1
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Pan Y, Wang Y, Gou S. Proteolysis targeting chimera, molecular glue degrader and hydrophobic tag tethering degrader for targeted protein degradation: Mechanisms, strategies and application. Bioorg Chem 2025; 161:108491. [PMID: 40306190 DOI: 10.1016/j.bioorg.2025.108491] [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: 12/03/2024] [Revised: 02/13/2025] [Accepted: 04/16/2025] [Indexed: 05/02/2025]
Abstract
Targeted protein degradation (TPD) represents a revolutionary approach to drug discovery, offering a novel mechanism that outperforms traditional inhibitors. This approach employs small molecule drugs to induce the ubiquitination and subsequent degradation of target protein via the proteasome or lysosomal pathways. Key strategies within TPD include proteolysis targeting chimeras (PROTACs), hydrophobic tag tethering degraders (HyTTDs), and molecular glue degraders (MGDs). PROTACs have been undergone clinical evaluations, MGDs have been used in the clinic, and HyTTDs have shown significant progress in cancer treatment. Each of these strategies presents unique advantages and approaches to target protein degradation. This review summarizes five years of research on PROTACs, HyTTDs, and MGDs, highlighting their design principles, advantages, limitations, and future challenges to provide clear guidance and in-depth insights for advancing drug development.
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Affiliation(s)
- Yanchang Pan
- Pharmaceutical Research Center and School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, PR China
| | - Yuanjiang Wang
- Pharmaceutical Research Center and School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, PR China; Jiangsu Province Hi-Tech Key Laboratory for Biomedical Research, Southeast University, Nanjing 211189, PR China
| | - Shaohua Gou
- Pharmaceutical Research Center and School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, PR China; Jiangsu Province Hi-Tech Key Laboratory for Biomedical Research, Southeast University, Nanjing 211189, PR China.
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2
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Tavassoli M, Abedi-Firoozjah R, Bahramian B, Hashemi M, Noori SMA, Oladzadabbasabadi N, Nagdalian A, Jafari SM. Glutaraldehyde cross-linking for improving the techno-functional properties of biopolymeric food packaging films; a comprehensive review. Food Chem 2025; 478:143740. [PMID: 40073600 DOI: 10.1016/j.foodchem.2025.143740] [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: 10/14/2024] [Revised: 02/11/2025] [Accepted: 03/02/2025] [Indexed: 03/14/2025]
Abstract
Biodegradable and/or edible films made from polysaccharides and proteins have gained attention for their potential to replace some traditional packaging materials in the food industry due to their abundance, biodegradability, and nutritional value. Glutaraldehyde (GLA), rapidly reacts with free deprotonated ε-amino groups in proteins, leading to crosslinking (CL) reactions. This review delves into the chemistry of GLA and explores the various biopolymeric food packaging materials crosslinked by GLA. Furthermore, it summarizes recent applications of active and intelligent food packaging based on GLA-CL of biopolymers for food preservation. The comprehensive enhancement of biopolymeric films through GLACL is evident, with the impact on their properties depending on the concentration of GLA and reaction state. GLACL with biopolymer molecules enhances the cohesion of the polymer network, with physical and chemical covalent CL being the primary phenomena. Notably, biopolymeric food packaging films/coatings fabricated by GLACL have proven highly effectiveness in preserving fresh foods.
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Affiliation(s)
- Milad Tavassoli
- Student Research Committee, Yasuj University of Medical Sciences, Yasuj, Iran; Department of Nutrition, Faculty of Health and Nutrition Sciences, Yasuj University of Medical Science, Yasuj, Iran
| | - Reza Abedi-Firoozjah
- Department of Food Science and Technology, School of Nutrition Sciences and Food Technology, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Behnam Bahramian
- Department of Food Sciences and Technology, Faculty of Nutrition and Food Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Hashemi
- Medical Toxicology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyyed Mohammad Ali Noori
- Toxicology Research Center, Medical Basic Sciences Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
| | - Nazila Oladzadabbasabadi
- Food Technology Division, School of Industrial Technology, Universiti Sains Malaysia, 11800 Penang, Malaysia.
| | - Andrey Nagdalian
- North Caucasus Federal University, Pushkina Street 1, 355009, Stavropol, Russia
| | - Seid Mahdi Jafari
- Department of Food Materials and Process Design Engineering, Gorgan University of Agricultural Sciences and Natural Resources, Gorgan, Iran; Halal Research Center of IRI, Iran Food and Drug Administration, Ministry of Health and Medical Education, Tehran, Iran.
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3
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Kotlyar M, Guo Z, Rao AVS, Peng H, Wang J, Ma Z, Schiene-Fischer C, Fischer G, Liu JO. Identification of Rapaglutin E as an Isoform-Specific Inhibitor of Glucose Transporter 1. ACS Chem Biol 2025; 20:1004-1009. [PMID: 40226990 DOI: 10.1021/acschembio.5c00152] [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: 04/15/2025]
Abstract
Natural products rapamycin and FK506 are macrocyclic compounds with therapeutic benefits whose unique scaffold inspired the generation and exploration of hybrid macrocycle rapafucins. From this library, a potent inhibitor of the facilitative glucose transporter (GLUT), rapaglutin A (RgA), was previously identified. RgA is a pan-GLUT inhibitor of Class I isoforms GLUT1, GLUT3, and GLUT4. Herein, we report the discovery of rapaglutin E (RgE). Unlike RgA, RgE is highly specific for GLUT1. Further characterization revealed that RgE and RgA likely bound to distinct sites on GLUT1 despite their shared FKBP-binding domain, suggesting that the distinct effector domains of RgE and RgA play key roles in the recognition of GLUTs.
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Affiliation(s)
- Marnie Kotlyar
- Chemistry Biology Interface Graduate Program, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Pharmacology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
- The SJ Yan and HJ Mao Laboratory of Chemical Biology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
| | - Zufeng Guo
- Department of Pharmacology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
- The SJ Yan and HJ Mao Laboratory of Chemical Biology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
| | - A V Subba Rao
- Department of Pharmacology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
- The SJ Yan and HJ Mao Laboratory of Chemical Biology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
| | - Hanjing Peng
- Department of Pharmacology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
- The SJ Yan and HJ Mao Laboratory of Chemical Biology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
| | - Jingxin Wang
- Department of Pharmacology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
- The SJ Yan and HJ Mao Laboratory of Chemical Biology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
| | - Zhongnan Ma
- Department of Pharmacology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
- The SJ Yan and HJ Mao Laboratory of Chemical Biology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
| | - Cordelia Schiene-Fischer
- Department of Enzymology, Institute for Biochemistry and Biotechnology, Martin Luther University Halle-Wittenberg, 06120 Halle, Germany
| | - Gunter Fischer
- Max Planck Institute for Multidisciplinary Sciences, 37077 Göttingen, Germany
| | - Jun O Liu
- Chemistry Biology Interface Graduate Program, Johns Hopkins University, Baltimore, Maryland 21218, United States
- The SJ Yan and HJ Mao Laboratory of Chemical Biology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
- Departments of Pharmacology and Oncology, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, United States
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4
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Salcius M, Tutter A, Fouché M, Koc H, King D, Dhembi A, Golosov A, Jahnke W, Henry C, Argoti D, Jia W, Pedro L, Connor L, Piechon P, Fabbiani F, Denay R, Sager E, Kuehnoel J, Lozach MA, Lima F, Vitrey A, Chen SY, Michaud G, Roth HJ. Identification and characterization of ternary complexes consisting of FKBP12, MAPRE1 and macrocyclic molecular glues. RSC Chem Biol 2025; 6:788-799. [PMID: 40059881 PMCID: PMC11883961 DOI: 10.1039/d4cb00279b] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2024] [Accepted: 01/31/2025] [Indexed: 05/10/2025] Open
Abstract
Many disease-relevant and functionally well-validated targets are difficult to drug. Their poorly defined 3D structure without deep hydrophobic pockets makes the development of ligands with low molecular weight and high affinity almost impossible. For these targets, incorporation into a ternary complex may be a viable alternative to modulate and in most cases inhibit their function. Therefore, we are interested in methods to identify and characterize molecular glues. In a protein array screen of 50 different macrocyclic FKBP12 ligands against 2500 different randomly selected proteins, a molecular glue compound was found to recruit a dimeric protein called MAPRE1 to FKBP12 in a compound-dependent manner. The corresponding ternary complex was characterized by TR-FRET proximity assay and native MS spectroscopy. Insights into the 3D structure of the ternary complex were obtained by 2D protein NMR spectroscopy and finally by an X-ray structure, which revealed the ternary complex as a 2 : 2 : 2 FKBP12 : molecular glue : MAPRE1 complex exhibiting multiple interactions that occur exclusively in the ternary complex and lead to significant cooperativity α. Using the X-ray structure, rationally guided synthesis of a series of analogues led to the cooperativity driven improvement in the stability of the ternary complex. Furthermore, the ternary complex formation of the series was confirmed by cellular NanoBiT assays, whose A max values correlate with those from the TR-FRET proximity assay. Furthermore, NanoBiT experiments showed the functional impact (inhibition) of these molecular glues on the interaction of MAPRE1 with its intracellular native partners.
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Affiliation(s)
- Michael Salcius
- Novartis Biomedical Research 181 Massachusetts Ave Cambridge USA
| | - Antonin Tutter
- Novartis Biomedical Research 181 Massachusetts Ave Cambridge USA
| | - Marianne Fouché
- Novartis Biomedical Research Fabrikstrasse 2 CH-4056 Basel Switzerland
| | - Halil Koc
- Novartis Biomedical Research Fabrikstrasse 2 CH-4056 Basel Switzerland
| | - Dan King
- Novartis Biomedical Research 181 Massachusetts Ave Cambridge USA
| | - Anxhela Dhembi
- Novartis Biomedical Research 181 Massachusetts Ave Cambridge USA
| | - Andrei Golosov
- Novartis Biomedical Research 181 Massachusetts Ave Cambridge USA
| | - Wolfgang Jahnke
- Novartis Biomedical Research Fabrikstrasse 2 CH-4056 Basel Switzerland
| | - Chrystèle Henry
- Novartis Biomedical Research Fabrikstrasse 2 CH-4056 Basel Switzerland
| | - Dayana Argoti
- Novartis Biomedical Research 5959 Horton Street Emeryville USA
| | - Weiping Jia
- Novartis Biomedical Research 5959 Horton Street Emeryville USA
| | - Liliana Pedro
- Novartis Biomedical Research 5959 Horton Street Emeryville USA
| | - Lauren Connor
- Novartis Biomedical Research Fabrikstrasse 2 CH-4056 Basel Switzerland
| | - Philippe Piechon
- Novartis Biomedical Research Fabrikstrasse 2 CH-4056 Basel Switzerland
| | | | - Regis Denay
- Novartis Biomedical Research Fabrikstrasse 2 CH-4056 Basel Switzerland
| | - Emine Sager
- Novartis Biomedical Research Fabrikstrasse 2 CH-4056 Basel Switzerland
| | - Juergen Kuehnoel
- Novartis Biomedical Research Fabrikstrasse 2 CH-4056 Basel Switzerland
| | - Marie-Anne Lozach
- Novartis Biomedical Research Fabrikstrasse 2 CH-4056 Basel Switzerland
| | - Fabio Lima
- Novartis Biomedical Research Fabrikstrasse 2 CH-4056 Basel Switzerland
| | - Angela Vitrey
- Novartis Biomedical Research Fabrikstrasse 2 CH-4056 Basel Switzerland
| | - Shu-Yu Chen
- Eidgenösisch Technische Hochschule, Inst. Mol. Phys. Wiss Zürich Switzerland
| | - Gregory Michaud
- Novartis Biomedical Research 181 Massachusetts Ave Cambridge USA
| | - Hans-Joerg Roth
- Novartis Biomedical Research Fabrikstrasse 2 CH-4056 Basel Switzerland
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5
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Coomar S, Gasser JA, Słabicki M, Donovan KA, Fischer ES, Ebert BL, Gillingham D, Thomä NH. Niclosamide: CRL4 AMBRA1 mediated degradation of cyclin D1 following mitochondrial membrane depolarization. RSC Med Chem 2025:d5md00054h. [PMID: 40337304 PMCID: PMC12054360 DOI: 10.1039/d5md00054h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2025] [Accepted: 04/19/2025] [Indexed: 05/09/2025] Open
Abstract
Targeted protein degradation has emerged as a promising approach in drug discovery, utilizing small molecules like molecular glue degraders to harness the ubiquitin-proteasome pathway for selective degradation of disease-driving proteins. Based on results from proteomics screens we investigated the potential of niclosamide, an FDA-approved anthelmintic drug with a 50 year history in treating tapeworm infections, as a molecular glue degrader targeting the proto-oncogene cyclin D1. Proteomics screens in HCT116 colon carcinoma and KELLY neuroblastoma cells, found that niclosamide induces rapid cyclin D1 degradation through a mechanism involving the ubiquitin-proteasome pathway. A genetic CRISPR screen identified the E3 ligase CRL4AMBRA1 as a key player in this process. Structure-activity relationship studies highlighted critical features of niclosamide necessary for cyclin D1 degradation, demonstrating a correlation between mitochondrial membrane potential (MMP) disruption and cyclin D1 downregulation. Notably, various mitochondrial uncouplers and other compounds with similar drug sensitivity profiles share this correlation suggesting that MMP disruption can trigger cyclin D1 degradation, and that the cellular signal driving the degradation differs from previously described mechanism involving CRL4AMBRA1. Our findings underscore the complexities of proteostatic mechanisms and the multitude of mechanisms that contribute to degrader drug action.
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Affiliation(s)
- Seemon Coomar
- Friedrich Miescher Institute for Biomedical Research Fabrikstrasse 24 Basel 4056 Switzerland
| | | | - Mikołaj Słabicki
- Broad Institute of MIT and Harvard Cambridge MA 02142 USA
- Department of Medical Oncology, Dana-Farber Cancer Institute Boston MA 02115 USA
- Krantz Family Center for Cancer Research, Massachusetts General Hospital Cancer Center Charlestown MA 02129 USA
| | - Katherine A Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute 450 Brookline Ave. Boston MA 02215 USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School 240 Longwood Ave. Boston MA 02215 USA
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute 450 Brookline Ave. Boston MA 02215 USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School 240 Longwood Ave. Boston MA 02215 USA
| | | | | | - Nicolas H Thomä
- Friedrich Miescher Institute for Biomedical Research Fabrikstrasse 24 Basel 4056 Switzerland
- Swiss Institute for Experimental Cancer Research (ISREC) EPFL, Station 19 Lausanne 1015 Switzerland
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6
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Zhu B, Wu Z, Shou Y, Zhao K, Lu Q, Qin JJ, Guo H. Harnessing the Power of Natural Products for Targeted Protein Degradation. Med Res Rev 2025. [PMID: 40304621 DOI: 10.1002/med.22113] [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: 03/27/2025] [Revised: 03/27/2025] [Accepted: 04/02/2025] [Indexed: 05/02/2025]
Abstract
Natural products have garnered significant attention due to their complex chemical structures and remarkable pharmacological activities. With inherent recognition capabilities for protein surfaces, natural products serve as ideal candidates for designing proteolysis-targeting chimeras (PROTACs). The utilization of natural products in PROTAC development offers distinct advantages, including their rich chemical diversity, multitarget activities, and sustainable sourcing. This comprehensive review explores the vast potential of harnessing natural products in PROTAC research. Moreover, the review discusses the application of natural degradant technology, which involves utilizing natural product-based compounds to selectively degrade disease-causing proteins, as well as the implementation of computer-aided drug design (CADD) technology in identifying suitable targets for degradation within the realm of natural products. By harnessing the power of natural products and leveraging computational tools, PROTACs derived from natural products have the potential to revolutionize drug discovery and provide innovative therapeutic interventions for various diseases.
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Affiliation(s)
- Bo Zhu
- Collaborative Innovation Centre of Regenerative Medicine and Medical BioResource Development and Application Co-constructed by the Province and Ministry, Guangxi Medical University, Nanning, Guangxi, China
| | - Zheng Wu
- Key Laboratory of Longevity and Aging-related Diseases of Chinese Ministry of Education, Guangxi Key Laboratory of Bioactive Molecules Research and Evaluation & College of Pharmacy, Guangxi Medical University, Nanning, Guangxi, China
| | - Yiwen Shou
- Key Laboratory of Longevity and Aging-related Diseases of Chinese Ministry of Education, Guangxi Key Laboratory of Bioactive Molecules Research and Evaluation & College of Pharmacy, Guangxi Medical University, Nanning, Guangxi, China
| | - Kaili Zhao
- Key Laboratory of Longevity and Aging-related Diseases of Chinese Ministry of Education, Guangxi Key Laboratory of Bioactive Molecules Research and Evaluation & College of Pharmacy, Guangxi Medical University, Nanning, Guangxi, China
| | - Qinpei Lu
- Key Laboratory of Longevity and Aging-related Diseases of Chinese Ministry of Education, Guangxi Key Laboratory of Bioactive Molecules Research and Evaluation & College of Pharmacy, Guangxi Medical University, Nanning, Guangxi, China
| | - Jiang-Jiang Qin
- Center for Innovative Drug Research, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Hongwei Guo
- Key Laboratory of Longevity and Aging-related Diseases of Chinese Ministry of Education, Guangxi Key Laboratory of Bioactive Molecules Research and Evaluation & College of Pharmacy, Guangxi Medical University, Nanning, Guangxi, China
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7
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Kordana N, Johnson A, Quinn K, Obar JJ, Cramer RA. Recent developments in Aspergillus fumigatus research: diversity, drugs, and disease. Microbiol Mol Biol Rev 2025; 89:e0001123. [PMID: 39927770 PMCID: PMC11948498 DOI: 10.1128/mmbr.00011-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2025] Open
Abstract
SUMMARYAdvances in modern medical therapies for many previously intractable human diseases have improved patient outcomes. However, successful disease treatment outcomes are often prevented due to invasive fungal infections caused by the environmental mold Aspergillus fumigatus. As contemporary antifungal therapies have not experienced the same robust advances as other medical therapies, defining mechanisms of A. fumigatus disease initiation and progression remains a critical research priority. To this end, the World Health Organization recently identified A. fumigatus as a research priority human fungal pathogen and the Centers for Disease Control has highlighted the emergence of triazole-resistant A. fumigatus isolates. The expansion in the diversity of host populations susceptible to aspergillosis and the complex and dynamic A. fumigatus genotypic and phenotypic diversity call for a reinvigorated assessment of aspergillosis pathobiological and drug-susceptibility mechanisms. Here, we summarize recent advancements in the field and discuss challenges in our understanding of A. fumigatus heterogeneity and its pathogenesis in diverse host populations.
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Affiliation(s)
- Nicole Kordana
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Angus Johnson
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Katherine Quinn
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Joshua J. Obar
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
| | - Robert A. Cramer
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, USA
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8
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Kapcan E, Krygier K, da Luz M, Serniuck NJ, Zhang A, Bramson J, Rullo AF. Mimicry of molecular glues using dual covalent chimeras. Nat Commun 2025; 16:2855. [PMID: 40128528 PMCID: PMC11933337 DOI: 10.1038/s41467-025-58083-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 03/07/2025] [Indexed: 03/26/2025] Open
Abstract
A special class of proximity inducing bifunctional molecules/chimeras called molecular glues leverage positive co-operativity to stabilize ternary complex formation and induce a biological response. Despite their utility, molecular glues remain challenging to rationally design. This is particularly true in the context of inducing cell-cell proximity which involve ternary complexes that comprise non- or negatively interacting proteins. In this work, we develop a dual proximity labeling strategy enabling a chimera to covalently crosslink a non-interacting serum antibody to a tumor surface protein, within a ternary complex. The resultant resistance to dissociation, including in the presence of competitor binding ligands, mimics molecular glue stabilization. We demonstrate these covalent glue mimics (CGMs) can induce cell-cell proximity in three distinct model systems of tumor-immune recognition, leading to significant functional enhancements. Collectively, this work underscores the utility of dual proximal covalent labeling as a potential general strategy to stabilize ternary complexes comprising non-interacting proteins and enforce cell-cell interactions.
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Affiliation(s)
- Eden Kapcan
- Center for Discovery in Cancer Research, McMaster University, Hamilton, ON, Canada
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Karolina Krygier
- Center for Discovery in Cancer Research, McMaster University, Hamilton, ON, Canada
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Maya da Luz
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada
| | - Nickolas J Serniuck
- Center for Discovery in Cancer Research, McMaster University, Hamilton, ON, Canada
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Ali Zhang
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Jonathan Bramson
- Center for Discovery in Cancer Research, McMaster University, Hamilton, ON, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
| | - Anthony F Rullo
- Center for Discovery in Cancer Research, McMaster University, Hamilton, ON, Canada.
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada.
- Department of Medicine, McMaster University, Hamilton, ON, Canada.
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada.
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9
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Tan ZY, Adade JKA, Gu X, Hecht CJS, Salcius M, Tong B, Liu S, Hwang S, Zécri FJ, Graham DB, Schreiber SL, Xavier RJ. Development of an FKBP12-recruiting chemical-induced proximity DNA-encoded library and its application to discover an autophagy potentiator. Cell Chem Biol 2025; 32:498-510.e35. [PMID: 39753134 PMCID: PMC11928285 DOI: 10.1016/j.chembiol.2024.12.002] [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: 05/31/2024] [Revised: 10/01/2024] [Accepted: 12/04/2024] [Indexed: 03/23/2025]
Abstract
Chemical inducers of proximity (CIPs) are molecules that recruit one protein to another and introduce new functionalities toward modulating protein states and activities. While CIP-mediated recruitment of E3 ligases is widely exploited for the development of degraders, other therapeutic modalities remain underexplored. We describe a non-degrader CIP-DNA-encoded library (CIP-DEL) that recruits FKBP12 to target proteins using non-traditional acyclic structures, with an emphasis on introducing stereochemically diverse and rigid connectors to attach the combinatorial library. We deployed this strategy to modulate ATG16L1 T300A, which confers genetic susceptibility to Crohn's disease (CD), and identified a compound that stabilizes the variant protein against caspase-3 (Casp3) cleavage in a FKBP12-independent manner. We demonstrate in cellular models that this compound potentiates autophagy, and reverses the xenophagy defects as well as increased cytokine secretion characteristic of ATG16L1 T300A. This study provides a platform to access unexplored chemical space for CIP design to develop therapeutic modalities guided by human genetics.
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Affiliation(s)
- Zher Yin Tan
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Joel K A Adade
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Xiebin Gu
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Cody J S Hecht
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael Salcius
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Bingqi Tong
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shuang Liu
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Seungmin Hwang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Frédéric J Zécri
- Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA
| | - Daniel B Graham
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Stuart L Schreiber
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Arena BioWorks, Cambridge, MA 02139, USA.
| | - Ramnik J Xavier
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA.
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10
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Liu H, Zhao X, Chen J, Win YY, Cai J. Unnatural foldamers as inhibitors of Aβ aggregation via stabilizing the Aβ helix. Chem Commun (Camb) 2025; 61:4586-4594. [PMID: 40035705 PMCID: PMC11878269 DOI: 10.1039/d4cc05280c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2024] [Accepted: 02/24/2025] [Indexed: 03/06/2025]
Abstract
Protein aggregation is a critical factor in the development and progression of several human diseases, including Alzheimer's disease (AD), Huntington's disease, Parkinson's disease, and type 2 diabetes. Among these conditions, AD is recognized as the most prevalent progressive neurodegenerative disorder, characterized by the accumulation of amyloid-beta (Aβ) peptides. Neuronal toxicity is likely driven by soluble oligomeric intermediates of the Aβ peptide, which are thought to play a central role in the cascade leading to neuronal dysfunction and cognitive decline. In response, numerous therapeutic strategies have been developed to inhibit Aβ oligomerization, as this is believed to delay the formation of Aβ protofibrils. Traditional research has focused on discovering small molecules or peptides that antagonize Aβ oligomerization. However, recent studies have explored an alternative approach-developing ligands that stabilize the Aβ peptide in its α-helical conformation. This stabilization is thought to alter the peptide's natural aggregation kinetics, shifting it away from toxic oligomer formation and toward less harmful states. Crucially, by maintaining Aβ in this α-helical form, these ligands have been shown to rescue the peptide's associated cytotoxicity, offering a promising mechanism to mitigate the detrimental effects of Aβ in AD. While challenges remain, including treatment costs and side effects like ARIA (amyloid-related imaging abnormalities), anti-Aβ drug development represents a major advancement in Alzheimer's research and therapeutic options. This brief review aims to highlight the development and potential of these α-helix-stabilizing ligands as antagonists of Aβ aggregation, focusing on their interactions with Aβ and how these compounds induce and maintain secondary structural changes in the Aβ peptide. Notably, this innovative strategy holds promise beyond Aβ-related pathology, as the fundamental principles could be applied to other amyloidogenic proteins implicated in various amyloid-related diseases, potentially broadening the scope of therapeutic intervention for multiple neurodegenerative conditions.
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Affiliation(s)
- Heng Liu
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, Tampa, FL, 33620, USA.
| | - Xue Zhao
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, Tampa, FL, 33620, USA.
| | - Jianyu Chen
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, Tampa, FL, 33620, USA.
| | - Yu Yu Win
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, Tampa, FL, 33620, USA.
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, 4202 E. Fowler Ave, Tampa, FL, 33620, USA.
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11
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Uliassi E, Bolognesi ML, Milelli A. Targeting Tau Protein with Proximity Inducing Modulators: A New Frontier to Combat Tauopathies. ACS Pharmacol Transl Sci 2025; 8:654-672. [PMID: 40109749 PMCID: PMC11915046 DOI: 10.1021/acsptsci.4c00733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2024] [Revised: 01/18/2025] [Accepted: 01/21/2025] [Indexed: 03/22/2025]
Abstract
Dysregulation of correct protein tau homeostasis represents the seed for the development of several devastating central nervous system disorders, known as tauopathies, that affect millions of people worldwide. Despite massive public and private support to research funding, these diseases still represent unmet medical needs. In fact, the tau-targeting tools developed to date have failed to translate into the clinic. Recently, taking advantage of the modes that nature uses to mediate the flow of information in cells, researchers have developed a new class of molecules, called proximity-inducing modulators, which exploit spatial proximity to modulate protein function(s) and redirect cellular processes. In this perspective, after a brief discussion about tau protein and the classic tau-targeting approaches, we will discuss the different classes of proximity-inducing modulators developed so far and highlight the applications to modulate tau protein's function and tau-induced toxicity.
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Affiliation(s)
- Elisa Uliassi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, Bologna 40126, Italy
| | - Maria Laura Bolognesi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Via Belmeloro 6, Bologna 40126, Italy
| | - Andrea Milelli
- Department for Life Quality Studies, Alma Mater Studiorum - University of Bologna, Corso d'Augusto 237, Rimini 47921, Italy
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12
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Rosen HT, Li K, Li EL, Currier B, Brittain SM, Garcia FJ, Beard DC, Haenni-Holzinger S, Dovala D, McKenna JM, Schirle M, Maimone TJ, Nomura DK. Sulfinyl Aziridines as Stereoselective Covalent Destabilizing Degraders of the Oncogenic Transcription Factor MYC. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.24.639755. [PMID: 40060528 PMCID: PMC11888305 DOI: 10.1101/2025.02.24.639755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 03/18/2025]
Abstract
While MYC is a significant oncogenic transcription factor driver of cancer, directly targeting MYC has remained challenging due to its intrinsic disorder and poorly defined structure, deeming it "undruggable." Whether transient pockets formed within intrinsically disordered and unstructured regions of proteins can be selectively targeted with small molecules remains an outstanding challenge. Here, we developed a bespoke stereochemically-paired spirocyclic oxindole aziridine covalent library and screened this library for degradation of MYC. Through this screen, we identified a hit covalent ligand KL2-236, bearing a unique sulfinyl aziridine warhead, that engaged MYC in vitro as pure MYC/MAX protein complex and in situ in cancer cells to destabilize MYC, inhibit MYC transcriptional activity and degrade MYC in a proteasome-dependent manner through targeting intrinsically disordered C203 and D205 residues. Notably, this reactivity was most pronounced for specific stereoisomers of KL2-236 with a diastereomer KL4-019 that was largely inactive. Mutagenesis of both C203 and D205 completely attenuated KL2-236-mediated MYC degradation. We have also optimized our initial KL2-236 hit compound to generate a more durable MYC degrader KL4-219A in cancer cells. Our results reveal a novel ligandable site within MYC and indicate that certain intrinsically disordered regions within high-value protein targets, such as MYC, can be interrogated by isomerically unique chiral small molecules, leading to destabilization and degradation.
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Affiliation(s)
- Hannah T. Rosen
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720 USA
| | - Kelvin Li
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720 USA
| | - Erin L. Li
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720 USA
| | - Brynne Currier
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720 USA
| | - Scott M. Brittain
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720 USA
- Novartis Biomedical Research, Emeryville, CA USA; Cambridge, MA USA; Basel, Switzerland
| | - Francisco J. Garcia
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720 USA
- Novartis Biomedical Research, Emeryville, CA USA; Cambridge, MA USA; Basel, Switzerland
| | - Diana C. Beard
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720 USA
- Novartis Biomedical Research, Emeryville, CA USA; Cambridge, MA USA; Basel, Switzerland
| | - Sandra Haenni-Holzinger
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720 USA
- Novartis Biomedical Research, Emeryville, CA USA; Cambridge, MA USA; Basel, Switzerland
| | - Dustin Dovala
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720 USA
- Novartis Biomedical Research, Emeryville, CA USA; Cambridge, MA USA; Basel, Switzerland
| | - Jeffrey M. McKenna
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720 USA
- Novartis Biomedical Research, Emeryville, CA USA; Cambridge, MA USA; Basel, Switzerland
| | - Markus Schirle
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720 USA
- Novartis Biomedical Research, Emeryville, CA USA; Cambridge, MA USA; Basel, Switzerland
| | - Thomas J. Maimone
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720 USA
| | - Daniel K. Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94720 USA
- Novartis-Berkeley Translational Chemical Biology Institute, Berkeley, CA 94720 USA
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13
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Nussinov R, Yavuz BR, Jang H. Allostery in Disease: Anticancer Drugs, Pockets, and the Tumor Heterogeneity Challenge. J Mol Biol 2025:169050. [PMID: 40021049 DOI: 10.1016/j.jmb.2025.169050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2025] [Accepted: 02/24/2025] [Indexed: 03/03/2025]
Abstract
Charting future innovations is challenging. Yet, allosteric and orthosteric anticancer drugs are undergoing a revolution and taxing unresolved dilemmas await. Among the imaginative innovations, here we discuss cereblon and thalidomide derivatives as a means of recruiting neosubstrates and their degradation, allosteric heterogeneous bifunctional drugs like PROTACs, drugging phosphatases, inducers of targeted posttranslational protein modifications, antibody-drug conjugates, exploiting membrane interactions to increase local concentration, stabilizing the folded state, and more. These couple with harnessing allosteric cryptic pockets whose discovery offers more options to modulate the affinity of orthosteric, active site inhibitors. Added to these are strategies to counter drug resistance through drug combinations co-targeting pathways to bypass signaling blockades. Here, we discuss on the molecular and cellular levels, such inspiring advances, provide examples of their applications, their mechanisms and rational. We start with an overview on difficult to target proteins and their properties-rarely, if ever-conceptualized before, discuss emerging innovative drugs, and proceed to the increasingly popular allosteric cryptic pockets-their advantages-and critically, issues to be aware of. We follow with drug resistance and in-depth discussion of tumor heterogeneity. Heterogeneity is a hallmark of highly aggressive cancers, the core of drug resistance unresolved challenge. We discuss potential ways to target heterogeneity by predicting it. The increase in experimental and clinical data, computed (cell-type specific) interactomes, capturing transient cryptic pockets, learned drug resistance, workings of regulatory mechanisms, heterogeneity, and resistance-based cell signaling drug combinations, assisted by AI-driven reasoning and recognition, couple with creative allosteric drug discovery, charting future innovations.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, the United States of America; Cancer Innovation Laboratory, National Cancer Institute at Frederick, Frederick, MD 21702, the United States of America; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel.
| | - Bengi Ruken Yavuz
- Cancer Innovation Laboratory, National Cancer Institute at Frederick, Frederick, MD 21702, the United States of America
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, the United States of America; Cancer Innovation Laboratory, National Cancer Institute at Frederick, Frederick, MD 21702, the United States of America
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14
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Zammit CM, Nadel CM, Lin Y, Koirala S, Potts PR, Nomura DK. Covalent Destabilizing Degrader of AR and AR-V7 in Androgen-Independent Prostate Cancer Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.02.12.637117. [PMID: 39990458 PMCID: PMC11844536 DOI: 10.1101/2025.02.12.637117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/25/2025]
Abstract
Androgen-independent prostate cancers, correlated with heightened aggressiveness and poor prognosis, are caused by mutations or deletions in the androgen receptor (AR) or expression of truncated variants of AR that are constitutively activated. Currently, drugs and drug candidates against AR target the steroid-binding domain to antagonize or degrade AR. However, these compounds cannot therapeutically access largely intrinsically disordered truncated splice variants of AR, such as AR-V7, that only possess the DNA binding domain and are missing the ligand binding domain. Targeting intrinsically disordered regions within transcription factors has remained challenging and is considered "undruggable". Herein, we leveraged a cysteine-reactive covalent ligand library in a cellular screen to identify degraders of AR and AR-V7 in androgen-independent prostate cancer cells. We identified a covalent compound EN1441 that selectively degrades AR and AR-V7 in a proteasome-dependent manner through direct covalent targeting of an intrinsically disordered cysteine C125 in AR and AR-V7. EN1441 causes significant and selective destabilization of AR and AR-V7, leading to aggregation of AR/AR-V7 and subsequent proteasome-mediated degradation. Consistent with targeting both AR and AR-V7, we find that EN1441 completely inhibits total AR transcriptional activity in androgen-independent prostate cancer cells expressing both AR and AR-V7 compared to AR antagonists or degraders that only target the ligand binding domain of full-length AR, such as enzalutamide and ARV-110. Our results put forth a pathfinder molecule EN1441 that targets an intrinsically disordered cysteine within AR to destabilize, degrade, and inhibit both AR and AR-V7 in androgen-independent prostate cancer cells and highlights the utility of covalent ligand discovery approaches in directly targeting, destabilizing, inhibiting, and degrading classically undruggable transcription factor targets.
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Affiliation(s)
- Charlotte M. Zammit
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94720 USA
| | - Cory M. Nadel
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320 USA
| | - Ying Lin
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320 USA
| | - Sajjan Koirala
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320 USA
| | | | - Daniel K. Nomura
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720 USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720 USA
- Innovative Genomics Institute, Berkeley, CA 94720 USA
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15
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Jochem M, Schrempf A, Wagner LM, Segal D, Cisneros J, Ng A, Winter GE, Krijgsveld J. Degradome analysis to identify direct protein substrates of small-molecule degraders. Cell Chem Biol 2025; 32:192-200.e6. [PMID: 39536762 DOI: 10.1016/j.chembiol.2024.10.007] [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: 02/09/2024] [Revised: 07/27/2024] [Accepted: 10/18/2024] [Indexed: 11/16/2024]
Abstract
Targeted protein degradation (TPD) has emerged as a powerful strategy to selectively eliminate cellular proteins using small-molecule degraders, offering therapeutic promise for targeting proteins that are otherwise undruggable. However, a remaining challenge is to unambiguously identify primary TPD targets that are distinct from secondary downstream effects in the proteome. Here we introduce an approach for selective analysis of protein degradation by mass spectrometry (DegMS) at proteomic scale, which derives its specificity from the exclusion of confounding effects of altered transcription and translation induced by target depletion. We show that the approach efficiently operates at the timescale of TPD (hours) and we demonstrate its utility by analyzing the cyclin K degraders dCeMM2 and dCeMM4, which induce widespread transcriptional downregulation, and the GSPT1 degrader CC-885, an inhibitor of protein translation. Additionally, we apply DegMS to characterize a previously uncharacterized degrader, and identify the zinc-finger protein FIZ1 as a degraded target.
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Affiliation(s)
- Marco Jochem
- German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Anna Schrempf
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | | | - Dmitri Segal
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Jose Cisneros
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Amanda Ng
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Jeroen Krijgsveld
- German Cancer Research Center (DKFZ), Heidelberg, Germany; Heidelberg University, Medical Faculty, Heidelberg, Germany.
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16
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Zhang Q, Yu J, You Q, Wang L. Modulating Phosphorylation by Proximity-Inducing Modalities for Cancer Therapy. J Med Chem 2024; 67:21695-21716. [PMID: 39648992 DOI: 10.1021/acs.jmedchem.4c02624] [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: 12/10/2024]
Abstract
Abnormal phosphorylation of proteins can lead to various diseases, particularly cancer. Therefore, the development of small molecules for precise regulation of protein phosphorylation holds great potential for drug design. While the traditional kinase/phosphatase small-molecule modulators have shown some success, achieving precise phosphorylation regulation has proven to be challenging. The emergence of heterobifunctional molecules, such as phosphorylation-inducing chimeric small molecules (PHICSs) and phosphatase recruiting chimeras (PHORCs), with proximity-inducing modalities is expected to lead to a breakthrough by specifically recruiting kinase or phosphatase to the protein of interest. Herein, we summarize the drug targets with aberrant phosphorylation in cancer and underscore the potential of correcting phosphorylation in cancer therapy. Through reported cases of heterobifunctional molecules targeting phosphorylation regulation, we highlight the current design strategies and features of these molecules. We also provide a systematic elaboration of the link between aberrantly phosphorylated targets and cancer as well as the existing challenges and future research directions for developing heterobifunctional molecular drugs for phosphorylation regulation.
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Affiliation(s)
- Qiuyue Zhang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Jia Yu
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Qidong You
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Lei Wang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 210009, China
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17
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Saha S, Cheloha RW. Chemically Induced Dimerization via Nanobody Binding Facilitates in Situ Ligand Assembly and On-Demand GPCR Activation. JACS AU 2024; 4:4780-4789. [PMID: 39735930 PMCID: PMC11673187 DOI: 10.1021/jacsau.4c00711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2024] [Revised: 11/16/2024] [Accepted: 11/18/2024] [Indexed: 12/31/2024]
Abstract
Methods that enable the on-demand synthesis of biologically active molecules offer the potential for a high degree of control over the timing and context of target activation; however, such approaches often require extensive engineering to implement. Tools to restrict the localization of assembly also remain limited. Here we present a new approach for stimulus-induced ligand assembly that helps to address these challenges. This methodology relies on the high affinity and specificity recognition exhibited by antibody fragments (nanobodies, Nbs). By using Nbs that recognize short peptide epitopes to create semisynthetic conjugates, we develop a bioengineering platform termed peptide epitope dimerization (PED) in which the addition of heterodimeric peptide composed of two Nb epitopes stimulates the proximity-induced synthesis of a functional ligand for the parathyroid hormone receptor-1, a G protein-coupled receptor. We further demonstrate that high efficiency assembly can be achieved on the cell surface via Nb-based delivery of template. This approach opens the door for the on-demand generation of bioactive receptor ligands preferentially at a desired biological niche.
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Affiliation(s)
- Shubhra
Jyoti Saha
- Laboratory
of Bioorganic Chemistry, National Institutes of Diabetes, Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892, United States
| | - Ross W. Cheloha
- Laboratory
of Bioorganic Chemistry, National Institutes of Diabetes, Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892, United States
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18
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Zhou Z, Huang Z, Tang Y, Zhu Y, Li J. Modulating membrane-bound enzyme activity with chemical stimuli. Eur J Med Chem 2024; 280:116964. [PMID: 39406113 DOI: 10.1016/j.ejmech.2024.116964] [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: 03/17/2024] [Revised: 10/10/2024] [Accepted: 10/11/2024] [Indexed: 11/25/2024]
Abstract
Membrane-bound enzymes play pivotal roles in various cellular processes, making their activity regulation essential for cellular homeostasis and signaling transduction. Given that dysregulation of membrane-bound enzymes involved in various disease, controlling enzyme activity offers valuable avenues for designing targeted therapies and novel pharmaceutical interventions. This review explores chemical stimuli-responsive strategies for modulating the activity of these enzymes, employing diverse stimuli such as small molecules, proteins, nucleic acids, and bifunctional molecules to either inhibit or enhance their catalytic function. We systematically delineate the mechanisms underlying enzyme activity regulation, including substrate binding site blockade, conformational changes, and local concentration of enzymes and substrates. Furthermore, based on some examples, we elucidate the binding modalities between stimuli and enzymes, along with potential modes of regulation, and discuss their potential medical applications and future prospects. This review underscores the significance of understanding and manipulating enzyme activity on the cell membrane for advancing biomedical research and therapeutic development.
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Affiliation(s)
- Zhilan Zhou
- Academy of Medical Engineering and Translational Medicine, Tianjin University, Tianjin, 300072, China; Zhejiang Cancer Hospital, The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Zening Huang
- Department of Gastric Surgery, Fujian Medical University Union Hospital, Fuzhou, Fujian, 350001, China
| | - Yiyuan Tang
- Zhejiang Cancer Hospital, The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Yingdi Zhu
- Zhejiang Cancer Hospital, The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310022, China
| | - Juan Li
- Zhejiang Cancer Hospital, The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, 310022, China.
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19
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Wang X, Shuai W, Yang P, Liu Y, Zhang Y, Wang G. Targeted protein degradation: expanding the technology to facilitate the clearance of neurotoxic proteins in neurodegenerative diseases. Ageing Res Rev 2024; 102:102584. [PMID: 39551160 DOI: 10.1016/j.arr.2024.102584] [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: 05/11/2024] [Revised: 10/30/2024] [Accepted: 11/12/2024] [Indexed: 11/19/2024]
Abstract
In neurodegenerative diseases (NDDs), disruptions in protein homeostasis hinder the clearance of misfolded proteins, causing the formation of misfolded protein oligomers and multimers. The accumulation of these abnormal proteins results in the onset and progression of NDDs. Removal of non-native protein is essential for cell to maintain proteostasis. In recent years, targeted protein degradation (TPD) technologies have become a novel means of treating NDDs by removing misfolded proteins through the intracellular protein quality control system. The TPD strategy includes the participation of two primary pathways, namely the ubiquitin-proteasome pathway (for instance, PROTAC, molecular glue and hydrophobic tag), and the autophagy-lysosome pathway (such as LYTAC, AUTAC and ATTEC). In this review, we systematically present the mechanisms of various TPD strategies employed for neurotoxic protein degradation in NDDs. The article provides an overview of the design, in vitro and in vivo anti-NDD activities and pharmacokinetic properties of these small-molecular degraders. Finally, the advantages, challenges and perspectives of these TPD technologies in NDDs therapy are discussed, providing ideas for further development of small molecule degraders in the realm of NDDs.
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Affiliation(s)
- Xin Wang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu 610041, China
| | - Wen Shuai
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu 610041, China
| | - Panpan Yang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu 610041, China
| | - Yinyang Liu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu 610041, China
| | - Yiwen Zhang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu 610041, China.
| | - Guan Wang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, Nursing Key Laboratory of Sichuan Province, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu 610041, China.
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20
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Ryu M, Oh S, Jeong KB, Hwang S, Kim JS, Chung M, Chi SW. Single-Molecule-Based, Label-Free Monitoring of Molecular Glue Efficacies for Promoting Protein-Protein Interactions Using YaxAB Nanopores. ACS NANO 2024; 18:31451-31465. [PMID: 39482865 PMCID: PMC11562796 DOI: 10.1021/acsnano.4c11436] [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: 08/19/2024] [Revised: 10/15/2024] [Accepted: 10/21/2024] [Indexed: 11/03/2024]
Abstract
Modulating protein-protein interactions (PPIs) is an attractive strategy in drug discovery. Molecular glues, bifunctional small-molecule drugs that promote PPIs, offer an approach to targeting traditionally undruggable targets. However, the efficient discovery of molecular glues has been hampered by the current limitations of conventional ensemble-averaging-based methods. In this study, we present a YaxAB nanopore for probing the efficacy of molecular glues in inducing PPIs. Using YaxAB nanopores, we demonstrate single-molecule-based, label-free monitoring of protein complex formation between mammalian target of rapamycin (mTOR) and FK506-binding proteins (FKBPs) triggered by the molecular glue, rapamycin. Owing to its wide entrance and adjustable pore size, in combination with potent electro-osmotic flow (EOF), a single funnel-shaped YaxAB nanopore enables the simultaneous detection and single-molecule-level quantification of multiprotein states, including single proteins, binary complexes, and ternary complexes induced by rapamycin. Notably, YaxAB nanopores could sensitively discriminate between the binary complexes or ternary complexes induced by rapamycin and its analogues, despite the subtle size differences of ∼122 or ∼116 Da, respectively. Taken together, our results provide proof-of-concept for single-molecule-based, label-free, and ultrasensitive screening and structure-activity relationship (SAR) analysis of molecular glues, which will contribute to low-cost, highly efficient discovery, and rational design of bifunctional modality of drugs, such as molecular glues.
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Affiliation(s)
- Minju Ryu
- Disease
Target Structure Research Center, Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology
(KRIBB), Daejeon 34141, Republic
of Korea
- Department
of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Sohee Oh
- Disease
Target Structure Research Center, Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology
(KRIBB), Daejeon 34141, Republic
of Korea
| | - Ki-Baek Jeong
- Disease
Target Structure Research Center, Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology
(KRIBB), Daejeon 34141, Republic
of Korea
- Critical
Diseases Diagnostics Convergence Research Center, KRIBB, Daejeon 34141, Republic of Korea
| | - Sungbo Hwang
- Disease
Target Structure Research Center, Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology
(KRIBB), Daejeon 34141, Republic
of Korea
| | - Jin-Sik Kim
- Disease
Target Structure Research Center, Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology
(KRIBB), Daejeon 34141, Republic
of Korea
- Critical
Diseases Diagnostics Convergence Research Center, KRIBB, Daejeon 34141, Republic of Korea
| | - Minji Chung
- Disease
Target Structure Research Center, Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology
(KRIBB), Daejeon 34141, Republic
of Korea
- Department
of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Seung-Wook Chi
- Disease
Target Structure Research Center, Division of Biomedical Research, Korea Research Institute of Bioscience and Biotechnology
(KRIBB), Daejeon 34141, Republic
of Korea
- Department
of Proteome Structural Biology, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34113, Republic of Korea
- School
of Pharmacy, Sungkyunkwan University, Suwon, Gyeonggi 16419, Republic
of Korea
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21
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Cui M, Zhang D, Zheng X, Zhai H, Xie M, Fan Q, Wang L, Fan C, Chao J. Intelligent Modular DNA Lysosome-Targeting Chimera Nanodevice for Precision Tumor Therapy. J Am Chem Soc 2024; 146:29609-29620. [PMID: 39428706 DOI: 10.1021/jacs.4c10010] [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: 10/22/2024]
Abstract
Lysosome targeting chimeras (LYTACs) have emerged as a powerful modality that can eliminate traditionally undruggable extracellular tumor-related pathogenic proteins, but their low bioavailability and nonspecific distribution significantly restrict their efficacy in precision tumor therapy. Developing a LYTAC system that can selectively target tumor tissues and enable a modular design is crucial but challenging. We here report a programmable nanoplatform for tumor-specific degradation of multipathogenic proteins using an intelligent modular DNA LYTAC (IMTAC) nanodevice. We employ circular DNA origami to integrate predesigned modular multitarget protein binding sites and pH-responsive protein degradation promoters that specifically recognize cell-surface lysosome-shuttling receptors in tumor tissues. By precisely manipulating the stoichiometry and modularity of promoters and ligands targeting diverse proteins, the IMTAC nanodevice enables accurate localization and delivery into tumor tissues, where the acidic tumor microenvironment triggers degradation switch activation, multivalent binding, and efficient degradation of various prespecified proteins. The tissue-specificity and multiple ligands in IMTACs significantly improve the drug utilization rate while reducing off-target effects. Importantly, this system demonstrates the capability of collabo-rative degradation of EGFR and PDL1 in tumor tissue for combined targeting and immunity therapy of hepatocellular carcinoma (HCC), resulting in obvious tumor necrosis and inhibition of tumor growth in vivo even at low concentrations. This study presents a unique strategy for building a general, intelligent, modular, and simple encoded nanoplatform for designing precision medicine degraders and developing proprietary antitumor drugs.
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Affiliation(s)
- Meirong Cui
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Dan Zhang
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Xian Zheng
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Huan Zhai
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Mo Xie
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Qin Fan
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Lianhui Wang
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Jie Chao
- State Key Laboratory of Organic Electronics and Information Displays & Institute of Advanced Materials (IAM), National Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing 210023, China
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22
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Krygier K, Wijetunge AN, Srayeddin A, Mccann H, Rullo AF. Leveraging Covalency to Stabilize Ternary Complex Formation For Cell-Cell "Induced Proximity". ACS Chem Biol 2024; 19:2103-2117. [PMID: 39325690 DOI: 10.1021/acschembio.4c00286] [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: 09/28/2024]
Abstract
Recent advances in the field of translational chemical biology use diverse "proximity-inducing" synthetic modalities to elicit new modes of "event driven" pharmacology. These include mechanisms of targeted protein degradation and immune clearance of pathogenic cells. Heterobifunctional "chimeric" compounds like Proteolysis TArgeting Chimeras (PROTACs) and Antibody Recruiting Molecules (ARMs) leverage these mechanisms, respectively. Both systems function through the formation of reversible "ternary" or higher-order biomolecular complexes. Critical to function are key parameters, such as bifunctional molecule affinity for endogenous proteins, target residence time, and turnover. To probe the mechanism and enhance function, covalent chemical approaches have been developed to kinetically stabilize ternary complexes. These include electrophilic PROTACs and Covalent Immune Recruiters (CIRs), the latter designed to uniquely enforce cell-cell induced proximity. Inducing cell-cell proximity is associated with key challenges arising from a combination of steric and/or mechanical based destabilizing forces on the ternary complex. These factors can attenuate the formation of ternary complexes driven by high affinity bifunctional/proximity inducing molecules. This Account describes initial efforts in our lab to address these challenges using the CIR strategy in antibody recruitment or receptor engineered T cell model systems of cell-cell induced proximity. ARMs form ternary complexes with serum antibodies and surface protein antigens on tumor cells that subsequently engage immune cells via Fc receptors. Binding and clustering of Fc receptors trigger immune cell killing of the tumor cell. We applied the CIR strategy to convert ARMs to covalent chimeras, which "irreversibly" recruit serum antibodies to tumor cells. These covalent chimeras leverage electrophile preorganization and kinetic effective molarity to achieve fast and selective covalent engagement of the target ternary complex protein, e.g., serum antibody. Importantly, covalent engagement can proceed via diverse binding site amino acids beyond cysteine. Covalent chimeras demonstrated striking functional enhancements compared to noncovalent ARM analogs in functional immune assays. We revealed this enhancement was in fact due to the increased kinetic stability and not concentration, of ternary complexes. This finding was recapitulated using analogous CIR modalities that integrate peptidic or carbohydrate binding ligands with Sulfur(VI) Fluoride Exchange (SuFEx) electrophiles to induce cell-cell proximity. Mechanistic studies in a distinct model system that uses T cells engineered with receptors that recognize covalent chimeras or ARMs, revealed covalent receptor engagement uniquely enforces downstream activation signaling. Finally, this Account discusses potential challenges and future directions for adapting and optimizing covalent chimeric/bifunctional molecules for diverse applications in cell-cell induced proximity.
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Affiliation(s)
- Karolina Krygier
- Center for Discovery in Cancer Research, Department of Biochemistry and Biomedical Sciences, Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada, L8S 4L8
| | - Anjalee N Wijetunge
- Center for Discovery in Cancer Research, Department of Biochemistry and Biomedical Sciences, Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada, L8S 4L8
| | - Arthur Srayeddin
- Center for Discovery in Cancer Research, Department of Biochemistry and Biomedical Sciences, Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada, L8S 4L8
| | - Harrison Mccann
- Center for Discovery in Cancer Research, Department of Biochemistry and Biomedical Sciences, Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada, L8S 4L8
| | - Anthony F Rullo
- Center for Discovery in Cancer Research, Department of Biochemistry and Biomedical Sciences, Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada, L8S 4L8
- Department of Medicine, McMaster University, Hamilton, Ontario, Canada, L8S 4L8
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23
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Zhou Y, Li C, Chen X, Zhao Y, Liao Y, Huang P, Wu W, Nieto NS, Li L, Tang W. Development of folate receptor targeting chimeras for cancer selective degradation of extracellular proteins. Nat Commun 2024; 15:8695. [PMID: 39379374 PMCID: PMC11461649 DOI: 10.1038/s41467-024-52685-9] [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: 12/15/2023] [Accepted: 09/19/2024] [Indexed: 10/10/2024] Open
Abstract
Targeted protein degradation has emerged as a novel therapeutic modality to treat human diseases by utilizing the cell's own disposal systems to remove protein target. Significant clinical benefits have been observed for degrading many intracellular proteins. Recently, the degradation of extracellular proteins in the lysosome has been developed. However, there have been limited successes in selectively degrading protein targets in disease-relevant cells or tissues, which would greatly enhance the development of precision medicine. Additionally, most degraders are not readily available due to their complexity. We report a class of easily accessible Folate Receptor TArgeting Chimeras (FRTACs) to recruit the folate receptor, primarily expressed on malignant cells, to degrade extracellular soluble and membrane cancer-related proteins in vitro and in vivo. Our results indicate that FRTAC is a general platform for developing more precise and effective chemical probes and therapeutics for the study and treatment of cancers.
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Affiliation(s)
- Yaxian Zhou
- Lachman Institute of Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Chunrong Li
- Lachman Institute of Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Xuankun Chen
- Lachman Institute of Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Yuan Zhao
- Lachman Institute of Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Yaxian Liao
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Penghsuan Huang
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Wenxin Wu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Nicholas S Nieto
- Lachman Institute of Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Lingjun Li
- Lachman Institute of Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Weiping Tang
- Lachman Institute of Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA.
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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24
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Serniuck NJ, Kapcan E, Moogk D, Moore AE, Lake BP, Denisova G, Hammill JA, Bramson JL, Rullo AF. Electrophilic proximity-inducing synthetic adapters enhance universal T cell function by covalently enforcing immune receptor signaling. MOLECULAR THERAPY. ONCOLOGY 2024; 32:200842. [PMID: 39045028 PMCID: PMC11264187 DOI: 10.1016/j.omton.2024.200842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 06/10/2024] [Accepted: 06/21/2024] [Indexed: 07/25/2024]
Abstract
Proximity-induction of cell-cell interactions via small molecules represents an emerging field in basic and translational sciences. Covalent anchoring of these small molecules represents a useful chemical strategy to enforce proximity; however, it remains largely unexplored for driving cell-cell interactions. In immunotherapeutic applications, bifunctional small molecules are attractive tools for inducing proximity between immune effector cells like T cells and tumor cells to induce tumoricidal function. We describe a two-component system composed of electrophilic bifunctional small molecules and paired synthetic antigen receptors (SARs) that elicit T cell activation. The molecules, termed covalent immune recruiters (CIRs), were designed to affinity label and covalently engage SARs. We evaluated the utility of CIRs to direct anti-tumor function of human T cells engineered with three biologically distinct classes of SAR. Irrespective of the electrophilic chemistry, tumor-targeting moiety, or SAR design, CIRs outperformed equivalent non-covalent bifunctional adapters, establishing a key role for covalency in maximizing functionality. We determined that covalent linkage enforced early T cell activation events in a manner that was dependent upon each SARs biology and signaling threshold. These results provide a platform to optimize universal SAR-T cell functionality and more broadly reveal new insights into how covalent adapters modulate cell-cell proximity-induction.
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Affiliation(s)
- Nickolas J. Serniuck
- Centre for Discovery in Cancer Research, McMaster University, Hamilton, ON, Canada
- McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada
| | - Eden Kapcan
- Centre for Discovery in Cancer Research, McMaster University, Hamilton, ON, Canada
- McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada
| | - Duane Moogk
- Centre for Discovery in Cancer Research, McMaster University, Hamilton, ON, Canada
- McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Allyson E. Moore
- Centre for Discovery in Cancer Research, McMaster University, Hamilton, ON, Canada
- McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Benjamin P.M. Lake
- Centre for Discovery in Cancer Research, McMaster University, Hamilton, ON, Canada
- McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada
| | - Galina Denisova
- McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada
| | - Joanne A. Hammill
- Centre for Discovery in Cancer Research, McMaster University, Hamilton, ON, Canada
- McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Jonathan L. Bramson
- Centre for Discovery in Cancer Research, McMaster University, Hamilton, ON, Canada
- McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Anthony F. Rullo
- Centre for Discovery in Cancer Research, McMaster University, Hamilton, ON, Canada
- McMaster Immunology Research Centre, McMaster University, Hamilton, ON, Canada
- Department of Medicine, McMaster University, Hamilton, ON, Canada
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada
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25
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Yvon R, Woo CM. Small molecules help misplaced proteins hitchhike around cells. Nature 2024; 633:773-774. [PMID: 39294281 DOI: 10.1038/d41586-024-02802-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/20/2024]
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26
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Yi S, Kim D, Cho W, Lee JH, Kwon JH, Kim J, Park SB. Rational Design of Pyrido[3,2- b]indolizine as a Tunable Fluorescent Scaffold for Fluorogenic Bioimaging. JACS AU 2024; 4:2896-2906. [PMID: 39211616 PMCID: PMC11350592 DOI: 10.1021/jacsau.4c00135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 05/24/2024] [Accepted: 05/29/2024] [Indexed: 09/04/2024]
Abstract
Novel fluorescent scaffolds are highly demanding for a wide range of applications in biomedical investigation. To meet this demand, the pyrido[3,2-b]indolizine scaffold was designed as a versatile organic fluorophore. With the aid of computational modeling, fluorophores offering tunable emission colors (blue to red) were constructed. Notably, constructed fluorophores absorb lights in the visible range (>400 nm) despite their small sizes (<300 g/mol). Among the fluorophores was discovered a highly fluorogenic fluorophore with a unique turn-on property, 1, and it was developed into a washing-free bioprobe for visualizing cellular lipid droplets in living cells. Furthermore, motivated by the core's compact size and structural analogy to indole, unprecedented tryptophan-analogous fluorogenic unnatural amino acids were constructed and incorporated into fluorogenic peptide probes for monitoring peptide-protein interactions.
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Affiliation(s)
- Sihyeong Yi
- CRI
Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Dahham Kim
- CRI
Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Wansang Cho
- CRI
Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Jung Ho Lee
- Department
of Biophysics and Chemical Biology, Seoul
National University, Seoul 08826, Korea
| | - Ji Hoon Kwon
- CRI
Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul 08826, Korea
| | - Jonghoon Kim
- Department
of Chemistry and Integrative Institute of Basic Science, Department
of Green Chemistry and Materials Engineering, Soongsil University, Seoul 06978, Korea
| | - Seung Bum Park
- CRI
Center for Chemical Proteomics, Department of Chemistry, Seoul National University, Seoul 08826, Korea
- Department
of Biophysics and Chemical Biology, Seoul
National University, Seoul 08826, Korea
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27
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Wang L, Lin H, Yang B, Jiang X, Chen J, Chowdhury SR, Cheng N, Nakata PA, Lonard DM, Wang MC, Wang J. Development of a Novel Amplifiable System to Quantify Hydrogen Peroxide in Living Cells. J Am Chem Soc 2024; 146:22396-22404. [PMID: 39079063 PMCID: PMC11722959 DOI: 10.1021/jacs.4c05366] [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: 08/15/2024]
Abstract
Although many redox signaling molecules are present at low concentrations, typically ranging from micromolar to submicromolar levels, they often play essential roles in a wide range of biological pathways and disease mechanisms. However, accurately measuring low-abundant analytes has been a significant challenge due to the lack of sensitivity and quantitative capability of existing measurement methods. In this study, we introduced a novel chemically induced amplifiable system for quantifying low-abundance redox signaling molecules in living cells. We utilized H2O2 as a proof-of-concept analyte and developed a probe that quantifies cellular peroxide levels by combining the NanoBiT system with androgen receptor dimerization as a reporting mechanism. Our system demonstrated a highly sensitive response to cellular peroxide changes induced both endogenously and exogenously. Furthermore, the system can be adapted for the quantification of other signaling molecules if provided with suitable probing chemistry.
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Affiliation(s)
- Lingfei Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Hanfeng Lin
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
- Center for NextGen Therapeutics, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Bin Yang
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
- Center for NextGen Therapeutics, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Xiqian Jiang
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Jianwei Chen
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Sandipan Roy Chowdhury
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
- Center for NextGen Therapeutics, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Ninghui Cheng
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Paul A. Nakata
- Department of Pediatrics, Baylor College of Medicine, Houston, Texas 77030, United States
| | - David M. Lonard
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Meng. C. Wang
- Department of Molecular and Human Genetics, Huffington Center on Aging, and Howard Hughes Medical Institute, Baylor College of Medicine, Houston, Texas 77030, United States
| | - Jin Wang
- Verna and Marrs McLean Department of Biochemistry and Molecular Pharmacology, Baylor College of Medicine, Houston, Texas 77030, United States
- Center for NextGen Therapeutics, Baylor College of Medicine, Houston, Texas 77030, United States
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas 77030, United States
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28
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Mitchell CL, Kurouski D. Novel strategies in Parkinson's disease treatment: a review. Front Mol Neurosci 2024; 17:1431079. [PMID: 39183754 PMCID: PMC11341544 DOI: 10.3389/fnmol.2024.1431079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Accepted: 07/29/2024] [Indexed: 08/27/2024] Open
Abstract
An unprecedented extension of life expectancy observed during the past century drastically increased the number of patients diagnosed with Parkinson's diseases (PD) worldwide. Estimated costs of PD alone reached $52 billion per year, making effective neuroprotective treatments an urgent and unmet need. Current treatments of both AD and PD focus on mitigating the symptoms associated with these pathologies and are not neuroprotective. In this review, we discuss the most advanced therapeutic strategies that can be used to treat PD. We also critically review the shift of the therapeutic paradigm from a small molecule-based inhibition of protein aggregation to the utilization of natural degradation pathways and immune cells that are capable of degrading toxic amyloid deposits in the brain of PD patients.
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Affiliation(s)
- Charles L. Mitchell
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, TX, United States
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
| | - Dmitry Kurouski
- Interdisciplinary Program in Genetics and Genomics, Texas A&M University, College Station, TX, United States
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, United States
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29
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Vetma V, Perez LC, Eliaš J, Stingu A, Kombara A, Gmaschitz T, Braun N, Ciftci T, Dahmann G, Diers E, Gerstberger T, Greb P, Kidd G, Kofink C, Puoti I, Spiteri V, Trainor N, Weinstabl H, Westermaier Y, Whitworth C, Ciulli A, Farnaby W, McAulay K, Frost AB, Chessum N, Koegl M. Confounding Factors in Targeted Degradation of Short-Lived Proteins. ACS Chem Biol 2024; 19:1484-1494. [PMID: 38958654 DOI: 10.1021/acschembio.4c00152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
Targeted protein degradation has recently emerged as a novel option in drug discovery. Natural protein half-life is expected to affect the efficacy of degrading agents, but to what extent it influences target protein degradation has not been systematically explored. Using simple mathematical modeling of protein degradation, we find that the natural half-life of a target protein has a dramatic effect on the level of protein degradation induced by a degrader agent which can pose significant hurdles to screening efforts. Moreover, we show that upon screening for degraders of short-lived proteins, agents that stall protein synthesis, such as GSPT1 degraders and generally cytotoxic compounds, deceptively appear as protein-degrading agents. This is exemplified by the disappearance of short-lived proteins such as MCL1 and MDM2 upon GSPT1 degradation and upon treatment with cytotoxic agents such as doxorubicin. These findings have implications for target selection as well as for the type of control experiments required to conclude that a novel agent works as a bona fide targeted protein degrader.
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Affiliation(s)
- Vesna Vetma
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ Dundee, Scotland, U.K
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dow Street, DD1 5EH Dundee, Scotland, U.K
| | - Laura Casares Perez
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ Dundee, Scotland, U.K
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dow Street, DD1 5EH Dundee, Scotland, U.K
| | - Ján Eliaš
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | - Andrea Stingu
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | - Anju Kombara
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | | | - Nina Braun
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | - Tuncay Ciftci
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | - Georg Dahmann
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | - Emelyne Diers
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dow Street, DD1 5EH Dundee, Scotland, U.K
| | | | - Peter Greb
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | - Giorgia Kidd
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ Dundee, Scotland, U.K
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dow Street, DD1 5EH Dundee, Scotland, U.K
| | | | - Ilaria Puoti
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ Dundee, Scotland, U.K
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dow Street, DD1 5EH Dundee, Scotland, U.K
| | - Valentina Spiteri
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ Dundee, Scotland, U.K
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dow Street, DD1 5EH Dundee, Scotland, U.K
| | - Nicole Trainor
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dow Street, DD1 5EH Dundee, Scotland, U.K
| | | | | | - Claire Whitworth
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dow Street, DD1 5EH Dundee, Scotland, U.K
| | - Alessio Ciulli
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ Dundee, Scotland, U.K
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dow Street, DD1 5EH Dundee, Scotland, U.K
| | - William Farnaby
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ Dundee, Scotland, U.K
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dow Street, DD1 5EH Dundee, Scotland, U.K
| | - Kirsten McAulay
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ Dundee, Scotland, U.K
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dow Street, DD1 5EH Dundee, Scotland, U.K
| | - Aileen B Frost
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ Dundee, Scotland, U.K
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dow Street, DD1 5EH Dundee, Scotland, U.K
| | - Nicola Chessum
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | - Manfred Koegl
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
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30
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Zhang S, Nie S, Ma G, Shen M, Kong L, Zuo Z, Li Y. Identification of novel GSPT1 degraders by virtual screening and bioassay. Eur J Med Chem 2024; 273:116524. [PMID: 38795517 DOI: 10.1016/j.ejmech.2024.116524] [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: 04/08/2024] [Revised: 05/11/2024] [Accepted: 05/20/2024] [Indexed: 05/28/2024]
Abstract
GSPT1 plays crucial physiological functions, such as terminating protein translation, overexpressed in various tumors. It is a promising anti-tumor target, but is also considered as an "undruggable" protein. Recent studies have found that a class of small molecules can degrade GSPT1 through the "molecular glue" mechanism with strong antitumor activity, which is expected to become a new therapy for hematological malignancies. Currently available GSPT1 degraders are mostly derived from the scaffold of immunomodulatory imide drug (IMiD), thus more active compounds with novel structure remain to be found. In this work, using computer-assisted multi-round virtual screening and bioassay, we identified a non-IMiD acylhydrazone compound, AN5782, which can reduce the protein level of GPST1 and obviously inhibit the proliferation of tumor cells. Some analogs were obtained by a substructure search of AN5782. The structure-activity relationship analysis revealed possible interactions between these compounds and CRBN-GSPT1. Further biological mechanistic studies showed that AN5777 decreased GSPT1 remarkably through the ubiquitin-proteasome system, and its effective cytotoxicity was CRBN- and GSPT1-dependent. Furthermore, AN5777 displayed good antiproliferative activities against U937 and OCI-AML-2 cells, and dose-dependently induced G1 phase arrest and apoptosis. The structure found in this work could be good start for antitumor drug development.
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Affiliation(s)
- Shuqun Zhang
- Key Laboratory of Phytochemistry and Natural Medicines, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Shiyun Nie
- Key Laboratory of Medicinal Chemistry for Natural Resource, Yunnan Key Laboratory of Research and Development for Natural Products, School of Pharmacy, Ministry of Education, Yunnan University, Kunming, 650500, China
| | - Guangchao Ma
- Key Laboratory of Medicinal Chemistry for Natural Resource, Yunnan Key Laboratory of Research and Development for Natural Products, School of Pharmacy, Ministry of Education, Yunnan University, Kunming, 650500, China
| | - Meiling Shen
- Key Laboratory of Phytochemistry and Natural Medicines, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lingmei Kong
- Key Laboratory of Medicinal Chemistry for Natural Resource, Yunnan Key Laboratory of Research and Development for Natural Products, School of Pharmacy, Ministry of Education, Yunnan University, Kunming, 650500, China
| | - Zhili Zuo
- Key Laboratory of Phytochemistry and Natural Medicines, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Yan Li
- Key Laboratory of Phytochemistry and Natural Medicines, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China; Key Laboratory of Medicinal Chemistry for Natural Resource, Yunnan Key Laboratory of Research and Development for Natural Products, School of Pharmacy, Ministry of Education, Yunnan University, Kunming, 650500, China.
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31
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Wozniak JM, Li W, Governa P, Chen LY, Jadhav A, Dongre A, Forli S, Parker CG. Enhanced mapping of small-molecule binding sites in cells. Nat Chem Biol 2024; 20:823-834. [PMID: 38167919 PMCID: PMC11213684 DOI: 10.1038/s41589-023-01514-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 11/29/2023] [Indexed: 01/05/2024]
Abstract
Photoaffinity probes are routinely utilized to identify proteins that interact with small molecules. However, despite this common usage, resolving the specific sites of these interactions remains a challenge. Here we developed a chemoproteomic workflow to determine precise protein binding sites of photoaffinity probes in cells. Deconvolution of features unique to probe-modified peptides, such as their tendency to produce chimeric spectra, facilitated the development of predictive models to confidently determine labeled sites. This yielded an expansive map of small-molecule binding sites on endogenous proteins and enabled the integration with multiplexed quantitation, increasing the throughput and dimensionality of experiments. Finally, using structural information, we characterized diverse binding sites across the proteome, providing direct evidence of their tractability to small molecules. Together, our findings reveal new knowledge for the analysis of photoaffinity probes and provide a robust method for high-resolution mapping of reversible small-molecule interactions en masse in native systems.
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Affiliation(s)
- Jacob M Wozniak
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Weichao Li
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Paolo Governa
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Li-Yun Chen
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Appaso Jadhav
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA, USA
| | - Ashok Dongre
- Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Stefano Forli
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
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32
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Chang X, Qu F, Li C, Zhang J, Zhang Y, Xie Y, Fan Z, Bian J, Wang J, Li Z, Xu X. Development and therapeutic potential of GSPT1 molecular glue degraders: A medicinal chemistry perspective. Med Res Rev 2024; 44:1727-1767. [PMID: 38314926 DOI: 10.1002/med.22024] [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: 09/20/2023] [Revised: 12/18/2023] [Accepted: 01/21/2024] [Indexed: 02/07/2024]
Abstract
Unprecedented therapeutic targeting of previously undruggable proteins has now been achieved by molecular-glue-mediated proximity-induced degradation. As a small GTPase, G1 to S phase transition 1 (GSPT1) interacts with eRF1, the translation termination factor, to facilitate the process of translation termination. Studied demonstrated that GSPT1 plays a vital role in the acute myeloid leukemia (AML) and MYC-driven lung cancer. Thus, molecular glue (MG) degraders targeting GSPT1 is a novel and promising approach for treating AML and MYC-driven cancers. In this Perspective, we briefly summarize the structural and functional aspects of GSPT1, highlighting the latest advances and challenges in MG degraders, as well as some representative patents. The structure-activity relationships, mechanism of action and pharmacokinetic features of MG degraders are emphasized to provide a comprehensive compendium on the rational design of GSPT1 MG degraders. We hope to provide an updated overview, and design guide for strategies targeting GSPT1 for the treatment of cancer.
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Affiliation(s)
- Xiujin Chang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Fangui Qu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Chunxiao Li
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Jingtian Zhang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Yanqing Zhang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Yuanyuan Xie
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Zhongpeng Fan
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Jinlei Bian
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Jubo Wang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Zhiyu Li
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Xi Xu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
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33
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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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34
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Schreiber SL. Molecular glues and bifunctional compounds: Therapeutic modalities based on induced proximity. Cell Chem Biol 2024; 31:1050-1063. [PMID: 38861986 DOI: 10.1016/j.chembiol.2024.05.004] [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: 03/29/2024] [Revised: 05/16/2024] [Accepted: 05/20/2024] [Indexed: 06/13/2024]
Abstract
This Perspective explores molecular glues and bifunctional compounds-proximity-inducing compounds-and offers a framework to understand and exploit their similarity to hotspots, missense mutations, and posttranslational modifications (PTMs). This view is also shown to be relevant to intramolecular glues, where compounds induce contacts between distinct domains of the same protein. A historical perspective of these compounds is presented that shows the field has come full circle from molecular glues targeting native proteins, to bifunctionals targeting fusion proteins, and back to molecular glues and bifunctionals targeting native proteins. Modern screening methods and data analyses with pre-selected target proteins are shown to yield either cooperative molecular glues or bifunctional compounds that induce proximity, thereby enabling novel functional outcomes.
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Affiliation(s)
- Stuart L Schreiber
- Arena BioWorks, Broad Institute, Harvard University, Cambridge, MA, USA.
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35
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Pedram K, Shon DJ, Tender GS, Mantuano NR, Northey JJ, Metcalf KJ, Wisnovsky SP, Riley NM, Forcina GC, Malaker SA, Kuo A, George BM, Miller CL, Casey KM, Vilches-Moure JG, Ferracane MJ, Weaver VM, Läubli H, Bertozzi CR. Design of a mucin-selective protease for targeted degradation of cancer-associated mucins. Nat Biotechnol 2024; 42:597-607. [PMID: 37537499 PMCID: PMC11018308 DOI: 10.1038/s41587-023-01840-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 05/22/2023] [Indexed: 08/05/2023]
Abstract
Targeted protein degradation is an emerging strategy for the elimination of classically undruggable proteins. Here, to expand the landscape of targetable substrates, we designed degraders that achieve substrate selectivity via recognition of a discrete peptide and glycan motif and achieve cell-type selectivity via antigen-driven cell-surface binding. We applied this approach to mucins, O-glycosylated proteins that drive cancer progression through biophysical and immunological mechanisms. Engineering of a bacterial mucin-selective protease yielded a variant for fusion to a cancer antigen-binding nanobody. The resulting conjugate selectively degraded mucins on cancer cells, promoted cell death in culture models of mucin-driven growth and survival, and reduced tumor growth in mouse models of breast cancer progression. This work establishes a blueprint for the development of biologics that degrade specific protein glycoforms on target cells.
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Affiliation(s)
- Kayvon Pedram
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - D Judy Shon
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Gabrielle S Tender
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Natalia R Mantuano
- Cancer Immunotherapy Laboratory, Department of Biomedicine, University of Basel, Basel, Switzerland
- Division of Oncology, Department of Theragnostics, University Hospital, Basel, Switzerland
| | - Jason J Northey
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Kevin J Metcalf
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Simon P Wisnovsky
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nicholas M Riley
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Giovanni C Forcina
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Stacy A Malaker
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Angel Kuo
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Benson M George
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | - Caitlyn L Miller
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Kerriann M Casey
- Department of Comparative Medicine, Stanford University, Stanford, CA, USA
| | | | | | - Valerie M Weaver
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco (UCSF), San Francisco, CA, USA
- Departments of Radiation Oncology and Bioengineering and Therapeutic Sciences, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, and Helen Diller Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Heinz Läubli
- Cancer Immunotherapy Laboratory, Department of Biomedicine, University of Basel, Basel, Switzerland
- Division of Oncology, Department of Theragnostics, University Hospital, Basel, Switzerland
| | - Carolyn R Bertozzi
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford, CA, USA.
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36
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Brennan PJ, Saunders RE, Spanou M, Serafini M, Sun L, Heger GP, Konopacka A, Beveridge RD, Gordon L, Bunally SB, Saudemont A, Benowitz AB, Martinez-Fleites C, Queisser MA, An H, Deane CM, Hann MM, Brayshaw LL, Conway SJ. Orthogonal IMiD-Degron Pairs Induce Selective Protein Degradation in Cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.15.585309. [PMID: 38559242 PMCID: PMC10979945 DOI: 10.1101/2024.03.15.585309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Immunomodulatory imide drugs (IMiDs) including thalidomide, lenalidomide, and pomalidomide, can be used to induce degradation of a protein of interest that is fused to a short zinc finger (ZF) degron motif. These IMiDs, however, also induce degradation of endogenous neosubstrates, including IKZF1 and IKZF3. To improve degradation selectivity, we took a bump-and-hole approach to design and screen bumped IMiD analogs against 8380 ZF mutants. This yielded a bumped IMiD analog that induces efficient degradation of a mutant ZF degron, while not affecting other cellular proteins, including IKZF1 and IKZF3. In proof-of-concept studies, this system was applied to induce efficient degradation of TRIM28, a disease-relevant protein with no known small molecule binders. We anticipate that this system will make a valuable addition to the current arsenal of degron systems for use in target validation.
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Affiliation(s)
- Patrick J. Brennan
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford; Oxford, UK
- Department of Chemistry & Biochemistry, University of California, Los Angeles; Los Angeles, USA
| | | | | | - Marta Serafini
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford; Oxford, UK
| | - Liang Sun
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center; New York, USA
| | | | | | - Ryan D. Beveridge
- Virus Screening Facility, Weatherall Institute of Molecular Medicine, University of Oxford; Oxford, UK
| | | | | | | | | | | | | | - Heeseon An
- Chemical Biology Program, Memorial Sloan Kettering Cancer Center; New York, USA
| | | | | | | | - Stuart J. Conway
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford; Oxford, UK
- Department of Chemistry & Biochemistry, University of California, Los Angeles; Los Angeles, USA
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37
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Chen QH, Munoz E, Ashong D. Insight into Recent Advances in Degrading Androgen Receptor for Castration-Resistant Prostate Cancer. Cancers (Basel) 2024; 16:663. [PMID: 38339414 PMCID: PMC10854644 DOI: 10.3390/cancers16030663] [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: 12/30/2023] [Revised: 01/28/2024] [Accepted: 02/03/2024] [Indexed: 02/12/2024] Open
Abstract
Induced protein degradation has emerged as an innovative drug discovery approach, complementary to the classical method of suppressing protein function. The androgen receptor signaling pathway has been identified as the primary driving force in the development and progression of lethal castration-resistant prostate cancer. Since androgen receptor degraders function differently from androgen receptor antagonists, they hold the promise to overcome the drug resistance challenges faced by current therapeutics. Proteolysis-targeting chimeras (PROTACs), monomeric degraders, hydrophobic tagging, molecular glues, and autophagic degradation have demonstrated their capability in downregulating intracellular androgen receptor concentrations. The potential of these androgen receptor degraders to treat castration-resistant prostate cancer is substantiated by the advancement of six PROTACs and two monomeric androgen receptor degraders into phase I or II clinical trials. Although the chemical structures, in vitro and in vivo data, and degradation mechanisms of androgen receptor degraders have been reviewed, it is crucial to stay updated on recent advances in this field as novel androgen receptor degraders and new strategies continue to emerge. This review thus provides insight into recent advancements in this paradigm, offering an overview of the progress made since 2020.
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Affiliation(s)
- Qiao-Hong Chen
- Department of Chemistry and Biochemistry, California State University, Fresno, CA 93740, USA; (E.M.); (D.A.)
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38
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Thomas K, Bouguenina H, Miller DSJ, Sialana FJ, Hayhow TG, Choudhary JS, Rossanese OW, Bellenie BR. Degradation by Design: New Cyclin K Degraders from Old CDK Inhibitors. ACS Chem Biol 2024; 19:173-184. [PMID: 38193430 PMCID: PMC10804372 DOI: 10.1021/acschembio.3c00616] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/22/2023] [Accepted: 12/27/2023] [Indexed: 01/10/2024]
Abstract
Small molecules that induce protein degradation hold the potential to overcome several limitations of the currently available inhibitors. Monovalent or molecular glue degraders, in particular, enable the benefits of protein degradation without the disadvantages of high molecular weight and the resulting challenge in drug development that are associated with bivalent molecules like Proteolysis Targeting Chimeras. One key challenge in designing monovalent degraders is how to build in the degrader activity─how can we convert an inhibitor into a degrader? If degradation activity requires very specific molecular features, it will be difficult to find new degraders and challenging to optimize those degraders toward drugs. Herein, we demonstrate that an unexpectedly wide range of modifications to the degradation-inducing group of the cyclin K degrader CR8 are tolerated, including both aromatic and nonaromatic groups. We used these findings to convert the pan-CDK inhibitors dinaciclib and AT-7519 to Cyclin K degraders, leading to a novel dinaciclib-based compound with improved degradation activity compared to CR8 and confirm the mechanism of degradation. These results suggest that general design principles can be generated for the development and optimization of monovalent degraders.
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Affiliation(s)
- Katie
L. Thomas
- Centre
for Cancer Drug Discovery, The Institute
of Cancer Research, London SM2 5NG, U.K.
| | - Habib Bouguenina
- Centre
for Cancer Drug Discovery, The Institute
of Cancer Research, London SM2 5NG, U.K.
| | - Daniel S. J. Miller
- Centre
for Cancer Drug Discovery, The Institute
of Cancer Research, London SM2 5NG, U.K.
| | - Fernando J. Sialana
- Functional
Proteomics Group, The Institute of Cancer
Research, London SW3 6JB, U.K.
| | - Thomas G. Hayhow
- Oncology
R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0AA, U.K.
| | - Jyoti S. Choudhary
- Functional
Proteomics Group, The Institute of Cancer
Research, London SW3 6JB, U.K.
| | - Olivia W. Rossanese
- Centre
for Cancer Drug Discovery, The Institute
of Cancer Research, London SM2 5NG, U.K.
| | - Benjamin R. Bellenie
- Centre
for Cancer Drug Discovery, The Institute
of Cancer Research, London SM2 5NG, U.K.
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39
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He T, Wen C, Yang G, Yang X. Targeted Protein Degradation: Principles, Strategies, and Applications. Adv Biol (Weinh) 2023; 7:e2300083. [PMID: 37518856 DOI: 10.1002/adbi.202300083] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 06/11/2023] [Indexed: 08/01/2023]
Abstract
Protein degradation is a general process to maintain cell homeostasis. The intracellular protein quality control system mainly includes the ubiquitin-proteasome system and the lysosome pathway. Inspired by the physiological process, strategies to degrade specific proteins have developed, which emerge as potent and effective tools in biological research and drug discovery. This review focuses on recent advances in targeted protein degradation techniques, summarizing the principles, advantages, and challenges. Moreover, the potential applications and future direction in biological science and clinics are also discussed.
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Affiliation(s)
- Ting He
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, 710032, P. R. China
| | - Chenxi Wen
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, 710032, P. R. China
| | - Guodong Yang
- The State Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, 710032, P. R. China
| | - Xuekang Yang
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, 710032, P. R. China
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40
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Xue G, Xie J, Hinterndorfer M, Cigler M, Dötsch L, Imrichova H, Lampe P, Cheng X, Adariani SR, Winter GE, Waldmann H. Discovery of a Drug-like, Natural Product-Inspired DCAF11 Ligand Chemotype. Nat Commun 2023; 14:7908. [PMID: 38036533 PMCID: PMC10689823 DOI: 10.1038/s41467-023-43657-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 11/15/2023] [Indexed: 12/02/2023] Open
Abstract
Targeted proteasomal and autophagic protein degradation, often employing bifunctional modalities, is a new paradigm for modulation of protein function. In an attempt to explore protein degradation by means of autophagy we combine arylidene-indolinones reported to bind the autophagy-related LC3B-protein and ligands of the PDEδ lipoprotein chaperone, the BRD2/3/4-bromodomain containing proteins and the BTK- and BLK kinases. Unexpectedly, the resulting bifunctional degraders do not induce protein degradation by means of macroautophagy, but instead direct their targets to the ubiquitin-proteasome system. Target and mechanism identification reveal that the arylidene-indolinones covalently bind DCAF11, a substrate receptor in the CUL4A/B-RBX1-DDB1-DCAF11 E3 ligase. The tempered α, β-unsaturated indolinone electrophiles define a drug-like DCAF11-ligand class that enables exploration of this E3 ligase in chemical biology and medicinal chemistry programs. The arylidene-indolinone scaffold frequently occurs in natural products which raises the question whether E3 ligand classes can be found more widely among natural products and related compounds.
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Affiliation(s)
- Gang Xue
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Jianing Xie
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Matthias Hinterndorfer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Marko Cigler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Lara Dötsch
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
- Technical University Dortmund, Faculty of Chemistry and Chemical Biology, Dortmund, Germany
| | - Hana Imrichova
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Philipp Lampe
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Xiufen Cheng
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Soheila Rezaei Adariani
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
| | - Herbert Waldmann
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
- Technical University Dortmund, Faculty of Chemistry and Chemical Biology, Dortmund, Germany.
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41
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Lake BM, Rullo AF. Offsetting Low-Affinity Carbohydrate Binding with Covalency to Engage Sugar-Specific Proteins for Tumor-Immune Proximity Induction. ACS CENTRAL SCIENCE 2023; 9:2064-2075. [PMID: 38033792 PMCID: PMC10683482 DOI: 10.1021/acscentsci.3c01052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Indexed: 12/02/2023]
Abstract
Carbohydrate-binding receptors are often used by the innate immune system to potentiate inflammation, target endocytosis/destruction, and adaptive immunity (e.g., CD206, DC-SIGN, MBL, and anticarbohydrate antibodies). To access this class of receptors for cancer immunotherapy, a growing repertoire of bifunctional proximity-inducing therapeutics use high-avidity multivalent carbohydrate binding domains to offset the intrinsically low affinity associated with monomeric carbohydrate-protein binding interactions (Kd ≈ 10-3-10-6 M). For applications aimed at recruiting anticarbohydrate antibodies to tumor cells, large synthetic scaffolds are used that contain both a tumor-binding domain (TBD) and a multivalent antibody-binding domain (ABD) comprising multiple l-rhamnose monosaccharides. This allows for stable bridging between tumor cells and antibodies, which activates tumoricidal immune function. Problematically, such multivalent macromolecules can face limitations including synthetic and/or structural complexity and the potential for off-target immune engagement. We envisioned that small bifunctional "proximity-inducing" molecules containing a low-affinity monovalent ABD could efficiently engage carbohydrate-binding receptors for tumor-immune proximity by coupling weak binding with covalent engagement. Typical covalent drugs and electrophilic chimeras use high-affinity ligands to promote the fast covalent engagement of target proteins (i.e., large kinact/KI), driven by a favorably small KI for binding. We hypothesized the much less favorable KI associated with carbohydrate-protein binding interactions can be offset by a favorably large kinact for the covalent labeling step. In the current study, we test this hypothesis in the context of a model system that uses rhamnose-specific antibodies to induce tumor-immune proximity and tumoricidal function. We discovered that synthetic chimeric molecules capable of preorganizing an optimal electrophile (i.e., SuFEx vs activated ester) for protein engagement can rapidly covalently engage natural sources of antirhamnose antibody using only a single low-affinity rhamnose monosaccharide ABD. Strikingly, we observe chimeric molecules lacking an electrophile, which can only noncovalently bind the antibody, completely lack tumoricidal function. This is in stark contrast to previous work targeting small molecule hapten and peptide-specific antibodies. Our findings underscore the utility of covalency as a strategy to engage low-affinity carbohydrate-specific proteins for tumor-immune proximity induction.
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Affiliation(s)
- Benjamin
P. M. Lake
- Department
of Medicine, McMaster Immunology Research Center, Center
for Discovery in Cancer Research, Department of Biochemistry and Biomedical
Sciences, and Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton Ontario, Canada
| | - Anthony F. Rullo
- Department
of Medicine, McMaster Immunology Research Center, Center
for Discovery in Cancer Research, Department of Biochemistry and Biomedical
Sciences, and Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton Ontario, Canada
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42
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Amirian R, Azadi Badrbani M, Izadi Z, Samadian H, Bahrami G, Sarvari S, Abdolmaleki S, Nabavi SM, Derakhshankhah H, Jaymand M. Targeted protein modification as a paradigm shift in drug discovery. Eur J Med Chem 2023; 260:115765. [PMID: 37659194 DOI: 10.1016/j.ejmech.2023.115765] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/24/2023] [Accepted: 08/24/2023] [Indexed: 09/04/2023]
Abstract
Targeted Protein Modification (TPM) is an umbrella term encompassing numerous tools and approaches that use bifunctional agents to induce a desired modification over the POI. The most well-known TPM mechanism is PROTAC-directed protein ubiquitination. PROTAC-based targeted degradation offers several advantages over conventional small-molecule inhibitors, has shifted the drug discovery paradigm, and is acquiring increasing interest as over ten PROTACs have entered clinical trials in the past few years. Targeting the protein of interest for proteasomal degradation by PROTACS was the pioneer of various toolboxes for selective protein degradation. Nowadays, the ever-increasing number of tools and strategies for modulating and modifying the POI has expanded far beyond protein degradation, which phosphorylation and de-phosphorylation of the protein of interest, targeted acetylation, and selective modification of protein O-GlcNAcylation are among them. These novel strategies have opened new avenues for achieving more precise outcomes while remaining feasible and minimizing side effects. This field, however, is still in its infancy and has a long way to precede widespread use and translation into clinical practice. Herein, we investigate the pros and cons of these novel strategies by exploring the latest advancements in this field. Ultimately, we briefly discuss the emerging potential applications of these innovations in cancer therapy, neurodegeneration, viral infections, and autoimmune and inflammatory diseases.
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Affiliation(s)
- Roshanak Amirian
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran; Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran; USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Mehdi Azadi Badrbani
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran; Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran; USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Zhila Izadi
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran; USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Hadi Samadian
- Research Center for Molecular Medicine, Hamadan University of Medical Sciences, Hamadan, Iran.
| | - Gholamreza Bahrami
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran; USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Sajad Sarvari
- Department of Pharmaceutical Science, School of Pharmacy, West Virginia University, Morgantown, WV, USA.
| | - Sara Abdolmaleki
- Department of Chemistry, Faculty of Science, University of Kurdistan, Sanandaj, Iran.
| | - Seyed Mohammad Nabavi
- Department of Science and Technology, University of Sannio, 82100, Benevento, Italy.
| | - Hossein Derakhshankhah
- Pharmaceutical Sciences Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran; USERN Office, Kermanshah University of Medical Sciences, Kermanshah, Iran.
| | - Mehdi Jaymand
- Nano Drug Delivery Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran.
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Mohammed A, Waddell MB, Sutkeviciute I, Danda A, Philips SJ, Lang W, Slavish PJ, Kietlinska SJ, Kaulage M, Das S, Ansari AZ. Domain-Selective BET Ligands Yield Next-Generation Synthetic Genome Readers/Regulators with Nonidentical Cellular Functions. J Am Chem Soc 2023:10.1021/jacs.3c06297. [PMID: 37923569 PMCID: PMC11957383 DOI: 10.1021/jacs.3c06297] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023]
Abstract
SynTEF1, a prototype synthetic genome reader/regulator (SynGR), was designed to target GAA triplet repeats and restore the expression of frataxin (FXN) in Friedreich's ataxia patients. It achieves this complex task by recruiting BRD4, via a pan-BET ligand (JQ1), to the GAA repeats by using a sequence-selective DNA-binding polyamide. When bound to specific genomic loci in this way, JQ1 functions as a chemical prosthetic for acetyl-lysine residues that are natural targets of the two tandem bromodomains (BD1 and BD2) in bromo- and extra-terminal domain (BET) proteins. As next-generation BET ligands were disclosed, we tested a select set with improved physicochemical, pharmacological, and bromodomain-selective properties as substitutes for JQ1 in the SynGR design. Here, we report two unexpected findings: (1) SynGRs bearing pan-BET or BD2-selective ligands license transcription at the FXN locus, whereas those bearing BD1-selective ligands do not, and (2) rather than being neutral or inhibitory, an untethered BD1-selective ligand (GSK778) substantively enhances the activity of all active SynGRs. The failure of BD1-selective SynGRs to recruit BRD4/BET proteins suggests that rather than functioning as "epigenetic/chromatin mimics," active SynGRs mimic the functions of natural transcription factors in engaging BET proteins through BD2 binding. Moreover, the enhanced activity of SynGRs upon cotreatment with the BD1-selective ligand suggests that natural transcription factors compete for a limited pool of nonchromatin-bound BET proteins, and blocking BD1 directs pan-BET ligands to more effectively engage BD2. Taken together, SynGRs as chemical probes provide unique insights into the molecular recognition principles utilized by natural factors to precisely regulate gene expression, and they guide the design of more sophisticated synthetic gene regulators with greater therapeutic potential.
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Affiliation(s)
- Ashraf Mohammed
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - M Brett Waddell
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Ieva Sutkeviciute
- Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Adithi Danda
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Steven J. Philips
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Walter Lang
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - P. Jake Slavish
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Sandra J. Kietlinska
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Mangesh Kaulage
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Sourav Das
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN, USA
| | - Aseem Z. Ansari
- Department of Chemical Biology and Therapeutics, St. Jude Children’s Research Hospital, Memphis, TN, USA
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44
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Chen X, Zhou Y, Zhao Y, Tang W. Targeted degradation of extracellular secreted and membrane proteins. Trends Pharmacol Sci 2023; 44:762-775. [PMID: 37758536 PMCID: PMC10591793 DOI: 10.1016/j.tips.2023.08.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 08/26/2023] [Accepted: 08/27/2023] [Indexed: 09/29/2023]
Abstract
Targeted protein degradation (TPD) involving chimeric molecules has emerged as one of the most promising therapeutic modalities in recent years. Among various reported TPD strategies, proteolysis-targeting chimeras (PROTACs) stand out as a significant breakthrough in small-molecule drug discovery and have garnered the most attention to date. However, PROTACs are mainly capable of depleting intracellular proteins. Given that many important therapeutic targets such as cytokines, growth factors, and numerous receptors are membrane proteins or secreted extracellularly, there is interest in the development of novel strategies to degrade these protein categories. We review advances in this emerging area and provide insights to enhance the development of novel TPDs targeting extracellular proteins.
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Affiliation(s)
- Xuankun Chen
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
| | - Yaxian Zhou
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
| | - Yuan Zhao
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA
| | - Weiping Tang
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705, USA; Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA.
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45
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Ma Z, Bolinger AA, Zhou J. RIPTACs: A groundbreaking approach to drug discovery. Drug Discov Today 2023; 28:103774. [PMID: 37734702 PMCID: PMC11144445 DOI: 10.1016/j.drudis.2023.103774] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/04/2023] [Accepted: 09/14/2023] [Indexed: 09/23/2023]
Abstract
Regulated induced proximity targeting chimeras (RIPTACs), a new class of heterobifunctional molecules, show promise in specifically targeting and eliminating cancer cells while leaving healthy cells unharmed. As a groundbreaking drug discovery approach, RIPTACs work by forming a stable complex with two proteins, one specifically found in cancer cells (target protein, TP) and the other pan-essential for cell survival (effector protein, EP), selectively disrupting the function of the EP in cancer cells and causing cell death. Interestingly, the TPs need not be linked to disease progression, broadening the spectrum of potential drug targets. This review summarizes the discovery and recent advances of the RIPTAC strategy. Additionally, it discusses the associated opportunities and challenges as well as future perspectives in this field.
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Affiliation(s)
- Zonghui Ma
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA
| | - Andrew A Bolinger
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA
| | - Jia Zhou
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA.
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46
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Visser EJ, Jaishankar P, Sijbesma E, Pennings MAM, Vandenboorn EMF, Guillory X, Neitz RJ, Morrow J, Dutta S, Renslo AR, Brunsveld L, Arkin MR, Ottmann C. From Tethered to Freestanding Stabilizers of 14-3-3 Protein-Protein Interactions through Fragment Linking. Angew Chem Int Ed Engl 2023; 62:e202308004. [PMID: 37455289 DOI: 10.1002/anie.202308004] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023]
Abstract
Small-molecule stabilization of protein-protein interactions (PPIs) is a promising strategy in chemical biology and drug discovery. However, the systematic discovery of PPI stabilizers remains a largely unmet challenge. Herein we report a fragment-linking approach targeting the interface of 14-3-3 and a peptide derived from the estrogen receptor alpha (ERα) protein. Two classes of fragments-a covalent and a noncovalent fragment-were co-crystallized and subsequently linked, resulting in a noncovalent hybrid molecule in which the original fragment interactions were largely conserved. Supported by 20 crystal structures, this initial hybrid molecule was further optimized, resulting in selective, 25-fold stabilization of the 14-3-3/ERα interaction. The high-resolution structures of both the single fragments, their co-crystal structures and those of the linked fragments document a feasible strategy to develop orthosteric PPI stabilizers by linking to an initial tethered fragment.
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Affiliation(s)
- Emira J Visser
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Den Dolech 2, 5612, AZ Eindhoven, The Netherlands
| | - Priyadarshini Jaishankar
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Centre (SMDC), University of California San Francisco (UCSF), San Francisco, CA, 94143, USA
| | - Eline Sijbesma
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Den Dolech 2, 5612, AZ Eindhoven, The Netherlands
| | - Marloes A M Pennings
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Den Dolech 2, 5612, AZ Eindhoven, The Netherlands
| | - Edmee M F Vandenboorn
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Den Dolech 2, 5612, AZ Eindhoven, The Netherlands
| | - Xavier Guillory
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Den Dolech 2, 5612, AZ Eindhoven, The Netherlands
| | - R Jeffrey Neitz
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Centre (SMDC), University of California San Francisco (UCSF), San Francisco, CA, 94143, USA
| | - John Morrow
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Centre (SMDC), University of California San Francisco (UCSF), San Francisco, CA, 94143, USA
| | - Shubhankar Dutta
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Centre (SMDC), University of California San Francisco (UCSF), San Francisco, CA, 94143, USA
| | - Adam R Renslo
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Centre (SMDC), University of California San Francisco (UCSF), San Francisco, CA, 94143, USA
| | - Luc Brunsveld
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Den Dolech 2, 5612, AZ Eindhoven, The Netherlands
| | - Michelle R Arkin
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Centre (SMDC), University of California San Francisco (UCSF), San Francisco, CA, 94143, USA
| | - Christian Ottmann
- Laboratory of Chemical Biology, Department of Biomedical Engineering and Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Den Dolech 2, 5612, AZ Eindhoven, The Netherlands
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47
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Li Z, Ma S, Zhang S, Ma Z, Du L, Li M. Degradation of extracellular and membrane proteins in targeted therapy: Status quo and quo vadis. Drug Discov Today 2023; 28:103716. [PMID: 37467880 DOI: 10.1016/j.drudis.2023.103716] [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: 02/19/2023] [Revised: 06/29/2023] [Accepted: 07/12/2023] [Indexed: 07/21/2023]
Abstract
Targeted protein degradation (TPD) strategies, such as proteolysis-targeting chimeras (PROTACs) only work for intracellular protein degradation because they involve the intracellular protein degradation machinery. Several new technologies have emerged in recent years for TPD of extracellular and membrane proteins. Even though some progress has been demonstrated in the extracellular and membrane protein degradation field, the application of these technologies is still in its infancy. In this review, we survey the therapeutic potential of existing technologies by summarizing and reviewing discoveries and hurdles in extracellular and membrane protein-of-interest (POI) degradation.
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Affiliation(s)
- Zhenzhen Li
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Siyue Ma
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Shuxin Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Zhao Ma
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China
| | - Lupei Du
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China.
| | - Minyong Li
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (MOE), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong 250012, China; Helmholtz International Lab, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, Shandong 266237, China.
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48
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Peterson AA, Liu DR. Small-molecule discovery through DNA-encoded libraries. Nat Rev Drug Discov 2023; 22:699-722. [PMID: 37328653 PMCID: PMC10924799 DOI: 10.1038/s41573-023-00713-6] [Citation(s) in RCA: 69] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/04/2023] [Indexed: 06/18/2023]
Abstract
The development of bioactive small molecules as probes or drug candidates requires discovery platforms that enable access to chemical diversity and can quickly reveal new ligands for a target of interest. Within the past 15 years, DNA-encoded library (DEL) technology has matured into a widely used platform for small-molecule discovery, yielding a wide variety of bioactive ligands for many therapeutically relevant targets. DELs offer many advantages compared with traditional screening methods, including efficiency of screening, easily multiplexed targets and library selections, minimized resources needed to evaluate an entire DEL and large library sizes. This Review provides accounts of recently described small molecules discovered from DELs, including their initial identification, optimization and validation of biological properties including suitability for clinical applications.
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Affiliation(s)
- Alexander A Peterson
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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49
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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: 22] [Impact Index Per Article: 11.0] [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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50
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Singh S, Tian W, Severance ZC, Chaudhary SK, Anokhina V, Mondal B, Pergu R, Singh P, Dhawa U, Singha S, Choudhary A. Proximity-inducing modalities: the past, present, and future. Chem Soc Rev 2023; 52:5485-5515. [PMID: 37477631 DOI: 10.1039/d2cs00943a] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023]
Abstract
Living systems use proximity to regulate biochemical processes. Inspired by this phenomenon, bifunctional modalities that induce proximity have been developed to redirect cellular processes. An emerging example of this class is molecules that induce ubiquitin-dependent proteasomal degradation of a protein of interest, and their initial development sparked a flurry of discovery for other bifunctional modalities. Recent advances in this area include modalities that can change protein phosphorylation, glycosylation, and acetylation states, modulate gene expression, and recruit components of the immune system. In this review, we highlight bifunctional modalities that perform functions other than degradation and have great potential to revolutionize disease treatment, while also serving as important tools in basic research to explore new aspects of biology.
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Affiliation(s)
- Sameek Singh
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Wenzhi Tian
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Zachary C Severance
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Santosh K Chaudhary
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Viktoriya Anokhina
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Basudeb Mondal
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Rajaiah Pergu
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Prashant Singh
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Uttam Dhawa
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Santanu Singha
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
| | - Amit Choudhary
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA 02115, USA
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