251
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Ghidini A, Cléry A, Halloy F, Allain FHT, Hall J. RNA‐PROTACs: Degraders of RNA‐Binding Proteins. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202012330] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Alice Ghidini
- Department of Chemistry and Applied Biosciences ETH Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | - Antoine Cléry
- Department of Biology ETH Zurich Hönggerbergring 64 8093 Zurich Switzerland
| | - François Halloy
- Department of Chemistry and Applied Biosciences ETH Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
| | | | - Jonathan Hall
- Department of Chemistry and Applied Biosciences ETH Zurich Vladimir-Prelog-Weg 4 8093 Zurich Switzerland
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252
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Ghidini A, Cléry A, Halloy F, Allain FHT, Hall J. RNA-PROTACs: Degraders of RNA-Binding Proteins. Angew Chem Int Ed Engl 2021; 60:3163-3169. [PMID: 33108679 PMCID: PMC7898822 DOI: 10.1002/anie.202012330] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/08/2020] [Indexed: 12/19/2022]
Abstract
Defects in the functions of RNA binding proteins (RBPs) are at the origin of many diseases; however, targeting RBPs with conventional drugs has proven difficult. PROTACs are a new class of drugs that mediate selective degradation of a target protein through a cell's ubiquitination machinery. PROTACs comprise a moiety that binds the selected protein, conjugated to a ligand of an E3 ligase. Herein, we introduce RNA-PROTACs as a new concept in the targeting of RBPs. These chimeric structures employ small RNA mimics as targeting groups that dock the RNA-binding site of the RBP, whereupon a conjugated E3-recruiting peptide derived from the HIF-1α protein directs the RBP for proteasomal degradation. We performed a proof-of-concept demonstration with the degradation of two RBPs-a stem cell factor LIN28 and a splicing factor RBFOX1-and showed their use in cancer cell lines. The RNA-PROTAC approach opens the way to rapid, selective targeting of RBPs in a rational and general fashion.
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Affiliation(s)
- Alice Ghidini
- Department of Chemistry and Applied BiosciencesETH ZurichVladimir-Prelog-Weg 48093ZurichSwitzerland
| | - Antoine Cléry
- Department of BiologyETH ZurichHönggerbergring 648093ZurichSwitzerland
| | - François Halloy
- Department of Chemistry and Applied BiosciencesETH ZurichVladimir-Prelog-Weg 48093ZurichSwitzerland
| | | | - Jonathan Hall
- Department of Chemistry and Applied BiosciencesETH ZurichVladimir-Prelog-Weg 48093ZurichSwitzerland
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253
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Recent insight into the role of RING-finger E3 ligases in glioma. Biochem Soc Trans 2021; 49:519-529. [PMID: 33544148 DOI: 10.1042/bst20201060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 01/07/2021] [Accepted: 01/12/2021] [Indexed: 12/17/2022]
Abstract
The ubiquitin proteasome system (UPS) serves as the major posttranslational modification system for the maintenance of protein homeostasis. The ubiquitin ligases (E3s) are responsible for the recognition and recruitment of specific substrate proteins for polyubiquitination. Really interesting new gene (RING) finger E3s account for the majority of E3s. The human genome encodes more than 600 RING E3s, which are divided into three subclasses: single polypeptide E3s, cullin-RING ligases (CRLs) and other multisubunit E3s. The abnormal regulation of RING E3s has been reported to disrupt normal biological processes and induce the occurrence of many human malignancies. Glioma is the most common type of malignant primary brain tumor. In the last few decades, patient prognosis has improved as novel targeted therapeutic agents have developed. In this review, we will summarize the current knowledge about the dysregulation of RING E3s and the altered stability of their substrates in glioma. We will further introduce and discuss the current status and future perspectives of the application of small inhibitors and proteolysis-targeting chimeric molecules (PROTACs) interfering with RING E3s as potential anticancer agents for glioma.
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254
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Expanding the role of proteasome homeostasis in Parkinson's disease: beyond protein breakdown. Cell Death Dis 2021; 12:154. [PMID: 33542205 PMCID: PMC7862491 DOI: 10.1038/s41419-021-03441-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 01/13/2021] [Accepted: 01/15/2021] [Indexed: 02/06/2023]
Abstract
Proteasome is the principal hydrolytic machinery responsible for the great majority of protein degradation. The past three decades have testified prominent advances about proteasome involved in almost every aspect of biological processes. Nonetheless, inappropriate increase or decrease in proteasome function is regarded as a causative factor in several diseases. Proteasome abundance and proper assembly need to be precisely controlled. Indeed, various neurodegenerative diseases including Parkinson's disease (PD) share a common pathological feature, intracellular protein accumulation such as α-synuclein. Proteasome activation may effectively remove aggregates and prevent the neurodegeneration in PD, which provides a potential application for disease-modifying treatment. In this review, we build on the valuable discoveries related to different types of proteolysis by distinct forms of proteasome, and how its regulatory and catalytic particles promote protein elimination. Additionally, we summarize the emerging ideas on the proteasome homeostasis regulation by targeting transcriptional, translational, and post-translational levels. Given the imbalanced proteostasis in PD, the strategies for intensifying proteasomal degradation are advocated as a promising approach for PD clinical intervention.
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255
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Dunbar K, Macartney TJ, Sapkota GP. IMiDs induce FAM83F degradation via an interaction with CK1α to attenuate Wnt signalling. Life Sci Alliance 2021; 4:e202000804. [PMID: 33361334 PMCID: PMC7768194 DOI: 10.26508/lsa.202000804] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 12/11/2020] [Accepted: 12/11/2020] [Indexed: 11/24/2022] Open
Abstract
Immunomodulatory imide drugs (IMiDs) bind CRBN, a substrate receptor of the Cul4A E3 ligase complex, enabling the recruitment of neo-substrates, such as CK1α, and their degradation via the ubiquitinproteasome system. Here, we report FAM83F as such a neo-substrate. The eight FAM83 proteins (A-H) interact with and regulate the subcellular distribution of CK1α. We demonstrate that IMiD-induced FAM83F degradation requires its association with CK1α. However, no other FAM83 protein is degraded by IMiDs. We have recently identified FAM83F as a mediator of the canonical Wnt signalling pathway. The IMiD-induced degradation of FAM83F attenuated Wnt signalling in colorectal cancer cells and removed CK1α from the plasma membrane, mirroring the phenotypes observed with genetic ablation of FAM83F. Intriguingly, the expression of FAM83G, which also binds to CK1α, appears to attenuate the IMiD-induced degradation of CK1α, suggesting a protective role for FAM83G on CK1α. Our findings reveal that the efficiency and extent of target protein degradation by IMiDs depends on the nature of inherent multiprotein complex in which the target protein is part of.
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Affiliation(s)
- Karen Dunbar
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Sir James Black Centre, Dundee, UK
| | - Thomas J Macartney
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Sir James Black Centre, Dundee, UK
| | - Gopal P Sapkota
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Sir James Black Centre, Dundee, UK
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256
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Zhao CX, Zeng CM, Wang K, He QJ, Yang B, Zhou FF, Zhu H. Ubiquitin-proteasome system-targeted therapy for uveal melanoma: what is the evidence? Acta Pharmacol Sin 2021; 42:179-188. [PMID: 32601365 DOI: 10.1038/s41401-020-0441-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 05/07/2020] [Accepted: 05/12/2020] [Indexed: 12/22/2022] Open
Abstract
Uveal melanoma (UM) is a rare ocular tumor. The loss of BRCA1-associated protein 1 (BAP1) and the aberrant activation of G protein subunit alpha q (GNAQ)/G protein subunit alpha 11 (GNA11) contribute to the frequent metastasis of UM. Thus far, limited molecular-targeted therapies have been developed for the clinical treatment of UM. However, an increasing number of studies have revealed the close relationship between the ubiquitin proteasome system (UPS) and the malignancy of UM. UPS consists of a three-enzyme cascade, i.e. ubiquitin-activating enzymes (E1s); ubiquitin-conjugating enzymes (E2s); and ubiquitin-protein ligases (E3s), as well as 26S proteasome and deubiquitinases (DUBs), which work coordinately to dictate the fate of intracellular proteins through regulating ubiquitination, thus influencing cell viability. Due to the critical role of UPS in tumors, we here provide an overview of the crosstalk between UPS and the malignancy of UM, discuss the current UPS-targeted therapies in UM and highlight its potential in developing novel regimens for UM.
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257
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Jiang T, Wang G, Liu Y, Feng L, Wang M, Liu J, Chen Y, Ouyang L. Development of small-molecule tropomyosin receptor kinase (TRK) inhibitors for NTRK fusion cancers. Acta Pharm Sin B 2021; 11:355-372. [PMID: 33643817 PMCID: PMC7893124 DOI: 10.1016/j.apsb.2020.05.004] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/29/2020] [Accepted: 05/06/2020] [Indexed: 02/08/2023] Open
Abstract
Tropomyosin receptor kinase A, B and C (TRKA, TRKB and TRKC), which are well-known members of the cell surface receptor tyrosine kinase (RTK) family, are encoded by the neurotrophic receptor tyrosine kinase 1, 2 and 3 (NTRK1, NTRK2 and NTRK3) genes, respectively. TRKs can regulate cell proliferation, differentiation and even apoptosis through the RAS/MAPKs, PI3K/AKT and PLCγ pathways. Gene fusions involving NTRK act as oncogenic drivers of a broad diversity of adult and pediatric tumors, and TRKs have become promising antitumor targets. Therefore, achieving a comprehensive understanding of TRKs and relevant TRK inhibitors should be urgently pursued for the further development of novel TRK inhibitors for potential clinical applications. This review focuses on summarizing the biological functions of TRKs and NTRK fusion proteins, the development of small-molecule TRK inhibitors with different chemotypes and their activity and selectivity, and the potential therapeutic applications of these inhibitors for future cancer drug discovery efforts.
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Key Words
- AFAP1, actin filament-associated protein 1
- AML, acute myeloid leukemia
- ARHGEF2, Rho/Rac guanine nucleotide exchange factor 2
- BCAN, brevican
- BDNF, brain-derived neurotrophic factor
- BTBD1, BTB (POZ) domain containing 1
- CDK-2, cyclin-dependent kinase 2
- CR, complete response
- CRC, colorectal cancer
- CTCs, sequencing of circulating tumor cells
- DFG, Asp-Phe-Gly
- DOR, durable objective responses
- ETV6, ETS translocation variant 6
- EWG, electron-withdrawing group
- FDA, U.S. Food and Drug Administration
- FISH, fluorescence in situ hybridization
- GBM, glioblastoma multiforme
- HNSCC, head and neck squamous cell carcinoma
- HTS, high-throughput screening
- ICC, intrahepatic cholangiocarcinoma
- IG-C2, Ig-like C2 type I
- LMNA, lamin A/C
- MASC, mammary analogue secretory carcinoma
- MPRIP, myosin phosphatase Rho interacting protein
- NACC2, NACC family member 2
- NCCN, National Comprehensive Cancer Network
- NFASC, neurofascin
- NGF, nerve growth factor
- NGS, next-generation sequencing of tumor tissue
- NSCLC, non-small cell lung cancer
- NT3, neurotrophin-3
- NTRK fusion cancer
- NTRK, neurotrophic receptor tyrosine kinase
- Neurotrophic receptor tyrosine kinase fusions
- OAK, osteoarthritis of the knee
- ORR, overall response rate
- PAN3, poly(A) nuclease 3
- PPL, periplakin
- PROTAC proteolysis targeting chimera, QKI
- RABGTPase activating protein 1-like, RFWD2
- RTK, receptor tyrosine kinase
- SAR, structure–activity relationship
- SBC, secretory breast carcinoma
- SCYL3, SCY1 like pseudokinase 3
- SQSTM1, sequestosome 1
- Small-molecule inhibitor
- TFG, TRK-fused gene
- TP53, tumor protein P53
- TPM3, tropomyosin 3
- TPR, translocated promoter region
- TRIM24, tripartite motif containing 24
- TRK, tropomyosin receptor kinase
- Tropomyosin receptor kinase
- VCL, vinculin
- VEGFR2, vascular endothelial growth factor receptor 2
- quaking I protein, RABGAP1L
- ring finger and WD repeat domain 2, E3 ubiquitin protein ligase
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Affiliation(s)
- Tingting Jiang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Guan Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Yao Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Lu Feng
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Meng Wang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Jie Liu
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Yi Chen
- State Key Laboratory of Biotherapy and Cancer Center and Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China
| | - Liang Ouyang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China
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258
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Ermondi G, Garcia-Jimenez D, Caron G. PROTACs and Building Blocks: The 2D Chemical Space in Very Early Drug Discovery. Molecules 2021; 26:672. [PMID: 33525371 PMCID: PMC7865272 DOI: 10.3390/molecules26030672] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 12/11/2022] Open
Abstract
Targeted protein degradation by PROTACs has emerged as a new modality for the knockdown of a range of proteins, and, more recently, it has become increasingly clear that the PROTAC chemical space requires characterization through a pool of ad hoc physicochemical descriptors. In this study, a new database named PROTAC-DB that provides extensive information about PROTACs and building blocks was used to obtain the 2D chemical structures of about 1600 PROTACs, 60 E3 ligands, 800 linkers, and 202 warheads. For every structure, we calculated a pool of seven 2D descriptors carefully identified as informative for large and flexible structures. For comparison purposes, the same procedure was applied to a dataset of about 50 bRo5 approved drugs reported in the literature. Correlation matrices, PCAs, box plots, and other graphical tools were used to define and understand the chemical space covered by PROTACs and building blocks in relation to other compounds. Results show that linkers have different properties than E3 ligands and warheads. Polar descriptors additivity is not respected when passing from building blocks to degraders. Moreover, a very preliminary analysis based on three PROTACs with high, intermediate, and low permeability showed how the most permeable compounds seem to occupy a region closer to bRo5 drugs and, thus, exhibit different properties than impermeable compounds. Finally, a second database, PROTACpedia, was used to discuss the relevance of physicochemical descriptors on degradation activity.
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Affiliation(s)
| | | | - Giulia Caron
- Molecular Biotechnology and Health Sciences Department, University of Torino, Via Quarello, 15, 10135 Torino, Italy; (G.E.); (D.G.-J.)
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259
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Pomplun S, Jbara M, Quartararo AJ, Zhang G, Brown JS, Lee YC, Ye X, Hanna S, Pentelute BL. De Novo Discovery of High-Affinity Peptide Binders for the SARS-CoV-2 Spike Protein. ACS CENTRAL SCIENCE 2021; 7:156-163. [PMID: 33527085 PMCID: PMC7755081 DOI: 10.1021/acscentsci.0c01309] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Indexed: 05/03/2023]
Abstract
The β-coronavirus SARS-CoV-2 has caused a global pandemic. Affinity reagents targeting the SARS-CoV-2 spike protein are of interest for the development of therapeutics and diagnostics. We used affinity selection-mass spectrometry for the rapid discovery of synthetic high-affinity peptide binders for the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. From library screening with 800 million synthetic peptides, we identified three sequences with nanomolar affinities (dissociation constants K d = 80-970 nM) for RBD and selectivity over human serum proteins. Nanomolar RBD concentrations in a biological matrix could be detected using the biotinylated lead peptide in ELISA format. These peptides do not compete for ACE2 binding, and their site of interaction on the SARS-CoV-2-spike-RBD might be unrelated to the ACE2 binding site, making them potential orthogonal reagents for sandwich immunoassays. These findings serve as a starting point for the development of SARS-CoV-2 diagnostics or conjugates for virus-directed delivery of therapeutics.
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Affiliation(s)
- Sebastian Pomplun
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Muhammad Jbara
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Anthony J. Quartararo
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Genwei Zhang
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Joseph S. Brown
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Yen-Chun Lee
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Xiyun Ye
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Stephanie Hanna
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Bradley L. Pentelute
- Department
of Chemistry, Massachusetts Institute of
Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- The
Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, Massachusetts 02142, United States
- Center
for Environmental Health Sciences, Massachusetts
Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Broad
Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
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260
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Chen Y, Ning Y, Bai G, Tong L, Zhang T, Zhou J, Zhang H, Xie H, Ding J, Duan W. Design, Synthesis, and Biological Evaluation of IRAK4-Targeting PROTACs. ACS Med Chem Lett 2021; 12:82-87. [PMID: 33488968 DOI: 10.1021/acsmedchemlett.0c00474] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 12/08/2020] [Indexed: 02/07/2023] Open
Abstract
Interleukin-1 receptor associated kinase 4 (IRAK4) is a promising therapeutic target for diffuse large B-cell lymphoma driven by MYD88 L265P mutant, acting both as a kinase and a scaffolding protein for downstream signaling molecules. While previous efforts to modulate IRAK4 activity with kinase inhibitors alone displayed moderate efficacy, protein degradation may offer a solution to blocking both IRAK4 kinase activity and scaffolding capabilities. To this end, the potent IRAK4 degrader 9 was discovered, and it effectively inhibited the activation of downstream NF-κB signaling and outperformed the parent compound 1. In addition, compound 9 displayed a substantial advantage in reduction of the viability of OCI-LY10 and TMD8 cells over the parent compound 1. These results underline the potential that eliminating both the kinase and scaffolding functions of IRAK4 may result in superior and broader efficacy than inhibiting the kinase activity alone.
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Affiliation(s)
- Yun Chen
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, P. R. China
| | - Yi Ning
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, P. R. China
| | - Gang Bai
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China
| | - Linjiang Tong
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China
| | - Tao Zhang
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China
| | - Jinpei Zhou
- Department of Medicinal Chemistry, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, P. R. China
| | - Huibin Zhang
- Center of Drug Discovery, State Key Laboratory of Natural Medicines, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, P. R. China
| | - Hua Xie
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China
| | - Jian Ding
- Division of Antitumor Pharmacology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China
- University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, P. R. China
| | - Wenhu Duan
- Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, P. R. China
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261
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Miyashita SI, Zhang J, Zhang S, Shoemaker CB, Dong M. Delivery of single-domain antibodies into neurons using a chimeric toxin-based platform is therapeutic in mouse models of botulism. Sci Transl Med 2021; 13:eaaz4197. [PMID: 33408184 DOI: 10.1126/scitranslmed.aaz4197] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 05/01/2020] [Indexed: 12/15/2022]
Abstract
Efficient penetration of cell membranes and specific targeting of a cell type represent major challenges for developing therapeutics toward intracellular targets. One example facing these hurdles is to develop post-exposure treatment for botulinum neurotoxins (BoNTs), a group of bacterial toxins (BoNT/A to BoNT/G) that are major potential bioterrorism agents. BoNTs enter motor neurons, block neurotransmitter release, and cause a paralytic disease botulism. Members of BoNTs such as BoNT/A exhibit extremely long half-life within neurons, resulting in persistent paralysis for months, yet there are no therapeutics that can inhibit BoNTs once they enter neurons. Here, we developed a chimeric toxin-based delivery platform by fusing the receptor-binding domain of a BoNT, which targets neurons, with the membrane translocation domain and inactivated protease domain of the recently discovered BoNT-like toxin BoNT/X, which can deliver cargoes across endosomal membranes into the cytosol. A therapeutic protein was then created by fusing a single-domain antibody (nanobody) against BoNT/A with the delivery platform. In vitro characterization demonstrated that nanobodies were delivered into cultured neurons and neutralized BoNT/A in neurons. Administration of this protein in mice shortened duration of local muscle paralysis, restoring muscle function within hours, and rescued mice from systemic toxicity of lethal doses of BoNT/A. Fusion of two nanobodies, one against BoNT/A and the other against BoNT/B, created a multivalent therapeutic protein able to neutralize both BoNT/A and BoNT/B in mice. These studies provide an effective post-exposure treatment for botulism and establish a platform for intracellular delivery of therapeutics targeting cytosolic proteins and processes.
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Affiliation(s)
- Shin-Ichiro Miyashita
- Department of Urology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Surgery and Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Jie Zhang
- Department of Urology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Surgery and Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Sicai Zhang
- Department of Urology, Boston Children's Hospital, Boston, MA 02115, USA
- Department of Surgery and Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Charles B Shoemaker
- Department of Infectious Diseases and Global Health, Cummings School of Veterinary Medicine at Tufts University, North Grafton, MA 01536, USA
| | - Min Dong
- Department of Urology, Boston Children's Hospital, Boston, MA 02115, USA.
- Department of Surgery and Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
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262
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Fuchs O, Bokorova R. Preclinical Studies of PROTACs in Hematological Malignancies. Cardiovasc Hematol Disord Drug Targets 2021; 21:7-22. [PMID: 33687890 DOI: 10.2174/1871529x21666210308111546] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 01/01/2021] [Accepted: 01/23/2021] [Indexed: 06/12/2023]
Abstract
Incorrectly expressed or mutated proteins associated with hematologic malignancies have been generally targeted by chemotherapy using small-molecule inhibitors or monoclonal antibodies. But the majority of these intracellular proteins are without active sites and antigens. PROTACs, proteolysis targeting chimeras, are bifunctional molecules designed to polyubiquitinate and degrade specific pathological proteins of interest (POIs) by hijacking the activity of E3-ubiquitin ligases for POI polyubiquitination and subsequent degradation by the proteasome. This strategy utilizes the ubiquitin-proteasome system for the degradation of specific proteins in the cell. In many cases, including hematologic malignancies, inducing protein degradation as a therapeutic strategy offers therapeutic benefits over classical enzyme inhibition connected with resistance to inhibitors. Limitations of small-molecule inhibitors are shown. PROTACs can polyubiquitinate and mark for degradation of "undruggable"proteins, e.g. transcription factor STAT3 and scaffold proteins. Today, this technology is used in preclinical studies in various hematologic malignancies, mainly for targeting drug-resistant bromodomain and extraterminal proteins and Bruton tyrosine kinase. Several mechanisms limiting selectivity and safety of PROTAC molecules function are also discussed.
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Affiliation(s)
- Ota Fuchs
- Department of Genomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
| | - Radka Bokorova
- Department of Genomics, Institute of Hematology and Blood Transfusion, Prague, Czech Republic
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263
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Casement R, Bond A, Craigon C, Ciulli A. Mechanistic and Structural Features of PROTAC Ternary Complexes. Methods Mol Biol 2021; 2365:79-113. [PMID: 34432240 DOI: 10.1007/978-1-0716-1665-9_5] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The rapid and ever-growing advancements from within the field of proteolysis-targeting chimeras (PROTAC)-induced protein degradation have driven considerable development to gain a deeper understanding of their mode of action. The ternary complex formed by PROTACs with their target protein and E3 ubiquitin ligase is the key species in their substoichiometric catalytic mechanism. Here, we describe the theoretical framework that underpins ternary complexes, including a current understanding of the three-component binding model, cooperativity, hook effect and structural considerations. We discuss in detail the biophysical methods used to interrogate ternary complex formation in vitro, including X-ray crystallography, AlphaLISA, FRET, FP, ITC and SPR. Finally, we provide detailed ITC methods and discuss approaches to assess binary and ternary target engagement, target ubiquitination and degradation that can be used to obtain a more holistic understanding of the mode of action within a cellular environment.
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Affiliation(s)
- Ryan Casement
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, Scotland, UK
| | - Adam Bond
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, Scotland, UK
| | - Conner Craigon
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, Scotland, UK
| | - Alessio Ciulli
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, Scotland, UK.
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264
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Zheng S, Wu Y, Li Z. Integrating cullin2-RING E3 ligase as a potential biomarker for glioblastoma multiforme prognosis and radiosensitivity profiling. Radiother Oncol 2021; 154:36-44. [DOI: 10.1016/j.radonc.2020.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 08/30/2020] [Accepted: 09/01/2020] [Indexed: 12/25/2022]
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265
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Mologni L, Marzaro G, Redaelli S, Zambon A. Dual Kinase Targeting in Leukemia. Cancers (Basel) 2021; 13:E119. [PMID: 33401428 PMCID: PMC7796318 DOI: 10.3390/cancers13010119] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 12/23/2020] [Accepted: 12/28/2020] [Indexed: 12/13/2022] Open
Abstract
Pharmacological cancer therapy is often based on the concurrent inhibition of different survival pathways to improve treatment outcomes and to reduce the risk of relapses. While this strategy is traditionally pursued only through the co-administration of several drugs, the recent development of multi-targeting drugs (i.e., compounds intrinsically able to simultaneously target several macromolecules involved in cancer onset) has had a dramatic impact on cancer treatment. This review focuses on the most recent developments in dual-kinase inhibitors used in acute myeloid leukemia (AML), chronic myelogenous leukemia (CML), and lymphoid tumors, giving details on preclinical studies as well as ongoing clinical trials. A brief overview of dual-targeting inhibitors (kinase/histone deacetylase (HDAC) and kinase/tubulin polymerization inhibitors) applied to leukemia is also given. Finally, the very recently developed Proteolysis Targeting Chimeras (PROTAC)-based kinase inhibitors are presented.
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Affiliation(s)
- Luca Mologni
- Department of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (L.M.); (S.R.)
| | - Giovanni Marzaro
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, via Marzolo 5, I-35131 Padova, Italy;
| | - Sara Redaelli
- Department of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy; (L.M.); (S.R.)
| | - Alfonso Zambon
- Department of Chemistry and Geological Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
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266
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Hu J, Wei J, Yim H, Wang L, Xie L, Jin MS, Kabir M, Qin L, Chen X, Liu J, Jin J. Potent and Selective Mitogen-Activated Protein Kinase Kinase 1/2 (MEK1/2) Heterobifunctional Small-molecule Degraders. J Med Chem 2020; 63:15883-15905. [PMID: 33284613 PMCID: PMC7770057 DOI: 10.1021/acs.jmedchem.0c01609] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Previously, we reported a first-in-class von Hippel-Lindau (VHL)-recruiting mitogen-activated protein kinase kinases 1 and 2 (MEK1/2) degrader, MS432. To date, only two MEK1/2 degrader papers have been published and very limited structure-activity relationships (SAR) have been reported. Here, we describe our extensive SAR studies exploring both von Hippel-Lindau (VHL) and cereblon (CRBN) E3 ligase ligands and a variety of linkers, which resulted in two novel, improved VHL-recruiting MEK1/2 degraders, 24 (MS928) and 27 (MS934), and the first CRBN-recruiting MEK1/2 degrader 50 (MS910). These compounds potently and selectively degraded MEK1/2 by hijacking the ubiquitin-proteasome system, inhibited downstream signaling, and suppressed cancer cell proliferation. Furthermore, concurrent inhibition of BRAF or PI3K significantly potentiated the antitumor activity of degrader 27, suggesting that the combination of MEK1/2 degradation with BRAF or PI3K inhibition may provide potential therapeutic benefits. Finally, besides being more potent, degrader 27 displayed improved plasma exposure levels in mice, representing the best MEK1/2 degrader to date for in vivo studies.
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Affiliation(s)
- Jianping Hu
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Jieli Wei
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Hyerin Yim
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Li Wang
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Ling Xie
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Margaret S Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Md Kabir
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Lihuai Qin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Xian Chen
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jing Liu
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
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267
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Du S, Liew SS, Zhang CW, Du W, Lang W, Yao CCY, Li L, Ge J, Yao SQ. Cell-Permeant Bioadaptors for Cytosolic Delivery of Native Antibodies: A "Mix-and-Go" Approach. ACS CENTRAL SCIENCE 2020; 6:2362-2376. [PMID: 33376798 PMCID: PMC7760483 DOI: 10.1021/acscentsci.0c01379] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Indexed: 05/05/2023]
Abstract
Antibodies are powerful tools that may potentially find wide applications in live-cell bioimaging, disease diagnostics, and therapeutics. Their practical applications have however remained limited thus far, owing to their inability to cross the cell membrane. Existing approaches for cytosolic delivery of functional antibodies are available, but they are constantly plagued by the need for chemical/genetic modifications, low delivery efficiency, and severe endolysosomal trapping. Consequently, it is of paramount importance to develop new strategies capable of highly efficient cytosolic delivery of native antibodies with immediate bioavailability. Herein, we report a modification-free, convenient "mix-and-go" strategy for the cytosolic delivery of native antibodies to different live mammalian cells efficiently, with minimal endolysosomal trapping and immediate bioavailability. By simply mixing a cell-permeant bioadaptor (derived from protein A or TRIM21) with a commercially available off-the-shelf antibody, the resulting noncovalent complex could be immediately used for intracellular delivery of native antibodies needed in subsequent cytosolic target engagement. The versatility of this approach was successfully illustrated in a number of applications, including antibody-based, live-cell imaging of the endogenous protein glutathionylation to detect oxidative cell stress, antibody-based activation of endogenous caspase-3, and inhibition of endogenous PTP1B activity, and finally TRIM21-mediated endogenous protein degradation for potential targeted therapy. Our results thus indicate this newly developed, "mix-and-go" antibody delivery method should have broad applications in chemical biology and future drug discovery.
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Affiliation(s)
- Shubo Du
- Department
of Chemistry, National University of Singapore, Singapore 117543, Singapore
| | - Si Si Liew
- Department
of Chemistry, National University of Singapore, Singapore 117543, Singapore
| | - Cheng-wu Zhang
- Department
of Chemistry, National University of Singapore, Singapore 117543, Singapore
| | - Wei Du
- Department
of Chemistry, National University of Singapore, Singapore 117543, Singapore
- Shaanxi
Institute of Flexible Electronics (SIFE) & Xi’an Key Laboratory
of Biomedical Materials & Engineering, Northwestern Polytechnical University (NPU), Xi’an 710072, China
| | - Wenjie Lang
- Key
Laboratory of Bioorganic Synthesis of Zhejiang Province, College of
Biotechnology and Bioengineering, Zhejiang
University of Technology, Hangzhou 310014, China
| | - Cassandra C. Y. Yao
- Department
of Chemistry, National University of Singapore, Singapore 117543, Singapore
| | - Lin Li
- Shaanxi
Institute of Flexible Electronics (SIFE) & Xi’an Key Laboratory
of Biomedical Materials & Engineering, Northwestern Polytechnical University (NPU), Xi’an 710072, China
| | - Jingyan Ge
- Key
Laboratory of Bioorganic Synthesis of Zhejiang Province, College of
Biotechnology and Bioengineering, Zhejiang
University of Technology, Hangzhou 310014, China
| | - Shao Q. Yao
- Department
of Chemistry, National University of Singapore, Singapore 117543, Singapore
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268
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Meng F, Liang Z, Zhao K, Luo C. Drug design targeting active posttranslational modification protein isoforms. Med Res Rev 2020; 41:1701-1750. [PMID: 33355944 DOI: 10.1002/med.21774] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/29/2020] [Accepted: 12/03/2020] [Indexed: 12/11/2022]
Abstract
Modern drug design aims to discover novel lead compounds with attractable chemical profiles to enable further exploration of the intersection of chemical space and biological space. Identification of small molecules with good ligand efficiency, high activity, and selectivity is crucial toward developing effective and safe drugs. However, the intersection is one of the most challenging tasks in the pharmaceutical industry, as chemical space is almost infinity and continuous, whereas the biological space is very limited and discrete. This bottleneck potentially limits the discovery of molecules with desirable properties for lead optimization. Herein, we present a new direction leveraging posttranslational modification (PTM) protein isoforms target space to inspire drug design termed as "Post-translational Modification Inspired Drug Design (PTMI-DD)." PTMI-DD aims to extend the intersections of chemical space and biological space. We further rationalized and highlighted the importance of PTM protein isoforms and their roles in various diseases and biological functions. We then laid out a few directions to elaborate the PTMI-DD in drug design including discovering covalent binding inhibitors mimicking PTMs, targeting PTM protein isoforms with distinctive binding sites from that of wild-type counterpart, targeting protein-protein interactions involving PTMs, and hijacking protein degeneration by ubiquitination for PTM protein isoforms. These directions will lead to a significant expansion of the biological space and/or increase the tractability of compounds, primarily due to precisely targeting PTM protein isoforms or complexes which are highly relevant to biological functions. Importantly, this new avenue will further enrich the personalized treatment opportunity through precision medicine targeting PTM isoforms.
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Affiliation(s)
- Fanwang Meng
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada
| | - Zhongjie Liang
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Kehao Zhao
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, China
| | - Cheng Luo
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
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269
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Liang Y, Nandakumar KS, Cheng K. Design and pharmaceutical applications of proteolysis-targeting chimeric molecules. Biochem Pharmacol 2020; 182:114211. [DOI: 10.1016/j.bcp.2020.114211] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 08/24/2020] [Accepted: 08/26/2020] [Indexed: 12/14/2022]
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270
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271
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Mapping the Degradable Kinome Provides a Resource for Expedited Degrader Development. Cell 2020; 183:1714-1731.e10. [DOI: 10.1016/j.cell.2020.10.038] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 09/09/2020] [Accepted: 10/22/2020] [Indexed: 01/11/2023]
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272
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Wang Y, Zhang Y, Du Y, Zhou M, Hu Y, Zhang S. Emerging roles of N6-methyladenosine (m 6A) modification in breast cancer. Cell Biosci 2020; 10:136. [PMID: 33292526 PMCID: PMC7690038 DOI: 10.1186/s13578-020-00502-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 11/19/2020] [Indexed: 02/06/2023] Open
Abstract
N6-Methyladenosine (m6A) is the most abundant, dynamic, and reversible epigenetic RNA modification that is found in coding and non-coding RNAs. Emerging studies have shown that m6A and its regulators affect multiple steps in RNA metabolism and play broad roles in various cancers. Worldwide, breast cancer is the most prevalent cancer in female. It is a very heterogeneous disease characterized by genetic and epigenetic variations in tumor cells. Increasing evidence has shown that the dysregulation of m6A-related effectors, as methyltransferases, demethylases, and m6A binding proteins, is pivotal in breast cancer pathogenesis. In this review, we have summarized the most up-to-date research on the biological functions of m6A modification in breast cancer and have discussed the potential clinical applications and future directions of m6A modification as a biomarker as well as a therapeutic target of breast cancer.
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Affiliation(s)
- Yanyan Wang
- Department of Breast Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China.
| | - Yujie Zhang
- Department of Orthopedic Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Yushen Du
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA, 90095, USA
| | - Meiqi Zhou
- Department of Breast Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Yue Hu
- Department of Breast Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
| | - Suzhan Zhang
- Department of Breast Surgery, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310009, Zhejiang, China
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273
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Goss KL, Koppenhafer SL, Waters T, Terry WW, Wen KK, Wu M, Ostergaard J, Gordon PM, Gordon DJ. The translational repressor 4E-BP1 regulates RRM2 levels and functions as a tumor suppressor in Ewing sarcoma tumors. Oncogene 2020; 40:564-577. [PMID: 33191406 PMCID: PMC7856031 DOI: 10.1038/s41388-020-01552-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 10/27/2020] [Accepted: 10/30/2020] [Indexed: 12/15/2022]
Abstract
Ribonucleotide reductase (RNR), which is a heterodimeric tetramer composed of RRM1 and RRM2 subunits, is the rate-limiting enzyme in the synthesis of deoxyribonucleoside triphosphates (dNTPs) and essential for both DNA replication and the repair of DNA damage. The activity of RNR is coordinated with the cell cycle and regulated by fluctuations in the level of the RRM2 subunit. Multiple cancer types, including Ewing sarcoma tumors, are sensitive to inhibitors of RNR or a reduction in the levels of either the RRM1 or RRM2 subunits of RNR. Here, we show that the expression of the RRM2 protein is dependent on active protein synthesis and that 4E-BP1, a repressor of cap-dependent protein translation, specifically regulates the level of the RRM2 protein. Furthermore, inhibition of mTORC1/2, but not mTORC1, activates 4E-BP1, inhibits protein synthesis, and reduces the level of the RRM2 protein in multiple sarcoma cell lines. This effect of mTORC1/2 inhibitors on protein synthesis and RRM2 levels was rescued in cell lines with the CRISPR/Cas9-mediated knockout of 4E-BP1. In addition, the inducible expression of a mutant 4E-BP1 protein that cannot be phosphorylated by mTOR blocked protein synthesis and inhibited the growth of Ewing sarcoma cells in vitro and in vivo in a xenograft. Overall, these results provide insight into the multifaceted regulation of RRM2 protein levels and identify a regulatory link between protein translation and DNA replication.
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Affiliation(s)
- Kelli L Goss
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Iowa, Iowa City, IA, 52242, USA
| | - Stacia L Koppenhafer
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Iowa, Iowa City, IA, 52242, USA
| | - Torin Waters
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Iowa, Iowa City, IA, 52242, USA
| | - William W Terry
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Iowa, Iowa City, IA, 52242, USA
| | - Kuo-Kuang Wen
- Department of Biochemistry, University of Iowa, Iowa City, IA, 52242, USA
| | - Meng Wu
- Department of Biochemistry, University of Iowa, Iowa City, IA, 52242, USA
| | - Jason Ostergaard
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - Peter M Gordon
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Minnesota, Minneapolis, MN, 55455, USA
| | - David J Gordon
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Iowa, Iowa City, IA, 52242, USA.
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274
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Affiliation(s)
- Jie Li
- School of Medicine Huaqiao University Quanzhou 362021 P. R. China
| | - Jieqing Liu
- School of Medicine Huaqiao University Quanzhou 362021 P. R. China
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275
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Gui W, Shen S, Zhuang Z. Photocaged Cell-Permeable Ubiquitin Probe for Temporal Profiling of Deubiquitinating Enzymes. J Am Chem Soc 2020; 142:19493-19501. [PMID: 33141564 DOI: 10.1021/jacs.9b12426] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Photocaged cell-permeable ubiquitin probe holds promise in profiling the activity of cellular deubiquitinating enzymes (DUBs) with the much needed temporal control. Here we report a new photocaged cell-permeable ubiquitin probe that undergoes photoactivation upon 365 nm UV treatment and enables intracellular deubiquitinating enzyme profiling. We used a semisynthetic approach to generate modular ubiquitin-based probe containing a tetrazole-derived warhead at the C-terminus of ubiquitin and employed a cyclic polyarginine cell-penetrating peptide (cR10) conjugated to the N-terminus of ubiquitin via a disulfide linkage to deliver the probe into live cells. Upon 365 nm UV irradiation, the tetrazole group is converted to a nitrilimine intermediate in situ, which reacts with nearby nucleophilic cysteine residue from the DUB active site. The new photocaged cell-permeable probe showed good reactivity toward purified DUBs, including USP2, UCHL1, and UCHL3, upon photoirradiation. The Ub-tetrazole probe was also assessed in HeLa cell lysate and showed robust labeling only upon photoactivation. We further carried out protein profiling in intact HeLa cells using the new photocaged cell-permeable ubiquitin probe and identified DUBs captured by the probe using label-free quantitative (LFQ) mass spectrometry. Importantly, the photocaged cell-permeable ubiquitin probe captured DUBs specifically in respective G1/S and G2/M phases in synchronized HeLa cells. Moreover, using this probe DUBs were profiled at different time points following the release of HeLa cells from G1/S phase. Our results showed that photocaged cell-permeable probe represents a valuable new tool for achieving a better understanding of the cellular functions of DUBs.
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Affiliation(s)
- Weijun Gui
- Department of Chemistry and Biochemistry, University of Delaware, 214A Drake Hall, Newark, Delaware 19716, United States
| | - Siqi Shen
- Department of Chemistry and Biochemistry, University of Delaware, 214A Drake Hall, Newark, Delaware 19716, United States
| | - Zhihao Zhuang
- Department of Chemistry and Biochemistry, University of Delaware, 214A Drake Hall, Newark, Delaware 19716, United States
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276
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Posternak G, Tang X, Maisonneuve P, Jin T, Lavoie H, Daou S, Orlicky S, Goullet de Rugy T, Caldwell L, Chan K, Aman A, Prakesch M, Poda G, Mader P, Wong C, Maier S, Kitaygorodsky J, Larsen B, Colwill K, Yin Z, Ceccarelli DF, Batey RA, Taipale M, Kurinov I, Uehling D, Wrana J, Durocher D, Gingras AC, Al-Awar R, Therrien M, Sicheri F. Functional characterization of a PROTAC directed against BRAF mutant V600E. Nat Chem Biol 2020; 16:1170-1178. [PMID: 32778845 PMCID: PMC7862923 DOI: 10.1038/s41589-020-0609-7] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 07/01/2020] [Indexed: 12/22/2022]
Abstract
The RAF family kinases function in the RAS-ERK pathway to transmit signals from activated RAS to the downstream kinases MEK and ERK. This pathway regulates cell proliferation, differentiation and survival, enabling mutations in RAS and RAF to act as potent drivers of human cancers. Drugs targeting the prevalent oncogenic mutant BRAF(V600E) have shown great efficacy in the clinic, but long-term effectiveness is limited by resistance mechanisms that often exploit the dimerization-dependent process by which RAF kinases are activated. Here, we investigated a proteolysis-targeting chimera (PROTAC) approach to BRAF inhibition. The most effective PROTAC, termed P4B, displayed superior specificity and inhibitory properties relative to non-PROTAC controls in BRAF(V600E) cell lines. In addition, P4B displayed utility in cell lines harboring alternative BRAF mutations that impart resistance to conventional BRAF inhibitors. This work provides a proof of concept for a substitute to conventional chemical inhibition to therapeutically constrain oncogenic BRAF.
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Affiliation(s)
- Ganna Posternak
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Xiaojing Tang
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Pierre Maisonneuve
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Ting Jin
- Institute for Research in Immunology and Cancer, Laboratory of Intracellular Signaling, Université de Montréal, Quebec, Montreal, Canada
| | - Hugo Lavoie
- Institute for Research in Immunology and Cancer, Laboratory of Intracellular Signaling, Université de Montréal, Quebec, Montreal, Canada
| | - Salima Daou
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Stephen Orlicky
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Theo Goullet de Rugy
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Lauren Caldwell
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Kin Chan
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Ahmed Aman
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Michael Prakesch
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Gennady Poda
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario, Canada
| | - Pavel Mader
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Cassandra Wong
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Stefan Maier
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Julia Kitaygorodsky
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Brett Larsen
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Karen Colwill
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Zhe Yin
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Derek F Ceccarelli
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Robert A Batey
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Mikko Taipale
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Donnelly Centre for Cellular and Biomolecular Research, Toronto, Ontario, Canada
| | - Igor Kurinov
- Department of Chemistry and Chemical Biology, Cornell University, NE-CAT, Argonne, IL, USA
| | - David Uehling
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Jeff Wrana
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Daniel Durocher
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Anne-Claude Gingras
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Rima Al-Awar
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Marc Therrien
- Institute for Research in Immunology and Cancer, Laboratory of Intracellular Signaling, Université de Montréal, Quebec, Montreal, Canada.
- Département de Pathologie et Biologie Cellulaire, University of Montréal, Quebec, Montreal, Canada.
| | - Frank Sicheri
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
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277
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Proteolysis targeting chimera (PROTAC) in drug discovery paradigm: Recent progress and future challenges. Eur J Med Chem 2020; 210:112981. [PMID: 33160761 DOI: 10.1016/j.ejmech.2020.112981] [Citation(s) in RCA: 112] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/23/2020] [Accepted: 10/27/2020] [Indexed: 02/07/2023]
Abstract
Proteolysis targeting chimera (PROTAC), hijacking protein of interest (POI) and recruiting E3 ligase for target degradation via the ubiquitin-proteasome pathway, is a novel drug discovery paradigm which has been widely used as biological tools and medicinal molecules with the potential of clinical application value. Currently, ARV-110, an orally small molecule PROTAC was designed to specifically target Androgen receptor (AR), firstly enters clinical phase I trials for the treatment of metastatic castration-resistant prostate cancer, which turns a new avenue for the development of PROTAC. We herein provide a detail summary on the latest one year progress of PROTAC target various proteins and elucidate the advantages of PROTAC technology. Finally, the potential challenges of this vibrant field are also discussed.
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278
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Goracci L, Desantis J, Valeri A, Castellani B, Eleuteri M, Cruciani G. Understanding the Metabolism of Proteolysis Targeting Chimeras (PROTACs): The Next Step toward Pharmaceutical Applications. J Med Chem 2020; 63:11615-11638. [PMID: 33026811 PMCID: PMC8015227 DOI: 10.1021/acs.jmedchem.0c00793] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Indexed: 12/15/2022]
Abstract
Hetero-bifunctional PROteolysis TArgeting Chimeras (PROTACs) represent a new emerging class of small molecules designed to induce polyubiquitylation and proteasomal-dependent degradation of a target protein. Despite the increasing number of publications about the synthesis, biological evaluation, and mechanism of action of PROTACs, the characterization of the pharmacokinetic properties of this class of compounds is still minimal. Here, we report a study on the metabolism of a series of 40 PROTACs in cryopreserved human hepatocytes at multiple time points. Our results indicated that the metabolism of PROTACs could not be predicted from that of their constituent ligands. Their linkers' chemical nature and length resulted in playing a major role in the PROTACs' liability. A subset of compounds was also tested for metabolism by human cytochrome P450 3A4 (CYP3A4) and human aldehyde oxidase (hAOX) for more in-depth data interpretation, and both enzymes resulted in active PROTAC metabolism.
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Affiliation(s)
- Laura Goracci
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
| | - Jenny Desantis
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
| | | | - Beatrice Castellani
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
| | - Michela Eleuteri
- Montelino
Therapeutics, LLC, 7
Powdermill Lane, Southborough, Massachusetts 01772 Unites States
| | - Gabriele Cruciani
- Department
of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
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279
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Powell CE, Du G, Che J, He Z, Donovan KA, Yue H, Wang ES, Nowak RP, Zhang T, Fischer ES, Gray NS. Selective Degradation of GSPT1 by Cereblon Modulators Identified via a Focused Combinatorial Library. ACS Chem Biol 2020; 15:2722-2730. [PMID: 32865967 DOI: 10.1021/acschembio.0c00520] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cereblon (CRBN) is an E3 ligase adapter protein that can be reprogrammed by imide-class compounds such as thalidomide, lenalidomide, and pomalidomide to induce the degradation of neo-substrate proteins. In order to identify additional small molecule CRBN modulators, we implemented a focused combinatorial library approach where we fused an imide-based CRBN-binding pharmacophore to a heterocyclic scaffold, which could be further elaborated. We screened the library for CRBN-dependent antiproliferative activity in the multiple myeloma cell line MM1.S and identified five hit compounds. Quantitative chemical proteomics of hit compounds revealed that they induced selective degradation of GSPT1, a translation termination factor that is currently being explored as a therapeutic target for the treatment of acute myeloid leukemia. Molecular docking studies with CRBN and GSPT1 followed by analogue synthesis identified a possible hydrogen bond interaction with the central pyrimidine ring as a molecular determinant of hit compounds' selectivity. This study demonstrates that a focused combinatorial library design, phenotypic screening, and chemical proteomics can provide a suitable workflow to efficiently identify novel CRBN modulators.
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Affiliation(s)
- Chelsea E. Powell
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Guangyan Du
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Jianwei Che
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Zhixiang He
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Katherine A. Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Hong Yue
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Eric S. Wang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Radosław P. Nowak
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Tinghu Zhang
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Eric S. Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
| | - Nathanael S. Gray
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02215, United States
- Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, United States
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280
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Lu Y, Sun H. Progress in the Development of Small Molecular Inhibitors of Focal Adhesion Kinase (FAK). J Med Chem 2020; 63:14382-14403. [PMID: 33058670 DOI: 10.1021/acs.jmedchem.0c01248] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Focal adhesion kinase (FAK) is a nonreceptor intracellular tyrosine kinase that plays an essential role in cancer cell adhesion, survival, proliferation, and migration through both its enzymatic activities and scaffolding functions. Overexpression of FAK has been found in many human cancer cells from different origins, which promotes tumor progression and influences clinical outcomes in different classes of human tumors. Therefore, FAK has been considered as a promising target for small molecule anticancer drug development. Many FAK inhibitors targeting different domains of FAK with various mechanisms of functions have been reported, including kinase domain inhibitors, FERM domain inhibitors, and FAT domain inhibitors. In addition, FAK-targeting PROTACs, which can induce the degradation of FAK, have also been developed. In this Perspective, we summarized the progress in the development of small molecular FAK inhibitors and proposed the perspectives for the future development of agents targeting FAK.
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Affiliation(s)
- Yang Lu
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
| | - Haiying Sun
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, China Pharmaceutical University, 639 Longmian Avenue, Nanjing 211198, China
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281
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Troup RI, Fallan C, Baud MGJ. Current strategies for the design of PROTAC linkers: a critical review. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2020; 1:273-312. [PMID: 36046485 PMCID: PMC9400730 DOI: 10.37349/etat.2020.00018] [Citation(s) in RCA: 137] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 08/23/2020] [Indexed: 12/11/2022] Open
Abstract
PROteolysis TArgeting Chimeras (PROTACs) are heterobifunctional molecules consisting of two ligands; an “anchor” to bind to an E3 ubiquitin ligase and a “warhead” to bind to a protein of interest, connected by a chemical linker. Targeted protein degradation by PROTACs has emerged as a new modality for the knock down of a range of proteins, with the first agents now reaching clinical evaluation. It has become increasingly clear that the length and composition of the linker play critical roles on the physicochemical properties and bioactivity of PROTACs. While linker design has historically received limited attention, the PROTAC field is evolving rapidly and currently undergoing an important shift from synthetically tractable alkyl and polyethylene glycol to more sophisticated functional linkers. This promises to unlock a wealth of novel PROTAC agents with enhanced bioactivity for therapeutic intervention. Here, the authors provide a timely overview of the diverse linker classes in the published literature, along with their underlying design principles and overall influence on the properties and bioactivity of the associated PROTACs. Finally, the authors provide a critical analysis of current strategies for PROTAC assembly. The authors highlight important limitations associated with the traditional “trial and error” approach around linker design and selection, and suggest potential future avenues to further inform rational linker design and accelerate the identification of optimised PROTACs. In particular, the authors believe that advances in computational and structural methods will play an essential role to gain a better understanding of the structure and dynamics of PROTAC ternary complexes, and will be essential to address the current gaps in knowledge associated with PROTAC design.
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Affiliation(s)
- Robert I. Troup
- School of Chemistry, University of Southampton, Highfield, SO17 1BJ Southampton, UK
| | - Charlene Fallan
- Medicinal Chemistry, Oncology R&D, AstraZeneca, Cambridge Science Park, Milton Road, CB4 0WG Cambridge, UK
| | - Matthias G. J. Baud
- School of Chemistry, University of Southampton, Highfield, SO17 1BJ Southampton, UK
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282
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Recent advances in small molecular modulators targeting histone deacetylase 6. FUTURE DRUG DISCOVERY 2020. [DOI: 10.4155/fdd-2020-0023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Histone deacetylase 6 (HDAC6) is a unique isozyme in the HDAC family with various distinguished characters. HDAC6 is predominantly localized in the cytoplasm and has several specific nonhistone substrates, such as α-tubulin, cortactin, Hsp90, tau and peroxiredoxins. Accumulating evidence reveals that targeting HDAC6 may serve as a promising therapeutic strategy for the treatment of cancers, neurological disorders and immune diseases, making the development of HDAC6 inhibitors particularly attractive. Recently, multitarget drug design and proteolysis targeting chimera technology have also been applied in the discovery of novel small molecular modulators targeting HDAC6. In this review, we briefly describe the structural features and biological functions of HDAC6 and discuss the recent advances in HDAC6 modulators, including selective inhibitors, chimeric inhibitors and proteolysis targeting chimeras for multiple therapeutic purposes.
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283
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Wang PF, Qiu HY, He Y, Zhu HL. Cyclin-dependent kinase 4/6 inhibitors for cancer therapy: a patent review (2015 - 2019). Expert Opin Ther Pat 2020; 30:795-805. [PMID: 32945222 DOI: 10.1080/13543776.2020.1825686] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Cyclin-dependent kinases 4 and 6 (CDK4/6) along with their upstream/downstream components are pivotal regulators for the cell cycle progression. The dysfunction of CDK4/6 is the common feature and promoting factor in various cancer types. In-depth research on CDK4/6 inhibitors has afforded therapeutic agents, while new challenges and ideas are emerging concomitantly. AREAS COVERED This review focuses on patent publications related to CDK4/6 inhibitors which could be utilized for anti-cancer purposes during the period 2015-2019. EXPERT OPINION The increasingly comprehensive and thorough understanding of CDK4/6 inhibitors facilitates them to break through the current limitations. Hence the utilization of CDK4/6 inhibitors for cancer therapy in the near future is likely to be performed in diverse forms and for distinct purposes. Selectivity over kinases is still crucial to new agent development but shall be prudently dealt with. The gradually revealing of resistance and adverse events proposed another issue that calls for new tackling strategies.
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Affiliation(s)
- Peng-Fei Wang
- School of Pharmaceutical Sciences and Innovative Drug Research Centre, Chongqing University , Chongqing, People's Republic of China
| | - Han-Yue Qiu
- School of Pharmaceutical Sciences and Innovative Drug Research Centre, Chongqing University , Chongqing, People's Republic of China
| | - Yun He
- School of Pharmaceutical Sciences and Innovative Drug Research Centre, Chongqing University , Chongqing, People's Republic of China
| | - Hai-Liang Zhu
- State Key Laboratory of Pharmaceutical Biotechnology, Nanjing University , Nanjing, People's Republic of China
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284
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Induced protein degradation of histone deacetylases 3 (HDAC3) by proteolysis targeting chimera (PROTAC). Eur J Med Chem 2020; 208:112800. [PMID: 32971411 DOI: 10.1016/j.ejmech.2020.112800] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 08/04/2020] [Accepted: 08/27/2020] [Indexed: 12/19/2022]
Abstract
Histone deacetylases (HDACs) play important roles in inflammatory diseases like asthma and chronic obstructive pulmonary disease (COPD). Unravelling of and interfering with the functions of specific isoenzymes contributing to inflammation provides opportunities for drug development. Here we synthesize proteolysis targeting chimeras (PROTACs) for degradation of class I HDACs in which o-aminoanilide-based class I HDAC inhibitors are tethered to the cereblon ligand pomalidomide. One of these PROTACs, denoted HD-TAC7, showed promising degradation effects for HDAC3 with a DC50 value of 0.32 μM. In contrast to biochemical evidence using siRNA, HD-TAC7 showed a minimal effect on gene expression in LPS/IFNγ-stimulated RAW 264.7 macrophages. The lack of effect can be attributed to downregulation of the NF-κB subunit p65, which is a known side effect of pomalidomide treatment. Altogether, we describe a novel PROTAC that enables selective downregulation of HDAC3 levels, however we note that concomitant downregulation of the NF-κB subunit p65 can confound the biological outcome.
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285
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Luh LM, Scheib U, Juenemann K, Wortmann L, Brands M, Cromm PM. Prey for the Proteasome: Targeted Protein Degradation-A Medicinal Chemist's Perspective. Angew Chem Int Ed Engl 2020; 59:15448-15466. [PMID: 32428344 PMCID: PMC7496094 DOI: 10.1002/anie.202004310] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Indexed: 12/12/2022]
Abstract
Targeted protein degradation (TPD), the ability to control a proteins fate by triggering its degradation in a highly selective and effective manner, has created tremendous excitement in chemical biology and drug discovery within the past decades. The TPD field is spearheaded by small molecule induced protein degradation with molecular glues and proteolysis targeting chimeras (PROTACs) paving the way to expand the druggable space and to create a new paradigm in drug discovery. However, besides the therapeutic angle of TPD a plethora of novel techniques to modulate and control protein levels have been developed. This enables chemical biologists to better understand protein function and to discover and verify new therapeutic targets. This Review gives a comprehensive overview of chemical biology techniques inducing TPD. It explains the strengths and weaknesses of these methods in the context of drug discovery and discusses their future potential from a medicinal chemist's perspective.
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Affiliation(s)
- Laura M. Luh
- Research and DevelopmentPharmaceuticalsBayer AG13353BerlinGermany
| | - Ulrike Scheib
- Research and DevelopmentPharmaceuticalsBayer AG13353BerlinGermany
| | - Katrin Juenemann
- Research and DevelopmentPharmaceuticalsBayer AG13353BerlinGermany
| | - Lars Wortmann
- Research and DevelopmentPharmaceuticalsBayer AG13353BerlinGermany
| | - Michael Brands
- Research and DevelopmentPharmaceuticalsBayer AG13353BerlinGermany
| | - Philipp M. Cromm
- Research and DevelopmentPharmaceuticalsBayer AG13353BerlinGermany
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286
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Shahar N, Larisch S. Inhibiting the inhibitors: Targeting anti-apoptotic proteins in cancer and therapy resistance. Drug Resist Updat 2020; 52:100712. [DOI: 10.1016/j.drup.2020.100712] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/29/2020] [Accepted: 06/05/2020] [Indexed: 12/14/2022]
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287
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Dyla M, Kjaergaard M. Intrinsically disordered linkers control tethered kinases via effective concentration. Proc Natl Acad Sci U S A 2020; 117:21413-21419. [PMID: 32817491 PMCID: PMC7474599 DOI: 10.1073/pnas.2006382117] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Kinase specificity is crucial to the fidelity of signaling pathways, yet many pathways use the same kinases to achieve widely different effects. Specificity arises in part from the enzymatic domain but also from the physical tethering of kinases to their substrates. Such tethering can occur via protein interaction domains in the kinase or via anchoring and scaffolding proteins and can drastically increase the kinetics of phosphorylation. However, we do not know how such intracomplex reactions depend on the link between enzyme and substrate. Here we show that the kinetics of tethered kinases follow a Michaelis-Menten-like dependence on effective concentration. We find that phosphorylation kinetics scale with the length of the intrinsically disordered linkers that join the enzyme and substrate but that the scaling differs between substrates. Steady-state kinetics can only partially predict rates of tethered reactions as product release may obscure the rate of phosphotransfer. Our results suggest that changes in signaling complex architecture not only enhance the rates of phosphorylation reactions but may also alter the relative substrate usage. This suggests a mechanism for how scaffolding proteins can allosterically modify the output from a signaling pathway.
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Affiliation(s)
- Mateusz Dyla
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
- Danish Research Institute of Translational Neuroscience - DANDRITE, Nordic-EMBL (European Molecular Biology Laboratory) Partnership for Molecular Medicine, DK-8000 Aarhus, Denmark
| | - Magnus Kjaergaard
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark;
- Danish Research Institute of Translational Neuroscience - DANDRITE, Nordic-EMBL (European Molecular Biology Laboratory) Partnership for Molecular Medicine, DK-8000 Aarhus, Denmark
- Center for Proteins in Memory, Danish National Research Foundation, DK-8000 Aarhus, Denmark
- Aarhus Institute of Advanced Studies, Aarhus University, DK-8000 Aarhus, Denmark
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288
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Han B. A suite of mathematical solutions to describe ternary complex formation and their application to targeted protein degradation by heterobifunctional ligands. J Biol Chem 2020; 295:15280-15291. [PMID: 32859748 PMCID: PMC7650257 DOI: 10.1074/jbc.ra120.014715] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 08/25/2020] [Indexed: 01/30/2023] Open
Abstract
Small molecule–induced targeted protein degradation by heterobifunctional ligands or molecular glues represents a new modality in drug development, allowing development of therapeutic agents for targets previously considered undruggable. Successful target engagement requires the formation of a ternary complex (TC) when the ligand brings its target protein in contact with an E3 ubiquitin ligase. Unlike traditional drugs, where target engagement can be described by a simple bimolecular equilibrium equation, similar mathematical tools are currently not available to describe TC formation in a universal manner. This current limitation substantially increases the challenges of developing drugs with targeted protein degradation mechanism. In this article, I provide a full, exact, and universal mathematical description of the TC system at equilibrium for the first time. I have also constructed a comprehensive suite of mathematical tools for quantitative measurement of target engagement and equilibrium constants from experimental data. Mechanistic explanations are provided for many common challenges associated with developing this type of therapeutic agent. Insights from these analyses provide testable hypotheses and grant direction to drug development efforts in this promising area. The mathematical and analytical tools described in this article may also have broader applications in other areas of biology and chemistry in which ternary complexes are observed.
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Affiliation(s)
- Bomie Han
- Department of Molecular Pharmacology, Discovery Chemistry Research and Technologies, Lilly Research Laboratories, Eli Lilly and Co., Indianapolis, Indiana, USA.
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289
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De Vita E, Maneiro M, Tate EW. The Missing Link between (Un)druggable and Degradable KRAS. ACS CENTRAL SCIENCE 2020; 6:1281-1284. [PMID: 32875070 PMCID: PMC7453419 DOI: 10.1021/acscentsci.0c00920] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Affiliation(s)
| | | | - Edward W. Tate
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, Wood Lane, London W12 0BZ, U.K.
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290
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Bond M, Chu L, Nalawansha DA, Li K, Crews CM. Targeted Degradation of Oncogenic KRAS G12C by VHL-Recruiting PROTACs. ACS CENTRAL SCIENCE 2020; 6:1367-1375. [PMID: 32875077 PMCID: PMC7453568 DOI: 10.1021/acscentsci.0c00411] [Citation(s) in RCA: 218] [Impact Index Per Article: 54.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Indexed: 05/16/2023]
Abstract
KRAS is mutated in ∼20% of human cancers and is one of the most sought-after targets for pharmacological modulation, despite having historically been considered "undruggable." The discovery of potent covalent inhibitors of the KRASG12C mutant in recent years has sparked a new wave of interest in small molecules targeting KRAS. While these inhibitors have shown promise in the clinic, we wanted to explore PROTAC-mediated degradation as a complementary strategy to modulate mutant KRAS. Herein, we report the development of LC-2, the first PROTAC capable of degrading endogenous KRASG12C. LC-2 covalently binds KRASG12C with a MRTX849 warhead and recruits the E3 ligase VHL, inducing rapid and sustained KRASG12C degradation leading to suppression of MAPK signaling in both homozygous and heterozygous KRASG12C cell lines. LC-2 demonstrates that PROTAC-mediated degradation is a viable option for attenuating oncogenic KRAS levels and downstream signaling in cancer cells.
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Affiliation(s)
- Michael
J. Bond
- Department
of Pharmacology, Yale University, New Haven, Connecticut 06511, United States
| | - Ling Chu
- Department
of Molecular, Cellular, and Developmental Biology, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06511, United States
| | - Dhanusha A. Nalawansha
- Department
of Molecular, Cellular, and Developmental Biology, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06511, United States
| | - Ke Li
- Department
of Molecular, Cellular, and Developmental Biology, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06511, United States
| | - Craig M. Crews
- Department
of Pharmacology, Yale University, New Haven, Connecticut 06511, United States
- Department
of Molecular, Cellular, and Developmental Biology, Yale University, 260 Whitney Avenue, New Haven, Connecticut 06511, United States
- Department
of Chemistry, Yale University, New Haven, Connecticut 06511, United States
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291
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Xiao Y, Wang J, Zhao LY, Chen X, Zheng G, Zhang X, Liao D. Discovery of histone deacetylase 3 (HDAC3)-specific PROTACs. Chem Commun (Camb) 2020; 56:9866-9869. [PMID: 32840532 PMCID: PMC7654701 DOI: 10.1039/d0cc03243c] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Histone deacetylases (HDACs) are validated drug targets for cancer treatment. Increased HDAC isozyme selectivity and novel strategies to inhibit HDAC activity could lead to safer and more effective drug candidates. Nonetheless, it is quite challenging to develop isozyme-specific HDACi due to the highly conserved catalytic domain. We discovered XZ9002, a first-in-class HDAC3-specific PROTAC that potently degraded HDAC3. Importantly, XZ9002 is more effective to inhibit cancer cell proliferation than its proteolysis-inactive counterpart, suggesting HDAC3 degradation is a novel and promising anticancer approach.
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Affiliation(s)
- Yufeng Xiao
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA.
| | - Jia Wang
- Department of Anatomy & Cell Biology, College of Medicine, UF Health Cancer Center, University of Florida, 2033 Mowry Road, Gainesville, FL 32610, USA. and Affiliated Dongzhimen Hospital, Beijing University of Chinses Medicine, Beijing, China and Department of Integrated Traditional and Western Medicine, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Lisa Y Zhao
- Department of Anatomy & Cell Biology, College of Medicine, UF Health Cancer Center, University of Florida, 2033 Mowry Road, Gainesville, FL 32610, USA.
| | - Xinyi Chen
- Affiliated Dongzhimen Hospital, Beijing University of Chinses Medicine, Beijing, China
| | - Guangrong Zheng
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA.
| | - Xuan Zhang
- Department of Medicinal Chemistry, College of Pharmacy, University of Florida, 1333 Center Drive, Gainesville, FL 32610, USA.
| | - Daiqing Liao
- Department of Anatomy & Cell Biology, College of Medicine, UF Health Cancer Center, University of Florida, 2033 Mowry Road, Gainesville, FL 32610, USA.
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292
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Zheng S, Tao W. Targeting Cullin-RING E3 Ligases for Radiosensitization: From NEDDylation Inhibition to PROTACs. Front Oncol 2020; 10:1517. [PMID: 32983997 PMCID: PMC7475704 DOI: 10.3389/fonc.2020.01517] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 07/15/2020] [Indexed: 12/24/2022] Open
Abstract
As a dynamic regulator for short-lived protein degradation and turnover, the ubiquitin-proteasome system (UPS) plays important roles in various biological processes, including response to cellular stress, regulation of cell cycle progression, and carcinogenesis. Over the past decade, research on targeting the cullin-RING (really interesting new gene) E3 ligases (CRLs) in the UPS has gained great momentum with the entry of late-phase clinical trials of its novel inhibitors MLN4924 (pevonedistat) and TAS4464. Several preclinical studies have demonstrated the efficacy of MLN4924 as a radiosensitizer, mainly due to its unique cytotoxic properties, including induction of DNA damage response, cell cycle checkpoints dysregulation, and inhibition of NF-κB and mTOR pathways. Recently, the PROteolysis TArgeting Chimeras (PROTACs) technology was developed to recruit the target proteins for CRL-mediated polyubiquitination, overcoming the resistance that develops inevitably with traditional targeted therapies. First-in-class cell-permeable PROTACs against critical radioresistance conferring proteins, including the epidermal growth factor receptor (EGFR), androgen receptor (AR) and estrogen receptor (ER), cyclin-dependent kinases (CDKs), MAP kinase kinase 1 (MEK1), and MEK2, have emerged in the past 5 years. In this review article, we will summarize the most important research findings of targeting CRLs for radiosensitization.
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Affiliation(s)
- Shuhua Zheng
- College of Osteopathic Medicine, Nova Southeastern University, Fort Lauderdale, FL, United States
| | - Wensi Tao
- Department of Radiation Oncology, University of Miami-Miller School of Medicine, Coral Gables, FL, United States
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293
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Jin J, Wu Y, Chen J, Shen Y, Zhang L, Zhang H, Chen L, Yuan H, Chen H, Zhang W, Luan X. The peptide PROTAC modality: a novel strategy for targeted protein ubiquitination. Theranostics 2020; 10:10141-10153. [PMID: 32929339 PMCID: PMC7481416 DOI: 10.7150/thno.46985] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 07/30/2020] [Indexed: 02/07/2023] Open
Abstract
Despite dramatic advances in drug discovery over the decades, effective therapeutic strategies for cancers treatment are still in urgent demands. PROteolysis TArgeting Chimera (PROTAC), a novel therapeutic modality, has been vigorously promoted in preclinical and clinical applications. Unlike small molecule PROTAC, peptide PROTAC (p-PROTAC) with advantages of high specificity and low toxicity, while avoiding the limitations of shallow binding pockets through large interacting surfaces, provides promising substitutions for E3 ubiquitin ligase complex-mediated ubiquitination of "undruggable proteins". It is worth noting that successful applications of p-PROTAC still have some obstacles, including low stability and poor membrane permeability. Hence, we highlight that p-PROTAC combined with cell-penetrating peptides, constrained conformation technique, and targeted delivery systems could be the future efforts for potential translational research.
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Affiliation(s)
- Jinmei Jin
- Institute of Interdisciplinary Integrative Medicine Research, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Ye Wu
- Institute of Interdisciplinary Integrative Medicine Research, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Jinjiao Chen
- Institute of Interdisciplinary Integrative Medicine Research, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
- Department of Pharmacology, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Yiwen Shen
- Institute of Interdisciplinary Integrative Medicine Research, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Lijun Zhang
- Institute of Interdisciplinary Integrative Medicine Research, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Hong Zhang
- Institute of Interdisciplinary Integrative Medicine Research, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Lili Chen
- Institute of Interdisciplinary Integrative Medicine Research, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Hebao Yuan
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109 US
| | - Hongzhuan Chen
- Institute of Interdisciplinary Integrative Medicine Research, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
- Department of Pharmacology and Chemical Biology, Shanghai Universities Collaborative Innovation Center for Translational Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Weidong Zhang
- Institute of Interdisciplinary Integrative Medicine Research, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
| | - Xin Luan
- Institute of Interdisciplinary Integrative Medicine Research, Shuguang Hospital, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
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294
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Cipriano A, Sbardella G, Ciulli A. Targeting epigenetic reader domains by chemical biology. Curr Opin Chem Biol 2020; 57:82-94. [DOI: 10.1016/j.cbpa.2020.05.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/17/2020] [Indexed: 12/17/2022]
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295
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Luh LM, Scheib U, Juenemann K, Wortmann L, Brands M, Cromm PM. Beute für das Proteasom: Gezielter Proteinabbau aus medizinalchemischer Perspektive. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004310] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Laura M. Luh
- Research and Development Pharmaceuticals Bayer AG 13353 Berlin Germany
| | - Ulrike Scheib
- Research and Development Pharmaceuticals Bayer AG 13353 Berlin Germany
| | - Katrin Juenemann
- Research and Development Pharmaceuticals Bayer AG 13353 Berlin Germany
| | - Lars Wortmann
- Research and Development Pharmaceuticals Bayer AG 13353 Berlin Germany
| | - Michael Brands
- Research and Development Pharmaceuticals Bayer AG 13353 Berlin Germany
| | - Philipp M. Cromm
- Research and Development Pharmaceuticals Bayer AG 13353 Berlin Germany
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296
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Functional characterization of SOX2 as an anticancer target. Signal Transduct Target Ther 2020; 5:135. [PMID: 32728033 PMCID: PMC7391717 DOI: 10.1038/s41392-020-00242-3] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/01/2020] [Accepted: 06/22/2020] [Indexed: 02/07/2023] Open
Abstract
SOX2 is a well-characterized pluripotent factor that is essential for stem cell self-renewal, reprogramming, and homeostasis. The cellular levels of SOX2 are precisely regulated by a complicated network at the levels of transcription, post-transcription, and post-translation. In many types of human cancer, SOX2 is dysregulated due to gene amplification and protein overexpression. SOX2 overexpression is associated with poor survival of cancer patients. Mechanistically, SOX2 promotes proliferation, survival, invasion/metastasis, cancer stemness, and drug resistance. SOX2 is, therefore, an attractive anticancer target. However, little progress has been made in the efforts to discover SOX2 inhibitors, largely due to undruggable nature of SOX2 as a transcription factor. In this review, we first briefly introduced SOX2 as a transcription factor, its domain structure, normal physiological functions, and its involvement in human cancers. We next discussed its role in embryonic development and stem cell-renewal. We then mainly focused on three aspects of SOX2: (a) the regulatory mechanisms of SOX2, including how SOX2 level is regulated, and how SOX2 cross-talks with multiple signaling pathways to control growth and survival; (b) the role of SOX2 in tumorigenesis and drug resistance; and (c) current drug discovery efforts on targeting SOX2, and the future perspectives to discover specific SOX2 inhibitors for effective cancer therapy.
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297
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Beveridge R, Kessler D, Rumpel K, Ettmayer P, Meinhart A, Clausen T. Native Mass Spectrometry Can Effectively Predict PROTAC Efficacy. ACS CENTRAL SCIENCE 2020; 6:1223-1230. [PMID: 32724856 PMCID: PMC7379389 DOI: 10.1021/acscentsci.0c00049] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Indexed: 05/16/2023]
Abstract
Protein degraders, also known as proteolysis targeting chimeras (PROTACs), are bifunctional small molecules that promote cellular degradation of a protein of interest (POI). PROTACs act as molecular mediators, bringing an E3 ligase and a POI into proximity, thus promoting ubiquitination and degradation of the targeted POI. Despite their great promise as next-generation pharmaceutical drugs, the development of new PROTACs is challenged by the complexity of the system, which involves binary and ternary interactions between components. Here, we demonstrate the strength of native mass spectrometry (nMS), a label-free technique, to provide novel insight into PROTAC-mediated protein interactions. We show that nMS can monitor the formation of ternary E3-PROTAC-POI complexes and detect various intermediate species in a single experiment. A unique benefit of the method is its ability to reveal preferentially formed E3-PROTAC-POI combinations in competition experiments with multiple substrate proteins, thereby positioning it as an ideal high-throughput screening strategy during the development of new PROTACs.
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Affiliation(s)
- Rebecca Beveridge
- Research
Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Dirk Kessler
- Discovery
Research, Boehringer Ingelheim Regional
Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Klaus Rumpel
- Discovery
Research, Boehringer Ingelheim Regional
Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Peter Ettmayer
- Discovery
Research, Boehringer Ingelheim Regional
Center Vienna GmbH & Co KG, 1120 Vienna, Austria
| | - Anton Meinhart
- Research
Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
| | - Tim Clausen
- Research
Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus-Vienna-Biocenter 1, 1030 Vienna, Austria
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298
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Abstract
In this issue of Cell Chemical Biology, Li et al. (2020), Hsu et al. (2020), and Potjewyd et al. (2020) expand the target spectrum amenable to protein degradation by designing degraders of the cell cycle checkpoint kinase Wee1 and the polycomb repressive complex 2 (PRC2) via its regulatory EED subunit.
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Affiliation(s)
- Martin G Jaeger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 AKH BT 25.3, 1090 Vienna, Austria
| | - Georg E Winter
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, Lazarettgasse 14 AKH BT 25.3, 1090 Vienna, Austria.
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299
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Pisa R, Kapoor TM. Chemical strategies to overcome resistance against targeted anticancer therapeutics. Nat Chem Biol 2020; 16:817-825. [PMID: 32694636 DOI: 10.1038/s41589-020-0596-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 06/17/2020] [Indexed: 12/12/2022]
Abstract
Emergence of resistance is a major factor limiting the efficacy of molecularly targeted anticancer drugs. Understanding the specific mutations, or other genetic or cellular changes, that confer drug resistance can help in the development of therapeutic strategies with improved efficacies. Here, we outline recent progress in understanding chemotype-specific mechanisms of resistance and present chemical strategies, such as designing drugs with distinct binding modes or using proteolysis targeting chimeras, to overcome resistance. We also discuss how targeting multiple binding sites with bifunctional inhibitors or identifying collateral sensitivity profiles can be exploited to limit the emergence of resistance. Finally, we highlight how incorporating analyses of resistance early in drug development can help with the design and evaluation of therapeutics that can have long-term benefits for patients.
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Affiliation(s)
- Rudolf Pisa
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY, USA.,Tri-Institutional PhD Program in Chemical Biology, The Rockefeller University, New York, NY, USA.,Department of Cell Biology, Harvard Medical School, Boston, MA, USA
| | - Tarun M Kapoor
- Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY, USA.
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300
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Yan Z, Shanmugasundaram K, Ma D, Luo J, Luo S, Rao H. The N-terminal domain of the non-receptor tyrosine kinase ABL confers protein instability and suppresses tumorigenesis. J Biol Chem 2020; 295:9069-9075. [PMID: 32439806 PMCID: PMC7335801 DOI: 10.1074/jbc.ra120.012821] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 05/20/2020] [Indexed: 11/06/2022] Open
Abstract
Chromosome translocation can lead to chimeric proteins that may become oncogenic drivers. A classic example is the fusion of the BCR activator of RhoGEF and GTPase and the ABL proto-oncogene nonreceptor tyrosine kinase, a result of a chromosome abnormality (Philadelphia chromosome) that causes leukemia. To unravel the mechanism underlying BCR-ABL-mediated tumorigenesis, here we compared the stability of ABL and the BCR-ABL fusion. Using protein degradation, cell proliferation, 5-ethynyl-2-deoxyuridine, and apoptosis assays, along with xenograft tumor analysis, we found that the N-terminal segment of ABL, which is lost in the BCR-ABL fusion, confers degradation capacity that is promoted by SMAD-specific E3 ubiquitin protein ligase 1. We further demonstrate that the N-terminal deletion renders ABL more stable and stimulates cell growth and tumorigenesis. The findings of our study suggest that altered protein stability may contribute to chromosome translocation-induced cancer development.
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Affiliation(s)
- Zhengwei Yan
- Center for Experimental Medicine, First Affiliated Hospital, Nanchang University, Nanchang, China
| | | | - Dongwen Ma
- Center for Experimental Medicine, First Affiliated Hospital, Nanchang University, Nanchang, China
| | - Jiayu Luo
- Center for Experimental Medicine, First Affiliated Hospital, Nanchang University, Nanchang, China
| | - Shiwen Luo
- Center for Experimental Medicine, First Affiliated Hospital, Nanchang University, Nanchang, China.
| | - Hai Rao
- Department of Molecular Medicine, University of Texas Health Science Center, San Antonio, Texas, USA.
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