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Ji M, Yu D, Liu X, Wang L, Zhang D, Yang Z, Huang W, Fan H, Wang L, Sun H. Glutathione-dependent degradation of SMARCA2/4 for targeted lung cancer therapy with improved selectivity. Eur J Med Chem 2024; 277:116751. [PMID: 39128328 DOI: 10.1016/j.ejmech.2024.116751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 07/20/2024] [Accepted: 08/03/2024] [Indexed: 08/13/2024]
Abstract
SMARCA2 and SMARCA4 are the mutually exclusive catalytic subunits of the mammalian Switch/Sucrose Non-Fermentable (SWI/SNF) chromatin remodeling complex, and have recently been considered as attractive synthetic lethal targets for PROTAC-based cancer therapy. However, the potential off-tissue toxicity towards normal tissues remains a concern. Here, we optimize a GSH-inducible SMARCA2/4-based PROTAC precursor with selective antitumor activity towards lung cancer cells and negligible cytotoxicity towards normal cells in both in vitro and in vivo studies. The precursor is not bioactive or cytotoxic, but preferentially responds to endogenous GSH in GSH-rich lung cancer cells, releasing active PROTAC to degrade SMARCA2/4 via PROTAC-mediated proteasome pathway. Subsequent xenograft model study reveals that selective SMARCA2/4 degradation in lung tumors triggers DNA damage and apoptosis, which significantly inhibits lung cancer cell proliferation without obvious adverse events towards normal tissues. This study exemplifies the targeted degradation of SMARCA2/4 in lung cancer cells by the GSH-responsive PROTAC precursor, highlighting its potential as an encouraging cancer therapeutic strategy.
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Affiliation(s)
- Ming Ji
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, Department of Chemical Biology, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Dehao Yu
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, Department of Chemical Biology, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Xinmin Liu
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, Department of Chemical Biology, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Luo Wang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, Department of Chemical Biology, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Dongli Zhang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, Department of Chemical Biology, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Zhengduo Yang
- Department of Pathology, Tianjin Union Medical Center, Tianjin, 300121, China
| | - Wanqiao Huang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, Department of Chemical Biology, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Heli Fan
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, Department of Chemical Biology, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China
| | - Lulu Wang
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, Department of Chemical Biology, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China.
| | - Huabing Sun
- The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Tianjin Key Laboratory on Technologies Enabling Development of Clinical Therapeutics and Diagnostics, Department of Chemical Biology, School of Pharmacy, Tianjin Medical University, Tianjin, 300070, China.
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2
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Cheng-Sánchez I, Gosselé K, Palaferri L, Laul E, Riccabella G, Bedi RK, Li Y, Müller A, Corbeski I, Caflisch A, Nevado C. Structure-Based Design of CBP/EP300 Degraders: When Cooperativity Overcomes Affinity. JACS AU 2024; 4:3466-3474. [PMID: 39328757 PMCID: PMC11423305 DOI: 10.1021/jacsau.4c00292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 06/25/2024] [Accepted: 07/03/2024] [Indexed: 09/28/2024]
Abstract
We present the development of dCE-2, a structurally novel PROTAC targeting the CREB-binding protein (CBP) and E1A-associated protein (EP300)-two homologous multidomain enzymes crucial for enhancer-mediated transcription. The design of dCE-2 was based on the crystal structure of an in-house bromodomain (BRD) inhibitor featuring a 3-methyl-cinnoline acetyl-lysine mimic acetyl-lysine mimic discovered by high-throughput fragment docking. Our study shows that, despite its modest binding affinity to CBP/EP300-BRD, dCE-2's remarkable protein degradation activity stems from its good cooperativity, which we demonstrate by the characterization of its ternary complex formation both in vitro and in cellulo. Molecular dynamics simulations indicate that in aqueous solvents, this active degrader populates both folded and extended conformations, which are likely to promote cell permeability and ternary complex formation, respectively.
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Affiliation(s)
- Iván Cheng-Sánchez
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Katherine Gosselé
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Leonardo Palaferri
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Eleen Laul
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Gionata Riccabella
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Rajiv K Bedi
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Yaozong Li
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Anna Müller
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Ivan Corbeski
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Amedeo Caflisch
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
| | - Cristina Nevado
- Department of Chemistry, University of Zurich, Winterthurerstrasse 190, Zurich CH-8057, Switzerland
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3
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Popow J, Farnaby W, Gollner A, Kofink C, Fischer G, Wurm M, Zollman D, Wijaya A, Mischerikow N, Hasenoehrl C, Prokofeva P, Arnhof H, Arce-Solano S, Bell S, Boeck G, Diers E, Frost AB, Goodwin-Tindall J, Karolyi-Oezguer J, Khan S, Klawatsch T, Koegl M, Kousek R, Kratochvil B, Kropatsch K, Lauber AA, McLennan R, Olt S, Peter D, Petermann O, Roessler V, Stolt-Bergner P, Strack P, Strauss E, Trainor N, Vetma V, Whitworth C, Zhong S, Quant J, Weinstabl H, Kuster B, Ettmayer P, Ciulli A. Targeting cancer with small-molecule pan-KRAS degraders. Science 2024; 385:1338-1347. [PMID: 39298590 DOI: 10.1126/science.adm8684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 07/23/2024] [Indexed: 09/22/2024]
Abstract
Mutations in the Kirsten rat sarcoma viral oncogene homolog (KRAS) protein are highly prevalent in cancer. However, small-molecule concepts that address oncogenic KRAS alleles remain elusive beyond replacing glycine at position 12 with cysteine (G12C), which is clinically drugged through covalent inhibitors. Guided by biophysical and structural studies of ternary complexes, we designed a heterobifunctional small molecule that potently degrades 13 out of 17 of the most prevalent oncogenic KRAS alleles. Compared with inhibition, KRAS degradation results in more profound and sustained pathway modulation across a broad range of KRAS mutant cell lines, killing cancer cells while sparing models without genetic KRAS aberrations. Pharmacological degradation of oncogenic KRAS was tolerated and led to tumor regression in vivo. Together, these findings unveil a new path toward addressing KRAS-driven cancers with small-molecule degraders.
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Affiliation(s)
- Johannes Popow
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | - William Farnaby
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee DD1 5JJ, UK
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, UK
| | | | | | | | - Melanie Wurm
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | - David Zollman
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee DD1 5JJ, UK
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, UK
| | - Andre Wijaya
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee DD1 5JJ, UK
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, UK
| | | | | | - Polina Prokofeva
- Proteomics and Bioanalytics, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | | | | | - Sammy Bell
- Boehringer Ingelheim Pharmaceuticals, Ridgefield, CT 06877, USA
| | - Georg Boeck
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | - Emelyne Diers
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, UK
| | - Aileen B Frost
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee DD1 5JJ, UK
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, UK
| | - Jake Goodwin-Tindall
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, UK
| | | | - Shakil Khan
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee DD1 5JJ, UK
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, UK
| | | | - Manfred Koegl
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | - Roland Kousek
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | | | | | - Arnel A Lauber
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | - Ross McLennan
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee DD1 5JJ, UK
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, UK
| | - Sabine Olt
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | - Daniel Peter
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | | | | | | | - Patrick Strack
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | - Eva Strauss
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | - Nicole Trainor
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, UK
| | - Vesna Vetma
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee DD1 5JJ, UK
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, UK
| | - Claire Whitworth
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, UK
| | - Siying Zhong
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, UK
| | - Jens Quant
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | | | - Bernhard Kuster
- Proteomics and Bioanalytics, School of Life Sciences, Technical University of Munich, 85354 Freising, Germany
| | - Peter Ettmayer
- Boehringer Ingelheim RCV GmbH & Co KG, 1221 Vienna, Austria
| | - Alessio Ciulli
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, Dundee DD1 5JJ, UK
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, James Black Centre, University of Dundee, Dundee DD1 5EH, UK
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4
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Pierri M, Liu X, Kroupova A, Rutter Z, Hallatt AJ, Ciulli A. Stereochemical inversion at a 1,4-cyclohexyl PROTAC linker fine-tunes conformation and binding affinity. Bioorg Med Chem Lett 2024; 110:129861. [PMID: 38942127 DOI: 10.1016/j.bmcl.2024.129861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 06/16/2024] [Accepted: 06/25/2024] [Indexed: 06/30/2024]
Abstract
Proteolysis targeting chimeras (PROTACs) are heterobifunctional small-molecule degraders made of a linker connecting a target-binding moiety to a ubiquitin E3 ligase-binding moiety. The linker unit is known to influence the physicochemical and pharmacokinetic properties of PROTACs, as well as the properties of ternary complexes, in turn impacting on their degradation activity in cells and in vivo. Our LRRK2 PROTAC XL01126, bearing a trans-cyclohexyl group in the linker, is a better and more cooperative degrader than its corresponding cis- analogue despite its much weaker binary binding affinities. Here, we investigate how this subtle stereocenter alteration in the linker affects the ligand binding affinity to the E3 ligase VHL. We designed a series of molecular matched pairs, truncating from the full PROTACs down to the VHL ligand, and find that across the series the trans-cyclohexyl compounds showed consistently weaker VHL-binding affinity compared to the cis- counterparts. High-resolution co-crystal structures revealed that the trans linker exhibits a rigid stick-out conformation, while the cis linker collapses into a folded-back conformation featuring a network of intramolecular contacts and long-range interactions with VHL. These observations are noteworthy as they reveal how a single stereochemical inversion within a PROTAC linker impacts conformational rigidity and binding mode, in turn fine-tuning differentiated propensity to binary and ternary complex formation, and ultimately cellular degradation activity.
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Affiliation(s)
- Martina Pierri
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ Dundee, United Kingdom
| | - Xingui Liu
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ Dundee, United Kingdom
| | - Alena Kroupova
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ Dundee, United Kingdom
| | - Zoe Rutter
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ Dundee, United Kingdom
| | - Alex J Hallatt
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ Dundee, United Kingdom
| | - Alessio Ciulli
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ Dundee, United Kingdom.
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5
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Tsai JM, Nowak RP, Ebert BL, Fischer ES. Targeted protein degradation: from mechanisms to clinic. Nat Rev Mol Cell Biol 2024; 25:740-757. [PMID: 38684868 DOI: 10.1038/s41580-024-00729-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2024] [Indexed: 05/02/2024]
Abstract
Targeted protein degradation refers to the use of small molecules to induce the selective degradation of proteins. In its most common form, this degradation is achieved through ligand-mediated neo-interactions between ubiquitin E3 ligases - the principal waste disposal machines of a cell - and the protein targets of interest, resulting in ubiquitylation and subsequent proteasomal degradation. Notable advances have been made in biological and mechanistic understanding of serendipitously discovered degraders. This improved understanding and novel chemistry has not only provided clinical proof of concept for targeted protein degradation but has also led to rapid growth of the field, with dozens of investigational drugs in active clinical trials. Two distinct classes of protein degradation therapeutics are being widely explored: bifunctional PROTACs and molecular glue degraders, both of which have their unique advantages and challenges. Here, we review the current landscape of targeted protein degradation approaches and how they have parallels in biological processes. We also outline the ongoing clinical exploration of novel degraders and provide some perspectives on the directions the field might take.
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Affiliation(s)
- Jonathan M Tsai
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Radosław P Nowak
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
- Institute of Structural Biology, Medical Faculty, University of Bonn, Bonn, Germany
| | - Benjamin L Ebert
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, MA, USA.
- Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Boston, MA, USA.
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.
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6
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Malone HA, Roberts CWM. Chromatin remodellers as therapeutic targets. Nat Rev Drug Discov 2024; 23:661-681. [PMID: 39014081 DOI: 10.1038/s41573-024-00978-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/28/2024] [Indexed: 07/18/2024]
Abstract
Large-scale cancer genome sequencing studies have revealed that chromatin regulators are frequently mutated in cancer. In particular, more than 20% of cancers harbour mutations in genes that encode subunits of SWI/SNF (BAF) chromatin remodelling complexes. Additional links of SWI/SNF complexes to disease have emerged with the findings that some oncogenes drive transformation by co-opting SWI/SNF function and that germline mutations in select SWI/SNF subunits are the basis of several neurodevelopmental disorders. Other chromatin remodellers, including members of the ISWI, CHD and INO80/SWR complexes, have also been linked to cancer and developmental disorders. Consequently, therapeutic manipulation of SWI/SNF and other remodelling complexes has become of great interest, and drugs that target SWI/SNF subunits have entered clinical trials. Genome-wide perturbation screens in cancer cell lines with SWI/SNF mutations have identified additional synthetic lethal targets and led to further compounds in clinical trials, including one that has progressed to FDA approval. Here, we review the progress in understanding the structure and function of SWI/SNF and other chromatin remodelling complexes, mechanisms by which SWI/SNF mutations cause cancer and neurological diseases, vulnerabilities that arise because of these mutations and efforts to target SWI/SNF complexes and synthetic lethal targets for therapeutic benefit.
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Affiliation(s)
- Hayden A Malone
- Division of Molecular Oncology, Department of Oncology, and Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN, USA
- St. Jude Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Charles W M Roberts
- Division of Molecular Oncology, Department of Oncology, and Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, TN, USA.
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7
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Kotagiri S, Wang Y, Han Y, Liang X, Blazanin N, Nguyen PK, Jiang Y, Lissanu Y. Discovery of Novel, Potent and Orally Bioavailable SMARCA2 PROTACs with Synergistic Anti-tumor Activity in Combination with KRAS G12C Inhibitors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.23.608456. [PMID: 39253520 PMCID: PMC11383272 DOI: 10.1101/2024.08.23.608456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/11/2024]
Abstract
Cancer genomic studies have identified frequent mutations in subunits of the SWI/SNF chromatin remodeling complex including SMARCA4 in non-small cell lung cancer with a frequency of up to 33% in advanced stage disease, making it the most frequently mutated complex in lung cancer. We and others have identified SMARCA2 to be synthetic lethal to SMARCA4, indicating SMARCA2 is a high value therapeutic target. Here, we disclose the discovery and characterization of potent, selective and orally bioavailable Cereblon-based SMARCA2 PROTACs. Biochemically, YDR1 and YD54 are potent SMARCA2 degraders with an average DC 50 of 7.7nM and 3.5nM respectively in SMARCA4 mutant lung cancer cells. Phenotypically, both YDR1 and YD54 selectively inhibited growth of SMARCA4 mutant cancer cells. Further, we showed anti-tumor growth inhibitory activity of YDR1 and YD54 in SMARCA4 mutant xenograft models of lung cancer. Finally, we show that YDR1 and YD54 synergize with the KRAS G12C inhibitor sotorasib to inhibit growth of SMARCA4 and KRAS G12C co-mutant lung cancer cells. These findings provide additional evidence for the utility of single agent or combination regimens containing SMARCA2 PROTACs as synthetic lethal therapeutics against SMARCA4 mutant cancers.
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8
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Xu M, Hong JJ, Zhang X, Sun M, Liu X, Kang J, Stack H, Fang W, Lei H, Lacoste X, Okada R, Jung R, Nguyen R, Shern JF, Thiele CJ, Liu Z. Targeting SWI/SNF ATPases reduces neuroblastoma cell plasticity. EMBO J 2024:10.1038/s44318-024-00206-1. [PMID: 39174852 DOI: 10.1038/s44318-024-00206-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 07/01/2024] [Accepted: 07/17/2024] [Indexed: 08/24/2024] Open
Abstract
Tumor cell heterogeneity defines therapy responsiveness in neuroblastoma (NB), a cancer derived from neural crest cells. NB consists of two primary subtypes: adrenergic and mesenchymal. Adrenergic traits predominate in NB tumors, while mesenchymal features becomes enriched post-chemotherapy or after relapse. The interconversion between these subtypes contributes to NB lineage plasticity, but the underlying mechanisms driving this phenotypic switching remain unclear. Here, we demonstrate that SWI/SNF chromatin remodeling complex ATPases are essential in establishing an mesenchymal gene-permissive chromatin state in adrenergic-type NB, facilitating lineage plasticity. Targeting SWI/SNF ATPases with SMARCA2/4 dual degraders effectively inhibits NB cell proliferation, invasion, and notably, cellular plasticity, thereby preventing chemotherapy resistance. Mechanistically, depletion of SWI/SNF ATPases compacts cis-regulatory elements, diminishes enhancer activity, and displaces core transcription factors (MYCN, HAND2, PHOX2B, and GATA3) from DNA, thereby suppressing transcriptional programs associated with plasticity. These findings underscore the pivotal role of SWI/SNF ATPases in driving intrinsic plasticity and therapy resistance in neuroblastoma, highlighting an epigenetic target for combinational treatments in this cancer.
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Affiliation(s)
- Man Xu
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Jason J Hong
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Xiyuan Zhang
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Ming Sun
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Xingyu Liu
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Jeeyoun Kang
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Hannah Stack
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Wendy Fang
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Haiyan Lei
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Xavier Lacoste
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Reona Okada
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Raina Jung
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Rosa Nguyen
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Jack F Shern
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Carol J Thiele
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
| | - Zhihui Liu
- Pediatric Oncology Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
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9
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Rovers E, Schapira M. Benchmarking Methods for PROTAC Ternary Complex Structure Prediction. J Chem Inf Model 2024; 64:6162-6173. [PMID: 39087481 DOI: 10.1021/acs.jcim.4c00426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2024]
Abstract
Proteolysis targeting chimeras (PROTACs) are bifunctional compounds that recruit an E3 ligase to a target protein to induce ubiquitination and degradation of the target. Rational optimization of PROTAC requires a structural model of the ternary complex. In the absence of an experimental structure, computational tools have emerged that attempt to predict PROTAC ternary complexes. Here, we systematically benchmark three commonly used tools: PRosettaC, MOE, and ICM. We find that these PROTAC-focused methods produce an array of ternary complex structures, including some that are observed experimentally, but also many that significantly deviate from the crystal structure. Molecular dynamics simulations show that PROTAC complexes may exist in a multiplicity of configurational states and question the use of experimentally observed structures as a reference for accurate predictions. The pioneering computational tools benchmarked here highlight the promises and challenges in the field and may be more valuable when guided by clear structural and biophysical data. The benchmarking data set that we provide may also be valuable for evaluating other and future computational tools for ternary complex modeling.
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Affiliation(s)
- Evianne Rovers
- Structural Genomics Consortium, Toronto M5G 1L7, Canada
- Department of Pharmacology, University of Toronto, Toronto M5G 1L7, Canada
| | - Matthieu Schapira
- Structural Genomics Consortium, Toronto M5G 1L7, Canada
- Department of Pharmacology, University of Toronto, Toronto M5G 1L7, Canada
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10
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Duplaquet L, So K, Ying AW, Pal Choudhuri S, Li X, Xu GD, Li Y, Qiu X, Li R, Singh S, Wu XS, Hamilton S, Chien VD, Liu Q, Qi J, Somerville TDD, Heiling HM, Mazzola E, Lee Y, Zoller T, Vakoc CR, Doench JG, Forrester WC, Abrams T, Long HW, Niederst MJ, Drapkin BJ, Kadoch C, Oser MG. Mammalian SWI/SNF complex activity regulates POU2F3 and constitutes a targetable dependency in small cell lung cancer. Cancer Cell 2024; 42:1352-1369.e13. [PMID: 39029464 DOI: 10.1016/j.ccell.2024.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 04/22/2024] [Accepted: 06/21/2024] [Indexed: 07/21/2024]
Abstract
Small cell lung cancers (SCLCs) are composed of heterogeneous subtypes marked by lineage-specific transcription factors, including ASCL1, NEUROD1, and POU2F3. POU2F3-positive SCLCs, ∼12% of all cases, are uniquely dependent on POU2F3 itself; as such, approaches to attenuate POU2F3 expression may represent new therapeutic opportunities. Here using genome-scale screens for regulators of POU2F3 expression and SCLC proliferation, we define mSWI/SNF complexes as top dependencies specific to POU2F3-positive SCLC. Notably, chemical disruption of mSWI/SNF ATPase activity attenuates proliferation of all POU2F3-positive SCLCs, while disruption of non-canonical BAF (ncBAF) via BRD9 degradation is effective in pure non-neuroendocrine POU2F3-SCLCs. mSWI/SNF targets to and maintains accessibility over gene loci central to POU2F3-mediated gene regulatory networks. Finally, clinical-grade pharmacologic disruption of SMARCA4/2 ATPases and BRD9 decreases POU2F3-SCLC tumor growth and increases survival in vivo. These results demonstrate mSWI/SNF-mediated governance of the POU2F3 oncogenic program and suggest mSWI/SNF inhibition as a therapeutic strategy for POU2F3-positive SCLCs.
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Affiliation(s)
- Leslie Duplaquet
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Kevin So
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Biological and Biomedical Sciences Graduate Program, Harvard Medical School, Boston, MA 02115, USA
| | - Alexander W Ying
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Shreoshi Pal Choudhuri
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Internal Medicine and Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xinyue Li
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Grace D Xu
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Yixiang Li
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Xintao Qiu
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Rong Li
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Shilpa Singh
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Xiaoli S Wu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY 11724, USA
| | - Seth Hamilton
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Internal Medicine and Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Victor D Chien
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Internal Medicine and Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Qi Liu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Jun Qi
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | - Hillary M Heiling
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Emanuele Mazzola
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Yenarae Lee
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Thomas Zoller
- Novartis BioMedical Research, Cambridge, MA 02139, USA
| | | | - John G Doench
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Tinya Abrams
- Novartis BioMedical Research, Cambridge, MA 02139, USA
| | - Henry W Long
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | | | - Benjamin J Drapkin
- Hamon Center for Therapeutic Oncology Research, University of Texas Southwestern Medical Center, Dallas, TX, USA; Department of Internal Medicine and Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Cigall Kadoch
- Department of Pediatric Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
| | - Matthew G Oser
- Department of Medical Oncology, Dana-Farber Cancer Institute and Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA; Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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11
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Kumar H, Sobhia ME. Interplay of PROTAC Complex Dynamics for Undruggable Targets: Insights into Ternary Complex Behavior and Linker Design. ACS Med Chem Lett 2024; 15:1306-1318. [PMID: 39140051 PMCID: PMC11317996 DOI: 10.1021/acsmedchemlett.4c00189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 07/25/2024] [Accepted: 07/25/2024] [Indexed: 08/15/2024] Open
Abstract
Protein degraders, such as bifunctional proteolysis-targeting chimeras (PROTACs), selectively eliminate target proteins by leveraging the natural protein degradation machinery. PROTACs bridge the target protein with an E3 ligase, which induces ubiquitination and degradation. Investigating ternary complex structures elucidates the molecular mechanisms of their formation and degradation. This study examines the binding dynamics of E3 ligases (VHL, CRBN, and cIAP) with proteins of interest, focusing on dynamics, cooperativity, selectivity, linker length, and PROTAC conformations. The influence of interface residues and linker lengths on specific conformations for target proteins and E3 ligases is highlighted. Utilizing molecular dynamics and steered molecular dynamics simulations, the study provides comprehensive parameters on the behavior and stability of diverse ternary complexes. These insights are crucial for designing PROTACs targeting disease-causing proteins and advancing the development of degradable ternary complexes for therapeutic applications.
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Affiliation(s)
- Harish Kumar
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and
Research (NIPER), Sector 67, S.A.S. Nagar (Mohali), 160062 Punjab, India
| | - Masilamani Elizabeth Sobhia
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and
Research (NIPER), Sector 67, S.A.S. Nagar (Mohali), 160062 Punjab, India
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12
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Trejo-Villegas OA, Heijink IH, Ávila-Moreno F. Preclinical evidence in the assembly of mammalian SWI/SNF complexes: Epigenetic insights and clinical perspectives in human lung disease therapy. Mol Ther 2024; 32:2470-2488. [PMID: 38910326 PMCID: PMC11405180 DOI: 10.1016/j.ymthe.2024.06.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 04/18/2024] [Accepted: 06/20/2024] [Indexed: 06/25/2024] Open
Abstract
The SWI/SNF complex, also known as the BRG1/BRM-associated factor (BAF) complex, represents a critical regulator of chromatin remodeling mechanisms in mammals. It is alternatively referred to as mSWI/SNF and has been suggested to be imbalanced in human disease compared with human health. Three types of BAF assemblies associated with it have been described, including (1) canonical BAF (cBAF), (2) polybromo-associated BAF (PBAF), and (3) non-canonical BAF (ncBAF) complexes. Each of these BAF assemblies plays a role, either functional or dysfunctional, in governing gene expression patterns, cellular processes, epigenetic mechanisms, and biological processes. Recent evidence increasingly links the dysregulation of mSWI/SNF complexes to various human non-malignant lung chronic disorders and lung malignant diseases. This review aims to provide a comprehensive general state-of-the-art and a profound examination of the current understanding of mSWI/SNF assembly processes, as well as the structural and functional organization of mSWI/SNF complexes and their subunits. In addition, it explores their intricate functional connections with potentially dysregulated transcription factors, placing particular emphasis on molecular and cellular pathogenic processes in lung diseases. These processes are reflected in human epigenome aberrations that impact clinical and therapeutic levels, suggesting novel perspectives on the diagnosis and molecular therapies for human respiratory diseases.
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Affiliation(s)
- Octavio A Trejo-Villegas
- Lung Diseases and Functional Epigenomics Laboratory (LUDIFE), Biomedicine Research Unit (UBIMED), Facultad de Estudios Superiores-Iztacala (FES-Iztacala), Universidad Nacional Autónoma de México (UNAM), Avenida de los Barrios #1, Colonia Los Reyes Iztacala, Tlalnepantla de Baz, 54090, Estado de México, México
| | - Irene H Heijink
- Departments of Pathology & Medical Biology and Pulmonology, GRIAC Research Institute, University Medical Center Groningen, University of Groningen, 9713 Groningen, the Netherlands
| | - Federico Ávila-Moreno
- Lung Diseases and Functional Epigenomics Laboratory (LUDIFE), Biomedicine Research Unit (UBIMED), Facultad de Estudios Superiores-Iztacala (FES-Iztacala), Universidad Nacional Autónoma de México (UNAM), Avenida de los Barrios #1, Colonia Los Reyes Iztacala, Tlalnepantla de Baz, 54090, Estado de México, México; Research Unit, Instituto Nacional de Enfermedades Respiratorias (INER), Ismael Cosío Villegas, 14080, Ciudad de México, México; Research Tower, Subdirección de Investigación Básica, Instituto Nacional de Cancerología (INCan), 14080, Ciudad de México, México.
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13
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Schade M, Scott JS, Hayhow TG, Pike A, Terstiege I, Ahlqvist M, Johansson JR, Diene CR, Fallan C, Balazs AYS, Chiarparin E, Wilson D. Structural and Physicochemical Features of Oral PROTACs. J Med Chem 2024. [PMID: 39078401 DOI: 10.1021/acs.jmedchem.4c01017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/31/2024]
Abstract
Achieving oral bioavailability with Proteolysis Targeting Chimeras (PROTACs) is a key challenge. Here, we report the in vivo pharmacokinetic properties in mouse, rat, and dog of four clinical oral PROTACs and compare with an internally derived data set. We use NMR to determine 3D molecular conformations and structural preorganization free in solution, and we introduce the new experimental descriptors, solvent-exposed H-bond donors (eHBD), and acceptors (eHBA). We derive an upper limit of eHBD ≤ 2 for oral PROTACs in apolar environments and show a greater tolerance for other properties (eHBA, polarity, lipophilicity, and molecular weight) than for Rule-of-5 compliant oral drugs. Within a set of structurally related PROTACs, we show that examples with eHBD > 2 have much lower oral bioavailability than those that have eHBD ≤ 2. We summarize our findings as an experimental "Rule-of-oral-PROTACs" in order to assist medicinal chemists to achieve oral bioavailability in this challenging space.
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Affiliation(s)
- Markus Schade
- Chemistry and DMPK, Oncology R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge CB2 0AA, United Kingdom
| | - James S Scott
- Chemistry and DMPK, Oncology R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge CB2 0AA, United Kingdom
| | - Thomas G Hayhow
- Chemistry and DMPK, Oncology R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge CB2 0AA, United Kingdom
| | - Andy Pike
- Chemistry and DMPK, Oncology R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge CB2 0AA, United Kingdom
| | - Ina Terstiege
- Chemistry and DMPK, Research and Early Development, Respiratory and Immunology, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, Mölndal 43183, Sweden
| | - Marie Ahlqvist
- Chemistry and DMPK, Research and Early Development, Respiratory and Immunology, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, Mölndal 43183, Sweden
| | - Johan R Johansson
- Chemistry and DMPK, Research and Early Development, Respiratory and Immunology, Cardiovascular, Renal and Metabolism, BioPharmaceuticals R&D, AstraZeneca, Pepparedsleden 1, Mölndal 43183, Sweden
| | - Coura R Diene
- Chemistry and DMPK, Oncology R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge CB2 0AA, United Kingdom
| | - Charlene Fallan
- Chemistry and DMPK, Oncology R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge CB2 0AA, United Kingdom
| | - Amber Y S Balazs
- Chemistry, Oncology R&D, AstraZeneca, Waltham, Massachusetts 02451, United States
| | - Elisabetta Chiarparin
- Chemistry and DMPK, Oncology R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge CB2 0AA, United Kingdom
| | - David Wilson
- Chemistry and DMPK, Oncology R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge CB2 0AA, United Kingdom
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14
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Previtali V, Bagnolini G, Ciamarone A, Ferrandi G, Rinaldi F, Myers SH, Roberti M, Cavalli A. New Horizons of Synthetic Lethality in Cancer: Current Development and Future Perspectives. J Med Chem 2024; 67:11488-11521. [PMID: 38955347 DOI: 10.1021/acs.jmedchem.4c00113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
In recent years, synthetic lethality has been recognized as a solid paradigm for anticancer therapies. The discovery of a growing number of synthetic lethal targets has led to a significant expansion in the use of synthetic lethality, far beyond poly(ADP-ribose) polymerase inhibitors used to treat BRCA1/2-defective tumors. In particular, molecular targets within DNA damage response have provided a source of inhibitors that have rapidly reached clinical trials. This Perspective focuses on the most recent progress in synthetic lethal targets and their inhibitors, within and beyond the DNA damage response, describing their design and associated therapeutic strategies. We will conclude by discussing the current challenges and new opportunities for this promising field of research, to stimulate discussion in the medicinal chemistry community, allowing the investigation of synthetic lethality to reach its full potential.
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Affiliation(s)
- Viola Previtali
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
| | - Greta Bagnolini
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Andrea Ciamarone
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Giovanni Ferrandi
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Francesco Rinaldi
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
| | - Samuel Harry Myers
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
| | - Marinella Roberti
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Andrea Cavalli
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
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15
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Zhao H. Structural Basis of Conformational Dynamics in the PROTAC-Induced Protein Degradation. ChemMedChem 2024; 19:e202400171. [PMID: 38655701 DOI: 10.1002/cmdc.202400171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/19/2024] [Accepted: 04/23/2024] [Indexed: 04/26/2024]
Abstract
Pronounced conformational dynamics is unveiled upon analyzing multiple crystal structures of the same proteins recruited to the same E3 ligases by PROTACs, and yet, is largely permissive for targeted protein degradation due to the intrinsic mobility of E3 assemblies creating a large ubiquitylation zone. Mathematical modelling of ternary dynamics on ubiquitylation probability confirms the experimental finding that ternary complex rigidification need not correlate with enhanced protein degradation. Salt bridges are found to prevail in the PROTAC-induced ternary complexes, and may contribute to a positive cooperativity and prolonged half-life. The analysis highlights the importance of presenting lysines close to the active site of the E2 enzyme while constraining ternary dynamics in PROTAC design to achieve high degradation efficiency.
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Affiliation(s)
- Hongtao Zhao
- Medicinal Chemistry, Research and Early Development, Respiratory and Immunology (R&I), BioPharmaceuticals R&D, AstraZeneca, Gothenburg, Sweden
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16
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Li Y, Qu J, Jiang L, Peng X, Wu K, Chen M, Peng Y, Cao X. Application and challenges of nitrogen heterocycles in PROTAC linker. Eur J Med Chem 2024; 273:116520. [PMID: 38788299 DOI: 10.1016/j.ejmech.2024.116520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 05/07/2024] [Accepted: 05/19/2024] [Indexed: 05/26/2024]
Abstract
The absence of effective active pockets makes traditional molecularly targeted drug strategies ineffective against 80 % of human disease-related proteins. The PROTAC technology effectively makes up for the deficiency of traditional molecular targeted drugs, which produces drug activity by degrading rather than inhibiting the target protein. The degradation of PROTAC is not only affected by POI ligand and E3 ligand, but by the selection of suitable linker which can play an important role in the efficiency and selectivity of the degradation. In the early exploring stage of the PROTAC, flexible chains were priorly applied as the linker of PROTAC. Although PROTAC with flexible chains as linkers sometimes perform well in vitro bioactivity evaluations, the introduction of lipophilic flexible chains reduces the hydrophilicity of these molecules, resulting in generally poor pharmacokinetic characteristics and pharmacological activities in vivo. In addition, recent reports have also shown that some PROTAC with flexible chains have some risks to causing hemolysis in vivo. Therefore, PROTAC with flexible chains show less druggability and large difficulty to entering the clinical trial stage. On the other hand, the application of nitrogen heterocycles in the design of PROTAC linkers has been widely reported in recent years. More and more reports have shown that the introduction of nitrogen heterocycles in the linker not only can effectively improves the metabolism of PROTAC in vivo, but also can enhance the degradation efficiency and selectivity of PROTAC. These PROTAC with nitrogen heterocycle linkers have attracted much attention of pharmaceutical chemists. The introduction of nitrogen heterocycles in the linker deserves priority consideration in the primary design of the PROTAC based on various druggabilities including pharmacokinetic characteristics and pharmacological activity. In this work, we summarized the optimization process and progress of nitrogen heterocyclic rings as the PROTAC linker in recent years. However, there were still limited understanding of how to discover, design and optimize PROTAC. For example, the selection of the types of nitrogen heterocycles and the optimization sites of this linker are challenges for researchers, choosing between four to six-membered nitrogen heterocycles, selecting from saturated to unsaturated ones, and even optimizing the length and extension angle of the linker. There is a truly need for theoretical explanation and elucidation of the PROTAC to guide the developing of more effective and valuable PROTAC.
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Affiliation(s)
- Yang Li
- Institute of Pharmacy and Pharmacology, Hunan Province, Cooperative Innovation Center for Molecular Target New Drug Study, College of Pharmacy, Hengyang Medical School, University of South China, Hengyang, 421001, China
| | - Junfeng Qu
- Institute of Pharmacy and Pharmacology, Hunan Province, Cooperative Innovation Center for Molecular Target New Drug Study, College of Pharmacy, Hengyang Medical School, University of South China, Hengyang, 421001, China
| | - Lizhi Jiang
- Institute of Pharmacy and Pharmacology, Hunan Province, Cooperative Innovation Center for Molecular Target New Drug Study, College of Pharmacy, Hengyang Medical School, University of South China, Hengyang, 421001, China
| | - Xiaoyu Peng
- Institute of Pharmacy and Pharmacology, Hunan Province, Cooperative Innovation Center for Molecular Target New Drug Study, College of Pharmacy, Hengyang Medical School, University of South China, Hengyang, 421001, China
| | - Kaiyue Wu
- Department of Pharmacy, Ezhou Central Hospital, Ezhou, Hubei, China
| | - Miaojia Chen
- Department of Pharmacy, The First People's Hospital, Pingjiang, Yueyang, Hunan, China
| | - Yuanyuan Peng
- School of Electrical and Automation Engineering, East China Jiaotong University, Nanchang, 330000, China
| | - Xuan Cao
- Institute of Pharmacy and Pharmacology, Hunan Province, Cooperative Innovation Center for Molecular Target New Drug Study, College of Pharmacy, Hengyang Medical School, University of South China, Hengyang, 421001, China.
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17
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Diehl CJ, Salerno A, Ciulli A. Ternary Complex-Templated Dynamic Combinatorial Chemistry for the Selection and Identification of Homo-PROTACs. Angew Chem Int Ed Engl 2024; 63:e202319456. [PMID: 38626385 DOI: 10.1002/anie.202319456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 04/08/2024] [Accepted: 04/15/2024] [Indexed: 04/18/2024]
Abstract
Dynamic combinatorial chemistry (DCC) leverages a reversible reaction to generate compound libraries from constituting building blocks under thermodynamic control. The position of this equilibrium can be biased by addition of a target macromolecule towards enrichment of bound ligands. While DCC has been applied to select ligands for a single target protein, its application to identifying chimeric molecules inducing proximity between two proteins is unprecedented. In this proof-of-concept study, we develop a DCC approach to select bifunctional proteolysis targeting chimeras (PROTACs) based on their ability to stabilize the ternary complex. We focus on VHL-targeting Homo-PROTACs as model system, and show that the formation of a VHL2 : Homo-PROTAC ternary complex reversibly assembled using thiol-disulfide exchange chemistry leads to amplification of potent VHL Homo-PROTACs with degradation activities which correlated well with their biophysical ability to dimerize VHL. Ternary complex templated dynamic combinatorial libraries allowed identification of novel Homo-PROTAC degraders. We anticipate future applications of ternary-complex directed DCC to early PROTAC screenings and expansion to other proximity-inducing modalities beyond PROTACs.
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Affiliation(s)
- Claudia J Diehl
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ, Dundee, Scotland, U.K
| | - Alessandra Salerno
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ, Dundee, Scotland, U.K
| | - Alessio Ciulli
- Centre for Targeted Protein Degradation, School of Life Sciences, University of Dundee, 1 James Lindsay Place, DD1 5JJ, Dundee, Scotland, U.K
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18
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Mabe NW, Perry JA, Malone CF, Stegmaier K. Pharmacological targeting of the cancer epigenome. NATURE CANCER 2024; 5:844-865. [PMID: 38937652 DOI: 10.1038/s43018-024-00777-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 04/19/2024] [Indexed: 06/29/2024]
Abstract
Epigenetic dysregulation is increasingly appreciated as a hallmark of cancer, including disease initiation, maintenance and therapy resistance. As a result, there have been advances in the development and evaluation of epigenetic therapies for cancer, revealing substantial promise but also challenges. Three epigenetic inhibitor classes are approved in the USA, and many more are currently undergoing clinical investigation. In this Review, we discuss recent developments for each epigenetic drug class and their implications for therapy, as well as highlight new insights into the role of epigenetics in cancer.
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Affiliation(s)
- Nathaniel W Mabe
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jennifer A Perry
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Clare F Malone
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kimberly Stegmaier
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.
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19
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Gold S, Shilatifard A. Therapeutic targeting of BET bromodomain and other epigenetic acetylrecognition domain-containing factors. Curr Opin Genet Dev 2024; 86:102181. [PMID: 38564841 DOI: 10.1016/j.gde.2024.102181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/03/2024] [Accepted: 03/04/2024] [Indexed: 04/04/2024]
Abstract
Development of cancer therapies targeting chromatin modifiers and transcriptional regulatory factors is rapidly expanding to include new targets and novel targeting strategies. At the same time, basic molecular research continues to refine our understanding of the epigenetic mechanisms regulating transcription, gene expression, and oncogenesis. This mini-review focuses on cancer therapies targeting the chromatin-associated factors that recognize histone lysine acetylation. Recently reported safety and efficacy are discussed for inhibitors targeting the bromodomains of bromodomain and extraterminal domain (BET) family proteins. In light of recent results indicating that the transcriptional regulator BRD4-PTEFb can function independently of BRD4's bromodomains, the clinical trial performance of these BET inhibitors is placed in a broader context of existing and potential strategies for targeting BRD4-PTEFb. Recently developed therapies targeting bromodomain-containing factors within the SWI/SNF (BAF) family of chromatin remodeling complexes are discussed, as is the potential for targeting the bromodomain-containing transcription factor TAF1 and the YEATS acetylrecognition domain-containing factor GAS41. Recent findings regarding the selectivity and combinatorial specificity of acetylrecognition are highlighted. In conclusion, the potential for further development is discussed with a focus on proximity-based therapies targeting this class of epigenetic factors.
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Affiliation(s)
- Sarah Gold
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA. https://twitter.com/@rwx_life
| | - Ali Shilatifard
- Department of Biochemistry and Molecular Genetics, Simpson Querrey Institute for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.
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20
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Stevens R, Thompson JDF, Fournier JCL, Burley GA, Battersby DJ, Miah AH. Innovative, combinatorial and high-throughput approaches to degrader synthesis. Chem Soc Rev 2024; 53:4838-4861. [PMID: 38596888 DOI: 10.1039/d3cs01127e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Targeted protein degraders such as PROTACs and molecular glues are a rapidly emerging therapeutic modality within industry and academia. Degraders possess unique mechanisms of action that lead to the removal of specific proteins by co-opting the cell's natural degradation mechanisms via induced proximity. Their optimisation thus far has often been largely empirical, requiring the synthesis and screening of a large number of analogues. In addition, the synthesis and development of degraders is often challenging, leading to lengthy optimisation campaigns to deliver candidate-quality compounds. This review highlights how the synthesis of degraders has evolved in recent years, in particular focusing on means of applying high-throughput chemistry and screening approaches to expedite these timelines, which we anticipate to be valuable in shaping the future of degrader optimisation campaigns.
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Affiliation(s)
- Rebecca Stevens
- Medicinal Chemistry, GSK, Stevenage, SG1 2NY, UK.
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, G1 1XQ, UK
| | | | | | - Glenn A Burley
- Department of Pure and Applied Chemistry, University of Strathclyde, Glasgow, G1 1XQ, UK
| | | | - Afjal H Miah
- Medicinal Chemistry, GSK, Stevenage, SG1 2NY, UK.
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21
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Zhang D, Ma B, Dragovich PS, Ma L, Chen S, Chen EC, Ye X, Liu J, Pizzano J, Bortolon E, Chan E, Zhang X, Chen YC, Levy ES, Yauch RL, Khojasteh SC, Hop CECA. Tissue distribution and retention drives efficacy of rapidly clearing VHL-based PROTACs. COMMUNICATIONS MEDICINE 2024; 4:87. [PMID: 38755248 PMCID: PMC11099041 DOI: 10.1038/s43856-024-00505-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 04/19/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND Proteolysis-targeting chimeras (PROTACs) are being developed for therapeutic use. However, they have poor pharmacokinetic profiles and their tissue distribution kinetics are not known. METHODS A typical von Hippel-Lindau tumor suppressor (VHL)-PROTAC 14C-A947 (BRM degrader)-was synthesized and its tissue distribution kinetics was studied by quantitative whole-body autoradiography (QWBA) and tissue excision in rats following IV dosing. Bile duct-cannulated (BDC) rats allowed the elucidation of in vivo clearance pathways. Distribution kinetics was evaluated in the tissues and tumors of mice to support PK-PD correlation. In vitro studies enabled the evaluation of cell uptake mechanisms and cell retention properties. RESULTS Here, we show that A947 quickly distributes into rat tissues after IV dosing, where it accumulates and is retained in tissues such as the lung and liver although it undergoes fast clearance from circulation. Similar uptake/retention kinetics enable tumor growth inhibition over 2-3 weeks in a lung cancer model. A947 quickly excretes in the bile of rats. Solute carrier (SLC) transporters are involved in hepatocyte uptake of PROTACs. Sustained BRM protein degradation is seen after extensive washout that supports prolonged cell retention of A947 in NCI-H1944 cells. A947 tissue exposure and pharmacodynamics are inversely correlated in tumors. CONCLUSIONS Plasma sampling for VHL-PROTAC does not represent the tissue concentrations necessary for efficacy. Understanding of tissue uptake and retention could enable less frequent IV administration to be used for therapeutic dosing.
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Affiliation(s)
- Donglu Zhang
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA.
| | - Bin Ma
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
| | | | - Li Ma
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Shu Chen
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Eugene C Chen
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Xiaofen Ye
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Joyce Liu
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Jennifer Pizzano
- Arvinas; 5 Science Park, 395 Winchester Ave, New Haven, CT, 06511, USA
| | | | - Emily Chan
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Xing Zhang
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
| | - Yi-Chen Chen
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
| | | | - Robert L Yauch
- Genentech; 1 DNA Way, South San Francisco, CA, 94080, USA
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22
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Gourisankar S, Krokhotin A, Wenderski W, Crabtree GR. Context-specific functions of chromatin remodellers in development and disease. Nat Rev Genet 2024; 25:340-361. [PMID: 38001317 DOI: 10.1038/s41576-023-00666-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2023] [Indexed: 11/26/2023]
Abstract
Chromatin remodellers were once thought to be highly redundant and nonspecific in their actions. However, recent human genetic studies demonstrate remarkable biological specificity and dosage sensitivity of the thirty-two adenosine triphosphate (ATP)-dependent chromatin remodellers encoded in the human genome. Mutations in remodellers produce many human developmental disorders and cancers, motivating efforts to investigate their distinct functions in biologically relevant settings. Exquisitely specific biological functions seem to be an emergent property in mammals, and in many cases are based on the combinatorial assembly of subunits and the generation of stable, composite surfaces. Critical interactions between remodelling complex subunits, the nucleosome and other transcriptional regulators are now being defined from structural and biochemical studies. In addition, in vivo analyses of remodellers at relevant genetic loci have provided minute-by-minute insights into their dynamics. These studies are proposing new models for the determinants of remodeller localization and function on chromatin.
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Affiliation(s)
- Sai Gourisankar
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Chemical Engineering, Stanford University, Stanford, CA, USA
| | - Andrey Krokhotin
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Wendy Wenderski
- Department of Pathology, Stanford University, Stanford, CA, USA
- Department of Developmental Biology, Stanford University, Stanford, CA, USA
| | - Gerald R Crabtree
- Department of Pathology, Stanford University, Stanford, CA, USA.
- Department of Developmental Biology, Stanford University, Stanford, CA, USA.
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23
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Rej RK, Allu SR, Roy J, Acharyya RK, Kiran INC, Addepalli Y, Dhamodharan V. Orally Bioavailable Proteolysis-Targeting Chimeras: An Innovative Approach in the Golden Era of Discovering Small-Molecule Cancer Drugs. Pharmaceuticals (Basel) 2024; 17:494. [PMID: 38675453 PMCID: PMC11054475 DOI: 10.3390/ph17040494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Revised: 04/02/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Proteolysis-targeting chimeras (PROTACs) are an emerging therapeutic modality that show promise to open a target space not accessible to conventional small molecules via a degradation-based mechanism. PROTAC degraders, due to their bifunctional nature, which is categorized as 'beyond the Rule of Five', have gained attention as a distinctive therapeutic approach for oral administration in clinical settings. However, the development of PROTACs with adequate oral bioavailability remains a significant hurdle, largely due to their large size and less than ideal physical and chemical properties. This review encapsulates the latest advancements in orally delivered PROTACs that have entered clinical evaluation as well as developments highlighted in recent scholarly articles. The insights and methodologies elaborated upon in this review could be instrumental in supporting the discovery and refinement of novel PROTAC degraders aimed at the treatment of various human cancers.
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Affiliation(s)
- Rohan Kalyan Rej
- Rogel Cancer Center, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; (S.R.A.); (R.K.A.)
| | - Srinivasa Rao Allu
- Rogel Cancer Center, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; (S.R.A.); (R.K.A.)
| | - Joyeeta Roy
- Rogel Cancer Center, Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109, USA;
| | - Ranjan Kumar Acharyya
- Rogel Cancer Center, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; (S.R.A.); (R.K.A.)
| | - I. N. Chaithanya Kiran
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02139, USA;
| | - Yesu Addepalli
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA;
| | - V. Dhamodharan
- Institute of Organic Chemistry, Center for Nanosystems Chemistry, University of Wuerzburg, Am Hubland, 97074 Würzburg, Germany;
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24
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Lucas SCC, Ahmed A, Ashraf SN, Argyrou A, Bauer MR, De Donatis GM, Demanze S, Eisele F, Fusani L, Hock A, Kadamur G, Li S, Macmillan-Jones A, Michaelides IN, Phillips C, Rehnström M, Richter M, Rodrigo-Brenni MC, Shilliday F, Wang P, Storer RI. Optimization of Potent Ligands for the E3 Ligase DCAF15 and Evaluation of Their Use in Heterobifunctional Degraders. J Med Chem 2024; 67:5538-5566. [PMID: 38513086 DOI: 10.1021/acs.jmedchem.3c02136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
Unlocking novel E3 ligases for use in heterobifunctional PROTAC degraders is of high importance to the pharmaceutical industry. Over-reliance on the current suite of ligands used to recruit E3 ligases could limit the potential of their application. To address this, potent ligands for DCAF15 were optimized using cryo-EM supported, structure-based design to improve on micromolar starting points. A potent binder, compound 24, was identified and subsequently conjugated into PROTACs against multiple targets. Following attempts on degrading a number of proteins using DCAF15 recruiting PROTACs, only degradation of BRD4 was observed. Deconvolution of the mechanism of action showed that this degradation was not mediated by DCAF15, thereby highlighting both the challenges faced when trying to expand the toolbox of validated E3 ligase ligands for use in PROTAC degraders and the pitfalls of using BRD4 as a model substrate.
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Affiliation(s)
- Simon C C Lucas
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Afshan Ahmed
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - S Neha Ashraf
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Argyrides Argyrou
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Matthias R Bauer
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | | | - Sylvain Demanze
- Oncology Chemistry, Oncology R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Frederik Eisele
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg SE-431 83,Sweden
| | - Lucia Fusani
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Andreas Hock
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Ganesh Kadamur
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Shuyou Li
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176, People's Republic of China
| | | | | | - Christopher Phillips
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Marie Rehnström
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Gothenburg SE-431 83, Sweden
| | - Magdalena Richter
- Discovery Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Monica C Rodrigo-Brenni
- Safety Innovation and PROTAC Safety, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Fiona Shilliday
- Mechanistic and Structural Biology, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
| | - Peng Wang
- Pharmaron Beijing Co., Ltd., 6 Taihe Road BDA, Beijing 100176, People's Republic of China
| | - R Ian Storer
- Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K
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25
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Price E, Weinheimer M, Rivkin A, Jenkins G, Nijsen M, Cox PB, DeGoey D. Beyond Rule of Five and PROTACs in Modern Drug Discovery: Polarity Reducers, Chameleonicity, and the Evolving Physicochemical Landscape. J Med Chem 2024; 67:5683-5698. [PMID: 38498697 DOI: 10.1021/acs.jmedchem.3c02332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
Developing orally bioavailable drugs demands an understanding of absorption in early drug development. Traditional methods and physicochemical properties optimize absorption for rule of five (Ro5) compounds; beyond rule of five (bRo5) drugs necessitate advanced tools like the experimental measure of exposed polarity (EPSA) and the AbbVie multiparametric score (AB-MPS). Analyzing AB-MPS and EPSA against ∼1000 compounds with human absorption data and ∼10,000 AbbVie tool compounds (∼1000 proteolysis targeting chimeras or PROTACs, ∼7000 Ro5s, and ∼2000 bRo5s) revealed new patterns of physicochemical trends. We introduced a high-throughput "polarity reduction" descriptor: ETR, the EPSA-to-topological polar surface area (TPSA) ratio, highlights unique bRo5 and PROTAC subsets for specialized drug design strategies for effective absorption. Our methods and guidelines refine drug design by providing innovative in vitro approaches, enhancing physicochemical property optimization, and enabling accurate predictions of intestinal absorption in the complex bRo5 domain.
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Affiliation(s)
- Edward Price
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Manuel Weinheimer
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Alexey Rivkin
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Gary Jenkins
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Marjoleen Nijsen
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - Philip B Cox
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
| | - David DeGoey
- Research and Development, AbbVie Inc., 1 North Waukegan Road, North Chicago, Illinois 60064, United States
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26
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Henick BS, Herzberg BO, Concepcion-Crisol CP, Taylor AM. Controlled Chaos: Parsing Acquired Immunoresistance in Lung Cancer. J Clin Oncol 2024; 42:1211-1214. [PMID: 38422476 PMCID: PMC11095881 DOI: 10.1200/jco.23.02339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/20/2023] [Accepted: 01/03/2024] [Indexed: 03/02/2024] Open
Affiliation(s)
- Brian S. Henick
- Herbert Irving Comprehensive Cancer Center, New York, NY
- Division of Hematology/Medical Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Benjamin O. Herzberg
- Herbert Irving Comprehensive Cancer Center, New York, NY
- Division of Hematology/Medical Oncology, Department of Medicine, Columbia University Irving Medical Center, New York, NY
| | - Carla P. Concepcion-Crisol
- Herbert Irving Comprehensive Cancer Center, New York, NY
- Department of Molecular Pharmacology & Therapeutics, Columbia University Irving Medical Center, New York, NY
| | - Alison M. Taylor
- Herbert Irving Comprehensive Cancer Center, New York, NY
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
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27
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He T, Cheng C, Qiao Y, Cho H, Young E, Mannan R, Mahapatra S, Miner SJ, Zheng Y, Kim N, Zeng VZ, Wisniewski JP, Hou S, Jackson B, Cao X, Su F, Wang R, Chang Y, Kuila B, Mukherjee S, Dukare S, Aithal KB, D.S. S, Abbineni C, Vaishampayan U, Lyssiotis CA, Parolia A, Xiao L, Chinnaiyan AM. Development of an orally bioavailable mSWI/SNF ATPase degrader and acquired mechanisms of resistance in prostate cancer. Proc Natl Acad Sci U S A 2024; 121:e2322563121. [PMID: 38557192 PMCID: PMC11009648 DOI: 10.1073/pnas.2322563121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 03/02/2024] [Indexed: 04/04/2024] Open
Abstract
Mammalian switch/sucrose nonfermentable (mSWI/SNF) ATPase degraders have been shown to be effective in enhancer-driven cancers by functioning to impede oncogenic transcription factor chromatin accessibility. Here, we developed AU-24118, an orally bioavailable proteolysis-targeting chimera (PROTAC) degrader of mSWI/SNF ATPases (SMARCA2 and SMARCA4) and PBRM1. AU-24118 demonstrated tumor regression in a model of castration-resistant prostate cancer (CRPC) which was further enhanced with combination enzalutamide treatment, a standard of care androgen receptor (AR) antagonist used in CRPC patients. Importantly, AU-24118 exhibited favorable pharmacokinetic profiles in preclinical analyses in mice and rats, and further toxicity testing in mice showed a favorable safety profile. As acquired resistance is common with targeted cancer therapeutics, experiments were designed to explore potential mechanisms of resistance that may arise with long-term mSWI/SNF ATPase PROTAC treatment. Prostate cancer cell lines exposed to long-term treatment with high doses of a mSWI/SNF ATPase degrader developed SMARCA4 bromodomain mutations and ABCB1 (ATP binding cassette subfamily B member 1) overexpression as acquired mechanisms of resistance. Intriguingly, while SMARCA4 mutations provided specific resistance to mSWI/SNF degraders, ABCB1 overexpression provided broader resistance to other potent PROTAC degraders targeting bromodomain-containing protein 4 and AR. The ABCB1 inhibitor, zosuquidar, reversed resistance to all three PROTAC degraders tested. Combined, these findings position mSWI/SNF degraders for clinical translation for patients with enhancer-driven cancers and define strategies to overcome resistance mechanisms that may arise.
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Affiliation(s)
- Tongchen He
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI48109
- Department of Pathology, University of Michigan, Ann Arbor, MI48109
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan410008, China
| | - Caleb Cheng
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI48109
- Medical Scientist Training Program, University of Michigan, Ann Arbor, MI48109
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI48109
| | - Yuanyuan Qiao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI48109
- Department of Pathology, University of Michigan, Ann Arbor, MI48109
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI48109
| | - Hanbyul Cho
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI48109
- Department of Pathology, University of Michigan, Ann Arbor, MI48109
| | - Eleanor Young
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI48109
- Department of Pathology, University of Michigan, Ann Arbor, MI48109
| | - Rahul Mannan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI48109
- Department of Pathology, University of Michigan, Ann Arbor, MI48109
| | - Somnath Mahapatra
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI48109
- Department of Pathology, University of Michigan, Ann Arbor, MI48109
| | - Stephanie J. Miner
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI48109
- Department of Pathology, University of Michigan, Ann Arbor, MI48109
| | - Yang Zheng
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI48109
- Department of Pathology, University of Michigan, Ann Arbor, MI48109
| | - NamHoon Kim
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI48109
| | - Victoria Z. Zeng
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI48109
| | - Jasmine P. Wisniewski
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI48109
| | - Siyu Hou
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI48109
| | - Bailey Jackson
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI48109
| | - Xuhong Cao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI48109
- Department of Pathology, University of Michigan, Ann Arbor, MI48109
- HHMI, University of Michigan, Ann Arbor, MI48109
| | - Fengyun Su
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI48109
- Department of Pathology, University of Michigan, Ann Arbor, MI48109
| | - Rui Wang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI48109
- Department of Pathology, University of Michigan, Ann Arbor, MI48109
| | - Yu Chang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI48109
- Department of Pathology, University of Michigan, Ann Arbor, MI48109
| | - Bilash Kuila
- Aurigene Oncology Limited, Bangalore, Karnataka560100, India
| | | | - Sandeep Dukare
- Aurigene Oncology Limited, Bangalore, Karnataka560100, India
| | - Kiran B. Aithal
- Aurigene Oncology Limited, Bangalore, Karnataka560100, India
| | - Samiulla D.S.
- Aurigene Oncology Limited, Bangalore, Karnataka560100, India
| | | | - Ulka Vaishampayan
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI48109
- Department of Internal Medicine, Division of Medical Oncology, University of Michigan, Ann Arbor, MI48109
| | - Costas A. Lyssiotis
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI48109
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI48109
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI 48109
| | - Abhijit Parolia
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI48109
- Department of Pathology, University of Michigan, Ann Arbor, MI48109
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI48109
| | - Lanbo Xiao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI48109
- Department of Pathology, University of Michigan, Ann Arbor, MI48109
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI48109
| | - Arul M. Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI48109
- Department of Pathology, University of Michigan, Ann Arbor, MI48109
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI48109
- HHMI, University of Michigan, Ann Arbor, MI48109
- Department of Urology, University of Michigan, Ann Arbor, MI 48109
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28
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Wang J, Lu D, Yu X, Qi X, Lin H, Holloman BL, Jin F, Xu L, Ding L, Peng W, Wang M, Chen X. Development of a First-in-Class RIPK1 Degrader to Enhance Antitumor Immunity. RESEARCH SQUARE 2024:rs.3.rs-4156736. [PMID: 38659866 PMCID: PMC11042424 DOI: 10.21203/rs.3.rs-4156736/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The scaffolding function of receptor interacting protein kinase 1 (RIPK1) confers intrinsic and extrinsic resistance to immune checkpoint blockades (ICBs) and has emerged as a promising target for improving cancer immunotherapies. To address the challenge posed by a poorly defined binding pocket within the intermediate domain, we harnessed proteolysis targeting chimera (PROTAC) technology to develop a first-in-class RIPK1 degrader, LD4172. LD4172 exhibited potent and selective RIPK1 degradation both in vitro and in vivo. Degradation of RIPK1 by LD4172 triggered immunogenic cell death (ICD) and enriched tumor-infiltrating lymphocytes and substantially sensitized the tumors to anti-PD1 therapy. This work reports the first RIPK1 degrader that serves as a chemical probe for investigating the scaffolding functions of RIPK1 and as a potential therapeutic agent to enhance tumor responses to immune checkpoint blockade therapy.
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Affiliation(s)
| | | | - Xin Yu
- Baylor College of Medicine
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29
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Chaudhri A, Lizee G, Hwu P, Rai K. Chromatin Remodelers Are Regulators of the Tumor Immune Microenvironment. Cancer Res 2024; 84:965-976. [PMID: 38266066 DOI: 10.1158/0008-5472.can-23-2244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/24/2023] [Accepted: 01/17/2024] [Indexed: 01/26/2024]
Abstract
Immune checkpoint inhibitors show remarkable responses in a wide range of cancers, yet patients develop adaptive resistance. This necessitates the identification of alternate therapies that synergize with immunotherapies. Epigenetic modifiers are potent mediators of tumor-intrinsic mechanisms and have been shown to regulate immune response genes, making them prime targets for therapeutic combinations with immune checkpoint inhibitors. Some success has been observed in early clinical studies that combined immunotherapy with agents targeting DNA methylation and histone modification; however, less is known about chromatin remodeler-targeted therapies. Here, we provide a discussion on the regulation of tumor immunogenicity by the chromatin remodeling SWI/SNF complex through multiple mechanisms associated with immunotherapy response that broadly include IFN signaling, DNA damage, mismatch repair, regulation of oncogenic programs, and polycomb-repressive complex antagonism. Context-dependent targeting of SWI/SNF subunits can elicit opportunities for synthetic lethality and reduce T-cell exhaustion. In summary, alongside the significance of SWI/SNF subunits in predicting immunotherapy outcomes, their ability to modulate the tumor immune landscape offers opportunities for therapeutic intervention.
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Affiliation(s)
- Apoorvi Chaudhri
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Medical Oncology, Dana Farber Cancer Institute, Boston, Massachusetts
| | - Gregory Lizee
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Kunal Rai
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
- MDACC Epigenomics Therapy Initiative, The University of Texas MD Anderson Cancer Center, Houston, Texas
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Hernández-Morán BA, Taylor G, Lorente-Macías Á, Wood AJ. Degron tagging for rapid protein degradation in mice. Dis Model Mech 2024; 17:dmm050613. [PMID: 38666498 PMCID: PMC11073515 DOI: 10.1242/dmm.050613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024] Open
Abstract
Degron tagging allows proteins of interest to be rapidly degraded, in a reversible and tuneable manner, in response to a chemical stimulus. This provides numerous opportunities for understanding disease mechanisms, modelling therapeutic interventions and constructing synthetic gene networks. In recent years, many laboratories have applied degron tagging successfully in cultured mammalian cells, spurred by rapid advances in the fields of genome editing and targeted protein degradation. In this At a Glance article, we focus on recent efforts to apply degron tagging in mouse models, discussing the distinct set of challenges and opportunities posed by the in vivo environment.
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Affiliation(s)
- Brianda A. Hernández-Morán
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh EH4, 2XR, UK
| | - Gillian Taylor
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh EH4, 2XR, UK
| | - Álvaro Lorente-Macías
- Edinburgh Cancer Research, Cancer Research UK Scotland Centre, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh EH4 2XR, UK
| | - Andrew J. Wood
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road, Edinburgh EH4, 2XR, UK
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Kumar Tiwari P, Reddy Doda S, Vannam R, Hudlikar M, Harrison DA, Ojeda S, Rai S, Koglin AS, Nguyen Gilbert A, Ott CJ. Exploration of bromodomain ligand-linker conjugation sites for efficient CBP/p300 heterobifunctional degrader activity. Bioorg Med Chem Lett 2024; 102:129676. [PMID: 38408512 DOI: 10.1016/j.bmcl.2024.129676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/13/2024] [Accepted: 02/22/2024] [Indexed: 02/28/2024]
Abstract
Synthesis of proteolysis targeting chimeras (PROTACs) involves conjugation of an E3 ligase binding ligand to a ligand targeting a protein of interest via a rigid or flexible chemical linker. The choice of linker conjugation site on these ligands can be informed by structural analysis of ligand-target binding modes, the feasibility of synthetic procedures to access specific sites, and computational modeling of predicted ternary complex formations. Small molecules that target bromodomains - epigenetic readers of lysine acetylation - typically offer several potential options for linker conjugation sites. Here we describe how varying the linker attachment site (exit vector) on a CBP/p300 bromodomain ligand along with linker length affects PROTAC degradation activity and ternary complex formation. Using kinetic live cell assays of endogenous CBP and p300 protein abundance and bead-based proximity assays for ternary complexes, we describe the structure-activity relationships of a diverse library of CBP/p300 degraders (dCBPs).
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Affiliation(s)
- Praveen Kumar Tiwari
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Sai Reddy Doda
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Raghu Vannam
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Manish Hudlikar
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Drew A Harrison
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
| | - Samuel Ojeda
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
| | - Sumit Rai
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA; Harvard Medical School, Boston, MA, USA
| | - Ann-Sophie Koglin
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA
| | | | - Christopher J Ott
- Krantz Family Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA, USA; Harvard Medical School, Boston, MA, USA.
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Apprato G, Poongavanam V, Garcia Jimenez D, Atilaw Y, Erdelyi M, Ermondi G, Caron G, Kihlberg J. Exploring the chemical space of orally bioavailable PROTACs. Drug Discov Today 2024; 29:103917. [PMID: 38360147 DOI: 10.1016/j.drudis.2024.103917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 02/05/2024] [Accepted: 02/09/2024] [Indexed: 02/17/2024]
Abstract
A principal challenge in the discovery of proteolysis targeting chimeras (PROTACs) as oral medications is their bioavailability. To facilitate drug design, it is therefore essential to identify the chemical space where orally bioavailable PROTACs are more likely to be situated. To this aim, we extracted structure-bioavailability insights from published data using traditional 2D descriptors, thereby shedding light on their potential and limitations as drug design tools. Subsequently, we describe cutting-edge experimental, computational and hybrid design strategies based on 3D descriptors, which show promise for enhancing the probability of discovering PROTACs with high oral bioavailability.
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Affiliation(s)
- Giulia Apprato
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Piazza Nizza 44bis, 10126 Torino, Italy
| | | | - Diego Garcia Jimenez
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Piazza Nizza 44bis, 10126 Torino, Italy
| | - Yoseph Atilaw
- Department of Chemistry - BMC, Uppsala University, SE-75123 Uppsala, Sweden
| | - Mate Erdelyi
- Department of Chemistry - BMC, Uppsala University, SE-75123 Uppsala, Sweden
| | - Giuseppe Ermondi
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Piazza Nizza 44bis, 10126 Torino, Italy
| | - Giulia Caron
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Piazza Nizza 44bis, 10126 Torino, Italy.
| | - Jan Kihlberg
- Department of Chemistry - BMC, Uppsala University, SE-75123 Uppsala, Sweden.
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Liu F, Xin M, Feng H, Zhang W, Liao Z, Sheng T, Wen P, Wu Q, Liang T, Shi J, Zhou R, He K, Gu Z, Li H. Cryo-shocked tumor cells deliver CRISPR-Cas9 for lung cancer regression by synthetic lethality. SCIENCE ADVANCES 2024; 10:eadk8264. [PMID: 38552011 PMCID: PMC10980270 DOI: 10.1126/sciadv.adk8264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 02/23/2024] [Indexed: 04/01/2024]
Abstract
Although CRISPR-mediated genome editing holds promise for cancer therapy, inadequate tumor targeting and potential off-target side effects hamper its outcomes. In this study, we present a strategy using cryo-shocked lung tumor cells as a CRISPR-Cas9 delivery system for cyclin-dependent kinase 4 (CDK4) gene editing, which initiates synthetic lethal in KRAS-mutant non-small cell lung cancer (NSCLC). By rapidly liquid nitrogen shocking, we effectively eliminate the pathogenicity of tumor cells while preserving their structure and surface receptor activity. This delivery system enables the loaded CRISPR-Cas9 to efficiently target to lung through the capture in pulmonary capillaries and interactions with endothelial cells. In a NSCLC-bearing mouse model, the drug accumulation is increased nearly fourfold in lung, and intratumoral CDK4 expression is substantially down-regulated compared to CRISPR-Cas9 lipofectamine nanoparticles administration. Furthermore, CRISPR-Cas9 editing-mediated CDK4 ablation triggers synthetic lethal in KRAS-mutant NSCLC and prolongs the survival of mice.
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Affiliation(s)
- Feng Liu
- National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China
| | - Minhang Xin
- National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Huiheng Feng
- National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China
| | - Wentao Zhang
- National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ziyan Liao
- National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China
| | - Tao Sheng
- National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ping Wen
- National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China
| | - Qing Wu
- National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China
| | - Tingxizi Liang
- National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China
| | - Jiaqi Shi
- National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China
| | - Ruyi Zhou
- National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
| | - Kaixin He
- National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Jinhua Institute of Zhejiang University, Jinhua 321299, China
| | - Zhen Gu
- National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China
- Jinhua Institute of Zhejiang University, Jinhua 321299, China
- Key Laboratory of Advanced Drug Delivery Systems of Zhejiang Province, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Department of General Surgery, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou 310016, China
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou 310027, China
| | - Hongjun Li
- National Key Laboratory of Advanced Drug Delivery and Release Systems, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou 311121, China
- Jinhua Institute of Zhejiang University, Jinhua 321299, China
- Key Laboratory of Advanced Drug Delivery Systems of Zhejiang Province, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China
- Department of Hepatobiliary and Pancreatic Surgery the Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310009, China
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He T, Cheng C, Qiao Y, Cho H, Young E, Mannan R, Mahapatra S, Miner SJ, Zheng Y, Kim N, Zeng VZ, Wisniewski JP, Hou S, Jackson B, Cao X, Su F, Wang R, Chang Y, Kuila B, Mukherjee S, Dukare S, Aithal KB, D.S. S, Abbineni C, Lyssiotis CA, Parolia A, Xiao L, Chinnaiyan AM. Development of an orally bioavailable mSWI/SNF ATPase degrader and acquired mechanisms of resistance in prostate cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.29.582768. [PMID: 38464081 PMCID: PMC10925251 DOI: 10.1101/2024.02.29.582768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Mammalian switch/sucrose non-fermentable (mSWI/SNF) ATPase degraders have been shown to be effective in enhancer-driven cancers by functioning to impede oncogenic transcription factor chromatin accessibility. Here, we developed AU-24118, a first-in-class, orally bioavailable proteolysis targeting chimera (PROTAC) degrader of mSWI/SNF ATPases (SMARCA2 and SMARCA4) and PBRM1. AU-24118 demonstrated tumor regression in a model of castration-resistant prostate cancer (CRPC) which was further enhanced with combination enzalutamide treatment, a standard of care androgen receptor (AR) antagonist used in CRPC patients. Importantly, AU-24118 exhibited favorable pharmacokinetic profiles in preclinical analyses in mice and rats, and further toxicity testing in mice showed a favorable safety profile. As acquired resistance is common with targeted cancer therapeutics, experiments were designed to explore potential mechanisms of resistance that may arise with long-term mSWI/SNF ATPase PROTAC treatment. Prostate cancer cell lines exposed to long-term treatment with high doses of a mSWI/SNF ATPase degrader developed SMARCA4 bromodomain mutations and ABCB1 overexpression as acquired mechanisms of resistance. Intriguingly, while SMARCA4 mutations provided specific resistance to mSWI/SNF degraders, ABCB1 overexpression provided broader resistance to other potent PROTAC degraders targeting bromodomain-containing protein 4 (BRD4) and AR. The ABCB1 inhibitor, zosuquidar, reversed resistance to all three PROTAC degraders tested. Combined, these findings position mSWI/SNF degraders for clinical translation for patients with enhancer-driven cancers and define strategies to overcome resistance mechanisms that may arise.
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Affiliation(s)
- Tongchen He
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Urology, Xiangya Hospital, Central South University, Changsha, Hunan, China
- These authors contributed equally
| | - Caleb Cheng
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Medical Scientist Training Program, University of Michigan, Ann Arbor, MI, USA
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, MI, USA
- These authors contributed equally
| | - Yuanyuan Qiao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Hanbyul Cho
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Eleanor Young
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Rahul Mannan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Somnath Mahapatra
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Stephanie J. Miner
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Yang Zheng
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - NamHoon Kim
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Victoria Z. Zeng
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Jasmine P. Wisniewski
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Siyu Hou
- Department of Biostatistics, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Bailey Jackson
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Xuhong Cao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
| | - Fengyun Su
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Rui Wang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | - Yu Chang
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
| | | | | | | | | | | | | | - Costas A. Lyssiotis
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
- Department of Molecular and Integrative Physiology, University of Michigan, Ann Arbor, MI, USA
- Department of Internal Medicine, Division of Gastroenterology, University of Michigan, Ann Arbor, MI, USA
| | - Abhijit Parolia
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Lanbo Xiao
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
| | - Arul M. Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan, Ann Arbor, MI, USA
- Department of Pathology, University of Michigan, Ann Arbor, MI, USA
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI, USA
- Howard Hughes Medical Institute, University of Michigan, Ann Arbor, MI, USA
- Department of Urology, University of Michigan, Ann Arbor, MI, USA
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Reichl KD, Lee ECY, Gopalsamy A. Synthetic lethality: targeting SMARCA2 ATPase in SMARCA4-deficient tumors - a review of patent literature from 2019-30 June 2023. Expert Opin Ther Pat 2024; 34:159-169. [PMID: 38578210 DOI: 10.1080/13543776.2024.2338111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 03/28/2024] [Indexed: 04/06/2024]
Abstract
INTRODUCTION The multi-subunit SWI/SNF chromatin remodeling complex is a key epigenetic regulator for many cellular processes, and several subunits are found to be mutated in human cancers. The inactivating mutations of SMARCA4, the ATPase subunit of the complex, result in cellular dependency on the paralog SMARCA2 for survival. This observed synthetic lethal relationship posits targeting SMARCA2 in SMARCA4-deficient settings as an attractive therapeutic target in oncology. AREAS COVERED This review covers patent literature disclosed during the 2019-30 June 2023 period which claim ATPase inhibitors and PROTAC degraders that bind to the ATPase domain of SMARCA2 and/or SMARCA4. A total of 16 documents from 6 applicants are presented. EXPERT OPINION The demonstration of cellular dependence on SMARCA2 ATPase activity in SMARCA4-deficient settings has prompted substantial research toward SMARCA2-targeting therapies. Although selectively targeting the ATPase domain of SMARCA2 is viewed as challenging, several ATPase inhibitor scaffolds have been disclosed within the last five years. Most early compounds are weakly selective, but these efforts have culminated in the first dual SMARCA2/SMARCA4 ATPase inhibitor to enter clinical trials. Data from the ongoing clinical trials, as well as continued advancement of SMARCA2-selective ATPase inhibitors, are anticipated to significantly impact the field of therapies, targeting SMARCA4-deficient tumors.
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Nalawansha DA, Mangano K, den Besten W, Potts PR. TAC-tics for Leveraging Proximity Biology in Drug Discovery. Chembiochem 2024; 25:e202300712. [PMID: 38015747 DOI: 10.1002/cbic.202300712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 11/30/2023]
Abstract
Chemically induced proximity (CIP) refers to co-opting naturally occurring biological pathways using synthetic molecules to recruit neosubstrates that are not normally encountered or to enhance the affinity of naturally occurring interactions. Leveraging proximity biology through CIPs has become a rapidly evolving field and has garnered considerable interest in basic research and drug discovery. PROteolysis TArgeting Chimera (PROTAC) is a well-established CIP modality that induces the proximity between a target protein and an E3 ubiquitin ligase, causing target protein degradation via the ubiquitin-proteasome system. Inspired by PROTACs, several other induced proximity modalities have emerged to modulate both proteins and RNA over recent years. In this review, we summarize the critical advances and opportunities in the field, focusing on protein degraders, RNA degraders and non-degrader modalities such as post-translational modification (PTM) and protein-protein interaction (PPI) modulators. We envision that these emerging proximity-based drug modalities will be valuable resources for both biological research and therapeutic discovery in the future.
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Affiliation(s)
| | - Kyle Mangano
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320, USA
| | - Willem den Besten
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320, USA
| | - Patrick Ryan Potts
- Induced Proximity Platform, Amgen Research, Thousand Oaks, CA 91320, USA
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Wang Y, Zheng J, Long Y, Wu W, Zhu Y. Direct degradation and stabilization of proteins: New horizons in treatment of nonalcoholic steatohepatitis. Biochem Pharmacol 2024; 220:115989. [PMID: 38122854 DOI: 10.1016/j.bcp.2023.115989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023]
Abstract
Nonalcoholic fatty liver disease (NAFLD) is featured with excessive hepatic lipid accumulation and its global prevalence is soaring. Nonalcoholic steatohepatitis (NASH), the severe systemic inflammatory subtype of NAFLD, is tightly associated with metabolic comorbidities, and the hepatocytes manifest severe inflammation and ballooning. Currently the therapeutic options for treating NASH are limited. Potent small molecules specifically intervene with the signaling pathways that promote pathogenesis of NASH. Nevertheless they have obvious adverse effects and show long-term ineffectiveness in clinical trials. It poses the fundamental question to efficiently and safely inhibit the pathogenic processes. Targeted protein degradation (TPD) belongs to the direct degradation strategies and is a burgeoning strategy. It utilizes the small molecules to bind to the target proteins and recruit the endogenous proteasome, lysosome and autophagosome-mediated degradation machineries. They effectively and specifically degrade the target proteins. It has exhibited promising therapeutic effects in treatment of cancer, neurodegenerative diseases and other diseases in a catalytic manner at low doses. We critically discuss the principles of multiple direct degradation strategies, especially PROTAC and ATTEC. We extensively analyze their emerging application in degradation of excessive pathogenic proteins and lipid droplets, which promote the progression of NASH. Moreover, we discuss the opposite strategy that utilizes the small molecules to recruit deubiquinases to stabilize the NASH/MASH-suppressing proteins. Their advantages, limitations, as well as the solutions to address the limitations have been analyzed. In summary, the innovative direct degradation strategies provide new insights into design of next-generation therapeutics to combat NASH with optimal safety paradigm and efficiency.
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Affiliation(s)
- Yibing Wang
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, PR China; Shanghai Frontiers Science Research Base of Exercise and Metabolic Health, PR China.
| | - Jianan Zheng
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, PR China
| | - Yun Long
- Department of Endocrinology, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510120, PR China
| | - Wenyi Wu
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, PR China
| | - Yutong Zhu
- School of Kinesiology, Shanghai University of Sport, Shanghai 200438, PR China
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Dai XJ, Ji SK, Fu MJ, Liu GZ, Liu HM, Wang SP, Shen L, Wang N, Herdewijn P, Zheng YC, Wang SQ, Chen XB. Degraders in epigenetic therapy: PROTACs and beyond. Theranostics 2024; 14:1464-1499. [PMID: 38389844 PMCID: PMC10879860 DOI: 10.7150/thno.92526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 01/21/2024] [Indexed: 02/24/2024] Open
Abstract
Epigenetics refers to the reversible process through which changes in gene expression occur without changing the nucleotide sequence of DNA. The process is currently gaining prominence as a pivotal objective in the treatment of cancers and other ailments. Numerous drugs that target epigenetic mechanisms have obtained approval from the Food and Drug Administration (FDA) for the therapeutic intervention of diverse diseases; many have drawbacks, such as limited applicability, toxicity, and resistance. Since the discovery of the first proteolysis-targeting chimeras (PROTACs) in 2001, studies on targeted protein degradation (TPD)-encompassing PROTACs, molecular glue (MG), hydrophobic tagging (HyT), degradation TAG (dTAG), Trim-Away, a specific and non-genetic inhibitor of apoptosis protein (IAP)-dependent protein eraser (SNIPER), antibody-PROTACs (Ab-PROTACs), and other lysosome-based strategies-have achieved remarkable progress. In this review, we comprehensively highlight the small-molecule degraders beyond PROTACs that could achieve the degradation of epigenetic proteins (including bromodomain-containing protein-related targets, histone acetylation/deacetylation-related targets, histone methylation/demethylation related targets, and other epigenetic targets) via proteasomal or lysosomal pathways. The present difficulties and forthcoming prospects in this domain are also deliberated upon, which may be valuable for medicinal chemists when developing more potent, selective, and drug-like epigenetic drugs for clinical applications.
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Affiliation(s)
- Xing-Jie Dai
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment; Key Laboratory of Henan Province for Drug Quality and Evaluation; Institute of Drug Discovery and Development; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Shi-Kun Ji
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment; Key Laboratory of Henan Province for Drug Quality and Evaluation; Institute of Drug Discovery and Development; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Meng-Jie Fu
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment; Key Laboratory of Henan Province for Drug Quality and Evaluation; Institute of Drug Discovery and Development; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Gao-Zhi Liu
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment; Key Laboratory of Henan Province for Drug Quality and Evaluation; Institute of Drug Discovery and Development; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Hui-Min Liu
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment; Key Laboratory of Henan Province for Drug Quality and Evaluation; Institute of Drug Discovery and Development; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Shao-Peng Wang
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment; Key Laboratory of Henan Province for Drug Quality and Evaluation; Institute of Drug Discovery and Development; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Liang Shen
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment; Key Laboratory of Henan Province for Drug Quality and Evaluation; Institute of Drug Discovery and Development; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Ning Wang
- The School of Chinese Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China
| | - Piet Herdewijn
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment; Key Laboratory of Henan Province for Drug Quality and Evaluation; Institute of Drug Discovery and Development; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
- XNA platform, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
- Rega Institute for Medical Research, Medicinal Chemistry, KU Leuven, Herestraat 49-Box 1041, 3000 Leuven, Belgium
| | - Yi-Chao Zheng
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, China; State Key Laboratory of Esophageal Cancer Prevention & Treatment; Key Laboratory of Henan Province for Drug Quality and Evaluation; Institute of Drug Discovery and Development; School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
- XNA platform, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Sai-Qi Wang
- Department of Oncology, the Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou University, Zhengzhou, China
- Department of Oncology, the Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Henan Engineering Research Center of Precision Therapy of Gastrointestinal Cancer & Zhengzhou Key Laboratory for Precision Therapy of Gastrointestinal Cancer, Zhengzhou, China
| | - Xiao-Bing Chen
- Department of Oncology, the Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou University, Zhengzhou, China
- Department of Oncology, the Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Henan Engineering Research Center of Precision Therapy of Gastrointestinal Cancer & Zhengzhou Key Laboratory for Precision Therapy of Gastrointestinal Cancer, Zhengzhou, China
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Berlin M, Cantley J, Bookbinder M, Bortolon E, Broccatelli F, Cadelina G, Chan EW, Chen H, Chen X, Cheng Y, Cheung TK, Davenport K, DiNicola D, Gordon D, Hamman BD, Harbin A, Haskell R, He M, Hole AJ, Januario T, Kerry PS, Koenig SG, Li L, Merchant M, Pérez-Dorado I, Pizzano J, Quinn C, Rose CM, Rousseau E, Soto L, Staben LR, Sun H, Tian Q, Wang J, Wang W, Ye CS, Ye X, Zhang P, Zhou Y, Yauch R, Dragovich PS. PROTACs Targeting BRM (SMARCA2) Afford Selective In Vivo Degradation over BRG1 (SMARCA4) and Are Active in BRG1 Mutant Xenograft Tumor Models. J Med Chem 2024; 67:1262-1313. [PMID: 38180485 DOI: 10.1021/acs.jmedchem.3c01781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2024]
Abstract
The identification of VHL-binding proteolysis targeting chimeras (PROTACs) that potently degrade the BRM protein (also known as SMARCA2) in SW1573 cell-based experiments is described. These molecules exhibit between 10- and 100-fold degradation selectivity for BRM over the closely related paralog protein BRG1 (SMARCA4). They also selectively impair the proliferation of the H1944 "BRG1-mutant" NSCLC cell line, which lacks functional BRG1 protein and is thus highly dependent on BRM for growth, relative to the wild-type Calu6 line. In vivo experiments performed with a subset of compounds identified PROTACs that potently and selectively degraded BRM in the Calu6 and/or the HCC2302 BRG1 mutant NSCLC xenograft models and also afforded antitumor efficacy in the latter system. Subsequent PK/PD analysis established a need to achieve strong BRM degradation (>95%) in order to trigger meaningful antitumor activity in vivo. Intratumor quantitation of mRNA associated with two genes whose transcription was controlled by BRM (PLAU and KRT80) also supported this conclusion.
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Affiliation(s)
- Michael Berlin
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Jennifer Cantley
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Mark Bookbinder
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Elizabeth Bortolon
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Fabio Broccatelli
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Greg Cadelina
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Emily W Chan
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Huifen Chen
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Xin Chen
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Yunxing Cheng
- Pharmaron Beijing, Co. Ltd., 6 Tai He Road, BDA, Beijing 100176, P. R. China
| | - Tommy K Cheung
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Kim Davenport
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Dean DiNicola
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Debbie Gordon
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Brian D Hamman
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Alicia Harbin
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Roy Haskell
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Mingtao He
- Pharmaron Beijing, Co. Ltd., 6 Tai He Road, BDA, Beijing 100176, P. R. China
| | - Alison J Hole
- Evotec (U.K.) Ltd., 95 Park Drive, Milton Park, Abingdon, Oxfordshire OX14 4RY, U.K
| | - Thomas Januario
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Philip S Kerry
- Evotec (U.K.) Ltd., 95 Park Drive, Milton Park, Abingdon, Oxfordshire OX14 4RY, U.K
| | - Stefan G Koenig
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Limei Li
- Pharmaron Beijing, Co. Ltd., 6 Tai He Road, BDA, Beijing 100176, P. R. China
| | - Mark Merchant
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | | | - Jennifer Pizzano
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Connor Quinn
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Christopher M Rose
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Emma Rousseau
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Leofal Soto
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Leanna R Staben
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Hongming Sun
- Pharmaron Beijing, Co. Ltd., 6 Tai He Road, BDA, Beijing 100176, P. R. China
| | - Qingping Tian
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Jing Wang
- Arvinas LLC, 5 Science Park, New Haven, Connecticut 06511, United States
| | - Weifeng Wang
- Pharmaron Beijing, Co. Ltd., 6 Tai He Road, BDA, Beijing 100176, P. R. China
| | - Crystal S Ye
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Xiaofen Ye
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Penghong Zhang
- Pharmaron Beijing, Co. Ltd., 6 Tai He Road, BDA, Beijing 100176, P. R. China
| | - Yuhui Zhou
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Robert Yauch
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Peter S Dragovich
- Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
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Duplaquet L, So K, Ying AW, Li X, Li Y, Qiu X, Li R, Singh S, Wu XS, Liu Q, Qi J, Somerville TDD, Heiling H, Mazzola E, Lee Y, Zoller T, Vakoc CR, Doench JG, Forrester WC, Abrams T, Long HW, Niederst MJ, Kadoch C, Oser MG. Mammalian SWI/SNF complex activity regulates POU2F3 and constitutes a targetable dependency in small cell lung cancer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.21.576304. [PMID: 38328215 PMCID: PMC10849479 DOI: 10.1101/2024.01.21.576304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Small cell lung cancers (SCLC) are comprised of heterogeneous subtypes marked by lineage-specific transcription factors, including ASCL1, NEUROD1, and POU2F3. POU2F3-positive SCLC, ∼12% of all cases, are uniquely dependent on POU2F3 itself; as such, approaches to attenuate POU2F3 expression may represent new therapeutic opportunities. Here using genome-scale screens for regulators of POU2F3 expression and SCLC proliferation, we define mSWI/SNF complexes, including non-canonical BAF (ncBAF) complexes, as top dependencies specific to POU2F3-positive SCLC. Notably, clinical-grade pharmacologic mSWI/SNF inhibition attenuates proliferation of all POU2F3-positive SCLCs, while disruption of ncBAF via BRD9 degradation is uniquely effective in pure non-neuroendocrine POU2F3-SCLCs. mSWI/SNF maintains accessibility over gene loci central to POU2F3-mediated gene regulatory networks. Finally, chemical targeting of SMARCA4/2 mSWI/SNF ATPases and BRD9 decrease POU2F3-SCLC tumor growth and increase survival in vivo . Taken together, these results characterize mSWI/SNF-mediated global governance of the POU2F3 oncogenic program and suggest mSWI/SNF inhibition as a therapeutic strategy for SCLC.
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Geiger TM, Walz M, Meyners C, Kuehn A, Dreizler JK, Sugiarto WO, Maciel EVS, Zheng M, Lermyte F, Hausch F. Discovery of a Potent Proteolysis Targeting Chimera Enables Targeting the Scaffolding Functions of FK506-Binding Protein 51 (FKBP51). Angew Chem Int Ed Engl 2024; 63:e202309706. [PMID: 37942685 DOI: 10.1002/anie.202309706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 11/01/2023] [Accepted: 11/03/2023] [Indexed: 11/10/2023]
Abstract
The FK506-binding protein 51 (FKBP51) is a promising target in a variety of disorders including depression, chronic pain, and obesity. Previous FKBP51-targeting strategies were restricted to occupation of the FK506-binding site, which does not affect core functions of FKBP51. Here, we report the discovery of the first FKBP51 proteolysis targeting chimera (PROTAC) that enables degradation of FKBP51 abolishing its scaffolding function. Initial synthesis of 220 FKBP-focused PROTACs yielded a plethora of active PROTACs for FKBP12, six for FKBP51, and none for FKBP52. Structural analysis of a binary FKBP12:PROTAC complex revealed the molecular basis for negative cooperativity. Linker-based optimization of first generation FKBP51 PROTACs led to the PROTAC SelDeg51 with improved cellular activity, selectivity, and high cooperativity. The structure of the ternary FKBP51:SelDeg51:VCB complex revealed how SelDeg51 establishes cooperativity by dimerizing FKBP51 and the von Hippel-Lindau protein (VHL) in a glue-like fashion. SelDeg51 efficiently depletes FKBP51 and reactivates glucocorticoid receptor (GR)-signalling, highlighting the enhanced efficacy of full protein degradation compared to classical FKBP51 binding.
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Affiliation(s)
- Thomas M Geiger
- Department of Chemistry and Biochemistry Clemens-Schöpf-Institute, Technical University Darmstadt, Peter-Grünberg-Straße 4, 64287, Darmstadt, Germany
| | - Michael Walz
- Department of Chemistry and Biochemistry Clemens-Schöpf-Institute, Technical University Darmstadt, Peter-Grünberg-Straße 4, 64287, Darmstadt, Germany
| | - Christian Meyners
- Department of Chemistry and Biochemistry Clemens-Schöpf-Institute, Technical University Darmstadt, Peter-Grünberg-Straße 4, 64287, Darmstadt, Germany
| | - Angela Kuehn
- Department of Chemistry and Biochemistry Clemens-Schöpf-Institute, Technical University Darmstadt, Peter-Grünberg-Straße 4, 64287, Darmstadt, Germany
| | - Johannes K Dreizler
- Department of Chemistry and Biochemistry Clemens-Schöpf-Institute, Technical University Darmstadt, Peter-Grünberg-Straße 4, 64287, Darmstadt, Germany
| | - Wisely O Sugiarto
- Department of Chemistry and Biochemistry Clemens-Schöpf-Institute, Technical University Darmstadt, Peter-Grünberg-Straße 4, 64287, Darmstadt, Germany
| | - Edvaldo V S Maciel
- Department of Chemistry and Biochemistry Clemens-Schöpf-Institute, Technical University Darmstadt, Peter-Grünberg-Straße 4, 64287, Darmstadt, Germany
| | - Min Zheng
- Department of Chemistry and Biochemistry Clemens-Schöpf-Institute, Technical University Darmstadt, Peter-Grünberg-Straße 4, 64287, Darmstadt, Germany
| | - Frederik Lermyte
- Department of Chemistry and Biochemistry Clemens-Schöpf-Institute, Technical University Darmstadt, Peter-Grünberg-Straße 4, 64287, Darmstadt, Germany
| | - Felix Hausch
- Department of Chemistry and Biochemistry Clemens-Schöpf-Institute, Technical University Darmstadt, Peter-Grünberg-Straße 4, 64287, Darmstadt, Germany
- Centre for Synthetic Biology, Technical University of Darmstadt, 64283, Darmstadt, Germany
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42
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Winter GE, Mayor-Ruiz C. Proximity-inducing pharmacology. Nat Chem Biol 2024; 20:13-14. [PMID: 37978259 DOI: 10.1038/s41589-023-01492-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Affiliation(s)
- Georg E Winter
- Research Center for Molecular Medicine (CeMM), Austrian Academy of Sciences, Vienna, Austria.
| | - Cristina Mayor-Ruiz
- Institute for Research in Biomedicine (IRB) Barcelona, Barcelona Institute of Technology (BIST), Barcelona, Spain.
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43
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Arndt CM, Bitai J, Brunner J, Opatz T, Martinelli P, Gollner A, Sokol KR, Krumb M. One-Pot Synthesis of Cereblon Proteolysis Targeting Chimeras via Photoinduced C(sp 2)-C(sp 3) Cross Coupling and Amide Formation for Proteolysis Targeting Chimera Library Synthesis. J Med Chem 2023; 66:16939-16952. [PMID: 38096359 DOI: 10.1021/acs.jmedchem.3c01613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
In this study, a one-pot synthesis via photoinduced C(sp2)-C(sp3) coupling followed by amide formation to access proteolysis targeting chimeras (PROTACs) was developed. The described protocol was studied on cereblon (CRBN)-based E3-ligase binders and (+)-JQ-1, a bromodomain inhibitor, to generate BET (bromodomain and extra terminal domain) targeting protein degraders. The generated PROTACs were profiled in vitro and tested for their degradation ability with several potent candidates identified. Upfront, the individual reactions of the one-pot transformation were carefully optimized for CRBN binder functionalization and multiple heterobifunctional linker moieties were designed and synthesized. Separate scopes detailing the C(sp2)-C(sp3) coupling and one-pot PROTAC synthesis are described in this report as well as a library miniaturization study showing the high-throughput compatibility. Overall, the developed protocol provides rapid access to PROTACs in a single process, thereby allowing efficient generation of CRBN-based PROTAC libraries.
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Affiliation(s)
- Christine M Arndt
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, Vienna 1121, Austria
- Department of Chemistry, Johannes Gutenberg-University, Duesbergweg 10-14, Mainz 55128, Germany
| | - Jacqueline Bitai
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, Vienna 1121, Austria
| | - Jessica Brunner
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, Vienna 1121, Austria
| | - Till Opatz
- Department of Chemistry, Johannes Gutenberg-University, Duesbergweg 10-14, Mainz 55128, Germany
| | - Paola Martinelli
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, Vienna 1121, Austria
| | - Andreas Gollner
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, Vienna 1121, Austria
| | - Kevin R Sokol
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, Vienna 1121, Austria
| | - Matthias Krumb
- Boehringer Ingelheim RCV GmbH & Co KG, Dr. Boehringer-Gasse 5-11, Vienna 1121, Austria
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44
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Zeng S, Ye Y, Xia H, Min J, Xu J, Wang Z, Pan Y, Zhou X, Huang W. Current advances and development strategies of orally bioavailable PROTACs. Eur J Med Chem 2023; 261:115793. [PMID: 37708797 DOI: 10.1016/j.ejmech.2023.115793] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/16/2023] [Accepted: 09/04/2023] [Indexed: 09/16/2023]
Abstract
Proteolysis-targeting chimeras (PROTACs) have been an area of intensive research with the potential to extend drug space not target to traditional molecules. In the last half decade, we have witnessed several PROTACs initiated phase I/II/III clinical trials, which inspired us a lot. However, the structure of PROTACs beyond "rule of 5" resulted in developing PROTACs with acceptable oral pharmacokinetic (PK) properties remain one of the biggest bottleneck tasks. Many reports have demonstrated that it is possible to access orally bioavailable PROTACs through rational ligand and linker modifications. In this review, we systematically reviewed and highlighted the most recent advances in orally bioavailable PROTACs development, especially focused on the medicinal chemistry campaign of discovery process and in vivo oral PK properties. Moreover, the constructive strategies for developing oral PROTACs were proposed comprehensively. Collectively, we believe that the strategies summarized here may provide references for further development of oral PROTACs.
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Affiliation(s)
- Shenxin Zeng
- Affiliated Yongkang First People's Hospital and School of Pharmaceutical Sciences, Hangzhou Medical College, Hangzhou, Zhejiang, 311399, China; School of Pharmaceutical Sciences, Hangzhou Medical College, Hangzhou, Zhejiang, 311399, China; Key Laboratory of Neuropsychiatric Drug Research of Zhejiang Province, School of Pharmacy, Hangzhou Medical College, Hangzhou, Zhejiang, 311399, China; Key Discipline of Zhejiang Province in Public Health and Preventive Medicine (First Class, Category A), Hangzhou Medical College, China.
| | - Yingqiao Ye
- Affiliated Yongkang First People's Hospital and School of Pharmaceutical Sciences, Hangzhou Medical College, Hangzhou, Zhejiang, 311399, China; School of Pharmaceutical Sciences, Hangzhou Medical College, Hangzhou, Zhejiang, 311399, China; Key Laboratory of Neuropsychiatric Drug Research of Zhejiang Province, School of Pharmacy, Hangzhou Medical College, Hangzhou, Zhejiang, 311399, China; Key Discipline of Zhejiang Province in Public Health and Preventive Medicine (First Class, Category A), Hangzhou Medical College, China
| | - Heye Xia
- Affiliated Yongkang First People's Hospital and School of Pharmaceutical Sciences, Hangzhou Medical College, Hangzhou, Zhejiang, 311399, China; School of Pharmaceutical Sciences, Hangzhou Medical College, Hangzhou, Zhejiang, 311399, China; Key Laboratory of Neuropsychiatric Drug Research of Zhejiang Province, School of Pharmacy, Hangzhou Medical College, Hangzhou, Zhejiang, 311399, China; Key Discipline of Zhejiang Province in Public Health and Preventive Medicine (First Class, Category A), Hangzhou Medical College, China
| | - Jingli Min
- Affiliated Yongkang First People's Hospital and School of Pharmaceutical Sciences, Hangzhou Medical College, Hangzhou, Zhejiang, 311399, China; School of Pharmaceutical Sciences, Hangzhou Medical College, Hangzhou, Zhejiang, 311399, China; Key Laboratory of Neuropsychiatric Drug Research of Zhejiang Province, School of Pharmacy, Hangzhou Medical College, Hangzhou, Zhejiang, 311399, China; Key Discipline of Zhejiang Province in Public Health and Preventive Medicine (First Class, Category A), Hangzhou Medical College, China
| | - Jiamei Xu
- Affiliated Yongkang First People's Hospital and School of Pharmaceutical Sciences, Hangzhou Medical College, Hangzhou, Zhejiang, 311399, China; School of Pharmaceutical Sciences, Hangzhou Medical College, Hangzhou, Zhejiang, 311399, China; Key Laboratory of Neuropsychiatric Drug Research of Zhejiang Province, School of Pharmacy, Hangzhou Medical College, Hangzhou, Zhejiang, 311399, China; Key Discipline of Zhejiang Province in Public Health and Preventive Medicine (First Class, Category A), Hangzhou Medical College, China
| | - Zunyuan Wang
- Affiliated Yongkang First People's Hospital and School of Pharmaceutical Sciences, Hangzhou Medical College, Hangzhou, Zhejiang, 311399, China; School of Pharmaceutical Sciences, Hangzhou Medical College, Hangzhou, Zhejiang, 311399, China; Key Laboratory of Neuropsychiatric Drug Research of Zhejiang Province, School of Pharmacy, Hangzhou Medical College, Hangzhou, Zhejiang, 311399, China; Key Discipline of Zhejiang Province in Public Health and Preventive Medicine (First Class, Category A), Hangzhou Medical College, China
| | - Youlu Pan
- Affiliated Yongkang First People's Hospital and School of Pharmaceutical Sciences, Hangzhou Medical College, Hangzhou, Zhejiang, 311399, China; School of Pharmaceutical Sciences, Hangzhou Medical College, Hangzhou, Zhejiang, 311399, China; Key Laboratory of Neuropsychiatric Drug Research of Zhejiang Province, School of Pharmacy, Hangzhou Medical College, Hangzhou, Zhejiang, 311399, China; Key Discipline of Zhejiang Province in Public Health and Preventive Medicine (First Class, Category A), Hangzhou Medical College, China
| | - Xinglu Zhou
- HealZen Therapeutics Co., Ltd., Hangzhou, Zhejiang, 310018, China.
| | - Wenhai Huang
- Affiliated Yongkang First People's Hospital and School of Pharmaceutical Sciences, Hangzhou Medical College, Hangzhou, Zhejiang, 311399, China; School of Pharmaceutical Sciences, Hangzhou Medical College, Hangzhou, Zhejiang, 311399, China; Key Laboratory of Neuropsychiatric Drug Research of Zhejiang Province, School of Pharmacy, Hangzhou Medical College, Hangzhou, Zhejiang, 311399, China; Key Discipline of Zhejiang Province in Public Health and Preventive Medicine (First Class, Category A), Hangzhou Medical College, China.
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Inam M, Yang Y, Hu J, Zheng J, Deng W, Zhou Y, Qi J, Xu C, Chai G, Dang Y, Chen W. Cocrystallization of Gefitinib Potentiate Single-Dose Oral Administration for Lung Tumor Eradication via Unbalancing the DNA Damage/Repair. Pharmaceutics 2023; 15:2713. [PMID: 38140054 PMCID: PMC10747925 DOI: 10.3390/pharmaceutics15122713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/27/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023] Open
Abstract
Gefitinib (GEF) is a clinical medication for the treatment of lung cancer targeting the epidermal growth factor receptor (EGFR). However, its efficacy is remarkably limited by low solubility and dissolution rates. In this study, two cocrystals of GEF with co-formers were successfully synthesized using the recrystallization method characterized via Powder X-ray Diffraction, Fourier Transform Infrared Spectroscopy, and 2D Nuclear Overhauser Effect Spectroscopy. The solubility and dissolution rates of cocrystals were found to be two times higher than those of free GEF. In vitro cytotoxicity studies revealed that the cocrystals enhanced the inhibition of cell proliferation and apoptosis in A549 and H1299 cells compared to free GEF. In mouse models, GEF@TSBO demonstrated targeted, safe, and effective antitumor activity with only one-dose administration. Mechanistically, the GEF cocrystals were shown to increase the cellular levels of damaged DNA, while potentially downregulating PARP, thereby impairing the DNA repair machinery and leading to an imbalance between DNA damage and restoration. These findings suggest that the cocrystallization of GEF could serve as a promising adjunct to significantly enhance the physicochemical and biopharmaceutical performance for lung cancer treatment, providing a facial strategy to improve GEF anticancer efficiency with high bioavailability that can be orally administrated with only one dose.
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Affiliation(s)
- Muhammad Inam
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State & NMPA Key Laboratory of Respiratory Disease, School of Pharmaceutical Science, The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, China; (M.I.); (Y.Y.); (J.H.); (J.Z.); (W.D.); (Y.Z.); (C.X.)
| | - Yi Yang
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State & NMPA Key Laboratory of Respiratory Disease, School of Pharmaceutical Science, The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, China; (M.I.); (Y.Y.); (J.H.); (J.Z.); (W.D.); (Y.Z.); (C.X.)
| | - Jialin Hu
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State & NMPA Key Laboratory of Respiratory Disease, School of Pharmaceutical Science, The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, China; (M.I.); (Y.Y.); (J.H.); (J.Z.); (W.D.); (Y.Z.); (C.X.)
| | - Jiena Zheng
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State & NMPA Key Laboratory of Respiratory Disease, School of Pharmaceutical Science, The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, China; (M.I.); (Y.Y.); (J.H.); (J.Z.); (W.D.); (Y.Z.); (C.X.)
| | - Wenxia Deng
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State & NMPA Key Laboratory of Respiratory Disease, School of Pharmaceutical Science, The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, China; (M.I.); (Y.Y.); (J.H.); (J.Z.); (W.D.); (Y.Z.); (C.X.)
| | - You Zhou
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State & NMPA Key Laboratory of Respiratory Disease, School of Pharmaceutical Science, The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, China; (M.I.); (Y.Y.); (J.H.); (J.Z.); (W.D.); (Y.Z.); (C.X.)
| | - Jialong Qi
- Yunnan Digestive Endoscopy Clinical Medical Center, Department of Gastroenterology, The First People’s Hospital of Yunnan Province, Kunming 650032, China;
| | - Chuanshan Xu
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State & NMPA Key Laboratory of Respiratory Disease, School of Pharmaceutical Science, The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, China; (M.I.); (Y.Y.); (J.H.); (J.Z.); (W.D.); (Y.Z.); (C.X.)
| | - Guihong Chai
- School of Pharmaceutical Science, Sun Yat-sen University, Guangzhou 510006, China;
| | - Yuanye Dang
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State & NMPA Key Laboratory of Respiratory Disease, School of Pharmaceutical Science, The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, China; (M.I.); (Y.Y.); (J.H.); (J.Z.); (W.D.); (Y.Z.); (C.X.)
| | - Wenjie Chen
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State & NMPA Key Laboratory of Respiratory Disease, School of Pharmaceutical Science, The Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, China; (M.I.); (Y.Y.); (J.H.); (J.Z.); (W.D.); (Y.Z.); (C.X.)
- Sydney Vital Translational Cancer Research Centre, Westbourne St., Sydney, NSW 2065, Australia
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46
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Stevens R, Bendito-Moll E, Battersby DJ, Miah AH, Wellaway N, Law RP, Stacey P, Klimaszewska D, Macina JM, Burley GA, Harling JD. Integrated Direct-to-Biology Platform for the Nanoscale Synthesis and Biological Evaluation of PROTACs. J Med Chem 2023; 66:15437-15452. [PMID: 37933562 DOI: 10.1021/acs.jmedchem.3c01604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Proteolysis targeting chimeras (PROTACs) are heterobifunctional molecules that co-opt the cell's natural proteasomal degradation mechanisms to degrade undesired proteins. A challenge associated with PROTACs is the time and resource-intensive optimization; thus, the development of high-throughput platforms for their synthesis and biological evaluation is required. In this study, we establish an ultra-high-throughput experimentation (ultraHTE) platform for PROTAC synthesis, followed by direct addition of the crude reaction mixtures to cellular degradation assays without any purification. This 'direct-to-biology' (D2B) approach was validated and then exemplified in a medicinal chemistry campaign to identify novel BRD4 PROTACs. Using the D2B platform, the synthesis of 650 PROTACs was carried out in a 1536-well plate, and subsequent biological evaluation was performed by a single scientist in less than 1 month. Due to its ability to hugely accelerate the optimization of new degraders, we anticipate our platform will transform the synthesis and testing of PROTACs.
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Affiliation(s)
- Rebecca Stevens
- Medicines Design, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - Enrique Bendito-Moll
- Medicines Design, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - David J Battersby
- Medicines Design, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Afjal H Miah
- Medicines Design, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Natalie Wellaway
- Medicines Design, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Robert P Law
- Medicines Design, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Peter Stacey
- Medicines Design, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Diana Klimaszewska
- Medicines Design, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Justyna M Macina
- Medicines Design, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
| | - Glenn A Burley
- Department of Pure and Applied Chemistry, University of Strathclyde, 295 Cathedral Street, Glasgow G1 1XL, United Kingdom
| | - John D Harling
- Medicines Design, GSK Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom
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47
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Sathe G, Sapkota GP. Proteomic approaches advancing targeted protein degradation. Trends Pharmacol Sci 2023; 44:786-801. [PMID: 37778939 DOI: 10.1016/j.tips.2023.08.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 08/18/2023] [Accepted: 08/25/2023] [Indexed: 10/03/2023]
Abstract
Targeted protein degradation (TPD) is an emerging modality for research and therapeutics. Most TPD approaches harness cellular ubiquitin-dependent proteolytic pathways. Proteolysis-targeting chimeras (PROTACs) and molecular glue (MG) degraders (MGDs) represent the most advanced TPD approaches, with some already used in clinical settings. Despite these advances, TPD still faces many challenges, pertaining to both the development of effective, selective, and tissue-penetrant degraders and understanding their mode of action. In this review, we focus on progress made in addressing these challenges. In particular, we discuss the utility and application of recent proteomic approaches as indispensable tools to enable insights into degrader development, including target engagement, degradation selectivity, efficacy, safety, and mode of action.
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Affiliation(s)
- Gajanan Sathe
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
| | - Gopal P Sapkota
- MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.
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48
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Xie H, Xu W, Liang J, Liu Y, Zhuo C, Zou X, Luo W, Xiao J, Lin Y, Chen L, Li H. Design, synthesis and evaluation of EZH2-based PROTACs targeting PRC2 complex in lymphoma. Bioorg Chem 2023; 140:106762. [PMID: 37572533 DOI: 10.1016/j.bioorg.2023.106762] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 07/19/2023] [Accepted: 08/01/2023] [Indexed: 08/14/2023]
Abstract
EZH2 is a member of PcG and can induce the occurrence of cancer when it is highly expressed. As an EZH2 inhibitor, Tazemetostat (EPZ6438) can inhibit the methylation catalytic activity of EZH2. However, many studies have shown that inhibition of EZH2 alone does not efficiently block tumor development. Therefore, in this study, proteolytic targeting chimera technology was employed to enhance the antiproliferative potency of EPZ6438 by degrading the oncogenic activity of EZH2. Several PROTACs have been synthesized by combining EPZ6438 with four E3 ligase ligands based on VHL, CRBN, MDM2, and cIAP E3 ligase systems. In our study, compound E-3P-MDM2 is the most active PROTAC molecule. It degraded EZH2 of the SU-DHL-6 cells in a concentration and dose-dependent manner and also degraded both EED and SUZ12 protein without affecting their mRNA levels, then significantly inhibited the expression of H3K27me3. The in vitro antiproliferative activity of E-3P-MDM2 was much stronger than that of EPZ6438.
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Affiliation(s)
- Huiru Xie
- Institute of Structural Pharmacology & TCM Chemical Biology, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China; Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Wei Xu
- Institute of Structural Pharmacology & TCM Chemical Biology, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China
| | - Jing Liang
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Yang Liu
- Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China
| | - Chenxi Zhuo
- Institute of Structural Pharmacology & TCM Chemical Biology, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China
| | - Xiaoxue Zou
- Institute of Structural Pharmacology & TCM Chemical Biology, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China
| | - Weihong Luo
- Institute of Structural Pharmacology & TCM Chemical Biology, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China
| | - Jianping Xiao
- The Affiliated Rehabilitation Hospital, Fujian University of Traditional Chinese Medicine, Fuzhou 350003, China.
| | - Yu Lin
- Institute of Structural Pharmacology & TCM Chemical Biology, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China.
| | - Lixia Chen
- Institute of Structural Pharmacology & TCM Chemical Biology, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China; Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China.
| | - Hua Li
- Institute of Structural Pharmacology & TCM Chemical Biology, College of Pharmacy, Fujian University of Traditional Chinese Medicine, Fuzhou 350122, China; Wuya College of Innovation, Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education, Shenyang Pharmaceutical University, Shenyang 110016, China.
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49
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Cooper MS, Norley MC, Armitage S, Cresser-Brown JO, Edmonds AK, Goggins S, Hopewell JP, Karadogan B, Knights KA, Nash TJ, Oakes CS, O'Neill WJ, Pridmore SJ, Maple HJ, Marsh GP. Efficient, multi-hundred-gram scale access to E3 ubiquitin ligase ligands for degrader development. Org Biomol Chem 2023; 21:8344-8352. [PMID: 37800999 DOI: 10.1039/d3ob00983a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/07/2023]
Abstract
Small molecule heterobifunctional degraders (commonly also known as PROTACs) offer tremendous potential to deliver new therapeutics in areas of unmet medical need. To deliver on this promise, a new discipline directed at degrader design and optimization has emerged within medicinal chemistry to address a central challenge, namely how to optimize relatively large, heterobifunctional molecules for activity, whilst maintaining drug-like properties. This process involves simultaneous optimization of the three principle degrader components: E3 ubiquitin ligase ligand, linker, and protein of interest (POI) ligand. A substantial degree of commonality exists with the E3 ligase ligands typically used at the early stages of degrader development, resulting in demand for these compounds as chemical building blocks in degrader research programs. We describe herein a collation of large scale, high-yielding syntheses to access the most utilized E3 ligase ligands to support early-stage degrader development.
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Affiliation(s)
- Mark S Cooper
- Bio-Techne (Tocris), The Watkins Building, Atlantic Road, Bristol, BS11 9QD, UK.
| | - Mark C Norley
- Bio-Techne (Tocris), The Watkins Building, Atlantic Road, Bristol, BS11 9QD, UK.
| | - Simon Armitage
- Bio-Techne (Tocris), The Watkins Building, Atlantic Road, Bristol, BS11 9QD, UK.
| | - Joel O Cresser-Brown
- Bio-Techne (Tocris), The Watkins Building, Atlantic Road, Bristol, BS11 9QD, UK.
| | - Anthony K Edmonds
- Bio-Techne (Tocris), The Watkins Building, Atlantic Road, Bristol, BS11 9QD, UK.
| | - Sean Goggins
- Bio-Techne (Tocris), The Watkins Building, Atlantic Road, Bristol, BS11 9QD, UK.
| | - Jonathan P Hopewell
- Bio-Techne (Tocris), The Watkins Building, Atlantic Road, Bristol, BS11 9QD, UK.
| | - Burhan Karadogan
- Bio-Techne (Tocris), The Watkins Building, Atlantic Road, Bristol, BS11 9QD, UK.
| | - Kevin A Knights
- Bio-Techne (Tocris), The Watkins Building, Atlantic Road, Bristol, BS11 9QD, UK.
| | - Toby J Nash
- Bio-Techne (Tocris), The Watkins Building, Atlantic Road, Bristol, BS11 9QD, UK.
| | - Catherine S Oakes
- Bio-Techne (Tocris), The Watkins Building, Atlantic Road, Bristol, BS11 9QD, UK.
| | - William J O'Neill
- Bio-Techne (Tocris), The Watkins Building, Atlantic Road, Bristol, BS11 9QD, UK.
| | - Simon J Pridmore
- Bio-Techne (Tocris), The Watkins Building, Atlantic Road, Bristol, BS11 9QD, UK.
| | - Hannah J Maple
- Bio-Techne (Tocris), The Watkins Building, Atlantic Road, Bristol, BS11 9QD, UK.
| | - Graham P Marsh
- Bio-Techne (Tocris), The Watkins Building, Atlantic Road, Bristol, BS11 9QD, UK.
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50
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Hales LT, Thompson PE. Solid-Phase Synthesis of PROTACs and SNIPERs on Backbone Amide Linked (BAL) Resin. Chemistry 2023; 29:e202301975. [PMID: 37526498 DOI: 10.1002/chem.202301975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/30/2023] [Accepted: 08/01/2023] [Indexed: 08/02/2023]
Abstract
Developing straightforward but flexible approaches to PROTAC synthesis that can incorporate the structural elements of emerging designs can improve the quality and efficiency of PROTAC development. Solid-phase approaches could offer many advantages over conventional PROTAC synthesis if diverse chemistries and topographies can be incorporated. We have exploited the backbone-amide-linked (BAL) resin to employ an array of solid-phase organic reactions, providing access to VHL- and IAP-targeting degraders using the BRD4-targeting JQ1 conjugates as examples.
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Affiliation(s)
- Liam Thomas Hales
- Medicinal Chemistry, Monash Institute of Pharmaceutical Science, Monash University, Parkville, VIC, Australia
| | - Philip Evan Thompson
- Medicinal Chemistry, Monash Institute of Pharmaceutical Science, Monash University, Parkville, VIC, Australia
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