1
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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. [PMID: 38981094 DOI: 10.1021/acs.jmedchem.4c00723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [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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Kagiou C, Cisneros JA, Farnung J, Liwocha J, Offensperger F, Dong K, Yang K, Tin G, Horstmann CS, Hinterndorfer M, Paulo JA, Scholes NS, Sanchez Avila J, Fellner M, Andersch F, Hannich JT, Zuber J, Kubicek S, Gygi SP, Schulman BA, Winter GE. Alkylamine-tethered molecules recruit FBXO22 for targeted protein degradation. Nat Commun 2024; 15:5409. [PMID: 38926334 PMCID: PMC11208438 DOI: 10.1038/s41467-024-49739-3] [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: 01/29/2024] [Accepted: 06/18/2024] [Indexed: 06/28/2024] Open
Abstract
Targeted protein degradation (TPD) relies on small molecules to recruit proteins to E3 ligases to induce their ubiquitylation and degradation by the proteasome. Only a few of the approximately 600 human E3 ligases are currently amenable to this strategy. This limits the actionable target space and clinical opportunities and thus establishes the necessity to expand to additional ligases. Here we identify and characterize SP3N, a specific degrader of the prolyl isomerase FKBP12. SP3N features a minimal design, where a known FKBP12 ligand is appended with a flexible alkylamine tail that conveys degradation properties. We found that SP3N is a precursor and that the alkylamine is metabolized to an active aldehyde species that recruits the SCFFBXO22 ligase for FKBP12 degradation. Target engagement occurs via covalent adduction of Cys326 in the FBXO22 C-terminal domain, which is critical for ternary complex formation, ubiquitylation and degradation. This mechanism is conserved for two recently reported alkylamine-based degraders of NSD2 and XIAP, thus establishing alkylamine tethering and covalent hijacking of FBXO22 as a generalizable TPD strategy.
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Affiliation(s)
- Chrysanthi Kagiou
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Jose A Cisneros
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Jakob Farnung
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Joanna Liwocha
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Fabian Offensperger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Kevin Dong
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Ka Yang
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Gary Tin
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Christina S Horstmann
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
- St. Anna Children's Cancer Research Institute, Vienna, Austria
| | - Matthias Hinterndorfer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Natalie S Scholes
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Juan Sanchez Avila
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Michaela Fellner
- Research Institute of Molecular Pathology, Vienna BioCenter, 1030, Vienna, Austria
| | - Florian Andersch
- Research Institute of Molecular Pathology, Vienna BioCenter, 1030, Vienna, Austria
| | - J Thomas Hannich
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Johannes Zuber
- Research Institute of Molecular Pathology, Vienna BioCenter, 1030, Vienna, Austria
| | - Stefan Kubicek
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Brenda A Schulman
- Department of Molecular Machines and Signaling, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria.
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3
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Robinson SA, Co JA, Banik SM. Molecular glues and induced proximity: An evolution of tools and discovery. Cell Chem Biol 2024; 31:1089-1100. [PMID: 38688281 DOI: 10.1016/j.chembiol.2024.04.001] [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: 07/25/2023] [Revised: 01/23/2024] [Accepted: 04/02/2024] [Indexed: 05/02/2024]
Abstract
Small molecule molecular glues can nucleate protein complexes and rewire interactomes. Molecular glues are widely used as probes for understanding functional proximity at a systems level, and the potential to instigate event-driven pharmacology has motivated their application as therapeutics. Despite advantages such as cell permeability and the potential for low off-target activity, glues are still rare when compared to canonical inhibitors in therapeutic development. Their often simple structure and specific ability to reshape protein-protein interactions pose several challenges for widespread, designer applications. Molecular glue discovery and design campaigns can find inspiration from the fields of synthetic biology and biophysics to mine chemical libraries for glue-like molecules.
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Affiliation(s)
| | | | - Steven Mark Banik
- Department of Chemistry, Stanford University, Stanford, CA, USA; Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
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4
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Konstantinidou M, Arkin MR. Molecular glues for protein-protein interactions: Progressing toward a new dream. Cell Chem Biol 2024; 31:1064-1088. [PMID: 38701786 PMCID: PMC11193649 DOI: 10.1016/j.chembiol.2024.04.002] [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: 01/04/2024] [Revised: 03/08/2024] [Accepted: 04/08/2024] [Indexed: 05/05/2024]
Abstract
The modulation of protein-protein interactions with small molecules is one of the most rapidly developing areas in drug discovery. In this review, we discuss advances over the past decade (2014-2023) focusing on molecular glues (MGs)-monovalent small molecules that induce proximity, either by stabilizing native interactions or by inducing neomorphic interactions. We include both serendipitous and rational discoveries and describe the different approaches that were used to identify them. We classify the compounds in three main categories: degradative MGs, non-degradative MGs or PPI stabilizers, and MGs that induce self-association. Diverse, illustrative examples with structural data are described in detail, emphasizing the elements of molecular recognition and cooperative binding at the interface that are fundamental for a MG mechanism of action.
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Affiliation(s)
- Markella Konstantinidou
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco, San Francisco, CA 94143, USA
| | - Michelle R Arkin
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco, San Francisco, CA 94143, USA.
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5
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Wang B, Cao S, Zheng N. Emerging strategies for prospective discovery of molecular glue degraders. Curr Opin Struct Biol 2024; 86:102811. [PMID: 38598983 DOI: 10.1016/j.sbi.2024.102811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/14/2024] [Accepted: 03/15/2024] [Indexed: 04/12/2024]
Abstract
Molecular glue (MG) degraders are monovalent small molecule compounds that co-opt E3 ubiquitin ligases to target neo-substrates for proteasomal degradation. Here, we provide a concise review of recent advances in rational MG discovery, which are categorized into two major strategies, ligand modification and de novo discovery. We also highlight the structural mechanisms underlying the formation of MG-enabled ternary complexes and their thermodynamic properties. Finally, we summarize the broader category of proximity inducers including MGs, proteolysis-targeting chimeras (PROTACs), peptides, and viral proteins. MGs are specified as a unique class of proximity inducers with chemical simplicity and a requirement of pre-existing weak protein-protein interactions. We propose that leveraging the weak basal interaction provides a starting point to prospectively develop MGs to degrade high-value therapeutic targets.
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Affiliation(s)
- Baiyun Wang
- Department of Pharmacology, Box 357280, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Shiyun Cao
- Department of Pharmacology, Box 357280, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Ning Zheng
- Department of Pharmacology, Box 357280, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
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6
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Chen Y, Xue H, Jin J. Applications of protein ubiquitylation and deubiquitylation in drug discovery. J Biol Chem 2024; 300:107264. [PMID: 38582446 PMCID: PMC11087986 DOI: 10.1016/j.jbc.2024.107264] [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: 07/09/2023] [Revised: 03/29/2024] [Accepted: 04/01/2024] [Indexed: 04/08/2024] Open
Abstract
The ubiquitin (Ub)-proteasome system (UPS) is the major machinery mediating specific protein turnover in eukaryotic cells. By ubiquitylating unwanted, damaged, or harmful proteins and driving their degradation, UPS is involved in many important cellular processes. Several new UPS-based technologies, including molecular glue degraders and PROTACs (proteolysis-targeting chimeras) to promote protein degradation, and DUBTACs (deubiquitinase-targeting chimeras) to increase protein stability, have been developed. By specifically inducing the interactions between different Ub ligases and targeted proteins that are not otherwise related, molecular glue degraders and PROTACs degrade targeted proteins via the UPS; in contrast, by inducing the proximity of targeted proteins to deubiquitinases, DUBTACs are created to clear degradable poly-Ub chains to stabilize targeted proteins. In this review, we summarize the recent research progress in molecular glue degraders, PROTACs, and DUBTACs and their applications. We discuss immunomodulatory drugs, sulfonamides, cyclin-dependent kinase-targeting molecular glue degraders, and new development of PROTACs. We also introduce the principle of DUBTAC and its applications. Finally, we propose a few future directions of these three technologies related to targeted protein homeostasis.
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Affiliation(s)
- Yilin Chen
- Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Haoan Xue
- Life Sciences Institute, Zhejiang University, Hangzhou, China; Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, China
| | - Jianping Jin
- Life Sciences Institute, Zhejiang University, Hangzhou, China; Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, China; Cancer Center, Zhejiang University, Hangzhou, China.
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7
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Tsai JM, Nowak RP, Ebert BL, Fischer ES. Targeted protein degradation: from mechanisms to clinic. Nat Rev Mol Cell Biol 2024:10.1038/s41580-024-00729-9. [PMID: 38684868 DOI: 10.1038/s41580-024-00729-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2024] [Indexed: 05/02/2024]
Abstract
Targeted protein degradation refers to the use of small molecules to induce the selective degradation of proteins. In its most common form, this degradation is achieved through ligand-mediated neo-interactions between ubiquitin E3 ligases - the principal waste disposal machines of a cell - and the protein targets of interest, resulting in ubiquitylation and subsequent proteasomal degradation. Notable advances have been made in biological and mechanistic understanding of serendipitously discovered degraders. This improved understanding and novel chemistry has not only provided clinical proof of concept for targeted protein degradation but has also led to rapid growth of the field, with dozens of investigational drugs in active clinical trials. Two distinct classes of protein degradation therapeutics are being widely explored: bifunctional PROTACs and molecular glue degraders, both of which have their unique advantages and challenges. Here, we review the current landscape of targeted protein degradation approaches and how they have parallels in biological processes. We also outline the ongoing clinical exploration of novel degraders and provide some perspectives on the directions the field might take.
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Affiliation(s)
- Jonathan M Tsai
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Radosław P Nowak
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Institute of Structural Biology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Benjamin L Ebert
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Boston, MA, USA.
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
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8
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Lucas SCC, Ahmed A, Ashraf SN, Argyrou A, Bauer MR, De Donatis GM, Demanze S, Eisele F, Fusani L, Hock A, Kadamur G, Li S, Macmillan-Jones A, Michaelides IN, Phillips C, Rehnström M, Richter M, Rodrigo-Brenni MC, Shilliday F, Wang P, Storer RI. Optimization of Potent Ligands for the E3 Ligase DCAF15 and Evaluation of Their Use in Heterobifunctional Degraders. J Med Chem 2024; 67:5538-5566. [PMID: 38513086 DOI: 10.1021/acs.jmedchem.3c02136] [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: 03/23/2024]
Abstract
Unlocking novel E3 ligases for use in heterobifunctional PROTAC degraders is of high importance to the pharmaceutical industry. Over-reliance on the current suite of ligands used to recruit E3 ligases could limit the potential of their application. To address this, potent ligands for DCAF15 were optimized using cryo-EM supported, structure-based design to improve on micromolar starting points. A potent binder, compound 24, was identified and subsequently conjugated into PROTACs against multiple targets. Following attempts on degrading a number of proteins using DCAF15 recruiting PROTACs, only degradation of BRD4 was observed. Deconvolution of the mechanism of action showed that this degradation was not mediated by DCAF15, thereby highlighting both the challenges faced when trying to expand the toolbox of validated E3 ligase ligands for use in PROTAC degraders and the pitfalls of using BRD4 as a model substrate.
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Affiliation(s)
- Simon C C Lucas
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Afshan Ahmed
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - S Neha Ashraf
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Argyrides Argyrou
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Matthias R Bauer
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | | | - Sylvain Demanze
- Oncology Chemistry, Oncology R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Frederik Eisele
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg SE-431 83,Sweden
| | - Lucia Fusani
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Andreas Hock
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Ganesh Kadamur
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Shuyou Li
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176, People's Republic of China
| | | | | | - Christopher Phillips
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Marie Rehnström
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg SE-431 83, Sweden
| | - Magdalena Richter
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Monica C Rodrigo-Brenni
- Safety Innovation and PROTAC Safety, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Fiona Shilliday
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Peng Wang
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176, People's Republic of China
| | - R Ian Storer
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
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9
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Giardina SF, Valdambrini E, Singh PK, Bacolod MD, Babu-Karunakaran G, Peel M, Warren JD, Barany F. Combinatorial Ubiquitination REal-time PROteolysis (CURE-PROs): A Modular Platform for Generating Reversible, Self-Assembling Bifunctional Targeted Degraders. J Med Chem 2024; 67:5473-5501. [PMID: 38554135 DOI: 10.1021/acs.jmedchem.3c02097] [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: 04/01/2024]
Abstract
Proteolysis-Targeting Chimeras (PROTACs) are bifunctional molecules that bring a target protein and an E3 ubiquitin ligase into proximity to append ubiquitin, thus directing target degradation. Although numerous PROTACs have entered clinical trials, their development remains challenging, and their large size can produce poor drug-like properties. To overcome these limitations, we have modified our Coferon platform to generate Combinatorial Ubiquitination REal-time PROteolysis (CURE-PROs). CURE-PROs are small molecule degraders designed to self-assemble through reversible bio-orthogonal linkers to form covalent heterodimers. By modifying known ligands for Cereblon, MDM2, VHL, and BRD with complementary phenylboronic acid and diol/catechol linkers, we have successfully created CURE-PROs that direct degradation of BRD4 both in vitro and in vivo. The combinatorial nature of our platform significantly reduces synthesis time and effort to identify the optimal linker length and E3 ligase partner to each target and is readily amenable to screening for new targets.
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Affiliation(s)
- Sarah F Giardina
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10065, United States
| | - Elena Valdambrini
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10065, United States
| | - Pradeep K Singh
- Department of Biochemistry, Weill Cornell Medicine, New York, New York 10065, United States
| | - Manny D Bacolod
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10065, United States
| | | | - Michael Peel
- MRP Pharma LLC, Chapel Hill, North Carolina 27514, United States
| | - J David Warren
- Department of Biochemistry, Weill Cornell Medicine, New York, New York 10065, United States
| | - Francis Barany
- Department of Microbiology and Immunology, Weill Cornell Medicine, New York, New York 10065, United States
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10
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Lemaitre T, Cornu M, Schwalen F, Since M, Kieffer C, Voisin-Chiret AS. Molecular glue degraders: exciting opportunities for novel drug discovery. Expert Opin Drug Discov 2024; 19:433-449. [PMID: 38240114 DOI: 10.1080/17460441.2024.2306845] [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: 10/06/2023] [Accepted: 01/15/2024] [Indexed: 01/25/2024]
Abstract
INTRODUCTION Molecular Glue Degraders (MGDs) is a concept that refers to a class of compounds that facilitate the interaction between two proteins or molecules within a cell. These compounds act as bridge that enhances specific Protein-Protein Interactions (PPIs). Over the past decade, this technology has gained attention as a potential strategy to target proteins that were traditionally considered undruggable using small molecules. AREAS COVERED This review presents the concept of cellular homeostasis and the balance between protein synthesis and protein degradation. The concept of protein degradation is concerned with molecular glues, which form part of the broader field of Targeted Protein Degradation (TPD). Next, pharmacochemical strategies for the rational design of MGDs are detailed and illustrated by examples of Ligand-Based (LBDD), Structure-Based (SBDD) and Fragment-Based Drug Design (FBDD). EXPERT OPINION Expanding the scope of what can be effectively targeted in the development of treatments for diseases that are incurable or resistant to conventional therapies offers new therapeutic options. The treatment of microbial infections and neurodegenerative diseases is a major societal challenge, and the discovery of MGDs appears to be a promising avenue. Combining different approaches to discover and exploit a variety of innovative therapeutic agents will create opportunities to treat diseases that are still incurable.
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Affiliation(s)
| | - Marie Cornu
- Normandie University, UNICAEN, CERMN, Caen, France
| | - Florian Schwalen
- Normandie University, UNICAEN, CERMN, Caen, France
- Department of Pharmacy, Caen University Hospital, Caen, France
| | - Marc Since
- Normandie University, UNICAEN, CERMN, Caen, France
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11
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Bouvier C, Lawrence R, Cavallo F, Xolalpa W, Jordan A, Hjerpe R, Rodriguez MS. Breaking Bad Proteins-Discovery Approaches and the Road to Clinic for Degraders. Cells 2024; 13:578. [PMID: 38607017 PMCID: PMC11011670 DOI: 10.3390/cells13070578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/12/2024] [Accepted: 03/18/2024] [Indexed: 04/13/2024] Open
Abstract
Proteolysis-targeting chimeras (PROTACs) describe compounds that bind to and induce degradation of a target by simultaneously binding to a ubiquitin ligase. More generally referred to as bifunctional degraders, PROTACs have led the way in the field of targeted protein degradation (TPD), with several compounds currently undergoing clinical testing. Alongside bifunctional degraders, single-moiety compounds, or molecular glue degraders (MGDs), are increasingly being considered as a viable approach for development of therapeutics, driven by advances in rational discovery approaches. This review focuses on drug discovery with respect to bifunctional and molecular glue degraders within the ubiquitin proteasome system, including analysis of mechanistic concepts and discovery approaches, with an overview of current clinical and pre-clinical degrader status in oncology, neurodegenerative and inflammatory disease.
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Affiliation(s)
- Corentin Bouvier
- Laboratoire de Chimie de Coordination LCC-UPR 8241-CNRS, 31077 Toulouse, France; (C.B.); (M.S.R.)
| | - Rachel Lawrence
- Sygnature Discovery, Bio City, Pennyfoot St., Nottingham NG1 1GR, UK (F.C.); (A.J.)
| | - Francesca Cavallo
- Sygnature Discovery, Bio City, Pennyfoot St., Nottingham NG1 1GR, UK (F.C.); (A.J.)
| | - Wendy Xolalpa
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62209, Morelos, Mexico;
| | - Allan Jordan
- Sygnature Discovery, Bio City, Pennyfoot St., Nottingham NG1 1GR, UK (F.C.); (A.J.)
| | - Roland Hjerpe
- Sygnature Discovery, Bio City, Pennyfoot St., Nottingham NG1 1GR, UK (F.C.); (A.J.)
| | - Manuel S. Rodriguez
- Laboratoire de Chimie de Coordination LCC-UPR 8241-CNRS, 31077 Toulouse, France; (C.B.); (M.S.R.)
- Pharmadev, UMR 152, Université de Toulouse, IRD, UT3, 31400 Toulouse, France
- B Molecular, Centre Pierre Potier, Canceropôle, 31106 Toulouse, France
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12
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Hsia O, Hinterndorfer M, Cowan AD, Iso K, Ishida T, Sundaramoorthy R, Nakasone MA, Imrichova H, Schätz C, Rukavina A, Husnjak K, Wegner M, Correa-Sáez A, Craigon C, Casement R, Maniaci C, Testa A, Kaulich M, Dikic I, Winter GE, Ciulli A. Targeted protein degradation via intramolecular bivalent glues. Nature 2024; 627:204-211. [PMID: 38383787 PMCID: PMC10917667 DOI: 10.1038/s41586-024-07089-6] [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: 02/18/2023] [Accepted: 01/18/2024] [Indexed: 02/23/2024]
Abstract
Targeted protein degradation is a pharmacological modality that is based on the induced proximity of an E3 ubiquitin ligase and a target protein to promote target ubiquitination and proteasomal degradation. This has been achieved either via proteolysis-targeting chimeras (PROTACs)-bifunctional compounds composed of two separate moieties that individually bind the target and E3 ligase, or via molecular glues that monovalently bind either the ligase or the target1-4. Here, using orthogonal genetic screening, biophysical characterization and structural reconstitution, we investigate the mechanism of action of bifunctional degraders of BRD2 and BRD4, termed intramolecular bivalent glues (IBGs), and find that instead of connecting target and ligase in trans as PROTACs do, they simultaneously engage and connect two adjacent domains of the target protein in cis. This conformational change 'glues' BRD4 to the E3 ligases DCAF11 or DCAF16, leveraging intrinsic target-ligase affinities that do not translate to BRD4 degradation in the absence of compound. Structural insights into the ternary BRD4-IBG1-DCAF16 complex guided the rational design of improved degraders of low picomolar potency. We thus introduce a new modality in targeted protein degradation, which works by bridging protein domains in cis to enhance surface complementarity with E3 ligases for productive ubiquitination and degradation.
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Affiliation(s)
- Oliver Hsia
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK
| | - Matthias Hinterndorfer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Angus D Cowan
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK
| | - Kentaro Iso
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK
- Tsukuba Research Laboratory, Eisai Co., Ibaraki, Japan
| | - Tasuku Ishida
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK
- Tsukuba Research Laboratory, Eisai Co., Ibaraki, Japan
| | | | - Mark A Nakasone
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK
| | - Hana Imrichova
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Caroline Schätz
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Andrea Rukavina
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Koraljka Husnjak
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Martin Wegner
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Alejandro Correa-Sáez
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK
| | - Conner Craigon
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK
| | - Ryan Casement
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK
| | - Chiara Maniaci
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK
- Medical Research Council (MRC) Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee, UK
| | - Andrea Testa
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK
- Amphista Therapeutics, Cambridge, UK
| | - Manuel Kaulich
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Ivan Dikic
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
| | - Alessio Ciulli
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee, UK.
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13
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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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14
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Nalawansha DA, Mangano K, den Besten W, Potts PR. TAC-tics for Leveraging Proximity Biology in Drug Discovery. Chembiochem 2024; 25:e202300712. [PMID: 38015747 DOI: 10.1002/cbic.202300712] [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: 10/17/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 11/30/2023]
Abstract
Chemically induced proximity (CIP) refers to co-opting naturally occurring biological pathways using synthetic molecules to recruit neosubstrates that are not normally encountered or to enhance the affinity of naturally occurring interactions. Leveraging proximity biology through CIPs has become a rapidly evolving field and has garnered considerable interest in basic research and drug discovery. PROteolysis TArgeting Chimera (PROTAC) is a well-established CIP modality that induces the proximity between a target protein and an E3 ubiquitin ligase, causing target protein degradation via the ubiquitin-proteasome system. Inspired by PROTACs, several other induced proximity modalities have emerged to modulate both proteins and RNA over recent years. In this review, we summarize the critical advances and opportunities in the field, focusing on protein degraders, RNA degraders and non-degrader modalities such as post-translational modification (PTM) and protein-protein interaction (PPI) modulators. We envision that these emerging proximity-based drug modalities will be valuable resources for both biological research and therapeutic discovery in the future.
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Affiliation(s)
| | - Kyle Mangano
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320, USA
| | - Willem den Besten
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320, USA
| | - Patrick Ryan Potts
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320, USA
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15
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Oleinikovas V, Gainza P, Ryckmans T, Fasching B, Thomä NH. From Thalidomide to Rational Molecular Glue Design for Targeted Protein Degradation. Annu Rev Pharmacol Toxicol 2024; 64:291-312. [PMID: 37585660 DOI: 10.1146/annurev-pharmtox-022123-104147] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
Thalidomide and its derivatives are powerful cancer therapeutics that are among the best-understood molecular glue degraders (MGDs). These drugs selectively reprogram the E3 ubiquitin ligase cereblon (CRBN) to commit target proteins for degradation by the ubiquitin-proteasome system. MGDs create novel recognition interfaces on the surface of the E3 ligase that engage in induced protein-protein interactions with neosubstrates. Molecular insight into their mechanism of action opens exciting opportunities to engage a plethora of targets through a specific recognition motif, the G-loop. Our analysis shows that current CRBN-based MGDs can in principle recognize over 2,500 proteins in the human proteome that contain a G-loop. We review recent advances in tuning the specificity between CRBN and its MGD-induced neosubstrates and deduce a set of simple rules that govern these interactions. We conclude that rational MGD design efforts will enable selective degradation of many more proteins, expanding this therapeutic modality to more disease areas.
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Affiliation(s)
| | | | | | | | - Nicolas H Thomä
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland;
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16
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Talukdar PD, Chatterji U. Transcriptional co-activators: emerging roles in signaling pathways and potential therapeutic targets for diseases. Signal Transduct Target Ther 2023; 8:427. [PMID: 37953273 PMCID: PMC10641101 DOI: 10.1038/s41392-023-01651-w] [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: 04/18/2023] [Revised: 08/27/2023] [Accepted: 09/10/2023] [Indexed: 11/14/2023] Open
Abstract
Specific cell states in metazoans are established by the symphony of gene expression programs that necessitate intricate synergic interactions between transcription factors and the co-activators. Deregulation of these regulatory molecules is associated with cell state transitions, which in turn is accountable for diverse maladies, including developmental disorders, metabolic disorders, and most significantly, cancer. A decade back most transcription factors, the key enablers of disease development, were historically viewed as 'undruggable'; however, in the intervening years, a wealth of literature validated that they can be targeted indirectly through transcriptional co-activators, their confederates in various physiological and molecular processes. These co-activators, along with transcription factors, have the ability to initiate and modulate transcription of diverse genes necessary for normal physiological functions, whereby, deregulation of such interactions may foster tissue-specific disease phenotype. Hence, it is essential to analyze how these co-activators modulate specific multilateral processes in coordination with other factors. The proposed review attempts to elaborate an in-depth account of the transcription co-activators, their involvement in transcription regulation, and context-specific contributions to pathophysiological conditions. This review also addresses an issue that has not been dealt with in a comprehensive manner and hopes to direct attention towards future research that will encompass patient-friendly therapeutic strategies, where drugs targeting co-activators will have enhanced benefits and reduced side effects. Additional insights into currently available therapeutic interventions and the associated constraints will eventually reveal multitudes of advanced therapeutic targets aiming for disease amelioration and good patient prognosis.
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Affiliation(s)
- Priyanka Dey Talukdar
- Cancer Research Laboratory, Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, West Bengal, India
| | - Urmi Chatterji
- Cancer Research Laboratory, Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, West Bengal, India.
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17
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Miao Q, Kadam VD, Mukherjee A, Tan Z, Teng M. Unlocking DCAFs To Catalyze Degrader Development: An Arena for Innovative Approaches. J Med Chem 2023; 66:13369-13383. [PMID: 37738232 DOI: 10.1021/acs.jmedchem.3c01209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
Chemically induced proximity-based targeted protein degradation (TPD) has become a prominent paradigm in drug discovery. With the clinical benefit demonstrated by certain small-molecule protein degraders that target the cullin-RING E3 ubiquitin ligases (CRLs), the field has proactively strategized to tackle anticipated drug resistance by harnessing additional E3 ubiquitin ligases to enrich the arsenal of this therapeutic approach. Here, we endeavor to explore the collaborative efforts involved in unlocking a broad range of CRL4DCAF for degrader drug development. Throughout the discussion, we also highlight how both conventional and innovative approaches in drug discovery can be taken to realize this objective. Moving ahead, we expect a greater allocation of resources in TPD to pursue these high-hanging fruits.
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Affiliation(s)
- Qi Miao
- Center for Drug Discovery, Department of Pathology & Immunology, and Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Vilas D Kadam
- Center for Drug Discovery, Department of Pathology & Immunology, and Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Ayan Mukherjee
- Center for Drug Discovery, Department of Pathology & Immunology, and Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Zhi Tan
- Center for Drug Discovery, Department of Pathology & Immunology, and Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Mingxing Teng
- Center for Drug Discovery, Department of Pathology & Immunology, and Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
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18
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Sarott RC, You I, Li YD, Toenjes ST, Donovan KA, Seo P, Ordonez M, Byun WS, Hassan MM, Wachter F, Chouchani ET, Słabicki M, Fischer ES, Ebert BL, Hinshaw SM, Gray NS. Chemical Specification of E3 Ubiquitin Ligase Engagement by Cysteine-Reactive Chemistry. J Am Chem Soc 2023; 145:21937-21944. [PMID: 37767920 DOI: 10.1021/jacs.3c06622] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2023]
Abstract
Targeted protein degradation relies on small molecules that induce new protein-protein interactions between targets and the cellular protein degradation machinery. Most of these small molecules feature specific ligands for ubiquitin ligases. Recently, the attachment of cysteine-reactive chemical groups to pre-existing small molecule inhibitors has been shown to drive specific target degradation. We demonstrate here that different cysteine-reactive groups can specify target degradation via distinct ubiquitin ligases. By focusing on the bromodomain ligand JQ1, we identify cysteine-reactive functional groups that drive BRD4 degradation by either DCAF16 or DCAF11. Unlike proteolysis-targeting chimeric molecules (PROTACs), the new compounds use a single small molecule ligand with a well-positioned cysteine-reactive group to induce protein degradation. The finding that nearly identical compounds can engage multiple ubiquitination pathways suggests that targeting cellular pathways that search for and eliminate chemically reactive proteins is a feasible avenue for converting existing small molecule drugs into protein degrader molecules.
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Affiliation(s)
- Roman C Sarott
- Department of Chemical and Systems Biology, ChEM-H, and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, California 94305, United States
| | - Inchul You
- Department of Chemical and Systems Biology, ChEM-H, and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, California 94305, United States
| | - Yen-Der Li
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138, United States
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, United States
| | - Sean T Toenjes
- Department of Chemical and Systems Biology, ChEM-H, and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, California 94305, United States
| | - Katherine A Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Pooreum Seo
- Department of Chemical and Systems Biology, ChEM-H, and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, California 94305, United States
| | - Martha Ordonez
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Pediatrics, Dana-Farber/Boston Children's Cancer and Blood Disorders Center and Harvard Medical School, Harvard University, Boston, Massachusetts 02215, United States
| | - Woong Sub Byun
- Department of Chemical and Systems Biology, ChEM-H, and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, California 94305, United States
| | - Muhammad Murtaza Hassan
- Department of Chemical and Systems Biology, ChEM-H, and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, California 94305, United States
| | - Franziska Wachter
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Pediatrics, Dana-Farber/Boston Children's Cancer and Blood Disorders Center and Harvard Medical School, Harvard University, Boston, Massachusetts 02215, United States
| | - Edward T Chouchani
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Mikołaj Słabicki
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, United States
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Benjamin L Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02141, United States
- Howard Hughes Medical Institute, Boston, Massachusetts 02115, United States
| | - Stephen M Hinshaw
- Department of Chemical and Systems Biology, ChEM-H, and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, California 94305, United States
| | - Nathanael S Gray
- Department of Chemical and Systems Biology, ChEM-H, and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, California 94305, United States
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19
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Hassan MM, Li YD, Ma MW, Teng M, Byun WS, Puvar K, Lumpkin R, Sandoval B, Rutter JC, Jin CY, Wang MY, Xu S, Schmoker AM, Cheong H, Groendyke BJ, Qi J, Fischer ES, Ebert BL, Gray NS. Exploration of the Tunability of BRD4 Degradation by DCAF16 Trans-labelling Covalent Glues. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.07.561308. [PMID: 37873358 PMCID: PMC10592706 DOI: 10.1101/2023.10.07.561308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Small molecules that can induce protein degradation by inducing proximity between a desired target and an E3 ligase have the potential to greatly expand the number of proteins that can be manipulated pharmacologically. Current strategies for targeted protein degradation are mostly limited in their target scope to proteins with preexisting ligands. Alternate modalities such as molecular glues, as exemplified by the glutarimide class of ligands for the CUL4CRBN ligase, have been mostly discovered serendipitously. We recently reported a trans-labelling covalent glue mechanism which we named 'Template-assisted covalent modification', where an electrophile decorated small molecule binder of BRD4 was effectively delivered to a cysteine residue on an E3 ligase DCAF16 as a consequence of a BRD4-DCAF16 protein-protein interaction. Herein, we report our medicinal chemistry efforts to evaluate how various electrophilic modifications to the BRD4 binder, JQ1, affect DCAF16 trans-labeling and subsequent BRD4 degradation efficiency. We discovered a decent correlation between the ability of the electrophilic small molecule to induce ternary complex formation between BRD4 and DCAF16 with its ability to induce BRD4 degradation. Moreover, we show that a more solvent-exposed warhead presentation is optimal for DCAF16 recruitment and subsequent BRD4 degradation. Unlike the sensitivity of CUL4CRBN glue degraders to chemical modifications, the diversity of covalent attachments in this class of BRD4 glue degraders suggests a high tolerance and tunability for the BRD4-DCAF16 interaction. This offers a potential new avenue for a rational design of covalent glue degraders by introducing covalent warheads to known binders.
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Affiliation(s)
- Muhammad Murtaza Hassan
- Department of Chemical and Systems Biology, ChEM-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA
| | - Yen-Der Li
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Michelle W. Ma
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Mingxing Teng
- Center for Drug Discovery, Department of Pathology & Immunology, and Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, TX
| | - Woong Sub Byun
- Department of Chemical and Systems Biology, ChEM-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA
| | - Kedar Puvar
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Ryan Lumpkin
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Brittany Sandoval
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Justine C. Rutter
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
| | - Cyrus Y. Jin
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Michelle Y. Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
| | - Shawn Xu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
| | - Anna M. Schmoker
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Hakyung Cheong
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | | | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
| | - Eric S. Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA
| | - Benjamin L. Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA
- Howard Hughes Medical Institute, Boston, MA
| | - Nathanael S. Gray
- Department of Chemical and Systems Biology, ChEM-H and Stanford Cancer Institute, Stanford School of Medicine, Stanford University, Stanford, CA
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20
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Teng M, Gray NS. The rise of degrader drugs. Cell Chem Biol 2023; 30:864-878. [PMID: 37494935 DOI: 10.1016/j.chembiol.2023.06.020] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/30/2023] [Accepted: 06/21/2023] [Indexed: 07/28/2023]
Abstract
The cancer genomics revolution has served up a plethora of promising and challenging targets for the drug discovery community. The field of targeted protein degradation (TPD) uses small molecules to reprogram the protein homeostasis system to destroy desired target proteins. In the last decade, remarkable progress has enabled the rational development of degraders for a large number of target proteins, with over 20 molecules targeting more than 12 proteins entering clinical development. While TPD has been fully credentialed by the prior development of immunomodulatory drug (IMiD) class for the treatment of multiple myeloma, the field is poised for a "Gleevec moment" in which robust clinical efficacy of a rationally developed novel degrader against a preselected target is firmly established. Here, we endeavor to provide a high-level evaluation of exciting developments in the field and comment on steps that may realize the full potential of this new therapeutic modality.
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Affiliation(s)
- Mingxing Teng
- Center for Drug Discovery, Department of Pathology & Immunology, and Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA.
| | - Nathanael S Gray
- Department of Chemical and Systems Biology, ChEM-H, Stanford Cancer Institute, School of Medicine, Stanford University, Stanford, CA 94305, USA.
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21
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Liu X, Ciulli A. Proximity-Based Modalities for Biology and Medicine. ACS CENTRAL SCIENCE 2023; 9:1269-1284. [PMID: 37521793 PMCID: PMC10375889 DOI: 10.1021/acscentsci.3c00395] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Indexed: 08/01/2023]
Abstract
Molecular proximity orchestrates biological function, and blocking existing proximities is an established therapeutic strategy. By contrast, strengthening or creating neoproximity with chemistry enables modulation of biological processes with high selectivity and has the potential to substantially expand the target space. A plethora of proximity-based modalities to target proteins via diverse approaches have recently emerged, opening opportunities for biopharmaceutical innovation. This Outlook outlines the diverse mechanisms and molecules based on induced proximity, including protein degraders, blockers, and stabilizers, inducers of protein post-translational modifications, and agents for cell therapy, and discusses opportunities and challenges that the field must address to mature and unlock translation in biology and medicine.
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22
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Abstract
Proteolysis-targeting chimeras (PROTACs) are heterobifunctional small molecules that induce the ternary complex formation between a protein-of-interest (POI) and an E3 ligase, leading to targeted polyubiquitination and degradation of the POI. Particularly, PROTACs have the distinct advantage of targeting both canonical and noncanonical functions of epigenetic targets over traditional inhibitors, which typically target canonical functions only, resulting in greater therapeutic efficacy. In this review, we methodically analyze published PROTAC degraders of epigenetic writer, reader, and eraser proteins and their in vitro and in vivo effects. We highlight the mechanism of action of these degraders and their advantages in targeting both canonical and noncanonical functions of epigenetic targets in the context of cancer treatment. Furthermore, we present a future outlook for this exciting field. Overall, pharmacological degradation of epigenetic targets has emerged as an effective and attractive strategy to thwart cancer progression and growth.
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Affiliation(s)
- Md Kabir
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.
| | - Xufen Yu
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.
| | - H Ümit Kaniskan
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences, Oncological Sciences and Neuroscience, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA.
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23
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Hu J, Hu B, Xu F, Wang M, Qin C, McEachern D, Stuckey J, Wang S. Precise Conformational Control Yielding Highly Potent and Exceptionally Selective BRD4 Degraders with Strong Antitumor Activity. J Med Chem 2023; 66:8222-8237. [PMID: 37289649 PMCID: PMC10436693 DOI: 10.1021/acs.jmedchem.3c00520] [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] [Indexed: 06/10/2023]
Abstract
Starting from a nonselective bromodomain and extraterminal (BET) inhibitor and a cereblon ligand, we have used precise conformational control for the development of two potent and highly selective BRD4 degraders, BD-7148 and BD-9136. These compounds induce rapid degradation of BRD4 protein in cells at concentrations as low as 1 nM and demonstrate ≥1000-fold degradation selectivity over BRD2 or BRD3 protein. Proteomic analysis of >5700 proteins confirmed their highly selective BRD4 degradation. A single dose of BD-9136 selectively and effectively depletes BRD4 protein in tumor tissues for >48 h. BD-9136 effectively inhibits tumor growth without adverse effects on mice and is more efficacious than the corresponding pan BET inhibitor. This study suggests selective degradation of BRD4 as a strategy for the treatment of human cancers and demonstrates a strategy for the design of highly selective PROTAC degraders.
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Affiliation(s)
- Jiantao Hu
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Biao Hu
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Fuming Xu
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Mi Wang
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Chong Qin
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Donna McEachern
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jeanne Stuckey
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Shaomeng Wang
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Pharmacology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Medicinal Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA
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24
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Toriki E, Papatzimas JW, Nishikawa K, Dovala D, Frank AO, Hesse MJ, Dankova D, Song JG, Bruce-Smythe M, Struble H, Garcia FJ, Brittain SM, Kile AC, McGregor LM, McKenna JM, Tallarico JA, Schirle M, Nomura DK. Rational Chemical Design of Molecular Glue Degraders. ACS CENTRAL SCIENCE 2023; 9:915-926. [PMID: 37252349 PMCID: PMC10214506 DOI: 10.1021/acscentsci.2c01317] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Indexed: 05/31/2023]
Abstract
Targeted protein degradation with molecular glue degraders has arisen as a powerful therapeutic modality for eliminating classically undruggable disease-causing proteins through proteasome-mediated degradation. However, we currently lack rational chemical design principles for converting protein-targeting ligands into molecular glue degraders. To overcome this challenge, we sought to identify a transposable chemical handle that would convert protein-targeting ligands into molecular degraders of their corresponding targets. Using the CDK4/6 inhibitor ribociclib as a prototype, we identified a covalent handle that, when appended to the exit vector of ribociclib, induced the proteasome-mediated degradation of CDK4 in cancer cells. Further modification of our initial covalent scaffold led to an improved CDK4 degrader with the development of a but-2-ene-1,4-dione ("fumarate") handle that showed improved interactions with RNF126. Subsequent chemoproteomic profiling revealed interactions of the CDK4 degrader and the optimized fumarate handle with RNF126 as well as additional RING-family E3 ligases. We then transplanted this covalent handle onto a diverse set of protein-targeting ligands to induce the degradation of BRD4, BCR-ABL and c-ABL, PDE5, AR and AR-V7, BTK, LRRK2, HDAC1/3, and SMARCA2/4. Our study undercovers a design strategy for converting protein-targeting ligands into covalent molecular glue degraders.
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Affiliation(s)
- Ethan
S. Toriki
- Department
of Chemistry, University of California,
Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Innovative
Genomics Institute, Berkeley, California 94704, United States
| | - James W. Papatzimas
- Department
of Chemistry, University of California,
Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Innovative
Genomics Institute, Berkeley, California 94704, United States
| | - Kaila Nishikawa
- Department
of Chemistry, University of California,
Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Innovative
Genomics Institute, Berkeley, California 94704, United States
| | - Dustin Dovala
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Novartis
Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Andreas O. Frank
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Novartis
Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Matthew J. Hesse
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Novartis
Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Daniela Dankova
- Department
of Chemistry, University of California,
Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Innovative
Genomics Institute, Berkeley, California 94704, United States
| | - Jae-Geun Song
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Novartis
Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Megan Bruce-Smythe
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Novartis
Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Heidi Struble
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Novartis
Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Francisco J. Garcia
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Novartis
Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Scott M. Brittain
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Novartis
Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Andrew C. Kile
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Novartis
Institutes for BioMedical Research, Emeryville, California 94608, United States
| | - Lynn M. McGregor
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Novartis
Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Jeffrey M. McKenna
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Novartis
Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - John A. Tallarico
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Novartis
Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Markus Schirle
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Novartis
Institutes for BioMedical Research, Cambridge, Massachusetts 02139, United States
| | - Daniel K. Nomura
- Department
of Chemistry, University of California,
Berkeley, Berkeley, California 94720, United States
- Novartis-Berkeley
Translational Chemical Biology Institute, Berkeley, California 94720, United States
- Innovative
Genomics Institute, Berkeley, California 94704, United States
- Department
of Molecular and Cell Biology, University
of California, Berkeley, Berkeley, California 94720, United States
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