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Chan P, Nagai Y, Wu Q, Hovsepyan A, Mkhitaryan S, Wang J, Karapetyan G, Kamenecka T, Solt LA, Cope J, Moats RA, Hirota T, Rich JN, Kay SA. Advancing Clinical Response Against Glioblastoma: Evaluating SHP1705 CRY2 Activator Efficacy in Preclinical Models and Safety in Phase I Trials. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.17.613520. [PMID: 39345648 PMCID: PMC11429762 DOI: 10.1101/2024.09.17.613520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
Background It has been reported that circadian clock components, Brain and Muscle ARNT-Like 1 (BMAL1) and Circadian Locomotor Output Cycles Kaput (CLOCK), are uniquely essential for glioblastoma (GBM) stem cell (GSC) biology and survival. Consequently, we developed a novel Cryptochrome (CRY) activator SHP1705, which inhibits BMAL1-CLOCK transcriptional activity. Methods We analyzed buffy coats isolated from Phase 1 clinical trial subjects' blood to assess any changes to circadian, housekeeping, and blood transcriptome-based biomarkers following SHP1705 treatment. We utilized GlioVis to determine which circadian genes are differentially expressed in non-tumor versus GBM tissues. We employed in vitro and in vivo methods to test the efficacy of SHP1705 against patient-derived GSCs and xenografts in comparison to earlier CRY activator scaffolds. Additionally, we applied a novel-REV-ERB agonist SR29065, which inhibits BMAL1 transcription, to determine whether targeting both negative limbs of the circadian transcription-translation feedback loop (TTFL) would yield synergistic effects against various GBM cells. Results SHP1705 is safe and well-tolerated in Phase I clinical trials. SHP1705 has increased selectivity for the CRY2 isoform and potency against GSC viability compared to previously published CRY activators. SHP1705 prolonged survival in mice bearing GBM tumors established with GSCs. When combined with the novel REV-ERB agonist SR29065, SHP1705 displayed synergy against multiple GSC lines and differentiated GSCs (DGCs). Conclusions These demonstrate the efficacy of SHP1705 against GSCs, which pose for GBM patient outcomes. They highlight the potential of novel circadian clock compounds in targeting GBM as single agents or in combination with each other or current standard-of-care. KEY POINTS SHP1705 is a novel CRY2 activator that has shown success in Phase 1 safety trialsSHP1705 has a significantly improved efficacy against GSCs and GBM PDX tumorsNovel REV-ERB agonist SR29065 and SHP1705 display synergistic effects against GSCs. IMPORTANCE OF THE STUDY CRY2 is decreased in GBM tissues compared to CRY1 suggesting that promoting CRY2 activity will be an efficacious GBM treatment paradigm. SHP1705, a CRY2 activator that has shown success in Phase 1 safety trials, has significantly improved preclinical efficacy. Novel REV-ERB agonist SR29065 displays synergistic effects against diverse GBM cells.
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Gabriel CH, del Olmo M, Rizki Widini A, Roshanbin R, Woyde J, Hamza E, Gutu NN, Zehtabian A, Ewers H, Granada A, Herzel H, Kramer A. Circadian period is compensated for repressor protein turnover rates in single cells. Proc Natl Acad Sci U S A 2024; 121:e2404738121. [PMID: 39141353 PMCID: PMC11348271 DOI: 10.1073/pnas.2404738121] [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: 03/06/2024] [Accepted: 07/07/2024] [Indexed: 08/15/2024] Open
Abstract
Most mammalian cells have molecular circadian clocks that generate widespread rhythms in transcript and protein abundance. While circadian clocks are robust to fluctuations in the cellular environment, little is known about the mechanisms by which the circadian period compensates for fluctuating metabolic states. Here, we exploit the heterogeneity of single cells both in circadian period and a metabolic parameter-protein stability-to study their interdependence without the need for genetic manipulation. We generated cells expressing key circadian proteins (CRYPTOCHROME1/2 (CRY1/2) and PERIOD1/2 (PER1/2)) as endogenous fusions with fluorescent proteins and simultaneously monitored circadian rhythms and degradation in thousands of single cells. We found that the circadian period compensates for fluctuations in the turnover rates of circadian repressor proteins and uncovered possible mechanisms using a mathematical model. In addition, the stabilities of the repressor proteins are circadian phase dependent and correlate with the circadian period in a phase-dependent manner, in contrast to the prevailing model.
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Affiliation(s)
- Christian H. Gabriel
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Division of Chronobiology, Berlin10117, Germany
| | - Marta del Olmo
- Institute for Theoretical Biology, Charité–Universitätsmedizin Berlin, Berlin10115, Germany
| | - Arunya Rizki Widini
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Division of Chronobiology, Berlin10117, Germany
| | - Rashin Roshanbin
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Division of Chronobiology, Berlin10117, Germany
| | - Jonas Woyde
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Division of Chronobiology, Berlin10117, Germany
| | - Ebrahim Hamza
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Division of Chronobiology, Berlin10117, Germany
| | - Nica-Nicoleta Gutu
- Charité Comprehensive Cancer Center, Charité–Universitätsmedizin Berlin, Berlin10117, Germany
| | - Amin Zehtabian
- Department of Biology, Chemistry and Pharmacy, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin14195, Germany
| | - Helge Ewers
- Department of Biology, Chemistry and Pharmacy, Institute for Chemistry and Biochemistry, Freie Universität Berlin, Berlin14195, Germany
| | - Adrian Granada
- Charité Comprehensive Cancer Center, Charité–Universitätsmedizin Berlin, Berlin10117, Germany
| | - Hanspeter Herzel
- Institute for Theoretical Biology, Charité–Universitätsmedizin Berlin, Berlin10115, Germany
| | - Achim Kramer
- Charité–Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Division of Chronobiology, Berlin10117, Germany
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DeOliveira CC, Crane BR. A structural decryption of cryptochromes. Front Chem 2024; 12:1436322. [PMID: 39220829 PMCID: PMC11362059 DOI: 10.3389/fchem.2024.1436322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 08/01/2024] [Indexed: 09/04/2024] Open
Abstract
Cryptochromes (CRYs), which are signaling proteins related to DNA photolyases, play pivotal roles in sensory responses throughout biology, including growth and development, metabolic regulation, circadian rhythm entrainment and geomagnetic field sensing. This review explores the evolutionary relationships and functional diversity of cryptochromes from the perspective of their molecular structures. In general, CRY biological activities derive from their core structural architecture, which is based on a Photolyase Homology Region (PHR) and a more variable and functionally specific Cryptochrome C-terminal Extension (CCE). The α/β and α-helical domains within the PHR bind FAD, modulate redox reactive residues, accommodate antenna cofactors, recognize small molecules and provide conformationally responsive interaction surfaces for a range of partners. CCEs add structural complexity and divergence, and in doing so, influence photoreceptor reactivity and tailor function. Primary and secondary pockets within the PHR bind myriad moieties and collaborate with the CCEs to tune recognition properties and propagate chemical changes to downstream partners. For some CRYs, changes in homo and hetero-oligomerization couple to light-induced conformational changes, for others, changes in posttranslational modifications couple to cascades of protein interactions with partners and effectors. The structural exploration of cryptochromes underscores how a broad family of signaling proteins with close relationship to light-dependent enzymes achieves a wide range of activities through conservation of key structural and chemical properties upon which function-specific features are elaborated.
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Affiliation(s)
| | - Brian R. Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, United States
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4
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Cho Y, Li K, Lee JH, Pack SP, Cho AE. Elucidating TH301's influence on the torsion angle of CRY1 W399 using replica exchange with solute tempering (REST) molecular dynamics (MD) simulations. Phys Chem Chem Phys 2023; 25:32648-32655. [PMID: 38010133 DOI: 10.1039/d3cp04092e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Cryptochrome 1 (CRY1) is a protein involved in the circadian clock and associated with various diseases. Targeting CRY1 for drug development requires the discovery of competitive inhibitors that target its FAD binding site through ubiquitination. During the development of compounds to regulate CRY1, an intriguing compound called TH301 was identified. Despite binding to CRY1, TH301 does not induce the expected reaction and is considered an inactive compound. However, it has been observed that TH301 affects the torsion angle of CRY1's W399 residue, which plays a crucial role in the regulation of ubiquitination by influencing the movement of the lid loop. In our research, we aimed to understand how TH301 induces the torsion angle of CRY1's W399 to shift to an "out-form" by performing REST-based MD simulations. The cyclopentane of TH301 tends to align parallel with W292, creating a repulsive force when W399 is in the "in-form", leading to a flip. In the "out-form", W399's side chain interacts with TH301's chlorobenzene through a π-π interaction, stabilizing this pose. This analysis helps identify compounds binding to CRY1 and filter out inactive ones. We found that assessing the interaction energy between TH301 and W399 is crucial to evaluate whether W399 flips or not. These findings contribute to the development of drugs targeting CRY1 and enhance our understanding of its regulatory mechanisms.
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Affiliation(s)
- Yeongrae Cho
- Department of Bioinformatics, Korea University, 2511 Sejong-ro, Sejong, 30119, Korea.
- Biological Clock-based Anti-aging Convergence RLRC, Korea University, Sejong, Republic of Korea
| | - Kexin Li
- Department of Bioinformatics, Korea University, 2511 Sejong-ro, Sejong, 30119, Korea.
- Biological Clock-based Anti-aging Convergence RLRC, Korea University, Sejong, Republic of Korea
| | - Jin Hyup Lee
- Department of Food and Biotechnology, 2511 Sejong-ro, Sejong, 30119, Korea
- Biological Clock-based Anti-aging Convergence RLRC, Korea University, Sejong, Republic of Korea
| | - Seung Pil Pack
- Department of Bioinformatics, Korea University, 2511 Sejong-ro, Sejong, 30119, Korea.
- Biological Clock-based Anti-aging Convergence RLRC, Korea University, Sejong, Republic of Korea
| | - Art E Cho
- Department of Bioinformatics, Korea University, 2511 Sejong-ro, Sejong, 30119, Korea.
- Biological Clock-based Anti-aging Convergence RLRC, Korea University, Sejong, Republic of Korea
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Surme S, Ergun C, Gul S, Akyel YK, Gul ZM, Ozcan O, Ipek OS, Akarlar BA, Ozlu N, Taskin AC, Turkay M, Gören AC, Baris I, Ozturk N, Guzel M, Aydin C, Okyar A, Kavakli IH. TW68, cryptochromes stabilizer, regulates fasting blood glucose levels in diabetic ob/ob and high fat-diet-induced obese mice. Biochem Pharmacol 2023; 218:115896. [PMID: 37898388 DOI: 10.1016/j.bcp.2023.115896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 10/30/2023]
Abstract
Cryptochromes (CRYs), transcriptional repressors of the circadian clock in mammals, inhibit cAMP production when glucagon activates G-protein coupled receptors. Therefore, molecules that modulate CRYs have the potential to regulate gluconeogenesis. In this study, we discovered a new molecule called TW68 that interacts with the primary pockets of mammalian CRY1/2, leading to reduced ubiquitination levels and increased stability. In cell-based circadian rhythm assays using U2OS Bmal1-dLuc cells, TW68 extended the period length of the circadian rhythm. Additionally, TW68 decreased the transcriptional levels of two genes, Phosphoenolpyruvate carboxykinase 1 (PCK1) and Glucose-6-phosphatase (G6PC), which play crucial roles in glucose biosynthesis during glucagon-induced gluconeogenesis in HepG2 cells. Oral administration of TW68 in mice showed good tolerance, a good pharmacokinetic profile, and remarkable bioavailability. Finally, when administered to fasting diabetic animals from ob/ob and HFD-fed obese mice, TW68 reduced blood glucose levels by enhancing CRY stabilization and subsequently decreasing the transcriptional levels of Pck1 and G6pc. These findings collectively demonstrate the antidiabetic efficacy of TW68 in vivo, suggesting its therapeutic potential for controlling fasting glucose levels in the treatment of type 2 diabetes mellitus.
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Affiliation(s)
- Saliha Surme
- Department of Molecular Biology and Genetics, Koc University, Rumelifeneri Yolu, Istanbul, Türkiye
| | - Cagla Ergun
- Department of Chemical and Biological Engineering, Koc University, Rumelifeneri Yolu, Istanbul, Türkiye
| | - Seref Gul
- Istanbul University, Department of Biology, Biotechnology Division, TR-34116 Beyazit-İstanbul, Türkiye; Current address: Bezmialem Vakif University, Institute of Life Sciences and Biotechnology, Beykoz, Istanbul, Türkiye
| | - Yasemin Kubra Akyel
- Istanbul Medipol University, School of Medicine, Department of Medical Pharmacology, İstanbul, Türkiye; Istanbul University, Faculty of Pharmacy Department of Pharmacology, TR-34116 Beyazit-İstanbul, Türkiye
| | - Zeynep Melis Gul
- Department of Molecular Biology and Genetics, Koc University, Rumelifeneri Yolu, Istanbul, Türkiye
| | - Onur Ozcan
- Department of Molecular Biology and Genetics, Koc University, Rumelifeneri Yolu, Istanbul, Türkiye
| | - Ozgecan Savlug Ipek
- Istanbul Medipol University, Regenerative and Restorative Medicine Research Center (REMER), Kavacik Campus, Kavacik-Beykoz/İstanbul 34810, Türkiye
| | - Busra Aytul Akarlar
- Department of Molecular Biology and Genetics, Koc University, Rumelifeneri Yolu, Istanbul, Türkiye
| | - Nurhan Ozlu
- Department of Molecular Biology and Genetics, Koc University, Rumelifeneri Yolu, Istanbul, Türkiye
| | - Ali Cihan Taskin
- Department of Laboratory Animal Science, Aziz Sancar Institute of Experimental Medicine, Istanbul University, Istanbul, Türkiye
| | - Metin Turkay
- Department of Industrial Engineering, Koc University, Rumelifeneri Yolu, İstanbul, Türkiye
| | - Ahmet Ceyhan Gören
- Gebze Technical University, Department of Chemistry, Gebze, Kocaeli, Türkiye
| | - Ibrahim Baris
- Department of Molecular Biology and Genetics, Koc University, Rumelifeneri Yolu, Istanbul, Türkiye
| | - Nuri Ozturk
- Gebze Technical University, Department of Molecular Biology and Genetics, Gebze, Kocaeli, Türkiye
| | - Mustafa Guzel
- Istanbul Medipol University, Regenerative and Restorative Medicine Research Center (REMER), Kavacik Campus, Kavacik-Beykoz/İstanbul 34810, Türkiye
| | - Cihan Aydin
- Department of Molecular Biology and Genetics, Istanbul Medeniyet University, Istanbul, Türkiye
| | - Alper Okyar
- Istanbul University, Faculty of Pharmacy Department of Pharmacology, TR-34116 Beyazit-İstanbul, Türkiye
| | - Ibrahim Halil Kavakli
- Department of Molecular Biology and Genetics, Koc University, Rumelifeneri Yolu, Istanbul, Türkiye; Department of Chemical and Biological Engineering, Koc University, Rumelifeneri Yolu, Istanbul, Türkiye.
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6
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Li W, Xiong X, Kiperman T, Ma K. Transcription Repression of CRY2 via PER2 Interaction Promotes Adipogenesis. Mol Cell Biol 2023; 43:500-514. [PMID: 37724597 PMCID: PMC10569361 DOI: 10.1080/10985549.2023.2253710] [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: 03/09/2023] [Accepted: 08/25/2023] [Indexed: 09/21/2023] Open
Abstract
The circadian clock is driven by a transcriptional-translational feedback loop, and cryptochrome 2 (CRY2) represses CLOCK/BMAL1-induced transcription activation. Despite the established role of clock in adipogenic regulation, whether the CRY2 repressor activity functions in adipocyte biology remains unclear. Here we identify a critical cysteine residue of CRY2 that mediates interaction with Period 2 (PER2). We further demonstrate that this mechanism is required for repressing circadian clock-controlled Wnt signaling to promote adipogenesis. CRY2 protein is enriched in white adipose depots and robustly induced by adipogenic differentiation. Via site-directed mutagenesis, we identified that a conserved CRY2 cysteine at 432 within the loop interfacing with PER2 mediates heterodimer complex formation that confers transcription repression. C432 mutation disrupted PER2 association without affecting BMAL1 binding, leading to loss of repression of clock transcription activation. In preadipocytes, whereas CRY2 enhanced adipocyte differentiation, the repression-defective C432 mutant suppressed this process. Furthermore, silencing of CRY2 attenuated, while stabilization of CRY2 by KL001 markedly augmented adipocyte maturation. Mechanistically, we show that transcriptional repression of Wnt pathway components underlies CRY2 modulation of adipogenesis. Collectively, our findings elucidate a CRY2-mediated repression mechanism that promotes adipocyte development, and implicate its potential as a clock intervention target for obesity.
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Affiliation(s)
- Weini Li
- Department of Diabetes Complications & Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, California, USA
| | - Xuekai Xiong
- Department of Diabetes Complications & Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, California, USA
| | - Tali Kiperman
- Department of Diabetes Complications & Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, California, USA
| | - Ke Ma
- Department of Diabetes Complications & Metabolism, Arthur Riggs Diabetes & Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, California, USA
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Laothamatas I, Rasmussen ES, Green CB, Takahashi JS. Metabolic and chemical architecture of the mammalian circadian clock. Cell Chem Biol 2023; 30:1033-1052. [PMID: 37708890 PMCID: PMC10631358 DOI: 10.1016/j.chembiol.2023.08.014] [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: 01/31/2023] [Revised: 07/20/2023] [Accepted: 08/23/2023] [Indexed: 09/16/2023]
Abstract
Circadian rhythms are endogenous periodic biological processes that occur on a daily timescale. These rhythms are generated by a transcriptional/translational feedback loop that consists of the CLOCK-BMAL1 heterodimeric transcriptional activator complex and the PER1/2-CRY1/2-CK1δ/ε repressive complex. The output pathways of this molecular feedback loop generate circadian rhythmicity in various biological processes. Among these, metabolism is a primary regulatory target of the circadian clock which can also feedback to modulate clock function. This intertwined relationship between circadian rhythms and metabolism makes circadian clock components promising therapeutic targets. Despite this, pharmacological therapeutics that target the circadian clock are relatively rare. In this review, we hope to stimulate interest in chemical chronobiology by providing a comprehensive background on the molecular mechanism of mammalian circadian rhythms and their connection to metabolism, highlighting important studies in the chemical approach to circadian research, and offering our perspectives on future developments in the field.
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Affiliation(s)
- Isara Laothamatas
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Emil Sjulstok Rasmussen
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Carla B Green
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA
| | - Joseph S Takahashi
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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Pan Y, van der Watt PJ, Kay SA. E-box binding transcription factors in cancer. Front Oncol 2023; 13:1223208. [PMID: 37601651 PMCID: PMC10437117 DOI: 10.3389/fonc.2023.1223208] [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: 05/15/2023] [Accepted: 06/27/2023] [Indexed: 08/22/2023] Open
Abstract
E-boxes are important regulatory elements in the eukaryotic genome. Transcription factors can bind to E-boxes through their basic helix-loop-helix or zinc finger domain to regulate gene transcription. E-box-binding transcription factors (EBTFs) are important regulators of development and essential for physiological activities of the cell. The fundamental role of EBTFs in cancer has been highlighted by studies on the canonical oncogene MYC, yet many EBTFs exhibit common features, implying the existence of shared molecular principles of how they are involved in tumorigenesis. A comprehensive analysis of TFs that share the basic function of binding to E-boxes has been lacking. Here, we review the structure of EBTFs, their common features in regulating transcription, their physiological functions, and their mutual regulation. We also discuss their converging functions in cancer biology, their potential to be targeted as a regulatory network, and recent progress in drug development targeting these factors in cancer therapy.
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Affiliation(s)
- Yuanzhong Pan
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Pauline J. van der Watt
- Division of Medical Biochemistry and Structural Biology, Department of Integrative Biomedical Sciences, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Steve A. Kay
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
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Civelek E, Ozturk Civelek D, Akyel YK, Kaleli Durman D, Okyar A. Circadian Dysfunction in Adipose Tissue: Chronotherapy in Metabolic Diseases. BIOLOGY 2023; 12:1077. [PMID: 37626963 PMCID: PMC10452180 DOI: 10.3390/biology12081077] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/26/2023] [Accepted: 07/28/2023] [Indexed: 08/27/2023]
Abstract
Essential for survival and reproduction, the circadian timing system (CTS) regulates adaptation to cyclical changes such as the light/dark cycle, temperature change, and food availability. The regulation of energy homeostasis possesses rhythmic properties that correspond to constantly fluctuating needs for energy production and consumption. Adipose tissue is mainly responsible for energy storage and, thus, operates as one of the principal components of energy homeostasis regulation. In accordance with its roles in energy homeostasis, alterations in adipose tissue's physiological processes are associated with numerous pathologies, such as obesity and type 2 diabetes. These alterations also include changes in circadian rhythm. In the current review, we aim to summarize the current knowledge regarding the circadian rhythmicity of adipogenesis, lipolysis, adipokine secretion, browning, and non-shivering thermogenesis in adipose tissue and to evaluate possible links between those alterations and metabolic diseases. Based on this evaluation, potential therapeutic approaches, as well as clock genes as potential therapeutic targets, are also discussed in the context of chronotherapy.
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Affiliation(s)
- Erkan Civelek
- Department of Pharmacology, Faculty of Pharmacy, Istanbul University, 34116 Istanbul, Turkey; (E.C.); (D.K.D.)
| | - Dilek Ozturk Civelek
- Department of Pharmacology, Faculty of Pharmacy, Bezmialem Vakıf University, 34093 Istanbul, Turkey;
| | - Yasemin Kubra Akyel
- Department of Medical Pharmacology, School of Medicine, Istanbul Medipol University, 34815 Istanbul, Turkey;
| | - Deniz Kaleli Durman
- Department of Pharmacology, Faculty of Pharmacy, Istanbul University, 34116 Istanbul, Turkey; (E.C.); (D.K.D.)
| | - Alper Okyar
- Department of Pharmacology, Faculty of Pharmacy, Istanbul University, 34116 Istanbul, Turkey; (E.C.); (D.K.D.)
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Kiperman T, Li W, Xiong X, Li H, Horne D, Ma K. Targeted screening and identification of chlorhexidine as a pro-myogenic circadian clock activator. Stem Cell Res Ther 2023; 14:190. [PMID: 37525228 PMCID: PMC10391781 DOI: 10.1186/s13287-023-03424-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 07/21/2023] [Indexed: 08/02/2023] Open
Abstract
BACKGROUND The circadian clock is an evolutionarily conserved mechanism that exerts pervasive temporal control in stem cell behavior. This time-keeping machinery is required for orchestrating myogenic progenitor properties in regenerative myogenesis that ameliorates muscular dystrophy. Here we report a screening platform to discover circadian clock modulators that promote myogenesis and identify chlorhexidine (CHX) as a clock-activating molecule with pro-myogenic activities. METHODS A high-throughput molecular docking pipeline was applied to identify compounds with a structural fit for a hydrophobic pocket within the key circadian transcription factor protein, Circadian Locomotor Output Cycles Kaput (CLOCK). These identified molecules were further screened for clock-modulatory activities and functional validations for pro-myogenic properties. RESULTS CHX was identified as a clock activator that promotes distinct aspects of myogenesis. CHX activated circadian clock that reduced cycling period length and augmented amplitude. This action was mediated by the targeted CLOCK structure via augmented interaction with heterodimer partner Bmal1, leading to enhanced CLOCK/Bmal1-controlled transcription with upregulation of core clock genes. Consistent with its clock-activating function, CHX displayed robust effects on stimulating myogenic differentiation in a clock-dependent manner. In addition, CHX augmented the proliferative and migratory activities of myoblasts. CONCLUSION Our findings demonstrate the feasibility of a screening platform to discover clock modulators with myogenic regulatory activities. Discovery of CHX as a pro-myogenic molecule could be applicable to promote regenerative capacities in ameliorating dystrophic or degenerative muscle diseases.
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Affiliation(s)
- Tali Kiperman
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Weini Li
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Xuekai Xiong
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Hongzhi Li
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - David Horne
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA
| | - Ke Ma
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute, Beckman Research Institute of City of Hope, Duarte, CA, 91010, USA.
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Hanić M, Antill LM, Gehrckens AS, Schmidt J, Görtemaker K, Bartölke R, El-Baba TJ, Xu J, Koch KW, Mouritsen H, Benesch JLP, Hore PJ, Solov'yov IA. Dimerization of European Robin Cryptochrome 4a. J Phys Chem B 2023. [PMID: 37428840 PMCID: PMC10364083 DOI: 10.1021/acs.jpcb.3c01305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
Homo-dimer formation is important for the function of many proteins. Although dimeric forms of cryptochromes (Cry) have been found by crystallography and were recently observed in vitro for European robin Cry4a, little is known about the dimerization of avian Crys and the role it could play in the mechanism of magnetic sensing in migratory birds. Here, we present a combined experimental and computational investigation of the dimerization of robin Cry4a resulting from covalent and non-covalent interactions. Experimental studies using native mass spectrometry, mass spectrometric analysis of disulfide bonds, chemical cross-linking, and photometric measurements show that disulfide-linked dimers are routinely formed, that their formation is promoted by exposure to blue light, and that the most likely cysteines are C317 and C412. Computational modeling and molecular dynamics simulations were used to generate and assess a number of possible dimer structures. The relevance of these findings to the proposed role of Cry4a in avian magnetoreception is discussed.
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Affiliation(s)
- Maja Hanić
- Institute of Physics, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26129, Germany
| | - Lewis M Antill
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Sakura Ward, Saitama 338-8570, Japan
- Japan Science and Technology Agency, Precursory Research for Embryonic Science and Technology, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Angela S Gehrckens
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Jessica Schmidt
- Department of Biology and Environmental Sciences, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26129, Germany
| | - Katharina Görtemaker
- Department of Neuroscience, Division of Biochemistry, Carl von Ossietzky University of Oldenburg, Oldenburg D-26111, Germany
| | - Rabea Bartölke
- Department of Biology and Environmental Sciences, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26129, Germany
| | - Tarick J El-Baba
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
- Kavli Institute for NanoScience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, U.K
| | - Jingjing Xu
- Department of Biology and Environmental Sciences, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26129, Germany
| | - Karl-Wilhelm Koch
- Department of Neuroscience, Division of Biochemistry, Carl von Ossietzky University of Oldenburg, Oldenburg D-26111, Germany
- Research Center for Neurosensory Sciences, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26111, Germany
| | - Henrik Mouritsen
- Department of Biology and Environmental Sciences, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26129, Germany
- Research Center for Neurosensory Sciences, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26111, Germany
| | - Justin L P Benesch
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
- Kavli Institute for NanoScience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, U.K
| | - P J Hore
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Ilia A Solov'yov
- Institute of Physics, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26129, Germany
- Research Center for Neurosensory Sciences, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26111, Germany
- Center for Nanoscale Dynamics (CENAD), Carl von Ossietzky Universität Oldenburg, Ammerländer Heerstr. 114-118, Oldenburg 26129, Germany
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12
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Peng X, Chen Y. The emerging role of circadian rhythms in the development and function of thermogenic fat. Front Endocrinol (Lausanne) 2023; 14:1175845. [PMID: 37293491 PMCID: PMC10244810 DOI: 10.3389/fendo.2023.1175845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/06/2023] [Indexed: 06/10/2023] Open
Abstract
Circadian rhythms regulate many biological processes in response to ambient influences. A disrupted circadian rhythm has been shown to be associated with obesity and obesity-related metabolic disorders. Thermogenic fat, including brown and beige fat, may play an important role in this process since it displays a high capacity to burn fat and release the stored energy as heat, contributing to the combat against obesity and its associated metabolic disorders. In this review, we summarize the relationship between the circadian clock and thermogenic fat and the prominent mechanisms which are involved in the regulation of the development and function of thermogenic fat by circadian rhythms, which may provide novel therapeutics for the prevention and treatment of metabolic diseases by targeting thermogenic fat in a circadian manner.
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Affiliation(s)
- Xuemin Peng
- Division of Endocrinology, Internal Medicine, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
- Laboratory of Endocrinology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
| | - Yong Chen
- Division of Endocrinology, Internal Medicine, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
- Laboratory of Endocrinology, Tongji Hospital, Huazhong University of Science and Technology, Wuhan, China
- Branch of National Clinical Research Center for Metabolic Diseases, Hubei, China
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13
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Li W, Xiong X, Kiperman T, Ma K. Transcription repression of Cry2 via Per2 interaction promotes adipogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.12.532323. [PMID: 36993226 PMCID: PMC10054956 DOI: 10.1101/2023.03.12.532323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
The circadian clock is driven by a transcriptional-translational feedback loop, and Cryptochrome 2 (Cry2) represses CLOCK/Bmal1-induced transcription activation. Despite the established role of clock in adipogenic regulation, whether the Cry2 repressor activity functions in adipocyte biology remains unclear. Here we identify a critical cysteine residue of Cry2 that mediates interaction with Per2, and demonstrate that this mechanism is required for clock transcriptional repression that inhibits Wnt signaling to promote adipogenesis. Cry2 protein is enriched in white adipose depots and was robustly induced by adipocyte differentiation. Via site-directed mutagenesis, we identified that a conserved Cry2 Cysteine at 432 within the loop interfacing with Per2 mediates heterodimer complex formation that confers transcription repression. C432 mutation disrupted Per2 association without affecting Bmal1 binding, leading to loss of repression of clock transcription activation. In preadipocytes, whereas Cry2 enhanced adipogenic differentiation, the repression-defective C432 mutant suppressed this process. Furthermore, silencing of Cry2 attenuated, while stabilization of Cry2 by KL001 markedly augmented adipocyte maturation. Mechanistically, we show that transcriptional repression of Wnt pathway components underlies Cry2 modulation of adipogenesis. Collectively, our findings elucidate a Cry2-mediated repression mechanism that promotes adipocyte development, and implicate its potential as a clock intervention target for obesity.
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14
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Katsioudi G, Dreos R, Arpa ES, Gaspari S, Liechti A, Sato M, Gabriel CH, Kramer A, Brown SA, Gatfield D. A conditional Smg6 mutant mouse model reveals circadian clock regulation through the nonsense-mediated mRNA decay pathway. SCIENCE ADVANCES 2023; 9:eade2828. [PMID: 36638184 PMCID: PMC9839329 DOI: 10.1126/sciadv.ade2828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
Nonsense-mediated messenger RNA (mRNA) decay (NMD) has been intensively studied as a surveillance pathway that degrades erroneous transcripts arising from mutations or RNA processing errors. While additional roles in physiological control of mRNA stability have emerged, possible functions in mammalian physiology in vivo remain unclear. Here, we created a conditional mouse allele that allows converting the NMD effector nuclease SMG6 from wild-type to nuclease domain-mutant protein. We find that NMD down-regulation affects the function of the circadian clock, a system known to require rapid mRNA turnover. Specifically, we uncover strong lengthening of free-running circadian periods for liver and fibroblast clocks and direct NMD regulation of Cry2 mRNA, encoding a key transcriptional repressor within the rhythm-generating feedback loop. Transcriptome-wide changes in daily mRNA accumulation patterns in the entrained liver, as well as an altered response to food entrainment, expand the known scope of NMD regulation in mammalian gene expression and physiology.
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Affiliation(s)
- Georgia Katsioudi
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - René Dreos
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Enes S. Arpa
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Sevasti Gaspari
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Angelica Liechti
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
| | - Miho Sato
- Chronobiology and Sleep Research Group, Institute of Pharmacology and Toxicology, University of Zürich, Zürich, Switzerland
| | - Christian H. Gabriel
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany
| | - Achim Kramer
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany
| | - Steven A. Brown
- Chronobiology and Sleep Research Group, Institute of Pharmacology and Toxicology, University of Zürich, Zürich, Switzerland
| | - David Gatfield
- Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland
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15
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Calloni G, Vabulas RM. The structural and functional roles of the flavin cofactor FAD in mammalian cryptochromes. Front Mol Biosci 2023; 9:1081661. [PMID: 36660433 PMCID: PMC9845712 DOI: 10.3389/fmolb.2022.1081661] [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: 10/27/2022] [Accepted: 12/19/2022] [Indexed: 01/06/2023] Open
Abstract
The importance of circadian rhythms in human health and disease calls for a thorough understanding of the underlying molecular machinery, including its key components, the flavin adenine dinucleotide (FAD)-containing flavoproteins cryptochrome 1 and 2. Contrary to their Drosophila counterparts, mammalian cryptochromes are direct suppressors of circadian transcription and act independently of light. Light-independence poses the question regarding the role of the cofactor FAD in mammalian cryptochromes. The weak binding of the cofactor in vitro argues against its relevance and might be a functionless evolutionary remnant. From the other side, the FAD-binding pocket constitutes the part of mammalian cryptochromes directly related to their ubiquitylation by the ubiquitin ligase Fbxl3 and is the target for protein-stabilizing small molecules. Increased supplies of FAD stabilize cryptochromes in cell culture, and the depletion of the FAD precursor riboflavin with simultaneous knock-down of riboflavin kinase affects the expression of circadian genes in mice. This review presents the classical and more recent studies in the field, which help to comprehend the role of FAD for the stability and function of mammalian cryptochromes.
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Affiliation(s)
| | - R. Martin Vabulas
- Institute of Biochemistry, Charité-Universitätsmedizin Berlin, Berlin, Germany,*Correspondence: R. Martin Vabulas,
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16
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Kim E, Yoo SH, Chen Z. Circadian stabilization loop: the regulatory hub and therapeutic target promoting circadian resilience and physiological health. F1000Res 2022; 11:1236. [PMID: 36415204 PMCID: PMC9652504.2 DOI: 10.12688/f1000research.126364.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/06/2022] [Indexed: 12/14/2022] Open
Abstract
The circadian clock is a fundamental biological mechanism that orchestrates essential cellular and physiological processes to optimize fitness and health. The basic functional unit is the cell-autonomous oscillator, consisting of intersecting negative feedback loops. Whereas the core loop is primarily responsible for rhythm generation, auxiliary loops, most notably the secondary or stabilization loop, play pivotal roles to confer temporal precision and molecular robustness. The stabilization loop contains opposing nuclear receptor subfamilies REV-ERBs and retinoic acid receptor-related orphan receptors (RORs), competing to modulate rhythmic expression of the basic helix-loop-helix ARNT like 1 ( Bmal1) genes in the core loop as well as other clock-controlled genes. Therefore, REV-ERBs and RORs are strategically located to interface the oscillator and the global transcriptomic network, promoting cellular homeostasis and physiological fitness throughout lifespan. Disruption of REV-ERB and ROR functions has been linked with diseases and aging, and pharmacological manipulation of these factors has shown promise in various mouse disease models. Nobiletin is a natural compound that directly binds to and activates RORα/γ, modulating circadian rhythms, and shows robust in vivo efficacies to combat clock-associated pathophysiologies and age-related decline. Results from several studies demonstrate an inverse relation between nobiletin efficacy and clock functional state, where nobiletin elicits little effect in young and healthy mice with growing efficacy as the clock is perturbed by environmental and genetic challenges. This mode of action is consistent with the function of the stabilization loop to promote circadian and physiological resilience. Future studies should further investigate the function and mechanism of REV-ERBs and RORs, and test strategies targeting these factors against disease and aging.
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Affiliation(s)
- Eunju Kim
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth Houston), Houston, TX, 77030, USA
| | - Seung-Hee Yoo
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth Houston), Houston, TX, 77030, USA
| | - Zheng Chen
- Department of Biochemistry and Molecular Biology, McGovern Medical School, The University of Texas Health Science Center at Houston (UTHealth Houston), Houston, TX, 77030, USA,
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17
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Gul S, Akyel YK, Gul ZM, Isin S, Ozcan O, Korkmaz T, Selvi S, Danis I, Ipek OS, Aygenli F, Taskin AC, Akarlar BA, Ozlu N, Ozturk N, Ozturk N, Ünal DÖ, Guzel M, Turkay M, Okyar A, Kavakli IH. Discovery of a small molecule that selectively destabilizes Cryptochrome 1 and enhances life span in p53 knockout mice. Nat Commun 2022; 13:6742. [PMID: 36347873 PMCID: PMC9643396 DOI: 10.1038/s41467-022-34582-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 10/31/2022] [Indexed: 11/09/2022] Open
Abstract
Cryptochromes are negative transcriptional regulators of the circadian clock in mammals. It is not clear how reducing the level of endogenous CRY1 in mammals will affect circadian rhythm and the relation of such a decrease with apoptosis. Here, we discovered a molecule (M47) that destabilizes Cryptochrome 1 (CRY1) both in vitro and in vivo. The M47 selectively enhanced the degradation rate of CRY1 by increasing its ubiquitination and resulted in increasing the circadian period length of U2OS Bmal1-dLuc cells. In addition, subcellular fractionation studies from mice liver indicated that M47 increased degradation of the CRY1 in the nucleus. Furthermore, M47-mediated CRY1 reduction enhanced oxaliplatin-induced apoptosis in Ras-transformed p53 null fibroblast cells. Systemic repetitive administration of M47 increased the median lifespan of p53-/- mice by ~25%. Collectively our data suggest that M47 is a promising molecule to treat forms of cancer depending on the p53 mutation.
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Affiliation(s)
- Seref Gul
- grid.15876.3d0000000106887552Department of Chemical and Biological Engineering, Koc University, 34450 Sariyer-Istanbul, Turkey ,grid.9601.e0000 0001 2166 6619Present Address: Department of Biology, Biotechnology Division, İstanbul University, TR-34116 Beyazit-Istanbul, Turkey
| | - Yasemin Kubra Akyel
- grid.9601.e0000 0001 2166 6619Faculty of Pharmacy, Department of Pharmacology, İstanbul University, TR-34116 Beyazit-Istanbul, Turkey ,grid.411781.a0000 0004 0471 9346Present Address: School of Medicine, Department of Medical Pharmacology, Istanbul Medipol University, Istanbul, Turkey
| | - Zeynep Melis Gul
- grid.15876.3d0000000106887552Department of Molecular Biology and Genetics, Koc University, İstanbul, Turkey
| | - Safak Isin
- grid.15876.3d0000000106887552Department of Molecular Biology and Genetics, Koc University, İstanbul, Turkey
| | - Onur Ozcan
- grid.15876.3d0000000106887552Department of Molecular Biology and Genetics, Koc University, İstanbul, Turkey
| | - Tuba Korkmaz
- grid.448834.70000 0004 0595 7127Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, 41400 Kocaeli, Turkey
| | - Saba Selvi
- grid.448834.70000 0004 0595 7127Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, 41400 Kocaeli, Turkey
| | - Ibrahim Danis
- grid.9601.e0000 0001 2166 6619Faculty of Pharmacy, Department of Analytical Chemistry, İstanbul University, TR-34116 Beyazit-Istanbul, Turkey ,grid.9601.e0000 0001 2166 6619İstanbul University Drug Research and Application Center (ILAM), TR-34116 Beyazıt-Istanbul, Turkey
| | - Ozgecan Savlug Ipek
- grid.411781.a0000 0004 0471 9346Regenerative and Restorative Medicine Research Center (REMER), İstanbul Medipol University, Kavacik Campus, Kavacik-Beykoz/Istanbul, 34810 Turkey ,grid.38575.3c0000 0001 2337 3561Department of Chemistry, Graduate School of Natural and Applied Sciences, Yildiz Technical University, Besiktas/Istanbul, 34349 Turkey
| | - Fatih Aygenli
- grid.448834.70000 0004 0595 7127Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, 41400 Kocaeli, Turkey
| | - Ali Cihan Taskin
- grid.15876.3d0000000106887552Animal Research Facility, Research Center for Translational Medicine, Koc University, Rumelifeneri yolu, 34450 Sariyer-Istanbul, Turkey
| | - Büşra Aytül Akarlar
- grid.15876.3d0000000106887552Department of Molecular Biology and Genetics, Koc University, İstanbul, Turkey
| | - Nurhan Ozlu
- grid.15876.3d0000000106887552Department of Molecular Biology and Genetics, Koc University, İstanbul, Turkey
| | - Nuri Ozturk
- grid.448834.70000 0004 0595 7127Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, 41400 Kocaeli, Turkey
| | - Narin Ozturk
- grid.9601.e0000 0001 2166 6619Faculty of Pharmacy, Department of Pharmacology, İstanbul University, TR-34116 Beyazit-Istanbul, Turkey
| | - Durişehvar Özer Ünal
- grid.9601.e0000 0001 2166 6619Faculty of Pharmacy, Department of Analytical Chemistry, İstanbul University, TR-34116 Beyazit-Istanbul, Turkey ,grid.9601.e0000 0001 2166 6619İstanbul University Drug Research and Application Center (ILAM), TR-34116 Beyazıt-Istanbul, Turkey
| | - Mustafa Guzel
- grid.411781.a0000 0004 0471 9346Regenerative and Restorative Medicine Research Center (REMER), İstanbul Medipol University, Kavacik Campus, Kavacik-Beykoz/Istanbul, 34810 Turkey ,grid.411781.a0000 0004 0471 9346International School of Medicine, Department of Medical Pharmacology, Kavacik Campus, İstanbul Medipol University, Kavacik-Beykoz/Istanbul, 34810 Turkey
| | - Metin Turkay
- grid.15876.3d0000000106887552Department of Industrial Engineering, Koc University, Istanbul, Turkey
| | - Alper Okyar
- grid.9601.e0000 0001 2166 6619Faculty of Pharmacy, Department of Pharmacology, İstanbul University, TR-34116 Beyazit-Istanbul, Turkey
| | - Ibrahim Halil Kavakli
- grid.15876.3d0000000106887552Department of Chemical and Biological Engineering, Koc University, 34450 Sariyer-Istanbul, Turkey ,grid.15876.3d0000000106887552Department of Molecular Biology and Genetics, Koc University, İstanbul, Turkey
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18
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Yagi M, Miller S, Nagai Y, Inuki S, Sato A, Hirota T. A methylbenzimidazole derivative regulates mammalian circadian rhythms by targeting Cryptochrome proteins. F1000Res 2022; 11:1016. [PMID: 36226040 PMCID: PMC9523283 DOI: 10.12688/f1000research.124658.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/26/2022] [Indexed: 01/13/2023] Open
Abstract
Background: Impairment of the circadian clock has been associated with numerous diseases, including sleep disorders and metabolic disease. Although small molecules that modulate clock function may form the basis of drug discovery of clock-related diseases, only a few compounds that selectively target core clock proteins have been identified. Three scaffolds were previously discovered as small-molecule activators of the clock protein Cryptochrome (CRY), and they have been providing powerful tools to understand and control the circadian clock system. Identifying new scaffolds will expand the possibilities of drug discovery. Methods: A methylbenzimidazole derivative TH401 identified from cell-based circadian screens was characterized. Effects of TH401 on circadian rhythms were evaluated in cellular assays. Functional assays and X-ray crystallography were used to elucidate the effects of the compound on CRY1 and CRY2 isoforms. Results: TH401 lengthened the period of circadian rhythms and stabilized both CRY1 and CRY2. The compound repressed Per2 reporter activity, which was reduced by Cry1 or Cry2 knockout and abolished by Cry1/Cry2 double knockout, indicating the dependence on CRY isoforms. Thermal shift assays showed slightly higher interaction of TH401 with CRY2 over CRY1. The crystal structure of CRY1 in complex with TH401 revealed a conformational change of the gatekeeper W399, which is involved in isoform-selectivity determination. Conclusions: The present study identified a new small molecule TH401 that targets both CRY isoforms. This compound has expanded the chemical diversity of CRY activators, and will ultimately aid in the development of therapeutics against circadian clock-related disorders.
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Affiliation(s)
- Moeri Yagi
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, 464-8601, Japan,Division of Biological Sciences, Graduate School of Science, Nagoya University, Nagoya, 464-8601, Japan
| | - Simon Miller
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, 464-8601, Japan
| | - Yoshiko Nagai
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, 464-8601, Japan
| | - Shinsuke Inuki
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
| | - Ayato Sato
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, 464-8601, Japan
| | - Tsuyoshi Hirota
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, 464-8601, Japan,Division of Biological Sciences, Graduate School of Science, Nagoya University, Nagoya, 464-8601, Japan,
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19
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CRY2 isoform selectivity of a circadian clock modulator with antiglioblastoma efficacy. Proc Natl Acad Sci U S A 2022; 119:e2203936119. [PMID: 36161947 PMCID: PMC9546630 DOI: 10.1073/pnas.2203936119] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The mammalian cryptochrome isoforms, CRY1 and CRY2, are core circadian clock regulators that work redundantly. Recent studies revealed distinct roles of these closely related homologs in clock output pathways. Isoform-selective control of CRY1 and CRY2 is critical for further understanding their redundant and distinct roles. KL001 was the first identified small-molecule CRY modulator that activates both CRY1 and CRY2. SHP656 is an orally available KL001 derivative and has shown efficacy in blood glucose control and inhibition of glioblastoma stem cell (GSC) growth in animal models. However, CRY isoform selectivity of SHP656 was uncharacterized, limiting understanding of the roles of CRY1 and CRY2. Here, we report the elucidation of CRY2 selectivity of SHP656. SHP656 lengthened cellular circadian period in a CRY2-dependent manner and selectively interacted with CRY2. By determining the X-ray crystal structure of CRY2 in complex with SHP656 and performing molecular dynamics simulations, we elucidated compound interaction mechanisms. SHP656 binding was compatible with the intrinsic CRY2 gatekeeper W417 "in" orientation and also a close "further in" conformation. Perturbation of W417 interaction with the lid loop resulted in a reduced effect of SHP656 on CRY2, supporting an important role of gatekeeper orientation in isoform selectivity. We also identified the R form of SHP656 (called SHP1703) as the active isomer. Treatment with SHP1703 effectively reduced GSC viability. Our results suggest a direct role of CRY2 in glioblastoma antitumorigenesis and provide a rationale for the selective modulation of CRY isoforms in the therapeutic treatment of glioblastoma and other circadian clock-related diseases.
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20
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Rasmussen ES, Takahashi JS, Green CB. Time to target the circadian clock for drug discovery. Trends Biochem Sci 2022; 47:745-758. [PMID: 35577675 PMCID: PMC9378619 DOI: 10.1016/j.tibs.2022.04.009] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 04/01/2022] [Accepted: 04/18/2022] [Indexed: 11/30/2022]
Abstract
The circadian clock is an intracellular timekeeping device that drives daily rhythms in diverse and extensive processes throughout the body. The clock mechanism comprises a core transcription/translation negative feedback loop that is modulated by a complex set of additional interlocking feedback loops. Pharmacological manipulation of the clock may be valuable for treating many maladies including jet lag, shift work and related sleep disorders, various metabolic diseases, and cancer. We review recent identification of small-molecule clock modulators and discuss the biochemical features of the core clock that may be amenable to future drug discovery.
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Affiliation(s)
- Emil Sjulstok Rasmussen
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Joseph S Takahashi
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Carla B Green
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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21
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Hatori M, Hirota T. Cell-Based Phenotypic Screens to Discover Circadian Clock-Modulating Compounds. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2482:95-104. [PMID: 35610421 DOI: 10.1007/978-1-0716-2249-0_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
There is increasing demand to control circadian clock functions in a conditional manner for deeper understanding of the circadian system as well as for potential treatment of clock-related diseases. Small-molecule compounds provide powerful tools to reveal novel functions of target proteins in the circadian clock mechanism, and can be great therapeutic candidates. Here we describe the detailed methods of measuring cellular circadian rhythms in a high-throughput manner for chemical screening to identify compounds that affect circadian rhythms by targeting clock-related proteins.
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Affiliation(s)
- Megumi Hatori
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan
| | - Tsuyoshi Hirota
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan.
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22
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Lin C, Schneps CM, Chandrasekaran S, Ganguly A, Crane BR. Mechanistic insight into light-dependent recognition of Timeless by Drosophila Cryptochrome. Structure 2022; 30:851-861.e5. [PMID: 35397203 DOI: 10.1016/j.str.2022.03.010] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/24/2022] [Accepted: 03/15/2022] [Indexed: 10/18/2022]
Abstract
Cryptochrome (CRY) entrains the fly circadian clock by binding to Timeless (TIM) in light. Undocking of a helical C-terminal tail (CTT) in response to photoreduction of the CRY flavin cofactor gates TIM recognition. We present a generally applicable select western-blot-free tagged-protein interaction (SWFTI) assay that allowed the quantification of CRY binding to TIM in dark and light. The assay was used to study CRY variants with residue substitutions in the flavin pocket and correlate their TIM affinities with CTT undocking, as measured by pulse-dipolar ESR spectroscopy and evaluated by molecular dynamics simulations. CRY variants with the CTT removed or undocked bound TIM constitutively, whereas those incapable of photoreduction bound TIM weakly. In response to the flavin redox state, two conserved histidine residues contributed to a robust on/off switch by mediating CTT interactions with the flavin pocket and TIM. Our approach provides an expeditious means to quantify the interactions of difficult-to-produce proteins.
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Affiliation(s)
- Changfan Lin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | - Connor M Schneps
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA
| | | | - Abir Ganguly
- Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ 08854, USA
| | - Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853, USA.
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23
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Identification of novel small molecules targeting core clock proteins to regulate circadian rhythm. Curr Opin Chem Eng 2022. [DOI: 10.1016/j.coche.2021.100730] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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24
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Fagiani F, Di Marino D, Romagnoli A, Travelli C, Voltan D, Mannelli LDC, Racchi M, Govoni S, Lanni C. Molecular regulations of circadian rhythm and implications for physiology and diseases. Signal Transduct Target Ther 2022; 7:41. [PMID: 35136018 PMCID: PMC8825842 DOI: 10.1038/s41392-022-00899-y] [Citation(s) in RCA: 92] [Impact Index Per Article: 46.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 01/18/2022] [Accepted: 01/18/2022] [Indexed: 12/11/2022] Open
Abstract
The term “circadian rhythms” describes endogenous oscillations with ca. 24-h period associated with the earth’s daily rotation and light/dark cycle. Such rhythms reflect the existence of an intrinsic circadian clock that temporally orchestrates physiological processes to adapt the internal environment with the external cues. At the molecular level, the circadian clock consists of multiple sets of transcription factors resulting in autoregulatory transcription-translation feedback loops. Notably, in addition to their primary role as generator of circadian rhythm, the biological clock plays a key role in controlling physiological functions of almost all tissues and organs. It regulates several intracellular signaling pathways, ranging from cell proliferation, DNA damage repair and response, angiogenesis, metabolic and redox homeostasis, to inflammatory and immune response. In this review, we summarize findings showing the crosstalk between the circadian molecular clock and some key intracellular pathways, describing a scenario wherein their reciprocal regulation impinges upon several aspects of mammalian physiology. Moreover, based on evidence indicating that circadian rhythms can be challenged by environmental factors, social behaviors, as well as pre-existing pathological conditions, we discuss implications of circadian misalignment in human pathologies, such as cancer and inflammatory diseases. Accordingly, disruption of circadian rhythm has been reported to affect several physiological processes that are relevant to human diseases. Expanding our understanding of this field represents an intriguing and transversal medicine challenge in order to establish a circadian precision medicine.
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Affiliation(s)
- Francesca Fagiani
- Department of Drug Sciences (Pharmacology Section), University of Pavia, V.le Taramelli 14, 27100, Pavia, Italy
| | - Daniele Di Marino
- Department of Life and Environmental Sciences, Polytechnic University of Marche, via Brecce Bianche, 60131, Ancona, Italy.,New York-Marche Structural Biology Center (NY-MaSBiC), Polytechnic University of Marche, via Brecce Bianche, 60131, Ancona, Italy
| | - Alice Romagnoli
- Department of Life and Environmental Sciences, Polytechnic University of Marche, via Brecce Bianche, 60131, Ancona, Italy.,New York-Marche Structural Biology Center (NY-MaSBiC), Polytechnic University of Marche, via Brecce Bianche, 60131, Ancona, Italy
| | - Cristina Travelli
- Department of Drug Sciences (Pharmacology Section), University of Pavia, V.le Taramelli 14, 27100, Pavia, Italy
| | - Davide Voltan
- Department of Drug Sciences (Pharmacology Section), University of Pavia, V.le Taramelli 14, 27100, Pavia, Italy
| | | | - Marco Racchi
- Department of Drug Sciences (Pharmacology Section), University of Pavia, V.le Taramelli 14, 27100, Pavia, Italy
| | - Stefano Govoni
- Department of Drug Sciences (Pharmacology Section), University of Pavia, V.le Taramelli 14, 27100, Pavia, Italy
| | - Cristina Lanni
- Department of Drug Sciences (Pharmacology Section), University of Pavia, V.le Taramelli 14, 27100, Pavia, Italy.
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25
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Miller S, Hirota T. Structural and Chemical Biology Approaches Reveal Isoform-Selective Mechanisms of Ligand Interactions in Mammalian Cryptochromes. Front Physiol 2022; 13:837280. [PMID: 35153842 PMCID: PMC8831909 DOI: 10.3389/fphys.2022.837280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 01/05/2022] [Indexed: 01/27/2023] Open
Abstract
Cryptochromes (CRYs) are core components of the circadian feedback loop in mammals, which regulates circadian rhythmicity in a variety of physiological processes including sleep–wake cycles and metabolism. Dysfunction of CRY1 and CRY2 isoforms has been associated with a host of diseases, such as sleep phase disorder and metabolic diseases. Accumulating evidence for distinct roles of CRY1 and CRY2 has highlighted the need for CRY isoform-selective regulation; however, highly conserved sequences in CRY ligand-binding sites have hindered the design of isoform-selective compounds. Chemical biology approaches have been identifying small-molecule modulators of CRY proteins, which act in isoform-non-selective and also isoform-selective manners. In this review, we describe advances in our understanding of CRY isoform selectivity by comparing X-ray crystal structures of mammalian CRY isoforms in apo form and in complexes with compounds. We discuss how intrinsic conformational differences in identical residues of CRY1 and CRY2 contribute to unique interactions with different compound moieties for isoform selectivity.
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26
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Gul S, Kavakli IH. The Structure-Based Molecular-Docking Screen Against Core Clock Proteins to Identify Small Molecules to Modulate the Circadian Clock. Methods Mol Biol 2022; 2482:15-34. [PMID: 35610417 DOI: 10.1007/978-1-0716-2249-0_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Circadian rhythms are part of the body's clock, which regulates several physiological and biochemical variables according to the 24-h cycle. Ample evidence indicated disturbance of the circadian clock leads to an increased susceptibility to several diseases. Therefore, a great effort has been made to find small molecules that regulate circadian rhythm by high-throughput methods. Having crystal structures of core clock proteins, makes them amenable to structure-based drug design studies. Here, we describe virtual screening methods that can be utilized for the identification of small molecules regulating the activity of core clock protein Cryptochrome 1.
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Affiliation(s)
- Seref Gul
- Chemical and Biological Engineering, Koç University, Istanbul, Turkey
| | - Ibrahim Halil Kavakli
- Chemical and Biological Engineering, Koç University, Istanbul, Turkey.
- Molecular Biology and Genetics, Koç University, Istanbul, Turkey.
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27
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Cellini A, Shankar MK, Wahlgren WY, Nimmrich A, Furrer A, James D, Wranik M, Aumonier S, Beale EV, Dworkowski F, Standfuss J, Weinert T, Westenhoff S. Structural basis of the radical pair state in photolyases and cryptochromes. Chem Commun (Camb) 2022; 58:4889-4892. [PMID: 35352724 PMCID: PMC9008703 DOI: 10.1039/d2cc00376g] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present the structure of a photoactivated animal (6-4) photolyase in its radical pair state, captured by serial crystallography. We observe how a conserved asparigine moves towards the semiquinone FAD chromophore and stabilizes it by hydrogen bonding. Several amino acids around the final tryptophan radical rearrange, opening it up to the solvent. The structure explains how the protein environment stabilizes the radical pair state, which is crucial for function of (6-4) photolyases and cryptochromes. The structural response of the drosophila (6-4) photolyase to photoinduced electron transfer along a chain of tryptophans is revealed using a serial crystallographic snapshot of the protein in its radical pair state.![]()
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Affiliation(s)
- Andrea Cellini
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden.
| | - Madan Kumar Shankar
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden.
| | - Weixiao Yuan Wahlgren
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden.
| | - Amke Nimmrich
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden.
| | - Antonia Furrer
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Daniel James
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Maximilian Wranik
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Sylvain Aumonier
- Photon Science Division - Laboratory for Macromolecules and Bioimaging (LSB), Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Emma V Beale
- Photon Science Division - Laboratory for Synchrotron Radiation and Femtochemistry (LSF), Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Florian Dworkowski
- Photon Science Division - Laboratory for Macromolecules and Bioimaging (LSB), Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Jörg Standfuss
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Tobias Weinert
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden.
- Department of Chemistry-BMC, University of Uppsala, Husargatan 3, 75237 Uppsala, Sweden
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28
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Abstract
Circadian clocks are biological timing mechanisms that generate 24-h rhythms of physiology and behavior, exemplified by cycles of sleep/wake, hormone release, and metabolism. The adaptive value of clocks is evident when internal body clocks and daily environmental cycles are mismatched, such as in the case of shift work and jet lag or even mistimed eating, all of which are associated with physiological disruption and disease. Studies with animal and human models have also unraveled an important role of functional circadian clocks in modulating cellular and organismal responses to physiological cues (ex., food intake, exercise), pathological insults (e.g. virus and parasite infections), and medical interventions (e.g. medication). With growing knowledge of the molecular and cellular mechanisms underlying circadian physiology and pathophysiology, it is becoming possible to target circadian rhythms for disease prevention and treatment. In this review, we discuss recent advances in circadian research and the potential for therapeutic applications that take patient circadian rhythms into account in treating disease.
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Affiliation(s)
- Yool Lee
- Department of Translational Medicine and Physiology, Elson S. Floyd College of Medicine, Washington State University, Spokane, Washington
| | - Jeffrey M. Field
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Amita Sehgal
- Howard Hughes Medical Institute, Chronobiology and Sleep Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
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29
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Gul S, Rahim F, Isin S, Yilmaz F, Ozturk N, Turkay M, Kavakli IH. Structure-based design and classifications of small molecules regulating the circadian rhythm period. Sci Rep 2021; 11:18510. [PMID: 34531414 PMCID: PMC8445970 DOI: 10.1038/s41598-021-97962-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 08/27/2021] [Indexed: 11/09/2022] Open
Abstract
Circadian rhythm is an important mechanism that controls behavior and biochemical events based on 24 h rhythmicity. Ample evidence indicates disturbance of this mechanism is associated with different diseases such as cancer, mood disorders, and familial delayed phase sleep disorder. Therefore, drug discovery studies have been initiated using high throughput screening. Recently the crystal structures of core clock proteins (CLOCK/BMAL1, Cryptochromes (CRY), Periods), responsible for generating circadian rhythm, have been solved. Availability of structures makes amenable core clock proteins to design molecules regulating their activity by using in silico approaches. In addition to that, the implementation of classification features of molecules based on their toxicity and activity will improve the accuracy of the drug discovery process. Here, we identified 171 molecules that target functional domains of a core clock protein, CRY1, using structure-based drug design methods. We experimentally determined that 115 molecules were nontoxic, and 21 molecules significantly lengthened the period of circadian rhythm in U2OS cells. We then performed a machine learning study to classify these molecules for identifying features that make them toxic and lengthen the circadian period. Decision tree classifiers (DTC) identified 13 molecular descriptors, which predict the toxicity of molecules with a mean accuracy of 79.53% using tenfold cross-validation. Gradient boosting classifiers (XGBC) identified 10 molecular descriptors that predict and increase in the circadian period length with a mean accuracy of 86.56% with tenfold cross-validation. Our results suggested that these features can be used in QSAR studies to design novel nontoxic molecules that exhibit period lengthening activity.
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Affiliation(s)
- Seref Gul
- Department of Chemical and Biological Engineering, Koc University, Rumelifeneri Yolu, Sariyer, Istabul, Turkey
| | - Fatih Rahim
- Department of Industrial Engineering, Koc University, Rumelifeneri Yolu, Sariyer, Istabul, Turkey
| | - Safak Isin
- Department of Molecular Biology and Genetics, Rumelifeneri Yolu, Sariyer, Istabul, Turkey
| | - Fatma Yilmaz
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, 41400, Kocaeli, Turkey
| | - Nuri Ozturk
- Department of Molecular Biology and Genetics, Gebze Technical University, Gebze, 41400, Kocaeli, Turkey
| | - Metin Turkay
- Department of Industrial Engineering, Koc University, Rumelifeneri Yolu, Sariyer, Istabul, Turkey.
| | - Ibrahim Halil Kavakli
- Department of Chemical and Biological Engineering, Koc University, Rumelifeneri Yolu, Sariyer, Istabul, Turkey.
- Department of Molecular Biology and Genetics, Rumelifeneri Yolu, Sariyer, Istabul, Turkey.
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30
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Iida M, Nakane Y, Yoshimura T, Hirota T. Effects of Cryptochrome-modulating compounds on circadian behavioral rhythms in zebrafish. J Biochem 2021; 171:501-507. [PMID: 34528676 DOI: 10.1093/jb/mvab096] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 09/01/2021] [Indexed: 02/02/2023] Open
Abstract
The circadian clock controls daily rhythms of various physiological processes, and impairment of its function causes many diseases including sleep disorders. Chemical compounds that regulate clock function are expected to be applied for treatment of circadian clock-related diseases. We previously identified small-molecule compounds KL001, KL101, and TH301 that lengthen the period of cellular circadian clock by directly targeting clock proteins Cryptochromes (CRYs) in mammals. KL001 targets both CRY1 and CRY2 isoforms, while KL101 and TH301 are isoform-selective compounds and require CRY C-terminal region for their effects. For further application of these compounds, the effects on locomotor activity rhythms at the organismal level need to be investigated. Here we used zebrafish larvae as an in vivo model system and found that KL001 lengthened the period of locomotor activity rhythms in a dose-dependent manner. In contrast, KL101 and TH301 showed no effect on the period. The amino acid sequences of CRY C-terminal regions are diverged in zebrafish and mammals, supporting the importance of this region for the effects of KL101 and TH301. This study demonstrated efficacy of CRY modulation for controlling circadian behavioral rhythms in organisms and suggested species-dependent differences in the effects of isoform-selective CRY-modulating compounds.
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Affiliation(s)
- Mui Iida
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan.,Division of Biological Sciences, Graduate School of Science, Nagoya University, Nagoya, Japan
| | - Yusuke Nakane
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan.,Laboratory of Animal Integrative Physiology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Takashi Yoshimura
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan.,Laboratory of Animal Integrative Physiology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Japan
| | - Tsuyoshi Hirota
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya, Japan.,Division of Biological Sciences, Graduate School of Science, Nagoya University, Nagoya, Japan
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31
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Structural differences in the FAD-binding pockets and lid loops of mammalian CRY1 and CRY2 for isoform-selective regulation. Proc Natl Acad Sci U S A 2021; 118:2026191118. [PMID: 34172584 PMCID: PMC8255803 DOI: 10.1073/pnas.2026191118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The circadian clock is a biological timekeeper that operates through transcription-translation feedback loops in mammals. Cryptochrome 1 (CRY1) and Cryptochrome 2 (CRY2) are highly conserved core clock components having redundant and distinct functions. We recently identified the CRY1- and CRY2-selective compounds KL101 and TH301, respectively, which provide useful tools for the exploration of isoform-selective CRY regulation. However, intrinsic differences in the compound-binding FAD (flavin adenine dinucleotide) pockets between CRY1 and CRY2 are not well understood, partly because of nonoptimal properties of previously reported apo form structures in this particular region constituted by almost identical sequences. Here, we show unliganded CRY1 and CRY2 crystal structures with well-defined electron densities that are largely free of crystal contacts at the FAD pocket and nearby lid loop. We revealed conformational isomerism in key residues. In particular, CRY1 W399 and corresponding CRY2 W417 in the FAD pocket had distinct conformations ("out" for CRY1 and "in" for CRY2) by interacting with the lid loop residues CRY1 Q407 and CRY2 F424, respectively, resulting in different overall lid loop structures. Molecular dynamics simulations supported that these conformations were energetically favorable to each isoform. Isoform-selective compounds KL101 and TH301 preferred intrinsic "out" and "in" conformations of the tryptophan residue in CRY1 and CRY2, respectively, while the nonselective compound KL001 fit to both conformations. Mutations of lid loop residues designed to perturb their isoform-specific interaction with the tryptophan resulted in reversed responses of CRY1 and CRY2 to KL101 and TH301. We propose that these intrinsic structural differences of CRY1 and CRY2 can be targeted for isoform-selective regulation.
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32
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Abstract
Disruption of circadian rhythms increases the risk of several types of cancer. Mammalian cryptochromes (CRY1 and CRY2) are circadian transcriptional repressors that are related to DNA-repair enzymes. While CRYs lack DNA-repair activity, they modulate the transcriptional response to DNA damage, and CRY2 can promote SKP1 cullin 1-F-box (SCF)FBXL3-mediated ubiquitination of c-MYC and other targets. Here, we characterize five mutations in CRY2 observed in human cancers in The Cancer Genome Atlas. We demonstrate that two orthologous mutations of mouse CRY2 (D325H and S510L) accelerate the growth of primary mouse fibroblasts expressing high levels of c-MYC. Neither mutant affects steady-state levels of overexpressed c-MYC, and they have divergent impacts on circadian rhythms and on the ability of CRY2 to interact with SCFFBXL3 Unexpectedly, stable expression of either CRY2 D325H or of CRY2 S510L robustly suppresses P53 target-gene expression, suggesting that this may be a primary mechanism by which they influence cell growth.
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33
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Gabriel CH, Del Olmo M, Zehtabian A, Jäger M, Reischl S, van Dijk H, Ulbricht C, Rakhymzhan A, Korte T, Koller B, Grudziecki A, Maier B, Herrmann A, Niesner R, Zemojtel T, Ewers H, Granada AE, Herzel H, Kramer A. Live-cell imaging of circadian clock protein dynamics in CRISPR-generated knock-in cells. Nat Commun 2021; 12:3796. [PMID: 34145278 PMCID: PMC8213786 DOI: 10.1038/s41467-021-24086-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 05/25/2021] [Indexed: 02/06/2023] Open
Abstract
The cell biology of circadian clocks is still in its infancy. Here, we describe an efficient strategy for generating knock-in reporter cell lines using CRISPR technology that is particularly useful for genes expressed transiently or at low levels, such as those coding for circadian clock proteins. We generated single and double knock-in cells with endogenously expressed PER2 and CRY1 fused to fluorescent proteins allowing us to simultaneously monitor the dynamics of CRY1 and PER2 proteins in live single cells. Both proteins are highly rhythmic in the nucleus of human cells with PER2 showing a much higher amplitude than CRY1. Surprisingly, CRY1 protein is nuclear at all circadian times indicating the absence of circadian gating of nuclear import. Furthermore, in the nucleus of individual cells CRY1 abundance rhythms are phase-delayed (~5 hours), and CRY1 levels are much higher (>5 times) compared to PER2 questioning the current model of the circadian oscillator.
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Affiliation(s)
- Christian H Gabriel
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Marta Del Olmo
- Institute for Theoretical Biology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Amin Zehtabian
- Institute for Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Marten Jäger
- Berlin Institute of Health (BIH) Core Genomics Facility, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Silke Reischl
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Hannah van Dijk
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Carolin Ulbricht
- Immune Dynamics, Rheumatology and Clinical Immunology, Charité - Universitätsmedizin Berlin, Berlin, Germany
- Immune Dynamics, Deutsches Rheuma-Forschungszentrum (DRFZ), a Leibniz Institute, Berlin, Germany
| | - Asylkhan Rakhymzhan
- Biophysical Analytics, Deutsches Rheuma-Forschungszentrum (DRFZ), a Leibniz Institute, Berlin, Germany
| | - Thomas Korte
- Molecular Biophysics, Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Barbara Koller
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Astrid Grudziecki
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Bert Maier
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany
- Berlin Institute of Health (BIH), Berlin, Germany
| | - Andreas Herrmann
- Molecular Biophysics, Department of Biology, Humboldt Universität zu Berlin, Berlin, Germany
| | - Raluca Niesner
- Biophysical Analytics, Deutsches Rheuma-Forschungszentrum (DRFZ), a Leibniz Institute, Berlin, Germany
- Dynamic and Functional in vivo Imaging, Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Tomasz Zemojtel
- Berlin Institute of Health (BIH) Core Genomics Facility, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Helge Ewers
- Institute for Chemistry and Biochemistry, Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Adrián E Granada
- Charité Comprehensive Cancer Center, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Hanspeter Herzel
- Institute for Theoretical Biology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Achim Kramer
- Charité Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Laboratory of Chronobiology, Berlin, Germany.
- Berlin Institute of Health (BIH), Berlin, Germany.
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34
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Reversible modulation of circadian time with chronophotopharmacology. Nat Commun 2021; 12:3164. [PMID: 34039965 PMCID: PMC8155176 DOI: 10.1038/s41467-021-23301-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 04/16/2021] [Indexed: 12/20/2022] Open
Abstract
The circadian clock controls daily rhythms of physiological processes. The presence of the clock mechanism throughout the body is hampering its local regulation by small molecules. A photoresponsive clock modulator would enable precise and reversible regulation of circadian rhythms using light as a bio-orthogonal external stimulus. Here we show, through judicious molecular design and state-of-the-art photopharmacological tools, the development of a visible light-responsive inhibitor of casein kinase I (CKI) that controls the period and phase of cellular and tissue circadian rhythms in a reversible manner. The dark isomer of photoswitchable inhibitor 9 exhibits almost identical affinity towards the CKIα and CKIδ isoforms, while upon irradiation it becomes more selective towards CKIδ, revealing the higher importance of CKIδ in the period regulation. Our studies enable long-term regulation of CKI activity in cells for multiple days and show the reversible modulation of circadian rhythms with a several hour period and phase change through chronophotopharmacology.
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35
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Jeong YU, Jin HE, Lim HY, Choi G, Joo H, Kang B, Lee GH, Liu KH, Maeng HJ, Chung S, Son GH, Jung JW. Development of Non-Ethoxypropanoic Acid Type Cryptochrome Inhibitors with Circadian Molecular Clock-Enhancing Activity by Bioisosteric Replacement. Pharmaceuticals (Basel) 2021; 14:ph14060496. [PMID: 34073760 PMCID: PMC8225008 DOI: 10.3390/ph14060496] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/17/2021] [Accepted: 05/18/2021] [Indexed: 12/26/2022] Open
Abstract
Circadian dysfunction is closely associated with an increased risk of various diseases. Considering that molecular clock machinery serves as an intrinsic time-keeping system underlying the circadian rhythm of biological processes, the modulation of the molecular clock machinery is an attractive therapeutic target with novel mechanisms of action. Based on the previous structure–activity relationship study of small molecule cryptochrome (CRY) inhibitors possessing an ethoxypropanoic acid moiety, non-ethoxypropanoic acid-type inhibitors have been developed by bioisosteric replacement. They were evaluated as potent and effective enhancers of E-box-mediated transcription, and, in particular, ester 5d and its hydrolysis product 2d exhibited desirable metabolic and pharmacokinetic profiles as promising drug candidates. Compound 2d directly bound to both CRY1 and 2 in surface plasmon resonance analyses, suggesting that the molecular target is CRY. Effects of compound 5d and 2d on suppressive action of CRY1 on CLOCK:BMAL1-activated E-box-LUC reporter activity revealed that both compounds inhibited the negative feedback actions of CRY on CLOCK:BMAL1. Most importantly, compounds 5d and 2d exhibited significant effects on molecular circadian rhythmicity to be considered circadian clock-enhancers, distinct from the previously developed CRY inhibitors possessing an ethoxypropanoic acid moiety.
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Affiliation(s)
- Yong Uk Jeong
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Kyungpook National University, Daegu 41566, Korea; (Y.U.J.); (G.C.); (H.J.); (B.K.); (G.-H.L.); (K.-H.L.)
- Vessel-Organ Interaction Research Center, Kyungpook National University, Daegu 41566, Korea
| | - Hyo-Eon Jin
- College of Pharmacy, Ajou University, Suwon 16499, Korea;
| | - Hye Young Lim
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul 02841, Korea;
| | - Goyeong Choi
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Kyungpook National University, Daegu 41566, Korea; (Y.U.J.); (G.C.); (H.J.); (B.K.); (G.-H.L.); (K.-H.L.)
| | - Hansol Joo
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Kyungpook National University, Daegu 41566, Korea; (Y.U.J.); (G.C.); (H.J.); (B.K.); (G.-H.L.); (K.-H.L.)
- Vessel-Organ Interaction Research Center, Kyungpook National University, Daegu 41566, Korea
| | - Bohun Kang
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Kyungpook National University, Daegu 41566, Korea; (Y.U.J.); (G.C.); (H.J.); (B.K.); (G.-H.L.); (K.-H.L.)
- Vessel-Organ Interaction Research Center, Kyungpook National University, Daegu 41566, Korea
| | - Ga-Hyun Lee
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Kyungpook National University, Daegu 41566, Korea; (Y.U.J.); (G.C.); (H.J.); (B.K.); (G.-H.L.); (K.-H.L.)
| | - Kwang-Hyeon Liu
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Kyungpook National University, Daegu 41566, Korea; (Y.U.J.); (G.C.); (H.J.); (B.K.); (G.-H.L.); (K.-H.L.)
| | - Han-Joo Maeng
- College of Pharmacy, Gachon University, Incheon 21936, Korea;
| | - Sooyoung Chung
- Department of Brain and Cognitive Sciences, Scranton College, Ewha Womans University, Seoul 03760, Korea;
| | - Gi Hoon Son
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul 02841, Korea;
- Correspondence: (G.H.S.); (J.-W.J.); Tel.: +82-2-2286-1147 (G.H.S.); +82-53-950-8578 (J.-W.J.)
| | - Jong-Wha Jung
- Research Institute of Pharmaceutical Sciences, College of Pharmacy, Kyungpook National University, Daegu 41566, Korea; (Y.U.J.); (G.C.); (H.J.); (B.K.); (G.-H.L.); (K.-H.L.)
- Vessel-Organ Interaction Research Center, Kyungpook National University, Daegu 41566, Korea
- Correspondence: (G.H.S.); (J.-W.J.); Tel.: +82-2-2286-1147 (G.H.S.); +82-53-950-8578 (J.-W.J.)
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36
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Karki N, Vergish S, Zoltowski BD. Cryptochromes: Photochemical and structural insight into magnetoreception. Protein Sci 2021; 30:1521-1534. [PMID: 33993574 DOI: 10.1002/pro.4124] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/10/2021] [Accepted: 05/11/2021] [Indexed: 12/21/2022]
Abstract
Cryptochromes (CRYs) function as blue light photoreceptors in diverse physiological processes in nearly all kingdoms of life. Over the past several decades, they have emerged as the most likely candidates for light-dependent magnetoreception in animals, however, a long history of conflicts between in vitro photochemistry and in vivo behavioral data complicate validation of CRYs as a magnetosensor. In this review, we highlight the origins of conflicts regarding CRY photochemistry and signal transduction, and identify recent data that provides clarity on potential mechanisms of signal transduction in magnetoreception. The review primarily focuses on examining differences in photochemistry and signal transduction in plant and animal CRYs, and identifies potential modes of convergent evolution within these independent lineages that may identify conserved signaling pathways.
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Affiliation(s)
- Nischal Karki
- Department of Chemistry, Southern Methodist University, Dallas, Texas, USA
| | - Satyam Vergish
- Department of Chemistry, Southern Methodist University, Dallas, Texas, USA
| | - Brian D Zoltowski
- Department of Chemistry, Southern Methodist University, Dallas, Texas, USA
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37
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Battaglin F, Chan P, Pan Y, Soni S, Qu M, Spiller ER, Castanon S, Roussos Torres ET, Mumenthaler SM, Kay SA, Lenz HJ. Clocking cancer: the circadian clock as a target in cancer therapy. Oncogene 2021; 40:3187-3200. [PMID: 33846572 PMCID: PMC8549632 DOI: 10.1038/s41388-021-01778-6] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/24/2021] [Accepted: 03/29/2021] [Indexed: 02/08/2023]
Abstract
Disruption of the cellular pathway modulating endogenous 24-h rhythms, referred to as "the circadian clock", has been recently proven to be associated with cancer risk, development, and progression. This pathway operates through a complex network of transcription-translation feedback loops generated by a set of interplaying proteins. The expression of core circadian clock genes is frequently dysregulated in human tumors; however, the specific effects and underlying mechanisms seem to vary depending on the cancer types and are not fully understood. In addition, specific oncogenes may differentially induce the dysregulation of the circadian clock in tumors. Pharmacological modulation of clock components has been shown to result in specific lethality in certain types of cancer cells, and thus holds great promise as a novel anti-cancer therapeutic approach. Here we present an overview of the rationale and current evidence for targeting the clock in cancer treatment.
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Affiliation(s)
- Francesca Battaglin
- Division of Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Priscilla Chan
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Yuanzhong Pan
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Shivani Soni
- Division of Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Meng Qu
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Erin R Spiller
- Lawrence J. Ellison Institute for Transformative Medicine, University of Southern California, Los Angeles, CA, USA
| | - Sofi Castanon
- Division of Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Evanthia T Roussos Torres
- Division of Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Shannon M Mumenthaler
- Division of Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Lawrence J. Ellison Institute for Transformative Medicine, University of Southern California, Los Angeles, CA, USA
| | - Steve A Kay
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Heinz-Josef Lenz
- Division of Oncology, Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.
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38
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Ribeiro RFN, Cavadas C, Silva MMC. Small-molecule modulators of the circadian clock: Pharmacological potentials in circadian-related diseases. Drug Discov Today 2021; 26:1620-1641. [PMID: 33781946 DOI: 10.1016/j.drudis.2021.03.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 02/20/2021] [Accepted: 03/16/2021] [Indexed: 12/29/2022]
Abstract
Disruption of circadian oscillations has a wide-ranging impact on health, with the potential to induce the development of clock-related diseases. Small-molecule modulators of the circadian clock (SMMCC) target core or noncore clock proteins, modulating physiological effects as a consequence of agonist, inverse agonist, or antagonist interference. These pharmacological modulators are usually identified using chemical screening of large libraries of active compounds. However, target-based screens, chemical optimization, and circadian crystallography have recently assisted in the identification of these compounds. In this review, we focus on established and novel SMMCCs targeting both core and noncore clock proteins, identifying their circadian targets, detailed circadian effects, and specific physiological effects. In addition, we discuss their therapeutic potential for the treatment of diverse clock-related disorders (such as metabolic-associated disorders, autoimmune diseases, mood disorders, and cancer) and as chronotherapeutics. Future perspectives are also considered, such as clinical trials, and potential safety hazards, including those in the absence of clinical trials.
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Affiliation(s)
- Rodrigo F N Ribeiro
- Centre for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal; Centre for Innovation in Biomedicine and Biotechnology (CIBB), University of Coimbra, Portugal; Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
| | - Cláudia Cavadas
- Centre for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal; Centre for Innovation in Biomedicine and Biotechnology (CIBB), University of Coimbra, Portugal; Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal.
| | - Maria Manuel C Silva
- Centre for Neuroscience and Cell Biology (CNC), University of Coimbra, Coimbra, Portugal; Centre for Innovation in Biomedicine and Biotechnology (CIBB), University of Coimbra, Portugal; Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal.
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39
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Crane BR. Winding Down: Selectively Drugging a Promiscuous Pocket in Cryptochrome Slows Circadian Rhythms. Cell Chem Biol 2021; 27:1109-1111. [PMID: 32946755 DOI: 10.1016/j.chembiol.2020.08.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Mammalian cryptochromes regulate sleep and metabolism as components of the circadian clock. In this issue of Cell Chemical Biology, Miller et al. (2020a) use phenotypic chemical screens to identify selective modulators of two cryptochrome isoforms. Binding specificity depends on conformational patterning of the ligand-binding pocket and a disordered C-terminal domain.
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Affiliation(s)
- Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14850 USA.
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40
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Chandrasekaran S, Schneps CM, Dunleavy R, Lin C, DeOliveira CC, Ganguly A, Crane BR. Tuning flavin environment to detect and control light-induced conformational switching in Drosophila cryptochrome. Commun Biol 2021; 4:249. [PMID: 33637846 PMCID: PMC7910608 DOI: 10.1038/s42003-021-01766-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 01/22/2021] [Indexed: 12/12/2022] Open
Abstract
Light-induction of an anionic semiquinone (SQ) flavin radical in Drosophila cryptochrome (dCRY) alters the dCRY conformation to promote binding and degradation of the circadian clock protein Timeless (TIM). Specific peptide ligation with sortase A attaches a nitroxide spin-probe to the dCRY C-terminal tail (CTT) while avoiding deleterious side reactions. Pulse dipolar electron-spin resonance spectroscopy from the CTT nitroxide to the SQ shows that flavin photoreduction shifts the CTT ~1 nm and increases its motion, without causing full displacement from the protein. dCRY engineered to form the neutral SQ serves as a dark-state proxy to reveal that the CTT remains docked when the flavin ring is reduced but uncharged. Substitutions of flavin-proximal His378 promote CTT undocking in the dark or diminish undocking in the light, consistent with molecular dynamics simulations and TIM degradation activity. The His378 variants inform on recognition motifs for dCRY cellular turnover and strategies for developing optogenetic tools. Chandrasekaran et al. engineered the Drosophila circadian clock protein Cryptochrome (dCRY) to form the neutral semiquinone, which serves as a dark-state proxy. They find that the C-terminal tail of dCRY remains docked when the flavin ring is reduced but uncharged. dCRY His378 variants provide insights into the recognition motifs for dCRY turnover and strategies for optogenetic tools.
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Affiliation(s)
| | - Connor M Schneps
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Robert Dunleavy
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | - Changfan Lin
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA
| | | | - Abir Ganguly
- Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ, USA
| | - Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, USA.
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41
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Ruan W, Yuan X, Eltzschig HK. Circadian rhythm as a therapeutic target. Nat Rev Drug Discov 2021; 20:287-307. [PMID: 33589815 DOI: 10.1038/s41573-020-00109-w] [Citation(s) in RCA: 178] [Impact Index Per Article: 59.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/09/2020] [Indexed: 12/20/2022]
Abstract
The circadian clock evolved in diverse organisms to integrate external environmental changes and internal physiology. The clock endows the host with temporal precision and robust adaptation to the surrounding environment. When circadian rhythms are perturbed or misaligned, as a result of jet lag, shiftwork or other lifestyle factors, adverse health consequences arise, and the risks of diseases such as cancer, cardiovascular diseases or metabolic disorders increase. Although the negative impact of circadian rhythm disruption is now well established, it remains underappreciated how to take advantage of biological timing, or correct it, for health benefits. In this Review, we provide an updated account of the circadian system and highlight several key disease areas with altered circadian signalling. We discuss environmental and lifestyle modifications of circadian rhythm and clock-based therapeutic strategies, including chronotherapy, in which dosing time is deliberately optimized for maximum therapeutic index, and pharmacological agents that target core clock components and proximal regulators. Promising progress in research, disease models and clinical applications should encourage a concerted effort towards a new era of circadian medicine.
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Affiliation(s)
- Wei Ruan
- Department of Anesthesiology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA.,Department of Anesthesiology, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Xiaoyi Yuan
- Department of Anesthesiology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Holger K Eltzschig
- Department of Anesthesiology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA.
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42
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Kolarski D, Miller S, Oshima T, Nagai Y, Aoki Y, Kobauri P, Srivastava A, Sugiyama A, Amaike K, Sato A, Tama F, Szymanski W, Feringa BL, Itami K, Hirota T. Photopharmacological Manipulation of Mammalian CRY1 for Regulation of the Circadian Clock. J Am Chem Soc 2021; 143:2078-2087. [PMID: 33464888 PMCID: PMC7863067 DOI: 10.1021/jacs.0c12280] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
CRY1
and CRY2 proteins are highly conserved components of the circadian
clock that controls daily physiological rhythms. Disruption of CRY
functions are related to many diseases, including circadian sleep
phase disorder. Development of isoform-selective and spatiotemporally
controllable tools will facilitate the understanding of shared and
distinct functions of CRY1 and CRY2. Here, we developed CRY1-selective
compounds that enable light-dependent manipulation of the circadian
clock. From phenotypic chemical screening in human cells, we identified
benzophenone derivatives that lengthened the circadian period. These
compounds selectively interacted with the CRY1 photolyase homology
region, resulting in activation of CRY1 but not CRY2. The benzophenone
moiety rearranged a CRY1 region called the “lid loop”
located outside of the compound-binding pocket and formed a unique
interaction with Phe409 in the lid loop. Manipulation of this key
interaction was achieved by rationally designed replacement of the
benzophenone with a switchable azobenzene moiety whose cis–trans isomerization can be controlled by light. The metastable cis form exhibited sufficiently high half-life in aqueous
solutions and structurally mimicked the benzophenone unit, enabling
reversible period regulation over days by cellular irradiation with
visible light. This study revealed an unprecedented role of the lid
loop in CRY-compound interaction and paves the way for spatiotemporal
regulation of CRY1 activity by photopharmacology for molecular understanding
of CRY1-dependent functions in health and disease.
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Affiliation(s)
- Dušan Kolarski
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Simon Miller
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
| | - Tsuyoshi Oshima
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan.,Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Yoshiko Nagai
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
| | - Yugo Aoki
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan.,Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Piermichele Kobauri
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Ashutosh Srivastava
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
| | - Akiko Sugiyama
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
| | - Kazuma Amaike
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan.,Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Ayato Sato
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
| | - Florence Tama
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan.,Department of Physics, Graduate School of Science, Nagoya University, Nagoya 464-8601, Japan.,Computational Structural Biology Unit, RIKEN-Center for Computational Science, Hyogo 650-0047, Japan
| | - Wiktor Szymanski
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Groningen 9747 AG, The Netherlands.,Department of Radiology, Medical Imaging Center, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Ben L Feringa
- Centre for Systems Chemistry, Stratingh Institute for Chemistry, University of Groningen, Groningen 9747 AG, The Netherlands
| | - Kenichiro Itami
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan.,Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya 464-8602, Japan
| | - Tsuyoshi Hirota
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
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43
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Kolarski D, Sugiyama A, Rodat T, Schulte A, Peifer C, Itami K, Hirota T, Feringa BL, Szymanski W. Reductive stability evaluation of 6-azopurine photoswitches for the regulation of CKIα activity and circadian rhythms. Org Biomol Chem 2021; 19:2312-2321. [DOI: 10.1039/d1ob00014d] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
6-Azopurines were evaluated for their reductive stability, and the ability to modulate CKIα activity and cellular circadian rhythms, revealing key challenges for long-term activity modulation utilizing chronophotopharmacology.
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Affiliation(s)
- Dušan Kolarski
- Stratingh Institute for Chemistry
- University of Groningen
- Groningen
- The Netherlands
| | - Akiko Sugiyama
- Institute of Transformative Bio-Molecules (WPI-ITbM)
- Nagoya University
- Nagoya 464-8601
- Japan
| | - Theo Rodat
- Department of Pharmaceutical and Medicinal Chemistry
- Christian-Albrechts-University of Kiel
- 24118 Kiel
- Germany
| | - Albert Schulte
- Stratingh Institute for Chemistry
- University of Groningen
- Groningen
- The Netherlands
| | - Christian Peifer
- Department of Pharmaceutical and Medicinal Chemistry
- Christian-Albrechts-University of Kiel
- 24118 Kiel
- Germany
| | - Kenichiro Itami
- Institute of Transformative Bio-Molecules (WPI-ITbM)
- Nagoya University
- Nagoya 464-8601
- Japan
| | - Tsuyoshi Hirota
- Institute of Transformative Bio-Molecules (WPI-ITbM)
- Nagoya University
- Nagoya 464-8601
- Japan
| | - Ben L. Feringa
- Stratingh Institute for Chemistry
- University of Groningen
- Groningen
- The Netherlands
| | - Wiktor Szymanski
- Stratingh Institute for Chemistry
- University of Groningen
- Groningen
- The Netherlands
- Medical Imaging Center
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44
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Huang S, Jiao X, Lu D, Pei X, Qi D, Li Z. Recent advances in modulators of circadian rhythms: an update and perspective. J Enzyme Inhib Med Chem 2020; 35:1267-1286. [PMID: 32506972 PMCID: PMC7717701 DOI: 10.1080/14756366.2020.1772249] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 04/29/2020] [Accepted: 05/08/2020] [Indexed: 12/23/2022] Open
Abstract
Circadian rhythm is a universal life phenomenon that plays an important role in maintaining the multiple physiological functions and regulating the adaptability to internal and external environments of flora and fauna. Circadian alignment in humans has the greatest effect on human health, and circadian misalignment is closely associated with increased risk for metabolic syndrome, cardiovascular diseases, neurological diseases, immune diseases, cancer, sleep disorders, and ophthalmic diseases. The recent description of clock proteins and related post-modification targets was involved in several diseases, and numerous lines of evidence are emerging that small molecule modulators of circadian rhythms can be used to rectify circadian disorder. Herein, we attempt to update the disclosures about the modulators targeting core clock proteins and related post-modification targets, as well as the relationship between circadian rhythm disorders and human health as well as the therapeutic role and prospect of these small molecule modulators in circadian rhythm related disease.
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Affiliation(s)
- Shenzhen Huang
- Henan Eye Institute, Henan Eye Hospital and Henan Key Laboratory of Ophthalmology and Visual Science, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, People’s Hospital of Henan University, Zhengzhou, China
| | - Xinwei Jiao
- Henan Eye Institute, Henan Eye Hospital and Henan Key Laboratory of Ophthalmology and Visual Science, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, People’s Hospital of Henan University, Zhengzhou, China
| | - Dingli Lu
- Henan Eye Institute, Henan Eye Hospital and Henan Key Laboratory of Ophthalmology and Visual Science, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, People’s Hospital of Henan University, Zhengzhou, China
| | - Xiaoting Pei
- Henan Eye Institute, Henan Eye Hospital and Henan Key Laboratory of Ophthalmology and Visual Science, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, People’s Hospital of Henan University, Zhengzhou, China
| | - Di Qi
- Henan Eye Institute, Henan Eye Hospital and Henan Key Laboratory of Ophthalmology and Visual Science, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, People’s Hospital of Henan University, Zhengzhou, China
| | - Zhijie Li
- Henan Eye Institute, Henan Eye Hospital and Henan Key Laboratory of Ophthalmology and Visual Science, Henan Provincial People’s Hospital, People’s Hospital of Zhengzhou University, People’s Hospital of Henan University, Zhengzhou, China
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45
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The circadian machinery links metabolic disorders and depression: A review of pathways, proteins and potential pharmacological interventions. Life Sci 2020; 265:118809. [PMID: 33249097 DOI: 10.1016/j.lfs.2020.118809] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/11/2020] [Accepted: 11/18/2020] [Indexed: 12/16/2022]
Abstract
Circadian rhythms are responsible for regulating a number of physiological processes. The central oscillator is located within the suprachiasmatic nucleus (SCN) of the hypothalamus and the SCN synchronises the circadian clocks that are found in our peripheral organs through neural and humoral signalling. At the molecular level, biological clocks consist of transcription-translation feedback loops (TTFLs) and these pathways are influenced by transcription factors, post-translational modifications, signalling pathways and epigenetic modifiers. When disruptions occur in the circadian machinery, the activities of the proteins implicated in this network and the expression of core clock or clock-controlled genes (CCGs) can be altered. Circadian misalignment can also arise when there is desychronisation between our internal clocks and environmental stimuli. There is evidence in the literature demonstrating that disturbances in the circadian rhythm contribute to the pathophysiology of several diseases and disorders. This includes the metabolic syndrome and recently, it has been suggested that the 'circadian syndrome' may be a more appropriate term to use to not only describe the cardio-metabolic risk factors but also the associated comorbidities. Here we overview the molecular architecture of circadian clocks in mammals and provide insight into the effects of shift work, exposure to artificial light, food intake and stress on the circadian rhythm. The relationship between circadian rhythms, metabolic disorders and depression is reviewed and this is a topic that requires further investigation. We also describe how particular proteins involved in the TTFLs can be potentially modulated by small molecules, including pharmacological interventions and dietary compounds.
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46
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Parico GCG, Partch CL. The tail of cryptochromes: an intrinsically disordered cog within the mammalian circadian clock. Cell Commun Signal 2020; 18:182. [PMID: 33198762 PMCID: PMC7667820 DOI: 10.1186/s12964-020-00665-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 09/22/2020] [Indexed: 12/23/2022] Open
Abstract
Cryptochrome (CRY) proteins play an essential role in regulating mammalian circadian rhythms. CRY is composed of a structured N-terminal domain known as the photolyase homology region (PHR), which is tethered to an intrinsically disordered C-terminal tail. The PHR domain is a critical hub for binding other circadian clock components such as CLOCK, BMAL1, PERIOD, or the ubiquitin ligases FBXL3 and FBXL21. While the isolated PHR domain is necessary and sufficient to generate circadian rhythms, removing or modifying the cryptochrome tails modulates the amplitude and/or periodicity of circadian rhythms, suggesting that they play important regulatory roles in the molecular circadian clock. In this commentary, we will discuss how recent studies of these intrinsically disordered tails are helping to establish a general and evolutionarily conserved model for CRY function, where the function of PHR domains is modulated by reversible interactions with their intrinsically disordered tails. Video abstract
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Affiliation(s)
| | - Carrie L Partch
- Department of Chemistry and Biochemistry, UC Santa Cruz, Santa Cruz, USA. .,Center for Circadian Biology, UC San Diego, La Jolla, USA.
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47
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Parico GCG, Perez I, Fribourgh JL, Hernandez BN, Lee HW, Partch CL. The human CRY1 tail controls circadian timing by regulating its association with CLOCK:BMAL1. Proc Natl Acad Sci U S A 2020; 117:27971-27979. [PMID: 33106415 PMCID: PMC7668087 DOI: 10.1073/pnas.1920653117] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Circadian rhythms are generated by interlocked transcription-translation feedback loops that establish cell-autonomous biological timing of ∼24 h. Mutations in core clock genes that alter their stability or affinity for one another lead to changes in circadian period. The human CRY1Δ11 mutant lengthens circadian period to cause delayed sleep phase disorder (DSPD), characterized by a very late onset of sleep. CRY1 is a repressor that binds to the transcription factor CLOCK:BMAL1 to inhibit its activity and close the core feedback loop. We previously showed how the PHR (photolyase homology region) domain of CRY1 interacts with distinct sites on CLOCK and BMAL1 to sequester the transactivation domain from coactivators. However, the Δ11 variant alters an intrinsically disordered tail in CRY1 downstream of the PHR. We show here that the CRY1 tail, and in particular the region encoded by exon 11, modulates the affinity of the PHR domain for CLOCK:BMAL1. The PHR-binding epitope in exon 11 is necessary and sufficient to disrupt the interaction between CRY1 and the subunit CLOCK. Moreover, PHR-tail interactions are conserved in the paralog CRY2 and reduced when either CRY is bound to the circadian corepressor PERIOD2. Discovery of this autoregulatory role for the mammalian CRY1 tail and conservation of PHR-tail interactions in both mammalian cryptochromes highlights functional conservation with plant and insect cryptochromes, which also utilize PHR-tail interactions to reversibly control their activity.
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Affiliation(s)
- Gian Carlo G Parico
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064
| | - Ivette Perez
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064
| | - Jennifer L Fribourgh
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064
| | - Britney N Hernandez
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064
| | - Hsiau-Wei Lee
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064
| | - Carrie L Partch
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064;
- Center for Circadian Biology, University of California San Diego, La Jolla, CA 92093
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Miller S, Aikawa Y, Sugiyama A, Nagai Y, Hara A, Oshima T, Amaike K, Kay SA, Itami K, Hirota T. An Isoform-Selective Modulator of Cryptochrome 1 Regulates Circadian Rhythms in Mammals. Cell Chem Biol 2020; 27:1192-1198.e5. [PMID: 32502390 DOI: 10.1016/j.chembiol.2020.05.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 04/12/2020] [Accepted: 05/15/2020] [Indexed: 02/07/2023]
Abstract
Cryptochrome 1 (CRY1) and CRY2 are core regulators of the circadian clock, and the development of isoform-selective modulators is important for the elucidation of their redundant and distinct functions. Here, we report the identification and functional characterization of a small-molecule modulator of the mammalian circadian clock that selectively controls CRY1. Cell-based circadian chemical screening identified a thienopyrimidine derivative KL201 that lengthened the period of circadian rhythms in cells and tissues. Functional assays revealed stabilization of CRY1 but not CRY2 by KL201. A structure-activity relationship study of KL201 derivatives in combination with X-ray crystallography of the CRY1-KL201 complex uncovered critical sites and interactions required for CRY1 regulation. KL201 bound to CRY1 in overlap with FBXL3, a subunit of ubiquitin ligase complex, and the effect of KL201 was blunted by knockdown of FBXL3. KL201 will facilitate isoform-selective regulation of CRY1 to accelerate chronobiology research and therapeutics against clock-related diseases.
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Affiliation(s)
- Simon Miller
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
| | - Yoshiki Aikawa
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
| | - Akiko Sugiyama
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
| | - Yoshiko Nagai
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
| | - Aya Hara
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan
| | - Tsuyoshi Oshima
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan; Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya 464-8601, Japan
| | - Kazuma Amaike
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan; Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya 464-8601, Japan
| | - Steve A Kay
- Department of Neurology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Kenichiro Itami
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan; Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya 464-8601, Japan
| | - Tsuyoshi Hirota
- Institute of Transformative Bio-Molecules, Nagoya University, Nagoya 464-8601, Japan.
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49
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Amaike K, Oshima T, Skoulding NS, Toyama Y, Hirota T, Itami K. Small Molecules Modulating Mammalian Biological Clocks: Exciting New Opportunities for Synthetic Chemistry. Chem 2020. [DOI: 10.1016/j.chempr.2020.08.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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50
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