1
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Scerba MT, Tweedie D, Greig NH. 2-(Piperidin-3-yl)phthalimides reduce classical markers of cellular inflammation in LPS-challenged RAW 264.7 cells and also demonstrate potentially relevant sigma and serotonin receptor affinity in membrane preparations. Bioorg Med Chem Lett 2024; 110:129885. [PMID: 38996940 DOI: 10.1016/j.bmcl.2024.129885] [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: 04/08/2024] [Revised: 06/28/2024] [Accepted: 07/08/2024] [Indexed: 07/14/2024]
Abstract
Herein, we report the synthesis of new 4-amino-2-(piperidin-3-yl)isoindoline-1,3-diones and their biological evaluation in a series of in vitro experiments. The synthetic production of these materials was initiated upon the condensation of appropriate nitrophthalic acid derivatives with various 3-aminopiperidines; subsequent reduction provided the final products in moderate to good yields. Readily available chiral pool reagents facilitated entry into optically enriched samples, while the piperidine scaffold furnished a variety of amide and alkylated entries. In total, 16 candidates were produced, and their ensuing treatment in LPS-challenged RAW cells effected slight reductions in secreted TNF-α but provided more robust and dose-dependent declines in nitrite and IL-6 levels relative to basal amounts, all concurrent with maintenance of cellular viability across the concentration ranges screened. The secondary amine cohort including rac-6, (R)-7, and (S)-8 rendered the most pronounced dose-dependent reductions in nitrite and IL-6. When dosed at 30 μM, (R)-7 demonstrated the most compelling effects, with decreases of 32 % and 40 % for nitrite and IL-6, respectively. Notable reductions in the inflammatory markers were also observed for 19 which effected declines in TNF-α (14 %), nitrite (19 %), and IL-6 (11 %) when treated at 30 μM. Additionally, four representative compounds were further evaluated against numerous CNS receptors, channels, and transporters, with 6, 9, and 19 demonstrating varying degrees of nanomolar-to-low-micromolar binding to the σ-1 and σ-2 receptors and also to serotonin receptors 5HT2A, 5HT2B and 5HT3. In this regard, 6 displayed perhaps the most noteworthy affinities, with binding at σ-2 (Ki = 2.2uM), 5HT2B (Ki = 561 nM) and 5HT3 (Ki = 536 nM). Furthermore, no pronounced or dose-dependent Cereblon/DDB1 binding was observed for the screened representative compounds 6, 9, 18 and 19.
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Affiliation(s)
- Michael T Scerba
- Drug Design & Development Section, Translational Gerontology Branch, Intramural Research Program, National Institute on Aging, National Institutes of Health, 251 Bayview Blvd, Baltimore, MD 21224, USA.
| | - David Tweedie
- Drug Design & Development Section, Translational Gerontology Branch, Intramural Research Program, National Institute on Aging, National Institutes of Health, 251 Bayview Blvd, Baltimore, MD 21224, USA
| | - Nigel H Greig
- Drug Design & Development Section, Translational Gerontology Branch, Intramural Research Program, National Institute on Aging, National Institutes of Health, 251 Bayview Blvd, Baltimore, MD 21224, USA
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2
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Barton BE, Collins MK, Chau CH, Choo-Wosoba H, Venzon DJ, Steinebach C, Garchitorena KM, Shah B, Sarin EL, Gütschow M, Figg WD. Preclinical Evaluation of a Novel Series of Polyfluorinated Thalidomide Analogs in Drug-Resistant Multiple Myeloma. Biomolecules 2024; 14:725. [PMID: 38927128 PMCID: PMC11201495 DOI: 10.3390/biom14060725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 06/09/2024] [Accepted: 06/13/2024] [Indexed: 06/28/2024] Open
Abstract
Immunomodulatory imide drugs (IMiDs) play a crucial role in the treatment landscape across various stages of multiple myeloma. Despite their evident efficacy, some patients may exhibit primary resistance to IMiD therapy, and acquired resistance commonly arises over time leading to inevitable relapse. It is critical to develop novel therapeutic options to add to the treatment arsenal to overcome IMiD resistance. We designed, synthesized, and screened a new class of polyfluorinated thalidomide analogs and investigated their anti-cancer, anti-angiogenic, and anti-inflammatory activity using in vitro and ex vivo biological assays. We identified four lead compounds that exhibit potent anti-myeloma, anti-angiogenic, anti-inflammatory properties using three-dimensional tumor spheroid models, in vitro tube formation, and ex vivo human saphenous vein angiogenesis assays, as well as the THP-1 inflammatory assay. Western blot analyses investigating the expression of proteins downstream of cereblon (CRBN) reveal that Gu1215, our primary lead candidate, exerts its activity through a CRBN-independent mechanism. Our findings demonstrate that the lead compound Gu1215 is a promising candidate for further preclinical development to overcome intrinsic and acquired IMiD resistance in multiple myeloma.
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Affiliation(s)
- Blaire E. Barton
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, Center for Cancer Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Matthew K. Collins
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, Center for Cancer Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Cindy H. Chau
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, Center for Cancer Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hyoyoung Choo-Wosoba
- Biostatics and Data Management Section, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David J. Venzon
- Biostatics and Data Management Section, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Christian Steinebach
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, 53121 Bonn, Germany
| | - Kathleen M. Garchitorena
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, Center for Cancer Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bhruga Shah
- Inova Heart and Vascular Institute, Inova Health System, Falls Church, VA 22042, USA
| | - Eric L. Sarin
- Inova Heart and Vascular Institute, Inova Health System, Falls Church, VA 22042, USA
| | - Michael Gütschow
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, 53121 Bonn, Germany
| | - William D. Figg
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, Center for Cancer Research, National Institutes of Health, Bethesda, MD 20892, USA
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3
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Han EJ, Jeong M, Lee SR, Sorensen EJ, Seyedsayamdost MR. Hirocidins, Cytotoxic Metabolites from Streptomyces hiroshimensis, Induce Mitochondrion-Mediated Apoptosis. Angew Chem Int Ed Engl 2024:e202405367. [PMID: 38898540 DOI: 10.1002/anie.202405367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 06/14/2024] [Accepted: 06/17/2024] [Indexed: 06/21/2024]
Abstract
Recent advances in whole genome sequencing have revealed an immense microbial potential for the production of therapeutic small molecules, even from well-known producers. To access this potential, we subjected prominent antimicrobial producers to alternative antiproliferative assays using persistent cancer cell lines. Described herein is our discovery of hirocidins, novel secondary metabolites from Streptomyces hiroshimensis with antiproliferative activities against colon and persistent breast cancer cells. Hirocidin A is an unusual nine-membered carbocyclic maleimide and hirocidins B and C are relatives with an unprecedented, bridged azamacrocyclic backbone. Mode of action studies show that hirocidins trigger mitochondrion-dependent apoptosis by inducing expression of the key apoptotic effector caspase-9. The discovery of new cytotoxins contributes to scaffold diversification in anticancer drug discovery and the reported modes of action and concise total synthetic route for variant A set the stage for unraveling specific targets and biochemical interactions of the hirocidins.
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Affiliation(s)
- Esther J Han
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Myungeun Jeong
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Seoung Rak Lee
- College of Pharmacy, Pusan National University, Busan, 46241, South Korea
| | - Erik J Sorensen
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Mohammad R Seyedsayamdost
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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4
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Nutt MJ, Stewart SG. Strengthening Molecular Glues: Design Strategies for Improving Thalidomide Analogs as Cereblon Effectors and Anticancer Agents. Drug Discov Today 2024; 29:104010. [PMID: 38704021 DOI: 10.1016/j.drudis.2024.104010] [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: 02/21/2024] [Revised: 04/19/2024] [Accepted: 04/26/2024] [Indexed: 05/06/2024]
Abstract
In the two decades since a novel thalidomide analog was last approved, many promising drug candidates have emerged with remarkable potency as targeted protein degraders. Likewise, the advent of PROTACs for suppressing 'undruggable' protein targets reinforces the need for new analogs with improved cereblon affinity, target selectivity and drug-like properties. However, thalidomide and its approved derivatives remain plagued by several shortcomings, such as structural instability and poor solubility. Herein, we present a review of strategies for mitigating these shortcomings and highlight contemporary drug discovery approaches that have generated novel thalidomide analogs with enhanced efficacy as cereblon effectors and/or anticancer agents.
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Affiliation(s)
- Michael J Nutt
- School of Molecular Sciences, University of Western Australia, 35 Stirling Hwy, Crawley 6009, Australia.
| | - Scott G Stewart
- School of Molecular Sciences, University of Western Australia, 35 Stirling Hwy, Crawley 6009, Australia.
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5
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Shevalev R, Bischof L, Sapegin A, Bunev A, Olga G, Kantin G, Kalinin S, Hartmann MD. Discovery and characterization of potent spiro-isoxazole-based cereblon ligands with a novel binding mode. Eur J Med Chem 2024; 270:116328. [PMID: 38552426 DOI: 10.1016/j.ejmech.2024.116328] [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: 12/27/2023] [Revised: 03/05/2024] [Accepted: 03/10/2024] [Indexed: 04/21/2024]
Abstract
The vast majority of current cereblon (CRBN) ligands is based on the thalidomide scaffold, relying on glutarimide as the core binding moiety. With this architecture, most of these ligands inherit the overall binding mode, interactions with neo-substrates, and thereby potentially also the cytotoxic and teratogenic properties of the parent thalidomide. In this work, by incorporating a spiro-linker to the glutarimide moiety, we have generated a new chemotype that exhibits an unprecedented binding mode for glutarimide-based CRBN ligands. In total, 16 spirocyclic glutarimide derivatives incorporating an isoxazole moiety were synthesized and tested for different criteria. In particular, all ligands showed a favorable lipophilicity, and several were able to outperform the binding affinity of thalidomide as a reference. In addition, all compounds showed favorable cytotoxicity profiles in myeloma cell lines and human peripheral blood mononuclear cells. The novel binding mode, which we determined in co-crystal structures, provides explanations for these improved properties: The incorporation of the spiro-isoxazole changes both the conformation of the glutarimide moiety within the canonical tri-trp pocket and the orientation of the protruding moiety. In this new orientation it forms additional hydrophobic interactions and is not available for direct interactions with the canonical neo-substrates. We therefore propose this chemotype as an attractive building block for the design of PROTACs.
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Affiliation(s)
- Robert Shevalev
- Institute of Chemistry, Saint Petersburg State University, Saint Petersburg, Russia
| | - Luca Bischof
- Department of Protein Evolution, Max Planck Institute for Biology, Tübingen, Germany
| | - Alexander Sapegin
- Institute of Chemistry, Saint Petersburg State University, Saint Petersburg, Russia
| | - Alexander Bunev
- Medicinal Chemistry Center, Togliatti State University, Togliatti, Russia
| | - Grigor'eva Olga
- Medicinal Chemistry Center, Togliatti State University, Togliatti, Russia
| | - Grigory Kantin
- Institute of Chemistry, Saint Petersburg State University, Saint Petersburg, Russia
| | - Stanislav Kalinin
- Institute of Chemistry, Saint Petersburg State University, Saint Petersburg, Russia.
| | - Marcus D Hartmann
- Department of Protein Evolution, Max Planck Institute for Biology, Tübingen, Germany.
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6
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Jiang W, Jiang Y, Luo Y, Qiao W, Yang T. Facilitating the development of molecular glues: Opportunities from serendipity and rational design. Eur J Med Chem 2024; 263:115950. [PMID: 37984298 DOI: 10.1016/j.ejmech.2023.115950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 11/09/2023] [Accepted: 11/09/2023] [Indexed: 11/22/2023]
Abstract
Molecular glues can specifically induce interactions between two or more proteins to modulate biological functions and have been proven to be a powerful therapeutic modality in drug discovery. It plays a variety of vital roles in several biological processes, such as complex stabilization, interactome modulation and transporter inhibition, thus enabling challenging therapeutic targets to be druggable. Most known molecular glues were identified serendipitously, such as IMiDs, auxin, and rapamycin. In recent years, more rational strategies were explored with the development of chemical biology and a deep understanding of the interaction between molecular glues and proteins, which led to the rational discovery of several molecular glues. Thus, in this review, we aim to highlight the discovery strategies of molecular glues from three aspects: serendipitous discovery, screening methods and rational design principles. We expect that this review will provide a reasonable reference and insights for the discovery of molecular glues.
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Affiliation(s)
- Weiqing Jiang
- Laboratory of Human Diseases and Immunotherapies, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China; Institute of Immunology and Inflammation, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Yunhan Jiang
- Laboratory of Human Diseases and Immunotherapies, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China; Institute of Immunology and Inflammation, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China; Cardiovascular Surgery Research Laboratory, West China Hospital, Sichuan University, Chengdu, 610041, China
| | - Youfu Luo
- Laboratory of Human Diseases and Immunotherapies, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Wenliang Qiao
- Lung Cancer Center, Laboratory of Lung Cancer, West China Hospital, Sichuan University, Chengdu, 610041, China.
| | - Tao Yang
- Laboratory of Human Diseases and Immunotherapies, and State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China; Institute of Immunology and Inflammation, Frontiers Science Center for Disease-related Molecular Network, West China Hospital, Sichuan University, Chengdu, 610041, China.
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7
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Steinebach C, Bricelj A, Murgai A, Sosič I, Bischof L, Ng YLD, Heim C, Maiwald S, Proj M, Voget R, Feller F, Košmrlj J, Sapozhnikova V, Schmidt A, Zuleeg MR, Lemnitzer P, Mertins P, Hansen FK, Gütschow M, Krönke J, Hartmann MD. Leveraging Ligand Affinity and Properties: Discovery of Novel Benzamide-Type Cereblon Binders for the Design of PROTACs. J Med Chem 2023; 66:14513-14543. [PMID: 37902300 PMCID: PMC10641816 DOI: 10.1021/acs.jmedchem.3c00851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 09/11/2023] [Accepted: 10/05/2023] [Indexed: 10/31/2023]
Abstract
Immunomodulatory imide drugs (IMiDs) such as thalidomide, pomalidomide, and lenalidomide are the most common cereblon (CRBN) recruiters in proteolysis-targeting chimera (PROTAC) design. However, these CRBN ligands induce the degradation of IMiD neosubstrates and are inherently unstable, degrading hydrolytically under moderate conditions. In this work, we simultaneously optimized physiochemical properties, stability, on-target affinity, and off-target neosubstrate modulation features to develop novel nonphthalimide CRBN binders. These efforts led to the discovery of conformationally locked benzamide-type derivatives that replicate the interactions of the natural CRBN degron, exhibit enhanced chemical stability, and display a favorable selectivity profile in terms of neosubstrate recruitment. The utility of the most potent ligands was demonstrated by their transformation into potent degraders of BRD4 and HDAC6 that outperform previously described reference PROTACs. Together with their significantly decreased neomorphic ligase activity on IKZF1/3 and SALL4, these ligands provide opportunities for the design of highly selective and potent chemically inert proximity-inducing compounds.
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Affiliation(s)
| | - Aleša Bricelj
- Faculty
of Pharmacy, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Arunima Murgai
- Department
of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin
Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, D-12203 Berlin, Germany
| | - Izidor Sosič
- Faculty
of Pharmacy, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Luca Bischof
- Max
Planck Institute for Biology Tübingen, D-72076 Tübingen, Germany
| | - Yuen Lam Dora Ng
- Department
of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin
Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, D-12203 Berlin, Germany
| | - Christopher Heim
- Max
Planck Institute for Biology Tübingen, D-72076 Tübingen, Germany
| | - Samuel Maiwald
- Max
Planck Institute for Biology Tübingen, D-72076 Tübingen, Germany
| | - Matic Proj
- Faculty
of Pharmacy, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Rabea Voget
- Pharmaceutical
Institute, University of Bonn, D-53121 Bonn, Germany
| | - Felix Feller
- Pharmaceutical
Institute, University of Bonn, D-53121 Bonn, Germany
| | - Janez Košmrlj
- Faculty
of Chemistry and Chemical Technology, University
of Ljubljana, SI 1000 Ljubljana, Slovenia
| | - Valeriia Sapozhnikova
- Department
of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin
Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, D-12203 Berlin, Germany
- Max
Delbrück
Center for Molecular Medicine, D-13125 Berlin, Germany
- German
Cancer Consortium (DKTK), Partner Site Berlin, DKFZ, D-69120 Heidelberg, Germany
| | - Annika Schmidt
- Department
of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin
Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, D-12203 Berlin, Germany
| | - Maximilian Rudolf Zuleeg
- Department
of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin
Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, D-12203 Berlin, Germany
| | - Patricia Lemnitzer
- Department
of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin
Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, D-12203 Berlin, Germany
| | - Philipp Mertins
- Max
Delbrück
Center for Molecular Medicine, D-13125 Berlin, Germany
- Berlin
Institute of Health, D-10178 Berlin, Germany
| | - Finn K. Hansen
- Pharmaceutical
Institute, University of Bonn, D-53121 Bonn, Germany
| | - Michael Gütschow
- Pharmaceutical
Institute, University of Bonn, D-53121 Bonn, Germany
| | - Jan Krönke
- Department
of Hematology, Oncology, and Cancer Immunology, Charité - Universitätsmedizin
Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, D-12203 Berlin, Germany
- German
Cancer Consortium (DKTK), Partner Site Berlin, DKFZ, D-69120 Heidelberg, Germany
| | - Marcus D. Hartmann
- Max
Planck Institute for Biology Tübingen, D-72076 Tübingen, Germany
- Interfaculty
Institute of Biochemistry, University of
Tübingen, D-72076 Tübingen, Germany
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8
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Elkady H, El-Adl K, Sakr H, Abdelraheem AS, Eissa SI, El-Zahabi MA. Novel promising benzoxazole/benzothiazole-derived immunomodulatory agents: Design, synthesis, anticancer evaluation, and in silico ADMET analysis. Arch Pharm (Weinheim) 2023; 356:e2300097. [PMID: 37379240 DOI: 10.1002/ardp.202300097] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 06/10/2023] [Accepted: 06/12/2023] [Indexed: 06/30/2023]
Abstract
Eleven novel benzoxazole/benzothiazole-based thalidomide analogs were designed and synthesized to obtain new effective antitumor immunomodulatory agents. The synthesized compounds were evaluated for their cytotoxic activities against HepG-2, HCT-116, PC3, and MCF-7 cells. Generally, the open analogs with semicarbazide and thiosemicarbazide moieties (10, 13a-c, 14, and 17a,b) exhibited higher cytotoxic activities than derivatives with closed glutarimide moiety (8a-d). In particular, compound 13a (IC50 = 6.14, 5.79, 10.26, and 4.71 µM against HepG-2, HCT-116, PC3, and MCF-7, respectively) and 14 (IC50 = 7.93, 8.23, 12.37, and 5.43 µM, respectively) exhibited the highest anticancer activities against the four tested cell lines. The most active compounds 13a and 14 were further evaluated for their in vitro immunomodulatory activities on tumor necrosis factor-alpha (TNF-α), caspase-8 (CASP8), vascular endothelial growth factor (VEGF), and nuclear factor kappa-B p65 (NF-κB p65) in HCT-116 cells. Compounds 13a and 14 showed a remarkable and significant reduction in TNF-α. Furthermore, they showed significant elevation in CASP8 levels. Also, they significantly inhibited VEGF. In addition, compound 13a showed significant decreases in the level of NF-κB p65 while compound 14 demonstrated an insignificant decrease with respect to thalidomide. Moreover, our derivatives exhibited good in silico absorption, distribution, metabolism, elimination, toxicity (ADMET) profiles.
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Affiliation(s)
- Hazem Elkady
- Pharmaceutical Medicinal Chemistry and Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, Egypt
| | - Khaled El-Adl
- Pharmaceutical Medicinal Chemistry and Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, Egypt
- Pharmaceutical Chemistry Department, Faculty of Pharmacy, Heliopolis University for Sustainable Development, Cairo, Egypt
| | - Helmy Sakr
- Pharmaceutical Medicinal Chemistry and Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, Egypt
| | - Adel S Abdelraheem
- Pharmaceutical Medicinal Chemistry and Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, Egypt
| | - Sally I Eissa
- Pharmaceutical Medicinal Chemistry and Drug Design Department, Faculty of Pharmacy (Girls), Al-Azhar University, Cairo, Egypt
| | - Mohamed Ayman El-Zahabi
- Pharmaceutical Medicinal Chemistry and Drug Design Department, Faculty of Pharmacy (Boys), Al-Azhar University, Cairo, Egypt
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9
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Pinheiro PDSM, Franco LS, Fraga CAM. The Magic Methyl and Its Tricks in Drug Discovery and Development. Pharmaceuticals (Basel) 2023; 16:1157. [PMID: 37631072 PMCID: PMC10457765 DOI: 10.3390/ph16081157] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/06/2023] [Accepted: 08/12/2023] [Indexed: 08/27/2023] Open
Abstract
One of the key scientific aspects of small-molecule drug discovery and development is the analysis of the relationship between its chemical structure and biological activity. Understanding the effects that lead to significant changes in biological activity is of paramount importance for the rational design and optimization of bioactive molecules. The "methylation effect", or the "magic methyl" effect, is a factor that stands out due to the number of examples that demonstrate profound changes in either pharmacodynamic or pharmacokinetic properties. In many cases, this has been carried out rationally, but in others it has been the product of serendipitous observations. This paper summarizes recent examples that provide an overview of the current state of the art and contribute to a better understanding of the methylation effect in bioactive small-molecule drug candidates.
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Affiliation(s)
- Pedro de Sena Murteira Pinheiro
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil; (P.d.S.M.P.); (L.S.F.)
| | - Lucas Silva Franco
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil; (P.d.S.M.P.); (L.S.F.)
- Instituto Nacional de Ciência e Tecnologia de Fármacos e Medicamentos (INCT-INOFAR), CCS, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro 21941-902, RJ, Brazil
| | - Carlos Alberto Manssour Fraga
- Laboratório de Avaliação e Síntese de Substâncias Bioativas (LASSBio), Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-902, RJ, Brazil; (P.d.S.M.P.); (L.S.F.)
- Instituto Nacional de Ciência e Tecnologia de Fármacos e Medicamentos (INCT-INOFAR), CCS, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro 21941-902, RJ, Brazil
- Programa de Pós-Graduação em Farmacologia e Química Medicinal, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Cidade Universitária, Rio de Janeiro 21941-902, RJ, Brazil
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10
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Liu M, Mirza A, McAndrew PC, Thapaliya A, Pierrat OA, Stubbs M, Hahner T, Chessum NEA, Innocenti P, Caldwell J, Cheeseman MD, Bellenie BR, van Montfort RLM, Newton GK, Burke R, Collins I, Hoelder S. Determination of Ligand-Binding Affinity ( Kd) Using Transverse Relaxation Rate ( R2) in the Ligand-Observed 1H NMR Experiment and Applications to Fragment-Based Drug Discovery. J Med Chem 2023; 66:10617-10627. [PMID: 37467168 PMCID: PMC10424183 DOI: 10.1021/acs.jmedchem.3c00758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Indexed: 07/21/2023]
Abstract
High hit rates from initial ligand-observed NMR screening can make it challenging to prioritize which hits to follow up, especially in cases where there are no available crystal structures of these hits bound to the target proteins or other strategies to provide affinity ranking. Here, we report a reproducible, accurate, and versatile quantitative ligand-observed NMR assay, which can determine Kd values of fragments in the affinity range of low μM to low mM using transverse relaxation rate R2 as the observable parameter. In this study, we examined the theory and proposed a mathematical formulation to obtain Kd values using non-linear regression analysis. We designed an assay format with automated sample preparation and simplified data analysis. Using tool compounds, we explored the assay reproducibility, accuracy, and detection limits. Finally, we used this assay to triage fragment hits, yielded from fragment screening against the CRBN/DDB1 complex.
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Affiliation(s)
- Manjuan Liu
- Centre
for Cancer Drug Discovery, The Institute
of Cancer Research, London SM2 5NG, U.K.
| | - Amin Mirza
- Centre
for Cancer Drug Discovery, The Institute
of Cancer Research, London SM2 5NG, U.K.
| | - P. Craig McAndrew
- Centre
for Cancer Drug Discovery, The Institute
of Cancer Research, London SM2 5NG, U.K.
| | - Arjun Thapaliya
- Centre
for Cancer Drug Discovery, The Institute
of Cancer Research, London SM2 5NG, U.K.
| | - Olivier A. Pierrat
- Centre
for Cancer Drug Discovery, The Institute
of Cancer Research, London SM2 5NG, U.K.
| | - Mark Stubbs
- Centre
for Cancer Drug Discovery, The Institute
of Cancer Research, London SM2 5NG, U.K.
| | - Tamas Hahner
- Centre
for Cancer Drug Discovery, The Institute
of Cancer Research, London SM2 5NG, U.K.
| | - Nicola E. A. Chessum
- Centre
for Cancer Drug Discovery, The Institute
of Cancer Research, London SM2 5NG, U.K.
| | - Paolo Innocenti
- Centre
for Cancer Drug Discovery, The Institute
of Cancer Research, London SM2 5NG, U.K.
| | - John Caldwell
- Centre
for Cancer Drug Discovery, The Institute
of Cancer Research, London SM2 5NG, U.K.
| | - Matthew D. Cheeseman
- Centre
for Cancer Drug Discovery, The Institute
of Cancer Research, London SM2 5NG, U.K.
| | - Benjamin R. Bellenie
- Centre
for Cancer Drug Discovery, The Institute
of Cancer Research, London SM2 5NG, U.K.
| | - Rob L. M. van Montfort
- Centre
for Cancer Drug Discovery, The Institute
of Cancer Research, London SM2 5NG, U.K.
- Division
of Structural Biology, The Institute of
Cancer Research, London SM2 5NG, U.K.
| | - Gary K. Newton
- Centre
for Cancer Drug Discovery, The Institute
of Cancer Research, London SM2 5NG, U.K.
| | - Rosemary Burke
- Centre
for Cancer Drug Discovery, The Institute
of Cancer Research, London SM2 5NG, U.K.
| | - Ian Collins
- Centre
for Cancer Drug Discovery, The Institute
of Cancer Research, London SM2 5NG, U.K.
| | - Swen Hoelder
- Centre
for Cancer Drug Discovery, The Institute
of Cancer Research, London SM2 5NG, U.K.
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11
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Michaelides IN, Collie GW. E3 Ligases Meet Their Match: Fragment-Based Approaches to Discover New E3 Ligands and to Unravel E3 Biology. J Med Chem 2023; 66:3173-3194. [PMID: 36821822 PMCID: PMC10009759 DOI: 10.1021/acs.jmedchem.2c01882] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Indexed: 02/25/2023]
Abstract
Ubiquitination is a key post-translational modification of proteins, affecting the regulation of multiple cellular processes. Cells are equipped with over 600 ubiquitin orchestrators, called E3 ubiquitin ligases, responsible for directing the covalent attachment of ubiquitin to substrate proteins. Due to their regulatory role in cells, significant efforts have been made to discover ligands for E3 ligases. The recent emergence of the proteolysis targeting chimera (PROTAC) and molecular glue degrader (MGD) modalities has further increased interest in E3 ligases as drug targets. This perspective focuses on how fragment based lead discovery (FBLD) methods have been used to discover new ligands for this important target class. In some cases these efforts have led to clinical candidates; in others, they have provided tools for deepening our understanding of E3 ligase biology. Recently, FBLD-derived ligands have inspired the design of PROTACs that are able to artificially modulate protein levels in cells.
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Affiliation(s)
- Iacovos N. Michaelides
- Discovery Sciences, BioPharmaceuticals
R&D, AstraZeneca, Cambridge, CB4 0WG, United
Kingdom
| | - Gavin W. Collie
- Discovery Sciences, BioPharmaceuticals
R&D, AstraZeneca, Cambridge, CB4 0WG, United
Kingdom
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12
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Kuchta R, Heim C, Herrmann A, Maiwald S, Ng YLD, Sosič I, Keuler T, Krönke J, Gütschow M, Hartmann MD, Steinebach C. Accessing three-branched high-affinity cereblon ligands for molecular glue and protein degrader design. RSC Chem Biol 2023; 4:229-234. [PMID: 36908700 PMCID: PMC9994103 DOI: 10.1039/d2cb00223j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/02/2023] [Indexed: 01/04/2023] Open
Abstract
The Petasis borono-Mannich reaction was employed for an alternative entry towards three-branched cereblon ligands. Such compounds are capabable of making multiple interactions with the protein surface and possess a suitable linker exit vector. The high-affinity ligands were used to assemble prototypic new molecular glues and proteolysis targeting chimeras (PROTACs) targeting BRD4 for degradation. Our results highlight the importance of multicomponent reactions (MCRs) in drug discovery and add new insights into the rapidly growing field of protein degraders.
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Affiliation(s)
- Robert Kuchta
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn An der Immenburg 4 Bonn D-53121 Germany
| | - Christopher Heim
- Max Planck Institute for Biology Tübingen Tübingen D-72076 Germany .,Interfaculty Institute of Biochemistry, University of Tübingen Tübingen 72076 Germany
| | | | - Samuel Maiwald
- Max Planck Institute for Biology Tübingen Tübingen D-72076 Germany
| | - Yuen Lam Dora Ng
- Charité, Department of Internal Medicine with Focus on Hematology, Oncology and Tumor Immunology Berlin D-12203 Germany
| | - Izidor Sosič
- Faculty of Pharmacy, University of Ljubljana Ljubljana SI-1000 Slovenia
| | - Tim Keuler
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn An der Immenburg 4 Bonn D-53121 Germany
| | - Jan Krönke
- Charité, Department of Internal Medicine with Focus on Hematology, Oncology and Tumor Immunology Berlin D-12203 Germany
| | - Michael Gütschow
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn An der Immenburg 4 Bonn D-53121 Germany
| | - Marcus D Hartmann
- Max Planck Institute for Biology Tübingen Tübingen D-72076 Germany .,Interfaculty Institute of Biochemistry, University of Tübingen Tübingen 72076 Germany
| | - Christian Steinebach
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn An der Immenburg 4 Bonn D-53121 Germany
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13
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Lecca D, Hsueh SC, Luo W, Tweedie D, Kim DS, Baig AM, Vargesson N, Kim YK, Hwang I, Kim S, Hoffer BJ, Chiang YH, Greig NH. Novel, thalidomide-like, non-cereblon binding drug tetrafluorobornylphthalimide mitigates inflammation and brain injury. J Biomed Sci 2023; 30:16. [PMID: 36872339 PMCID: PMC9987061 DOI: 10.1186/s12929-023-00907-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 02/09/2023] [Indexed: 03/07/2023] Open
Abstract
BACKGROUND Quelling microglial-induced excessive neuroinflammation is a potential treatment strategy across neurological disorders, including traumatic brain injury (TBI), and can be achieved by thalidomide-like drugs albeit this approved drug class is compromised by potential teratogenicity. Tetrafluorobornylphthalimide (TFBP) and tetrafluoronorbornylphthalimide (TFNBP) were generated to retain the core phthalimide structure of thalidomide immunomodulatory imide drug (IMiD) class. However, the classical glutarimide ring was replaced by a bridged ring structure. TFBP/TFNBP were hence designed to retain beneficial anti-inflammatory properties of IMiDs but, importantly, hinder cereblon binding that underlies the adverse action of thalidomide-like drugs. METHODS TFBP/TFNBP were synthesized and evaluated for cereblon binding and anti-inflammatory actions in human and rodent cell cultures. Teratogenic potential was assessed in chicken embryos, and in vivo anti-inflammatory actions in rodents challenged with either lipopolysaccharide (LPS) or controlled cortical impact (CCI) moderate traumatic brain injury (TBI). Molecular modeling was performed to provide insight into drug/cereblon binding interactions. RESULTS TFBP/TFNBP reduced markers of inflammation in mouse macrophage-like RAW264.7 cell cultures and in rodents challenged with LPS, lowering proinflammatory cytokines. Binding studies demonstrated minimal interaction with cereblon, with no resulting degradation of teratogenicity-associated transcription factor SALL4 or of teratogenicity in chicken embryo assays. To evaluate the biological relevance of its anti-inflammatory actions, two doses of TFBP were administered to mice at 1 and 24 h post-injury following CCI TBI. Compared to vehicle treatment, TFBP reduced TBI lesion size together with TBI-induction of an activated microglial phenotype, as evaluated by immunohistochemistry 2-weeks post-injury. Behavioral evaluations at 1- and 2-weeks post-injury demonstrated TFBP provided more rapid recovery of TBI-induced motor coordination and balance impairments, versus vehicle treated mice. CONCLUSION TFBP and TFNBP represent a new class of thalidomide-like IMiDs that lower proinflammatory cytokine generation but lack binding to cereblon, the main teratogenicity-associated mechanism. This aspect makes TFBP and TFNBP potentially safer than classic IMiDs for clinical use. TFBP provides a strategy to mitigate excessive neuroinflammation associated with moderate severity TBI to, thereby, improve behavioral outcome measures and warrants further investigation in neurological disorders involving a neuroinflammatory component.
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Affiliation(s)
- Daniela Lecca
- Drug Design and Development Section, Translational Gerontology Branch, Intramural Research Program National Institute On Aging, NIH, Baltimore, MD, 21224, USA
| | - Shih-Chang Hsueh
- Drug Design and Development Section, Translational Gerontology Branch, Intramural Research Program National Institute On Aging, NIH, Baltimore, MD, 21224, USA
| | - Weiming Luo
- Drug Design and Development Section, Translational Gerontology Branch, Intramural Research Program National Institute On Aging, NIH, Baltimore, MD, 21224, USA
| | - David Tweedie
- Drug Design and Development Section, Translational Gerontology Branch, Intramural Research Program National Institute On Aging, NIH, Baltimore, MD, 21224, USA
| | - Dong Seok Kim
- Aevisbio Inc., Gaithersburg, MD, 20878, USA
- Aevis Bio Inc., Daejeon, 34141, Republic of Korea
| | - Abdul Mannan Baig
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi, 74800, Pakistan
| | - Neil Vargesson
- School of Medicine, Medical Sciences and Nutrition, Institute of Medical Sciences, University of Aberdeen, Aberdeen, AB25 2ZD, Scotland, UK
| | - Yu Kyung Kim
- Aevis Bio Inc., Daejeon, 34141, Republic of Korea
| | - Inho Hwang
- Aevis Bio Inc., Daejeon, 34141, Republic of Korea
| | - Sun Kim
- Aevis Bio Inc., Daejeon, 34141, Republic of Korea
| | - Barry J Hoffer
- Department of Neurological Surgery, Case Western Reserve University School of Medicine, Cleveland, OH, 44106, USA
| | - Yung-Hsiao Chiang
- Neuroscience Research Center, Taipei Medical University, Taipei, 110, Taiwan.
- Department of Neurosurgery, Taipei Medical University Hospital, Department of Surgery, School of Medicine, College of Medicine, Taipei Medical University, Taipei, 110, Taiwan.
| | - Nigel H Greig
- Drug Design and Development Section, Translational Gerontology Branch, Intramural Research Program National Institute On Aging, NIH, Baltimore, MD, 21224, USA.
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14
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Heim C, Spring AK, Kirchgäßner S, Schwarzer D, Hartmann MD. Cereblon neo-substrate binding mimics the recognition of the cyclic imide degron. Biochem Biophys Res Commun 2023; 646:30-35. [PMID: 36701892 DOI: 10.1016/j.bbrc.2023.01.051] [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: 12/31/2022] [Accepted: 01/17/2023] [Indexed: 01/19/2023]
Abstract
In targeted protein degradation, immunomodulatory drugs (IMiDs) or cereblon (CRBN) E3 ligase modulatory drugs (CELMoDs) recruit neo-substrate proteins to the E3 ubiquitin ligase receptor CRBN for ubiquitination and subsequent proteasomal degradation. While the structural basis of this mechanism is generally understood, we have only recently described the recognition mode of the natural CRBN degron. In this communication, we reveal that the IMiD- or CELMoD-mediated binding of neo-substrates closely mimics the recognition of natural degrons. In crystal structures, we identify a conserved binding mode for natural degron peptides with an elaborate hydrogen bonding network involving the backbone of each of the six C-terminal degron residues, without the involvement of side chains. In a structural comparison, we show that neo-substrates recruited by IMiDs or CELMoDs emulate every single hydrogen bond of this network and thereby explain the origins of the largely sequence-independent recognition of neo-substrates. Our results imply that the V388I substitution in CRBN does not impair natural degron recognition and complete the structural basis for the rational design of CRBN effectors.
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Affiliation(s)
- Christopher Heim
- Max Planck Institute for Biology, Tübingen, Germany; Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany; NanoTemper Technologies GmbH, Munich, Germany
| | | | - Sören Kirchgäßner
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Dirk Schwarzer
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Marcus D Hartmann
- Max Planck Institute for Biology, Tübingen, Germany; Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany.
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15
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Xie H, Li C, Tang H, Tandon I, Liao J, Roberts BL, Zhao Y, Tang W. Development of Substituted Phenyl Dihydrouracil as the Novel Achiral Cereblon Ligands for Targeted Protein Degradation. J Med Chem 2023; 66:2904-2917. [PMID: 36749666 PMCID: PMC10398712 DOI: 10.1021/acs.jmedchem.2c01941] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Glutarimides such as thalidomide, pomalidomide, and lenalidomide are the most frequently used ligands to recruit E3 ubiquitin ligase cereblon (CRBN) for the development of proteolysis-targeting chimeras (PROTACs). Due to the rapid and spontaneous racemization of glutarimides, most CRBN-recruiting PROTACs are synthesized as a mixture of racemates or diastereomers. Since the (S)-enantiomer is primarily responsible for binding to CRBN, the existence of the largely inactive (R)-enantiomer complicates the drug development process. Herein, we report that substituted achiral phenyl dihydrouracil (PDHU) can be used as a novel class of CRBN ligands for the development of PROTACs. Although the parent PDHU has a minimal binding affinity to CRBN, we found that some substituted PDHUs had a comparable binding affinity to lenalidomide. Structural modeling provided a further understanding of the molecular interactions between PDHU ligands and CRBN. PDHUs also have greater stability than lenalidomide. Finally, potent BRD4 degraders were developed by employing trisubstituted PDHUs.
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Affiliation(s)
- Haibo Xie
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705 (USA)
| | - Chunrong Li
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705 (USA)
| | - Hua Tang
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705 (USA)
| | - Ira Tandon
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705 (USA)
| | - Junzhuo Liao
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705 (USA)
| | - Brett L. Roberts
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705 (USA)
| | - Yu Zhao
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705 (USA)
| | - Weiping Tang
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53705 (USA)
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706 (USA)
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16
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Krasavin M, Adamchik M, Bubyrev A, Heim C, Maiwald S, Zhukovsky D, Zhmurov P, Bunev A, Hartmann MD. Synthesis of novel glutarimide ligands for the E3 ligase substrate receptor Cereblon (CRBN): Investigation of their binding mode and antiproliferative effects against myeloma cell lines. Eur J Med Chem 2023; 246:114990. [PMID: 36476642 DOI: 10.1016/j.ejmech.2022.114990] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 11/04/2022] [Accepted: 11/28/2022] [Indexed: 12/05/2022]
Abstract
To expand the chemical toolkit for targeted protein degradation, we report the generation of a new series of non-thalidomide Cereblon (CRBN) ligands. Readily available 2-methylidene glutarimide was converted to a series of 2-((hetero)aryl(methyl))thio glutarimides via the thio-Michael addition reaction. The compounds thus synthesized were evaluated for their affinity to the thalidomide-binding domain of human CRBN and their binding modes studied via X-ray crystallography. This helped identify several promising glutarimide derivatives which bind stronger to CRBN compared to thalidomide and contain a functional group which permits further chemical conjugation. Oxidation of the sulfur atom in a select group of 2-((hetero)aryl(methyl))thio glutarimides produced the respective sulfones which were found to possess a markedly stronger antiproliferative profile against multiple myeloma cell lines and a sophisticated structural binding mode with additional hydrogen bonding interactions. The newly identified Cereblon ligands form the basis for the synthesis of novel PROTAC protein degraders.
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Affiliation(s)
- Mikhail Krasavin
- Saint Petersburg State University, Saint Petersburg, 199034, Russian Federation; Immanuel Kant Baltic Federal University, Kaliningrad, 236041, Russian Federation.
| | - Maria Adamchik
- Saint Petersburg State University, Saint Petersburg, 199034, Russian Federation
| | - Andrey Bubyrev
- Saint Petersburg State University, Saint Petersburg, 199034, Russian Federation
| | - Christopher Heim
- Department of Protein Evolution, Max Planck Institute for Biology, Tübingen, Germany; Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Samuel Maiwald
- Department of Protein Evolution, Max Planck Institute for Biology, Tübingen, Germany
| | - Daniil Zhukovsky
- Saint Petersburg State University, Saint Petersburg, 199034, Russian Federation
| | - Petr Zhmurov
- Saint Petersburg State University, Saint Petersburg, 199034, Russian Federation
| | - Alexander Bunev
- Medicinal Chemistry Center, Togliatti State University, Togliatti, 445020, Russian Federation
| | - Marcus D Hartmann
- Department of Protein Evolution, Max Planck Institute for Biology, Tübingen, Germany; Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany.
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17
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Synthesis of novel glutarimide derivatives via the Michael addition of (hetero)aromatic thiols: pronounced effect of sulfur oxidation on cytotoxicity towards multiple myeloma cell lines. MENDELEEV COMMUNICATIONS 2023. [DOI: 10.1016/j.mencom.2023.01.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
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18
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Nayek U, Basheer Ahamed SI, Mansoor Hussain UH, Unnikrishnan MK, Abdul Salam AA. Computational investigations of indanedione and indanone derivatives in drug discovery: Indanone derivatives inhibits cereblon, an E3 ubiquitin ligase component. Comput Biol Chem 2022; 101:107776. [PMID: 36252444 DOI: 10.1016/j.compbiolchem.2022.107776] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/30/2022] [Accepted: 10/05/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND Cereblon, an extensively studied multifunctional protein, is a Cullin 4-RING E3 ubiquitin ligase complex component. Cereblon is a well-known target of thalidomide and its derivatives. Cereblon is involved in multiple myeloma cell apoptosis. When ligands such as thalidomide and lenalidomide bind to cereblon, it recognizes various neosubstrates based on the ligand shape and properties. We have identified novel CRBN inhibitors, namely DHFO and its analogs, with structural features that are slightly different from thalidomide but stronger cereblon-binding affinity. We selected indanedione and indanone derivatives from the literature to understand and compare their cereblon-mediated substrate recognition potential. METHODS Computational investigations of possible CRBN inhibitors were investigated by molecular docking with Autodock Vina and DockThor programs. The properties of the compounds' ADME/T and drug-likeness were investigated. A molecular dynamics study was carried out for four selected molecules, and the molecular interactions were analyzed using PCA-based FEL methods. The binding affinity was calculated using the MM/PBSA method. RESULTS We conducted computational investigations on 68 indanedione and indanone derivatives binding with cereblon. Ten molecules showed better CRBN binding affinity than thalidomide. We studied the drug-likeness properties of the selected ten molecules, and four of the most promising molecules (DHFO, THOH, DIMS, and DTIN) were chosen for molecular dynamics studies. The MM/PBSA calculations showed that the DHFO, already shown to be a 5-LOX/COX2 inhibitor, has the highest binding affinity of - 163.16 kJ/mol with cereblon. CONCLUSION The selected CRBN inhibitor DHFO has demonstrated the highest binding affinity with cereblon protein compared to other molecules. Thalidomide and its derivatives have a new substitute in the form of DHFO, which produces an interaction hotspot on the surface of the cereblon. Ease of chemical synthesis, low toxicity, versatile therapeutic options, and pleiotropism of DHFO analogs provide an opportunity for exploring clinical alternatives with versatile therapeutic potential for a new category of indanedione molecules as novel modulators of E3 ubiquitin ligases.
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19
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Heim C, Spring AK, Kirchgäßner S, Schwarzer D, Hartmann MD. Identification and structural basis of C-terminal cyclic imides as natural degrons for cereblon. Biochem Biophys Res Commun 2022; 637:66-72. [DOI: 10.1016/j.bbrc.2022.11.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 11/02/2022] [Indexed: 11/06/2022]
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20
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Barkhatova D, Zhukovsky D, Heim C, Maiwald S, Hartmann MD, Krasavin M. Synthesis of novel glutarimide derivatives via the Ugi multicomponent reaction: affinity towards the E3 ubiquitin ligase substrate receptor Cereblon. MENDELEEV COMMUNICATIONS 2022. [DOI: 10.1016/j.mencom.2022.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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21
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Hsueh SC, Scerba MT, Tweedie D, Lecca D, Kim DS, Baig AM, Kim YK, Hwang I, Kim S, Selman WR, Hoffer BJ, Greig NH. Activity of a Novel Anti-Inflammatory Agent F-3,6'-dithiopomalidomide as a Treatment for Traumatic Brain Injury. Biomedicines 2022; 10:2449. [PMID: 36289711 PMCID: PMC9598880 DOI: 10.3390/biomedicines10102449] [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: 08/20/2022] [Revised: 09/01/2022] [Accepted: 09/17/2022] [Indexed: 11/16/2022] Open
Abstract
Traumatic brain injury (TBI) is a major risk factor for several neurodegenerative disorders, including Parkinson's disease (PD) and Alzheimer's disease (AD). Neuroinflammation is a cause of later secondary cell death following TBI, has the potential to aggravate the initial impact, and provides a therapeutic target, albeit that has failed to translate into clinical trial success. Thalidomide-like compounds have neuroinflammation reduction properties across cellular and animal models of TBI and neurodegenerative disorders. They lower the generation of proinflammatory cytokines, particularly TNF-α which is pivotal in microglial cell activation. Unfortunately, thalidomide-like drugs possess adverse effects in humans before achieving anti-inflammatory drug levels. We developed F-3,6'-dithiopomalidomide (F-3,6'-DP) as a novel thalidomide-like compound to ameliorate inflammation. F-3,6'-DP binds to cereblon but does not efficiently trigger the degradation of the transcription factors (SALL4, Ikaros, and Aiolos) associated with the teratogenic and anti-proliferative responses of thalidomide-like drugs. We utilized a phenotypic drug discovery approach that employed cellular and animal models in the selection and development of F-3,6'-DP. F-3,6'-DP significantly mitigated LPS-induced inflammatory markers in RAW 264.7 cells, and lowered proinflammatory cytokine/chemokine levels in the plasma and brain of rats challenged with systemic LPS. We subsequently examined immunohistochemical, biochemical, and behavioral measures following controlled cortical impact (CCI) in mice, a model of moderate TBI known to induce inflammation. F-3,6'-DP decreased CCI-induced neuroinflammation, neuronal loss, and behavioral deficits when administered after TBI. F-3,6'-DP represents a novel class of thalidomide-like drugs that do not lower classical cereblon-associated transcription factors but retain anti-inflammatory actions and possess efficacy in the treatment of TBI and potentially longer-term neurodegenerative disorders.
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Affiliation(s)
- Shih Chang Hsueh
- Drug Design & Development Section, Translational Gerontology Branch, Intramural Research Program National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Michael T. Scerba
- Drug Design & Development Section, Translational Gerontology Branch, Intramural Research Program National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - David Tweedie
- Drug Design & Development Section, Translational Gerontology Branch, Intramural Research Program National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Daniela Lecca
- Drug Design & Development Section, Translational Gerontology Branch, Intramural Research Program National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Dong Seok Kim
- AevisBio, Inc., Gaithersburg, MD 20878, USA
- Aevis Bio, Inc., Daejeon 34141, Korea
| | - Abdul Mannan Baig
- Department of Biological and Biomedical Sciences, Aga Khan University, Karachi 74800, Pakistan
| | | | | | - Sun Kim
- Aevis Bio, Inc., Daejeon 34141, Korea
| | - Warren R. Selman
- Department of Neurological Surgery, Case Western Reserve University and University Hospitals, Cleveland, OH 44106, USA
| | - Barry J. Hoffer
- Department of Neurological Surgery, Case Western Reserve University and University Hospitals, Cleveland, OH 44106, USA
| | - Nigel H. Greig
- Drug Design & Development Section, Translational Gerontology Branch, Intramural Research Program National Institute on Aging, NIH, Baltimore, MD 21224, USA
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22
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Huber A, Li Y, Lin W, Galbraith AN, Mishra A, Porter SN, Wu J, Florke Gee RR, Zhuang W, Pruett-Miller SM, Peng J, Chen T. SJPYT-195: A Designed Nuclear Receptor Degrader That Functions as a Molecular Glue Degrader of GSPT1. ACS Med Chem Lett 2022; 13:1311-1320. [PMID: 35978691 PMCID: PMC9377019 DOI: 10.1021/acsmedchemlett.2c00223] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 07/12/2022] [Indexed: 12/13/2022] Open
Abstract
We previously reported a specific inverse agonist (SPA70) of the nuclear receptor pregnane X receptor (PXR). However, derivatization of SPA70 yielded only agonists and neutral antagonists, suggesting that inverse agonism of PXR is difficult to achieve. Therefore, we sought to design proteolysis targeting chimeras (PROTACs) aimed at inducing PXR degradation. Conjugation of a SPA70 derivative to ligands of the E3 substrate receptor cereblon (CRBN) resulted in one molecule, SJPYT-195, that reduced PXR protein level in an optimized degradation assay described here. Further analysis revealed that SJPYT-195 was a molecular glue degrader of the translation termination factor GSPT1 and that GSPT1 degradation resulted in subsequent reduction of PXR protein. GSPT1 has recently gained interest as an anticancer target, and our results give new insights into chemical determinants of drug-induced GSPT1 degradation. Additionally, we have developed assays and cell models for PXR degrader discovery that can be applied to additional protein targets.
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Affiliation(s)
- Andrew
D. Huber
- Department
of Chemical Biology and Therapeutics, St.
Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Yongtao Li
- Department
of Chemical Biology and Therapeutics, St.
Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Wenwei Lin
- Department
of Chemical Biology and Therapeutics, St.
Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Annalise N. Galbraith
- Department
of Chemical Biology and Therapeutics, St.
Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Ashutosh Mishra
- Center
for Proteomics and Metabolomics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Shaina N. Porter
- Department
of Cell and Molecular Biology, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105, United States
- Center
for Advanced Genome Engineering, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Jing Wu
- Department
of Chemical Biology and Therapeutics, St.
Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Rebecca R. Florke Gee
- Department
of Chemical Biology and Therapeutics, St.
Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
- Graduate
School of Biomedical Sciences, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Wei Zhuang
- Department
of Chemical Biology and Therapeutics, St.
Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Shondra M. Pruett-Miller
- Department
of Cell and Molecular Biology, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105, United States
- Center
for Advanced Genome Engineering, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Junmin Peng
- Center
for Proteomics and Metabolomics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105, United States
- Department
of Structural Biology, St. Jude Children’s
Research Hospital, Memphis, Tennessee 38105, United States
- Department
of Developmental Neurobiology, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Taosheng Chen
- Department
of Chemical Biology and Therapeutics, St.
Jude Children’s Research Hospital, Memphis, Tennessee 38105, United States
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23
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Yamamoto J, Ito T, Yamaguchi Y, Handa H. Discovery of CRBN as a target of thalidomide: a breakthrough for progress in the development of protein degraders. Chem Soc Rev 2022; 51:6234-6250. [PMID: 35796627 DOI: 10.1039/d2cs00116k] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Progress in strategies aimed at breaking down therapeutic target proteins has led to a paradigm shift in drug discovery. Thalidomide and its derivatives are the only protein degraders currently used in clinical practice. Our understanding of the molecular mechanism of action of thalidomide and its derivatives has advanced dramatically since the identification of cereblon (CRBN) as their direct target. The binding of thalidomide derivatives to CRBN, a substrate recognition receptor for Cullin 4 RING E3 ubiquitin ligase (CRL4), induces the recruitment of non-native substrates to CRL4CRBN and their subsequent degradation. This discovery was a breakthrough in the current rapid development of protein-degrading agents because clarification of the mechanism of action of thalidomide derivatives has demonstrated the clinical value of these compounds. This review provides an overview of the mechanism of action of thalidomide and its derivatives and describes perspectives for protein degraders.
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Affiliation(s)
- Junichi Yamamoto
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Takumi Ito
- Institute of Medical Science, Tokyo Medical University, Shinjuku, Tokyo 160-8402, Japan
| | - Yuki Yamaguchi
- School of Life Science and Technology, Tokyo Institute of Technology, Yokohama 226-8501, Japan
| | - Hiroshi Handa
- Center for Future Medical Research, Tokyo Medical University, Shinjuku, Tokyo 160-8402, Japan.
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24
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Hendrick CE, Jorgensen JR, Chaudhry C, Strambeanu II, Brazeau JF, Schiffer J, Shi Z, Venable JD, Wolkenberg SE. Direct-to-Biology Accelerates PROTAC Synthesis and the Evaluation of Linker Effects on Permeability and Degradation. ACS Med Chem Lett 2022; 13:1182-1190. [PMID: 35859867 PMCID: PMC9290060 DOI: 10.1021/acsmedchemlett.2c00124] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Charles E. Hendrick
- Discovery Chemistry, Therapeutics Discovery, Janssen Research & Development, LLC,Welsh & McKean Roads, Spring House, Pennsylvania 19477, United States
| | - Jeff R. Jorgensen
- Discovery Technology and Molecular Pharmacology, Therapeutics Discovery, Janssen Research & Development, LLC, Welsh & McKean Roads, Spring House, Pennsylvania 19477, United States
| | - Charu Chaudhry
- Discovery Technology and Molecular Pharmacology, Therapeutics Discovery, Janssen Research & Development, LLC, Welsh & McKean Roads, Spring House, Pennsylvania 19477, United States
| | - Iulia I. Strambeanu
- Discovery Chemistry, Therapeutics Discovery, Janssen Research & Development, LLC,Welsh & McKean Roads, Spring House, Pennsylvania 19477, United States
| | - Jean-Francois Brazeau
- Discovery Chemistry, Therapeutics Discovery, Janssen Research & Development, LLC, 3210 Merryfield Row, La Jolla, California 92121, United States
| | - Jamie Schiffer
- Computational Chemistry, Therapeutics Discovery, Janssen Research & Development, LLC, 3210 Merryfield Row, La Jolla, California 92121, United States
| | - Zhicai Shi
- Discovery Chemistry, Therapeutics Discovery, Janssen Research & Development, LLC,Welsh & McKean Roads, Spring House, Pennsylvania 19477, United States
| | - Jennifer D. Venable
- Discovery Chemistry, Therapeutics Discovery, Janssen Research & Development, LLC, 3210 Merryfield Row, La Jolla, California 92121, United States
| | - Scott E. Wolkenberg
- Discovery Chemistry, Therapeutics Discovery, Janssen Research & Development, LLC,Welsh & McKean Roads, Spring House, Pennsylvania 19477, United States
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25
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Sosič I, Bricelj A, Steinebach C. E3 ligase ligand chemistries: from building blocks to protein degraders. Chem Soc Rev 2022; 51:3487-3534. [PMID: 35393989 DOI: 10.1039/d2cs00148a] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In recent years, proteolysis-targeting chimeras (PROTACs), capable of achieving targeted protein degradation, have proven their great therapeutic potential and usefulness as molecular biology tools. These heterobifunctional compounds are comprised of a protein-targeting ligand, an appropriate linker, and a ligand binding to the E3 ligase of choice. A successful PROTAC induces the formation of a ternary complex, leading to the E3 ligase-mediated ubiquitination of the targeted protein and its proteasomal degradation. In over 20 years since the concept was first demonstrated, the field has grown substantially, mainly due to the advancements in the discovery of non-peptidic E3 ligase ligands. Development of small-molecule E3 binders with favourable physicochemical profiles aided the design of PROTACs, which are known for breaking the rules of established guidelines for discovering small molecules. Synthetic accessibility of the ligands and numerous successful applications led to the prevalent use of cereblon and von Hippel-Lindau as the hijacked E3 ligase. However, the pool of over 600 human E3 ligases is full of untapped potential, which is why expanding the artillery of E3 ligands could contribute to broadening the scope of targeted protein degradation. In this comprehensive review, we focus on the chemistry aspect of the PROTAC design process by providing an overview of liganded E3 ligases, their chemistries, appropriate derivatisation, and synthetic approaches towards their incorporation into heterobifunctional degraders. By covering syntheses of both established and underexploited E3 ligases, this review can serve as a chemistry blueprint for PROTAC researchers during their future ventures into the complex field of targeted protein degradation.
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Affiliation(s)
- Izidor Sosič
- Faculty of Pharmacy, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Aleša Bricelj
- Faculty of Pharmacy, University of Ljubljana, SI-1000 Ljubljana, Slovenia
| | - Christian Steinebach
- Pharmaceutical Institute, Pharmaceutical & Medicinal Chemistry, University of Bonn, An der Immenburg 4, D-53121 Bonn, Germany
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26
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Heim C, Hartmann MD. High-resolution structures of the bound effectors avadomide (CC-122) and iberdomide (CC-220) highlight advantages and limitations of the MsCI4 soaking system. ACTA CRYSTALLOGRAPHICA SECTION D STRUCTURAL BIOLOGY 2022; 78:290-298. [PMID: 35234143 PMCID: PMC8900816 DOI: 10.1107/s2059798322000092] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 01/04/2022] [Indexed: 11/15/2022]
Abstract
Using the MsCI4 soaking system, the binding of the next-generation thalidomide-derived immunomodulatory drugs avadomide (CC-122) and iberdomide (CC-220) to cereblon was characterized at high resolution, highlighting the utility of the MsCI4 system for studies of the structure–activity relationship of cereblon effectors. Cereblon (CRBN) is the substrate receptor of the CRL4CRBN E3 ubiquitin ligase and is a central player in targeted protein degradation. It is the target of the thalidomide-derived immunomodulatory drugs (IMiDs) and is one of the most widely employed receptors for proteolysis-targeting chimeras (PROTACs), both of which induce the ubiquitination and subsequent proteasomal degradation of target proteins. Structural studies of ligand binding to CRBN are crucial to elucidate the mechanisms of action and for mediation of side effects, ultimately aiding the development of next-generation IMiDs and PROTACs. With this aim, a crystal-soaking system based on the single-domain bacterial homologue MsCI4 has previously been established and used to delineate the binding modes of several classes of small molecules, including FDA-approved drugs, at the molecular level. Here, this system was used to characterize the binding of the next-generation IMiDs avadomide (CC-122) and iberdomide (CC-220) at high resolution, highlighting the advantages and limitations of the MsCI4 system and its implications for the development of future cereblon effectors.
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27
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Abstract
INTRODUCTION Cereblon (CRBN), the substrate receptor of the CRL4CRBN E3 ubiquitin ligase has been extensively studied due to its involvement in many biological processes. It has also been identified as the target for immunomodulatory drugs (IMiDs). CRBN ligands are also important components of proteolysis-targeting chimeras (PROTACs), special bifunctional constructs capable of targeted degradation of aberrantly acting proteins using the cell's ubiquitin-proteasome machinery. AREAS COVERED Due to upsurge of the PROTAC technology, the patenting activity of new CRBN ligands has been on the rise in the last 5 years. The present review covers two broadly defined areas of CRBN ligand design. One covers 'thalidomide-like' molecules representing modifications of various parts of classical IMiDs. The other areas - non-thalidomide-like compounds - are compounds that are structurally distinct from the classical IMiDs. Efforts toward creating new CRBN ligands reflected in non-patent literature are briefly discussed with emphasis on the rational, crystallography-driven approaches. EXPERT OPINION The chemical space of CRBN ligands which is related to the classical IMiDs (thalidomide/lenalidomide/pomalidomide) is comprehensively covered by the current patent literature. The promising area of research is in the identification of non-thalidomide-like chemotypes capable of binding to CRBN. Rational, crystallography-driven approaches currently exploited in academia will significantly aid in this endeavor.
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Affiliation(s)
- Alexander Kazantsev
- Institute of Chemistry, Saint Petersburg State University, Saint Petersburg, Russian Federation
| | - Mikhail Krasavin
- Institute of Chemistry, Saint Petersburg State University, Saint Petersburg, Russian Federation
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28
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Ito T, Yamaguchi Y, Handa H. Exploiting ubiquitin ligase cereblon as a target for small-molecule compounds in medicine and chemical biology. Cell Chem Biol 2021; 28:987-999. [PMID: 34033753 DOI: 10.1016/j.chembiol.2021.04.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 04/08/2021] [Accepted: 04/20/2021] [Indexed: 12/24/2022]
Abstract
Cereblon (CRBN), originally identified as a gene associated with intellectual disability, was identified as primary target of thalidomide. Accumulating evidence has shown that CRBN is a substrate receptor of Cullin Ring E3 ubiquitin ligase 4 (CRL4) containing DDB1, CUL4, and RBX1, which recognizes specific neosubstrates in the presence of thalidomide or its analogs and induces their ubiquitination and proteasomal degradation. A set of small-molecule, CRBN-binding drugs are known as molecular glue degraders because these compounds promote the interaction between CRBN and its neosubstrates. Moreover, CRBN-based proteolysis-targeting chimeras, heterobifunctional molecules hijacking CRBN and inducing degradation of proteins of interest, have emerged as a promising modality in drug development and are being actively investigated. Meanwhile, the original functions and regulations of CRBN are still largely elusive. In this review, we describe key findings surrounding CRBN since its discovery and then discuss a few unanswered issues.
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Affiliation(s)
- Takumi Ito
- Department of Chemical Biology, Tokyo Medical University, 6-1-1, Shinjuku, Shinjuku-ku 160-8402, Japan
| | - Yuki Yamaguchi
- School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Hiroshi Handa
- Department of Chemical Biology, Tokyo Medical University, 6-1-1, Shinjuku, Shinjuku-ku 160-8402, Japan.
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29
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Hsueh SC, Luo W, Tweedie D, Kim DS, Kim YK, Hwang I, Gil JE, Han BS, Chiang YH, Selman W, Hoffer BJ, Greig NH. N-Adamantyl Phthalimidine: A New Thalidomide-like Drug That Lacks Cereblon Binding and Mitigates Neuronal and Synaptic Loss, Neuroinflammation, and Behavioral Deficits in Traumatic Brain Injury and LPS Challenge. ACS Pharmacol Transl Sci 2021; 4:980-1000. [PMID: 33860215 DOI: 10.1021/acsptsci.1c00042] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Indexed: 02/07/2023]
Abstract
Neuroinflammation contributes to delayed secondary cell death following traumatic brain injury (TBI), has the potential to chronically exacerbate the initial insult, and represents a therapeutic target that has largely failed to translate into human efficacy. Thalidomide-like drugs have effectively mitigated neuroinflammation across cellular and animal models of TBI and neurodegeneration but are complicated by adverse actions in humans. We hence developed N-adamantyl phthalimidine (NAP) as a new thalidomide-like drug to mitigate inflammation without binding to cereblon, a key target associated with the antiproliferative, antiangiogenic, and teratogenic actions seen in this drug class. We utilized a phenotypic drug discovery approach that employed multiple cellular and animal models and ultimately examined immunohistochemical, biochemical, and behavioral measures following controlled cortical impact (CCI) TBI in mice. NAP mitigated LPS-induced inflammation across cellular and rodent models and reduced oligomeric α-synuclein and amyloid-β mediated inflammation. Following CCI TBI, NAP mitigated neuronal and synaptic loss, neuroinflammation, and behavioral deficits, and is unencumbered by cereblon binding, a key protein underpinning the teratogenic and adverse actions of thalidomide-like drugs in humans. In summary, NAP represents a new class of thalidomide-like drugs with anti-inflammatory actions for promising efficacy in the treatment of TBI and potentially longer-term neurodegenerative disorders.
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Affiliation(s)
- Shih Chang Hsueh
- Drug Design & Development Section, Translational Gerontology Branch, Intramural Research Program National Institute on Aging, NIH, Baltimore, Maryland 21224, United States
| | - Weiming Luo
- Drug Design & Development Section, Translational Gerontology Branch, Intramural Research Program National Institute on Aging, NIH, Baltimore, Maryland 21224, United States
| | - David Tweedie
- Drug Design & Development Section, Translational Gerontology Branch, Intramural Research Program National Institute on Aging, NIH, Baltimore, Maryland 21224, United States
| | - Dong Seok Kim
- AevisBio, Inc., Gaithersburg Maryland 20878, United States.,Aevis Bio, Inc., Daejeon 34141, Republic of Korea
| | - Yu Kyung Kim
- Aevis Bio, Inc., Daejeon 34141, Republic of Korea
| | - Inho Hwang
- Aevis Bio, Inc., Daejeon 34141, Republic of Korea
| | - Jung-Eun Gil
- Aevis Bio, Inc., Daejeon 34141, Republic of Korea
| | - Baek-Soo Han
- Research Center for Biodefence, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Republic of Korea
| | - Yung-Hsiao Chiang
- Department of Neurosurgery, Taipei Medical University Hospital, Taipei 110, Taiwan.,Neuroscience Research Center, Taipei Medical University, Taipei 110, Taiwan.,Graduate Institute of Medical Sciences, Taipei Medical University, Taipei 110, Taiwan
| | - Warren Selman
- Department of Neurological Surgery, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Barry J Hoffer
- Department of Neurological Surgery, Case Western Reserve University, Cleveland, Ohio 44106, United States
| | - Nigel H Greig
- Drug Design & Development Section, Translational Gerontology Branch, Intramural Research Program National Institute on Aging, NIH, Baltimore, Maryland 21224, United States
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30
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Heim C, Maiwald S, Steinebach C, Collins MK, Strope J, Chau CH, Figg WD, Gütschow M, Hartmann MD. On the correlation of cereblon binding, fluorination and antiangiogenic properties of immunomodulatory drugs. Biochem Biophys Res Commun 2021; 534:67-72. [PMID: 33310190 PMCID: PMC7815984 DOI: 10.1016/j.bbrc.2020.11.117] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 11/27/2020] [Indexed: 11/26/2022]
Abstract
Cereblon (CRBN), the substrate receptor of an E3 ubiquitin ligase complex, is a target of thalidomide and thalidomide-derived immunomodulatory drugs (IMiDs). The binding of these IMiDs to CRBN alters the substrate specificity of the ligase, thereby mediating multiple effects that are exploited in cancer therapy. However, to date, it is not clear which other possible targets might be involved in the efficacy of IMiDs. One especially prominent effect of a number of thalidomide analogs is their ability to inhibit angiogenesis, which is typically enhanced in fluorinated analogs. So far, the involvement of CRBN in antiangiogenic effects is under debate. Here, starting from a systematic set of thalidomide analogs and employing a quantitative in vitro CRBN-binding assay, we study the correlation of fluorination, CRBN binding and antiangiogenic effects. We clearly identify fluorination to correlate both with CRBN binding affinity and with antiangiogenic effects, but do not find a correlation between the latter two phenomena, indicating that the main target for the antiangiogenic effects of thalidomide analogs still remains to be identified.
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Affiliation(s)
- Christopher Heim
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Samuel Maiwald
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | | | - Matthew K Collins
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Jonathan Strope
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Cindy H Chau
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - William D Figg
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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31
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Zhao Z, Yue J, Ji X, Nian M, Kang K, Qiao H, Zheng X. Research progress in biological activities of succinimide derivatives. Bioorg Chem 2020; 108:104557. [PMID: 33376010 DOI: 10.1016/j.bioorg.2020.104557] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/03/2020] [Accepted: 12/10/2020] [Indexed: 12/11/2022]
Abstract
Succinimides are well recognized heterocyclic compounds in drug discovery which produce diverse therapeutically related applications in pharmacological practices. Researches in medicinal chemistry field have isolated and synthesized succinimide derivatives with multiple medicinal properties including anticonvulsant, anti-inflammatory, antitumor and antimicrobial agents, 5-HT receptor ligands and enzyme inhibitors. Simultaneously, SAR (Structure-Activity Relationship) analysis has been gradually possessed, along with a great deal of derivatives have been derived for potential targets. In this article, we comprehensively summarize the biological activities and SAR for succinimide derivatives, along with the featuring bioactive molecules reported in patents, wishing to provide an overall retrospect and prospect on the succinimide analogues.
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Affiliation(s)
- Zefeng Zhao
- College of Acupuncture & Massage, Shaanxi University of Chinese Medicine, Xixian New Area, Shaanxi Province 712046, PR China; Shaanxi Key Laboratory of Acupuncture & Medicine, Xixian New Area, Shaanxi Province 712046, PR China; School of Pharmacy, Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Biomedicine Key Laboratory of Shaanxi Province, Northwest University, 229 Taibai Road, Xi'an 710069, PR China
| | - Jiangxin Yue
- Shaanxi Key Laboratory of Acupuncture & Medicine, Xixian New Area, Shaanxi Province 712046, PR China
| | - Xiaotong Ji
- Shaanxi Key Laboratory of Acupuncture & Medicine, Xixian New Area, Shaanxi Province 712046, PR China
| | - Meng Nian
- Shaanxi Key Laboratory of Acupuncture & Medicine, Xixian New Area, Shaanxi Province 712046, PR China
| | - Kaiwen Kang
- Shaanxi Key Laboratory of Acupuncture & Medicine, Xixian New Area, Shaanxi Province 712046, PR China
| | - Haifa Qiao
- College of Acupuncture & Massage, Shaanxi University of Chinese Medicine, Xixian New Area, Shaanxi Province 712046, PR China; Shaanxi Key Laboratory of Acupuncture & Medicine, Xixian New Area, Shaanxi Province 712046, PR China.
| | - Xiaohui Zheng
- School of Pharmacy, Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, Biomedicine Key Laboratory of Shaanxi Province, Northwest University, 229 Taibai Road, Xi'an 710069, PR China
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32
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Maiwald S, Heim C, Hernandez Alvarez B, Hartmann MD. Sweet and Blind Spots in E3 Ligase Ligand Space Revealed by a Thermophoresis-Based Assay. ACS Med Chem Lett 2020; 12:74-81. [PMID: 33488967 PMCID: PMC7812675 DOI: 10.1021/acsmedchemlett.0c00440] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 11/25/2020] [Indexed: 12/22/2022] Open
Abstract
![]()
Repurposing E3 ubiquitin ligases
for targeted protein degradation
via customized molecular glues or proteolysis-targeting chimeras (PROTACs)
is an increasingly important therapeutic modality. Currently, a major
limitation in the design of suitable molecular glues and PROTACs is
our fragmentary understanding of E3 ligases and their ligand space.
We here describe a quantitative assay for the discovery and characterization
of E3 ligase ligands that is based on the thermophoretic behavior
of a custom reporter ligand. Thereby, it is orthogonal to commonly
employed fluorescence-based assays and less affected by the optical
properties of test compounds. It can be employed for the high-throughput
screening of compound libraries for a given ligase but also for hit
validation, which we demonstrate with the identification of unexpected
well-binders and non-binders, yielding new insights into the ligand
space of cereblon (CRBN).
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Affiliation(s)
- Samuel Maiwald
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Christopher Heim
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Birte Hernandez Alvarez
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Marcus D. Hartmann
- Department of Protein Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
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33
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Peach ML, Beedie SL, Chau CH, Collins MK, Markolovic S, Luo W, Tweedie D, Steinebach C, Greig NH, Gütschow M, Vargesson N, Nicklaus MC, Figg WD. Antiangiogenic Activity and in Silico Cereblon Binding Analysis of Novel Thalidomide Analogs. Molecules 2020; 25:E5683. [PMID: 33276504 PMCID: PMC7730988 DOI: 10.3390/molecules25235683] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/25/2020] [Accepted: 11/27/2020] [Indexed: 12/14/2022] Open
Abstract
Due to its antiangiogenic and anti-immunomodulatory activity, thalidomide continues to be of clinical interest despite its teratogenic actions, and efforts to synthesize safer, clinically active thalidomide analogs are continually underway. In this study, a cohort of 27 chemically diverse thalidomide analogs was evaluated for antiangiogenic activity in an ex vivo rat aorta ring assay. The protein cereblon has been identified as the target for thalidomide, and in silico pharmacophore analysis and molecular docking with a crystal structure of human cereblon were used to investigate the cereblon binding abilities of the thalidomide analogs. The results suggest that not all antiangiogenic thalidomide analogs can bind cereblon, and multiple targets and mechanisms of action may be involved.
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Affiliation(s)
- Megan L. Peach
- Basic Science Program, Chemical Biology Laboratory, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21701, USA;
| | - Shaunna L. Beedie
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA; (S.L.B.); (C.H.C.); (M.K.C.); (S.M.)
- School of Medicine, Medical Sciences & Nutrition, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, UK;
| | - Cindy H. Chau
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA; (S.L.B.); (C.H.C.); (M.K.C.); (S.M.)
| | - Matthew K. Collins
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA; (S.L.B.); (C.H.C.); (M.K.C.); (S.M.)
| | - Suzana Markolovic
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA; (S.L.B.); (C.H.C.); (M.K.C.); (S.M.)
| | - Weiming Luo
- Drug Design & Development Section, Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD 21224, USA; (W.L.); (D.T.); (N.H.G.)
| | - David Tweedie
- Drug Design & Development Section, Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD 21224, USA; (W.L.); (D.T.); (N.H.G.)
| | - Christian Steinebach
- Pharmaceutical Institute, University of Bonn, 53121 Bonn, Germany; (C.S.); (M.G.)
| | - Nigel H. Greig
- Drug Design & Development Section, Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD 21224, USA; (W.L.); (D.T.); (N.H.G.)
| | - Michael Gütschow
- Pharmaceutical Institute, University of Bonn, 53121 Bonn, Germany; (C.S.); (M.G.)
| | - Neil Vargesson
- School of Medicine, Medical Sciences & Nutrition, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, UK;
| | - Marc C. Nicklaus
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, NIH, Frederick, MD 21701, USA;
| | - William D. Figg
- Molecular Pharmacology Section, Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA; (S.L.B.); (C.H.C.); (M.K.C.); (S.M.)
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Design and Applications of Bifunctional Small Molecules in Biology. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2020; 1869:140534. [PMID: 32871274 DOI: 10.1016/j.bbapap.2020.140534] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 08/17/2020] [Accepted: 08/27/2020] [Indexed: 12/12/2022]
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Asatsuma-Okumura T, Ito T, Handa H. Molecular Mechanisms of the Teratogenic Effects of Thalidomide. Pharmaceuticals (Basel) 2020; 13:ph13050095. [PMID: 32414180 PMCID: PMC7281272 DOI: 10.3390/ph13050095] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/08/2020] [Accepted: 05/11/2020] [Indexed: 12/13/2022] Open
Abstract
Thalidomide was sold worldwide as a sedative over 60 years ago, but it was quickly withdrawn from the market due to its teratogenic effects. Thalidomide was later found to have therapeutic effects in several diseases, although the molecular mechanisms remained unclear. The discovery of cereblon (CRBN), the direct target of thalidomide, a decade ago greatly improved our understanding of its mechanism of action. Accumulating evidence has shown that CRBN functions as a substrate of Cullin RING E3 ligase (CRL4CRBN), whose specificity is controlled by ligands such as thalidomide. For example, lenalidomide and pomalidomide, well-known thalidomide derivatives, degrade the neosubstrates Ikaros and Aiolos, resulting in anti-proliferative effects in multiple myeloma. Recently, novel CRBN-binding drugs have been developed. However, for the safe handling of thalidomide and its derivatives, a greater understanding of the mechanisms of its adverse effects is required. The teratogenic effects of thalidomide occur in multiple tissues in the developing fetus and vary in phenotype, making it difficult to clarify this issue. Recently, several CRBN neosubstrates (e.g., SALL4 (Spalt Like Transcription Factor 4) and p63 (Tumor Protein P63)) have been identified as candidate mediators of thalidomide teratogenicity. In this review, we describe the current understanding of molecular mechanisms of thalidomide, particularly in the context of its teratogenicity.
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Affiliation(s)
| | - Takumi Ito
- Correspondence: ; Tel.: +81-3-9323-3250; Fax: +81-3-9323-3251
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Design and synthesis of α-naphthoflavone chimera derivatives able to eliminate cytochrome P450 (CYP)1B1-mediated drug resistance via targeted CYP1B1 degradation. Eur J Med Chem 2020; 189:112028. [PMID: 31945665 DOI: 10.1016/j.ejmech.2019.112028] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/29/2019] [Accepted: 12/30/2019] [Indexed: 01/31/2023]
Abstract
Extrahepatic cytochrome P450 1B1 (CYP1B1), which is highly expressed in various tumors, is an attractive and potential target for cancer prevention, therapy, and reversal of drug resistance. CYP1B1 inhibition is the current predominant therapeutic paradigm to treating CYP1B1-mediated malignancy, but therapeutic effect has little success. Herein, we reported CYP1B1 degradation in place of CYP1B1 inhibition for reversing drug resistance toward docetaxel in CYP1B1-overexpressing prostate cancer cell line DU145 using a PROTAC strategy. Replacing chlorine atom of a CYP1B1 selective inhibitor we found previously with ethynyl, we got the resulting α-naphthoflavone derivative 5 which kept strong inhibition against CYP1B1 (IC50 = 0.4 ± 0.2 nM) and high selectivity. Coupling of 5 with thalidomide derivatives of varying chain lengths afforded conjugates 6A-Dvia click reaction. In vitro cell-based assay indicated that 6C was more effective in eliminating drug resistance of CYP1B1-overexpressed DU145 cells compared with other analogues. Western blotting analysis showed CYP1B1 degradation was one main reason for the reversal of drug resistance to docetaxel and the effect was obtained in a concentration-dependent manner. This work is the first attempt to overcome CYP1B1-mediated drug resistance via CYP1B1 degradation instead of CYP1B1 inhibition, which could provide a new direction toward eliminating drug resistance.
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ITO T, HANDA H. Molecular mechanisms of thalidomide and its derivatives. PROCEEDINGS OF THE JAPAN ACADEMY. SERIES B, PHYSICAL AND BIOLOGICAL SCIENCES 2020; 96:189-203. [PMID: 32522938 PMCID: PMC7298168 DOI: 10.2183/pjab.96.016] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Thalidomide, originally developed as a sedative drug, causes multiple defects due to severe teratogenicity, but it has been re-purposed for treating multiple myeloma, and derivatives such as lenalidomide and pomalidomide have been developed for treating blood cancers. Although the molecular mechanisms of thalidomide and its derivatives remained poorly understood until recently, we identified cereblon (CRBN), a primary direct target of thalidomide, using ferrite glycidyl methacrylate (FG) beads. CRBN is a ligand-dependent substrate receptor of the E3 ubiquitin ligase complex cullin-RING ligase 4 (CRL4CRBN). When a ligand such as thalidomide binds to CRBN, it recognizes various 'neosubstrates' depending on the shape of the ligand. CRL4CRBN binds many neosubstrates in the presence of various ligands. CRBN has been utilized in a novel protein knockdown technology named proteolysis targeting chimeras (PROTACs). Heterobifunctional molecules such as dBET1 are being developed to specifically degrade proteins of interest. Herein, we review recent advances in CRBN research.
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Affiliation(s)
- Takumi ITO
- Department of Chemical Biology, Tokyo Medical University, Tokyo, Japan
| | - Hiroshi HANDA
- Department of Chemical Biology, Tokyo Medical University, Tokyo, Japan
- Correspondence should be addressed: H. Handa, Department of Chemical Biology, Tokyo Medical University, 6-1-1 Shinjuku, Shinjuku-ku, Tokyo 160-8402, Japan (e-mail: )
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Konstantinidou M, Li J, Zhang B, Wang Z, Shaabani S, Ter Brake F, Essa K, Dömling A. PROTACs- a game-changing technology. Expert Opin Drug Discov 2019; 14:1255-1268. [PMID: 31538491 PMCID: PMC7008130 DOI: 10.1080/17460441.2019.1659242] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Introduction: Proteolysis – targeting chimeras (PROTACs) have emerged as a new modality with the potential to revolutionize drug discovery. PROTACs are heterobifunctional molecules comprising of a ligand targeting a protein of interest, a ligand targeting an E3 ligase and a connecting linker. The aim is instead of inhibiting the target to induce its proteasomal degradation. Areas covered: PROTACs, due to their bifunctional design, possess properties that differentiate them from classical inhibitors. A structural analysis, based on published crystal aspects, kinetic features and aspects of selectivity are discussed. Specific types such as homoPROTACs, PROTACs targeting Tau protein and the first PROTACs recently entering clinical trials are examined. Expert opinion: PROTACs have shown remarkable biological responses in challenging targets, including an unprecedented selectivity over protein family members and even efficacy starting from weak or unspecific binders. Moreover, PROTACs are standing out from classical pharmacology by inducing the degradation of the target protein and not merely its inhibition. However, there are also challenges in the field, such as the rational structure optimization, the evolution of computational tools, limited structural data and the greatly anticipated clinical data. Despite the remaining hurdles, PROTACs are expected to soon become a new therapeutic category of drugs.
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Affiliation(s)
| | - Jingyao Li
- Drug Design, University of Groningen , Groningen , The Netherlands
| | - Bidong Zhang
- Drug Design, University of Groningen , Groningen , The Netherlands
| | - Zefeng Wang
- Drug Design, University of Groningen , Groningen , The Netherlands
| | - Shabnam Shaabani
- Drug Design, University of Groningen , Groningen , The Netherlands
| | - Frans Ter Brake
- Drug Design, University of Groningen , Groningen , The Netherlands
| | - Khaled Essa
- Drug Design, University of Groningen , Groningen , The Netherlands
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39
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Heim C, Pliatsika D, Mousavizadeh F, Bär K, Hernandez Alvarez B, Giannis A, Hartmann MD. De-Novo Design of Cereblon (CRBN) Effectors Guided by Natural Hydrolysis Products of Thalidomide Derivatives. J Med Chem 2019; 62:6615-6629. [PMID: 31251063 PMCID: PMC6750895 DOI: 10.1021/acs.jmedchem.9b00454] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Indexed: 12/16/2022]
Abstract
Targeted protein degradation via cereblon (CRBN), a substrate receptor of an E3 ubiquitin ligase complex, is an increasingly important strategy in various clinical settings, in which the substrate specificity of CRBN is altered via the binding of small-molecule effectors. To date, such effectors are derived from thalidomide and confer a broad substrate spectrum that is far from being fully characterized. Here, we employed a rational and modular approach to design novel and minimalistic CRBN effectors. In this approach, we took advantage of the binding modes of hydrolyzed metabolites of several thalidomide-derived effectors, which we elucidated via crystallography. These yielded key insights for the optimization of the minimal core binding moiety and its linkage to a chemical moiety that imparts substrate specificity. Based on this scaffold, we present a first active de-novo CRBN effector that is able to degrade the neo-substrate IKZF3 in the cell culture.
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Affiliation(s)
- Christopher Heim
- Department
of Protein Evolution, Max Planck Institute
for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Dimanthi Pliatsika
- Faculty
for Chemistry und Mineralogy, Institute of Organic Chemistry, University of Leipzig, Johannisallee 29, 04103 Leipzig, Germany
| | - Farnoush Mousavizadeh
- Faculty
for Chemistry und Mineralogy, Institute of Organic Chemistry, University of Leipzig, Johannisallee 29, 04103 Leipzig, Germany
| | - Kerstin Bär
- Department
of Protein Evolution, Max Planck Institute
for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Birte Hernandez Alvarez
- Department
of Protein Evolution, Max Planck Institute
for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
| | - Athanassios Giannis
- Faculty
for Chemistry und Mineralogy, Institute of Organic Chemistry, University of Leipzig, Johannisallee 29, 04103 Leipzig, Germany
| | - Marcus D. Hartmann
- Department
of Protein Evolution, Max Planck Institute
for Developmental Biology, Max-Planck-Ring 5, 72076 Tübingen, Germany
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Steinebach C, Sosič I, Lindner S, Bricelj A, Kohl F, Ng YLD, Monschke M, Wagner KG, Krönke J, Gütschow M. A MedChem toolbox for cereblon-directed PROTACs. MEDCHEMCOMM 2019; 10:1037-1041. [PMID: 31304001 PMCID: PMC6596386 DOI: 10.1039/c9md00185a] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 05/27/2019] [Indexed: 12/12/2022]
Abstract
A modular chemistry toolbox was developed for cereblon-directed PROTACs. A variety of linkers was attached to a CRBN ligand via the 4-amino position of pomalidomide. We used linkers of different constitution to modulate physicochemical properties. We equipped one terminus of the linker with a set of functional groups, e.g. protected amines, protected carboxylic acids, alkynes, chloroalkanes, and protected alcohols, all of which are considered to be attractive for PROTAC design. We also highlight different opportunities for the expansion of the medicinal chemists' PROTAC toolbox towards heterobifunctional molecules, e.g. with biotin, fluorescent, hydrophobic and peptide tags.
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Affiliation(s)
- Christian Steinebach
- Pharmaceutical Institute , Pharmaceutical Chemistry I , University of Bonn , An der Immenburg 4 , 53121 Bonn , Germany .
| | - Izidor Sosič
- Faculty of Pharmacy , University of Ljubljana , 1000 Ljubljana , Slovenia
| | - Stefanie Lindner
- Department of Internal Medicine III , University Hospital Ulm , Albert-Einstein-Allee 23 , 89081 Ulm , Germany
| | - Aleša Bricelj
- Faculty of Pharmacy , University of Ljubljana , 1000 Ljubljana , Slovenia
| | - Franziska Kohl
- Pharmaceutical Institute , Pharmaceutical Chemistry I , University of Bonn , An der Immenburg 4 , 53121 Bonn , Germany .
| | - Yuen Lam Dora Ng
- Department of Internal Medicine III , University Hospital Ulm , Albert-Einstein-Allee 23 , 89081 Ulm , Germany
| | - Marius Monschke
- Pharmaceutical Institute , Pharmaceutical Technology , University of Bonn , Gerhard-Domagk-Straße 3 , 53121 Bonn , Germany
| | - Karl G Wagner
- Pharmaceutical Institute , Pharmaceutical Technology , University of Bonn , Gerhard-Domagk-Straße 3 , 53121 Bonn , Germany
| | - Jan Krönke
- Department of Internal Medicine III , University Hospital Ulm , Albert-Einstein-Allee 23 , 89081 Ulm , Germany
| | - Michael Gütschow
- Pharmaceutical Institute , Pharmaceutical Chemistry I , University of Bonn , An der Immenburg 4 , 53121 Bonn , Germany .
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41
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Steinebach C, Kehm H, Lindner S, Vu LP, Köpff S, López Mármol Á, Weiler C, Wagner KG, Reichenzeller M, Krönke J, Gütschow M. PROTAC-mediated crosstalk between E3 ligases. Chem Commun (Camb) 2019; 55:1821-1824. [DOI: 10.1039/c8cc09541h] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Small-molecule heterobifunctional degraders can effectively control protein levels and are useful research tools.
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