1
|
Di Girolamo D, Di Iorio E, Missero C. Molecular and Cellular Function of p63 in Skin Development and Genetic Diseases. J Invest Dermatol 2024:S0022-202X(24)02076-1. [PMID: 39340489 DOI: 10.1016/j.jid.2024.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Revised: 08/02/2024] [Accepted: 08/16/2024] [Indexed: 09/30/2024]
Abstract
The transcription factor p63 is a master regulator of multiple ectodermal derivatives. During epidermal commitment, p63 interacts with several chromatin remodeling complexes to transactivate epidermal-specific genes and repress transcription of simple epithelial and nonepithelial genes. In the postnatal epidermis, p63 is required to control the proliferative potential of progenitor cells, maintain epidermal integrity, and contribute to epidermal differentiation. Autosomal dominant sequence variant in p63 cause a spectrum of syndromic disorders that affect several tissues, including or derived from stratified epithelia. In this review, we describe the recent studies that have provided novel insights into disease pathogenesis and potential therapeutic targets.
Collapse
Affiliation(s)
- Daniela Di Girolamo
- CEINGE Biotecnologie Avanzate Franco Salvatore, Naples, Italy; Biology Department, University of Naples Federico II, Naples, Italy
| | - Enzo Di Iorio
- Clinical Genetics Unit, University Hospital of Padua, Padua, Italy; Department of Molecular Medicine, University of Padua, Padua, Italy
| | - Caterina Missero
- CEINGE Biotecnologie Avanzate Franco Salvatore, Naples, Italy; Biology Department, University of Naples Federico II, Naples, Italy.
| |
Collapse
|
2
|
Monteonofrio L, Virdia I, Pozzi S, Quadri R, Amendolare A, Marzano F, Braile M, Sulfaro V, Paroni M, Tullo A, Soddu S, Guerrini L. Molecular mechanisms of thalidomide effectiveness on COVID-19 patients explained: ACE2 is a new ΔNp63α target gene. J Mol Med (Berl) 2024:10.1007/s00109-024-02485-x. [PMID: 39294414 DOI: 10.1007/s00109-024-02485-x] [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: 03/26/2024] [Revised: 08/31/2024] [Accepted: 09/04/2024] [Indexed: 09/20/2024]
Abstract
COVID-19 pandemic is caused by the SARS-CoV-2 virus, whose internalization and infection are mediated by the angiotensin-converting enzyme 2 (ACE2). The identification of novel approaches to tackle this step is instrumental for the development of therapies for the management of COVID-19 and other diseases with a similar mechanism of infection. Thalidomide, a drug sadly known for its teratogenic effects, has potent immunomodulatory and anti-inflammatory properties. Treatment with this drug has been shown to improve the immune functions of COVID-19 patients and proposed for the management of COVID-19 in clinical practice through drug repositioning. Here, we investigated the molecular details linking thalidomide to ACE2 and COVID-19, showing that in conditions mimicking SARS-CoV-2-associated cytokine storm, the transcription factor ΔNp63α and ACE2 are stabilized, and IL-8 production is increased. In such conditions, we found p63 to bind to and regulate the expression of the ACE2 gene. We previously showed that ΔNp63α is degraded upon thalidomide treatment and now found that treatment with this drug-or with its analogue lenalidomide-downregulates ACE2 in a p63-dependent manner. Finally, we found that thalidomide treatment reduces in vitro infection by pseudo-SARS-CoV-2, a baculovirus pseudotyped with the SARS-CoV-2 spike protein. Overall, we propose the dual effect of thalidomide in reducing SARS-CoV-2 viral re-entry and inflammation through p63 degradation to weaken SARS-CoV-2 entry into host cells and mitigate lung inflammation, making it a valuable option in clinical management of COVID-19. KEY MESSAGES: Thalidomide treatment results in p63-dependent ACE2 downregulation. ACE2 is a p63 transcriptional target. Thalidomide reduces the "cytokine storm" associated to COVID-19. Thalidomide prevents viral re-entry of SARS-CoV-2 by p63-dependent ACE2 downregulation. Thalidomide is a modulator of SARS-CoV-2 or other ACE2-dependent infections. ACE2 is modulated by a pharmacological substance.
Collapse
Affiliation(s)
- Laura Monteonofrio
- Dipartimento Di Ricerca E Tecnologie Avanzate, Istituto Nazionale Tumori Regina Elena IRCCS, 00144, Rome, Italy
| | - Ilaria Virdia
- Dipartimento Di Ricerca E Tecnologie Avanzate, Istituto Nazionale Tumori Regina Elena IRCCS, 00144, Rome, Italy
| | - Sara Pozzi
- Dipartimento Di Bioscienze, Università Degli Studi Di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Roberto Quadri
- Dipartimento Di Bioscienze, Università Degli Studi Di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Alessandra Amendolare
- Istituto Di Biomembrane, Bioenergetica E Biotecnologie Molecolari (IBIOM), Consiglio Nazionale Delle Ricerche, 70025, Bari, Italy
| | - Flaviana Marzano
- Istituto Di Biomembrane, Bioenergetica E Biotecnologie Molecolari (IBIOM), Consiglio Nazionale Delle Ricerche, 70025, Bari, Italy
| | - Micaela Braile
- Dipartimento Di Bioscienze, Università Degli Studi Di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Virginia Sulfaro
- Dipartimento Di Bioscienze, Università Degli Studi Di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Moira Paroni
- Dipartimento Di Bioscienze, Università Degli Studi Di Milano, Via Celoria 26, 20133, Milan, Italy
| | - Apollonia Tullo
- Istituto Di Biomembrane, Bioenergetica E Biotecnologie Molecolari (IBIOM), Consiglio Nazionale Delle Ricerche, 70025, Bari, Italy
| | - Silvia Soddu
- Dipartimento Di Ricerca E Tecnologie Avanzate, Istituto Nazionale Tumori Regina Elena IRCCS, 00144, Rome, Italy
| | - Luisa Guerrini
- Dipartimento Di Bioscienze, Università Degli Studi Di Milano, Via Celoria 26, 20133, Milan, Italy.
| |
Collapse
|
3
|
Pliatsika D, Blatter C, Riedl R. Targeted protein degradation: current molecular targets, localization, and strategies. Drug Discov Today 2024; 29:104178. [PMID: 39276920 DOI: 10.1016/j.drudis.2024.104178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 08/23/2024] [Accepted: 09/10/2024] [Indexed: 09/17/2024]
Abstract
Targeted protein degradation (TPD) has revolutionized drug discovery by selectively eliminating specific proteins within and outside the cellular context. Over the past two decades, TPD has expanded its focus beyond well-established targets, exploring diverse proteins beyond cancer-related ones. This evolution extends the potential of TPD to various diseases. Notably, TPD can target proteins at demanding locations, such as the extracellular matrix (ECM) and cellular membranes, presenting both opportunities and challenges for future research. In this review, we comprehensively examine the exciting opportunities in the burgeoning field of TPD, highlighting different targets, their cellular environment, and innovative strategies for modern drug discovery.
Collapse
Affiliation(s)
- Dimanthi Pliatsika
- Institute of Chemistry and Biotechnology, Competence Center for Drug Discovery, Zurich University of Applied Sciences, CH-8820 Wädenswil, Switzerland
| | - Cindy Blatter
- Institute of Chemistry and Biotechnology, Competence Center for Drug Discovery, Zurich University of Applied Sciences, CH-8820 Wädenswil, Switzerland
| | - Rainer Riedl
- Institute of Chemistry and Biotechnology, Competence Center for Drug Discovery, Zurich University of Applied Sciences, CH-8820 Wädenswil, Switzerland.
| |
Collapse
|
4
|
Li P, Hu X, Fan Z, Sun S, Ran Q, Wei T, Wei P, Jiang Q, Yan J, Yang N, Jia C, Yang T, Mao Y, Cai X, Xu T, Zhao Z, Qian X, Qin W, Zhuang X, Fan F, Xiao J, Zheng Z, Li S. Novel potent molecular glue degraders against broad range of hematological cancer cell lines via multiple neosubstrates degradation. J Hematol Oncol 2024; 17:77. [PMID: 39218923 PMCID: PMC11367868 DOI: 10.1186/s13045-024-01592-z] [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: 06/22/2024] [Accepted: 08/05/2024] [Indexed: 09/04/2024] Open
Abstract
BACKGROUND Targeted protein degradation of neosubstrates plays a crucial role in hematological cancer treatment involving immunomodulatory imide drugs (IMiDs) therapy. Nevertheless, the persistence of inevitable drug resistance and hematological toxicities represents a significant obstacle to their clinical effectiveness. METHODS Phenotypic profiling of a small molecule compounds library in multiple hematological cancer cell lines was conducted to screen for hit degraders. Molecular dynamic-based rational design and cell-based functional assays were conducted to develop more potent degraders. Multiple myeloma (MM) tumor xenograft models were employed to investigate the antitumor efficacy of the degraders as single or combined agents with standard of care agents. Unbiased proteomics was employed to identify multiple therapeutically relevant neosubstrates targeted by the degraders. MM patient-derived cell lines (PDCs) and a panel of solid cancer cell lines were utilized to investigate the effects of candidate degrader on different stage of MM cells and solid malignancies. Unbiased proteomics of IMiDs-resistant MM cells, cell-based functional assays and RT-PCR analysis of clinical MM specimens were utilized to explore the role of BRD9 associated with IMiDs resistance and MM progression. RESULTS We identified a novel cereblon (CRBN)-dependent lead degrader with phthalazinone scaffold, MGD-4, which induced the degradation of Ikaros proteins. We further developed a novel potent candidate, MGD-28, significantly inhibited the growth of hematological cancer cells and induced the degradation of IKZF1/2/3 and CK1α with nanomolar potency via a Cullin-CRBN dependent pathway. Oral administration of MGD-4 and MGD-28 effectively inhibited MM tumor growth and exhibited significant synergistic effects with standard of care agents. MGD-28 exhibited preferentially profound cytotoxicity towards MM PDCs at different disease stages and broad antiproliferative activity in multiple solid malignancies. BRD9 modulated IMiDs resistance, and the expression of BRD9 was significant positively correlated with IKZF1/2/3 and CK1α in MM specimens at different stages. We also observed pronounced synergetic efficacy between the BRD9 inhibitor and MGD-28 for MM treatment. CONCLUSIONS Our findings present a strategy for the multi-targeted degradation of Ikaros proteins and CK1α against hematological cancers, which may be expanded to additional targets and indications. This strategy may enhance efficacy treatment against multiple hematological cancers and solid tumors.
Collapse
Affiliation(s)
- Pengyun Li
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
- State Key Laboratory of National Security Specially Needed Medicines, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Xiaotong Hu
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
- State Key Laboratory of National Security Specially Needed Medicines, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Zhiya Fan
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Shiyang Sun
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
- State Key Laboratory of National Security Specially Needed Medicines, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Qijie Ran
- Department of Clinical Laboratory, Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100039, China
- Department of Hematology, General Hospital of Central Theater Command, Wuhan, 430012, China
| | - Ting Wei
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
- State Key Laboratory of National Security Specially Needed Medicines, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Pengli Wei
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
- State Key Laboratory of National Security Specially Needed Medicines, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Qiyu Jiang
- Department of Clinical Laboratory, Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100039, China
| | - Jian Yan
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
- State Key Laboratory of National Security Specially Needed Medicines, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Ning Yang
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
- State Key Laboratory of National Security Specially Needed Medicines, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Changkai Jia
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
- State Key Laboratory of National Security Specially Needed Medicines, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Tingting Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing, 100191, China
| | - Yaqiu Mao
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
- State Key Laboratory of National Security Specially Needed Medicines, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Xu Cai
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
- State Key Laboratory of National Security Specially Needed Medicines, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Tingting Xu
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
- State Key Laboratory of National Security Specially Needed Medicines, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Zhiyuan Zhao
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
- State Key Laboratory of National Security Specially Needed Medicines, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| | - Xiaohong Qian
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Weijie Qin
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Xiaomei Zhuang
- State Key Laboratory of National Security Specially Needed Medicines, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China.
| | - Feng Fan
- Department of Clinical Laboratory, Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100039, China.
| | - Junhai Xiao
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China.
- State Key Laboratory of National Security Specially Needed Medicines, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China.
| | - Zhibing Zheng
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China.
- State Key Laboratory of National Security Specially Needed Medicines, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China.
| | - Song Li
- National Engineering Research Center for Strategic Drugs, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
- State Key Laboratory of National Security Specially Needed Medicines, Beijing Institute of Pharmacology and Toxicology, Beijing, 100850, China
| |
Collapse
|
5
|
Shiraki K, Mishima M, Sato N, Imoto Y, Nishiwaki K. Convenient screening of the reproductive toxicity of favipiravir and antiviral drugs in Caenorhabditis elegans. Heliyon 2024; 10:e35331. [PMID: 39165990 PMCID: PMC11334893 DOI: 10.1016/j.heliyon.2024.e35331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 07/23/2024] [Accepted: 07/26/2024] [Indexed: 08/22/2024] Open
Abstract
Reproductive toxicity is one of the major concerns in drug development. Thus, we have developed its screening system using Caenorhabditis elegans, which has a life cycle of three days and similar coding genes as humans. Antiviral nucleoside analogs used for acute infections are known to cause reproductive toxicity, contraindicated for pregnant women, and are used for comparing their reproductive toxicity in C. elegans and experimental animals. None of the drug treatments affected the number of offspring and the concentrations without toxicity to nematodes were consistent with no cytotoxicity or toxicity in experimental animals or humans. Favipiravir, ribavirin, molnupiravir (NHC), acyclovir, ganciclovir, zidovudine, and thalidomide significantly increased the incidence of arrested embryos but amenamevir, letermovir, and guanosine did not. RNA-dependent RNA polymerase (RdRp) inhibitors, in the order of favipiravir, ribavirin, and NHC increased the incidence of arrested embryos, possibly due to the specificity of favipiravir for RdRp and less cytotoxicity. RdRp inhibitors would impair RNA interference through RdRp expressed by telomerase reverse transcriptase during embryogenesis and cause embryo-fetal toxicity. The incidence of arrested embryos may be affected by differences in the substrate specificity of DNA polymerases and metabolism between C. elegans, animals, and humans. The concordance between the results of the screening system for reproductive toxicity of antivirals in C. elegans and those in experimental animals based on the International Council for Harmonisation of Technical Requirements for Pharmaceuticals for Human Use, reproductive toxicology confirms its appropriateness as a screening system for reproductive toxicity. Favipiravir and zidovudine were the least toxic to C. e legans among the antiviral drugs examined.
Collapse
Affiliation(s)
| | - Mizuki Mishima
- Department of Bioscience, School of Science and Technology, Kwansei Gakuin University, 2-1 Gakuen, Sanda, 669-1339, Japan
| | - Noriaki Sato
- Division of Health Medical Intelligence, Human Genome Center, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan
| | - Yasuo Imoto
- Japan Textile Products Quality and Technology Center, 5-7-3 Shimoyamatedori, Chuo-ku, Kobe, 650-0011, Japan
| | - Kiyoji Nishiwaki
- Department of Bioscience, School of Science and Technology, Kwansei Gakuin University, 2-1 Gakuen, Sanda, 669-1339, Japan
| |
Collapse
|
6
|
Brodermann MH, Henderson EK, Sellar RS. The emerging role of targeted protein degradation to treat and study cancer. J Pathol 2024; 263:403-417. [PMID: 38886898 DOI: 10.1002/path.6301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 04/18/2024] [Accepted: 04/30/2024] [Indexed: 06/20/2024]
Abstract
The evolution of cancer treatment has provided increasingly targeted strategies both in the upfront and relapsed disease settings. Small-molecule inhibitors and immunotherapy have risen to prominence with chimeric antigen receptor T-cells, checkpoint inhibitors, kinase inhibitors, and monoclonal antibody therapies being deployed across a range of solid organ and haematological malignancies. However, novel approaches are required to target transcription factors and oncogenic fusion proteins that are central to cancer biology and have generally eluded successful drug development. Thalidomide analogues causing protein degradation have been a cornerstone of treatment in multiple myeloma, but a lack of in-depth mechanistic understanding initially limited progress in the field. When the protein cereblon (CRBN) was found to mediate thalidomide analogues' action and CRBN's neo-targets were identified, existing and novel drug development accelerated, with applications outside multiple myeloma, including non-Hodgkin's lymphoma, myelodysplastic syndrome, and acute leukaemias. Critically, transcription factors were the first canonical targets described. In addition to broadening the application of protein-degrading drugs, resistance mechanisms are being overcome and targeted protein degradation is widening the scope of druggable proteins against which existing approaches have been ineffective. Examples of targeted protein degraders include molecular glues and proteolysis targeting chimeras (PROTACs): heterobifunctional molecules that bind to proteins of interest and cause proximity-induced ubiquitination and proteasomal degradation via a linked E3 ligase. Twenty years since their inception, PROTACs have begun progressing through clinical trials, with early success in targeting the oestrogen receptor and androgen receptor in breast and prostate cancer respectively. This review explores important developments in targeted protein degradation to both treat and study cancer. It also considers the potential advantages and challenges in the translational aspects of developing new treatments. © 2024 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
Collapse
Affiliation(s)
| | - Elizabeth K Henderson
- Department of Haematology, UCL Cancer Institute, University College London, London, UK
| | - Rob S Sellar
- Department of Haematology, UCL Cancer Institute, University College London, London, UK
| |
Collapse
|
7
|
Federspiel JD, Catlin NR, Nowland WS, Stethem CM, Mathialagan N, Fernandez Ocaña M, Bowman CJ. Differential Analysis of Cereblon Neosubstrates in Rabbit Embryos Using Targeted Proteomics. Mol Cell Proteomics 2024; 23:100797. [PMID: 38866076 PMCID: PMC11263748 DOI: 10.1016/j.mcpro.2024.100797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2024] [Revised: 05/31/2024] [Accepted: 06/06/2024] [Indexed: 06/14/2024] Open
Abstract
Targeted protein degradation is the selective removal of a protein of interest through hijacking intracellular protein cleanup machinery. This rapidly growing field currently relies heavily on the use of the E3 ligase cereblon (CRBN) to target proteins for degradation, including the immunomodulatory drugs (IMiDs) thalidomide, lenalidomide, and pomalidomide which work through a molecular glue mechanism of action with CRBN. While CRBN recruitment can result in degradation of a specific protein of interest (e.g., efficacy), degradation of other proteins (called CRBN neosubstrates) also occurs. Degradation of one or more of these CRBN neosubstrates is believed to play an important role in thalidomide-related developmental toxicity observed in rabbits and primates. We identified a set of 25 proteins of interest associated with CRBN-related protein homeostasis and/or embryo/fetal development. We developed a targeted assay for these proteins combining peptide immunoaffinity enrichment and high-resolution mass spectrometry and successfully applied this assay to rabbit embryo samples from pregnant rabbits dosed with three IMiDs. We confirmed previously reported in vivo decreases in neosubstrates like SALL4, as well as provided evidence of neosubstrate changes for proteins only examined in vitro previously. While there were many proteins that were similarly decreased by all three IMiDs, no compound had the exact same neosubstrate degradation profile as another. We compared our data to previous literature reports of IMiD-induced degradation and known developmental biology associations. Based on our observations, we recommend monitoring at least a major subset of these neosubstrates in a developmental test system to improve CRBN-binding compound-specific risk assessment. A strength of our assay is that it is configurable, and the target list can be readily adapted to focus on only a subset of proteins of interest or expanded to incorporate new findings as additional information about CRBN biology is discovered.
Collapse
Affiliation(s)
- Joel D Federspiel
- Drug Safety Research & Development, Pfizer, Inc, Andover, Massachusetts, USA
| | - Natasha R Catlin
- Drug Safety Research & Development, Pfizer, Inc, Groton, Connecticut, USA
| | - William S Nowland
- Drug Safety Research & Development, Pfizer, Inc, Groton, Connecticut, USA
| | | | | | | | | |
Collapse
|
8
|
Zhang C, Liu Y, Li G, Yang Z, Han C, Sun X, Sheng C, Ding K, Rao Y. Targeting the undruggables-the power of protein degraders. Sci Bull (Beijing) 2024; 69:1776-1797. [PMID: 38614856 DOI: 10.1016/j.scib.2024.03.056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 03/06/2024] [Accepted: 03/25/2024] [Indexed: 04/15/2024]
Abstract
Undruggable targets typically refer to a class of therapeutic targets that are difficult to target through conventional methods or have not yet been targeted, but are of great clinical significance. According to statistics, over 80% of disease-related pathogenic proteins cannot be targeted by current conventional treatment methods. In recent years, with the advancement of basic research and new technologies, the development of various new technologies and mechanisms has brought new perspectives to overcome challenging drug targets. Among them, targeted protein degradation technology is a breakthrough drug development strategy for challenging drug targets. This technology can specifically identify target proteins and directly degrade pathogenic target proteins by utilizing the inherent protein degradation pathways within cells. This new form of drug development includes various types such as proteolysis targeting chimera (PROTAC), molecular glue, lysosome-targeting Chimaera (LYTAC), autophagosome-tethering compound (ATTEC), autophagy-targeting chimera (AUTAC), autophagy-targeting chimera (AUTOTAC), degrader-antibody conjugate (DAC). This article systematically summarizes the application of targeted protein degradation technology in the development of degraders for challenging drug targets. Finally, the article looks forward to the future development direction and application prospects of targeted protein degradation technology.
Collapse
Affiliation(s)
- Chao Zhang
- Changping Laboratory, Beijing 102206, China
| | - Yongbo Liu
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Guangchen Li
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Zhouli Yang
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Chi Han
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Xiuyun Sun
- Changping Laboratory, Beijing 102206, China
| | - Chunquan Sheng
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China.
| | - Ke Ding
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 200032, China.
| | - Yu Rao
- State Key Laboratory of Molecular Oncology, MOE Key Laboratory of Protein Sciences, MOE Key Laboratory of Bioorganic Phosphorus Chemistry & Chemical Biology, School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China; Changping Laboratory, Beijing 102206, China.
| |
Collapse
|
9
|
Ito T. Protein degraders - from thalidomide to new PROTACs. J Biochem 2024; 175:507-519. [PMID: 38140952 DOI: 10.1093/jb/mvad113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/07/2023] [Accepted: 12/12/2023] [Indexed: 12/24/2023] Open
Abstract
Recently, the development of protein degraders (protein-degrading compounds) has prominently progressed. There are two remarkable classes of protein degraders: proteolysis-targeting chimeras (PROTACs) and molecular glue degraders (MGDs). Almost 70 years have passed since thalidomide was initially developed as a sedative-hypnotic drug, which is currently recognized as one of the most well-known MGDs. During the last two decades, a myriad of PROTACs and MGDs have been developed, and the molecular mechanism of action (MOA) of thalidomide was basically elucidated, including identifying its molecular target cereblon (CRBN). CRBN forms a Cullin Ring Ligase 4 with Cul4 and DDB1, whose substrate specificity is controlled by its binding ligands. Thalidomide, lenalidomide and pomalidomide, three CRBN-binding MGDs, were clinically approved to treat several intractable diseases (including multiple myeloma). Several other MGDs and CRBN-based PROTACs (ARV-110 and AVR-471) are undergoing clinical trials. In addition, several new related technologies regarding PROTACs and MGDs have also been developed, and achievements of protein degraders impact not only therapeutic fields but also basic biological science. In this article, I introduce the history of protein degraders, from the development of thalidomide to the latest PROTACs and related technologies.
Collapse
Affiliation(s)
- Takumi Ito
- Institute of Medical Science, Tokyo Medical University, 6-1-1, Shinjuku, Shinjuku-ku, Tokyo 160-8402, Japan
| |
Collapse
|
10
|
Costas-Insua C, Hermoso-López A, Moreno E, Montero-Fernández C, Álvaro-Blázquez A, Maroto IB, Sánchez-Ruiz A, Diez-Alarcia R, Blázquez C, Morales P, Canela EI, Casadó V, Urigüen L, Perea G, Bellocchio L, Rodríguez-Crespo I, Guzmán M. The CB 1 receptor interacts with cereblon and drives cereblon deficiency-associated memory shortfalls. EMBO Mol Med 2024; 16:755-783. [PMID: 38514794 PMCID: PMC11018632 DOI: 10.1038/s44321-024-00054-w] [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: 07/24/2023] [Revised: 02/26/2024] [Accepted: 03/05/2024] [Indexed: 03/23/2024] Open
Abstract
Cereblon/CRBN is a substrate-recognition component of the Cullin4A-DDB1-Roc1 E3 ubiquitin ligase complex. Destabilizing mutations in the human CRBN gene cause a form of autosomal recessive non-syndromic intellectual disability (ARNSID) that is modelled by knocking-out the mouse Crbn gene. A reduction in excitatory neurotransmission has been proposed as an underlying mechanism of the disease. However, the precise factors eliciting this impairment remain mostly unknown. Here we report that CRBN molecules selectively located on glutamatergic neurons are necessary for proper memory function. Combining various in vivo approaches, we show that the cannabinoid CB1 receptor (CB1R), a key suppressor of synaptic transmission, is overactivated in CRBN deficiency-linked ARNSID mouse models, and that the memory deficits observed in these animals can be rescued by acute CB1R-selective pharmacological antagonism. Molecular studies demonstrated that CRBN interacts physically with CB1R and impairs the CB1R-Gi/o-cAMP-PKA pathway in a ubiquitin ligase-independent manner. Taken together, these findings unveil that CB1R overactivation is a driving mechanism of CRBN deficiency-linked ARNSID and anticipate that the antagonism of CB1R could constitute a new therapy for this orphan disease.
Collapse
Affiliation(s)
- Carlos Costas-Insua
- Department of Biochemistry and Molecular Biology, Instituto Universitario de Investigación Neuroquímica (IUIN), Complutense University, 28040, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, 28029, Madrid, Spain
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034, Madrid, Spain
| | - Alba Hermoso-López
- Department of Biochemistry and Molecular Biology, Instituto Universitario de Investigación Neuroquímica (IUIN), Complutense University, 28040, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, 28029, Madrid, Spain
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034, Madrid, Spain
| | - Estefanía Moreno
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology and Institute of Biomedicine of the University of Barcelona, University of Barcelona, 08028, Barcelona, Spain
| | - Carlos Montero-Fernández
- Department of Biochemistry and Molecular Biology, Instituto Universitario de Investigación Neuroquímica (IUIN), Complutense University, 28040, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, 28029, Madrid, Spain
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034, Madrid, Spain
| | - Alicia Álvaro-Blázquez
- Department of Biochemistry and Molecular Biology, Instituto Universitario de Investigación Neuroquímica (IUIN), Complutense University, 28040, Madrid, Spain
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034, Madrid, Spain
| | - Irene B Maroto
- Department of Biochemistry and Molecular Biology, Instituto Universitario de Investigación Neuroquímica (IUIN), Complutense University, 28040, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, 28029, Madrid, Spain
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034, Madrid, Spain
| | | | - Rebeca Diez-Alarcia
- Department of Pharmacology, University of the Basque Country/Euskal Herriko Unibertsitatea, 48940, Leioa, Spain
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), 28029, Madrid, Spain
- BioBizkaia Health Research Institute, 48903, Barakaldo, Bizkaia, Spain
| | - Cristina Blázquez
- Department of Biochemistry and Molecular Biology, Instituto Universitario de Investigación Neuroquímica (IUIN), Complutense University, 28040, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, 28029, Madrid, Spain
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034, Madrid, Spain
| | - Paula Morales
- Instituto de Química Médica, CSIC, 28006, Madrid, Spain
| | - Enric I Canela
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology and Institute of Biomedicine of the University of Barcelona, University of Barcelona, 08028, Barcelona, Spain
| | - Vicent Casadó
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology and Institute of Biomedicine of the University of Barcelona, University of Barcelona, 08028, Barcelona, Spain
| | - Leyre Urigüen
- Department of Pharmacology, University of the Basque Country/Euskal Herriko Unibertsitatea, 48940, Leioa, Spain
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), 28029, Madrid, Spain
- BioBizkaia Health Research Institute, 48903, Barakaldo, Bizkaia, Spain
| | | | - Luigi Bellocchio
- Institut National de la Santé et de la Recherche Médicale (INSERM) and University of Bordeaux, NeuroCentre Magendie, Physiopathologie de la Plasticité Neuronale, U1215, 33077, Bordeaux, France
| | - Ignacio Rodríguez-Crespo
- Department of Biochemistry and Molecular Biology, Instituto Universitario de Investigación Neuroquímica (IUIN), Complutense University, 28040, Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, 28029, Madrid, Spain
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034, Madrid, Spain
| | - Manuel Guzmán
- Department of Biochemistry and Molecular Biology, Instituto Universitario de Investigación Neuroquímica (IUIN), Complutense University, 28040, Madrid, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, 28029, Madrid, Spain.
- Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034, Madrid, Spain.
| |
Collapse
|
11
|
Setia N, Almuqdadi HTA, Abid M. Journey of Von Hippel-Lindau (VHL) E3 ligase in PROTACs design: From VHL ligands to VHL-based degraders. Eur J Med Chem 2024; 265:116041. [PMID: 38199162 DOI: 10.1016/j.ejmech.2023.116041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 12/08/2023] [Accepted: 12/08/2023] [Indexed: 01/12/2024]
Abstract
The scientific community has shown considerable interest in proteolysis-targeting chimeras (PROTACs) in the last decade, indicating their remarkable potential as a means of achieving targeted protein degradation (TPD). Not only are PROTACs seen as valuable tools in molecular biology but their emergence as a modality for drug discovery has also garnered significant attention. PROTACs bind to E3 ligases and target proteins through respective ligands connected via a linker to induce proteasome-mediated protein degradation. The discovery of small molecule ligands for E3 ligases has led to the prevalent use of various E3 ligases in PROTAC design. Furthermore, the incorporation of different types of linkers has proven beneficial in enhancing the efficacy of PROTACs. By far more than 3300 PROTACs have been reported in the literature. Notably, Von Hippel-Lindau (VHL)-based PROTACs have surfaced as a propitious strategy for targeting proteins, even encompassing those that were previously considered non-druggable. VHL is extensively utilized as an E3 ligase in the advancement of PROTACs owing to its widespread expression in various tissues and well-documented binders. Here, we review the discovery of VHL ligands, the types of linkers employed to develop VHL-based PROTACs, and their subsequent modulation to design advanced non-conventional degraders to target various disease-causing proteins. Furthermore, we provide an overview of other E3 ligases recruited in the field of PROTAC technology.
Collapse
Affiliation(s)
- Nisha Setia
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | | | - Mohammad Abid
- Medicinal Chemistry Laboratory, Department of Biosciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India.
| |
Collapse
|
12
|
Oleinikovas V, Gainza P, Ryckmans T, Fasching B, Thomä NH. From Thalidomide to Rational Molecular Glue Design for Targeted Protein Degradation. Annu Rev Pharmacol Toxicol 2024; 64:291-312. [PMID: 37585660 DOI: 10.1146/annurev-pharmtox-022123-104147] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
Thalidomide and its derivatives are powerful cancer therapeutics that are among the best-understood molecular glue degraders (MGDs). These drugs selectively reprogram the E3 ubiquitin ligase cereblon (CRBN) to commit target proteins for degradation by the ubiquitin-proteasome system. MGDs create novel recognition interfaces on the surface of the E3 ligase that engage in induced protein-protein interactions with neosubstrates. Molecular insight into their mechanism of action opens exciting opportunities to engage a plethora of targets through a specific recognition motif, the G-loop. Our analysis shows that current CRBN-based MGDs can in principle recognize over 2,500 proteins in the human proteome that contain a G-loop. We review recent advances in tuning the specificity between CRBN and its MGD-induced neosubstrates and deduce a set of simple rules that govern these interactions. We conclude that rational MGD design efforts will enable selective degradation of many more proteins, expanding this therapeutic modality to more disease areas.
Collapse
Affiliation(s)
| | | | | | | | - Nicolas H Thomä
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland;
| |
Collapse
|
13
|
Nishiguchi G, Mascibroda LG, Young SM, Caine EA, Abdelhamed S, Kooijman JJ, Miller DJ, Das S, McGowan K, Mayasundari A, Shi Z, Barajas JM, Hiltenbrand R, Aggarwal A, Chang Y, Mishra V, Narina S, Thomas M, Loughran AJ, Kalathur R, Yu K, Zhou S, Wang X, High AA, Peng J, Pruett-Miller SM, Daniels DL, Urh M, Shelat AA, Mullighan CG, Riching KM, Zaman GJR, Fischer M, Klco JM, Rankovic Z. Selective CK1α degraders exert antiproliferative activity against a broad range of human cancer cell lines. Nat Commun 2024; 15:482. [PMID: 38228616 PMCID: PMC10791743 DOI: 10.1038/s41467-024-44698-1] [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: 05/01/2023] [Accepted: 12/21/2023] [Indexed: 01/18/2024] Open
Abstract
Molecular-glue degraders are small molecules that induce a specific interaction between an E3 ligase and a target protein, resulting in the target proteolysis. The discovery of molecular glue degraders currently relies mostly on screening approaches. Here, we describe screening of a library of cereblon (CRBN) ligands against a panel of patient-derived cancer cell lines, leading to the discovery of SJ7095, a potent degrader of CK1α, IKZF1 and IKZF3 proteins. Through a structure-informed exploration of structure activity relationship (SAR) around this small molecule we develop SJ3149, a selective and potent degrader of CK1α protein in vitro and in vivo. The structure of SJ3149 co-crystalized in complex with CK1α + CRBN + DDB1 provides a rationale for the improved degradation properties of this compound. In a panel of 115 cancer cell lines SJ3149 displays a broad antiproliferative activity profile, which shows statistically significant correlation with MDM2 inhibitor Nutlin-3a. These findings suggest potential utility of selective CK1α degraders for treatment of hematological cancers and solid tumors.
Collapse
Affiliation(s)
- Gisele Nishiguchi
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Lauren G Mascibroda
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Sarah M Young
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Elizabeth A Caine
- Promega Corporation, 5430 East Cheryl Drive, Madison, WI, 53711, USA
| | - Sherif Abdelhamed
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | | | - Darcie J Miller
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Sourav Das
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Kevin McGowan
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Anand Mayasundari
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Zhe Shi
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Juan M Barajas
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Ryan Hiltenbrand
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Anup Aggarwal
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Yunchao Chang
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Vibhor Mishra
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Shilpa Narina
- Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Melvin Thomas
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Allister J Loughran
- Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Ravi Kalathur
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Kaiwen Yu
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Suiping Zhou
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Xusheng Wang
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Anthony A High
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Junmin Peng
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
- Center for Proteomics and Metabolomics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Shondra M Pruett-Miller
- Center for Advanced Genome Engineering, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Memphis, TN, 38105, USA
| | - Danette L Daniels
- Promega Corporation, 5430 East Cheryl Drive, Madison, WI, 53711, USA
| | - Marjeta Urh
- Promega Corporation, 5430 East Cheryl Drive, Madison, WI, 53711, USA
| | - Anang A Shelat
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Kristin M Riching
- Promega Corporation, 5430 East Cheryl Drive, Madison, WI, 53711, USA
| | - Guido J R Zaman
- Oncolines B.V., Kloosterstraat 9, 5349 AB, Oss, The Netherlands
| | - Marcus Fischer
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
| | - Jeffery M Klco
- Department of Pathology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
| | - Zoran Rankovic
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
| |
Collapse
|
14
|
He T, Wen C, Yang G, Yang X. Targeted Protein Degradation: Principles, Strategies, and Applications. Adv Biol (Weinh) 2023; 7:e2300083. [PMID: 37518856 DOI: 10.1002/adbi.202300083] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 06/11/2023] [Indexed: 08/01/2023]
Abstract
Protein degradation is a general process to maintain cell homeostasis. The intracellular protein quality control system mainly includes the ubiquitin-proteasome system and the lysosome pathway. Inspired by the physiological process, strategies to degrade specific proteins have developed, which emerge as potent and effective tools in biological research and drug discovery. This review focuses on recent advances in targeted protein degradation techniques, summarizing the principles, advantages, and challenges. Moreover, the potential applications and future direction in biological science and clinics are also discussed.
Collapse
Affiliation(s)
- Ting He
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, 710032, P. R. China
| | - Chenxi Wen
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, 710032, P. R. China
| | - Guodong Yang
- The State Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, 710032, P. R. China
| | - Xuekang Yang
- Department of Burns and Cutaneous Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, 710032, P. R. China
| |
Collapse
|
15
|
Vargesson N, Hooper G, Giddins G, Hunter A, Stirling P, Lam W. Thalidomide upper limb embryopathy - pathogenesis, past and present management and future considerations. J Hand Surg Eur Vol 2023; 48:699-709. [PMID: 37226469 PMCID: PMC10466950 DOI: 10.1177/17531934231177425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 04/27/2023] [Accepted: 05/04/2023] [Indexed: 05/26/2023]
Abstract
This review article provides a comprehensive overview of thalidomide upper limb embryopathy including updates about its pathogenesis, a historical account of the management of the paediatric thalidomide patient, experience with management of the adult patient, as well as creating awareness about early onset age-related changes associated with limb differences. Despite its withdrawal from the market in November 1961, novel discoveries have meant thalidomide is licensed again and currently still in use to treat a variety of conditions, including inflammatory disorders and some cancers. Yet, if not used safely, thalidomide still has the potential to cause damage to the embryo. Recent work identifying thalidomide analogues that retain clinical benefits yet without the harmful effects are showing great promise. Understanding the problems thalidomide survivors face as they age can allow surgeons to support their unique healthcare issues and translate these principles of care to other congenital upper limb differences.
Collapse
Affiliation(s)
- Neil Vargesson
- School of Medicine Medical Sciences & Nutrition. Institute of Medical Sciences. University of Aberdeen. Aberdeen, UK
| | | | | | - Alastair Hunter
- Department of Trauma and Orthopaedics, University College London Hospitals, London, UK
| | - Paul Stirling
- Fife Hand Clinic, Queen Margaret Hospital, Dunfermline, UK
| | - Wee Lam
- Royal Hospital for Children and Young People, Edinburgh, UK
| |
Collapse
|
16
|
Yamanaka S, Furihata H, Yanagihara Y, Taya A, Nagasaka T, Usui M, Nagaoka K, Shoya Y, Nishino K, Yoshida S, Kosako H, Tanokura M, Miyakawa T, Imai Y, Shibata N, Sawasaki T. Lenalidomide derivatives and proteolysis-targeting chimeras for controlling neosubstrate degradation. Nat Commun 2023; 14:4683. [PMID: 37596276 PMCID: PMC10439208 DOI: 10.1038/s41467-023-40385-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 07/21/2023] [Indexed: 08/20/2023] Open
Abstract
Lenalidomide, an immunomodulatory drug (IMiD), is commonly used as a first-line therapy in many haematological cancers, such as multiple myeloma (MM) and 5q myelodysplastic syndromes (5q MDS), and it functions as a molecular glue for the protein degradation of neosubstrates by CRL4CRBN. Proteolysis-targeting chimeras (PROTACs) using IMiDs with a target protein binder also induce the degradation of target proteins. The targeted protein degradation (TPD) of neosubstrates is crucial for IMiD therapy. However, current IMiDs and IMiD-based PROTACs also break down neosubstrates involved in embryonic development and disease progression. Here, we show that 6-position modifications of lenalidomide are essential for controlling neosubstrate selectivity; 6-fluoro lenalidomide induced the selective degradation of IKZF1, IKZF3, and CK1α, which are involved in anti-haematological cancer activity, and showed stronger anti-proliferative effects on MM and 5q MDS cell lines than lenalidomide. PROTACs using these lenalidomide derivatives for BET proteins induce the selective degradation of BET proteins with the same neosubstrate selectivity. PROTACs also exert anti-proliferative effects in all examined cell lines. Thus, 6-position-modified lenalidomide is a key molecule for selective TPD using thalidomide derivatives and PROTACs.
Collapse
Affiliation(s)
- Satoshi Yamanaka
- Division of Cell-Free Sciences, Proteo-Science Center, Ehime University, Matsuyama, 790-8577, Japan
- Division of Proteo-Interactome, Proteo-Science Center, Ehime University, Matsuyama, 790-8577, Japan
| | - Hirotake Furihata
- Division of Cell-Free Sciences, Proteo-Science Center, Ehime University, Matsuyama, 790-8577, Japan
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Yuta Yanagihara
- Division of Integrative Pathophysiology, Proteo-Science Center, Ehime University, Toon, 791-0295, Japan
| | - Akihito Taya
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, 466-8555, Japan
| | - Takato Nagasaka
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, 466-8555, Japan
| | - Mai Usui
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, 466-8555, Japan
| | - Koya Nagaoka
- Division of Cell-Free Sciences, Proteo-Science Center, Ehime University, Matsuyama, 790-8577, Japan
| | - Yuki Shoya
- Division of Cell-Free Sciences, Proteo-Science Center, Ehime University, Matsuyama, 790-8577, Japan
| | - Kohei Nishino
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Shuhei Yoshida
- Division of Integrative Pathophysiology, Proteo-Science Center, Ehime University, Toon, 791-0295, Japan
| | - Hidetaka Kosako
- Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Tokushima University, Tokushima, 770-8503, Japan
| | - Masaru Tanokura
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
| | - Takuya Miyakawa
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan
- Graduate School of Biostudies, Kyoto University, Kyoto, 606-8502, Japan
| | - Yuuki Imai
- Division of Integrative Pathophysiology, Proteo-Science Center, Ehime University, Toon, 791-0295, Japan
| | - Norio Shibata
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Nagoya, 466-8555, Japan
| | - Tatsuya Sawasaki
- Division of Cell-Free Sciences, Proteo-Science Center, Ehime University, Matsuyama, 790-8577, Japan.
| |
Collapse
|
17
|
Kowalski TW, Feira MF, Lord VO, Gomes JDA, Giudicelli GC, Fraga LR, Sanseverino MTV, Recamonde-Mendoza M, Schuler-Faccini L, Vianna FSL. A New Strategy for the Old Challenge of Thalidomide: Systems Biology Prioritization of Potential Immunomodulatory Drug (IMiD)-Targeted Transcription Factors. Int J Mol Sci 2023; 24:11515. [PMID: 37511270 PMCID: PMC10380514 DOI: 10.3390/ijms241411515] [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: 06/01/2023] [Revised: 07/06/2023] [Accepted: 07/08/2023] [Indexed: 07/30/2023] Open
Abstract
Several molecular mechanisms of thalidomide embryopathy (TE) have been investigated, from anti-angiogenesis to oxidative stress to cereblon binding. Recently, it was discovered that thalidomide and its analogs, named immunomodulatory drugs (IMiDs), induced the degradation of C2H2 transcription factors (TFs). This mechanism might impact the strict transcriptional regulation of the developing embryo. Hence, this study aims to evaluate the TFs altered by IMiDs, prioritizing the ones associated with embryogenesis through transcriptome and systems biology-allied analyses. This study comprises only the experimental data accessed through bioinformatics databases. First, proteins and genes reported in the literature as altered/affected by the IMiDs were annotated. A protein systems biology network was evaluated. TFs beta-catenin (CTNNB1) and SP1 play more central roles: beta-catenin is an essential protein in the network, while SP1 is a putative C2H2 candidate for IMiD-induced degradation. Separately, the differential expressions of the annotated genes were analyzed through 23 publicly available transcriptomes, presenting 8624 differentially expressed genes (2947 in two or more datasets). Seventeen C2H2 TFs were identified as related to embryonic development but not studied for IMiD exposure; these TFs are potential IMiDs degradation neosubstrates. This is the first study to suggest an integration of IMiD molecular mechanisms through C2H2 TF degradation.
Collapse
Affiliation(s)
- Thayne Woycinck Kowalski
- Graduate Program in Genetics and Molecular Biology, Genetics Department, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91501-970, Brazil
- Teratogen Information System (SIAT), Medical Genetics Service, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
- Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
- Bioinformatics Core, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
- Biomedical Sciences Course, Centro Universitário CESUCA, Cachoeirinha 94935-630, Brazil
| | - Mariléa Furtado Feira
- Graduate Program in Genetics and Molecular Biology, Genetics Department, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91501-970, Brazil
- Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
| | - Vinícius Oliveira Lord
- Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
- Biomedical Sciences Course, Centro Universitário CESUCA, Cachoeirinha 94935-630, Brazil
| | - Julia do Amaral Gomes
- Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
| | - Giovanna Câmara Giudicelli
- Graduate Program in Genetics and Molecular Biology, Genetics Department, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91501-970, Brazil
- Bioinformatics Core, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
| | - Lucas Rosa Fraga
- Teratogen Information System (SIAT), Medical Genetics Service, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
- Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
- Post-Graduation Program in Medicine, Medical Sciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 90035-003, Brazil
- Department of Morphological Sciences, Institute of Health Sciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 90010-150, Brazil
| | - Maria Teresa Vieira Sanseverino
- Graduate Program in Genetics and Molecular Biology, Genetics Department, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91501-970, Brazil
- Teratogen Information System (SIAT), Medical Genetics Service, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
- School of Medicine, Pontifícia Universidade Católica do Rio Grande do Sul (PUCRS), Porto Alegre 90619-900, Brazil
| | - Mariana Recamonde-Mendoza
- Bioinformatics Core, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
- Post-Graduation Program in Computer Science, Institute of Informatics, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91501-970, Brazil
| | - Lavinia Schuler-Faccini
- Graduate Program in Genetics and Molecular Biology, Genetics Department, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91501-970, Brazil
- Teratogen Information System (SIAT), Medical Genetics Service, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
| | - Fernanda Sales Luiz Vianna
- Graduate Program in Genetics and Molecular Biology, Genetics Department, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 91501-970, Brazil
- Teratogen Information System (SIAT), Medical Genetics Service, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
- Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre (HCPA), Porto Alegre 90035-903, Brazil
- Post-Graduation Program in Medicine, Medical Sciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre 90035-003, Brazil
| |
Collapse
|
18
|
Kodytková A, Dušátková P, Amaratunga SA, Plachý L, Průhová Š, Lebl J. Integrative Role of the SALL4 Gene: From Thalidomide Embryopathy to Genetic Defects of the Upper Limb, Internal Organs, Cerebral Midline, and Pituitary. Horm Res Paediatr 2023; 97:106-112. [PMID: 37285827 PMCID: PMC11008716 DOI: 10.1159/000531452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 05/30/2023] [Indexed: 06/09/2023] Open
Abstract
BACKGROUND The thalidomide disaster resulted in tremendous congenital malformations in more than 10,000 children in the late 1950s and early 1960s. SUMMARY Although numerous putative mechanisms were proposed to explain thalidomide teratogenicity, it was confirmed only recently that thalidomide, rather its derivative 5-hydroxythalidomide (5HT) in a complex with the cereblon protein, interferes with early embryonic transcriptional regulation. 5HT induces selective degradation of SALL4, a principal transcriptional factor of early embryogenesis. Genetic syndromes caused by pathogenic variants of the SALL4 gene phenocopy thalidomide embryopathy with congenital malformations ranging from phocomelia, reduced radial ray, to defects of the heart, kidneys, ear, eye, and possibly cerebral midline and pituitary. SALL4 interacts with TBX5 and a handful of other transcriptional regulators and downregulates the Sonic hedgehog signaling pathway. Cranial midline defects, microcephaly, and short stature due to growth hormone deficiency have been occasionally reported in children carrying SALL4 pathogenic variants associated with generalized stunting of growth rather than just the loss of height attributable to the shortening of leg bones in many children with thalidomide embryopathy. KEY MESSAGES Thus, SALL4 joins the candidate gene list for monogenic syndromic pituitary insufficiency. In this review, we summarize the journey from the thalidomide disaster through the functions of the SALL4 gene to its link to the hormonal regulation of growth.
Collapse
Affiliation(s)
- Aneta Kodytková
- Department of Paediatrics, 2nd Faculty of Medicine, Charles University, and University Hospital Motol, Prague, Czechia
| | - Petra Dušátková
- Department of Paediatrics, 2nd Faculty of Medicine, Charles University, and University Hospital Motol, Prague, Czechia
| | - Shenali Anne Amaratunga
- Department of Paediatrics, 2nd Faculty of Medicine, Charles University, and University Hospital Motol, Prague, Czechia
| | - Lukáš Plachý
- Department of Paediatrics, 2nd Faculty of Medicine, Charles University, and University Hospital Motol, Prague, Czechia
| | - Štěpánka Průhová
- Department of Paediatrics, 2nd Faculty of Medicine, Charles University, and University Hospital Motol, Prague, Czechia
| | - Jan Lebl
- Department of Paediatrics, 2nd Faculty of Medicine, Charles University, and University Hospital Motol, Prague, Czechia,
| |
Collapse
|
19
|
Dsouza NN, Alampady V, Baby K, Maity S, Byregowda BH, Nayak Y. Thalidomide interaction with inflammation in idiopathic pulmonary fibrosis. Inflammopharmacology 2023; 31:1167-1182. [PMID: 36966238 PMCID: PMC10039777 DOI: 10.1007/s10787-023-01193-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 03/04/2023] [Indexed: 03/27/2023]
Abstract
The "Thalidomide tragedy" is a landmark in the history of the pharmaceutical industry. Despite limited clinical trials, there is a continuous effort to investigate thalidomide as a drug for cancer and inflammatory diseases such as rheumatoid arthritis, lepromatous leprosy, and COVID-19. This review focuses on the possibilities of targeting inflammation by repurposing thalidomide for the treatment of idiopathic pulmonary fibrosis (IPF). Articles were searched from the Scopus database, sorted, and selected articles were reviewed. The content includes the proven mechanisms of action of thalidomide relevant to IPF. Inflammation, oxidative stress, and epigenetic mechanisms are major pathogenic factors in IPF. Transforming growth factor-β (TGF-β) is the major biomarker of IPF. Thalidomide is an effective anti-inflammatory drug in inhibiting TGF-β, interleukins (IL-6 and IL-1β), and tumour necrosis factor-α (TNF-α). Thalidomide binds cereblon, a process that is involved in the proposed mechanism in specific cancers such as breast cancer, colon cancer, multiple myeloma, and lung cancer. Cereblon is involved in activating AMP-activated protein kinase (AMPK)-TGF-β/Smad signalling, thereby attenuating fibrosis. The past few years have witnessed an improvement in the identification of biomarkers and diagnostic technologies in respiratory diseases, partly because of the COVID-19 pandemic. Hence, investment in clinical trials with a systematic plan can help repurpose thalidomide for pulmonary fibrosis.
Collapse
Affiliation(s)
- Nikitha Naomi Dsouza
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Varun Alampady
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Krishnaprasad Baby
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Swastika Maity
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Bharath Harohalli Byregowda
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Yogendra Nayak
- Department of Pharmacology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India.
| |
Collapse
|
20
|
Kopp KO, Greer ME, Glotfelty EJ, Hsueh SC, Tweedie D, Kim DS, Reale M, Vargesson N, Greig NH. A New Generation of IMiDs as Treatments for Neuroinflammatory and Neurodegenerative Disorders. Biomolecules 2023; 13:biom13050747. [PMID: 37238617 DOI: 10.3390/biom13050747] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/14/2023] [Accepted: 04/21/2023] [Indexed: 05/28/2023] Open
Abstract
The immunomodulatory imide drug (IMiD) class, which includes the founding drug member thalidomide and later generation drugs, lenalidomide and pomalidomide, has dramatically improved the clinical treatment of specific cancers, such as multiple myeloma, and it combines potent anticancer and anti-inflammatory actions. These actions, in large part, are mediated by IMiD binding to the human protein cereblon that forms a critical component of the E3 ubiquitin ligase complex. This complex ubiquitinates and thereby regulates the levels of multiple endogenous proteins. However, IMiD-cereblon binding modifies cereblon's normal targeted protein degradation towards a new set of neosubstrates that underlies the favorable pharmacological action of classical IMiDs, but also their adverse actions-in particular, their teratogenicity. The ability of classical IMiDs to reduce the synthesis of key proinflammatory cytokines, especially TNF-α levels, makes them potentially valuable to reposition as drugs to mitigate inflammatory-associated conditions and, particularly, neurological disorders driven by an excessive neuroinflammatory element, as occurs in traumatic brain injury, Alzheimer's and Parkinson's diseases, and ischemic stroke. The teratogenic and anticancer actions of classical IMiDs are substantial liabilities for effective drugs in these disorders and can theoretically be dialed out of the drug class. We review a select series of novel IMiDs designed to avoid binding with human cereblon and/or evade degradation of downstream neosubstrates considered to underpin the adverse actions of thalidomide-like drugs. These novel non-classical IMiDs hold potential as new medications for erythema nodosum leprosum (ENL), a painful inflammatory skin condition associated with Hansen's disease for which thalidomide remains widely used, and, in particular, as a new treatment strategy for neurodegenerative disorders in which neuroinflammation is a key component.
Collapse
Affiliation(s)
- Katherine O Kopp
- Drug Design & Development Section, Translational Gerontology Branch, Intramural Research Program National Institute on Aging, Biomedical Research Center, 251 Bayview Blvd., NIH, Baltimore, MD 21224, USA
| | - Margaret E Greer
- Drug Design & Development Section, Translational Gerontology Branch, Intramural Research Program National Institute on Aging, Biomedical Research Center, 251 Bayview Blvd., NIH, Baltimore, MD 21224, USA
- Faculty of Medicine, Georgetown University School of Medicine, Washington, DC 20007, USA
| | - Elliot J Glotfelty
- Drug Design & Development Section, Translational Gerontology Branch, Intramural Research Program National Institute on Aging, Biomedical Research Center, 251 Bayview Blvd., NIH, Baltimore, MD 21224, USA
- Department of Neuroscience, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Shih-Chang Hsueh
- Drug Design & Development Section, Translational Gerontology Branch, Intramural Research Program National Institute on Aging, Biomedical Research Center, 251 Bayview Blvd., NIH, Baltimore, MD 21224, USA
| | - David Tweedie
- Drug Design & Development Section, Translational Gerontology Branch, Intramural Research Program National Institute on Aging, Biomedical Research Center, 251 Bayview Blvd., NIH, Baltimore, MD 21224, USA
| | - Dong Seok Kim
- Aevisbio Inc., Gaithersburg, MD 20878, USA
- Aevis Bio Inc., Daejeon 34141, Republic of Korea
| | - Marcella Reale
- Department of Innovative Technologies in Medicine and Dentistry, G. d'Annunzio University of Chieti and Pescara, 66100 Chieti, Italy
| | - Neil Vargesson
- School of Medicine, Medical Sciences and Nutrition, Institute of Medical Sciences, University of Aberdeen, Aberdeen AB25 2ZD, UK
| | - Nigel H Greig
- Drug Design & Development Section, Translational Gerontology Branch, Intramural Research Program National Institute on Aging, Biomedical Research Center, 251 Bayview Blvd., NIH, Baltimore, MD 21224, USA
| |
Collapse
|
21
|
Fisher ML, Balinth S, Mills AA. ΔNp63α in cancer: importance and therapeutic opportunities. Trends Cell Biol 2023; 33:280-292. [PMID: 36115734 PMCID: PMC10011024 DOI: 10.1016/j.tcb.2022.08.003] [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: 05/20/2022] [Revised: 08/09/2022] [Accepted: 08/22/2022] [Indexed: 10/14/2022]
Abstract
Our understanding of cancer and the key pathways that drive cancer survival has expanded rapidly over the past several decades. However, there are still important challenges that continue to impair patient survival, including our inability to target cancer stem cells (CSCs), metastasis, and drug resistance. The transcription factor p63 is a p53 family member with multiple isoforms that carry out a wide array of functions. Here, we discuss the critical importance of the ΔNp63α isoform in cancer and potential therapeutic strategies to target ΔNp63α expression to impair the CSC population, as well as to prevent metastasis and drug resistance to improve patient survival.
Collapse
Affiliation(s)
- Matthew L Fisher
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Seamus Balinth
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA; Molecular and Cellular Biology Program, Stony Brook University, Stony Brook, NY 11794, USA
| | - Alea A Mills
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.
| |
Collapse
|
22
|
Peng Y, Liu J, Inuzuka H, Wei W. Targeted protein posttranslational modifications by chemically induced proximity for cancer therapy. J Biol Chem 2023; 299:104572. [PMID: 36870680 PMCID: PMC10050664 DOI: 10.1016/j.jbc.2023.104572] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/17/2023] [Accepted: 02/22/2023] [Indexed: 03/06/2023] Open
Abstract
Post-translational modifications (PTMs) regulate all aspects of protein function. Therefore, upstream regulators of PTMs, such as kinases, acetyltransferases, or methyltransferases, are potential therapeutic targets for human diseases, including cancer. To date, multiple inhibitors and/or agonists of these PTM upstream regulators are in clinical use, while others are still in development. However, these upstream regulators control not only the PTMs of disease-related target proteins but also other disease-irrelevant substrate proteins. Thus, nontargeted perturbing activities may introduce unwanted off-target toxicity issues that limit the use of these drugs in successful clinical applications. Therefore, alternative drugs that solely regulate a specific PTM of the disease-relevant protein target may provide a more precise effect in treating disease with relatively low side effects. To this end, chemically induced proximity has recently emerged as a powerful research tool, and several chemical inducers of proximity (CIPs) have been used to target and regulate protein ubiquitination, phosphorylation, acetylation, and glycosylation. These CIPs have a high potential to be translated into clinical drugs and several examples such as PROTACs and MGDs are now in clinical trials. Hence, more CIPs need to be developed to cover all types of PTMs, such as methylation and palmitoylation, thus providing a full spectrum of tools to regulate protein PTM in basic research and also in clinical application for effective cancer treatment.
Collapse
Affiliation(s)
- Yunhua Peng
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA; The Key Laboratory of Biomedical Information Engineering of Ministry of Education, Center for Mitochondrial Biology and Medicine, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Jing Liu
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Hiroyuki Inuzuka
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA.
| |
Collapse
|
23
|
Cheng J, Jiang J, He B, Lin WJ, Li Y, Duan J, Li H, Huang X, Cai J, Xie J, Zhang Z, Yang Y, Xu Y, Hu X, Wu M, Zhuo X, Liu Q, Shi Z, Yu P, Rong X, Ye X, Saw PE, Wu LJ, Simone CB, Chua MLK, Mai HQ, Tang Y. A phase 2 study of thalidomide for the treatment of radiation-induced blood-brain barrier injury. Sci Transl Med 2023; 15:eabm6543. [PMID: 36812346 DOI: 10.1126/scitranslmed.abm6543] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Radiation-induced brain injury (RIBI) is a debilitating sequela after radiotherapy to treat head and neck cancer, and 20 to 30% of patients with RIBI fail to respond to or have contraindications to the first-line treatments of bevacizumab and corticosteroids. Here, we reported a Simon's minmax two-stage, single-arm, phase 2 clinical trial (NCT03208413) to assess the efficacy of thalidomide in patients with RIBI who were unresponsive to or had contraindications to bevacizumab and corticosteroid therapies. The trial met its primary endpoint, with 27 of 58 patients enrolled showing ≥25% reduction in the volume of cerebral edema on fluid-attenuated inversion recovery-magnetic resonance imaging (FLAIR-MRI) after treatment (overall response rate, 46.6%; 95% CI, 33.3 to 60.1%). Twenty-five (43.1%) patients demonstrated a clinical improvement based on the Late Effects Normal Tissues-Subjective, Objective, Management, Analytic (LENT/SOMA) scale, and 36 (62.1%) experienced cognitive improvement based on the Montreal Cognitive Assessment (MoCA) scores. In a mouse model of RIBI, thalidomide restored the blood-brain barrier and cerebral perfusion, which were attributed to the functional rescue of pericytes secondary to elevation of platelet-derived growth factor receptor β (PDGFRβ) expression by thalidomide. Our data thus demonstrate the therapeutic potential of thalidomide for the treatment of radiation-induced cerebral vasculature impairment.
Collapse
Affiliation(s)
- Jinping Cheng
- Department of Neurology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.,Brain Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Jingru Jiang
- Department of Neurology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.,Brain Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Baixuan He
- Department of Neurology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.,Brain Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Wei-Jye Lin
- Brain Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.,Guangdong Province Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China.,Nanhai Translational Innovation Center of Precision Immunology, Sun Yat-sen Memorial Hospital, Foshan 528200, China
| | - Yi Li
- Department of Neurology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.,Brain Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Jingjing Duan
- Department of Anatomy and Neurobiology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
| | - Honghong Li
- Department of Neurology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.,Brain Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Xiaolong Huang
- Department of Neurology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.,Brain Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Jinhua Cai
- Department of Neurology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.,Brain Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Jiatian Xie
- Department of Neurology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.,Brain Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Zhan Zhang
- Department of Neurology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.,Brain Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Yuhua Yang
- Department of Neurology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.,Brain Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Yongteng Xu
- Department of Neurology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.,Brain Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Xia Hu
- Department of Neurology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.,Brain Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Minyi Wu
- Department of Neurology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.,Brain Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Xiaohuang Zhuo
- Department of Neurology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.,Brain Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Qiang Liu
- Department of Neurology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.,Brain Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Zhongshan Shi
- Department of Neurology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.,Brain Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Pei Yu
- Department of Neurology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.,Brain Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Xiaoming Rong
- Department of Neurology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.,Brain Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Xiaojing Ye
- Guangdong Province Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China.,Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Phei Er Saw
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Long-Jun Wu
- Department of Neurology, Mayo Clinic, Rochester, MN 55905, USA.,Department of Neuroscience, Mayo Clinic, Jacksonville, FL 32224, USA.,Department of Immunology, Mayo Clinic, Rochester, MN 55905, USA
| | - Charles B Simone
- Department of Radiation Oncology, New York Proton Center, New York, NY 10035, USA
| | - Melvin L K Chua
- Department of Head and Neck and Thoracic Cancers, Division of Radiation Oncology, National Cancer Centre Singapore, Singapore 169610, Singapore.,Division of Medical Sciences, National Cancer Centre Singapore, Singapore 169610, Singapore.,Oncology Academic Programme, Duke-NUS Medical School, Singapore 169857, Singapore
| | - Hai-Qiang Mai
- Department of Nasopharyngeal Carcinoma, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou 510060, China
| | - Yamei Tang
- Department of Neurology, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.,Brain Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong-Hong Kong Joint Laboratory for RNA Medicine, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.,Guangdong Province Key Laboratory of Brain Function and Disease, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China.,Nanhai Translational Innovation Center of Precision Immunology, Sun Yat-sen Memorial Hospital, Foshan 528200, China
| |
Collapse
|
24
|
O'Brien Laramy MN, Luthra S, Brown MF, Bartlett DW. Delivering on the promise of protein degraders. Nat Rev Drug Discov 2023; 22:410-427. [PMID: 36810917 DOI: 10.1038/s41573-023-00652-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2023] [Indexed: 02/23/2023]
Abstract
Over the past 3 years, the first bivalent protein degraders intentionally designed for targeted protein degradation (TPD) have advanced to clinical trials, with an initial focus on established targets. Most of these clinical candidates are designed for oral administration, and many discovery efforts appear to be similarly focused. As we look towards the future, we propose that an oral-centric discovery paradigm will overly constrain the chemical designs that are considered and limit the potential to drug novel targets. In this Perspective, we summarize the current state of the bivalent degrader modality and propose three categories of degrader designs, based on their likely route of administration and requirement for drug delivery technologies. We then describe a vision for how parenteral drug delivery, implemented early in research and supported by pharmacokinetic-pharmacodynamic modelling, can enable exploration of a broader drug design space, expand the scope of accessible targets and deliver on the promise of protein degraders as a therapeutic modality.
Collapse
Affiliation(s)
| | - Suman Luthra
- Discovery Pharmaceutical Sciences, Merck & Co., Inc., Boston, MA, USA
| | - Matthew F Brown
- Discovery Sciences, Worldwide Research, Development, and Medical, Pfizer Inc., Groton, CT, USA
| | - Derek W Bartlett
- Pharmacokinetics, Dynamics, & Metabolism, Worldwide Research, Development, and Medical, Pfizer Inc., San Diego, CA, USA
| |
Collapse
|
25
|
Fuchs O. Targeting cereblon in hematologic malignancies. Blood Rev 2023; 57:100994. [PMID: 35933246 DOI: 10.1016/j.blre.2022.100994] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/26/2022] [Accepted: 07/27/2022] [Indexed: 01/28/2023]
Abstract
The protein cereblon (CRBN) is a substrate receptor of the cullin 4-really interesting new gene (RING) E3 ubiquitin ligase complex CRL4CRBN. Targeting CRBN mediates selective protein ubiquitination and subsequent degradation via the proteasome. This review describes novel thalidomide analogs, immunomodulatory drugs, also known as CRBN E3 ubiquitin ligase modulators or molecular glues (avadomide, iberdomide, CC-885, CC-90009, BTX-1188, CC-92480, CC-99282, CFT7455, and CC-91633), and CRBN-based proteolysis targeting chimeras (PROTACs) with increased efficacy and potent activity for application in hematologic malignancies. Both types of CRBN-binding drugs, molecular glues, and PROTACs stimulate the interaction between CRBN and its neosubstrates, recruiting target disease-promoting proteins and the E3 ubiquitin ligase CRL4CRBN. Proteins that are traditionally difficult to target (transcription factors and oncoproteins) can be polyubiquitinated and degraded in this way. The competition of CRBN neosubstrates with endogenous CRBN-interacting proteins and the pharmacology and rational combination therapies of and mechanisms of resistance to CRL4CRBN modulators or CRBN-based PROTACs are described.
Collapse
Affiliation(s)
- Ota Fuchs
- Institute of Hematology and Blood Transfusion, U Nemocnice 1, 12800 Praha 2, Czech Republic.
| |
Collapse
|
26
|
Ha S, Luo G, Xiang H. A Comprehensive Overview of Small-Molecule Androgen Receptor Degraders: Recent Progress and Future Perspectives. J Med Chem 2022; 65:16128-16154. [PMID: 36459083 DOI: 10.1021/acs.jmedchem.2c01487] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Prostate cancer (PC), the second most prevalent malignancy in men worldwide, has been proven to depend on the aberrant activation of androgen receptor (AR) signaling. Long-term androgen deprivation for the treatment of PC inevitably leads to castration-resistant prostate cancer (CRPC) in which AR remains a crucial oncogenic driver. Thus, there is an urgent need to develop new strategies to address this unmet medical need. Targeting AR for degradation has recently been in a vigorous development stage, and accumulating clinical studies have highlighted the benefits of AR degraders in CRPC patients. Herein, we provide a comprehensive summary of small-molecule AR degraders with diverse mechanisms of action including proteolysis-targeting chimeras (PROTACs), selective AR degraders (SARDs), hydrophobic tags (HyT), and other AR degraders with distinct mechanisms. Accordingly, their structure-activity relationships, biomedical applications, and therapeutic values are also dissected to provide insights into the future development of promising AR degradation-based therapeutics for CRPC.
Collapse
Affiliation(s)
- Si Ha
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, P. R. China
| | - Guoshun Luo
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, P. R. China
| | - Hua Xiang
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 211198, P. R. China
| |
Collapse
|
27
|
Lin Z, Shen D, Yang B, Woo CM. Molecular and Structural Characterization of Lenalidomide-Mediated Sequestration of eIF3i. ACS Chem Biol 2022; 17:3229-3237. [PMID: 36325969 DOI: 10.1021/acschembio.2c00706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Lenalidomide is a ligand of the E3 ligase substrate adapter cereblon (CRBN) that achieves its clinical effects in part by the promotion of substrate recruitment and degradation. In contrast to prior targets, eIF3i is recruited but not degraded upon complex formation with lenalidomide and CRBN, although the structural details and mechanistic outcomes of this interaction are unresolved. Here, we characterize the structural basis and mechanistic outcomes of lenalidomide-induced sequestration of eIF3i from the eIF3 complex. Identification of the binding interface on eIF3i by a covalent lenalidomide probe and mass spectrometry rationalizes the sequestration event. We further connect eIF3i and CRBN to lenalidomide-driven effects on angiogenic markers, Akt1 phosphorylation, and associated antiangiogenesis phenotypes. Finally, we find that eIF3i sequestration is observed in MM.1S and MOLM13 cells after the degradation of other substrates, such as IKZF1. The defined binding interface elucidated by chemical proteomics and the observation of eIF3i sequestration as a lenalidomide function open future directions in designing new chemical adapters for protein sequestration as a strategy to selectively control protein functions.
Collapse
Affiliation(s)
- Zhi Lin
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Dacheng Shen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Bo Yang
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Christina M Woo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| |
Collapse
|
28
|
Kudo KI, Tsuyama N, Nagata K, Imaoka T, Iizuka D, Sugai-Takahashi M, Muramatsu M, Sakai A. ΔNp63α transcriptionally represses p53 target genes involved in the radiation-induced DNA damage response : ΔNp63α may cause genomic instability in epithelial stem cells. Radiat Oncol 2022; 17:183. [PMID: 36380314 PMCID: PMC9667649 DOI: 10.1186/s13014-022-02139-7] [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: 06/07/2022] [Accepted: 10/05/2022] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The DNA damage response (DDR) is a mechanism that protects cells against radiation-induced oxidative DNA damage by causing cell cycle arrest and apoptosis. TP63 is a member of the tumour suppressor TP53 gene family, and ΔNp63α, a TP63 splicing variant, is constitutively expressed in the stem cell-containing basal layer of stratified epithelial tissues, including the mammary gland, where it plays a critical role in stemness and tissue development. ΔNp63α has been reported to transcriptionally inhibit the tumour suppression protein p53. This p53-repressive activity may cause genomic instability in epithelial stem cells exposed to radiation. In this study, we analysed the inhibitory effect of ΔNp63α on radiation-induced DDR. METHODS To elucidate the role of the p53-repressive effect of ΔNp63α in radiation response, we performed a p63-siRNA knockdown experiment using human mammary epithelial cells (HMECs) expressing ΔNp63α and then performed ectopic and entopic expression experiments using human induced pluripotent stem cells (hiPSCs). After irradiation, the expression of DDR-related genes and proteins in ΔNp63α-expressing and control cells was analysed by RT-qPCR, Western blotting, and flow cytometry. RESULTS The mRNA/protein expression levels of BAX and p21 were significantly increased in p63-siRNA-treated HMECs (sip63) after X-ray irradiation (4 Gy, 0.7 Gy/min) but not in scramble-siRNA treated HMECs (scr). Transcriptomic analysis showed decreased RNA expression of cell cycle-related genes and increased expression of programmed cell death-related genes in sip63 cells compared to scr cells. Furthermore, flow cytometric analysis revealed an increase in apoptotic cells and a decrease in 5-ethynyl-2´-deoxyuridine uptake in sip63 cells compared to scr cells. On the other hand, both the ectopic and entopic expression of ΔNp63α in apoptosis-sensitive hiPSCs reduced the expression levels of BAX after irradiation and significantly decreased the number of apoptotic cells induced by radiation. CONCLUSION Taken together, these results indicate that ΔNp63α represses p53-related radiation-induced DDR, thereby potentially causing genomic instability in epithelial stem cells.
Collapse
Affiliation(s)
- Ken-Ichi Kudo
- Department of Radiation Life Sciences, Fukushima Medical University School of Medicine, Fukushima, Japan.
| | - Naohiro Tsuyama
- Department of Radiation Life Sciences, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Kento Nagata
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Tatsuhiko Imaoka
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Daisuke Iizuka
- Department of Radiation Effects Research, National Institute of Radiological Sciences, National Institutes for Quantum Science and Technology, Chiba, Japan
| | - Misaki Sugai-Takahashi
- Department of Radiation Life Sciences, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Moe Muramatsu
- Department of Diagnostic Pathology, Fukushima Medical University School of Medicine, Fukushima, Japan
| | - Akira Sakai
- Department of Radiation Life Sciences, Fukushima Medical University School of Medicine, Fukushima, Japan
| |
Collapse
|
29
|
Ruffilli C, Roth S, Rodrigo M, Boyd H, Zelcer N, Moreau K. Proteolysis Targeting Chimeras (PROTACs): A Perspective on Integral Membrane Protein Degradation. ACS Pharmacol Transl Sci 2022; 5:849-858. [PMID: 36268122 PMCID: PMC9578132 DOI: 10.1021/acsptsci.2c00142] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Indexed: 11/28/2022]
Abstract
Targeted protein degradation (TPD) is a promising therapeutic modality to modulate protein levels and its application promises to reduce the "undruggable" proteome. Among TPD strategies, Proteolysis TArgeting Chimera (PROTAC) technology has shown a tremendous potential with attractive advantages when compared to the inhibition of the same target. While PROTAC technology has had a significant impact in scientific research, its application to degrade integral membrane proteins (IMPs) is still in its beginnings. Among the 15 compounds having entered clinical trials by the end of 2021, only two targets are membrane-associated proteins. In this review we are discussing the potential reasons which may underlie this, and we are presenting new tools that have been recently developed to solve these limitations and to empower the use of PROTACs to target IMPs.
Collapse
Affiliation(s)
- Camilla Ruffilli
- Safety
Innovation and PROTAC Safety, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, Cambridge CB2 0SL, United Kingdom
- Department
of Medical Biochemistry, Amsterdam UMC,
University of Amsterdam, Amsterdam 1000 GG, The Netherlands
| | - Sascha Roth
- Safety
Innovation and PROTAC Safety, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, Cambridge CB2 0SL, United Kingdom
| | - Monica Rodrigo
- Safety
Innovation and PROTAC Safety, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, Cambridge CB2 0SL, United Kingdom
| | - Helen Boyd
- Precision
Medicine & Biosamples, R&D, AstraZeneca, Cambridge CB2 0SL, United Kingdom
| | - Noam Zelcer
- Department
of Medical Biochemistry, Amsterdam UMC,
University of Amsterdam, Amsterdam 1000 GG, The Netherlands
| | - Kevin Moreau
- Safety
Innovation and PROTAC Safety, Clinical Pharmacology & Safety Sciences, R&D, AstraZeneca, Cambridge CB2 0SL, United Kingdom
| |
Collapse
|
30
|
Ichikawa S, Flaxman HA, Xu W, Vallavoju N, Lloyd HC, Wang B, Shen D, Pratt MR, Woo CM. The E3 ligase adapter cereblon targets the C-terminal cyclic imide degron. Nature 2022; 610:775-782. [PMID: 36261529 PMCID: PMC10316063 DOI: 10.1038/s41586-022-05333-5] [Citation(s) in RCA: 64] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 09/09/2022] [Indexed: 12/22/2022]
Abstract
The ubiquitin E3 ligase substrate adapter cereblon (CRBN) is a target of thalidomide and lenalidomide1, therapeutic agents used in the treatment of haematopoietic malignancies2-4 and as ligands for targeted protein degradation5-7. These agents are proposed to mimic a naturally occurring degron; however, the structural motif recognized by the thalidomide-binding domain of CRBN remains unknown. Here we report that C-terminal cyclic imides, post-translational modifications that arise from intramolecular cyclization of glutamine or asparagine residues, are physiological degrons on substrates for CRBN. Dipeptides bearing the C-terminal cyclic imide degron substitute for thalidomide when embedded within bifunctional chemical degraders. Addition of the degron to the C terminus of proteins induces CRBN-dependent ubiquitination and degradation in vitro and in cells. C-terminal cyclic imides form adventitiously on physiologically relevant timescales throughout the human proteome to afford a degron that is endogenously recognized and removed by CRBN. The discovery of the C-terminal cyclic imide degron defines a regulatory process that may affect the physiological function and therapeutic engagement of CRBN.
Collapse
Affiliation(s)
- Saki Ichikawa
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Hope A Flaxman
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Wenqing Xu
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Nandini Vallavoju
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Hannah C Lloyd
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Binyou Wang
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA
| | - Dacheng Shen
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Matthew R Pratt
- Department of Chemistry, University of Southern California, Los Angeles, CA, USA.,Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Christina M Woo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
| |
Collapse
|
31
|
CRL4 CRBN E3 Ligase Complex as a Therapeutic Target in Multiple Myeloma. Cancers (Basel) 2022; 14:cancers14184492. [PMID: 36139651 PMCID: PMC9496858 DOI: 10.3390/cancers14184492] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/14/2022] [Accepted: 09/14/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Immunomodulatory drugs (IMiDs) are effective in the treatment of multiple myeloma (MM) and other hematological malignancies. Cereblon (CRBN), a target of IMiDs, forms the CRL4 E3 ubiquitin ligase complex (CRL4CRBN) with DDB1, CUL4A and RBX1. The insight into the molecular mechanism of IMiDs action has advanced dramatically since the identification of cereblon (CRBN) as their direct target. Targeting CRBN by IMiDs modifies CRL4CRBN substrate specificity towards non-physiological protein targets which are subsequently ubiquitinated and degraded by the proteasome. To date, IMiDs are the only known group of protein degraders used in clinical practice. This review provides the current state of knowledge about thalidomide and its derivatives’ mechanisms of action, and highlights the future perspectives for targeted protein degraders. Abstract Multiple myeloma (MM) is the second most common hematological malignancy with a recurrent clinical course. The introduction of immunomodulatory drugs (IMiDs) was one of the milestones in MM therapy leading to a significant improvement in patients’ prognosis. Currently, IMiDs are the backbone of MM therapy in newly diagnosed and relapsed/refractory settings. It is now known that IMiDs exert their anti-myeloma activity mainly by binding cereblon (CRBN), the substrate receptor protein of the CRL4 E3 ubiquitin ligase (CRL4CRBN) complex. By binding CRBN, IMiDs alter its substrate specificity, leading to ubiquitination and proteasomal degradation of proteins essential for MM cell survival. Following the success of IMiDs, it is not surprising that the possibility of using the CRL4CRBN complex’s activity to treat MM is being further explored. In this review, we summarize the current state of knowledge about novel players in the MM therapeutic landscape, namely the CRBN E3 ligase modulators (CELMoDs), the next generation of IMiDs with broader biological activity. In addition, we discuss a new strategy of tailored proteolysis called proteolysis targeting chimeras (PROTACs) using the CRL4CRBN to degrade typically undruggable proteins, which may have relevance for the treatment of MM and other malignancies in the future.
Collapse
|
32
|
Shen C, Nayak A, Neitzel LR, Yang F, Li B, Williams CH, Hong CC, Ahmed Y, Lee E, Robbins DJ. The Casein kinase 1α agonist pyrvinium attenuates Wnt-mediated CK1α degradation via interaction with the E3 ubiquitin ligase component Cereblon. J Biol Chem 2022; 298:102227. [PMID: 35780831 PMCID: PMC9352546 DOI: 10.1016/j.jbc.2022.102227] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 06/23/2022] [Accepted: 06/27/2022] [Indexed: 12/04/2022] Open
Abstract
The Cullin-RING ligase 4 E3 ubiquitin ligase component Cereblon (CRBN) is a well-established target for a class of small molecules termed immunomodulatory drugs (IMiDs). These drugs drive CRBN to modulate the degradation of a number of neosubstrates required for the growth of multiple cancers. Whereas the mechanism underlying the activation of CRBN by IMiDs is well described, the normal physiological regulation of CRBN is poorly understood. We recently showed that CRBN is activated following exposure to Wnt ligands and subsequently mediates the degradation of a subset of physiological substrates. Among the Wnt-dependent substrates of CRBN is Casein kinase 1α (CK1α), a known negative regulator of Wnt signaling. Wnt-mediated degradation of CK1α occurs via its association with CRBN at a known IMiD binding pocket. Herein, we demonstrate that a small-molecule CK1α agonist, pyrvinium, directly prevents the Wnt-dependent interaction of CRBN with CK1α, attenuating the consequent CK1α degradation. We further show that pyrvinium disrupts the ability of CRBN to interact with CK1α at the IMiD binding pocket within the CRBN-CK1α complex. Of note, this function of pyrvinium is independent of its previously reported ability to enhance CK1α kinase activity. Furthermore, we also demonstrate that pyrvinium attenuates CRBN-induced Wnt pathway activation in vivo. Collectively, these results reveal a novel dual mechanism through which pyrvinium inhibits Wnt signaling by both attenuating the CRBN-mediated destabilization of CK1α and activating CK1α kinase activity.
Collapse
Affiliation(s)
- Chen Shen
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia, USA; Molecular Oncology Program, The DeWitt Daughtry Family Department of Surgery, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Anmada Nayak
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia, USA; Molecular Oncology Program, The DeWitt Daughtry Family Department of Surgery, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Leif R Neitzel
- Department of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Fan Yang
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia, USA; Molecular Oncology Program, The DeWitt Daughtry Family Department of Surgery, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Bin Li
- Molecular Oncology Program, The DeWitt Daughtry Family Department of Surgery, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Charles H Williams
- Department of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Charles C Hong
- Department of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Yashi Ahmed
- Department of Molecular and Systems Biology and the Norris Cotton Cancer Center, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA
| | - Ethan Lee
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, Tennessee, USA
| | - David J Robbins
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia, USA.
| |
Collapse
|
33
|
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.
Collapse
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.
| |
Collapse
|
34
|
Lin Z, Woo CM. Methods to characterize and discover molecular degraders in cells. Chem Soc Rev 2022; 51:7115-7137. [PMID: 35899832 DOI: 10.1039/d2cs00261b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cells use many post-translational modifications (PTMs) to tailor proteins and transduce cellular signals. Recent years have witnessed the rapid growth of small molecule and enzymatic strategies to purposely manipulate one particular PTM, ubiquitination, on desired target proteins in cells. These approaches typically act by induced proximity between an E3 ligase and a target protein resulting in ubiquitination and degradation of the substrate in cells. In this review, we cover recent approaches to study molecular degraders and discover their induced substrates in vitro and in live cells. Methods that have been adapted and applied to the development of molecular degraders are described, including global proteomics, affinity-purification, chemical proteomics and enzymatic strategies. Extension of these strategies to edit additional PTMs in cells is also discussed. This review is intended to assist researchers who are interested in editing PTMs with new modalities to select suitable method(s) and guide their studies.
Collapse
Affiliation(s)
- Zhi Lin
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
| | - Christina M Woo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA.
| |
Collapse
|
35
|
Distinct interactors define the p63 transcriptional signature in epithelial development or cancer. Biochem J 2022; 479:1375-1392. [PMID: 35748701 PMCID: PMC9250260 DOI: 10.1042/bcj20210737] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/01/2022] [Accepted: 06/06/2022] [Indexed: 11/24/2022]
Abstract
The TP63 is an indispensable transcription factor for development and homeostasis of epithelia and its derived glandular tissue. It is also involved in female germline cell quality control, muscle and thymus development. It is expressed as multiple isoforms transcribed by two independent promoters, in addition to alternative splicing occurring at the mRNA 3′-UTR. Expression of the TP63 gene, specifically the amino-deleted p63 isoform, ΔNp63, is required to regulate numerous biological activities, including lineage specification, self-renewal capacity of epithelial stem cells, proliferation/expansion of basal keratinocytes, differentiation of stratified epithelia. In cancer, ΔNp63 is implicated in squamous cancers pathogenesis of different origin including skin, head and neck and lung and in sustaining self-renewal of cancer stem cells. How this transcription factor can control such a diverse set of biological pathways is central to the understanding of the molecular mechanisms through which p63 acquires oncogenic activity, profoundly changing its down-stream transcriptional signature. Here, we highlight how different proteins interacting with p63 allow it to regulate the transcription of several central genes. The interacting proteins include transcription factors/regulators, epigenetic modifiers, and post-transcriptional modifiers. Moreover, as p63 depends on its interactome, we discuss the hypothesis to target the protein interactors to directly affect p63 oncogenic activities and p63-related diseases.
Collapse
|
36
|
Molecular glues modulate protein functions by inducing protein aggregation: A promising therapeutic strategy of small molecules for disease treatment. Acta Pharm Sin B 2022; 12:3548-3566. [PMID: 36176907 PMCID: PMC9513498 DOI: 10.1016/j.apsb.2022.03.019] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/15/2022] [Accepted: 03/22/2022] [Indexed: 11/24/2022] Open
Abstract
Molecular glues can specifically induce aggregation between two or more proteins to modulate biological functions. In recent years, molecular glues have been widely used as protein degraders. In addition, however, molecular glues play a variety of vital roles, such as complex stabilization, interactome modulation and transporter inhibition, enabling challenging therapeutic targets to be druggable and offering an exciting novel approach for drug discovery. Since most molecular glues are identified serendipitously, exploration of their systematic discovery and rational design are important. In this review, representative examples of molecular glues with various physiological functions are divided into those mediating homo-dimerization, homo-polymerization and hetero-dimerization according to their aggregation modes, and we attempt to elucidate their mechanisms of action. In particular, we aim to highlight some biochemical techniques typically exploited within these representative studies and classify them in terms of three stages of molecular glue development: starting point, optimization and identification.
Collapse
|
37
|
Establishment of a developmental toxicity assay based on human iPSC reporter to detect FGF signal disruption. iScience 2022; 25:103770. [PMID: 35146387 PMCID: PMC8819105 DOI: 10.1016/j.isci.2022.103770] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 12/13/2021] [Accepted: 01/11/2022] [Indexed: 12/15/2022] Open
Abstract
The number of man-made chemicals has increased exponentially recently, and exposure to some of them can induce fetal malformations. Because complex and precisely programmed signaling pathways play important roles in developmental processes, their disruption by external chemicals often triggers developmental toxicity. However, highly accurate and high-throughput screening assays for potential developmental toxicants are currently lacking. In this study, we propose a reporter assay that utilizes human-induced pluripotent stem cells (iPSCs) to detect changes in fibroblast growth factor signaling, which is essential for limb morphogenesis. The dynamics of this signaling after exposure to a chemical were integrated to estimate the degree of signaling disruption, which afforded a good prediction of the capacity of chemicals listed in the ECVAM International Validation Study that induce limb malformations. This study presents an initial report of a human iPSC-based signaling disruption assay, which could be useful for the screening of potential developmental toxicants. Human iPSC-based FGF signal disruption reporter system was established FGF signal disruption was a good indicator of limb malformation-related toxicants Integration of dynamic FGF signal disruption results improved assay performance
Collapse
|
38
|
The ubiquitination-dependent and -independent functions of cereblon in cancer and neurological diseases. J Mol Biol 2022; 434:167457. [PMID: 35045330 DOI: 10.1016/j.jmb.2022.167457] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/21/2021] [Accepted: 01/10/2022] [Indexed: 12/24/2022]
Abstract
Cereblon (CRBN) mediates the teratogenic effect of thalidomide in zebrafish, chicken, and humans. It additionally modulates the anti-myeloma effect of the immunomodulatory drugs (IMiDs) thalidomide, lenalidomide, and pomalidomide. IMiDs bind to CRBN and recruit neo-substrates for their ubiquitination and proteasome-mediated degradation, which significantly expands the application of proteolysis-targeting chimeras (PROTACs) for targeted drug discovery. However, the underlying molecular mechanisms by which CRBN mediates the teratogenicity and anti-myeloma effect of IMiDs are not fully elucidated. Furthermore, the normal physiological functions of endogenous CRBN have not been extensively studied, which precludes the thorough assessment of side effects of the CRBN ligand-based PROTACs in the treatment of cancer and neurological diseases. To advance our understanding of the diverse functions of CRBN, in this review, we will survey the ubiquitination-dependent and -independent functions of CRBN, summarize recent advances in the discovery of constitutive and neo-substrates of CRBN, and explore the molecular functions of CRBN in cancer treatment and in the development of neurological diseases. We will also discuss the potential future directions towards the identification of CRBN substrates and interacting proteins, and CRBN-ligand-based drug discovery in the treatment of cancer and neurological diseases.
Collapse
|
39
|
Lin Z, Amako Y, Kabir F, Flaxman HA, Budnik B, Woo CM. Development of Photolenalidomide for Cellular Target Identification. J Am Chem Soc 2022; 144:606-614. [PMID: 34978798 DOI: 10.1021/jacs.1c11920] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The thalidomide analogue lenalidomide (Len) is a clinical therapeutic that alters the substrate engagement of cereblon (CRBN), a substrate receptor for the CRL4 E3 ubiquitin ligase. Here, we report the development of photolenalidomide (pLen), a Len probe with a photoaffinity label and enrichment handle, designed for target identification by chemical proteomics. pLen preserves the substrate degradation profile, phenotypic antiproliferative and immunomodulatory properties of Len, and enhances interactions with the thalidomide-binding domain of CRBN, as revealed by binding site mapping and molecular modeling. Using pLen, we captured the known targets IKZF1 and CRBN from multiple myeloma MM.1S cells and further identified a new target, eukaryotic translation initiation factor 3 subunit i (eIF3i), from HEK293T cells. eIF3i is directly labeled by pLen and forms a ternary complex with CRBN in the presence of Len across several epithelial cell lines but is itself not ubiquitylated or degraded. These data point to the existence of a broader array of targets induced by ligands to CRBN that may or may not be degraded, which can be identified by the highly translatable application of pLen to additional biological systems.
Collapse
Affiliation(s)
- Zhi Lin
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Yuka Amako
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Farah Kabir
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Hope A Flaxman
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Bogdan Budnik
- Mass Spectrometry and Proteomics Resource (MSPRL), Division of Science, Faculty of Arts and Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Christina M Woo
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| |
Collapse
|
40
|
Frere GA, de Araujo ED, Gunning PT. Emerging mechanisms of targeted protein degradation by molecular glues. Methods Cell Biol 2022; 169:1-26. [DOI: 10.1016/bs.mcb.2022.01.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
41
|
Bansal M, Upadhyay C, Poonam, Kumar S, Rathi B. Phthalimide analogs for antimalarial drug discovery. RSC Med Chem 2021; 12:1854-1867. [PMID: 34825184 DOI: 10.1039/d1md00244a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 08/03/2021] [Indexed: 11/21/2022] Open
Abstract
Malaria remains one of the world's most life-threatening diseases and, thus, it is a major public health concern all around the world. The disease can become devastating if not treated with proper medication in a timely manner. Currently, the number of viable treatment therapies is in continuous decline due to compromised effectiveness, probably owing to the complex life cycle of Plasmodium falciparum. The factors responsible for the unclear status of malaria eradication programmes include ever-developing parasite resistance to the most effective treatments used on the frontline (i.e., artemisinin derivatives) and the paucity of new effective therapeutics. Due to these circumstances, the development of novel effective drug candidates with unique modes of action is essential for overcoming the listed obstacles. As such, the discovery of novel chemical compounds based on validated pharmacophores remains an unmet need in the field of medicinal chemistry. In this area, functionalized phthalimide (Pht) analogs have been explored as potential candidates against various diseases, including malaria. Pht presents a promising bioactive scaffold that can be easily functionalized and thus utilized as a starting point for the development of new antimalarial candidates suitable for preclinical and clinical studies. In this short review, we highlight a wide range of Pht analogs that have been investigated for their activity against various strains of Plasmodium falciparum.
Collapse
Affiliation(s)
- Meenakshi Bansal
- Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College University Enclave, University of Delhi Delhi 110007 India .,Department of Chemistry, Deenbandhu Chhotu Ram University of Science and Technology Murthal Sonepat-131039 Haryana India
| | - Charu Upadhyay
- Department of Chemistry, Miranda House, University of Delhi Delhi 110007 India
| | - Poonam
- Department of Chemistry, Miranda House, University of Delhi Delhi 110007 India
| | - Sumit Kumar
- Department of Chemistry, Deenbandhu Chhotu Ram University of Science and Technology Murthal Sonepat-131039 Haryana India
| | - Brijesh Rathi
- Laboratory for Translational Chemistry and Drug Discovery, Department of Chemistry, Hansraj College University Enclave, University of Delhi Delhi 110007 India
| |
Collapse
|
42
|
Molecular Mechanisms of Cereblon-Interacting Small Molecules in Multiple Myeloma Therapy. J Pers Med 2021; 11:jpm11111185. [PMID: 34834536 PMCID: PMC8623651 DOI: 10.3390/jpm11111185] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/08/2021] [Accepted: 11/08/2021] [Indexed: 12/12/2022] Open
Abstract
Thalidomide analogues (or immunomodulatory imide drugs, IMiDs) are cornerstones in the treatment of multiple myeloma (MM). These drugs bind Cereblon (CRBN), a receptor for the Cullin-ring 4 ubiquitin-ligase (CRL4) complex, to modify its substrate specificity. IMiDs mediate CRBN-dependent engagement and proteasomal degradation of ‘neosubstrates’, Ikaros (IKZF1) and Aiolos (IKZF3), conveying concurrent antimyeloma activity and T-cell costimulation. There is now a greater understanding of physiological CRBN functions, including endogenous substrates and chaperone activity. CRISPR Cas9-based genome-wide screening has further elucidated the complex cellular machinery implicated in IMiD sensitivity, including IKZF1/3-independent mechanisms. New-generation IMiD derivatives with more potent anti-cancer properties—the CELMoDs (Cereblon E3 ligase modulators)—are now being evaluated. Rational drug design also allows ‘hijacking’ of CRL4CRBN utilising proteolysis targeting chimeras (PROTACs) to convey entirely distinct substrate repertoires. As all these chemotypes—thalidomide, IMiDs, CELMoDs and PROTACs—engage CRBN and modify its functions, we describe them here in aggregate as ‘CRBN-interacting small molecules’ (CISMs). In this review, we provide a contemporary summary of the biological consequences of CRBN modulation by CISMs. Detailed molecular insight into CRBN–CISM interactions now provides an opportunity to more effectively target previously elusive cancer dependencies, representing a new and powerful tool for the implementation of precision medicine.
Collapse
|
43
|
PLZF and its fusion proteins are pomalidomide-dependent CRBN neosubstrates. Commun Biol 2021; 4:1277. [PMID: 34764413 PMCID: PMC8586336 DOI: 10.1038/s42003-021-02801-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 10/22/2021] [Indexed: 12/12/2022] Open
Abstract
Pomalidomide and lenalidomide are immunomodulatory agents that were derived from thalidomide. Cereblon (CRBN) is a common direct target of thalidomide and related compounds and works as a Cullin Ring 4 E3 ubiquitin ligase (CRL4) with DDB1, CUL4, and ROC1. The substrate specificity of CRL4CRBN is modulated by thalidomide-related compounds. While lenalidomide is approved for the treatment of several diseases including multiple myeloma, 5q- syndrome, mantle cell lymphoma, and follicular lymphoma, pomalidomide is approved only for the treatment of lenalidomide-resistant multiple myeloma. Here we show that PLZF/ZBTB16 and its fusion proteins are pomalidomide-dependent neosubstrates of CRL4CRBN. PLZF joins to RARα or potentially other partner genes, and the translocation causes leukemias, such as acute promyelocytic leukemia and T-cell acute lymphoblastic leukemia. We demonstrate that pomalidomide treatment induces PLZF-RARα degradation, resulting in antiproliferation of leukemic cells expressing PLZF-RARα. This study highlights a potential therapeutic role of pomalidomide as a degrader of leukemogenic fusion proteins.
Collapse
|
44
|
Rana S, Mallareddy JR, Singh S, Boghean L, Natarajan A. Inhibitors, PROTACs and Molecular Glues as Diverse Therapeutic Modalities to Target Cyclin-Dependent Kinase. Cancers (Basel) 2021; 13:5506. [PMID: 34771669 PMCID: PMC8583118 DOI: 10.3390/cancers13215506] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 10/27/2021] [Accepted: 10/29/2021] [Indexed: 12/25/2022] Open
Abstract
The cyclin-dependent kinase (CDK) family of proteins play prominent roles in transcription, mRNA processing, and cell cycle regulation, making them attractive cancer targets. Palbociclib was the first FDA-approved CDK inhibitor that non-selectively targets the ATP binding sites of CDK4 and CDK6. In this review, we will briefly inventory CDK inhibitors that are either part of over 30 active clinical trials or recruiting patients. The lack of selectivity among CDKs and dose-limiting toxicities are major challenges associated with the development of CDK inhibitors. Proteolysis Targeting Chimeras (PROTACs) and Molecular Glues have emerged as alternative therapeutic modalities to target proteins. PROTACs and Molecular glues utilize the cellular protein degradation machinery to destroy the target protein. PROTACs are heterobifunctional molecules that form a ternary complex with the target protein and E3-ligase by making two distinct small molecule-protein interactions. On the other hand, Molecular glues function by converting the target protein into a "neo-substrate" for an E3 ligase. Unlike small molecule inhibitors, preclinical studies with CDK targeted PROTACs have exhibited improved CDK selectivity. Moreover, the efficacy of PROTACs and molecular glues are not tied to the dose of these molecular entities but to the formation of the ternary complex. Here, we provide an overview of PROTACs and molecular glues that modulate CDK function as emerging therapeutic modalities.
Collapse
Affiliation(s)
- Sandeep Rana
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD 20850, USA;
| | - Jayapal Reddy Mallareddy
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA; (J.R.M.); (S.S.); (L.B.)
| | - Sarbjit Singh
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA; (J.R.M.); (S.S.); (L.B.)
| | - Lidia Boghean
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA; (J.R.M.); (S.S.); (L.B.)
| | - Amarnath Natarajan
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA; (J.R.M.); (S.S.); (L.B.)
- Pharmaceutical Sciences and University of Nebraska Medical Center, Omaha, NE 68198, USA
- Genetics Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Fred and Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| |
Collapse
|
45
|
Dale B, Cheng M, Park KS, Kaniskan HÜ, Xiong Y, Jin J. Advancing targeted protein degradation for cancer therapy. Nat Rev Cancer 2021; 21:638-654. [PMID: 34131295 PMCID: PMC8463487 DOI: 10.1038/s41568-021-00365-x] [Citation(s) in RCA: 274] [Impact Index Per Article: 91.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/23/2021] [Indexed: 02/05/2023]
Abstract
The human proteome contains approximately 20,000 proteins, and it is estimated that more than 600 of them are functionally important for various types of cancers, including nearly 400 non-enzyme proteins that are challenging to target by traditional occupancy-driven pharmacology. Recent advances in the development of small-molecule degraders, including molecular glues and heterobifunctional degraders such as proteolysis-targeting chimeras (PROTACs), have made it possible to target many proteins that were previously considered undruggable. In particular, PROTACs form a ternary complex with a hijacked E3 ubiquitin ligase and a target protein, leading to polyubiquitination and degradation of the target protein. The broad applicability of this approach is facilitated by the flexibility of individual E3 ligases to recognize different substrates. The vast majority of the approximately 600 human E3 ligases have not been explored, thus presenting enormous opportunities to develop degraders that target oncoproteins with tissue, tumour and subcellular selectivity. In this Review, we first discuss the molecular basis of targeted protein degradation. We then offer a comprehensive account of the most promising degraders in development as cancer therapies to date. Lastly, we provide an overview of opportunities and challenges in this exciting field.
Collapse
Affiliation(s)
- Brandon Dale
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Meng Cheng
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kwang-Su Park
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - H Ümit Kaniskan
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Yue Xiong
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
- Cullgen Inc., San Diego, CA, USA.
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
- Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
| |
Collapse
|
46
|
Kim HK, Seol JE, Ahn SW, Jeon S, Park CS, Han J. Cereblon: promise and challenges for combating human diseases. Pflugers Arch 2021; 473:1695-1711. [PMID: 34553266 DOI: 10.1007/s00424-021-02624-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/12/2021] [Accepted: 09/14/2021] [Indexed: 12/18/2022]
Abstract
Cereblon (CRBN) is a substrate recognition protein in the E3-ligase ubiquitin complex. The binding target of CRBN varies according to tissues and cells, and the protein regulates various biological functions by regulating tissue-specific targets. As new endogenous targets of CRBN have been identified over the past decade, the physiological and pathological functions of CRBN and its potential as a therapeutic target in various diseases have greatly expanded. For this purpose, in this review article, we introduce the basic principle of the ubiquitin-proteasome system, the regulation of physiological/pathological functions related to the endogenous substrate of CRBN, and the discovery of immunomodulatory imide drug-mediated neo-substrates of CRBN. In addition, the development of CRBN-based proteolysis-targeting chimeras, which has been actively researched recently, and strategies for developing therapeutic agents using them are introduced. These recent updates on CRBN will be useful in the establishment of strategies for disease treatment and utilization of CRBNs in biomedical engineering and clinical medicine.
Collapse
Affiliation(s)
- Hyoung Kyu Kim
- Department of Physiology, College of Medicine, Cardiovascular and Metabolic Disease Center, Smart Marine Therapeutic Center, Department of Health Sciences and Technology, Graduate School, Inje University, 47392, Busan, Korea
| | - Jung Eun Seol
- Department of Physiology, College of Medicine, Cardiovascular and Metabolic Disease Center, Smart Marine Therapeutic Center, Department of Health Sciences and Technology, Graduate School, Inje University, 47392, Busan, Korea
- Department of Dermatology, Inje University Busan Paik Hospital, Inje University, 47392, Busan, Korea
| | - Sang Woo Ahn
- Department of Dermatology, Inje University Busan Paik Hospital, Inje University, 47392, Busan, Korea
| | - Seungje Jeon
- Department of Physiology, College of Medicine, Cardiovascular and Metabolic Disease Center, Smart Marine Therapeutic Center, Department of Health Sciences and Technology, Graduate School, Inje University, 47392, Busan, Korea
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Korea
| | - Chul-Seung Park
- School of Life Sciences, Gwangju Institute of Science and Technology (GIST), Gwangju, Korea
| | - Jin Han
- Department of Physiology, College of Medicine, Cardiovascular and Metabolic Disease Center, Smart Marine Therapeutic Center, Department of Health Sciences and Technology, Graduate School, Inje University, 47392, Busan, Korea.
| |
Collapse
|
47
|
Chen H, Liu J, Kaniskan HÜ, Wei W, Jin J. Folate-Guided Protein Degradation by Immunomodulatory Imide Drug-Based Molecular Glues and Proteolysis Targeting Chimeras. J Med Chem 2021; 64:12273-12285. [PMID: 34378936 DOI: 10.1021/acs.jmedchem.1c00901] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Molecular glues and proteolysis targeting chimeras (PROTACs) are promising new therapeutic modalities. However, the lack of specificity for molecular glue- or PROTAC-mediated proteolysis in cancer cells versus normal cells raises potential toxicity concerns that will likely limit their clinical applications. Here, we developed a general strategy to deliver immunomodulatory imide drug (IMiD)-based molecular glues and PROTACs to folate receptor α (FOLR1)-positive cancer cells. Specifically, we designed a folate-caged pomalidomide prodrug, FA-S2-POMA, by incorporating a folate group as a caging and guiding element and validated its degradation effect on its neo-substrates in FOLR1-positive cancer cells in a FOLR1-dependent manner. We also developed a folate-caged pomalidomide-based anaplastic lymphoma kinase (ALK) PROTAC, FA-S2-MS4048, which effectively degraded ALK fusion proteins in cancer cells, again in a FOLR1-dependent manner. This novel approach provides a generalizable platform for the targeted delivery of IMiD-based molecular glues and PROTACs to FOLR1-expressing cancer cells with the potential to ameliorate toxicity.
Collapse
Affiliation(s)
- He Chen
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Jing Liu
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - H Ümit Kaniskan
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts 02215, United States
| | - Jian Jin
- Mount Sinai Center for Therapeutics Discovery, Departments of Pharmacological Sciences and Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, United States
| |
Collapse
|
48
|
Fu L, Zhang J, Shen B, Kong L, Liu Y, Tu W, Wang W, Cai X, Wang X, Cheng N, Xia M, Zhou T, Liu Q, Xu Y, Yang J, Gavine P, Philippar U, Attar R, Edwards JP, Venable JD, Dai X. Discovery of Highly Potent and Selective IRAK1 Degraders to Probe Scaffolding Functions of IRAK1 in ABC DLBCL. J Med Chem 2021; 64:10878-10889. [PMID: 34279092 DOI: 10.1021/acs.jmedchem.1c00103] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
MyD88 gene mutation has been identified as one of the most prevalent driver mutations in the activated B-cell-like diffuse large B-cell lymphoma (ABC DLBCL). The published literature suggests that interleukin-1 receptor-associated kinase 1 (IRAK1) is an essential gene for ABC DLBCL harboring MyD88 mutation. Importantly, the scaffolding function of IRAK1, rather than its kinase activity, is required for tumor cell survival. Herein, we present our design, synthesis, and biological evaluation of a novel series of potent and selective IRAK1 degraders. One of the most potent compounds, Degrader-3 (JNJ-1013), effectively degraded cellular IRAK1 protein with a DC50 of 3 nM in HBL-1 cells. Furthermore, JNJ-1013 potently inhibited IRAK1 downstream signaling pathways and demonstrated strong anti-proliferative effects in ABC DLBCL cells with MyD88 mutation. This work suggests that IRAK1 degraders have the potential for treating cancers that are dependent on the IRAK1 scaffolding function.
Collapse
Affiliation(s)
- Liqiang Fu
- Discovery Chemistry, Janssen Research & Development, Shanghai 201210, China
| | - Jing Zhang
- Department of Biology, Janssen Research & Development, Shanghai 201210, China
| | - Bin Shen
- Department of Biology, Janssen Research & Development, Shanghai 201210, China
| | - Linglong Kong
- Discovery Chemistry, Janssen Research & Development, Shanghai 201210, China
| | - Yingtao Liu
- Discovery Chemistry, Janssen Research & Development, Shanghai 201210, China
| | - Wangyang Tu
- Discovery Chemistry, Janssen Research & Development, Shanghai 201210, China
| | - Wenqian Wang
- Department of Biology, Janssen Research & Development, Shanghai 201210, China
| | - Xin Cai
- Department of Biomarker, Janssen Research & Development, Shanghai 201210, China
| | - Xiaotao Wang
- Department of Biomarker, Janssen Research & Development, Shanghai 201210, China
| | - Na Cheng
- Department of Biology, Janssen Research & Development, Shanghai 201210, China
| | - Mingxuan Xia
- Department of Biology, Janssen Research & Development, Shanghai 201210, China
| | - Tianyuan Zhou
- Department of Biology, Janssen Research & Development, Shanghai 201210, China
| | - Qian Liu
- Discovery Chemistry, Janssen Research & Development, Shanghai 201210, China
| | - Yanping Xu
- Discovery Chemistry, Janssen Research & Development, Shanghai 201210, China
| | - Jennifer Yang
- Department of Biology, Janssen Research & Development, Shanghai 201210, China
| | - Paul Gavine
- Department of Biology, Janssen Research & Development, Shanghai 201210, China
| | - Ulrike Philippar
- Janssen Pharmaceutical Research & Development, Beerse 2340, Belgium
| | - Ricardo Attar
- Janssen Pharmaceutical Research & Development, Spring House, Pennsylvania 19477, United States
| | - James P Edwards
- Discovery Sciences, Janssen Research & Development, San Diego, California 92121, United States
| | - Jennifer D Venable
- Discovery Sciences, Janssen Research & Development, San Diego, California 92121, United States
| | - Xuedong Dai
- Discovery Sciences, Janssen (China) Research & Development, Shanghai 201210, P.R. China.,Discovery Chemistry, Janssen Research & Development, Shanghai 201210, China
| |
Collapse
|
49
|
Liu J, Peng Y, Wei W. Light-Controllable PROTACs for Temporospatial Control of Protein Degradation. Front Cell Dev Biol 2021; 9:678077. [PMID: 34350175 PMCID: PMC8326567 DOI: 10.3389/fcell.2021.678077] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/14/2021] [Indexed: 12/25/2022] Open
Abstract
PROteolysis-TArgeting Chimeras (PROTACs) is an emerging and promising approach to target intracellular proteins for ubiquitination-mediated degradation, including those so-called undruggable protein targets, such as transcriptional factors and scaffold proteins. To date, plenty of PROTACs have been developed to degrade various disease-relevant proteins, such as estrogen receptor (ER), androgen receptor (AR), RTK, and CDKs. However, the on-target off-tissue and off-target effect is one of the major limitation that prevents the usage of PROTACs in clinic. To this end, we and several other groups have recently developed light-controllable PROTACs, as the representative for the third generation controllable PROTACs, by using either photo-caging or photo-switch approaches. In this review, we summarize the emerging light-controllable PROTACs and the prospective for other potential ways to achieve temporospatial control of PROTACs.
Collapse
Affiliation(s)
- Jing Liu
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Yunhua Peng
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, United States
| |
Collapse
|
50
|
Kowalski TW, Caldas-Garcia GB, Gomes JDA, Fraga LR, Schuler-Faccini L, Recamonde-Mendoza M, Paixão-Côrtes VR, Vianna FSL. Comparative Genomics Identifies Putative Interspecies Mechanisms Underlying Crbn-Sall4-Linked Thalidomide Embryopathy. Front Genet 2021; 12:680217. [PMID: 34249098 PMCID: PMC8262662 DOI: 10.3389/fgene.2021.680217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 05/18/2021] [Indexed: 11/21/2022] Open
Abstract
The identification of thalidomide–Cereblon-induced SALL4 degradation has brought new understanding for thalidomide embryopathy (TE) differences across species. Some questions, however, regarding species variability, still remain. The aim of this study was to detect sequence divergences between species, affected or not by TE, and to evaluate the regulated gene co-expression in a murine model. Here, we performed a comparative analysis of proteins experimentally established as affected by thalidomide exposure, evaluating 14 species. The comparative analysis, regarding synteny, neighborhood, and protein conservation, was performed in 42 selected genes. Differential co-expression analysis was performed, using a publicly available assay, GSE61306, which evaluated mouse embryonic stem cells (mESC) exposed to thalidomide. The comparative analyses evidenced 20 genes in the upstream neighborhood of NOS3, which are different between the species who develop, or not, the classic TE phenotype. Considering protein sequence alignments, RECQL4, SALL4, CDH5, KDR, and NOS2 proteins had the biggest number of variants reported in unaffected species. In co-expression analysis, Crbn was a gene identified as a driver of the co-expression of other genes implicated in genetic, non-teratogenic, limb reduction defects (LRD), such as Tbx5, Esco2, Recql4, and Sall4; Crbn and Sall4 were shown to have a moderate co-expression correlation, which is affected after thalidomide exposure. Hence, even though the classic TE phenotype is not identified in mice, a deregulatory Crbn-induced mechanism is suggested in this animal. Functional studies are necessary, especially evaluating the genes responsible for LRD syndromes and their interaction with thalidomide–Cereblon.
Collapse
Affiliation(s)
- Thayne Woycinck Kowalski
- Post-Graduation Program in Genetics and Molecular Biology, PPGBM, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre, Brazil.,Laboratory of Medical Genetics and Evolution, Genetics Department, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre, Brazil.,Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre, HCPA, Porto Alegre, Brazil.,National Institute of Medical Population Genetics, INAGEMP, Porto Alegre, Brazil.,Bioinformatics Core, Hospital de Clínicas de Porto Alegre, HCPA, Porto Alegre, Brazil.,Centro Universitário CESUCA, Cachoeirinha, Brazil
| | - Gabriela Barreto Caldas-Garcia
- Post-Graduation Program in Genetics and Molecular Biology, PPGBM, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre, Brazil.,Post-Graduation Program in Biodiversity and Evolution, PPGBioEvo Institute of Biology, Universidade Federal da Bahia, UFBA, Salvador, Brazil
| | - Julia do Amaral Gomes
- Post-Graduation Program in Genetics and Molecular Biology, PPGBM, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre, Brazil.,Laboratory of Medical Genetics and Evolution, Genetics Department, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre, Brazil.,Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre, HCPA, Porto Alegre, Brazil.,National Institute of Medical Population Genetics, INAGEMP, Porto Alegre, Brazil
| | - Lucas Rosa Fraga
- Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre, HCPA, Porto Alegre, Brazil.,National Institute of Medical Population Genetics, INAGEMP, Porto Alegre, Brazil.,Department of Morphological Sciences, Institute of Health Sciences, Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, Brazil.,Post-Graduation Program in Medical Science, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre, Brazil.,Teratogen Information System, SIAT, Medical Genetics Service, Hospital de Clínicas de Porto Alegre, HCPA, Porto Alegre, Brazil
| | - Lavínia Schuler-Faccini
- Post-Graduation Program in Genetics and Molecular Biology, PPGBM, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre, Brazil.,Laboratory of Medical Genetics and Evolution, Genetics Department, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre, Brazil.,National Institute of Medical Population Genetics, INAGEMP, Porto Alegre, Brazil.,Teratogen Information System, SIAT, Medical Genetics Service, Hospital de Clínicas de Porto Alegre, HCPA, Porto Alegre, Brazil
| | - Mariana Recamonde-Mendoza
- Bioinformatics Core, Hospital de Clínicas de Porto Alegre, HCPA, Porto Alegre, Brazil.,Institute of Informatics, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre, Brazil
| | - Vanessa Rodrigues Paixão-Côrtes
- Post-Graduation Program in Biodiversity and Evolution, PPGBioEvo Institute of Biology, Universidade Federal da Bahia, UFBA, Salvador, Brazil
| | - Fernanda Sales Luiz Vianna
- Post-Graduation Program in Genetics and Molecular Biology, PPGBM, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre, Brazil.,Laboratory of Medical Genetics and Evolution, Genetics Department, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre, Brazil.,Laboratory of Genomic Medicine, Center of Experimental Research, Hospital de Clínicas de Porto Alegre, HCPA, Porto Alegre, Brazil.,National Institute of Medical Population Genetics, INAGEMP, Porto Alegre, Brazil.,Post-Graduation Program in Medical Science, Universidade Federal do Rio Grande do Sul, UFRGS, Porto Alegre, Brazil.,Teratogen Information System, SIAT, Medical Genetics Service, Hospital de Clínicas de Porto Alegre, HCPA, Porto Alegre, Brazil
| |
Collapse
|