1
|
Xiao Q, Wang L, Wang J, Wang M, Wang DW, Ding H. A novel lncRNA GM47544 modulates triglyceride metabolism by inducing ubiquitination-dependent protein degradation of APOC3. Mol Metab 2024; 88:102011. [PMID: 39173944 PMCID: PMC11399561 DOI: 10.1016/j.molmet.2024.102011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Revised: 08/09/2024] [Accepted: 08/12/2024] [Indexed: 08/24/2024] Open
Abstract
OBJECTIVE Emerging evidence highlights the pivotal roles of long non-coding RNAs (lncRNAs) in lipid metabolism. Apoprotein C3 (ApoC3) is a well-established therapeutic target for hypertriglyceridemia and exhibits a strong association with cardiovascular disease. However, the exact mechanisms via which the lncRNAs control ApoC3 expression remain unclear. METHODS We identified a novel long noncoding RNA (lncRNA), GM47544, within the ApoA1/C3/A4/A5 gene cluster. Subsequently, the effect of GM47544 on intracellular triglyceride metabolism was analyzed. The diet-induced mouse models of hyperlipidemia and atherosclerosis were established to explore the effect of GM47544 on dyslipidemia and plaque formation in vivo. The molecular mechanism was explored through RNA sequencing, immunoprecipitation, RNA pull-down assay, and RNA immunoprecipitation. RESULTS GM47544 was overexpressed under high-fat stimulation. GM47544 effectively improved hepatic steatosis, reduced blood lipid levels, and alleviated atherosclerosis in vitro and in vivo. Mechanistically, GM47544 directly bound to ApoC3 and facilitated the ubiquitination at lysine 79 in ApoC3, thereby facilitating ApoC3 degradation via the ubiquitin-proteasome pathway. Moreover, we identified AP006216.5 as the human GM47544 transcript, which fulfills a comparable function in human hepatocytes. CONCLUSIONS The identification of GM47544 as a lncRNA modulator of ApoC3 reveals a novel mechanism of post-translational modification, with significant clinical implications for the treatment of hypertriglyceridemia and atherosclerosis.
Collapse
Affiliation(s)
- Qianqian Xiao
- Division of Cardiology, Departments of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, PR China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, 430030, PR China
| | - Luyun Wang
- Division of Cardiology, Departments of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, PR China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, 430030, PR China; Genetic Diagnosis Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, PR China
| | - Jing Wang
- Division of Cardiology, Departments of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, PR China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, 430030, PR China; Genetic Diagnosis Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, PR China
| | - Man Wang
- Division of Cardiology, Departments of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, PR China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, 430030, PR China
| | - Dao Wen Wang
- Division of Cardiology, Departments of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, PR China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, 430030, PR China; Genetic Diagnosis Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, PR China.
| | - Hu Ding
- Division of Cardiology, Departments of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, PR China; Hubei Key Laboratory of Genetics and Molecular Mechanisms of Cardiological Disorders, Wuhan, 430030, PR China; Genetic Diagnosis Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, PR China; Key Laboratory of Vascular Aging, Ministry of Education, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, PR China.
| |
Collapse
|
2
|
Winter GE. Extrapolating Lessons from Targeted Protein Degradation to Other Proximity-Inducing Drugs. ACS Chem Biol 2024. [PMID: 39264973 DOI: 10.1021/acschembio.4c00191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2024]
Abstract
Targeted protein degradation (TPD) is an emerging pharmacologic strategy. It relies on small-molecule "degraders" that induce proximity of a component of an E3 ubiquitin ligase complex and a target protein to induce target ubiquitination and subsequent proteasomal degradation. Essentially, degraders thus expand the function of E3 ligases, allowing them to degrade proteins they would not recognize in the absence of the small molecule. Over the past decade, insights gained from identifying, designing, and characterizing various degraders have significantly enhanced our understanding of TPD mechanisms, precipitating in rational degrader discovery strategies. In this Account, I aim to explore how these insights can be extrapolated to anticipate both opportunities and challenges of utilizing the overarching concept of proximity-inducing pharmacology to manipulate other cellular circuits for the dissection of biological mechanisms and for therapeutic purposes.
Collapse
Affiliation(s)
- Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| |
Collapse
|
3
|
Shan J, Li F, Lou H, Tang Y. Valorization of residual lignin from corncob residues into thermosensitive lignin-based "molecular glues" for recycling cellulase. Int J Biol Macromol 2024; 279:135474. [PMID: 39251003 DOI: 10.1016/j.ijbiomac.2024.135474] [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: 06/12/2024] [Revised: 08/26/2024] [Accepted: 09/06/2024] [Indexed: 09/11/2024]
Abstract
The cost of enzymolysis is a major bottleneck for the industrialisation of lignocellulosic enzymatic hydrolysis technology, and recycling cellulase can reduce this cost. Herein, a sulfobetaine prepolymer (CPS) with terminal chlorine was grafted onto enzymatic hydrolysis residual lignin (EHL) from corncob to construct thermosensitive lignin-based "molecular glues" (lignin-based sulfobetaine polymers, L-CPS) that were used to recover and recycle cellulase. L-CPS2 (1.0 g/L) was added to the corncob residue (CCR) enzymolysis system (50 °C, pH 4.5). After hydrolysis, L-CPS2 co-precipitated with cellulase through hydrophobic binding when cooling to 25 °C. This co-precipitation decreased the amount of cellulase by 40 %. In summary, a thermally responsive lignin-based molecular glue was constructed for green recycling of cellulase, providing a new approach to decreasing the cost of lignocellulosic enzymolysis and high value utilisation of industrial lignin.
Collapse
Affiliation(s)
- Jinxian Shan
- College of Textile Science and Engineering (International Institute of Silk), Zhejiang Sci-Tech University, Hangzhou 310018, PR China
| | - Feiyun Li
- College of Textile Science and Engineering (International Institute of Silk), Zhejiang Sci-Tech University, Hangzhou 310018, PR China.
| | - Hongming Lou
- School of Chemistry and Chemical Engineering, Guangdong Provincial Engineering Research Center for Green Fine Chemicals, South China University of Technology, Guangzhou 510641, PR China
| | - Yanjun Tang
- College of Textile Science and Engineering (International Institute of Silk), Zhejiang Sci-Tech University, Hangzhou 310018, PR China.
| |
Collapse
|
4
|
Huang Y, Liu W, Zhao C, Shi X, Zhao Q, Jia J, Wang A. Targeting cyclin-dependent kinases: From pocket specificity to drug selectivity. Eur J Med Chem 2024; 275:116547. [PMID: 38852339 DOI: 10.1016/j.ejmech.2024.116547] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/28/2024] [Accepted: 05/28/2024] [Indexed: 06/11/2024]
Abstract
The development of selective modulators of cyclin-dependent kinases (CDKs), a kinase family with numerous members and functional variations, is a significant preclinical challenge. Recent advancements in crystallography have revealed subtle differences in the highly conserved CDK pockets. Exploiting these differences has proven to be an effective strategy for achieving excellent drug selectivity. While previous reports briefly discussed the structural features that lead to selectivity in individual CDK members, attaining inhibitor selectivity requires consideration of not only the specific structures of the target CDK but also the features of off-target members. In this review, we summarize the structure-activity relationships (SARs) that influence selectivity in CDK drug development and analyze the pocket features that lead to selectivity using molecular-protein binding models. In addition, in recent years, novel CDK modulators have been developed, providing more avenues for achieving selectivity. These cases were also included. We hope that these efforts will assist in the development of novel CDK drugs.
Collapse
Affiliation(s)
- Yaoguang Huang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Wenwu Liu
- School of Pharmaceutical Sciences, Tsinghua University, Haidian Dist., Beijing, 100084, People's Republic of China
| | - Changhao Zhao
- Department of Pharmacy, General Hospital of Northern Theater Command, Shenyang, 110840, People's Republic of China
| | - Xiaoyu Shi
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China
| | - Qingchun Zhao
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China; Department of Pharmacy, General Hospital of Northern Theater Command, Shenyang, 110840, People's Republic of China.
| | - Jingming Jia
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China.
| | - Anhua Wang
- School of Traditional Chinese Materia Medica, Shenyang Pharmaceutical University, Shenyang, 110016, People's Republic of China.
| |
Collapse
|
5
|
Tsai JM, Nowak RP, Ebert BL, Fischer ES. Targeted protein degradation: from mechanisms to clinic. Nat Rev Mol Cell Biol 2024; 25:740-757. [PMID: 38684868 DOI: 10.1038/s41580-024-00729-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [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
|
6
|
Cheng J, Bin X, Tang Z. Cullin-RING Ligase 4 in Cancer: Structure, Functions, and Mechanisms. Biochim Biophys Acta Rev Cancer 2024; 1879:189169. [PMID: 39117093 DOI: 10.1016/j.bbcan.2024.189169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 07/29/2024] [Accepted: 08/05/2024] [Indexed: 08/10/2024]
Abstract
Cullin-RING ligase 4 (CRL4) has attracted enormous attentions because of its extensive regulatory roles in a wide variety of biological and pathological events, especially cancer-associated events. CRL4 exerts pleiotropic effects by targeting various substrates for proteasomal degradation or changes in activity through different internal compositions to regulate diverse events in cancer progression. In this review, we summarize the structure of CRL4 with manifold compositional modes and clarify the emerging functions and molecular mechanisms of CRL4 in a series of cancer-associated events.
Collapse
Affiliation(s)
- Jingyi Cheng
- Xiangya Stomatological Hospital & Xiangya School of Stomatology, Central South University, Changsha 410008, Hunan, China; Hunan Key Laboratory of Oral Health Research & Hunan Clinical Research Center of Oral Major Diseases and Oral Health & Academician Workstation for Oral-maxilofacial and Regenerative Medicine, Central South University, Changsha 410008, Hunan, China
| | - Xin Bin
- Xiangya Stomatological Hospital & Xiangya School of Stomatology, Central South University, Changsha 410008, Hunan, China; Hunan Key Laboratory of Oral Health Research & Hunan Clinical Research Center of Oral Major Diseases and Oral Health & Academician Workstation for Oral-maxilofacial and Regenerative Medicine, Central South University, Changsha 410008, Hunan, China.
| | - Zhangui Tang
- Xiangya Stomatological Hospital & Xiangya School of Stomatology, Central South University, Changsha 410008, Hunan, China; Hunan Key Laboratory of Oral Health Research & Hunan Clinical Research Center of Oral Major Diseases and Oral Health & Academician Workstation for Oral-maxilofacial and Regenerative Medicine, Central South University, Changsha 410008, Hunan, China.
| |
Collapse
|
7
|
Schwalm MP, Saxena K, Müller S, Knapp S. Luciferase- and HaloTag-based reporter assays to measure small-molecule-induced degradation pathway in living cells. Nat Protoc 2024; 19:2317-2357. [PMID: 38637703 DOI: 10.1038/s41596-024-00979-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 01/31/2024] [Indexed: 04/20/2024]
Abstract
The rational development of small-molecule degraders (e.g., proteolysis targeting chimeras) remains a challenge as the rate-limiting steps that determine degrader efficiency are largely unknown. Standard methods in the field of targeted protein degradation mostly rely on classical, low-throughput endpoint assays such as western blots or quantitative proteomics. Here we applied NanoLuciferase- and HaloTag-based screening technologies to determine the kinetics and stability of small-molecule-induced ternary complex formation between a protein of interest and a selected E3 ligase. A collection of live-cell assays were designed to probe the most critical steps of the degradation process while minimizing the number of required expression constructs, making the proposed assay pipeline flexible and adaptable to the requirements of the users. This approach evaluates the underlying mechanism of selective target degraders and reveals the exact characteristics of the developed degrader molecules in living cells. The protocol allows scientists trained in basic cell culture and molecular biology to carry out small-molecule proximity-inducer screening via tracking of the ternary complex formation within 2 weeks of establishment, while degrader screening using the HiBiT system requires a CRISPR-Cas9 engineered cell line whose generation can take up to 3 months. After cell-line generation, degrader screening and validation can be carried out in high-throughput manner within days.
Collapse
Affiliation(s)
- Martin P Schwalm
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany.
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Frankfurt am Main, Germany.
- German Cancer Consortium (DKTK)/German Cancer Research Center (DKFZ), DTKT Site Frankfurt-Mainz, Heidelberg, Germany.
| | - Krishna Saxena
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Frankfurt am Main, Germany
| | - Susanne Müller
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Frankfurt am Main, Germany
| | - Stefan Knapp
- Institute for Pharmaceutical Chemistry, Johann Wolfgang Goethe-University, Frankfurt am Main, Germany.
- Structural Genomics Consortium (SGC), Buchmann Institute for Life Sciences, Frankfurt am Main, Germany.
- German Cancer Consortium (DKTK)/German Cancer Research Center (DKFZ), DTKT Site Frankfurt-Mainz, Heidelberg, Germany.
| |
Collapse
|
8
|
Chen YF, Shen Y, Yan DF, Ghazala M, Scemama de Gialluly MA, Srinivasan R, Farrar AN, Friedrich RM, Adams DJ. Electrophile Determines Cellular Phenotypes among XPO1-Targeting Small Molecules. J Med Chem 2024; 67:12033-12054. [PMID: 39005064 DOI: 10.1021/acs.jmedchem.4c00754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Covalent drug discovery has experienced a renaissance, with numerous electrophilic small molecules recently gaining FDA approval. Many structurally diverse electrophilic small molecules target exportin-1 (XPO1/CRM1) at cysteine 528, including the selective inhibitor of nuclear export (SINE) selinexor, which was FDA-approved as an anticancer agent in 2019. Emerging evidence supports additional pharmacological classes of XPO1 modulators targeting Cys528, including the selective inhibitors of transcriptional activation (SITAs) and probes that induce rapid degradation of XPO1. Here, we analyzed structure-activity relationships across multiple structural series of XPO1 Cys528-targeting probes. We observe that the electrophilic moiety of Cys528-targeting small molecules plays a decisive role in the cellular behavior observed, with subtle changes in electrophile structure being sufficient to convert XPO1-targeting probes to different pharmacological classes. This investigation represents a unique case study in which the electrophile functionality used to target a specific cysteine determines the pharmacological effect among diverse XPO1-targeting small molecules.
Collapse
Affiliation(s)
- Yi Fan Chen
- Department of Genetics and Genome Sciences and Chemical Biology Program, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, United States
| | - Yanqiu Shen
- Department of Genetics and Genome Sciences and Chemical Biology Program, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, United States
| | - David F Yan
- Department of Genetics and Genome Sciences and Chemical Biology Program, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, United States
| | - Maryam Ghazala
- Department of Genetics and Genome Sciences and Chemical Biology Program, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, United States
| | - Marc A Scemama de Gialluly
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, United States
| | - Ramya Srinivasan
- Department of Genetics and Genome Sciences and Chemical Biology Program, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, United States
| | - Amanda N Farrar
- Department of Genetics and Genome Sciences and Chemical Biology Program, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, United States
| | - Ryan M Friedrich
- Department of Genetics and Genome Sciences and Chemical Biology Program, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, United States
| | - Drew J Adams
- Department of Genetics and Genome Sciences and Chemical Biology Program, Case Western Reserve University School of Medicine, Cleveland, Ohio 44106, United States
| |
Collapse
|
9
|
Xiao Y, Yuan Y, Liu Y, Lin Z, Zheng G, Zhou D, Lv D. Targeted Protein Degradation: Current and Emerging Approaches for E3 Ligase Deconvolution. J Med Chem 2024; 67:11580-11596. [PMID: 38981094 DOI: 10.1021/acs.jmedchem.4c00723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
Targeted protein degradation (TPD), including the use of proteolysis-targeting chimeras (PROTACs) and molecular glue degraders (MGDs) to degrade proteins, is an emerging strategy to develop novel therapies for cancer and beyond. PROTACs or MGDs function by inducing the proximity between an E3 ligase and a protein of interest (POI), leading to ubiquitination and consequent proteasomal degradation of the POI. Notably, one major issue in TPD is the lack of ligandable E3 ligases, as current studies predominantly use CUL4CRBN and CUL2VHL. The TPD community is seeking to expand the landscape of ligandable E3 ligases, but most discoveries rely on phenotypic screens or serendipity, necessitating systematic target deconvolution. Here, we examine and discuss both current and emerging E3 ligase deconvolution approaches for degraders discovered from phenotypic screens or monovalent glue chemistry campaigns, highlighting future prospects for identifying more ligandable E3 ligases.
Collapse
Affiliation(s)
- Yufeng Xiao
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, Florida 32610, United States
| | - Yaxia Yuan
- Department of Biochemistry and Structural Biology and Center for Innovative Drug Discovery, School of Medicine, University of Texas Health San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
- Mays Cancer Center, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
| | - Yi Liu
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, Florida 32610, United States
| | - Zongtao Lin
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St. Louis, Missouri 63110, United States
| | - Guangrong Zheng
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, Florida 32610, United States
| | - Daohong Zhou
- Department of Biochemistry and Structural Biology and Center for Innovative Drug Discovery, School of Medicine, University of Texas Health San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
- Mays Cancer Center, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
| | - Dongwen Lv
- Department of Biochemistry and Structural Biology and Center for Innovative Drug Discovery, School of Medicine, University of Texas Health San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
- Mays Cancer Center, University of Texas Health Science Center at San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States
| |
Collapse
|
10
|
Vetma V, Perez LC, Eliaš J, Stingu A, Kombara A, Gmaschitz T, Braun N, Ciftci T, Dahmann G, Diers E, Gerstberger T, Greb P, Kidd G, Kofink C, Puoti I, Spiteri V, Trainor N, Weinstabl H, Westermaier Y, Whitworth C, Ciulli A, Farnaby W, McAulay K, Frost AB, Chessum N, Koegl M. Confounding Factors in Targeted Degradation of Short-Lived Proteins. ACS Chem Biol 2024; 19:1484-1494. [PMID: 38958654 DOI: 10.1021/acschembio.4c00152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
Targeted protein degradation has recently emerged as a novel option in drug discovery. Natural protein half-life is expected to affect the efficacy of degrading agents, but to what extent it influences target protein degradation has not been systematically explored. Using simple mathematical modeling of protein degradation, we find that the natural half-life of a target protein has a dramatic effect on the level of protein degradation induced by a degrader agent which can pose significant hurdles to screening efforts. Moreover, we show that upon screening for degraders of short-lived proteins, agents that stall protein synthesis, such as GSPT1 degraders and generally cytotoxic compounds, deceptively appear as protein-degrading agents. This is exemplified by the disappearance of short-lived proteins such as MCL1 and MDM2 upon GSPT1 degradation and upon treatment with cytotoxic agents such as doxorubicin. These findings have implications for target selection as well as for the type of control experiments required to conclude that a novel agent works as a bona fide targeted protein degrader.
Collapse
Affiliation(s)
- Vesna Vetma
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ Dundee, Scotland, U.K
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dow Street, DD1 5EH Dundee, Scotland, U.K
| | - Laura Casares Perez
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ Dundee, Scotland, U.K
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dow Street, DD1 5EH Dundee, Scotland, U.K
| | - Ján Eliaš
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | - Andrea Stingu
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | - Anju Kombara
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | | | - Nina Braun
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | - Tuncay Ciftci
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | - Georg Dahmann
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | - Emelyne Diers
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dow Street, DD1 5EH Dundee, Scotland, U.K
| | | | - Peter Greb
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | - Giorgia Kidd
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ Dundee, Scotland, U.K
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dow Street, DD1 5EH Dundee, Scotland, U.K
| | | | - Ilaria Puoti
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ Dundee, Scotland, U.K
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dow Street, DD1 5EH Dundee, Scotland, U.K
| | - Valentina Spiteri
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ Dundee, Scotland, U.K
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dow Street, DD1 5EH Dundee, Scotland, U.K
| | - Nicole Trainor
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dow Street, DD1 5EH Dundee, Scotland, U.K
| | | | | | - Claire Whitworth
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dow Street, DD1 5EH Dundee, Scotland, U.K
| | - Alessio Ciulli
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ Dundee, Scotland, U.K
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dow Street, DD1 5EH Dundee, Scotland, U.K
| | - William Farnaby
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ Dundee, Scotland, U.K
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dow Street, DD1 5EH Dundee, Scotland, U.K
| | - Kirsten McAulay
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ Dundee, Scotland, U.K
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dow Street, DD1 5EH Dundee, Scotland, U.K
| | - Aileen B Frost
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ Dundee, Scotland, U.K
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dow Street, DD1 5EH Dundee, Scotland, U.K
| | - Nicola Chessum
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | - Manfred Koegl
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| |
Collapse
|
11
|
Chen YF, Rahman A, Sax JL, Atala Pleshinger MJ, Friedrich RM, Adams DJ. C646 degrades Exportin-1 to modulate p300 chromatin occupancy and function. Cell Chem Biol 2024; 31:1363-1372.e8. [PMID: 38917791 PMCID: PMC11268802 DOI: 10.1016/j.chembiol.2024.05.016] [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: 11/10/2023] [Revised: 03/13/2024] [Accepted: 05/28/2024] [Indexed: 06/27/2024]
Abstract
Molecular glues can induce proximity between a target protein and ubiquitin ligases to induce target degradation, but strategies for their discovery remain limited. We screened 3,200 bioactive small molecules and identified that C646 requires neddylation-dependent protein degradation to induce cytotoxicity. Although the histone acetyltransferase p300 is the canonical target of C646, we provide extensive evidence that C646 directly targets and degrades Exportin-1 (XPO1). Multiple cellular phenotypes induced by C646 were abrogated in cells expressing the known XPO1C528S drug-resistance allele. While XPO1 catalyzes nuclear-to-cytoplasmic transport of many cargo proteins, it also directly binds chromatin. We demonstrate that p300 and XPO1 co-occupy hundreds of chromatin loci. Degrading XPO1 using C646 or the known XPO1 modulator S109 diminishes the chromatin occupancy of both XPO1 and p300, enabling direct targeting of XPO1 to phenocopy p300 inhibition. This work highlights the utility of drug-resistant alleles and further validates XPO1 as a targetable regulator of chromatin state.
Collapse
Affiliation(s)
- Yi Fan Chen
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Chemical Biology Program, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Atikur Rahman
- Chemical Biology Program, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Joel L Sax
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Chemical Biology Program, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Matthew J Atala Pleshinger
- Chemical Biology Program, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Ryan M Friedrich
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Chemical Biology Program, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA
| | - Drew J Adams
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Chemical Biology Program, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA.
| |
Collapse
|
12
|
Tin G, Cigler M, Hinterndorfer M, Dong KD, Imrichova H, Gygi SP, Winter GE. Discovery of a DCAF11-dependent cyanoacrylamide-containing covalent degrader of BET-proteins. Bioorg Med Chem Lett 2024; 107:129779. [PMID: 38729317 DOI: 10.1016/j.bmcl.2024.129779] [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: 01/18/2024] [Revised: 04/08/2024] [Accepted: 04/29/2024] [Indexed: 05/12/2024]
Abstract
Targeted protein degradation is mediated by small molecules that induce or stabilize protein-protein interactions between targets and the ubiquitin-proteasome machinery. Currently, there remains a need to expand the repertoire of viable E3 ligases available for hijacking. Notably, covalent chemistry has been employed to engage a handful of E3 ligases, including DCAF11. Here, we disclose a covalent PROTAC that enables DCAF11-dependent degradation, featuring a cyanoacrylamide warhead. Our findings underscore DCAF11 as an interesting candidate with a capacity to accommodate diverse electrophilic chemistries compatible with targeted protein degradation.
Collapse
Affiliation(s)
- Gary Tin
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Marko Cigler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
| | - Matthias Hinterndorfer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Kevin D Dong
- Department of Cell Biology, Harvard Medical School, Boston, USA
| | - Hana Imrichova
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, USA
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
| |
Collapse
|
13
|
Chang X, Qu F, Li C, Zhang J, Zhang Y, Xie Y, Fan Z, Bian J, Wang J, Li Z, Xu X. Development and therapeutic potential of GSPT1 molecular glue degraders: A medicinal chemistry perspective. Med Res Rev 2024; 44:1727-1767. [PMID: 38314926 DOI: 10.1002/med.22024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 12/18/2023] [Accepted: 01/21/2024] [Indexed: 02/07/2024]
Abstract
Unprecedented therapeutic targeting of previously undruggable proteins has now been achieved by molecular-glue-mediated proximity-induced degradation. As a small GTPase, G1 to S phase transition 1 (GSPT1) interacts with eRF1, the translation termination factor, to facilitate the process of translation termination. Studied demonstrated that GSPT1 plays a vital role in the acute myeloid leukemia (AML) and MYC-driven lung cancer. Thus, molecular glue (MG) degraders targeting GSPT1 is a novel and promising approach for treating AML and MYC-driven cancers. In this Perspective, we briefly summarize the structural and functional aspects of GSPT1, highlighting the latest advances and challenges in MG degraders, as well as some representative patents. The structure-activity relationships, mechanism of action and pharmacokinetic features of MG degraders are emphasized to provide a comprehensive compendium on the rational design of GSPT1 MG degraders. We hope to provide an updated overview, and design guide for strategies targeting GSPT1 for the treatment of cancer.
Collapse
Affiliation(s)
- Xiujin Chang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Fangui Qu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Chunxiao Li
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Jingtian Zhang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Yanqing Zhang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Yuanyuan Xie
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Zhongpeng Fan
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Jinlei Bian
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Jubo Wang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Zhiyu Li
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| | - Xi Xu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, China
| |
Collapse
|
14
|
Li Z, Wang Z, Zhong C, Zhang H, Liu R, An P, Ma Z, Lu J, Pan C, Zhang Z, Cao Z, Hu J, Xing D, Fei Y, Ding Y, Lu B. P53 upregulation by USP7-engaging molecular glues. Sci Bull (Beijing) 2024; 69:1936-1953. [PMID: 38734583 DOI: 10.1016/j.scib.2024.04.017] [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: 08/07/2023] [Revised: 02/01/2024] [Accepted: 02/19/2024] [Indexed: 05/13/2024]
Abstract
Molecular glues are typically small chemical molecules that act at the interface between a target protein and degradation machinery to trigger ternary complex formation. Identifying molecular glues is challenging. There is a scarcity of target-specific upregulating molecular glues, which are highly anticipated for numerous targets, including P53. P53 is degraded in proteasomes through polyubiquitination by specific E3 ligases, whereas deubiquitinases (DUBs) remove polyubiquitination conjugates to counteract these E3 ligases. Thus, small-molecular glues that enhance P53 anchoring to DUBs may stabilize P53 through deubiquitination. Here, using small-molecule microarray-based technology and unbiased screening, we identified three potential molecular glues that may tether P53 to the DUB, USP7, and elevate the P53 level. Among the molecular glues, bromocriptine (BC) is an FDA-approved drug with the most robust effects. BC was further verified to increase P53 stability via the predicted molecular glue mechanism engaging USP7. Consistent with P53 upregulation in cancer cells, BC was shown to inhibit the proliferation of cancer cells in vitro and suppress tumor growth in a xenograft model. In summary, we established a potential screening platform and identified potential molecular glues upregulating P53. Similar strategies could be applied to the identification of other types of molecular glues that may benefit drug discovery and chemical biology studies.
Collapse
Affiliation(s)
- Zhaoyang Li
- The State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Huashan Hospital, the Institutes of Brain Science, School of Life Sciences, Fudan University, Shanghai 200438, China.
| | - Ziying Wang
- The State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Huashan Hospital, the Institutes of Brain Science, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Chao Zhong
- The State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Huashan Hospital, the Institutes of Brain Science, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Hang Zhang
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Fudan University, Shanghai 200438, China
| | - Rui Liu
- The State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Huashan Hospital, the Institutes of Brain Science, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ping An
- The State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Huashan Hospital, the Institutes of Brain Science, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Zhiqiang Ma
- The State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Huashan Hospital, the Institutes of Brain Science, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Junmei Lu
- The State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Huashan Hospital, the Institutes of Brain Science, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Chengfang Pan
- The State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Huashan Hospital, the Institutes of Brain Science, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Zhaolin Zhang
- The State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Huashan Hospital, the Institutes of Brain Science, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Zhiyuan Cao
- The State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Huashan Hospital, the Institutes of Brain Science, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jianyi Hu
- The State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Huashan Hospital, the Institutes of Brain Science, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Dong Xing
- Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China
| | - Yiyan Fei
- Department of Optical Science and Engineering, Shanghai Engineering Research Center of Ultra-Precision Optical Manufacturing, Key Laboratory of Micro and Nano Photonic Structures (Ministry of Education), Fudan University, Shanghai 200438, China.
| | - Yu Ding
- The State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Huashan Hospital, the Institutes of Brain Science, School of Life Sciences, Fudan University, Shanghai 200438, China.
| | - Boxun Lu
- The State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Huashan Hospital, the Institutes of Brain Science, School of Life Sciences, Fudan University, Shanghai 200438, China.
| |
Collapse
|
15
|
Robinson SA, Co JA, Banik SM. Molecular glues and induced proximity: An evolution of tools and discovery. Cell Chem Biol 2024; 31:1089-1100. [PMID: 38688281 DOI: 10.1016/j.chembiol.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 01/23/2024] [Accepted: 04/02/2024] [Indexed: 05/02/2024]
Abstract
Small molecule molecular glues can nucleate protein complexes and rewire interactomes. Molecular glues are widely used as probes for understanding functional proximity at a systems level, and the potential to instigate event-driven pharmacology has motivated their application as therapeutics. Despite advantages such as cell permeability and the potential for low off-target activity, glues are still rare when compared to canonical inhibitors in therapeutic development. Their often simple structure and specific ability to reshape protein-protein interactions pose several challenges for widespread, designer applications. Molecular glue discovery and design campaigns can find inspiration from the fields of synthetic biology and biophysics to mine chemical libraries for glue-like molecules.
Collapse
Affiliation(s)
| | | | - Steven Mark Banik
- Department of Chemistry, Stanford University, Stanford, CA, USA; Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
| |
Collapse
|
16
|
Konstantinidou M, Arkin MR. Molecular glues for protein-protein interactions: Progressing toward a new dream. Cell Chem Biol 2024; 31:1064-1088. [PMID: 38701786 PMCID: PMC11193649 DOI: 10.1016/j.chembiol.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/08/2024] [Accepted: 04/08/2024] [Indexed: 05/05/2024]
Abstract
The modulation of protein-protein interactions with small molecules is one of the most rapidly developing areas in drug discovery. In this review, we discuss advances over the past decade (2014-2023) focusing on molecular glues (MGs)-monovalent small molecules that induce proximity, either by stabilizing native interactions or by inducing neomorphic interactions. We include both serendipitous and rational discoveries and describe the different approaches that were used to identify them. We classify the compounds in three main categories: degradative MGs, non-degradative MGs or PPI stabilizers, and MGs that induce self-association. Diverse, illustrative examples with structural data are described in detail, emphasizing the elements of molecular recognition and cooperative binding at the interface that are fundamental for a MG mechanism of action.
Collapse
Affiliation(s)
- Markella Konstantinidou
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco, San Francisco, CA 94143, USA
| | - Michelle R Arkin
- Department of Pharmaceutical Chemistry and Small Molecule Discovery Center (SMDC), University of California, San Francisco, San Francisco, CA 94143, USA.
| |
Collapse
|
17
|
Huang X, Wu F, Ye J, Wang L, Wang X, Li X, He G. Expanding the horizons of targeted protein degradation: A non-small molecule perspective. Acta Pharm Sin B 2024; 14:2402-2427. [PMID: 38828146 PMCID: PMC11143490 DOI: 10.1016/j.apsb.2024.01.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/22/2023] [Accepted: 01/16/2024] [Indexed: 06/05/2024] Open
Abstract
Targeted protein degradation (TPD) represented by proteolysis targeting chimeras (PROTACs) marks a significant stride in drug discovery. A plethora of innovative technologies inspired by PROTAC have not only revolutionized the landscape of TPD but have the potential to unlock functionalities beyond degradation. Non-small-molecule-based approaches play an irreplaceable role in this field. A wide variety of agents spanning a broad chemical spectrum, including peptides, nucleic acids, antibodies, and even vaccines, which not only prove instrumental in overcoming the constraints of conventional small molecule entities but also provided rapidly renewing paradigms. Herein we summarize the burgeoning non-small molecule technological platforms inspired by PROTACs, including three major trajectories, to provide insights for the design strategies based on novel paradigms.
Collapse
Affiliation(s)
- Xiaowei Huang
- Department of Pharmacy and Department of Dermatology & Venerology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Fengbo Wu
- Department of Pharmacy and Department of Dermatology & Venerology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Jing Ye
- Department of Pharmacy and Department of Dermatology & Venerology, West China Hospital, Sichuan University, Chengdu 610041, China
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology, Frontiers Science Center for Disease-Related Molecular Network and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Lian Wang
- Department of Pharmacy and Department of Dermatology & Venerology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xiaoyun Wang
- Department of Pharmacy and Department of Dermatology & Venerology, West China Hospital, Sichuan University, Chengdu 610041, China
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology, Frontiers Science Center for Disease-Related Molecular Network and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xiang Li
- Department of Urology, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Gu He
- Department of Pharmacy and Department of Dermatology & Venerology, West China Hospital, Sichuan University, Chengdu 610041, China
- Laboratory of Dermatology, Clinical Institute of Inflammation and Immunology, Frontiers Science Center for Disease-Related Molecular Network and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 610041, China
| |
Collapse
|
18
|
Stevens R, Thompson JDF, Fournier JCL, Burley GA, Battersby DJ, Miah AH. Innovative, combinatorial and high-throughput approaches to degrader synthesis. Chem Soc Rev 2024; 53:4838-4861. [PMID: 38596888 DOI: 10.1039/d3cs01127e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Targeted protein degraders such as PROTACs and molecular glues are a rapidly emerging therapeutic modality within industry and academia. Degraders possess unique mechanisms of action that lead to the removal of specific proteins by co-opting the cell's natural degradation mechanisms via induced proximity. Their optimisation thus far has often been largely empirical, requiring the synthesis and screening of a large number of analogues. In addition, the synthesis and development of degraders is often challenging, leading to lengthy optimisation campaigns to deliver candidate-quality compounds. This review highlights how the synthesis of degraders has evolved in recent years, in particular focusing on means of applying high-throughput chemistry and screening approaches to expedite these timelines, which we anticipate to be valuable in shaping the future of degrader optimisation campaigns.
Collapse
Affiliation(s)
- Rebecca Stevens
- Medicinal Chemistry, GSK, Stevenage, SG1 2NY, UK.
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, G1 1XQ, UK
| | | | | | - Glenn A Burley
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, G1 1XQ, UK
| | | | - Afjal H Miah
- Medicinal Chemistry, GSK, Stevenage, SG1 2NY, UK.
| |
Collapse
|
19
|
Haridas V, Dutta S, Munjal A, Singh S. Inhibitors to degraders: Changing paradigm in drug discovery. iScience 2024; 27:109574. [PMID: 38646175 PMCID: PMC11031827 DOI: 10.1016/j.isci.2024.109574] [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] [Indexed: 04/23/2024] Open
Abstract
The chemical understanding of biological processes provides not only a deeper insight but also a solution to abnormal biological functioning. Protein degradation, a natural biological process for debris removal in the cell, has been studied for years. The recent finding that natural degradation pathways can be utilized for therapeutic purposes is a paradigm shift in the drug discovery approach. Methods such as Proteolysis Targeting Chimera (PROTAC), lysosomal targeting chimera, hydrophobic tagging, AUtophagy TArgeting Chimera, AUTOphagy TArgeting Chimera and several other variants of these methods have made a considerable impact on the way of drug design. Few selected examples testify that a huge wave of change is on the way. The drug design based on the targeted protein degradation is a powerful tool in our arsenal. More molecules will be invented that will uncover the hidden secrets of biological functioning and provide enduring solutions to several unmet medical needs.
Collapse
Affiliation(s)
- V. Haridas
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
- Department of Chemistry, Indian Institute of Technology Palakkad, Palakkad, Kerala 678623, India
| | - Souvik Dutta
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Akshay Munjal
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, New Delhi 110067, India
| | - Shailja Singh
- Special Centre for Molecular Medicine, Jawaharlal Nehru University, New Delhi, New Delhi 110067, India
| |
Collapse
|
20
|
Sun Y, Wang H, Li Y, Li Z, Mao Z, Zhang M, Shao Y, Ye J, Li D, Shan L. The design, synthesis and bioactivity evaluation of novel androgen receptor degraders based on hydrophobic tagging. Bioorg Chem 2024; 146:107309. [PMID: 38537338 DOI: 10.1016/j.bioorg.2024.107309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/11/2024] [Accepted: 03/22/2024] [Indexed: 04/13/2024]
Abstract
Prostate Cancer (PCa) easily progress to metastatic Castration-Resistant Prostate Cancer (mCRPC) that remains a significant cause of cancer-related death. Androgen receptor (AR)-dependent transcription is a major driver of prostate tumor cell proliferation. Proteolysis-targeting chimaera (PROTAC) technology based on Hydrophobic Tagging (HyT) represents an intriguing strategy to regulate the function of therapeutically androgen receptor proteins. In the present study, we have designed, synthesized, and evaluated a series of PROTAC-HyT AR degraders using AR antagonists, RU59063, which were connected with adamantane-based hydrophobic moieties by different alkyl chains. Compound D-4-6 exhibited significant AR protein degradation activity, with a degradation rate of 57 % at 5 μM and nearly 90 % at 20 μM in 24 h, and inhibited the proliferation of LNCaP cells significantly with an IC50 value of 4.77 ± 0.26 μM in a time-concentration-dependent manner. In conclusion, the present study lays the foundation for the development of a completely new class of therapeutic agents for the treatment of mCRPC, and further design and synthesis of AR-targeting degraders are currently in progress for better degradation rate.
Collapse
Affiliation(s)
- Ying Sun
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Huating Wang
- Key Laboratory of Advanced Drug Delivery Systems of Zhejiang Province, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yaru Li
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Zhaoxiang Li
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Zhihui Mao
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Mengyao Zhang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Yixian Shao
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Jiaqi Ye
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Dan Li
- Key Laboratory of Advanced Drug Delivery Systems of Zhejiang Province, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China; Jinhua Institute of Zhejiang University, Jinhua 321000, Zhejiang, China.
| | - Lihong Shan
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China; Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education of China, Zhengzhou 450001, China.
| |
Collapse
|
21
|
Ito T. Protein degraders - from thalidomide to new PROTACs. J Biochem 2024; 175:507-519. [PMID: 38140952 DOI: 10.1093/jb/mvad113] [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: 11/15/2023] [Revised: 12/07/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Recently, the development of protein degraders (protein-degrading compounds) has prominently progressed. There are two remarkable classes of protein degraders: proteolysis-targeting chimeras (PROTACs) and molecular glue degraders (MGDs). Almost 70 years have passed since thalidomide was initially developed as a sedative-hypnotic drug, which is currently recognized as one of the most well-known MGDs. During the last two decades, a myriad of PROTACs and MGDs have been developed, and the molecular mechanism of action (MOA) of thalidomide was basically elucidated, including identifying its molecular target cereblon (CRBN). CRBN forms a Cullin Ring Ligase 4 with Cul4 and DDB1, whose substrate specificity is controlled by its binding ligands. Thalidomide, lenalidomide and pomalidomide, three CRBN-binding MGDs, were clinically approved to treat several intractable diseases (including multiple myeloma). Several other MGDs and CRBN-based PROTACs (ARV-110 and AVR-471) are undergoing clinical trials. In addition, several new related technologies regarding PROTACs and MGDs have also been developed, and achievements of protein degraders impact not only therapeutic fields but also basic biological science. In this article, I introduce the history of protein degraders, from the development of thalidomide to the latest PROTACs and related technologies.
Collapse
Affiliation(s)
- Takumi Ito
- Institute of Medical Science, Tokyo Medical University, 6-1-1, Shinjuku, Shinjuku-ku, Tokyo 160-8402, Japan
| |
Collapse
|
22
|
An J, Zhang X. Crbn-based molecular Glues: Breakthroughs and perspectives. Bioorg Med Chem 2024; 104:117683. [PMID: 38552596 DOI: 10.1016/j.bmc.2024.117683] [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: 12/11/2023] [Revised: 03/12/2024] [Accepted: 03/13/2024] [Indexed: 04/20/2024]
Abstract
CRBN is a substrate receptor for the Cullin Ring E3 ubiquitin ligase 4 (CRL4) complex. It has been observed that CRBN can be exploited by small molecules to facilitate the recruitment and ubiquitination of non-natural CRL4 substrates, resulting in the degradation of neosubstrate through the ubiquitin-proteasome system. This phenomenon, known as molecular glue-induced protein degradation, has emerged as an innovative therapeutic approach in contrast to traditional small-molecule drugs. One key advantage of molecular glues, in comparison to conventional small-molecule drugs adhering to Lipinski's Rule of Five, is their ability to operate without the necessity for specific binding pockets on target proteins. This unique characteristic empowers molecular glues to interact with conventionally intractable protein targets, such as transcription factors and scaffold proteins. The ability to induce the degradation of these previously elusive targets by hijacking the ubiquitin-proteasome system presents a promising avenue for the treatment of recalcitrant diseases. Nevertheless, the rational design of molecular glues remains a formidable challenge due to the limited understanding of their mechanisms and actions. This review offers an overview of recent advances and breakthroughs in the field of CRBN-based molecular glues, while also exploring the prospects for a systematic approach to designing these compounds.
Collapse
Affiliation(s)
- Juzeng An
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
| | | |
Collapse
|
23
|
Kim J, Byun I, Kim DY, Joh H, Kim HJ, Lee MJ. Targeted protein degradation directly engaging lysosomes or proteasomes. Chem Soc Rev 2024; 53:3253-3272. [PMID: 38369971 DOI: 10.1039/d3cs00344b] [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: 02/20/2024]
Abstract
Targeted protein degradation (TPD) has been established as a viable alternative to attenuate the function of a specific protein of interest in both biological and clinical contexts. The unique TPD mode-of-action has allowed previously undruggable proteins to become feasible targets, expanding the landscape of "druggable" properties and "privileged" target proteins. As TPD continues to evolve, a range of innovative strategies, which do not depend on recruiting E3 ubiquitin ligases as in proteolysis-targeting chimeras (PROTACs), have emerged. Here, we present an overview of direct lysosome- and proteasome-engaging modalities and discuss their perspectives, advantages, and limitations. We outline the chemical composition, biochemical activity, and pharmaceutical characteristics of each degrader. These alternative TPD approaches not only complement the first generation of PROTACs for intracellular protein degradation but also offer unique strategies for targeting pathologic proteins located on the cell membrane and in the extracellular space.
Collapse
Affiliation(s)
- Jiseong Kim
- Department of Biochemistry & Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea.
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea
| | - Insuk Byun
- Department of Biochemistry & Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea.
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea
| | - Do Young Kim
- Department of Chemistry, College of Science, Korea University, Seoul 02841, Korea.
| | - Hyunhi Joh
- Department of Chemistry, College of Science, Korea University, Seoul 02841, Korea.
| | - Hak Joong Kim
- Department of Chemistry, College of Science, Korea University, Seoul 02841, Korea.
| | - Min Jae Lee
- Department of Biochemistry & Molecular Biology, Seoul National University College of Medicine, Seoul 03080, Korea.
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul 03080, Korea
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| |
Collapse
|
24
|
Poirson J, Cho H, Dhillon A, Haider S, Imrit AZ, Lam MHY, Alerasool N, Lacoste J, Mizan L, Wong C, Gingras AC, Schramek D, Taipale M. Proteome-scale discovery of protein degradation and stabilization effectors. Nature 2024; 628:878-886. [PMID: 38509365 DOI: 10.1038/s41586-024-07224-3] [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: 10/25/2022] [Accepted: 02/22/2024] [Indexed: 03/22/2024]
Abstract
Targeted protein degradation and stabilization are promising therapeutic modalities because of their potency, versatility and their potential to expand the druggable target space1,2. However, only a few of the hundreds of E3 ligases and deubiquitinases in the human proteome have been harnessed for this purpose, which substantially limits the potential of the approach. Moreover, there may be other protein classes that could be exploited for protein stabilization or degradation3-5, but there are currently no methods that can identify such effector proteins in a scalable and unbiased manner. Here we established a synthetic proteome-scale platform to functionally identify human proteins that can promote the degradation or stabilization of a target protein in a proximity-dependent manner. Our results reveal that the human proteome contains a large cache of effectors of protein stability. The approach further enabled us to comprehensively compare the activities of human E3 ligases and deubiquitinases, identify and characterize non-canonical protein degraders and stabilizers and establish that effectors have vastly different activities against diverse targets. Notably, the top degraders were more potent against multiple therapeutically relevant targets than the currently used E3 ligases cereblon and VHL. Our study provides a functional catalogue of stability effectors for targeted protein degradation and stabilization and highlights the potential of induced proximity screens for the discovery of new proximity-dependent protein modulators.
Collapse
Affiliation(s)
- Juline Poirson
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Hanna Cho
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Akashdeep Dhillon
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Shahan Haider
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Ahmad Zoheyr Imrit
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Mandy Hiu Yi Lam
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Nader Alerasool
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Jessica Lacoste
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Lamisa Mizan
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Cassandra Wong
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Daniel Schramek
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Mikko Taipale
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
| |
Collapse
|
25
|
Barbosa BMG, Sfyaki A, Rafael S, José-Duran F, Pous J, Sánchez-Zarzalejo C, Perez-Lopez C, Vilanova M, Cigler M, Gay M, Vilaseca M, Winter GE, Riera A, Mayor-Ruiz C. Discovery and Mechanistic Elucidation of NQO1-Bioactivatable Small Molecules That Overcome Resistance to Degraders. Angew Chem Int Ed Engl 2024; 63:e202316730. [PMID: 38153885 DOI: 10.1002/anie.202316730] [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: 11/05/2023] [Revised: 12/21/2023] [Accepted: 12/28/2023] [Indexed: 12/30/2023]
Abstract
Degraders hold the promise to efficiently inactivate previously intractable disease-relevant targets. Unlike traditional inhibitors, degraders act substoichiometrically and rely on the hijacked proteolysis machinery, which can also act as an entry point for resistance. To fully harness the potential of targeted protein degradation, it is crucial to comprehend resistance mechanisms and formulate effective strategies to overcome them. We conducted a chemical screening to identify synthetic lethal vulnerabilities of cancer cells that exhibit widespread resistance to degraders. Comparative profiling followed by tailored optimization delivered the small molecule RBS-10, which shows preferential cytotoxicity against cells pan-resistant to degraders. Multiomics deconvolution of the mechanism of action revealed that RBS-10 acts as a prodrug bioactivated by the oxidoreductase enzyme NQO1, which is highly overexpressed in our resistance models. Collectively, our work informs on NQO1 as an actionable vulnerability to overcome resistance to degraders and as a biomarker to selectively exploit bioactivatable prodrugs in cancer.
Collapse
Affiliation(s)
- Bárbara M G Barbosa
- Institute for Research in Biomedicine (IRB Barcelona), the, Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
| | - Aikaterini Sfyaki
- Institute for Research in Biomedicine (IRB Barcelona), the, Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
| | - Sergi Rafael
- Institute for Research in Biomedicine (IRB Barcelona), the, Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
| | - Ferran José-Duran
- Institute for Research in Biomedicine (IRB Barcelona), the, Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
| | - Joan Pous
- Institute for Research in Biomedicine (IRB Barcelona), the, Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
| | - Carolina Sánchez-Zarzalejo
- Institute for Research in Biomedicine (IRB Barcelona), the, Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
| | - Carles Perez-Lopez
- Institute for Research in Biomedicine (IRB Barcelona), the, Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
| | - Mar Vilanova
- Institute for Research in Biomedicine (IRB Barcelona), the, Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
| | - Marko Cigler
- Research Center for Molecular Medicine of the Austrian Academy of Sciences (CeMM), 1090, Vienna, Austria
| | - Marina Gay
- Institute for Research in Biomedicine (IRB Barcelona), the, Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
| | - Marta Vilaseca
- Institute for Research in Biomedicine (IRB Barcelona), the, Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
| | - Georg E Winter
- Research Center for Molecular Medicine of the Austrian Academy of Sciences (CeMM), 1090, Vienna, Austria
| | - Antoni Riera
- Institute for Research in Biomedicine (IRB Barcelona), the, Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
- Departament de Química Inorgànica i Orgànica, Secció Química Orgànica, Universitat de Barcelona, Martí i Franquès 1, 08028, Barcelona, Spain
| | - Cristina Mayor-Ruiz
- Institute for Research in Biomedicine (IRB Barcelona), the, Barcelona Institute of Science and Technology (BIST), 08028, Barcelona, Spain
| |
Collapse
|
26
|
Bertran-Mostazo A, Putriūtė G, Álvarez-Berbel I, Busquets MA, Galdeano C, Espargaró A, Sabate R. Proximity-Induced Pharmacology for Amyloid-Related Diseases. Cells 2024; 13:449. [PMID: 38474412 DOI: 10.3390/cells13050449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 02/19/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
Proximity-induced pharmacology (PIP) for amyloid-related diseases is a cutting-edge approach to treating conditions such as Alzheimer's disease and other forms of dementia. By bringing small molecules close to amyloid-related proteins, these molecules can induce a plethora of effects that can break down pathogenic proteins and reduce the buildup of plaques. One of the most promising aspects of this drug discovery modality is that it can be used to target specific types of amyloid proteins, such as the beta-amyloid protein that is commonly associated with Alzheimer's disease. This level of specificity could allow for more targeted and effective treatments. With ongoing research and development, it is hoped that these treatments can be refined and optimized to provide even greater benefits to patients. As our understanding of the underlying mechanisms of these diseases continues to grow, proximity-induced pharmacology treatments may become an increasingly important tool in the fight against dementia and other related conditions.
Collapse
Affiliation(s)
- Andrea Bertran-Mostazo
- Department of Pharmacy and Pharmaceutical Technology and Physical-Chemistry, School of Pharmacy, University of Barcelona, 08028 Barcelona, Spain
- Institute of Biomedicine (IBUB), University of Barcelona, 08028 Barcelona, Spain
| | - Gabrielė Putriūtė
- Department of Pharmacy and Pharmaceutical Technology and Physical-Chemistry, School of Pharmacy, University of Barcelona, 08028 Barcelona, Spain
| | - Irene Álvarez-Berbel
- Department of Pharmacy and Pharmaceutical Technology and Physical-Chemistry, School of Pharmacy, University of Barcelona, 08028 Barcelona, Spain
| | - Maria Antònia Busquets
- Department of Pharmacy and Pharmaceutical Technology and Physical-Chemistry, School of Pharmacy, University of Barcelona, 08028 Barcelona, Spain
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, 08028 Barcelona, Spain
| | - Carles Galdeano
- Department of Pharmacy and Pharmaceutical Technology and Physical-Chemistry, School of Pharmacy, University of Barcelona, 08028 Barcelona, Spain
- Institute of Biomedicine (IBUB), University of Barcelona, 08028 Barcelona, Spain
| | - Alba Espargaró
- Department of Pharmacy and Pharmaceutical Technology and Physical-Chemistry, School of Pharmacy, University of Barcelona, 08028 Barcelona, Spain
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, 08028 Barcelona, Spain
| | - Raimon Sabate
- Department of Pharmacy and Pharmaceutical Technology and Physical-Chemistry, School of Pharmacy, University of Barcelona, 08028 Barcelona, Spain
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, 08028 Barcelona, Spain
| |
Collapse
|
27
|
Holdgate GA, Bardelle C, Berry SK, Lanne A, Cuomo ME. Screening for molecular glues - Challenges and opportunities. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:100136. [PMID: 38104659 DOI: 10.1016/j.slasd.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/03/2023] [Accepted: 12/14/2023] [Indexed: 12/19/2023]
Abstract
Molecular glues are small molecules, typically smaller than PROTACs, and usually with improved physicochemical properties that aim to stabilise the interaction between two proteins. Most often this approach is used to improve or induce an interaction between the target and an E3 ligase, but other interactions which stabilise interactions to increase activity or to inhibit binding to a natural effector have also been demonstrated. This review will describe the effects of induced proximity, discuss current methods used to identify molecular glues and introduce approaches that could be adapted for molecular glue screening.
Collapse
Affiliation(s)
| | - Catherine Bardelle
- High-throughput Screening, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
| | - Sophia K Berry
- High-throughput Screening, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
| | - Alice Lanne
- High-throughput Screening, Discovery Sciences, R&D, AstraZeneca, Alderley Park, UK
| | | |
Collapse
|
28
|
Menendez JA, Cuyàs E, Encinar JA, Vander Steen T, Verdura S, Llop‐Hernández À, López J, Serrano‐Hervás E, Osuna S, Martin‐Castillo B, Lupu R. Fatty acid synthase (FASN) signalome: A molecular guide for precision oncology. Mol Oncol 2024; 18:479-516. [PMID: 38158755 PMCID: PMC10920094 DOI: 10.1002/1878-0261.13582] [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: 10/02/2023] [Revised: 10/27/2023] [Accepted: 12/28/2023] [Indexed: 01/03/2024] Open
Abstract
The initial excitement generated more than two decades ago by the discovery of drugs targeting fatty acid synthase (FASN)-catalyzed de novo lipogenesis for cancer therapy was short-lived. However, the advent of the first clinical-grade FASN inhibitor (TVB-2640; denifanstat), which is currently being studied in various phase II trials, and the exciting advances in understanding the FASN signalome are fueling a renewed interest in FASN-targeted strategies for the treatment and prevention of cancer. Here, we provide a detailed overview of how FASN can drive phenotypic plasticity and cell fate decisions, mitochondrial regulation of cell death, immune escape and organ-specific metastatic potential. We then present a variety of FASN-targeted therapeutic approaches that address the major challenges facing FASN therapy. These include limitations of current FASN inhibitors and the lack of precision tools to maximize the therapeutic potential of FASN inhibitors in the clinic. Rethinking the role of FASN as a signal transducer in cancer pathogenesis may provide molecularly driven strategies to optimize FASN as a long-awaited target for cancer therapeutics.
Collapse
Affiliation(s)
- Javier A. Menendez
- Metabolism & Cancer Group, Program Against Cancer Therapeutic Resistance (ProCURE)Catalan Institute of OncologyGironaSpain
- Girona Biomedical Research InstituteGironaSpain
| | - Elisabet Cuyàs
- Metabolism & Cancer Group, Program Against Cancer Therapeutic Resistance (ProCURE)Catalan Institute of OncologyGironaSpain
- Girona Biomedical Research InstituteGironaSpain
| | - Jose Antonio Encinar
- Institute of Research, Development and Innovation in Biotechnology of Elche (IDiBE) and Molecular and Cell Biology Institute (IBMC)Miguel Hernández University (UMH)ElcheSpain
| | - Travis Vander Steen
- Division of Experimental Pathology, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMNUSA
- Mayo Clinic Cancer CenterRochesterMNUSA
- Department of Biochemistry and Molecular Biology LaboratoryMayo Clinic LaboratoryRochesterMNUSA
| | - Sara Verdura
- Metabolism & Cancer Group, Program Against Cancer Therapeutic Resistance (ProCURE)Catalan Institute of OncologyGironaSpain
- Girona Biomedical Research InstituteGironaSpain
| | - Àngela Llop‐Hernández
- Metabolism & Cancer Group, Program Against Cancer Therapeutic Resistance (ProCURE)Catalan Institute of OncologyGironaSpain
- Girona Biomedical Research InstituteGironaSpain
| | - Júlia López
- Metabolism & Cancer Group, Program Against Cancer Therapeutic Resistance (ProCURE)Catalan Institute of OncologyGironaSpain
- Girona Biomedical Research InstituteGironaSpain
| | - Eila Serrano‐Hervás
- Metabolism & Cancer Group, Program Against Cancer Therapeutic Resistance (ProCURE)Catalan Institute of OncologyGironaSpain
- Girona Biomedical Research InstituteGironaSpain
- CompBioLab Group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de QuímicaUniversitat de GironaGironaSpain
| | - Sílvia Osuna
- CompBioLab Group, Institut de Química Computacional i Catàlisi (IQCC) and Departament de QuímicaUniversitat de GironaGironaSpain
- ICREABarcelonaSpain
| | - Begoña Martin‐Castillo
- Metabolism & Cancer Group, Program Against Cancer Therapeutic Resistance (ProCURE)Catalan Institute of OncologyGironaSpain
- Girona Biomedical Research InstituteGironaSpain
- Unit of Clinical ResearchCatalan Institute of OncologyGironaSpain
| | - Ruth Lupu
- Division of Experimental Pathology, Department of Laboratory Medicine and PathologyMayo ClinicRochesterMNUSA
- Mayo Clinic Cancer CenterRochesterMNUSA
- Department of Biochemistry and Molecular Biology LaboratoryMayo Clinic LaboratoryRochesterMNUSA
| |
Collapse
|
29
|
Jiang X, Yang L, Chen G, Feng X, Liu Y, Gao Q, Mai M, Chen CYC, Ye S, Yang Z. Discovery of Kinetin in inhibiting colorectal cancer progression via enhancing PSMB1-mediated RAB34 degradation. Cancer Lett 2024; 584:216600. [PMID: 38159835 DOI: 10.1016/j.canlet.2023.216600] [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: 09/19/2023] [Revised: 11/29/2023] [Accepted: 12/12/2023] [Indexed: 01/03/2024]
Abstract
Colorectal cancer (CRC) is one of the most prevalent malignancies worldwide. Understanding the underlying mechanism driving CRC progression and identifying potential therapeutic drug targets are of utmost urgency. We previously utilized LC-MS-based proteomic profiling to identify proteins associated with postoperative progression in stage II/III CRC. Here, we revealed that proteasome subunit beta type-1 (PSMB1) is an independent predictor for postoperative progression in stage II/III CRC. Mechanistically, PSMB1 binds directly to onco-protein RAB34 and promotes its proteasome-dependent degradation, potentially leading to the inactivation of the MEK/ERK signaling pathway and inhibition of CRC progression. To further identify potential anticancer drugs, we screened a library of 2509 FDA-approved drugs using computer-aided drug design (CADD) and identified Kinetin as a potentiating agent for PSMB1. Functional assays confirmed that Kinetin enhanced the interaction between PSMB1 and RAB34, hence facilitated the degradation of RAB34 protein and decreased the MEK/ERK phosphorylation. Kinetin suppresses CRC progression in patient-derived xenograft (PDX) and liver metastasis models. Conclusively, our study identifies PSMB1 as a potential biomarker and therapeutic target for CRC, and Kinetin as an anticancer drug by enhancing proteasome-dependent onco-protein degradation.
Collapse
Affiliation(s)
- Xuefei Jiang
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510655, China
| | - Lanlan Yang
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510655, China
| | - Guanxing Chen
- Artificial Intelligence Medical Research Center, School of Intelligent Systems Engineering, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong, 510275, China
| | - Xingzhi Feng
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510655, China; Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510655, China
| | - Yiting Liu
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510655, China; Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510655, China
| | - Qianling Gao
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510655, China; Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510655, China
| | - Mingru Mai
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510655, China; Biomedical Innovation Center, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510655, China
| | - Calvin Yu-Chian Chen
- Department of AI for Science, School of Electronic and Computer Engineering, Peking University Shenzhen Graduate School, Shenzhen, Guangdong, 518055, China
| | - Shubiao Ye
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510655, China; Department of General Surgery (Colorectal Surgery), The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510655, China
| | - Zihuan Yang
- Guangdong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, Guangdong Institute of Gastroenterology, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510655, China; Department of Clinical Laboratory, The Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, 510655, China.
| |
Collapse
|
30
|
Whelan R, Mayor-Ruiz C. Chemical rewiring of ubiquitination by degraders and their selectivity routes. Nat Struct Mol Biol 2024; 31:205-207. [PMID: 38366231 DOI: 10.1038/s41594-024-01215-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2024]
Affiliation(s)
- Rory Whelan
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Technology (BIST), Baldiri Reixac, Barcelona, Spain
| | - Cristina Mayor-Ruiz
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Technology (BIST), Baldiri Reixac, Barcelona, Spain.
| |
Collapse
|
31
|
Peng X, Hu Z, Zeng L, Zhang M, Xu C, Lu B, Tao C, Chen W, Hou W, Cheng K, Bi H, Pan W, Chen J. Overview of epigenetic degraders based on PROTAC, molecular glue, and hydrophobic tagging technologies. Acta Pharm Sin B 2024; 14:533-578. [PMID: 38322348 PMCID: PMC10840439 DOI: 10.1016/j.apsb.2023.09.003] [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: 06/10/2023] [Revised: 07/21/2023] [Accepted: 08/30/2023] [Indexed: 02/08/2024] Open
Abstract
Epigenetic pathways play a critical role in the initiation, progression, and metastasis of cancer. Over the past few decades, significant progress has been made in the development of targeted epigenetic modulators (e.g., inhibitors). However, epigenetic inhibitors have faced multiple challenges, including limited clinical efficacy, toxicities, lack of subtype selectivity, and drug resistance. As a result, the design of new epigenetic modulators (e.g., degraders) such as PROTACs, molecular glue, and hydrophobic tagging (HyT) degraders has garnered significant attention from both academia and pharmaceutical industry, and numerous epigenetic degraders have been discovered in the past decade. In this review, we aim to provide an in-depth illustration of new degrading strategies (2017-2023) targeting epigenetic proteins for cancer therapy, focusing on the rational design, pharmacodynamics, pharmacokinetics, clinical status, and crystal structure information of these degraders. Importantly, we also provide deep insights into the potential challenges and corresponding remedies of this approach to drug design and development. Overall, we hope this review will offer a better mechanistic understanding and serve as a useful guide for the development of emerging epigenetic-targeting degraders.
Collapse
Affiliation(s)
- Xiaopeng Peng
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Zhihao Hu
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Limei Zeng
- College of Basic Medicine, Gannan Medical University, Ganzhou 314000, China
| | - Meizhu Zhang
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Congcong Xu
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Benyan Lu
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Chengpeng Tao
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Weiming Chen
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Wen Hou
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Kui Cheng
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Huichang Bi
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Wanyi Pan
- College of Pharmacy, Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases of Ministry of Education, Gannan Medical University, Ganzhou 314000, China
| | - Jianjun Chen
- Guangdong Provincial Key Laboratory of New Drug Screening, NMPA Key Laboratory for Research and Evaluation of Drug Metabolism, School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, China
| |
Collapse
|
32
|
Li D, Peng X, Hu Z, Li S, Chen J, Pan W. Small molecules targeting selected histone methyltransferases (HMTs) for cancer treatment: Current progress and novel strategies. Eur J Med Chem 2024; 264:115982. [PMID: 38056296 DOI: 10.1016/j.ejmech.2023.115982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/17/2023] [Accepted: 11/19/2023] [Indexed: 12/08/2023]
Abstract
Histone methyltransferases (HMTs) play a critical role in gene post-translational regulation and diverse physiological processes, and are implicated in a plethora of human diseases, especially cancer. Increasing evidences demonstrate that HMTs may serve as a potential therapeutic target for cancer treatment. Thus, the development of HMTs inhibitor have been pursued with steadily increasing interest over the past decade. However, the disadvantages such as insufficient clinical efficacy, moderate selectivity, and propensity for acquired resistance have hindered the development of conventional HMT inhibitors. New technologies and methods are imperative to enhance the anticancer activity of HMT inhibitors. In this review, we first review the structure and biological functions of the several essential HMTs, such as EZH2, G9a, PRMT5, and DOT1L. The internal relationship between these HMTs and cancer is also expounded. Next, we mainly focus on the latest progress in the development of HMT modulators encompassing dual-target inhibitors, targeted protein degraders and covalent inhibitors from perspectives such as rational design, pharmacodynamics, pharmacokinetics, and clinical status. Lastly, we also discuss the challenges and future directions for HMT-based drug discovery for cancer therapy.
Collapse
Affiliation(s)
- Deping Li
- Department of Pharmacy, First Affiliated Hospital of Gannan Medical University, Ganzhou, 341000, PR China
| | - Xiaopeng Peng
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, School of Pharmacy, Gannan Medical University, Ganzhou, 341000, PR China
| | - Zhihao Hu
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, School of Pharmacy, Gannan Medical University, Ganzhou, 341000, PR China
| | - Shuqing Li
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, School of Pharmacy, Gannan Medical University, Ganzhou, 341000, PR China
| | - Jianjun Chen
- School of Pharmaceutical Sciences, Guangdong Provincial Key Laboratory of New Drug Screening, Southern Medical University, Guangzhou, 516000, PR China.
| | - Wanyi Pan
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, School of Pharmacy, Gannan Medical University, Ganzhou, 341000, PR China.
| |
Collapse
|
33
|
Jiang W, Jiang Y, Luo Y, Qiao W, Yang T. Facilitating the development of molecular glues: Opportunities from serendipity and rational design. Eur J Med Chem 2024; 263:115950. [PMID: 37984298 DOI: 10.1016/j.ejmech.2023.115950] [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: 08/28/2023] [Revised: 11/09/2023] [Accepted: 11/09/2023] [Indexed: 11/22/2023]
Abstract
Molecular glues can specifically induce interactions between two or more proteins to modulate biological functions and have been proven to be a powerful therapeutic modality in drug discovery. It plays a variety of vital roles in several biological processes, such as complex stabilization, interactome modulation and transporter inhibition, thus enabling challenging therapeutic targets to be druggable. Most known molecular glues were identified serendipitously, such as IMiDs, auxin, and rapamycin. In recent years, more rational strategies were explored with the development of chemical biology and a deep understanding of the interaction between molecular glues and proteins, which led to the rational discovery of several molecular glues. Thus, in this review, we aim to highlight the discovery strategies of molecular glues from three aspects: serendipitous discovery, screening methods and rational design principles. We expect that this review will provide a reasonable reference and insights for the discovery of molecular glues.
Collapse
Affiliation(s)
- Weiqing Jiang
- Laboratory of Human Diseases and Immunotherapies, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China; Institute of Immunology and Inflammation, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yunhan Jiang
- Laboratory of Human Diseases and Immunotherapies, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China; Institute of Immunology and Inflammation, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China; Cardiovascular Surgery Research Laboratory, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Youfu Luo
- Laboratory of Human Diseases and Immunotherapies, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Wenliang Qiao
- Lung Cancer Center, Laboratory of Lung Cancer, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Tao Yang
- Laboratory of Human Diseases and Immunotherapies, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China; Institute of Immunology and Inflammation, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China.
| |
Collapse
|
34
|
Kozicka Z, Suchyta DJ, Focht V, Kempf G, Petzold G, Jentzsch M, Zou C, Di Genua C, Donovan KA, Coomar S, Cigler M, Mayor-Ruiz C, Schmid-Burgk JL, Häussinger D, Winter GE, Fischer ES, Słabicki M, Gillingham D, Ebert BL, Thomä NH. Design principles for cyclin K molecular glue degraders. Nat Chem Biol 2024; 20:93-102. [PMID: 37679459 PMCID: PMC10746543 DOI: 10.1038/s41589-023-01409-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 07/24/2023] [Indexed: 09/09/2023]
Abstract
Molecular glue degraders are an effective therapeutic modality, but their design principles are not well understood. Recently, several unexpectedly diverse compounds were reported to deplete cyclin K by linking CDK12-cyclin K to the DDB1-CUL4-RBX1 E3 ligase. Here, to investigate how chemically dissimilar small molecules trigger cyclin K degradation, we evaluated 91 candidate degraders in structural, biophysical and cellular studies and reveal all compounds acquire glue activity via simultaneous CDK12 binding and engagement of DDB1 interfacial residues, in particular Arg928. While we identify multiple published kinase inhibitors as cryptic degraders, we also show that these glues do not require pronounced inhibitory properties for activity and that the relative degree of CDK12 inhibition versus cyclin K degradation is tuneable. We further demonstrate cyclin K degraders have transcriptional signatures distinct from CDK12 inhibitors, thereby offering unique therapeutic opportunities. The systematic structure-activity relationship analysis presented herein provides a conceptual framework for rational molecular glue design.
Collapse
Affiliation(s)
- Zuzanna Kozicka
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Department of Biology, University of Basel, Basel, Switzerland
| | - Dakota J Suchyta
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Department of Chemistry, University of Basel, Basel, Switzerland
| | - Vivian Focht
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Georg Kempf
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Georg Petzold
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
- Monte Rosa Therapeutics, Basel, Switzerland
| | - Marius Jentzsch
- Institute of Clinical Chemistry and Clinical Pharmacology, University and University Hospital Bonn, Bonn, Germany
| | - Charles Zou
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Yale University, New Haven, CT, USA
| | - Cristina Di Genua
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- VantAI, New York, NY, USA
| | - Katherine A Donovan
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Seemon Coomar
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Marko Cigler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Cristina Mayor-Ruiz
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
- IRB Barcelona-Institute for Research in Biomedicine, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Jonathan L Schmid-Burgk
- Institute of Clinical Chemistry and Clinical Pharmacology, University and University Hospital Bonn, Bonn, Germany
| | | | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Eric S Fischer
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mikołaj Słabicki
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | | | - Benjamin L Ebert
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Nicolas H Thomä
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland.
| |
Collapse
|
35
|
Wang Z, Shaabani S, Gao X, Ng YLD, Sapozhnikova V, Mertins P, Krönke J, Dömling A. Direct-to-biology, automated, nano-scale synthesis, and phenotypic screening-enabled E3 ligase modulator discovery. Nat Commun 2023; 14:8437. [PMID: 38114468 PMCID: PMC10730884 DOI: 10.1038/s41467-023-43614-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 11/09/2023] [Indexed: 12/21/2023] Open
Abstract
Thalidomide and its analogs are molecular glues (MGs) that lead to targeted ubiquitination and degradation of key cancer proteins via the cereblon (CRBN) E3 ligase. Here, we develop a direct-to-biology (D2B) approach for accelerated discovery of MGs. In this platform, automated, high throughput, and nano scale synthesis of hundreds of pomalidomide-based MGs was combined with rapid phenotypic screening, enabling an unprecedented fast identification of potent CRBN-acting MGs. The small molecules were further validated by degradation profiling and anti-cancer activity. This revealed E14 as a potent MG degrader targeting IKZF1/3, GSPT1 and 2 with profound effects on a panel of cancer cells. In a more generalized view, integration of automated, nanoscale synthesis with phenotypic assays has the potential to accelerate MGs discovery.
Collapse
Affiliation(s)
- Zefeng Wang
- University of Groningen, Department of Drug Design, A. Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Shabnam Shaabani
- University of Groningen, Department of Drug Design, A. Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Xiang Gao
- Department of Internal Medicine III, University Hospital Ulm, 89081, Ulm, Germany
| | - Yuen Lam Dora Ng
- Department of Hematology, Oncology and Cancer Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Valeriia Sapozhnikova
- Department of Hematology, Oncology and Cancer Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium (DKTK) partner site Berlin and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
| | - Philipp Mertins
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Jan Krönke
- Department of Hematology, Oncology and Cancer Immunology, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
- German Cancer Consortium (DKTK) partner site Berlin and German Cancer Research Center (DKFZ), Heidelberg, Germany.
| | - Alexander Dömling
- University of Groningen, Department of Drug Design, A. Deusinglaan 1, 9713 AV, Groningen, The Netherlands.
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry and Czech Advanced Technology and Research Institute, Palackӯ University in Olomouc, Olomouc, Czech Republic.
| |
Collapse
|
36
|
Tao AJ, Jiang J, Gadbois GE, Goyal P, Boyle BT, Mumby EJ, Myers SA, English JG, Ferguson FM. A biotin targeting chimera (BioTAC) system to map small molecule interactomes in situ. Nat Commun 2023; 14:8016. [PMID: 38049406 PMCID: PMC10695998 DOI: 10.1038/s41467-023-43507-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 11/12/2023] [Indexed: 12/06/2023] Open
Abstract
Understanding how small molecules bind to specific protein complexes in living cells is critical to understanding their mechanism-of-action. Unbiased chemical biology strategies for direct readout of protein interactome remodelling by small molecules would provide advantages over target-focused approaches, including the ability to detect previously unknown ligand targets and complexes. However, there are few current methods for unbiased profiling of small molecule interactomes. To address this, we envisioned a technology that would combine the sensitivity and live-cell compatibility of proximity labelling coupled to mass spectrometry, with the specificity and unbiased nature of chemoproteomics. In this manuscript, we describe the BioTAC system, a small-molecule guided proximity labelling platform that can rapidly identify both direct and complexed small molecule binding proteins. We benchmark the system against µMap, photoaffinity labelling, affinity purification coupled to mass spectrometry and proximity labelling coupled to mass spectrometry datasets. We also apply the BioTAC system to provide interactome maps of Trametinib and analogues. The BioTAC system overcomes a limitation of current approaches and supports identification of both inhibitor bound and molecular glue bound complexes.
Collapse
Affiliation(s)
- Andrew J Tao
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Jiewei Jiang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Gillian E Gadbois
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Pavitra Goyal
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Bridget T Boyle
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA
| | - Elizabeth J Mumby
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA
| | - Samuel A Myers
- Laboratory for Immunochemical Circuits, La Jolla Institute for Immunology, La Jolla, CA, 92037, USA
| | - Justin G English
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, 84112, USA.
| | - Fleur M Ferguson
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, 92093, USA.
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA, 92093, USA.
| |
Collapse
|
37
|
Zhu L, Zhou Y, Zhang B, Luo Y, Fang C, Yan X, Cai Y, Jiang L, Ge J. Conjugation with glucagon like peptide-1 enables targeted protein degradation. Bioorg Chem 2023; 141:106908. [PMID: 37827016 DOI: 10.1016/j.bioorg.2023.106908] [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: 08/04/2023] [Revised: 09/23/2023] [Accepted: 10/06/2023] [Indexed: 10/14/2023]
Abstract
Lysosome-targeting chimeras (LYTACs) have emerged as a promising technique to extend the scope of targeted protein degradation to extracellular proteins, e.g., secreted proteins and membrane-anchored proteins. However, up to now, only a small number of lysosomal targeting receptors (LTRs), such as cation-independent mannose 6-phosphate receptor (CI-M6PR) and asialoglycoprotein receptor (ASGPR), were reported to build LYTACs for degradation of extracellular proteins. Therefore, it is important to explore more functionalized ligands for the relevant LTRs to expand the LYTAC framework. Herein, we demonstrate a new LTR ligand-glucagon like peptide 1 (GLP-1) based targeted degradation platform, termed GLP-1 receptor-targeting chimeras (GLP-1-LYTAC). GLP-1-LYTACs are formed by conjugating GLP-1 with targeted binder (such as antibody) through Click Chemistry, showing efficiently lysosomal degradation of both extracellular proteins (GFP and Neutravidin) as well as cell membrane proteins (EGFR and PD-L1). We believe that this novel GLP-1-LYTAC will open up a new dimension for targeted protein breakdown.
Collapse
Affiliation(s)
- Liquan Zhu
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Yiyu Zhou
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Bei Zhang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Yin Luo
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Chen Fang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xiaoqiao Yan
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Yefeng Cai
- Department of Thyroid Surgery, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang 325000, China
| | - Linye Jiang
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Jingyan Ge
- Key Laboratory of Bioorganic Synthesis of Zhejiang Province, College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou 310014, China.
| |
Collapse
|
38
|
Xue G, Xie J, Hinterndorfer M, Cigler M, Dötsch L, Imrichova H, Lampe P, Cheng X, Adariani SR, Winter GE, Waldmann H. Discovery of a Drug-like, Natural Product-Inspired DCAF11 Ligand Chemotype. Nat Commun 2023; 14:7908. [PMID: 38036533 PMCID: PMC10689823 DOI: 10.1038/s41467-023-43657-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Accepted: 11/15/2023] [Indexed: 12/02/2023] Open
Abstract
Targeted proteasomal and autophagic protein degradation, often employing bifunctional modalities, is a new paradigm for modulation of protein function. In an attempt to explore protein degradation by means of autophagy we combine arylidene-indolinones reported to bind the autophagy-related LC3B-protein and ligands of the PDEδ lipoprotein chaperone, the BRD2/3/4-bromodomain containing proteins and the BTK- and BLK kinases. Unexpectedly, the resulting bifunctional degraders do not induce protein degradation by means of macroautophagy, but instead direct their targets to the ubiquitin-proteasome system. Target and mechanism identification reveal that the arylidene-indolinones covalently bind DCAF11, a substrate receptor in the CUL4A/B-RBX1-DDB1-DCAF11 E3 ligase. The tempered α, β-unsaturated indolinone electrophiles define a drug-like DCAF11-ligand class that enables exploration of this E3 ligase in chemical biology and medicinal chemistry programs. The arylidene-indolinone scaffold frequently occurs in natural products which raises the question whether E3 ligand classes can be found more widely among natural products and related compounds.
Collapse
Affiliation(s)
- Gang Xue
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Jianing Xie
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Matthias Hinterndorfer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Marko Cigler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Lara Dötsch
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
- Technical University Dortmund, Faculty of Chemistry and Chemical Biology, Dortmund, Germany
| | - Hana Imrichova
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria
| | - Philipp Lampe
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Xiufen Cheng
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Soheila Rezaei Adariani
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Vienna, Austria.
| | - Herbert Waldmann
- Department of Chemical Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
- Technical University Dortmund, Faculty of Chemistry and Chemical Biology, Dortmund, Germany.
| |
Collapse
|
39
|
McGibbon M, Shave S, Dong J, Gao Y, Houston DR, Xie J, Yang Y, Schwaller P, Blay V. From intuition to AI: evolution of small molecule representations in drug discovery. Brief Bioinform 2023; 25:bbad422. [PMID: 38033290 PMCID: PMC10689004 DOI: 10.1093/bib/bbad422] [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: 09/01/2023] [Revised: 10/13/2023] [Accepted: 11/01/2023] [Indexed: 12/02/2023] Open
Abstract
Within drug discovery, the goal of AI scientists and cheminformaticians is to help identify molecular starting points that will develop into safe and efficacious drugs while reducing costs, time and failure rates. To achieve this goal, it is crucial to represent molecules in a digital format that makes them machine-readable and facilitates the accurate prediction of properties that drive decision-making. Over the years, molecular representations have evolved from intuitive and human-readable formats to bespoke numerical descriptors and fingerprints, and now to learned representations that capture patterns and salient features across vast chemical spaces. Among these, sequence-based and graph-based representations of small molecules have become highly popular. However, each approach has strengths and weaknesses across dimensions such as generality, computational cost, inversibility for generative applications and interpretability, which can be critical in informing practitioners' decisions. As the drug discovery landscape evolves, opportunities for innovation continue to emerge. These include the creation of molecular representations for high-value, low-data regimes, the distillation of broader biological and chemical knowledge into novel learned representations and the modeling of up-and-coming therapeutic modalities.
Collapse
Affiliation(s)
- Miles McGibbon
- Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, Scotland EH9 3BF, United Kingdom
| | - Steven Shave
- Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, Scotland EH9 3BF, United Kingdom
| | - Jie Dong
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, 410013, China
| | - Yumiao Gao
- Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, Scotland EH9 3BF, United Kingdom
| | - Douglas R Houston
- Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, Scotland EH9 3BF, United Kingdom
| | - Jiancong Xie
- Key Laboratory of Machine Intelligence and Advanced Computing, Sun Yat-Sen University, Guangzhou, 510000, China
| | - Yuedong Yang
- Key Laboratory of Machine Intelligence and Advanced Computing, Sun Yat-Sen University, Guangzhou, 510000, China
| | - Philippe Schwaller
- Laboratory of Artificial Chemical Intelligence (LIAC), Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Vincent Blay
- Institute of Quantitative Biology, Biochemistry and Biotechnology, University of Edinburgh, Edinburgh, Scotland EH9 3BF, United Kingdom
| |
Collapse
|
40
|
Talukdar PD, Chatterji U. Transcriptional co-activators: emerging roles in signaling pathways and potential therapeutic targets for diseases. Signal Transduct Target Ther 2023; 8:427. [PMID: 37953273 PMCID: PMC10641101 DOI: 10.1038/s41392-023-01651-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 08/27/2023] [Accepted: 09/10/2023] [Indexed: 11/14/2023] Open
Abstract
Specific cell states in metazoans are established by the symphony of gene expression programs that necessitate intricate synergic interactions between transcription factors and the co-activators. Deregulation of these regulatory molecules is associated with cell state transitions, which in turn is accountable for diverse maladies, including developmental disorders, metabolic disorders, and most significantly, cancer. A decade back most transcription factors, the key enablers of disease development, were historically viewed as 'undruggable'; however, in the intervening years, a wealth of literature validated that they can be targeted indirectly through transcriptional co-activators, their confederates in various physiological and molecular processes. These co-activators, along with transcription factors, have the ability to initiate and modulate transcription of diverse genes necessary for normal physiological functions, whereby, deregulation of such interactions may foster tissue-specific disease phenotype. Hence, it is essential to analyze how these co-activators modulate specific multilateral processes in coordination with other factors. The proposed review attempts to elaborate an in-depth account of the transcription co-activators, their involvement in transcription regulation, and context-specific contributions to pathophysiological conditions. This review also addresses an issue that has not been dealt with in a comprehensive manner and hopes to direct attention towards future research that will encompass patient-friendly therapeutic strategies, where drugs targeting co-activators will have enhanced benefits and reduced side effects. Additional insights into currently available therapeutic interventions and the associated constraints will eventually reveal multitudes of advanced therapeutic targets aiming for disease amelioration and good patient prognosis.
Collapse
Affiliation(s)
- Priyanka Dey Talukdar
- Cancer Research Laboratory, Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, West Bengal, India
| | - Urmi Chatterji
- Cancer Research Laboratory, Department of Zoology, University of Calcutta, 35 Ballygunge Circular Road, Kolkata, 700019, West Bengal, India.
| |
Collapse
|
41
|
Csorba N, Ábrányi-Balogh P, Keserű GM. Covalent fragment approaches targeting non-cysteine residues. Trends Pharmacol Sci 2023; 44:802-816. [PMID: 37770315 DOI: 10.1016/j.tips.2023.08.014] [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: 06/10/2023] [Revised: 08/28/2023] [Accepted: 08/30/2023] [Indexed: 09/30/2023]
Abstract
Covalent fragment approaches combine advantages of covalent binders and fragment-based drug discovery (FBDD) for target identification and validation. Although early applications focused mostly on cysteine labeling, the chemistries of available warheads that target other orthosteric and allosteric protein nucleophiles has recently been extended. The range of different warheads and labeling chemistries provide unique opportunities for screening and optimizing warheads necessary for targeting non-cysteine residues. In this review, we discuss these recently developed amino-acid-specific and promiscuous warheads, as well as emerging labeling chemistries, which includes novel transition metal catalyzed, photoactive, electroactive, and noncatalytic methodologies. We also highlight recent applications of covalent fragments for the development of molecular glues and proteolysis-targeting chimeras (PROTACs), and their utility in chemical proteomics-based target identification and validation.
Collapse
Affiliation(s)
- Noémi Csorba
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary; National Laboratory for Drug Research and Development, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary; Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Szent Gellért tér 4, 1111 Budapest, Hungary
| | - Péter Ábrányi-Balogh
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary; National Laboratory for Drug Research and Development, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary; Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Szent Gellért tér 4, 1111 Budapest, Hungary
| | - György M Keserű
- Medicinal Chemistry Research Group, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary; National Laboratory for Drug Research and Development, Research Centre for Natural Sciences, Magyar tudósok krt. 2, 1117, Budapest, Hungary; Department of Organic Chemistry and Technology, Budapest University of Technology and Economics, Szent Gellért tér 4, 1111 Budapest, Hungary.
| |
Collapse
|
42
|
Liu C, Hu L, Jia H, Zhang J, Dong G, da Silva-Júnior EF, Liu X, Zhan P. Unveiling innovative anti-influenza agents through modern medicinal chemistry approaches (2019-2023 updates). Future Med Chem 2023; 15:1915-1917. [PMID: 37929606 DOI: 10.4155/fmc-2023-0258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2023] Open
Affiliation(s)
- Chuanfeng Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan, Shandong, 250012, P.R. China
- Suzhou Research Institute of Shandong University, Room 607, Building B of NUSP, No. 388 Ruoshui Road, SIP, Suzhou, Jiangsu, 215123, P.R. China
| | - Lide Hu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan, Shandong, 250012, P.R. China
| | - Huinan Jia
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan, Shandong, 250012, P.R. China
| | - Jiwei Zhang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan, Shandong, 250012, P.R. China
| | - Guanyu Dong
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan, Shandong, 250012, P.R. China
| | - Edeildo Ferreira da Silva-Júnior
- Biological & Molecular Chemistry Research Group, Institute of Chemistry & Biotechnology, Federal University of Alagoas, Lourival Melo Mota Avenue, AC. Simoesõ Campus, Alagoas, Maceió, 57072-970, Brazil
| | - Xinyong Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan, Shandong, 250012, P.R. China
| | - Peng Zhan
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, 44 West Culture Road, Jinan, Shandong, 250012, P.R. China
| |
Collapse
|
43
|
Xiang H, Zhou M, Li Y, Zhou L, Wang R. Drug discovery by targeting the protein-protein interactions involved in autophagy. Acta Pharm Sin B 2023; 13:4373-4390. [PMID: 37969735 PMCID: PMC10638514 DOI: 10.1016/j.apsb.2023.07.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 05/31/2023] [Accepted: 07/10/2023] [Indexed: 11/17/2023] Open
Abstract
Autophagy is a cellular process in which proteins and organelles are engulfed in autophagosomal vesicles and transported to the lysosome/vacuole for degradation. Protein-protein interactions (PPIs) play a crucial role at many stages of autophagy, which present formidable but attainable targets for autophagy regulation. Moreover, selective regulation of PPIs tends to have a lower risk in causing undesired off-target effects in the context of a complicated biological network. Thus, small-molecule regulators, including peptides and peptidomimetics, targeting the critical PPIs involved in autophagy provide a new opportunity for innovative drug discovery. This article provides general background knowledge of the critical PPIs involved in autophagy and reviews a range of successful attempts on discovering regulators targeting those PPIs. Successful strategies and existing limitations in this field are also discussed.
Collapse
Affiliation(s)
- Honggang Xiang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Mi Zhou
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Yan Li
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Lu Zhou
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Renxiao Wang
- Department of Medicinal Chemistry, School of Pharmacy, Fudan University, Shanghai 201203, China
| |
Collapse
|
44
|
Taherbhoy AM, Daniels DL. Harnessing UBR5 for targeted protein degradation of key transcriptional regulators. Trends Pharmacol Sci 2023; 44:758-761. [PMID: 37770316 DOI: 10.1016/j.tips.2023.09.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/05/2023] [Accepted: 09/05/2023] [Indexed: 09/30/2023]
Abstract
Targeted protein degradation (TPD) has opened the door for drugging transcriptional regulators, yet the number of proteins targeted and E3 ligases utilized remain limited. Here, we highlight UBR5 and propose multiple strategies by which this E3 ligase could be modulated to drive degradation of key transcriptional targets implicated in disease.
Collapse
Affiliation(s)
- Asad M Taherbhoy
- Foghorn Therapeutics, 500 Technology Square Suite 700, Cambridge, MA 02139, USA
| | - Danette L Daniels
- Foghorn Therapeutics, 500 Technology Square Suite 700, Cambridge, MA 02139, USA.
| |
Collapse
|
45
|
Ciulli A, O'Connor S, Chung CW, Hartung IV, Testa A, Daniels DL, Heitman LH. The 17 th EFMC Short Course on Medicinal Chemistry on Small Molecule Protein Degraders. ChemMedChem 2023; 18:e202300464. [PMID: 37817354 DOI: 10.1002/cmdc.202300464] [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: 08/28/2023] [Revised: 09/10/2023] [Indexed: 10/12/2023]
Abstract
The 17th EFMC Short Course on Medicinal Chemistry took place April 23-26, 2023 in Oegstgeest, near Leiden in the Netherlands. It covered for the first time the exciting topic of Targeted Protein Degradation (full title: Small Molecule Protein Degraders: A New Opportunity for Drug Design and Development). The course was oversubscribed, with 35 attendees and 6 instructors mainly from Europe but also from the US and South Africa, and representing both industry and academia. This report summarizes the successful event, key lectures given and topics discussed.
Collapse
Affiliation(s)
- Alessio Ciulli
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee, DD1 5JJ Scotland, UK
| | - Suzanne O'Connor
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, Dundee, DD1 5JJ Scotland, UK
| | | | - Ingo V Hartung
- Merck Healthcare KGaA, Frankfurter Straße 250, 64293, Darmstadt, Germany
| | - Andrea Testa
- Amphista Therapeutics Ltd., Cori Building, Granta Park, Great Abington, Cambridge, CB21 6GQ, UK
| | - Danette L Daniels
- Foghorn Therapeutics, 500 Technology Square, Cambridge, MA 02139, USA
| | - Laura H Heitman
- Oncode Institute & Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research (LACDR), P. O. Box 9502, 2300RA, Leiden, The Netherlands
| |
Collapse
|
46
|
Li J, Li C, Zhang Z, Zhang Z, Wu Z, Liao J, Wang Z, McReynolds M, Xie H, Guo L, Fan Q, Peng J, Tang W. A platform for the rapid synthesis of molecular glues (Rapid-Glue) under miniaturized conditions for direct biological screening. Eur J Med Chem 2023; 258:115567. [PMID: 37390512 PMCID: PMC10529953 DOI: 10.1016/j.ejmech.2023.115567] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 05/20/2023] [Accepted: 06/12/2023] [Indexed: 07/02/2023]
Abstract
Molecular glues, functioning via inducing degradation of the target protein while having similar molecular weight as traditional small molecule drugs, are emerging as a promising modality for the development of therapeutic agents. However, the development of molecular glues is limited by the lack of general principles and systematic methods. Not surprisingly, most molecular glues have been identified serendipitously or through phenotypic screening of large libraries. However, the preparation of large and diverse molecular glue libraries is not an easy task and requires extensive resources. We previously developed platforms for rapid synthesis of proteolysis targeting chimeras (PROTACs) that can be used directly for biological screening with minimal resources. Herein, we report a platform of rapid synthesis of molecular glues (Rapid-Glue) via a micromolar scale coupling reaction between hydrazide motif on the E3 ligase ligands and commercially available aldehydes with diverse structures. A pilot library of 1520 compounds is generated under miniaturized conditions in a high throughput manner without any further manipulation including purification after the synthesis. Through this platform, we identified two highly selective GSPT1 molecular glues through direct screening in cell-based assays. Three additional analogues were prepared from readily available starting materials by replacing the hydrolytic labile acylhydrazone linker with a more stable amide linker based on the two hits. All three analogues showed significant GSPT1 degradation activity and two of them possess comparable activity to the corresponding hit. The feasibility of our strategy is thus verified. Further studies by increasing the diversity and size of the library followed by appropriate assays will likely yield distinct molecular glues targeting novel neo-substrates.
Collapse
Affiliation(s)
- Jingyao Li
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI, 53705, USA
| | - Chunrong Li
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI, 53705, USA
| | - Zhongrui Zhang
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI, 53705, USA
| | - Zhen Zhang
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI, 53705, USA
| | - Zhiping Wu
- Department of Structural Biology, Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Junzhuo Liao
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI, 53705, USA
| | - Zhen Wang
- Department of Structural Biology, Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Meghan McReynolds
- Department of Structural Biology, Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Haibo Xie
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI, 53705, USA
| | - Le Guo
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI, 53705, USA
| | - Qiuhua Fan
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI, 53705, USA
| | - Junmin Peng
- Department of Structural Biology, Department of Developmental Neurobiology, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Weiping Tang
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI, 53705, USA; Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI, 53706, USA.
| |
Collapse
|
47
|
Wu D, Li Y, Zheng L, Xiao H, Ouyang L, Wang G, Sun Q. Small molecules targeting protein-protein interactions for cancer therapy. Acta Pharm Sin B 2023; 13:4060-4088. [PMID: 37799384 PMCID: PMC10547922 DOI: 10.1016/j.apsb.2023.05.035] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/28/2023] [Accepted: 05/22/2023] [Indexed: 10/07/2023] Open
Abstract
Protein-protein interactions (PPIs) are fundamental to many biological processes that play an important role in the occurrence and development of a variety of diseases. Targeting the interaction between tumour-related proteins with emerging small molecule drugs has become an attractive approach for treatment of human diseases, especially tumours. Encouragingly, selective PPI-based therapeutic agents have been rapidly advancing over the past decade, providing promising perspectives for novel therapies for patients with cancer. In this review we comprehensively clarify the discovery and development of small molecule modulators of PPIs from multiple aspects, focusing on PPIs in disease, drug design and discovery strategies, structure-activity relationships, inherent dilemmas, and future directions.
Collapse
Affiliation(s)
- Defa Wu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu 610041, China
| | - Yang Li
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu 610041, China
| | - Lang Zheng
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu 610041, China
| | - Huan Xiao
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu 610041, China
| | - Liang Ouyang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu 610041, China
| | - Guan Wang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu 610041, China
| | - Qiu Sun
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy, Innovation Center of Nursing Research, West China Hospital, Sichuan University /West China School of Nursing, Sichuan University, Chengdu 610041, China
- West China Medical Publishers, West China Hospital, Sichuan University, Chengdu 610041, China
| |
Collapse
|
48
|
Sun S, Shen J, Jiang J, Wang F, Min J. Targeting ferroptosis opens new avenues for the development of novel therapeutics. Signal Transduct Target Ther 2023; 8:372. [PMID: 37735472 PMCID: PMC10514338 DOI: 10.1038/s41392-023-01606-1] [Citation(s) in RCA: 68] [Impact Index Per Article: 68.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 07/24/2023] [Accepted: 08/11/2023] [Indexed: 09/23/2023] Open
Abstract
Ferroptosis is an iron-dependent form of regulated cell death with distinct characteristics, including altered iron homeostasis, reduced defense against oxidative stress, and abnormal lipid peroxidation. Recent studies have provided compelling evidence supporting the notion that ferroptosis plays a key pathogenic role in many diseases such as various cancer types, neurodegenerative disease, diseases involving tissue and/or organ injury, and inflammatory and infectious diseases. Although the precise regulatory networks that underlie ferroptosis are largely unknown, particularly with respect to the initiation and progression of various diseases, ferroptosis is recognized as a bona fide target for the further development of treatment and prevention strategies. Over the past decade, considerable progress has been made in developing pharmacological agonists and antagonists for the treatment of these ferroptosis-related conditions. Here, we provide a detailed overview of our current knowledge regarding ferroptosis, its pathological roles, and its regulation during disease progression. Focusing on the use of chemical tools that target ferroptosis in preclinical studies, we also summarize recent advances in targeting ferroptosis across the growing spectrum of ferroptosis-associated pathogenic conditions. Finally, we discuss new challenges and opportunities for targeting ferroptosis as a potential strategy for treating ferroptosis-related diseases.
Collapse
Affiliation(s)
- Shumin Sun
- The First Affiliated Hospital, Institute of Translational Medicine, The Second Affiliated Hospital, School of Public Health, Cancer Center, State Key Laboratory of Experimental Hematology, Zhejiang University School of Medicine, Hangzhou, China
| | - Jie Shen
- The First Affiliated Hospital, Institute of Translational Medicine, The Second Affiliated Hospital, School of Public Health, Cancer Center, State Key Laboratory of Experimental Hematology, Zhejiang University School of Medicine, Hangzhou, China
| | - Jianwei Jiang
- The First Affiliated Hospital, Institute of Translational Medicine, The Second Affiliated Hospital, School of Public Health, Cancer Center, State Key Laboratory of Experimental Hematology, Zhejiang University School of Medicine, Hangzhou, China
| | - Fudi Wang
- The First Affiliated Hospital, Institute of Translational Medicine, The Second Affiliated Hospital, School of Public Health, Cancer Center, State Key Laboratory of Experimental Hematology, Zhejiang University School of Medicine, Hangzhou, China.
| | - Junxia Min
- The First Affiliated Hospital, Institute of Translational Medicine, The Second Affiliated Hospital, School of Public Health, Cancer Center, State Key Laboratory of Experimental Hematology, Zhejiang University School of Medicine, Hangzhou, China.
| |
Collapse
|
49
|
Zhang D, Zhang J, Wang Y, Wang G, Tang P, Liu Y, Zhang Y, Ouyang L. Targeting epigenetic modifications in Parkinson's disease therapy. Med Res Rev 2023; 43:1748-1777. [PMID: 37119043 DOI: 10.1002/med.21962] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 01/10/2023] [Accepted: 04/12/2023] [Indexed: 04/30/2023]
Abstract
Parkinson's disease (PD) is a multifactorial disease due to a complex interplay between genetic and epigenetic factors. Recent efforts shed new light on the epigenetic mechanisms involved in regulating pathways related to the development of PD, including DNA methylation, posttranslational modifications of histones, and the presence of microRNA (miRNA or miR). Epigenetic regulators are potential therapeutic targets for neurodegenerative disorders. In the review, we aim to summarize mechanisms of epigenetic regulation in PD, and describe how the DNA methyltransferases, histone deacetylases, and histone acetyltransferases that mediate the key processes of PD are attractive therapeutic targets. We discuss the use of inhibitors and/or activators of these regulators in PD models or patients, and how these small molecule epigenetic modulators elicit neuroprotective effects. Further more, given the importance of miRNAs in PD, their contributions to the underlying mechanisms of PD will be discussed as well, together with miRNA-based therapies.
Collapse
Affiliation(s)
- Dan Zhang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics,West China Hospital, Sichuan University, Sichuan, Chengdu, China
| | - Jifa Zhang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics,West China Hospital, Sichuan University, Sichuan, Chengdu, China
| | - Yuxi Wang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics,West China Hospital, Sichuan University, Sichuan, Chengdu, China
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-Related Molecular Network, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Guan Wang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics,West China Hospital, Sichuan University, Sichuan, Chengdu, China
| | - Pan Tang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics,West China Hospital, Sichuan University, Sichuan, Chengdu, China
| | - Yun Liu
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics,West China Hospital, Sichuan University, Sichuan, Chengdu, China
| | - Yiwen Zhang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics,West China Hospital, Sichuan University, Sichuan, Chengdu, China
| | - Liang Ouyang
- Department of Biotherapy, Cancer Center and State Key Laboratory of Biotherapy and Joint Research Institution of Altitude Health and National Clinical Research Center for Geriatrics,West China Hospital, Sichuan University, Sichuan, Chengdu, China
| |
Collapse
|
50
|
Tao AJ, Jiang J, Gadbois GE, Goyal P, Boyle BT, Mumby EJ, Myers SA, English JG, Ferguson FM. A Biotin Targeting Chimera (BioTAC) System to Map Small Molecule Interactomes in situ. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.21.554211. [PMID: 37662262 PMCID: PMC10473607 DOI: 10.1101/2023.08.21.554211] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Unbiased chemical biology strategies for direct readout of protein interactome remodelling by small molecules provide advantages over target-focused approaches, including the ability to detect previously unknown targets, and the inclusion of chemical off-compete controls leading to high-confidence identifications. We describe the BioTAC system, a small-molecule guided proximity labelling platform, to rapidly identify both direct and complexed small molecule binding proteins. The BioTAC system overcomes a limitation of current approaches, and supports identification of both inhibitor bound and molecular glue bound complexes.
Collapse
Affiliation(s)
- Andrew J. Tao
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Jiewei Jiang
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Gillian E. Gadbois
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Pavitra Goyal
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Bridget T. Boyle
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
| | - Elizabeth J. Mumby
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Samuel A Myers
- Laboratory for Immunochemical Circuits, La Jolla Institute for Immunology, La Jolla, CA 92037
| | - Justin G. English
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Fleur M. Ferguson
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, CA 92093
| |
Collapse
|