Tian
- Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Wenhuaxi Road 44, Jinan, 250012, China
- Department of Immunology, Key Laboratory for Experimental Teratology of Ministry of Education, Shandong Provincial Key Laboratory of Infection & Immunology, School of Basic Medical Sciences, Shandong University, Wenhuaxi Road 44, Jinan, 250012, China
| | - Maximilian Seifermann
- Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Liana Bauer
- Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Charlotte Luchena
- Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Janne J Wiedmann
- Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Stefan Schmidt
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), University of Applied Sciences Mannheim, Paul-Wittsack-Straße 10, 68163, Mannheim, Germany
| | - Alexander Geisel
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), University of Applied Sciences Mannheim, Paul-Wittsack-Straße 10, 68163, Mannheim, Germany
| | - Sergii Afonin
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), POB 3640, 76021, Karlsruhe, Germany
| | - Julius Höpfner
- Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Marius Brehm
- Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Shandong University, Wenhuaxi Road 44, Jinan, 250012, China
| | - Carsten Hopf
- Center for Mass Spectrometry and Optical Spectroscopy (CeMOS), University of Applied Sciences Mannheim, Paul-Wittsack-Straße 10, 68163, Mannheim, Germany
- Medical Faculty, Heidelberg University, Im Neuenheimer Feld 280, 69117, Heidelberg, Germany
- Mannheim Center for Translational Neuroscience (MCTN), Medical Faculty Mannheim, Heidelberg University, Theodor Kutzer-Ufer 1-3, 68167, Mannheim, Germany
| | - Anna A Popova
- Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
| | - Pavel A Levkin
- Institute of Biological and Chemical Systems-Functional Molecular Systems (IBCS-FMS), Karlsruhe Institute of Technology (KIT), Hermann-von Helmholtz-Platz 1, 76344, Eggenstein-Leopoldshafen, Germany
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8
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Huang X, Chen Y, Xiao Q, Shang X, Liu Y. Chemical inhibitors targeting histone methylation readers. Pharmacol Ther 2024; 256:108614. [PMID: 38401773 DOI: 10.1016/j.pharmthera.2024.108614] [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: 12/19/2023] [Revised: 02/01/2024] [Accepted: 02/15/2024] [Indexed: 02/26/2024]
Abstract
Histone methylation reader domains are protein modules that recognize specific histone methylation marks, such as methylated or unmethylated lysine or arginine residues on histones. These reader proteins play crucial roles in the epigenetic regulation of gene expression, chromatin structure, and DNA damage repair. Dysregulation of these proteins has been linked to various diseases, including cancer, neurodegenerative diseases, and developmental disorders. Therefore, targeting these proteins with chemical inhibitors has emerged as an attractive approach for therapeutic intervention, and significant progress has been made in this area. In this review, we will summarize the development of inhibitors targeting histone methylation readers, including MBT domains, chromodomains, Tudor domains, PWWP domains, PHD fingers, and WD40 repeat domains. For each domain, we will briefly discuss its identification and biological/biochemical functions, and then focus on the discovery of inhibitors tailored to target this domain, summarizing the property and potential application of most inhibitors. We will also discuss the structural basis for the potency and selectivity of these inhibitors, which will aid in further lead generation and optimization. Finally, we will also address the challenges and strategies involved in the development of these inhibitors. It should facilitate the rational design and development of novel chemical scaffolds and new targeting strategies for histone methylation reader domains with the help of this body of data.
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Affiliation(s)
- Xiaolei Huang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Yichang Chen
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Qin Xiao
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Xinci Shang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, PR China
| | - Yanli Liu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, PR China.
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9
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Weissmiller AM, Fesik SW, Tansey WP. WD Repeat Domain 5 Inhibitors for Cancer Therapy: Not What You Think. J Clin Med 2024; 13:274. [PMID: 38202281 PMCID: PMC10779565 DOI: 10.3390/jcm13010274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 12/14/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
WDR5 is a conserved nuclear protein that scaffolds the assembly of epigenetic regulatory complexes and moonlights in functions ranging from recruiting MYC oncoproteins to chromatin to facilitating the integrity of mitosis. It is also a high-value target for anti-cancer therapies, with small molecule WDR5 inhibitors and degraders undergoing extensive preclinical assessment. WDR5 inhibitors were originally conceived as epigenetic modulators, proposed to inhibit cancer cells by reversing oncogenic patterns of histone H3 lysine 4 methylation-a notion that persists to this day. This premise, however, does not withstand contemporary inspection and establishes expectations for the mechanisms and utility of WDR5 inhibitors that can likely never be met. Here, we highlight salient misconceptions regarding WDR5 inhibitors as epigenetic modulators and provide a unified model for their action as a ribosome-directed anti-cancer therapy that helps focus understanding of when and how the tumor-inhibiting properties of these agents can best be understood and exploited.
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Affiliation(s)
- April M. Weissmiller
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN 32132, USA;
| | - Stephen W. Fesik
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA;
- Department of Pharmacology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
- Department of Chemistry, Vanderbilt University, Nashville, TN 37232, USA
| | - William P. Tansey
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37232, USA;
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
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10
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Schwalm MP, Dopfer J, Knapp S, Rogov VV. High-Throughput Screening for LC3/GABARAP Binders Utilizing the Fluorescence Polarization Assay. Methods Mol Biol 2024; 2845:203-218. [PMID: 39115669 DOI: 10.1007/978-1-0716-4067-8_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/18/2024]
Abstract
The characterization of interactions between autophagy modifiers (Atg8-family proteins) and their natural ligands (peptides and proteins) or small molecules is important for a detailed understanding of selective autophagy mechanisms and for the design of potential Atg8 inhibitors that affect the autophagy processes in cells. The fluorescence polarization (FP) assay is a rapid, cost-effective, and robust method that provides affinity and selectivity information for small molecules and peptide ligands targeting human Atg8 proteins.This chapter introduces the basic principles of FP assays. In addition, a case study on peptide interaction with human Atg8 proteins (LC3/GABARAPs) is described. Finally, data analysis and quality control of FP assays are discussed for the proper calculation of Ki values for the measured compounds.
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Affiliation(s)
- Martin P Schwalm
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
- Structural Genomics Consortium, BMLS, Goethe University Frankfurt, Frankfurt, Germany
| | - Johannes Dopfer
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
- Structural Genomics Consortium, BMLS, Goethe University Frankfurt, Frankfurt, Germany
| | - Stefan Knapp
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt, Germany
- Structural Genomics Consortium, BMLS, Goethe University Frankfurt, Frankfurt, Germany
| | - Vladimir V Rogov
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Frankfurt, Germany.
- Structural Genomics Consortium, BMLS, Goethe University Frankfurt, Frankfurt, Germany.
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11
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Brownsey DK, Gafuik CJ, Kim DS, O'Sullivan L, Gorobets E, Krukowski S, Turk M, Jenne CN, Mahoney DJ, Derksen DJ. Utilising the intrinsic fluorescence of pomalidomide for imaging applications. Chem Commun (Camb) 2023; 59:14532-14535. [PMID: 38019727 DOI: 10.1039/d3cc04314b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023]
Abstract
Optimisation of protein degraders requires balancing multiple factors including potency, cell permeability and solubility. Here we show that the fluorescence of pomalidomide can be used in high-throughput screening assays to rapidly assess cellular penetration of degrader candidates. In addition, this technique can be paired with endocytosis inhibitors to gain insight into potential mechanisms of candidates entering a target cell. A model library of pomalidomide conjugates was synthesised and evaluated using high-throughput fluorescence microscopy. This technique based on intrinsic fluorescence can be used to guide rational design of pomalidomide conjugates without the need for additional labels or tags.
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Affiliation(s)
- Duncan K Brownsey
- Department of Chemistry, University of Calgary, Calgary, AB, Canada
- Alberta Children's Health Research Institute (ACHRI), University of Calgary, Calgary, AB, Canada
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB, Canada
| | - Christopher J Gafuik
- Alberta Children's Health Research Institute (ACHRI), University of Calgary, Calgary, AB, Canada
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB, Canada
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada
- Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Dae-Sun Kim
- Alberta Children's Health Research Institute (ACHRI), University of Calgary, Calgary, AB, Canada
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB, Canada
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada
- Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Leonie O'Sullivan
- Department of Chemistry, University of Calgary, Calgary, AB, Canada
- Alberta Children's Health Research Institute (ACHRI), University of Calgary, Calgary, AB, Canada
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB, Canada
| | - Evgueni Gorobets
- Department of Chemistry, University of Calgary, Calgary, AB, Canada
- Alberta Children's Health Research Institute (ACHRI), University of Calgary, Calgary, AB, Canada
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB, Canada
| | - Samuel Krukowski
- Department of Chemistry, University of Calgary, Calgary, AB, Canada
- Alberta Children's Health Research Institute (ACHRI), University of Calgary, Calgary, AB, Canada
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB, Canada
| | - Madison Turk
- Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
- Calvin, Phoebe, and Joan Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada
| | - Craig N Jenne
- Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
- Calvin, Phoebe, and Joan Snyder Institute for Chronic Diseases, University of Calgary, Calgary, AB, Canada
| | - Douglas J Mahoney
- Alberta Children's Health Research Institute (ACHRI), University of Calgary, Calgary, AB, Canada
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB, Canada
- Department of Biochemistry and Molecular Biology, University of Calgary, Calgary, AB, Canada
- Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Alberta, Canada
| | - Darren J Derksen
- Department of Chemistry, University of Calgary, Calgary, AB, Canada
- Alberta Children's Health Research Institute (ACHRI), University of Calgary, Calgary, AB, Canada
- Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, AB, Canada
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