1
|
Wang B, Cao S, Zheng N. Emerging strategies for prospective discovery of molecular glue degraders. Curr Opin Struct Biol 2024; 86:102811. [PMID: 38598983 DOI: 10.1016/j.sbi.2024.102811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/14/2024] [Accepted: 03/15/2024] [Indexed: 04/12/2024]
Abstract
Molecular glue (MG) degraders are monovalent small molecule compounds that co-opt E3 ubiquitin ligases to target neo-substrates for proteasomal degradation. Here, we provide a concise review of recent advances in rational MG discovery, which are categorized into two major strategies, ligand modification and de novo discovery. We also highlight the structural mechanisms underlying the formation of MG-enabled ternary complexes and their thermodynamic properties. Finally, we summarize the broader category of proximity inducers including MGs, proteolysis-targeting chimeras (PROTACs), peptides, and viral proteins. MGs are specified as a unique class of proximity inducers with chemical simplicity and a requirement of pre-existing weak protein-protein interactions. We propose that leveraging the weak basal interaction provides a starting point to prospectively develop MGs to degrade high-value therapeutic targets.
Collapse
Affiliation(s)
- Baiyun Wang
- Department of Pharmacology, Box 357280, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Shiyun Cao
- Department of Pharmacology, Box 357280, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Ning Zheng
- Department of Pharmacology, Box 357280, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA.
| |
Collapse
|
2
|
Cui F, Wang W, Zhuang C, He D, Wang P. RBM39 is a potential prognostic biomarker with functional significance in hepatocellular carcinoma. Transl Cancer Res 2024; 13:1606-1622. [PMID: 38737697 PMCID: PMC11082663 DOI: 10.21037/tcr-23-2252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 03/14/2024] [Indexed: 05/14/2024]
Abstract
Background RNA-binding motif protein 39 (RBM39) is a well-known RNA-binding protein involved in tumorigenesis; however, its role in hepatocellular carcinoma (HCC) remains unclear. The aim of this study was to investigate the role of RBM39 in HCC. Methods The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases were used to analyze the differential expression of RBM39 in HCC and normal tissues. The prognostic and diagnostic value of RBM39 in HCC was accessed by Kaplan-Meier analysis, Cox regression, and receiver operating characteristic (ROC) curve analyses. Quantitative real-time polymerase chain reaction (qRT-PCR) and immunohistochemistry were used to validate the mRNA and protein expression of RBM39 in HCC. Moreover, gene set enrichment analysis (GSEA) was performed to identify key pathways related to RBM39. The correlation between RBM39 expression and immune cell infiltration was evaluated using a single-sample gene set enrichment analysis (ssGSEA). CCK8 and wound healing assays were performed to investigate the proliferation and migration abilities of HCC cells with RBM39 knockdown. Results RBM39 expression was upregulated in the HCC tissues. High RBM39 expression was significantly associated with advanced T stage, histological grade, and pathological stage and predicted poor overall survival (OS), disease-specific survival (DSS), and progress-free interval (PFI) in HCC patients. The upregulation of RBM39 expression was an independent prognostic factor for OS. Moreover, GSEA enrichment analysis indicated that RBM39 was functionally involved in pathways associated with the cell cycle, DNA replication, the p53 signaling pathway, and primary immunodeficiency. RBM39 expression was associated with infiltration of Th2 cells and dendritic cells (DC). RBM39 knockdown significantly inhibited the proliferation and migration of HCC cells. Conclusions These findings suggest that high RBM39 expression is associated with poor prognosis and promotes HCC cell proliferation and migration. Based on these results, RBM39 is a promising prognostic biomarker with functional significance for HCC.
Collapse
Affiliation(s)
- Fangfang Cui
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Academy of Medical Sciences of Zhengzhou University, Zhengzhou, China
| | - Wenling Wang
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Chunbo Zhuang
- Department of Clinical Laboratory, Key Clinical Laboratory of Henan Province, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Dezhi He
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Pei Wang
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| |
Collapse
|
3
|
Tsai JM, Nowak RP, Ebert BL, Fischer ES. Targeted protein degradation: from mechanisms to clinic. Nat Rev Mol Cell Biol 2024:10.1038/s41580-024-00729-9. [PMID: 38684868 DOI: 10.1038/s41580-024-00729-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2024] [Indexed: 05/02/2024]
Abstract
Targeted protein degradation refers to the use of small molecules to induce the selective degradation of proteins. In its most common form, this degradation is achieved through ligand-mediated neo-interactions between ubiquitin E3 ligases - the principal waste disposal machines of a cell - and the protein targets of interest, resulting in ubiquitylation and subsequent proteasomal degradation. Notable advances have been made in biological and mechanistic understanding of serendipitously discovered degraders. This improved understanding and novel chemistry has not only provided clinical proof of concept for targeted protein degradation but has also led to rapid growth of the field, with dozens of investigational drugs in active clinical trials. Two distinct classes of protein degradation therapeutics are being widely explored: bifunctional PROTACs and molecular glue degraders, both of which have their unique advantages and challenges. Here, we review the current landscape of targeted protein degradation approaches and how they have parallels in biological processes. We also outline the ongoing clinical exploration of novel degraders and provide some perspectives on the directions the field might take.
Collapse
Affiliation(s)
- Jonathan M Tsai
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Radosław P Nowak
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Institute of Structural Biology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Benjamin L Ebert
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Boston, MA, USA.
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
4
|
Bouton L, Ecoutin A, Malard F, Campagne S. Small molecules modulating RNA splicing: a review of targets and future perspectives. RSC Med Chem 2024; 15:1109-1126. [PMID: 38665842 PMCID: PMC11042171 DOI: 10.1039/d3md00685a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 01/03/2024] [Indexed: 04/28/2024] Open
Abstract
In eukaryotic cells, RNA splicing is crucial for gene expression. Dysregulation of this process can result in incorrect mRNA processing, leading to aberrant gene expression patterns. Such abnormalities are implicated in many inherited diseases and cancers. Historically, antisense oligonucleotides, which bind to specific RNA targets, have been used to correct these splicing abnormalities. Despite their high specificity of action, these oligonucleotides have drawbacks, such as lack of oral bioavailability and the need for chemical modifications to enhance cellular uptake and stability. As a result, recent efforts focused on the development of small organic molecules that can correct abnormal RNA splicing event under disease conditions. This review discusses known and potential targets of these molecules, including RNA structures, trans-acting splicing factors, and the spliceosome - the macromolecular complex responsible for RNA splicing. We also rely on recent advances to discuss therapeutic applications of RNA-targeting small molecules in splicing correction. Overall, this review presents an update on strategies for RNA splicing modulation, emphasizing the therapeutic promise of small molecules.
Collapse
Affiliation(s)
- Léa Bouton
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux 146 rue Léo Saignat 33076 Bordeaux Cedex France
- Institut Européen de Chimie et de Biologie F-33600 Pessac France
| | - Agathe Ecoutin
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux 146 rue Léo Saignat 33076 Bordeaux Cedex France
- Institut Européen de Chimie et de Biologie F-33600 Pessac France
| | - Florian Malard
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux 146 rue Léo Saignat 33076 Bordeaux Cedex France
- Institut Européen de Chimie et de Biologie F-33600 Pessac France
| | - Sébastien Campagne
- Inserm U1212, CNRS UMR5320, ARNA Laboratory, University of Bordeaux 146 rue Léo Saignat 33076 Bordeaux Cedex France
- Institut Européen de Chimie et de Biologie F-33600 Pessac France
| |
Collapse
|
5
|
Lucas SCC, Ahmed A, Ashraf SN, Argyrou A, Bauer MR, De Donatis GM, Demanze S, Eisele F, Fusani L, Hock A, Kadamur G, Li S, Macmillan-Jones A, Michaelides IN, Phillips C, Rehnström M, Richter M, Rodrigo-Brenni MC, Shilliday F, Wang P, Storer RI. Optimization of Potent Ligands for the E3 Ligase DCAF15 and Evaluation of Their Use in Heterobifunctional Degraders. J Med Chem 2024; 67:5538-5566. [PMID: 38513086 DOI: 10.1021/acs.jmedchem.3c02136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
Unlocking novel E3 ligases for use in heterobifunctional PROTAC degraders is of high importance to the pharmaceutical industry. Over-reliance on the current suite of ligands used to recruit E3 ligases could limit the potential of their application. To address this, potent ligands for DCAF15 were optimized using cryo-EM supported, structure-based design to improve on micromolar starting points. A potent binder, compound 24, was identified and subsequently conjugated into PROTACs against multiple targets. Following attempts on degrading a number of proteins using DCAF15 recruiting PROTACs, only degradation of BRD4 was observed. Deconvolution of the mechanism of action showed that this degradation was not mediated by DCAF15, thereby highlighting both the challenges faced when trying to expand the toolbox of validated E3 ligase ligands for use in PROTAC degraders and the pitfalls of using BRD4 as a model substrate.
Collapse
Affiliation(s)
- Simon C C Lucas
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Afshan Ahmed
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - S Neha Ashraf
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Argyrides Argyrou
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Matthias R Bauer
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | | | - Sylvain Demanze
- Oncology Chemistry, Oncology R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Frederik Eisele
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg SE-431 83,Sweden
| | - Lucia Fusani
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Andreas Hock
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Ganesh Kadamur
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Shuyou Li
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176, People's Republic of China
| | | | | | - Christopher Phillips
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Marie Rehnström
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg SE-431 83, Sweden
| | - Magdalena Richter
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Monica C Rodrigo-Brenni
- Safety Innovation and PROTAC Safety, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Fiona Shilliday
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Peng Wang
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176, People's Republic of China
| | - R Ian Storer
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| |
Collapse
|
6
|
Lemaitre T, Cornu M, Schwalen F, Since M, Kieffer C, Voisin-Chiret AS. Molecular glue degraders: exciting opportunities for novel drug discovery. Expert Opin Drug Discov 2024; 19:433-449. [PMID: 38240114 DOI: 10.1080/17460441.2024.2306845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 01/15/2024] [Indexed: 01/25/2024]
Abstract
INTRODUCTION Molecular Glue Degraders (MGDs) is a concept that refers to a class of compounds that facilitate the interaction between two proteins or molecules within a cell. These compounds act as bridge that enhances specific Protein-Protein Interactions (PPIs). Over the past decade, this technology has gained attention as a potential strategy to target proteins that were traditionally considered undruggable using small molecules. AREAS COVERED This review presents the concept of cellular homeostasis and the balance between protein synthesis and protein degradation. The concept of protein degradation is concerned with molecular glues, which form part of the broader field of Targeted Protein Degradation (TPD). Next, pharmacochemical strategies for the rational design of MGDs are detailed and illustrated by examples of Ligand-Based (LBDD), Structure-Based (SBDD) and Fragment-Based Drug Design (FBDD). EXPERT OPINION Expanding the scope of what can be effectively targeted in the development of treatments for diseases that are incurable or resistant to conventional therapies offers new therapeutic options. The treatment of microbial infections and neurodegenerative diseases is a major societal challenge, and the discovery of MGDs appears to be a promising avenue. Combining different approaches to discover and exploit a variety of innovative therapeutic agents will create opportunities to treat diseases that are still incurable.
Collapse
Affiliation(s)
| | - Marie Cornu
- Normandie University, UNICAEN, CERMN, Caen, France
| | - Florian Schwalen
- Normandie University, UNICAEN, CERMN, Caen, France
- Department of Pharmacy, Caen University Hospital, Caen, France
| | - Marc Since
- Normandie University, UNICAEN, CERMN, Caen, France
| | | | | |
Collapse
|
7
|
Hou C, Wu X, Shi R, Xing X, Tian S, Eléouët M, Qiao C, Ma J, Xu G. Subtle structural alteration in indisulam switches the molecular mechanisms for the inhibitory effect on the migration of gastric cancer cells. Biomed Pharmacother 2024; 172:116259. [PMID: 38359488 DOI: 10.1016/j.biopha.2024.116259] [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: 12/10/2023] [Revised: 02/03/2024] [Accepted: 02/06/2024] [Indexed: 02/17/2024] Open
Abstract
Gastric cancer is a highly metastatic malignant tumor with high morbidity and mortality globally. Recent studies reported that sulfonamide derivatives such as indisulam exhibited inhibitory effects on the viability and migration of cancer cells. However, multiple clinical trials revealed that indisulam did not significantly prevent cancer progression due to metastasis and drug resistance. Therefore, it is necessary to discover new potent derivatives to explore alternative therapeutic strategies. Here, we synthesize multiple indisulam derivatives and examine their inhibitory effects on the viability and migration of gastric cancer cells. Among them, compounds SR-3-65 and WXM-1-170 exhibit better inhibitory effects on the migration of gastric cancer cells than indisulam. Mechanistically, we discover that they could attenuate the PI3K/AKT/GSK-3β/β-catenin signaling pathway and lead to the suppression of epithelial-to-mesenchymal transition (EMT)-related transcription factors. The influence of SR-3-65 on the migration of gastric cancer cells is blocked by the PI3K inhibitor LY294002 while SR-3-65 and WXM-1-170 reverse the effect of PI3K activator 740 Y-P on the migration of gastric cancer cells. Molecular docking and molecular dynamics simulation further confirm that PI3K is the target of SR-3-65. Our study unveils a novel mechanism by which SR-3-65 and WXM-1-170 inhibit the migration of gastric cancer cells. Together with the previous discovery, we reveal that subtle structural change in indisulam results in a striking switch on the molecular targets and their associated signaling pathways for the inhibition of the migration of gastric cancer cells. These findings might provide informative insights for the development of targeted therapy for gastric cancer.
Collapse
Affiliation(s)
- Changxu Hou
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, Jiangsu 215123, China
| | - Xiaomei Wu
- College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Rui Shi
- College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Xiaoqi Xing
- College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Sheng Tian
- College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China
| | - Morgane Eléouët
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, Jiangsu 215123, China; Synbio Technologies Company, BioBay C20, 218 Xinghu Street, Suzhou, Jiangsu, 215123, China
| | - Chunhua Qiao
- College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China.
| | - Jingjing Ma
- Department of Pharmacy, The Fourth Affiliated Hospital of Soochow University, Suzhou Dushu Lake Hospital, Medical Center of Soochow University, Suzhou, Jiangsu 215123, China.
| | - Guoqiang Xu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, Jiangsu 215123, China; Suzhou International Joint Laboratory for Diagnosis and Treatment of Brain Diseases, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu 215123, China; MOE Key Laboratory of Geriatric Diseases and Immunology, Suzhou Medical College of Soochow University, Suzhou, Jiangsu 215123, China.
| |
Collapse
|
8
|
Dou Z, Lei H, Su W, Zhang T, Chen X, Yu B, Zhen X, Si J, Sun C, Zhang H, Di C. Modification of BCLX pre-mRNA splicing has antitumor efficacy alone or in combination with radiotherapy in human glioblastoma cells. Cell Death Dis 2024; 15:160. [PMID: 38383492 PMCID: PMC10881996 DOI: 10.1038/s41419-024-06507-x] [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: 08/15/2023] [Revised: 01/24/2024] [Accepted: 01/26/2024] [Indexed: 02/23/2024]
Abstract
Dysregulation of anti-apoptotic and pro-apoptotic protein isoforms arising from aberrant splicing is a crucial hallmark of cancers and may contribute to therapeutic resistance. Thus, targeting RNA splicing to redirect isoform expression of apoptosis-related genes could lead to promising anti-cancer phenotypes. Glioblastoma (GBM) is the most common type of malignant brain tumor in adults. In this study, through RT-PCR and Western Blot analysis, we found that BCLX pre-mRNA is aberrantly spliced in GBM cells with a favored splicing of anti-apoptotic Bcl-xL. Modulation of BCLX pre-mRNA splicing using splice-switching oligonucleotides (SSOs) efficiently elevated the pro-apoptotic isoform Bcl-xS at the expense of the anti-apoptotic Bcl-xL. Induction of Bcl-xS by SSOs activated apoptosis and autophagy in GBM cells. In addition, we found that ionizing radiation could also modulate the alternative splicing of BCLX. In contrast to heavy (carbon) ion irradiation, low energy X-ray radiation-induced an increased ratio of Bcl-xL/Bcl-xS. Inhibiting Bcl-xL through splicing regulation can significantly enhance the radiation sensitivity of 2D and 3D GBM cells. These results suggested that manipulation of BCLX pre-mRNA alternative splicing by splice-switching oligonucleotides is a novel approach to inhibit glioblastoma tumorigenesis alone or in combination with radiotherapy.
Collapse
Affiliation(s)
- Zhihui Dou
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China
- Advanced Energy Science and Technology Guangdong Laboratory, Huizhou, 516029, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, 730000, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Huiwen Lei
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China
- Advanced Energy Science and Technology Guangdong Laboratory, Huizhou, 516029, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, 730000, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Wei Su
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China
- Advanced Energy Science and Technology Guangdong Laboratory, Huizhou, 516029, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, 730000, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Taotao Zhang
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China
- Advanced Energy Science and Technology Guangdong Laboratory, Huizhou, 516029, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, 730000, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Xiaohua Chen
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China
- Advanced Energy Science and Technology Guangdong Laboratory, Huizhou, 516029, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, 730000, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Boyi Yu
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China
- Advanced Energy Science and Technology Guangdong Laboratory, Huizhou, 516029, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, 730000, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Xiaogang Zhen
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China
- Advanced Energy Science and Technology Guangdong Laboratory, Huizhou, 516029, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, 730000, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Jing Si
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China
- Advanced Energy Science and Technology Guangdong Laboratory, Huizhou, 516029, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, 730000, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Chao Sun
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China
- Advanced Energy Science and Technology Guangdong Laboratory, Huizhou, 516029, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, 730000, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Hong Zhang
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China.
- Advanced Energy Science and Technology Guangdong Laboratory, Huizhou, 516029, China.
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, 730000, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China.
| | - Cuixia Di
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China.
- Advanced Energy Science and Technology Guangdong Laboratory, Huizhou, 516029, China.
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, 730000, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China.
| |
Collapse
|
9
|
Setia N, Almuqdadi HTA, Abid M. Journey of Von Hippel-Lindau (VHL) E3 ligase in PROTACs design: From VHL ligands to VHL-based degraders. Eur J Med Chem 2024; 265:116041. [PMID: 38199162 DOI: 10.1016/j.ejmech.2023.116041] [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: 10/02/2023] [Revised: 12/08/2023] [Accepted: 12/08/2023] [Indexed: 01/12/2024]
Abstract
The scientific community has shown considerable interest in proteolysis-targeting chimeras (PROTACs) in the last decade, indicating their remarkable potential as a means of achieving targeted protein degradation (TPD). Not only are PROTACs seen as valuable tools in molecular biology but their emergence as a modality for drug discovery has also garnered significant attention. PROTACs bind to E3 ligases and target proteins through respective ligands connected via a linker to induce proteasome-mediated protein degradation. The discovery of small molecule ligands for E3 ligases has led to the prevalent use of various E3 ligases in PROTAC design. Furthermore, the incorporation of different types of linkers has proven beneficial in enhancing the efficacy of PROTACs. By far more than 3300 PROTACs have been reported in the literature. Notably, Von Hippel-Lindau (VHL)-based PROTACs have surfaced as a propitious strategy for targeting proteins, even encompassing those that were previously considered non-druggable. VHL is extensively utilized as an E3 ligase in the advancement of PROTACs owing to its widespread expression in various tissues and well-documented binders. Here, we review the discovery of VHL ligands, the types of linkers employed to develop VHL-based PROTACs, and their subsequent modulation to design advanced non-conventional degraders to target various disease-causing proteins. Furthermore, we provide an overview of other E3 ligases recruited in the field of PROTAC technology.
Collapse
Affiliation(s)
- Nisha Setia
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | | | - Mohammad Abid
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India.
| |
Collapse
|
10
|
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: 0] [Impact Index Per Article: 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.
Collapse
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
| |
Collapse
|
11
|
Mossmann D, Müller C, Park S, Ryback B, Colombi M, Ritter N, Weißenberger D, Dazert E, Coto-Llerena M, Nuciforo S, Blukacz L, Ercan C, Jimenez V, Piscuoglio S, Bosch F, Terracciano LM, Sauer U, Heim MH, Hall MN. Arginine reprograms metabolism in liver cancer via RBM39. Cell 2023; 186:5068-5083.e23. [PMID: 37804830 PMCID: PMC10642370 DOI: 10.1016/j.cell.2023.09.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 06/01/2023] [Accepted: 09/12/2023] [Indexed: 10/09/2023]
Abstract
Metabolic reprogramming is a hallmark of cancer. However, mechanisms underlying metabolic reprogramming and how altered metabolism in turn enhances tumorigenicity are poorly understood. Here, we report that arginine levels are elevated in murine and patient hepatocellular carcinoma (HCC), despite reduced expression of arginine synthesis genes. Tumor cells accumulate high levels of arginine due to increased uptake and reduced arginine-to-polyamine conversion. Importantly, the high levels of arginine promote tumor formation via further metabolic reprogramming, including changes in glucose, amino acid, nucleotide, and fatty acid metabolism. Mechanistically, arginine binds RNA-binding motif protein 39 (RBM39) to control expression of metabolic genes. RBM39-mediated upregulation of asparagine synthesis leads to enhanced arginine uptake, creating a positive feedback loop to sustain high arginine levels and oncogenic metabolism. Thus, arginine is a second messenger-like molecule that reprograms metabolism to promote tumor growth.
Collapse
Affiliation(s)
- Dirk Mossmann
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | | | - Sujin Park
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Brendan Ryback
- Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Marco Colombi
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | | | | | - Eva Dazert
- Biozentrum, University of Basel, 4056 Basel, Switzerland
| | - Mairene Coto-Llerena
- Institute of Medical Genetics and Pathology, University Hospital Basel, 4031 Basel, Switzerland; Department of Biomedicine, University of Basel, 4031 Basel, Switzerland
| | - Sandro Nuciforo
- Department of Biomedicine, Hepatology Laboratory, University and University Hospital Basel, 4031 Basel, Switzerland
| | - Lauriane Blukacz
- Department of Biomedicine, Hepatology Laboratory, University and University Hospital Basel, 4031 Basel, Switzerland
| | - Caner Ercan
- Institute of Medical Genetics and Pathology, University Hospital Basel, 4031 Basel, Switzerland
| | - Veronica Jimenez
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193 Barcelona, Spain
| | - Salvatore Piscuoglio
- Institute of Medical Genetics and Pathology, University Hospital Basel, 4031 Basel, Switzerland; Department of Biomedicine, University of Basel, 4031 Basel, Switzerland
| | - Fatima Bosch
- Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, 08193 Barcelona, Spain
| | - Luigi M Terracciano
- Institute of Medical Genetics and Pathology, University Hospital Basel, 4031 Basel, Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Markus H Heim
- Department of Biomedicine, Hepatology Laboratory, University and University Hospital Basel, 4031 Basel, Switzerland; Clarunis University Center for Gastrointestinal and Liver Diseases, 4031 Basel, Switzerland
| | - Michael N Hall
- Biozentrum, University of Basel, 4056 Basel, Switzerland.
| |
Collapse
|
12
|
Xu Y, Spear S, Ma Y, Lorentzen MP, Gruet M, McKinney F, Xu Y, Wickremesinghe C, Shepherd MR, McNeish I, Keun HC, Nijhuis A. Pharmacological depletion of RNA splicing factor RBM39 by indisulam synergizes with PARP inhibitors in high-grade serous ovarian carcinoma. Cell Rep 2023; 42:113307. [PMID: 37858464 DOI: 10.1016/j.celrep.2023.113307] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 09/04/2023] [Accepted: 10/04/2023] [Indexed: 10/21/2023] Open
Abstract
Ovarian high-grade serous carcinoma (HGSC) is the most common subtype of ovarian cancer with limited therapeutic options and a poor prognosis. In recent years, poly-ADP ribose polymerase (PARP) inhibitors have demonstrated significant clinical benefits, especially in patients with BRCA1/2 mutations. However, acquired drug resistance and relapse is a major challenge. Indisulam (E7070) has been identified as a molecular glue that brings together splicing factor RBM39 and DCAF15 E3 ubiquitin ligase resulting in polyubiquitination, degradation, and subsequent RNA splicing defects. In this work, we demonstrate that the loss of RBM39 induces splicing defects in key DNA damage repair genes in ovarian cancer, leading to increased sensitivity to cisplatin and various PARP inhibitors. The addition of indisulam also improved olaparib response in mice bearing PARP inhibitor-resistant tumors. These findings demonstrate that combining RBM39 degraders and PARP inhibitors is a promising therapeutic approach to improve PARP inhibitor response in ovarian HGSC.
Collapse
Affiliation(s)
- Yuewei Xu
- Department of Surgery & Cancer, Imperial College London, London, UK
| | - Sarah Spear
- Department of Surgery & Cancer, Imperial College London, London, UK; Ovarian Cancer Action Research Centre, Department of Surgery & Cancer, Imperial College London, London, UK
| | - Yurui Ma
- Department of Surgery & Cancer, Imperial College London, London, UK
| | - Marc P Lorentzen
- Department of Surgery & Cancer, Imperial College London, London, UK; Ovarian Cancer Action Research Centre, Department of Surgery & Cancer, Imperial College London, London, UK
| | - Michael Gruet
- Department of Surgery & Cancer, Imperial College London, London, UK
| | - Flora McKinney
- Department of Surgery & Cancer, Imperial College London, London, UK
| | - Yitao Xu
- Department of Surgery & Cancer, Imperial College London, London, UK
| | - Chiharu Wickremesinghe
- Department of Surgery & Cancer, Imperial College London, London, UK; Ovarian Cancer Action Research Centre, Department of Surgery & Cancer, Imperial College London, London, UK
| | | | - Iain McNeish
- Department of Surgery & Cancer, Imperial College London, London, UK; Ovarian Cancer Action Research Centre, Department of Surgery & Cancer, Imperial College London, London, UK
| | - Hector C Keun
- Department of Surgery & Cancer, Imperial College London, London, UK; Ovarian Cancer Action Research Centre, Department of Surgery & Cancer, Imperial College London, London, UK.
| | - Anke Nijhuis
- Department of Surgery & Cancer, Imperial College London, London, UK; Ovarian Cancer Action Research Centre, Department of Surgery & Cancer, Imperial College London, London, UK.
| |
Collapse
|
13
|
Campagne S, Jutzi D, Malard F, Matoga M, Romane K, Feldmuller M, Colombo M, Ruepp MD, Allain FHT. Molecular basis of RNA-binding and autoregulation by the cancer-associated splicing factor RBM39. Nat Commun 2023; 14:5366. [PMID: 37666821 PMCID: PMC10477243 DOI: 10.1038/s41467-023-40254-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 07/14/2023] [Indexed: 09/06/2023] Open
Abstract
Pharmacologic depletion of RNA-binding motif 39 (RBM39) using aryl sulfonamides represents a promising anti-cancer therapy but requires high levels of the adaptor protein DCAF15. Consequently, novel approaches to deplete RBM39 in an DCAF15-independent manner are required. Here, we uncover that RBM39 autoregulates via the inclusion of a poison exon into its own pre-mRNA and identify the cis-acting elements that govern this regulation. We also determine the NMR solution structures of RBM39's tandem RNA recognition motifs (RRM1 and RRM2) bound to their respective RNA targets, revealing how RRM1 recognises RNA stem loops whereas RRM2 binds specifically to single-stranded N(G/U)NUUUG. Our results support a model where RRM2 selects the 3'-splice site of a poison exon and the RRM3 and RS domain stabilise the U2 snRNP at the branchpoint. Our work provides molecular insights into RBM39-dependent 3'-splice site selection and constitutes a solid basis to design alternative anti-cancer therapies.
Collapse
Affiliation(s)
- Sébastien Campagne
- ETH Zurich, Department of Biology, Institute of Biochemistry, 8093, Zurich, Switzerland.
- University of Bordeaux, Inserm U1212, CNRS UMR5320, ARNA Laboratory, 33077, Bordeaux, France.
| | - Daniel Jutzi
- United Kingdom Dementia Research Institute Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, SE5 9NU, UK
| | - Florian Malard
- ETH Zurich, Department of Biology, Institute of Biochemistry, 8093, Zurich, Switzerland
- University of Bordeaux, Inserm U1212, CNRS UMR5320, ARNA Laboratory, 33077, Bordeaux, France
| | - Maja Matoga
- ETH Zurich, Department of Biology, Institute of Biochemistry, 8093, Zurich, Switzerland
| | - Ksenija Romane
- ETH Zurich, Department of Biology, Institute of Biochemistry, 8093, Zurich, Switzerland
| | - Miki Feldmuller
- ETH Zurich, Department of Biology, Institute of Biochemistry, 8093, Zurich, Switzerland
| | - Martino Colombo
- University of Bern, Department of Chemistry and Biochemistry, 3012, Bern, Switzerland
- Celgene Institute of Translational Research in Europe (CITRE), Bristol Myers Squibb, 41092, Seville, Spain
| | - Marc-David Ruepp
- United Kingdom Dementia Research Institute Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, Maurice Wohl Clinical Neuroscience Institute, London, SE5 9NU, UK.
| | - Frédéric H-T Allain
- ETH Zurich, Department of Biology, Institute of Biochemistry, 8093, Zurich, Switzerland.
| |
Collapse
|
14
|
Coomar S, Mota P, Penson A, Schwaller J, Abdel-Wahab O, Gillingham D. Overlaid Transcriptional and Proteome Analyses Identify Mitotic Kinesins as Important Targets of Arylsulfonamide-Mediated RBM39 Degradation. Mol Cancer Res 2023; 21:768-778. [PMID: 37255411 PMCID: PMC10395616 DOI: 10.1158/1541-7786.mcr-22-0541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 03/16/2023] [Accepted: 05/09/2023] [Indexed: 05/14/2023]
Abstract
Certain arylsulfonamides (ArSulf) induce an interaction between the E3 ligase substrate adaptor DCAF15 and the critical splicing factor RBM39, ultimately causing its degradation. However, degradation of a splicing factor introduces complex pleiotropic effects that are difficult to untangle, since, aside from direct protein degradation, downstream transcriptional effects also influence the proteome. By overlaying transcriptional data and proteome datasets, we distinguish transcriptional from direct degradation effects, pinpointing those proteins most impacted by splicing changes. Using our workflow, we identify and validate the upregulation of the arginine-and-serine rich protein (RSRP1) and the downregulation of the key kinesin motor proteins KIF20A and KIF20B due to altered splicing in the absence of RBM39. We further show that kinesin downregulation is connected to the multinucleation phenotype observed upon RBM39 depletion by ArSulfs. Our approach should be helpful in the assessment of potential cancer drug candidates which target splicing factors. IMPLICATIONS Our approach provides a workflow for identifying and studying the most strongly modulated proteins when splicing is altered. The work also uncovers a splicing-based approach toward pharmacologic targeting of mitotic kinesins.
Collapse
Affiliation(s)
- Seemon Coomar
- Department of Chemistry, University of Basel, Basel, Switzerland
| | - Pedro Mota
- Department of Chemistry, University of Basel, Basel, Switzerland
| | - Alexander Penson
- Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jürg Schwaller
- Department of Biomedicine, University Children's Hospital (UKBB), University of Basel, Basel, Switzerland
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | | |
Collapse
|
15
|
Dou Z, Zhang X, Su W, Zhang T, Ye F, Zhao D, Chen X, Li Q, Zhang H, Di C. Indisulam exerts anticancer effects via modulation of transcription, translation and alternative splicing on human cervical cancer cells. Am J Cancer Res 2023; 13:2922-2937. [PMID: 37559979 PMCID: PMC10408480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 06/06/2023] [Indexed: 08/11/2023] Open
Abstract
Indisulam is a synthetic sulfonamides drug with anticancer activity in various tumors. However, the effect and molecular mechanism of indisulam have still not been studied in human cervical cancer. We treated human cervical cancer cell lines (HeLa and C33A) with indisulam, evaluated its efficacy, and investigated its molecular targets. Indisulam inhibited tumor growth and induced RBM39 degradation in a dose-dependent manner. RNA-seq and proteomics analysis revealed that indisulam disrupted transcriptional regulation pathways related to mRNA splicing and apoptosis. More importantly, indisulam caused mis-splicing of RNA transcripts including p73 isoforms ΔNp73 and TAp73 which have opposite roles in apoptosis regulation. Indisulam increased TAp73 expression and triggered mitochondrial apoptosis independent of p53 status in HeLa cells. In summary, our data suggests that indisulam has therapeutic potential in cervical cancer, representing an attractive strategy in p53-disrupted cancers and should be further investigated.
Collapse
Affiliation(s)
- Zhihui Dou
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of SciencesLanzhou 730000, Gansu, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of SciencesLanzhou 730000, Gansu, China
- College of Life Sciences, University of Chinese Academy of SciencesBeijing 100039, China
- School of Nuclear Science and Technology, University of Chinese Academy of SciencesBeijing 100039, China
| | - Xuetian Zhang
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of SciencesLanzhou 730000, Gansu, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of SciencesLanzhou 730000, Gansu, China
- College of Life Sciences, University of Chinese Academy of SciencesBeijing 100039, China
- School of Nuclear Science and Technology, University of Chinese Academy of SciencesBeijing 100039, China
| | - Wei Su
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of SciencesLanzhou 730000, Gansu, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of SciencesLanzhou 730000, Gansu, China
- College of Life Sciences, University of Chinese Academy of SciencesBeijing 100039, China
- School of Nuclear Science and Technology, University of Chinese Academy of SciencesBeijing 100039, China
| | - Taotao Zhang
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of SciencesLanzhou 730000, Gansu, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of SciencesLanzhou 730000, Gansu, China
- College of Life Sciences, University of Chinese Academy of SciencesBeijing 100039, China
- School of Nuclear Science and Technology, University of Chinese Academy of SciencesBeijing 100039, China
| | - Fei Ye
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of SciencesLanzhou 730000, Gansu, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of SciencesLanzhou 730000, Gansu, China
- College of Life Sciences, University of Chinese Academy of SciencesBeijing 100039, China
- School of Nuclear Science and Technology, University of Chinese Academy of SciencesBeijing 100039, China
| | - Dapeng Zhao
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of SciencesLanzhou 730000, Gansu, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of SciencesLanzhou 730000, Gansu, China
- College of Life Sciences, University of Chinese Academy of SciencesBeijing 100039, China
- School of Nuclear Science and Technology, University of Chinese Academy of SciencesBeijing 100039, China
| | - Xiaohua Chen
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of SciencesLanzhou 730000, Gansu, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of SciencesLanzhou 730000, Gansu, China
- College of Life Sciences, University of Chinese Academy of SciencesBeijing 100039, China
- School of Nuclear Science and Technology, University of Chinese Academy of SciencesBeijing 100039, China
| | - Qiang Li
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of SciencesLanzhou 730000, Gansu, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of SciencesLanzhou 730000, Gansu, China
- College of Life Sciences, University of Chinese Academy of SciencesBeijing 100039, China
- School of Nuclear Science and Technology, University of Chinese Academy of SciencesBeijing 100039, China
| | - Hong Zhang
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of SciencesLanzhou 730000, Gansu, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of SciencesLanzhou 730000, Gansu, China
- College of Life Sciences, University of Chinese Academy of SciencesBeijing 100039, China
- School of Nuclear Science and Technology, University of Chinese Academy of SciencesBeijing 100039, China
| | - Cuixia Di
- Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of SciencesLanzhou 730000, Gansu, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of SciencesLanzhou 730000, Gansu, China
- College of Life Sciences, University of Chinese Academy of SciencesBeijing 100039, China
- School of Nuclear Science and Technology, University of Chinese Academy of SciencesBeijing 100039, China
| |
Collapse
|
16
|
Flemington EK, Flemington SA, O’Grady TM, Baddoo M, Nguyen T, Dong Y, Ungerleider N. SpliceTools, a suite of downstream RNA splicing analysis tools to investigate mechanisms and impact of alternative splicing. Nucleic Acids Res 2023; 51:e42. [PMID: 36864749 PMCID: PMC10123099 DOI: 10.1093/nar/gkad111] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/06/2023] [Indexed: 03/04/2023] Open
Abstract
As a fundamental aspect of normal cell signaling and disease states, there is great interest in determining alternative splicing (AS) changes in physiologic, pathologic, and pharmacologic settings. High throughput RNA sequencing and specialized software to detect AS has greatly enhanced our ability to determine transcriptome-wide splicing changes. Despite the richness of this data, deriving meaning from sometimes thousands of AS events is a substantial bottleneck for most investigators. We present SpliceTools, a suite of data processing modules that arms investigators with the ability to quickly produce summary statistics, mechanistic insights, and functional significance of AS changes through command line or through an online user interface. Utilizing RNA-seq datasets for 186 RNA binding protein knockdowns, nonsense mediated RNA decay inhibition, and pharmacologic splicing inhibition, we illustrate the utility of SpliceTools to distinguish splicing disruption from regulated transcript isoform changes, we show the broad transcriptome footprint of the pharmacologic splicing inhibitor, indisulam, we illustrate the utility in uncovering mechanistic underpinnings of splicing inhibition, we identify predicted neo-epitopes in pharmacologic splicing inhibition, and we show the impact of splicing alterations induced by indisulam on cell cycle progression. Together, SpliceTools puts rapid and easy downstream analysis at the fingertips of any investigator studying AS.
Collapse
Affiliation(s)
| | | | - Tina M O’Grady
- Department of Pathology, Tulane University, New Orleans, LA, USA
| | - Melody Baddoo
- Department of Pathology, Tulane University, New Orleans, LA, USA
| | - Trang Nguyen
- Department of Pathology, Tulane University, New Orleans, LA, USA
| | - Yan Dong
- Department of Structural and Cellular Biology, Tulane University, New Orleans, LA, USA
| | | |
Collapse
|
17
|
Xue Y, Bolinger AA, Zhou J. Novel approaches to targeted protein degradation technologies in drug discovery. Expert Opin Drug Discov 2023; 18:467-483. [PMID: 36895136 PMCID: PMC11089573 DOI: 10.1080/17460441.2023.2187777] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 03/02/2023] [Indexed: 03/11/2023]
Abstract
INTRODUCTION Target protein degradation (TPD) provides a novel therapeutic modality, other than inhibition, through the direct depletion of target proteins. Two primary human protein homeostasis mechanisms are exploited: the ubiquitin-proteasome system (UPS) and the lysosomal system. TPD technologies based on these two systems are progressing at an impressive pace. AREAS COVERED This review focuses on the TPD strategies based on UPS and lysosomal system, mainly classified into three types: Molecular Glue (MG), PROteolysis Targeting Chimera (PROTAC), and lysosome-mediated TPD. Starting with a brief background introduction of each strategy, exciting examples and perspectives on these novel approaches are provided. EXPERT OPINION MGs and PROTACs are two major UPS-based TPD strategies that have been extensively investigated in the past decade. Despite some clinical trials, several critical issues remain, among which is emphasized by the limitation of targets. Recently developed lysosomal system-based approaches provide alternative solutions for TPD beyond UPS' capability. The newly emerging novel approaches may partially address issues that have long plagued researchers, such as low potency, poor cell permeability, on-/off-target toxicity, and delivery efficiency. Comprehensive considerations for the rational design of protein degraders and continuous efforts to seek effective solutions are imperative to advance these strategies into clinical medications.
Collapse
Affiliation(s)
- Yu Xue
- Chemical Biology Program, Department of Pharmacology and Toxicology University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Andrew A. Bolinger
- Chemical Biology Program, Department of Pharmacology and Toxicology University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Jia Zhou
- Chemical Biology Program, Department of Pharmacology and Toxicology University of Texas Medical Branch, Galveston, TX 77555, USA
| |
Collapse
|
18
|
Abstract
Alternative splicing (AS) of mRNAs is an essential regulatory mechanism in eukaryotic gene expression. AS misregulation, caused by either dysregulation or mutation of splicing factors, has been shown to be involved in cancer development and progression, making splicing factors suitable targets for cancer therapy. In recent years, various types of pharmacological modulators, such as small molecules and oligonucleotides, targeting distinct components of the splicing machinery, have been under development to treat multiple disorders. Although these approaches have promise, targeting the core spliceosome components disrupts the early stages of spliceosome assembly and can lead to nonspecific and toxic effects. New research directions have been focused on targeting specific splicing factors for a more precise effect. In this Perspective, we will highlight several approaches for targeting splicing factors and their functions and suggest ways to improve their specificity.
Collapse
Affiliation(s)
- Ariel Bashari
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel-Canada, Hebrew University Hadassah Medical School, Jerusalem 9112001, Israel
| | - Zahava Siegfried
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel-Canada, Hebrew University Hadassah Medical School, Jerusalem 9112001, Israel
| | - Rotem Karni
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel-Canada, Hebrew University Hadassah Medical School, Jerusalem 9112001, Israel
| |
Collapse
|
19
|
Rui H, Ashton KS, Min J, Wang C, Potts PR. Protein-protein interfaces in molecular glue-induced ternary complexes: classification, characterization, and prediction. RSC Chem Biol 2023; 4:192-215. [PMID: 36908699 PMCID: PMC9994104 DOI: 10.1039/d2cb00207h] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 01/02/2023] [Indexed: 01/04/2023] Open
Abstract
Molecular glues are a class of small molecules that stabilize the interactions between proteins. Naturally occurring molecular glues are present in many areas of biology where they serve as central regulators of signaling pathways. Importantly, several clinical compounds act as molecular glue degraders that stabilize interactions between E3 ubiquitin ligases and target proteins, leading to their degradation. Molecular glues hold promise as a new generation of therapeutic agents, including those molecular glue degraders that can redirect the protein degradation machinery in a precise way. However, rational discovery of molecular glues is difficult in part due to the lack of understanding of the protein-protein interactions they stabilize. In this review, we summarize the structures of known molecular glue-induced ternary complexes and the interface properties. Detailed analysis shows different mechanisms of ternary structure formation. Additionally, we also review computational approaches for predicting protein-protein interfaces and highlight the promises and challenges. This information will ultimately help inform future approaches for rational molecular glue discovery.
Collapse
Affiliation(s)
- Huan Rui
- Center for Research Acceleration by Digital Innovation, Amgen Research Thousand Oaks CA 91320 USA
| | - Kate S Ashton
- Medicinal Chemistry, Amgen Research Thousand Oaks CA 91320 USA
| | - Jaeki Min
- Induced Proximity Platform, Amgen Research Thousand Oaks CA 91320 USA
| | - Connie Wang
- Digital, Technology & Innovation, Amgen Thousand Oaks CA 91320 USA
| | | |
Collapse
|
20
|
Eléouët M, Lu C, Zhou Y, Yang P, Ma J, Xu G. Insights on the biological functions and diverse regulation of RNA-binding protein 39 and their implication in human diseases. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2023; 1866:194902. [PMID: 36535628 DOI: 10.1016/j.bbagrm.2022.194902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/24/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022]
Abstract
RNA-binding protein 39 (RBM39) involves in pre-mRNA splicing and transcriptional regulation. RBM39 is dysregulated in many cancers and its upregulation enhances cancer cell proliferation. Recently, it has been discovered that aryl sulfonamides act as molecular glues to recruit RBM39 to the CRL4DCAF15 E3 ubiquitin ligase complex for its ubiquitination and proteasomal degradation. Therefore, various studies have focused on the degradation of RBM39 by aryl sulfonamides in the aim of finding new cancer therapeutics. These discoveries also attracted focus for thorough study on the biological functions of RBM39. RBM39 was found to regulate the splicing and transcription of genes mainly involved in pre-mRNA splicing, cell cycle regulation, DNA damage response, and metabolism, but the understanding of these regulations is still in its infancy. This article reviews the advances of the current literature and discusses the remaining key issues on the biological function and dynamic regulation of RBM39 at the post-translational level.
Collapse
Affiliation(s)
- Morgane Eléouët
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, 199 Ren'ai Road, Suzhou, Jiangsu 215123, China; Synbio Technologies Company, BioBay C20, 218 Xinghu Street, Suzhou, Jiangsu 215123, China
| | - Chengpiao Lu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, 199 Ren'ai Road, Suzhou, Jiangsu 215123, China
| | - Yijia Zhou
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, 199 Ren'ai Road, Suzhou, Jiangsu 215123, China
| | - Ping Yang
- Synbio Technologies Company, BioBay C20, 218 Xinghu Street, Suzhou, Jiangsu 215123, China
| | - Jingjing Ma
- Department of Pharmacy, Medical Center of Soochow University, Dushu Lake Hospital Affiliated to Soochow University, Suzhou, Jiangsu 215123, China.
| | - Guoqiang Xu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, 199 Ren'ai Road, Suzhou, Jiangsu 215123, China.
| |
Collapse
|
21
|
Abstract
Dysregulated RNA splicing is a molecular feature that characterizes almost all tumour types. Cancer-associated splicing alterations arise from both recurrent mutations and altered expression of trans-acting factors governing splicing catalysis and regulation. Cancer-associated splicing dysregulation can promote tumorigenesis via diverse mechanisms, contributing to increased cell proliferation, decreased apoptosis, enhanced migration and metastatic potential, resistance to chemotherapy and evasion of immune surveillance. Recent studies have identified specific cancer-associated isoforms that play critical roles in cancer cell transformation and growth and demonstrated the therapeutic benefits of correcting or otherwise antagonizing such cancer-associated mRNA isoforms. Clinical-grade small molecules that modulate or inhibit RNA splicing have similarly been developed as promising anticancer therapeutics. Here, we review splicing alterations characteristic of cancer cell transcriptomes, dysregulated splicing's contributions to tumour initiation and progression, and existing and emerging approaches for targeting splicing for cancer therapy. Finally, we discuss the outstanding questions and challenges that must be addressed to translate these findings into the clinic.
Collapse
Affiliation(s)
- Robert K Bradley
- Computational Biology Program, Public Health Sciences Division and Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
| | - Olga Anczuków
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA.
| |
Collapse
|
22
|
Nguyen TP, Fang M, Kim J, Wang B, Lin E, Khivansara V, Barrows N, Rivera-Cancel G, Goralski M, Cervantes CL, Xie S, Peterson JM, Povedano JM, Antczak MI, Posner BA, McFadden DG, Ready JM, De Brabander JK, Nijhawan D. Inducible mismatch repair streamlines forward genetic approaches to target identification of cytotoxic small molecules. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.21.529401. [PMID: 36865268 PMCID: PMC9980046 DOI: 10.1101/2023.02.21.529401] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Orphan cytotoxins are small molecules for which the mechanism of action (MoA) is either unknown or ambiguous. Unveiling the mechanism of these compounds may lead to useful tools for biological investigation and in some cases, new therapeutic leads. In select cases, the DNA mismatch repair-deficient colorectal cancer cell line, HCT116, has been used as a tool in forward genetic screens to identify compound-resistant mutations, which have ultimately led to target identification. To expand the utility of this approach, we engineered cancer cell lines with inducible mismatch repair deficits, thus providing temporal control over mutagenesis. By screening for compound resistance phenotypes in cells with low or high rates of mutagenesis, we increased both the specificity and sensitivity of identifying resistance mutations. Using this inducible mutagenesis system, we implicate targets for multiple orphan cytotoxins, including a natural product and compounds emerging from a high-throughput screen, thus providing a robust tool for future MoA studies.
Collapse
|
23
|
Shergalis AG, Marin VL, Rhee DY, Senaweera S, McCloud RL, Ronau JA, Hutchins CW, McLoughlin S, Woller KR, Warder SE, Vasudevan A, Reitsma JM. CRISPR Screen Reveals BRD2/4 Molecular Glue-like Degrader via Recruitment of DCAF16. ACS Chem Biol 2023; 18:331-339. [PMID: 36656921 DOI: 10.1021/acschembio.2c00747] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Molecular glues (MGs) are monovalent small molecules that induce an interaction between proteins (native or non-native partners) by altering the protein-protein interaction (PPI) interface toward a higher-affinity state. Enhancing the PPI between a protein and E3 ubiquitin ligase can lead to degradation of the partnering protein. Over the past decade, retrospective studies of clinical drugs identified that immunomodulatory drugs (e.g., thalidomide and analogues) and indisulam exhibit a molecular glue effect by driving the interaction between non-native substrates to CRBN and DCAF15 ligases, respectively. Ensuing reports of phenotypic screens focused on MG discovery have suggested that these molecules may be more common than initially anticipated. However, prospective discovery of MGs remains challenging. Thus, expanding the repertoire of MGs will enhance our understanding of principles for prospective design. Herein, we report the results of a CRISPR/Cas9 knockout screen of over 1000 ligases and ubiquitin proteasome system components in a BRD4 degradation assay with a JQ1-based monovalent degrader, compound 1a. We identified DCAF16, a substrate recognition component of the Cul4 ligase complex, as essential for compound activity, and we demonstrate that compound 1a drives the interaction between DCAF16 and BRD2/4 to promote target degradation. Taken together, our data suggest that compound 1a functions as an MG degrader between BRD2/4 and DCAF16 and provides a foundation for further mechanistic dissection to advance prospective MG discovery.
Collapse
Affiliation(s)
- Andrea G Shergalis
- Drug Discovery Science & Technology, AbbVie Inc, North Chicago, Illinois 60064, United States
| | - Violeta L Marin
- Drug Discovery Science & Technology, AbbVie Inc, North Chicago, Illinois 60064, United States
| | - David Y Rhee
- Drug Discovery Science & Technology, AbbVie Inc, North Chicago, Illinois 60064, United States
| | - Sameera Senaweera
- Drug Discovery Science & Technology, AbbVie Inc, North Chicago, Illinois 60064, United States
| | - Rebecca L McCloud
- Drug Discovery Science & Technology, AbbVie Inc, North Chicago, Illinois 60064, United States
| | - Judith A Ronau
- Drug Discovery Science & Technology, AbbVie Inc, North Chicago, Illinois 60064, United States
| | - Charles W Hutchins
- Drug Discovery Science & Technology, AbbVie Inc, North Chicago, Illinois 60064, United States
| | - Shaun McLoughlin
- Drug Discovery Science & Technology, AbbVie Inc, North Chicago, Illinois 60064, United States
| | - Kevin R Woller
- Drug Discovery Science & Technology, AbbVie Inc, North Chicago, Illinois 60064, United States
| | - Scott E Warder
- Drug Discovery Science & Technology, AbbVie Inc, North Chicago, Illinois 60064, United States
| | - Anil Vasudevan
- Drug Discovery Science & Technology, AbbVie Inc, North Chicago, Illinois 60064, United States
| | - Justin M Reitsma
- Drug Discovery Science & Technology, AbbVie Inc, North Chicago, Illinois 60064, United States
| |
Collapse
|
24
|
Lu J, Li D, Jiang H, Li Y, Lu C, Chen T, Wang Y, Wang X, Sun W, Pu Z, Qiao C, Ma J, Xu G. The aryl sulfonamide indisulam inhibits gastric cancer cell migration by promoting the ubiquitination and degradation of the transcription factor ZEB1. J Biol Chem 2023; 299:103025. [PMID: 36805336 PMCID: PMC10040736 DOI: 10.1016/j.jbc.2023.103025] [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: 10/03/2022] [Revised: 01/20/2023] [Accepted: 01/22/2023] [Indexed: 02/17/2023] Open
Abstract
Gastric cancer is one of the cancers with high morbidity and mortality worldwide. The aryl sulfonamide indisulam inhibits the proliferation of several types of cancer cells through its function as a molecular glue to promote the ubiquitination and degradation of RNA-binding motif protein 39 (RBM39). However, it is unknown whether and how indisulam regulates the migration of cancer cells. In this work, using label-free quantitative proteomics, we discover that indisulam significantly attenuates N-cadherin, a marker for epithelial to mesenchymal transition and migration of cancer cells. Our bioinformatics analysis and biochemical experiments reveal that indisulam promotes the interaction between the zinc finger E-box-binding homeobox 1 (ZEB1), a transcription factor of N-cadherin, and DCAF15, a substrate receptor of CRL4 E3 ubiquitin ligase, and enhances ZEB1 ubiquitination and proteasomal degradation. In addition, our cell line-based experiments demonstrate that indisulam inhibits the migration of gastric cancer cells in a ZEB1-dependent manner. Analyses of patient samples and datasets in public databases reveal that tumor tissues from patients with gastric cancer express high ZEB1 mRNA and this high expression reduces patient survival rate. Finally, we show that treatment of gastric tumor samples with indisulam significantly reduces ZEB1 protein levels. Therefore, this work discloses a new mechanism by which indisulam inhibits the migration of gastric cancer cells, indicating that indisulam exhibits different biological functions through distinct signaling molecules.
Collapse
Affiliation(s)
- Jiaqi Lu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, Jiangsu, China
| | - Dan Li
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, Jiangsu, China
| | - Honglv Jiang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, Jiangsu, China
| | - Yue Li
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, Jiangsu, China
| | - Chengpiao Lu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, Jiangsu, China
| | - Tao Chen
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Yuhong Wang
- Department of Pathology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Xiaohui Wang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, Jiangsu, China
| | - Wenzhao Sun
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, Jiangsu, China
| | - Zhongjian Pu
- Department of Oncology, Haian Hospital of Traditional Chinese Medicine, Haian, Jiangsu, China
| | - Chunhua Qiao
- College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Jingjing Ma
- Department of Pharmacy, Medical Center of Soochow University, Dushu Lake Hospital Affiliated to Soochow University, Suzhou, Jiangsu, China.
| | - Guoqiang Xu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Province Engineering Research Center of Precision Diagnostics and Therapeutics Development, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Suzhou Key Laboratory of Drug Research for Prevention and Treatment of Hyperlipidemic Diseases, Soochow University, Suzhou, Jiangsu, China.
| |
Collapse
|
25
|
Chakravarty A, Yang PL. Targeted protein degradation as an antiviral approach. Antiviral Res 2023; 210:105480. [PMID: 36567024 PMCID: PMC10178900 DOI: 10.1016/j.antiviral.2022.105480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 12/01/2022] [Indexed: 12/24/2022]
Abstract
Targeted protein degradation (TPD) has emerged as a new modality in drug discovery. In this approach, small molecules are used to drive degradation of the target protein of interest. Whereas most direct-acting antivirals (DAAs) inhibit or derange the activity of their viral protein targets and have occupancy-driven pharmacology, small molecules with a TPD-based mechanism have event-driven pharmacology exerted through their ability to induce target degradation. These contrasting mechanisms can result in significant differences in drug efficacy and pharmacodynamics that may be useful in the development of new classes of antivirals. While now being widely pursued in cancer biology and autoimmune disease, TPD has not yet been widely applied as an antiviral strategy. Here, we briefly review TPD pharmacology along with the current status of tools available for developing small molecules that achieve antiviral activity through a TPD mechanism. We also highlight aspects of TPD that may be especially useful in the development of antivirals and that we hope will motivate pursuit of TPD-based antivirals by the antivirals research community.
Collapse
Affiliation(s)
- Antara Chakravarty
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Priscilla L Yang
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| |
Collapse
|
26
|
Duran-Frigola M, Cigler M, Winter GE. Advancing Targeted Protein Degradation via Multiomics Profiling and Artificial Intelligence. J Am Chem Soc 2023; 145:2711-2732. [PMID: 36706315 PMCID: PMC9912273 DOI: 10.1021/jacs.2c11098] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Only around 20% of the human proteome is considered to be druggable with small-molecule antagonists. This leaves some of the most compelling therapeutic targets outside the reach of ligand discovery. The concept of targeted protein degradation (TPD) promises to overcome some of these limitations. In brief, TPD is dependent on small molecules that induce the proximity between a protein of interest (POI) and an E3 ubiquitin ligase, causing ubiquitination and degradation of the POI. In this perspective, we want to reflect on current challenges in the field, and discuss how advances in multiomics profiling, artificial intelligence, and machine learning (AI/ML) will be vital in overcoming them. The presented roadmap is discussed in the context of small-molecule degraders but is equally applicable for other emerging proximity-inducing modalities.
Collapse
Affiliation(s)
- Miquel Duran-Frigola
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria,Ersilia
Open Source Initiative, 28 Belgrave Road, CB1 3DE, Cambridge, United Kingdom,
| | - Marko Cigler
- 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,
| |
Collapse
|
27
|
Hanzl A, Barone E, Bauer S, Yue H, Nowak RP, Hahn E, Pankevich EV, Koren A, Kubicek S, Fischer ES, Winter GE. E3-Specific Degrader Discovery by Dynamic Tracing of Substrate Receptor Abundance. J Am Chem Soc 2023; 145:1176-1184. [PMID: 36602777 PMCID: PMC9853857 DOI: 10.1021/jacs.2c10784] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Indexed: 01/06/2023]
Abstract
Targeted protein degradation (TPD) is a new pharmacology based on small-molecule degraders that induce proximity between a protein of interest (POI) and an E3 ubiquitin ligase. Of the approximately 600 E3s encoded in the human genome, only around 2% can be co-opted with degraders. This underrepresentation is caused by a paucity of discovery approaches to identify degraders for defined E3s. This hampers a rational expansion of the druggable proteome and stymies critical advancements in the field, such as tissue- and cell-specific degradation. Here, we focus on dynamic NEDD8 conjugation, a post-translational, regulatory circuit that controls the activity of 250 cullin RING E3 ligases (CRLs). Leveraging this regulatory layer enabled us to develop a scalable assay to identify compounds that alter the interactome of an E3 of interest by tracing their abundance after pharmacologically induced auto-degradation. Initial validation studies are performed for CRBN and VHL, but proteomics studies indicate broad applicability for many CRLs. Among amenable ligases, we select CRLDCAF15 for a proof-of-concept screen, leading to the identification of a novel DCAF15-dependent molecular glue degrader inducing the degradation of RBM23 and RBM39. Together, this strategy empowers the scalable identification of degraders specific to a ligase of interest.
Collapse
Affiliation(s)
- Alexander Hanzl
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria
| | - Eleonora Barone
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria
| | - Sophie Bauer
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria
| | - Hong Yue
- Department
of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department
of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Radosław P. Nowak
- Department
of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department
of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Elisa Hahn
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria
| | - Eugenia V. Pankevich
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria
| | - Anna Koren
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria
| | - Stefan Kubicek
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria
| | - Eric S. Fischer
- Department
of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department
of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Georg E. Winter
- CeMM
Research Center for Molecular Medicine of the Austrian Academy of
Sciences, 1090 Vienna, Austria
| |
Collapse
|
28
|
Barraza SJ, Bhattacharyya A, Trotta CR, Woll MG. Targeting strategies for modulating pre-mRNA splicing with small molecules: Recent advances. Drug Discov Today 2023; 28:103431. [PMID: 36356786 DOI: 10.1016/j.drudis.2022.103431] [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: 08/03/2022] [Revised: 10/27/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022]
Abstract
The concept of using small molecules to therapeutically modulate pre-mRNA splicing was validated with the US Food and Drug Administration (FDA) approval of Evrysdi® (risdiplam) in 2020. Since then, efforts have continued unabated toward the discovery of new splicing-modulating drugs. However, the drug development world has evolved in the 10 years since risdiplam precursors were first identified in high-throughput screening (HTS). Now, new mechanistic insights into RNA-processing pathways and regulatory networks afford increasingly feasible targeted approaches. In this review, organized into classes of biological target, we compile and summarize small molecules discovered, devised, and developed since 2020 to alter pre-mRNA splicing.
Collapse
Affiliation(s)
- Scott J Barraza
- PTC Therapeutics, Inc., 100 Corporate Court, South Plainfield, NJ, USA.
| | | | | | - Matthew G Woll
- PTC Therapeutics, Inc., 100 Corporate Court, South Plainfield, NJ, USA
| |
Collapse
|
29
|
Srivastava R, Fernández-Ginés R, Encinar JA, Cuadrado A, Wells G. The current status and future prospects for therapeutic targeting of KEAP1-NRF2 and β-TrCP-NRF2 interactions in cancer chemoresistance. Free Radic Biol Med 2022; 192:246-260. [PMID: 36181972 DOI: 10.1016/j.freeradbiomed.2022.09.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/12/2022] [Accepted: 09/20/2022] [Indexed: 10/31/2022]
Abstract
Drug resistance is one of the biggest challenges in cancer treatment and limits the potential to cure patients. In many tumors, sustained activation of the protein NRF2 makes tumor cells resistant to chemo- and radiotherapy. Thus, blocking inappropriate NRF2 activity in cancers has been shown to reduce resistance in models of the disease. There is a growing scientific interest in NRF2 inhibitors. However, the compounds developed so far are not target-specific and are associated with a high degree of toxicity, hampering clinical applications. Compounds that can enhance the binding of NRF2 to its ubiquitination-facilitating regulator proteins, either KEAP1 or β-TrCP, have the potential to increase NRF2 degradation and may be of value as potential chemosensitising agents in cancer treatment. Approaches based on molecular glue-type mechanisms, in which ligands stabilise a ternary complex between a protein and its binding partner have shown to enhance β-catenin degradation by stabilising its interaction with β-TrCP. This strategy could be applied to rationally discover degradative β-TrCP-NRF2 and KEAP1-NRF2 protein-protein interaction enhancers. We are proposing a novel approach to selectively suppress NRF2 activity in tumors. It is based on recent methodology and has the potential to be a promising new addition to the arsenal of anticancer agents.
Collapse
Affiliation(s)
- Rohini Srivastava
- UCL School of Pharmacy, University College London, 29/39 Brunswick Square, London, WC1N 1AX, UK
| | - Raquel Fernández-Ginés
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Instituto de Investigación Sanitaria La Paz (IdiPaz), Department of Biochemistry and Instituto de Investigaciones Biomédicas Alberto Sols UAM-CSIC, Faculty of Medicine, Autonomous University of Madrid, Madrid, Spain
| | - José Antonio Encinar
- Institute of Molecular and Cell Biology (IBMC), Miguel Hernández University (UMH), Avda. Universidad s/n, Elche, 03202, Spain
| | - Antonio Cuadrado
- Centro de Investigación Biomédica en Red Sobre Enfermedades Neurodegenerativas (CIBERNED), Instituto de Investigación Sanitaria La Paz (IdiPaz), Department of Biochemistry and Instituto de Investigaciones Biomédicas Alberto Sols UAM-CSIC, Faculty of Medicine, Autonomous University of Madrid, Madrid, Spain
| | - Geoff Wells
- UCL School of Pharmacy, University College London, 29/39 Brunswick Square, London, WC1N 1AX, UK.
| |
Collapse
|
30
|
Zhang R, Wang W, Zhang N, Chen X, Liu W, Zhang L, Liu N. Systematic pan-cancer analysis identifies RBM39 as an immunological and prognostic biomarker. J Cell Mol Med 2022; 26:4859-4871. [PMID: 35989423 PMCID: PMC9465192 DOI: 10.1111/jcmm.17517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 07/21/2022] [Accepted: 08/08/2022] [Indexed: 11/27/2022] Open
Abstract
RNA‐binding Motif Protein39 (RBM39) is identified as a splicing factor and transcription coactivator. Despite mounting evidence that RBM39 plays a critical role in the development of specific malignancies, no systematic pan‐cancer investigation of RBM39 has been conducted. As a result, we set out to investigate RBM39’s prognostic significance and putative immunological activities in 33 different cancers. Based on TCGA and CCLE, GTEx, cBioportal and HPA, we used a series of bioinformatics approaches to explore the potential oncogenic role of RBM39, including analysis of the expression of the pan‐cancer species RBM39, the prognostic relationship between RBM39 expression and overall survival (OS), disease‐specific survival (DSS) and progression‐free interval (PFI), the relationship between RBM39 expression and clinical phenotype, analysis of the relationship between RBM39 expression and tumour mutational burden (TMB), microsatellite instability (MSI), DNA methylation and immune cell infiltration. Our results showed that RBM39 is overexpressed in most cancers. RBM39 was positively or negatively correlated with the prognosis of different tumours. RBM39 expression was associated with TMB and MSI in 9 and 12 cancer types. In addition, RBM39 expression was associated with DNA methylation in almost all tumours. There are eight tumours were screened for further study, including BRCA, COAD, HNSC, LIHC, LUSC, SKCM, STAD, UCEC. In the screed tumours, RBM39 was found to be negatively correlated with the infiltration of most immune cells. In addition, the correlation with RBM39 expression varied by immune cell subtype. Based on RBM39’s role in tumorigenesis and tumour immunity, we suggest it can serve as a surrogate prognostic marker.
Collapse
Affiliation(s)
- Rui Zhang
- Cancer Institute, Xuzhou Medical University, Xuzhou, China
| | - Wei Wang
- Cancer Institute, Xuzhou Medical University, Xuzhou, China
| | - Nie Zhang
- Cancer Institute, Xuzhou Medical University, Xuzhou, China
| | - Xueting Chen
- Cancer Institute, Xuzhou Medical University, Xuzhou, China
| | - Wanming Liu
- Cancer Institute, Xuzhou Medical University, Xuzhou, China
| | - Longzhen Zhang
- Department of Radiation Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China.,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| | - Nianli Liu
- Cancer Institute, Xuzhou Medical University, Xuzhou, China.,Center of Clinical Oncology, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China
| |
Collapse
|
31
|
A Comprehensive Review of BET-targeting PROTACs for Cancer Therapy. Bioorg Med Chem 2022; 73:117033. [DOI: 10.1016/j.bmc.2022.117033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/11/2022] [Accepted: 09/22/2022] [Indexed: 11/23/2022]
|
32
|
Sasso J, Tenchov R, Wang D, Johnson LS, Wang X, Zhou QA. Molecular Glues: The Adhesive Connecting Targeted Protein Degradation to the Clinic. Biochemistry 2022; 62:601-623. [PMID: 35856839 PMCID: PMC9910052 DOI: 10.1021/acs.biochem.2c00245] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Targeted protein degradation is a rapidly exploding drug discovery strategy that uses small molecules to recruit disease-causing proteins for rapid destruction mainly via the ubiquitin-proteasome pathway. It shows great potential for treating diseases such as cancer and infectious, inflammatory, and neurodegenerative diseases, especially for those with "undruggable" pathogenic protein targets. With the recent rise of the "molecular glue" type of protein degraders, which tighten and simplify the connection of an E3 ligase with a disease-causing protein for ubiquitination and subsequent degradation, new therapies for unmet medical needs are being designed and developed. Here we use data from the CAS Content Collection and the publication landscape of recent research on targeted protein degraders to provide insights into these molecules, with a special focus on molecular glues. We also outline the advantages of the molecular glues and summarize the advances in drug discovery practices for molecular glue degraders. We further provide a thorough review of drug candidates in targeted protein degradation through E3 ligase recruitment. Finally, we highlight the progression of molecular glues in drug discovery pipelines and their targeted diseases. Overall, our paper provides a comprehensive reference to support the future development of molecular glues in medicine.
Collapse
|
33
|
Riching KM, Caine EA, Urh M, Daniels DL. The importance of cellular degradation kinetics for understanding mechanisms in targeted protein degradation. Chem Soc Rev 2022; 51:6210-6221. [PMID: 35792307 DOI: 10.1039/d2cs00339b] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Targeted protein degradation has exploded over the past several years due to preclinical and early clinical therapeutic success of numerous compounds, and the emergence of new degradation modalities, which has broadened the definition of what a degrader is. The most characterized and well-studied small molecule degraders are molecular glues and proteolysis targeting chimeras (PROTACs). These degraders induce a ternary complex between a target protein, degrader, and E3 ligase component, resulting in ubiquitination and subsequent degradation of the target protein via the ubiquitin proteasomal system (UPS). This event-driven process requires success at all steps through a complex cascade of events. As more systems, degraders, and targets are tested, it has become increasingly clear that achieving degradation is only the first critical milestone in a degrader development program. Rather highly efficacious degraders require a combination of multiple optimized parameters: rapid degradation, high potency, high maximal degradation (Dmax), and sustained loss of target without re-dosing. Success to meet these more rigorous goals depends upon the ability to characterize and understand the dynamic cellular degradation profiles and relate them to the underlying mechanism for any given target treated with a specific concentration of degrader. From this starting point, optimization and fine tuning of multiple kinetic parameters such as how fast degradation occurs (the rate), how much of the target is degraded (the extent), and how long the target remains degraded (the duration) can be performed. In this review we explore the diversity of cellular kinetic degradation profiles which can arise after molecular glue and PROTAC treatment and the potential implications of these varying responses. As the overall degradation kinetics are a sum of individual mechanistic steps, each with their own kinetic contributions, we discuss the ways in which changes at any one of these steps could potentially influence the resultant kinetic degradation profiles. Looking forward, we address the importance in characterizing the kinetics of target protein loss in the early stages of degrader design and how this will enable more rapid discovery of therapeutic agents to elicit desired phenotypic outcomes.
Collapse
Affiliation(s)
- Kristin M Riching
- Promega Corporation, 5430 East Cheryl Drive, Madison, WI, 53711, USA.
| | - Elizabeth A Caine
- Promega Corporation, 5430 East Cheryl Drive, Madison, WI, 53711, USA.
| | - Marjeta Urh
- Promega Corporation, 5430 East Cheryl Drive, Madison, WI, 53711, USA.
| | - Danette L Daniels
- Promega Corporation, 5430 East Cheryl Drive, Madison, WI, 53711, USA.
| |
Collapse
|
34
|
Pogacar Z, Groot K, Jochems F, Dos Santos Dias M, Mulero-Sánchez A, Morris B, Roosen M, Wardak L, De Conti G, Velds A, Lieftink C, Thijssen B, Beijersbergen RL, Bernards R, Leite de Oliveira R. Genetic and compound screens uncover factors modulating cancer cell response to indisulam. Life Sci Alliance 2022; 5:5/9/e202101348. [PMID: 35534224 PMCID: PMC9095732 DOI: 10.26508/lsa.202101348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 04/26/2022] [Accepted: 04/26/2022] [Indexed: 11/28/2022] Open
Abstract
The authors identify that loss of SRPK1 sensitises cancer cells to indisulam treatment and loss of CAND1 confers resistance. Resistance is mediated through RBM39. Furthermore, pharmacological Bcl-xL inhibition prevents acquired resistance to indisulam. Discovering biomarkers of drug response and finding powerful drug combinations can support the reuse of previously abandoned cancer drugs in the clinic. Indisulam is an abandoned drug that acts as a molecular glue, inducing degradation of splicing factor RBM39 through interaction with CRL4DCAF15. Here, we performed genetic and compound screens to uncover factors mediating indisulam sensitivity and resistance. First, a dropout CRISPR screen identified SRPK1 loss as a synthetic lethal interaction with indisulam that can be exploited therapeutically by the SRPK1 inhibitor SPHINX31. Moreover, a CRISPR resistance screen identified components of the degradation complex that mediate resistance to indisulam: DCAF15, DDA1, and CAND1. Last, we show that cancer cells readily acquire spontaneous resistance to indisulam. Upon acquiring indisulam resistance, pancreatic cancer (Panc10.05) cells still degrade RBM39 and are vulnerable to BCL-xL inhibition. The better understanding of the factors that influence the response to indisulam can assist rational reuse of this drug in the clinic.
Collapse
Affiliation(s)
- Ziva Pogacar
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Kelvin Groot
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Fleur Jochems
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Matheus Dos Santos Dias
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Antonio Mulero-Sánchez
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ben Morris
- The Netherlands Cancer Institute Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Mieke Roosen
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Leyma Wardak
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Giulia De Conti
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Arno Velds
- Genomics Core Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Cor Lieftink
- The Netherlands Cancer Institute Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Bram Thijssen
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Roderick L Beijersbergen
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,The Netherlands Cancer Institute Robotics and Screening Center, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Genomics Core Facility, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - René Bernards
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Rodrigo Leite de Oliveira
- Division of Molecular Carcinogenesis, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| |
Collapse
|
35
|
The state of the art of PROTAC technologies for drug discovery. Eur J Med Chem 2022; 235:114290. [DOI: 10.1016/j.ejmech.2022.114290] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 03/10/2022] [Accepted: 03/11/2022] [Indexed: 12/20/2022]
|
36
|
Stanley RF, Abdel-Wahab O. Dysregulation and therapeutic targeting of RNA splicing in cancer. NATURE CANCER 2022; 3:536-546. [PMID: 35624337 PMCID: PMC9551392 DOI: 10.1038/s43018-022-00384-z] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 04/22/2022] [Indexed: 05/15/2023]
Abstract
High-throughput sequencing and functional characterization of the cancer transcriptome have uncovered cancer-specific dysregulation of RNA splicing across a variety of cancers. Alterations in the cancer genome and dysregulation of RNA splicing factors lead to missplicing, splicing alteration-dependent gene expression and, in some cases, generation of novel splicing-derived proteins. Here, we review recent advances in our understanding of aberrant splicing in cancer pathogenesis and present strategies to harness cancer-specific aberrant splicing for therapeutic intent.
Collapse
Affiliation(s)
- Robert F Stanley
- Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| |
Collapse
|
37
|
Gosavi P, Ngan KC, Yeo MJR, Su C, Li J, Lue NZ, Hoenig SM, Liau BB. Profiling the Landscape of Drug Resistance Mutations in Neosubstrates to Molecular Glue Degraders. ACS CENTRAL SCIENCE 2022; 8:417-429. [PMID: 35505873 PMCID: PMC9052798 DOI: 10.1021/acscentsci.1c01603] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Indexed: 05/31/2023]
Abstract
Targeted protein degradation (TPD) holds immense promise for drug discovery, but mechanisms of acquired resistance to degraders remain to be fully identified. Here, we used clustered regularly interspaced short palindromic repeats (CRISPR)-suppressor scanning to identify mechanistic classes of drug resistance mutations to molecular glue degraders in GSPT1 and RBM39, neosubstrates targeted by E3 ligase substrate receptors cereblon and DCAF15, respectively. While many mutations directly alter the ternary complex heterodimerization surface, distal resistance sites were also identified. Several distal mutations in RBM39 led to modest decreases in degradation, yet can enable cell survival, underscoring how small differences in degradation can lead to resistance. Integrative analysis of resistance sites across GSPT1 and RBM39 revealed varying levels of sequence conservation and mutational constraint that control the emergence of different resistance mechanisms, highlighting that many regions co-opted by TPD are nonessential. Altogether, our study identifies common resistance mechanisms for molecular glue degraders and outlines a general approach to survey neosubstrate requirements necessary for effective degradation.
Collapse
Affiliation(s)
- Pallavi
M. Gosavi
- Department
of Chemistry and Chemical Biology, Harvard
University, Cambridge, Massachusetts 02138, United States
- Broad
Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
| | - Kevin C. Ngan
- Department
of Chemistry and Chemical Biology, Harvard
University, Cambridge, Massachusetts 02138, United States
- Broad
Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
| | - Megan J. R. Yeo
- Department
of Chemistry and Chemical Biology, Harvard
University, Cambridge, Massachusetts 02138, United States
- Broad
Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
| | - Cindy Su
- Department
of Chemistry and Chemical Biology, Harvard
University, Cambridge, Massachusetts 02138, United States
- Broad
Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
| | - Jiaming Li
- Department
of Chemistry and Chemical Biology, Harvard
University, Cambridge, Massachusetts 02138, United States
- Broad
Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
| | - Nicholas Z. Lue
- Department
of Chemistry and Chemical Biology, Harvard
University, Cambridge, Massachusetts 02138, United States
- Broad
Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
| | - Samuel M. Hoenig
- Department
of Chemistry and Chemical Biology, Harvard
University, Cambridge, Massachusetts 02138, United States
- Broad
Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
| | - Brian B. Liau
- Department
of Chemistry and Chemical Biology, Harvard
University, Cambridge, Massachusetts 02138, United States
- Broad
Institute of Harvard and MIT, Cambridge, Massachusetts 02142, United States
| |
Collapse
|
38
|
Sette C, Paronetto MP. Somatic Mutations in Core Spliceosome Components Promote Tumorigenesis and Generate an Exploitable Vulnerability in Human Cancer. Cancers (Basel) 2022; 14:cancers14071827. [PMID: 35406598 PMCID: PMC8997811 DOI: 10.3390/cancers14071827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/30/2022] [Accepted: 03/30/2022] [Indexed: 12/02/2022] Open
Abstract
Simple Summary High throughput exome sequencing approaches have disclosed recurrent cancer-associated mutations in spliceosomal components, which drive aberrant pre-mRNA processing events and support the tumor phenotype. At the same time, mutations in spliceosome genes and aberrant splicing regulation establish a selective vulnerability of cancer cells to splicing-targeting approaches, which could be exploited therapeutically. It is conceivable that a better understanding of the mechanisms and roles of abnormal splicing in tumor metabolism will facilitate the development of a novel generation of tumor-targeting drugs. In this review, we describe recent advances in the elucidation of the biological impact and biochemical effects of somatic mutations in core spliceosome components on splicing choices and their associated targetable vulnerabilities. Abstract Alternative pre-mRNA processing enables the production of distinct mRNA and protein isoforms from a single gene, thus greatly expanding the coding potential of eukaryotic genomes and fine-tuning gene expression programs. Splicing is carried out by the spliceosome, a complex molecular machinery which assembles step-wise on mRNA precursors in the nucleus of eukaryotic cells. In the last decade, exome sequencing technologies have allowed the identification of point mutations in genes encoding splicing factors as a recurrent hallmark of human cancers, with higher incidence in hematological malignancies. These mutations lead to production of splicing factors that reduce the fidelity of the splicing process and yield splicing variants that are often advantageous for cancer cells. However, at the same time, these mutations increase the sensitivity of transformed cells to splicing inhibitors, thus offering a therapeutic opportunity for novel targeted strategies. Herein, we review the recent literature documenting cancer-associated mutations in components of the early spliceosome complex and discuss novel therapeutic strategies based on small-molecule spliceosome inhibitors that exhibit strong anti-tumor effects, particularly against cancer cells harboring mutations in spliceosomal components.
Collapse
Affiliation(s)
- Claudio Sette
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy;
- GSTEP-Organoids Core Facility, Fondazione Policlinico Agostino Gemelli IRCCS, 00168 Rome, Italy
| | - Maria Paola Paronetto
- Department of Movement, Human and Health Sciences, University of Rome “Foro Italico”, Piazza Lauro De Bosis, 6, 00135 Rome, Italy
- Laboratory of Molecular and Cellular Neurobiology, Fondazione Santa Lucia, IRCCS, Via del Fosso di Fiorano 64, 00143 Rome, Italy
- Correspondence:
| |
Collapse
|
39
|
Abstract
Targeted protein degradation (TPD) is an emerging therapeutic modality with the potential to tackle disease-causing proteins that have historically been highly challenging to target with conventional small molecules. In the 20 years since the concept of a proteolysis-targeting chimera (PROTAC) molecule harnessing the ubiquitin-proteasome system to degrade a target protein was reported, TPD has moved from academia to industry, where numerous companies have disclosed programmes in preclinical and early clinical development. With clinical proof-of-concept for PROTAC molecules against two well-established cancer targets provided in 2020, the field is poised to pursue targets that were previously considered 'undruggable'. In this Review, we summarize the first two decades of PROTAC discovery and assess the current landscape, with a focus on industry activity. We then discuss key areas for the future of TPD, including establishing the target classes for which TPD is most suitable, expanding the use of ubiquitin ligases to enable precision medicine and extending the modality beyond oncology.
Collapse
Affiliation(s)
| | | | - Craig M Crews
- Department of Molecular, Cellular & Developmental Biology, Yale University, New Haven, CT, USA.
- Department of Pharmacology, Yale University, New Haven, CT, USA.
- Department of Chemistry, Yale University, New Haven, CT, USA.
| |
Collapse
|
40
|
Cao S, Kang S, Mao H, Yao J, Gu L, Zheng N. Defining molecular glues with a dual-nanobody cannabidiol sensor. Nat Commun 2022; 13:815. [PMID: 35145136 PMCID: PMC8831599 DOI: 10.1038/s41467-022-28507-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 01/27/2022] [Indexed: 12/14/2022] Open
Abstract
"Molecular glue" (MG) is a term coined to describe the mechanism of action of the plant hormone auxin and subsequently used to characterize synthetic small molecule protein degraders exemplified by immune-modulatory imide drugs (IMiDs). Prospective development of MGs, however, has been hampered by its elusive definition and thermodynamic characteristics. Here, we report the crystal structure of a dual-nanobody cannabidiol-sensing system, in which the ligand promotes protein-protein interaction in a manner analogous to auxin. Through quantitative analyses, we draw close parallels among the dual-nanobody cannabidiol sensor, the auxin perception complex, and the IMiDs-bound CRL4CRBN E3, which can bind and ubiquitinate "neo-substrates". All three systems, including the recruitment of IKZF1 and CK1α to CRBN, are characterized by the lack of ligand binding activity in at least one protein partner and an under-appreciated preexisting low micromolar affinity between the two proteinaceous subunits that is enhanced by the ligand to reach the nanomolar range. These two unifying features define MGs as a special class of proximity inducers distinct from bifunctional compounds and can be used as criteria to guide target selection for future rational discovery of MGs.
Collapse
Affiliation(s)
- Shiyun Cao
- Howard Hughes Medical Institute, Department of Pharmacology, University of Washington, Seattle, WA, 98195, USA
| | - Shoukai Kang
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Haibin Mao
- Howard Hughes Medical Institute, Department of Pharmacology, University of Washington, Seattle, WA, 98195, USA
| | - Jiayu Yao
- Howard Hughes Medical Institute, Department of Pharmacology, University of Washington, Seattle, WA, 98195, USA
| | - Liangcai Gu
- Department of Biochemistry and Institute for Protein Design, University of Washington, Seattle, WA, 98195, USA
| | - Ning Zheng
- Howard Hughes Medical Institute, Department of Pharmacology, University of Washington, Seattle, WA, 98195, USA.
| |
Collapse
|
41
|
Krymov SK, Scherbakov AM, Salnikova DI, Sorokin DV, Dezhenkova LG, Ivanov IV, Vullo D, De Luca V, Capasso C, Supuran CT, Shchekotikhin AE. Synthesis, biological evaluation, and in silico studies of potential activators of apoptosis and carbonic anhydrase inhibitors on isatin-5-sulfonamide scaffold. Eur J Med Chem 2022; 228:113997. [PMID: 34902732 DOI: 10.1016/j.ejmech.2021.113997] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 11/08/2021] [Accepted: 11/11/2021] [Indexed: 02/09/2023]
Abstract
Carbonic anhydrase IX is a promising target for the search for new antitumor compounds with improved properties. Using the molecular hybridization approach, on the basis of structures of a selective carbonic anhydrase IX inhibitor 3 and an activator of apoptosis 2 (1), a series of 1-substituted isatin-5-sulfonamides 5a-5u were designed and synthesized. The study of the inhibitory activity of isatin-5-sulfonamides showed the ability to inhibit I, II, IX, XII isoforms at nano- and micromolar concentrations. Docking of compounds 5e and 5k into the active site of II and IX carbonic anhydrase isoforms showed the coordination of sulfonamidate anions with zinc cations, as well as a number of additional hydrophobic interactions. The trifluoromethylthio derivative 5r suppressed the growth of tumor cells at low micromolar concentrations, maintaining activity on resistant lines and under hypoxic conditions. Immunoblotting of MCF7 cells treated with the 5r revealed its antiestrogenic activity and ability to activate apoptosis in tumor cells.
Collapse
Affiliation(s)
- Stepan K Krymov
- Gause Institute of New Antibiotics, 11 B. Pirogovskaya Street, Moscow, 119021, Russia
| | - Alexander M Scherbakov
- Blokhin National Medical Center of Oncology, 24 Kashirskoye Shosse, Moscow, 115522, Russia
| | - Diana I Salnikova
- Blokhin National Medical Center of Oncology, 24 Kashirskoye Shosse, Moscow, 115522, Russia
| | - Danila V Sorokin
- Blokhin National Medical Center of Oncology, 24 Kashirskoye Shosse, Moscow, 115522, Russia
| | - Lyubov G Dezhenkova
- Gause Institute of New Antibiotics, 11 B. Pirogovskaya Street, Moscow, 119021, Russia
| | - Ivan V Ivanov
- Gause Institute of New Antibiotics, 11 B. Pirogovskaya Street, Moscow, 119021, Russia
| | - Daniela Vullo
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Florence, Italy
| | - Viviana De Luca
- Institute of Biosciences and Bioresources, CNR, Via Pietro Castellino 111, 80131, Napoli, Italy
| | - Clemente Capasso
- Institute of Biosciences and Bioresources, CNR, Via Pietro Castellino 111, 80131, Napoli, Italy
| | - Claudiu T Supuran
- Department of NEUROFARBA, Section of Pharmaceutical and Nutraceutical Sciences, University of Florence, Florence, Italy.
| | | |
Collapse
|
42
|
Yamanaka S, Horiuchi Y, Matsuoka S, Kido K, Nishino K, Maeno M, Shibata N, Kosako H, Sawasaki T. A proximity biotinylation-based approach to identify protein-E3 ligase interactions induced by PROTACs and molecular glues. Nat Commun 2022; 13:183. [PMID: 35013300 PMCID: PMC8748630 DOI: 10.1038/s41467-021-27818-z] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 12/02/2021] [Indexed: 12/24/2022] Open
Abstract
Proteolysis-targeting chimaeras (PROTACs) as well as molecular glues such as immunomodulatory drugs (IMiDs) and indisulam are drugs that induce interactions between substrate proteins and an E3 ubiquitin ligases for targeted protein degradation. Here, we develop a workflow based on proximity-dependent biotinylation by AirID to identify drug-induced neo-substrates of the E3 ligase cereblon (CRBN). Using AirID-CRBN, we detect IMiD-dependent biotinylation of CRBN neo-substrates in vitro and identify biotinylated peptides of well-known neo-substrates by mass spectrometry with high specificity and selectivity. Additional analyses reveal ZMYM2 and ZMYM2-FGFR1 fusion protein-responsible for the 8p11 syndrome involved in acute myeloid leukaemia-as CRBN neo-substrates. Furthermore, AirID-DCAF15 and AirID-CRBN biotinylate neo-substrates targeted by indisulam and PROTACs, respectively, suggesting that this approach has the potential to serve as a general strategy for characterizing drug-inducible protein-protein interactions in cells.
Collapse
Affiliation(s)
- Satoshi Yamanaka
- Division of Cell-Free Sciences, Proteo-Science Center, Ehime University, Matsuyama, 790-8577, Japan
| | - Yuto Horiuchi
- Division of Cell-Free Sciences, Proteo-Science Center, Ehime University, Matsuyama, 790-8577, Japan
| | - Saya Matsuoka
- Division of Cell-Free Sciences, Proteo-Science Center, Ehime University, Matsuyama, 790-8577, Japan
| | - Kohki Kido
- Division of Cell-Free Sciences, Proteo-Science Center, Ehime University, Matsuyama, 790-8577, Japan
| | - Kohei Nishino
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Mayaka Maeno
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Nagoya, 466-8555, Japan
| | - Norio Shibata
- Department of Nanopharmaceutical Sciences, Nagoya Institute of Technology, Nagoya, 466-8555, Japan
| | - Hidetaka Kosako
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Tatsuya Sawasaki
- Division of Cell-Free Sciences, Proteo-Science Center, Ehime University, Matsuyama, 790-8577, Japan.
| |
Collapse
|
43
|
Frere GA, de Araujo ED, Gunning PT. Emerging mechanisms of targeted protein degradation by molecular glues. Methods Cell Biol 2022; 169:1-26. [DOI: 10.1016/bs.mcb.2022.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
44
|
Freedy AM, Liau BB. Discovering new biology with drug-resistance alleles. Nat Chem Biol 2021; 17:1219-1229. [PMID: 34799733 PMCID: PMC9530778 DOI: 10.1038/s41589-021-00865-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 07/21/2021] [Indexed: 02/08/2023]
Abstract
Small molecule drugs form the backbone of modern medicine's therapeutic arsenal. Often less appreciated is the role that small molecules have had in advancing basic biology. In this Review, we highlight how resistance mutations have unlocked the potential of small molecule chemical probes to discover new biology. We describe key instances in which resistance mutations and related genetic variants yielded foundational biological insight and categorize these examples on the basis of their role in the discovery of novel molecular mechanisms, protein allostery, physiology and cell signaling. Next, we suggest ways in which emerging technologies can be leveraged to systematically introduce and characterize resistance mutations to catalyze basic biology research and drug discovery. By recognizing how resistance mutations have propelled biological discovery, we can better harness new technologies and maximize the potential of small molecules to advance our understanding of biology and improve human health.
Collapse
Affiliation(s)
- Allyson M. Freedy
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Brian B. Liau
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Correspondence should be addressed to Brian B. Liau,
| |
Collapse
|
45
|
Dale B, Cheng M, Park KS, Kaniskan HÜ, Xiong Y, Jin J. Advancing targeted protein degradation for cancer therapy. Nat Rev Cancer 2021; 21:638-654. [PMID: 34131295 PMCID: PMC8463487 DOI: 10.1038/s41568-021-00365-x] [Citation(s) in RCA: 238] [Impact Index Per Article: 79.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/23/2021] [Indexed: 02/05/2023]
Abstract
The human proteome contains approximately 20,000 proteins, and it is estimated that more than 600 of them are functionally important for various types of cancers, including nearly 400 non-enzyme proteins that are challenging to target by traditional occupancy-driven pharmacology. Recent advances in the development of small-molecule degraders, including molecular glues and heterobifunctional degraders such as proteolysis-targeting chimeras (PROTACs), have made it possible to target many proteins that were previously considered undruggable. In particular, PROTACs form a ternary complex with a hijacked E3 ubiquitin ligase and a target protein, leading to polyubiquitination and degradation of the target protein. The broad applicability of this approach is facilitated by the flexibility of individual E3 ligases to recognize different substrates. The vast majority of the approximately 600 human E3 ligases have not been explored, thus presenting enormous opportunities to develop degraders that target oncoproteins with tissue, tumour and subcellular selectivity. In this Review, we first discuss the molecular basis of targeted protein degradation. We then offer a comprehensive account of the most promising degraders in development as cancer therapies to date. Lastly, we provide an overview of opportunities and challenges in this exciting field.
Collapse
Affiliation(s)
- Brandon Dale
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Meng Cheng
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kwang-Su Park
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - H Ümit Kaniskan
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yue Xiong
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Cullgen Inc., San Diego, CA, USA.
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| |
Collapse
|
46
|
Lu J, Jiang H, Li D, Chen T, Wang Y, Pu Z, Xu G. Proximity Labeling, Quantitative Proteomics, and Biochemical Studies Revealed the Molecular Mechanism for the Inhibitory Effect of Indisulam on the Proliferation of Gastric Cancer Cells. J Proteome Res 2021; 20:4462-4474. [PMID: 34420308 DOI: 10.1021/acs.jproteome.1c00437] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Indisulam exhibits antitumor activity against several cancer cells. Although the DCAF15-indisulam-RBM39 axis has been well documented in the inhibition of cancer cell growth, it is unknown whether RBM39 degradation alone is the mechanism of action of indisulam. Here, we verified the inhibitory effect of indisulam on the proliferation of gastric cancer cells and its dependence on DCAF15. Proximity-dependent biotin labeling with TurboID and quantitative proteomics revealed that indisulam indeed promoted the interaction between DCAF15 and RBM39. Immunoblotting and immunofluorescence also revealed that indisulam promoted the ubiquitin-mediated RBM39 degradation and RBM39 colocalized with DCAF15 in the nucleus. DCAF15 knockdown almost completely abolished the indisulam-mediated RBM39 reduction. Further knockdown of RBM39 eliminated the effect of DCAF15 on the proliferation of gastric cancer cells upon indisulam treatment. Immunoblotting of gastric tumor tissues confirmed the downregulation of RBM39 by indisulam. Database analysis unveiled that RBM39 was highly expressed in gastric cancer tissues and its high expression significantly shortened the survival time of gastric cancer patients. Taken together, we demonstrated that indisulam enhanced RBM39 ubiquitination and degradation by promoting its interaction with DCAF15, thus inhibiting the proliferation of gastric cancer cells. This work may provide valuable information for drug discovery through proteolysis targeting chimeras. MS data were deposited in ProteomeXchange (Dataset identifier: PXD024168).
Collapse
Affiliation(s)
- Jiaqi Lu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, Jiangsu 215123, China
| | - Honglv Jiang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, Jiangsu 215123, China
| | - Dan Li
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, Jiangsu 215123, China
| | - Tao Chen
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, China
| | - Yuhong Wang
- Department of Pathology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu 215006, China
| | - Zhongjian Pu
- Department of Oncology, Haian Hospital of Traditional Chinese Medicine, Haian, Jiangsu 226600, China
| | - Guoqiang Xu
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Jiangsu Key Laboratory of Preventive and Translational Medicine for Geriatric Diseases, Soochow University, Suzhou, Jiangsu 215123, China
| |
Collapse
|
47
|
RNA-binding protein 39: a promising therapeutic target for cancer. Cell Death Discov 2021; 7:214. [PMID: 34389703 PMCID: PMC8363639 DOI: 10.1038/s41420-021-00598-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 03/04/2021] [Accepted: 05/29/2021] [Indexed: 12/14/2022] Open
Abstract
RNA-binding motif protein 39 (RBM39), as a key factor in tumor-targeted mRNA and protein expression, not only plays a vital role in tumorigenesis, but also has broad development prospects in clinical treatment and drug research. Moreover, since RBM39 was identified as a target of sulfonamides, it has played a key role in the emerging field of molecule drug development. Hence, it is of great significance to study the interaction between RBM39 and tumors and the clinical application of drug-targeted therapy. In this paper, we describe the possible multi-level regulation of RBM39, including gene transcription, protein translation, and alternative splicing. Importantly, the molecular function of RBM39 as an important splicing factor in most common tumors is systematically outlined. Furthermore, we briefly introduce RBM39’s tumor-targeted drug research and its clinical application, hoping to give reference significance for the molecular mechanism of RBM39 in tumors, and provide reliable ideas for in-depth research for future therapeutic strategies.
Collapse
|
48
|
Dong G, Ding Y, He S, Sheng C. Molecular Glues for Targeted Protein Degradation: From Serendipity to Rational Discovery. J Med Chem 2021; 64:10606-10620. [PMID: 34319094 DOI: 10.1021/acs.jmedchem.1c00895] [Citation(s) in RCA: 124] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Targeted protein degradation is a promising area in the discovery and development of innovative therapeutics. Molecular glues mediate proximity-induced protein degradation and have intrinsic advantages over heterobifunctional proteolysis-targeting chimeras, including unprecedented mechanisms, distinct biological activities, and favorable physicochemical properties. Classical molecular glue degraders have been identified serendipitously, but rational discovery and design strategies are emerging rapidly. In this review, we aim to highlight the recent advances in molecular glues for targeted protein degradation and discuss the challenges in developing molecular glues into therapeutic agents. In particular, discovery strategies, action mechanisms, and representative case studies will be addressed.
Collapse
Affiliation(s)
- Guoqiang Dong
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China
| | - Yu Ding
- Neurology Department at Huashan Hospital, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Institutes of Brain Science, School of Life Sciences, Fudan University, 220 Handan Road, Shanghai 200433, China
| | - Shipeng He
- Institute of Translational Medicine, Shanghai University, 99 Shangda Road, Shanghai 200444, China
| | - Chunquan Sheng
- School of Pharmacy, Second Military Medical University, 325 Guohe Road, Shanghai 200433, China
| |
Collapse
|
49
|
Scholes NS, Mayor-Ruiz C, Winter GE. Identification and selectivity profiling of small-molecule degraders via multi-omics approaches. Cell Chem Biol 2021; 28:1048-1060. [PMID: 33811812 DOI: 10.1016/j.chembiol.2021.03.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/18/2021] [Accepted: 03/10/2021] [Indexed: 12/12/2022]
Abstract
The therapeutic modality of targeted protein degradation promises to overcome limitations of traditional pharmacology. Small-molecule degraders recruit disease-causing proteins to E3 ubiquitin ligases, prompting their ubiquitination and degradation by the proteasome. The discovery, mechanistic elucidation, and selectivity profiling of novel degraders are often conducted in cellular systems. This highlights the need for unbiased multi-omics strategies that inform on the functionally involved components. Here, we review how proteomics and functional genomics can be integrated to identify and mechanistically understand degraders, their target selectivity as well as putative resistance mechanisms.
Collapse
Affiliation(s)
- Natalie S Scholes
- CeMM - Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Cristina Mayor-Ruiz
- CeMM - Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria; IRB Barcelona - Institute for Research in Biomedicine, 08028 Barcelona, Spain
| | - Georg E Winter
- CeMM - Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria.
| |
Collapse
|
50
|
Jan M, Sperling AS, Ebert BL. Cancer therapies based on targeted protein degradation - lessons learned with lenalidomide. Nat Rev Clin Oncol 2021; 18:401-417. [PMID: 33654306 PMCID: PMC8903027 DOI: 10.1038/s41571-021-00479-z] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/25/2021] [Indexed: 02/08/2023]
Abstract
For decades, anticancer targeted therapies have been designed to inhibit kinases or other enzyme classes and have profoundly benefited many patients. However, novel approaches are required to target transcription factors, scaffolding proteins and other proteins central to cancer biology that typically lack catalytic activity and have remained mostly recalcitrant to drug development. The selective degradation of target proteins is an attractive approach to expand the druggable proteome, and the selective oestrogen receptor degrader fulvestrant served as an early example of this concept. Following a long and tragic history in the clinic, the immunomodulatory imide drug (IMiD) thalidomide was discovered to exert its therapeutic activity via a novel and unexpected mechanism of action: targeting proteins to an E3 ubiquitin ligase for subsequent proteasomal degradation. This discovery has paralleled and directly catalysed myriad breakthroughs in drug development, leading to the rapid maturation of generalizable chemical platforms for the targeted degradation of previously undruggable proteins. Decades of clinical experience have established front-line roles for thalidomide analogues, including lenalidomide and pomalidomide, in the treatment of haematological malignancies. With a new generation of 'degrader' drugs currently in development, this experience provides crucial insights into class-wide features of degraders, including a unique pharmacology, mechanisms of resistance and emerging therapeutic opportunities. Herein, we review these past experiences and discuss their application in the clinical development of novel degrader therapies.
Collapse
Affiliation(s)
- Max Jan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Adam S Sperling
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Benjamin L Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Boston, MA, USA.
| |
Collapse
|