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Purushothaman K, Sivasankar E, Krishnamoorthy M, Karunakaran K, Muniyan R. Computational identification of potential tau tubulin kinase 1 (TTBK1) inhibitors: a structural analog approach. In Silico Pharmacol 2024; 12:66. [PMID: 39050776 PMCID: PMC11264489 DOI: 10.1007/s40203-024-00242-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 07/14/2024] [Indexed: 07/27/2024] Open
Abstract
Abnormal deposition or aggregation of protein alpha-synuclein and tau in the brain leads to neurodegenerative disorders. Excessive hyperphosphorylation of tau protein and aggregations destroys the microtubule structure resulting in neurofibrillary tangles in neurons and affecting cytoskeleton structure, mitochondrial axonal transport, and loss of synapses in neuronal cells. Tau tubulin kinase 1 (TTBK1), a specific neuronal kinase is a potential therapeutic target for neurodegenerative disorders as it is involved in hyperphosphorylation and aggregation of tau protein. TTBK inhibitors are now the subject of intense study, but limited numbers are found. Hence, this study involves structure-based virtual screening of TTBK1 inhibitor analogs to obtain efficient compounds targeting the TTBK1 using docking, molecular dynamics simulation and protein-ligand interaction profile. The initial analogs set containing 3884 compounds was subjected to Lipinski rule and the non-violated compounds were selected. Docking analysis was done on 2772 compounds through Autodock vina and Autodock 4.2. Data Warrior and SwissADME was utilized to filter the toxic compounds. The stability and protein-ligand interaction of the docked complex was analyzed through Gromacs and VMD. Molecular simulation results such as RMSD, Rg, and hydrogen bond interaction along with pharmacokinetic properties showed CID70794974 as the potential hit targeting TTBKl prompting the need for further experimental investigation to evaluate their potential therapeutic efficacy in Alzheimer's disease. Graphical Abstract Supplementary Information The online version contains supplementary material available at 10.1007/s40203-024-00242-z.
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Affiliation(s)
- Kaathambari Purushothaman
- School of BioSciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014 India
| | - Esaimozhi Sivasankar
- School of BioSciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014 India
| | - Monika Krishnamoorthy
- School of BioSciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014 India
| | - Keerthana Karunakaran
- School of BioSciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014 India
| | - Rajiniraja Muniyan
- School of BioSciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014 India
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2
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Ahamad S, Junaid IT, Gupta D. Computational Design of Novel Tau-Tubulin Kinase 1 Inhibitors for Neurodegenerative Diseases. Pharmaceuticals (Basel) 2024; 17:952. [PMID: 39065802 PMCID: PMC11280166 DOI: 10.3390/ph17070952] [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: 05/20/2024] [Revised: 06/14/2024] [Accepted: 06/20/2024] [Indexed: 07/28/2024] Open
Abstract
The tau-tubulin kinase 1 (TTBK1) protein is a casein kinase 1 superfamily member located at chromosome 6p21.1. It is expressed explicitly in the brain, particularly in the cytoplasm of cortical and hippocampal neurons. TTBK1 has been implicated in the phosphorylation and aggregation of tau in Alzheimer's disease (AD). Considering its significance in AD, TTBK1 has emerged as a promising target for AD treatment. In the present study, we identified novel TTBK1 inhibitors using various computational techniques. We performed a virtual screening-based docking study followed by E-pharmacophore modeling, cavity-based pharmacophore, and ligand design techniques and found ZINC000095101333, LD7, LD55, and LD75 to be potential novel TTBK1 lead inhibitors. The docking results were complemented by Molecular Mechanics/Generalized Born Surface Area (MMGBSA) calculations. The molecular dynamics (MD) simulation studies at a 500 ns scale were carried out to monitor the behavior of the protein toward the identified ligands. Pharmacological and ADME/T studies were carried out to check the drug-likeness of the compounds. In summary, we identified a new series of compounds that could effectively bind the TTBK1 receptor. The newly designed compounds are promising candidates for developing therapeutics targeting TTBK1 for AD.
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Affiliation(s)
- Shahzaib Ahamad
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Iqbal Taliy Junaid
- Malaria Biology, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India;
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
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3
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Wei Y, Zhong S, Yang H, Wang X, Lv B, Bian Y, Pei Y, Xu C, Zhao Q, Wu Y, Luo D, Wang F, Sun H, Chen Y. Current therapy in amyotrophic lateral sclerosis (ALS): A review on past and future therapeutic strategies. Eur J Med Chem 2024; 272:116496. [PMID: 38759454 DOI: 10.1016/j.ejmech.2024.116496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 05/11/2024] [Accepted: 05/11/2024] [Indexed: 05/19/2024]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease that affects the first and second motoneurons (MNs), associated with muscle weakness, paralysis and finally death. The exact etiology of the disease still remains unclear. Currently, efforts to develop novel ALS treatments which target specific pathomechanisms are being studied. The mechanisms of ALS pathogenesis involve multiple factors, such as protein aggregation, glutamate excitotoxicity, oxidative stress, mitochondrial dysfunction, apoptosis, inflammation etc. Unfortunately, to date, there are only two FDA-approved drugs for ALS, riluzole and edavarone, without curative treatment for ALS. Herein, we give an overview of the many pathways and review the recent discovery and preclinical characterization of neuroprotective compounds. Meanwhile, drug combination and other therapeutic approaches are also reviewed. In the last part, we analyze the reasons of clinical failure and propose perspective on the treatment of ALS in the future.
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Affiliation(s)
- Yuqing Wei
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Sheng Zhong
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Huajing Yang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Xueqing Wang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Bingbing Lv
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yaoyao Bian
- Jiangsu Provincial Engineering Center of TCM External Medication Researching and Industrializing, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yuqiong Pei
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Chunlei Xu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Qun Zhao
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Yulan Wu
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Daying Luo
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Fan Wang
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Haopeng Sun
- School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
| | - Yao Chen
- School of Pharmacy, Nanjing University of Chinese Medicine, Nanjing, 210023, China.
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4
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Flax RG, Rosston P, Rocha C, Anderson B, Capener JL, Durcan TM, Drewry DH, Prinos P, Axtman AD. Illumination of understudied ciliary kinases. Front Mol Biosci 2024; 11:1352781. [PMID: 38523660 PMCID: PMC10958382 DOI: 10.3389/fmolb.2024.1352781] [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: 12/08/2023] [Accepted: 01/29/2024] [Indexed: 03/26/2024] Open
Abstract
Cilia are cellular signaling hubs. Given that human kinases are central regulators of signaling, it is not surprising that kinases are key players in cilia biology. In fact, many kinases modulate ciliogenesis, which is the generation of cilia, and distinct ciliary pathways. Several of these kinases are understudied with few publications dedicated to the interrogation of their function. Recent efforts to develop chemical probes for members of the cyclin-dependent kinase like (CDKL), never in mitosis gene A (NIMA) related kinase (NEK), and tau tubulin kinase (TTBK) families either have delivered or are working toward delivery of high-quality chemical tools to characterize the roles that specific kinases play in ciliary processes. A better understanding of ciliary kinases may shed light on whether modulation of these targets will slow or halt disease onset or progression. For example, both understudied human kinases and some that are more well-studied play important ciliary roles in neurons and have been implicated in neurodevelopmental, neurodegenerative, and other neurological diseases. Similarly, subsets of human ciliary kinases are associated with cancer and oncological pathways. Finally, a group of genetic disorders characterized by defects in cilia called ciliopathies have associated gene mutations that impact kinase activity and function. This review highlights both progress related to the understanding of ciliary kinases as well as in chemical inhibitor development for a subset of these kinases. We emphasize known roles of ciliary kinases in diseases of the brain and malignancies and focus on a subset of poorly characterized kinases that regulate ciliary biology.
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Affiliation(s)
- Raymond G. Flax
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Peter Rosston
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Cecilia Rocha
- The Neuro’s Early Drug Discovery Unit (EDDU), McGill University, Montreal, QC, Canada
| | - Brian Anderson
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Jacob L. Capener
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Thomas M. Durcan
- The Neuro’s Early Drug Discovery Unit (EDDU), McGill University, Montreal, QC, Canada
| | - David H. Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
- UNC Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Panagiotis Prinos
- Structural Genomics Consortium, University of Toronto, Toronto, ON, Canada
| | - Alison D. Axtman
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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Wang J, Lin Y, Xu X, Wang Y, Xie Q. Identification of tau-tubulin kinase 1 inhibitors by microfluidics-based mobility shift assay from a kinase inhibitor library. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2023; 28:385-393. [PMID: 37399991 DOI: 10.1016/j.slasd.2023.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/22/2023] [Accepted: 06/27/2023] [Indexed: 07/05/2023]
Abstract
Tau tubulin kinase 1 (TTBK1) is a serine/threonine/tyrosine kinase that phosphorylates multiple residues in tau protein. Hyperphosphorylated tau is the main cause of tauopathy, such as Alzheimer's disease (AD). Therefore, preventing tau phosphorylation by inhibiting TTBK1 has been proposed as a therapeutic strategy for AD. However, few substrates of TTBK1 are reported for a biochemical assay and few inhibitors targeting TTBK1 have been reported so far. In this study, we identified a fluorescein amidite (FAM)-labeled peptide 15 from a small peptide library as the optimal peptide substrate for human TTBK1 (hTTBK1). We then developed and validated a microfluidics-based mobility shift assay (MMSA) with peptide 15. We further confirmed that peptide 15 could also be used in the ADP-Glo kinase assay. The established MMSA was applied for screening of a 427-compound kinase inhibitor library, yielding five compounds with IC50s of several micro molars against hTTBK1. Among them, three compounds, AZD5363, A-674,563 and GSK690693 inhibited hTTBK1 in an ATP competitive manner and molecular docking simulations revealed that they enter the ATP pocket and form one or two hydrogen bonds to the hinge region with hTTBK1. Another hit compound, piceatannol, showed non-ATP competitive inhibitory effect on hTTBK1 and may serve as a starting point to develop highly selective hTTBK1 inhibitors. Altogether, this study provided a new in vitro platform for the development of novel hTTBK1 inhibitors that might have potential applications in AD prevention.
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Affiliation(s)
- Jinlei Wang
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, PR China; Shanghai ChemPartner Co. Ltd., 2727/2728 Jinke Road, Shanghai 201203, PR China
| | - Ying Lin
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, PR China
| | - Xiaoyu Xu
- Shanghai ChemPartner Co. Ltd., 2727/2728 Jinke Road, Shanghai 201203, PR China
| | - Yonghui Wang
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, PR China.
| | - Qiong Xie
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, PR China.
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6
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Yukawa K, Yamamoto-Mcguire S, Cafaro L, Hong C, Kamme F, Ikezu T, Ikezu S. Antisense oligonucleotide-based targeting of Tau-tubulin kinase 1 prevents hippocampal accumulation of phosphorylated tau in PS19 tauopathy mice. Acta Neuropathol Commun 2023; 11:166. [PMID: 37853497 PMCID: PMC10585748 DOI: 10.1186/s40478-023-01661-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 09/29/2023] [Indexed: 10/20/2023] Open
Abstract
Tau tubulin kinase-1 (TTBK1), a neuron-specific tau kinase, is highly expressed in the entorhinal cortex and hippocampal regions, where early tau pathology evolves in Alzheimer's disease (AD). The protein expression level of TTBK1 is elevated in the cortex brain tissues with AD patients compared to the control subjects. We therefore hypothesized that antisense oligonucleotide (ASO) based targeting Ttbk1 could prevent the accumulation of phosphorylated tau, thereby delaying the development of tau pathology in AD. Here we show that in vivo administration of ASO targeting mouse Ttbk1 (ASO-Ttbk1) specifically suppressed the expression of Ttbk1 without affecting Ttbk2 expression in the temporal cortex of PS19 tau transgenic mice. Central administration of ASO-Ttbk1 in PS19 mice significantly reduced the expression level of representative phosphor-tau epitopes relevant to AD at 8 weeks post-dose, including pT231, pT181, and pS396 in the sarkosyl soluble and insoluble fractions isolated from hippocampal tissues as determined by ELISA and pS422 in soluble fractions as determined by western blotting. Immunofluorescence demonstrated that ASO-Ttbk1 significantly reduced pS422 phosphorylated tau intensity in mossy fibers region of the dentate gyrus in PS19 mice. RNA-sequence analysis of the temporal cortex tissue revealed significant enrichment of interferon-gamma and complement pathways and increased expression of antigen presenting molecules (Cd86, Cd74, and H2-Aa) in PS19 mice treated with ASO-Ttbk1, suggesting its potential effect on microglial phenotype although neurotoxic effect was absent. These data suggest that TTBK1 is an attractive therapeutic target to suppress TTBK1 without compromising TTBK2 expression and pathological tau phosphorylation in the early stages of AD.
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Affiliation(s)
- Kayo Yukawa
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Satomi Yamamoto-Mcguire
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Louis Cafaro
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, 02118, USA
| | | | | | - Tsuneya Ikezu
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, 02118, USA.
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, 32224, USA.
- Regenerative Science Graduate Program, Mayo Clinic Graduate School of Biomedical Sciences, Rochester, MN, 55905, USA.
- Mayo Clinic Alzheimer's Disease Research Center, Rochester, MN, 55905, USA.
- Robert and Arlene Kogod Center on Aging, Mayo Clinic, Rochester, MN, 55905, USA.
| | - Seiko Ikezu
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine, Boston, MA, 02118, USA.
- Department of Neuroscience, Mayo Clinic Florida, Jacksonville, FL, 32224, USA.
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7
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Bashore FM, Marquez AB, Chaikuad A, Howell S, Dunn AS, Beltran AA, Smith JL, Drewry DH, Beltran AS, Axtman AD. Modulation of tau tubulin kinases (TTBK1 and TTBK2) impacts ciliogenesis. Sci Rep 2023; 13:6118. [PMID: 37059819 PMCID: PMC10104807 DOI: 10.1038/s41598-023-32854-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 04/03/2023] [Indexed: 04/16/2023] Open
Abstract
Tau tubulin kinase 1 and 2 (TTBK1/2) are highly homologous kinases that are expressed and mediate disease-relevant pathways predominantly in the brain. Distinct roles for TTBK1 and TTBK2 have been delineated. While efforts have been devoted to characterizing the impact of TTBK1 inhibition in diseases like Alzheimer's disease and amyotrophic lateral sclerosis, TTBK2 inhibition has been less explored. TTBK2 serves a critical function during cilia assembly. Given the biological importance of these kinases, we designed a targeted library from which we identified several chemical tools that engage TTBK1 and TTBK2 in cells and inhibit their downstream signaling. Indolyl pyrimidinamine 10 significantly reduced the expression of primary cilia on the surface of human induced pluripotent stem cells (iPSCs). Furthermore, analog 10 phenocopies TTBK2 knockout in iPSCs, confirming a role for TTBK2 in ciliogenesis.
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Affiliation(s)
- Frances M Bashore
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Ariana B Marquez
- Human Pluripotent Cell Core, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Apirat Chaikuad
- Institute of Pharmaceutical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
- Structural Genomics Consortium, Buchmann Institute for Life Sciences, Goethe University Frankfurt, Max-von-Laue-Strabe 15, 60438, Frankfurt, Germany
| | - Stefanie Howell
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Andrea S Dunn
- Department of Computer Science, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Alvaro A Beltran
- Human Pluripotent Cell Core, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Jeffery L Smith
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - David H Drewry
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- UNC Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Adriana S Beltran
- Human Pluripotent Cell Core, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA
| | - Alison D Axtman
- Structural Genomics Consortium, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599, USA.
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8
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Baier A, Szyszka R. CK2 and protein kinases of the CK1 superfamily as targets for neurodegenerative disorders. Front Mol Biosci 2022; 9:916063. [PMID: 36275622 PMCID: PMC9582958 DOI: 10.3389/fmolb.2022.916063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 08/02/2022] [Indexed: 11/13/2022] Open
Abstract
Casein kinases are involved in a variety of signaling pathways, and also in inflammation, cancer, and neurological diseases. Therefore, they are regarded as potential therapeutic targets for drug design. Recent studies have highlighted the importance of the casein kinase 1 superfamily as well as protein kinase CK2 in the development of several neurodegenerative pathologies, such as Alzheimer's disease, Parkinson's disease, Huntington's disease, and amyotrophic lateral sclerosis. CK1 kinases and their closely related tau tubulin kinases as well as CK2 are found to be overexpressed in the mammalian brain. Numerous substrates have been detected which play crucial roles in neuronal and synaptic network functions and activities. The development of new substances for the treatment of these pathologies is in high demand. The impact of these kinases in the progress of neurodegenerative disorders, their bona fide substrates, and numerous natural and synthetic compounds which are able to inhibit CK1, TTBK, and CK2 are discussed in this review.
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Affiliation(s)
- Andrea Baier
- Institute of Biological Sciences, The John Paul II Catholic University of Lublin, Lublin, Poland
| | - Ryszard Szyszka
- Institute of Biological Sciences, The John Paul II Catholic University of Lublin, Lublin, Poland
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9
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TDP-43 Modulation by Tau-Tubulin Kinase 1 Inhibitors: A New Avenue for Future Amyotrophic Lateral Sclerosis Therapy. J Med Chem 2022; 65:1585-1607. [PMID: 34978799 DOI: 10.1021/acs.jmedchem.1c01942] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease without any effective treatment. Protein TDP-43 is a pathological hallmark of ALS in both sporadic and familiar patients. Post-translational modifications of TDP-43 promote its aggregation in the cytoplasm. Tau-Tubulin kinase (TTBK1) phosphorylates TDP-43 in cellular and animal models; thus, TTBK1 inhibitors emerge as a promising therapeutic strategy for ALS. The design, synthesis, biological evaluation, kinase-ligand complex structure determination, and molecular modeling studies confirmed novel pyrrolopyrimidine derivatives as valuable inhibitors for further development. Moreover, compound 29 revealed good brain penetration in vivo and was able to reduce TDP-43 phosphorylation not only in cell cultures but also in the spinal cord of transgenic TDP-43 mice. A shift to M2 anti-inflammatory microglia was also demonstrated in vivo. Both these activities led to motor neuron preservation in mice, proposing pyrrolopyrimidine 29 as a valuable lead compound for future ALS therapy.
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10
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Ahamad S, Hema K, Kumar V, Gupta D. The structural, functional, and dynamic effect of Tau tubulin kinase1 upon a mutation: A neuro-degenerative hotspot. J Cell Biochem 2021; 122:1653-1664. [PMID: 34297427 DOI: 10.1002/jcb.30112] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 07/03/2021] [Accepted: 07/07/2021] [Indexed: 12/27/2022]
Abstract
Alzheimer's disease (AD) is a progressive disorder that causes brain cells to degenerate and die. AD is one of the common causes of dementia that leads to a decline in thinking, behavioral and social skills that disrupts a person's ability to function independently. Tau-tubulin kinase1 (TTBK1) is a crucial disease regulating AD protein, which is majorly responsible for the phosphorylation and accumulation of tau protein at specific Serine/Threonine residues found in paired helical filaments, suggesting its role in tauopathy. TTBK1 involvement in many diseases and the restricted expression of TTBK1 to the central nervous system (CNS) makes TTBK1 an attractive therapeutic target for tauopathies. The genetic variations in TTBK1 are primarily involved in the TTBK1 pathogenesis. This study highlighted the destabilizing, damaging and deleterious effect of the mutation R142Q on TTBK1 structure through computational predictions and molecular dynamics simulations. The protein deviation, fluctuations, conformational dynamics, solvent accessibility, hydrogen bonding, and the residue-residue mapping confirmed the mutant effect to cause structural aberrations, suggesting overall destabilization due to the protein mutation. The presence of well-defined free energy minima was observed in TTBK1-wild type, as opposed to that in the R142Q mutant, reflecting structural deterioration. The overall findings from the study reveal that the presence of R142Q mutation on TTBK1 is responsible for the structural instability, leading to disruption of its biological functions. The mutation could be used as future diagnostic markers in treating AD.
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Affiliation(s)
- Shahzaib Ahamad
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Kanipakam Hema
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Vijay Kumar
- Amity Institute of Neuropsychology & Neurosciences, Amity University, Noida, Uttar Pradesh, India
| | - Dinesh Gupta
- Translational Bioinformatics Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
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11
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Halkina T, Henderson JL, Lin EY, Himmelbauer MK, Jones JH, Nevalainen M, Feng J, King K, Rooney M, Johnson JL, Marcotte DJ, Chodaparambil JV, Kumar PR, Patterson TA, Murugan P, Schuman E, Wong L, Hesson T, Lamore S, Bao C, Calhoun M, Certo H, Amaral B, Dillon GM, Gilfillan R, de Turiso FGL. Discovery of Potent and Brain-Penetrant Tau Tubulin Kinase 1 (TTBK1) Inhibitors that Lower Tau Phosphorylation In Vivo. J Med Chem 2021; 64:6358-6380. [PMID: 33944571 DOI: 10.1021/acs.jmedchem.1c00382] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Structural analysis of the known NIK inhibitor 3 bound to the kinase domain of TTBK1 led to the design and synthesis of a novel class of azaindazole TTBK1 inhibitors exemplified by 8 (cell IC50: 571 nM). Systematic optimization of this series of analogs led to the discovery of 31, a potent (cell IC50: 315 nM) and selective TTBK inhibitor with suitable CNS penetration (rat Kp,uu: 0.32) for in vivo proof of pharmacology studies. The ability of 31 to inhibit tau phosphorylation at the disease-relevant Ser 422 epitope was demonstrated in both a mouse hypothermia and a rat developmental model and provided evidence that modulation of this target may be relevant in the treatment of Alzheimer's disease and other tauopathies.
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Affiliation(s)
- Tamara Halkina
- Department of Medicinal Chemistry, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Jaclyn L Henderson
- Department of Medicinal Chemistry, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Edward Y Lin
- Department of Medicinal Chemistry, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Martin K Himmelbauer
- Department of Medicinal Chemistry, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - J Howard Jones
- Department of Medicinal Chemistry, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Marta Nevalainen
- Department of Medicinal Chemistry, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Jun Feng
- Department of Medicinal Chemistry, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Kristopher King
- Department of Drug Metabolism and Pharmacokinetics, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Michael Rooney
- Department of Drug Metabolism and Pharmacokinetics, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Joshua L Johnson
- Department of Drug Metabolism and Pharmacokinetics, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Douglas J Marcotte
- Department of Physical Biochemistry and Molecular Design, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Jayanth V Chodaparambil
- Department of Physical Biochemistry and Molecular Design, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - P Rajesh Kumar
- Department of Physical Biochemistry and Molecular Design, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Thomas A Patterson
- Department of Physical Biochemistry and Molecular Design, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Paramasivam Murugan
- Department of Bioassays, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Eli Schuman
- Department of Bioassays, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - LaiYee Wong
- Department of Bioassays, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Thomas Hesson
- Department of Bioassays, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Sarah Lamore
- Department of Preclinical Safety, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Channa Bao
- Department of Emerging Neurosciences Research Unit, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Michael Calhoun
- Department of Emerging Neurosciences Research Unit, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Hannah Certo
- Department of Emerging Neurosciences Research Unit, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Brenda Amaral
- Department of Emerging Neurosciences Research Unit, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Gregory M Dillon
- Department of Emerging Neurosciences Research Unit, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
| | - Rab Gilfillan
- Department of Medicinal Chemistry, Biogen, 225 Binney Street, Cambridge, Massachusetts 02142, United States
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12
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Bao C, Bajrami B, Marcotte DJ, Chodaparambil JV, Kerns HM, Henderson J, Wei R, Gao B, Dillon GM. Mechanisms of Regulation and Diverse Activities of Tau-Tubulin Kinase (TTBK) Isoforms. Cell Mol Neurobiol 2021; 41:669-685. [PMID: 32424773 DOI: 10.1007/s10571-020-00875-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 05/11/2020] [Indexed: 10/24/2022]
Abstract
Tau-tubulin kinase 1 (TTBK1) is a CNS-specific, kinase that has been implicated in the pathological phosphorylation of tau in Alzheimer's Disease (AD) and Frontotemporal Dementia (FTD). TTBK1 is a challenging therapeutic target because it shares a highly conserved catalytic domain with its homolog, TTBK2, a ubiquitously expressed kinase genetically linked to the disease spinocerebellar ataxia type 11. The present study attempts to elucidate the functional distinctions between the TTBK isoforms and increase our understanding of them as distinct targets for the treatment of neurodegenerative disease. We demonstrate that in cortical neurons, TTBK1, not TTBK2, is the isoform responsible for tau phosphorylation at epitopes enriched in tauopathies such as Serine 422. In addition, although our elucidation of the crystal structure of the TTBK2 kinase domain indicates almost identical structural similarity with TTBK1, biochemical and cellular assays demonstrate that the enzymatic activity of these two proteins is regulated by a combination of unique extra-catalytic sequences and autophosphorylation events. Finally, we have identified an unbiased list of neuronal interactors and phosphorylation substrates for TTBK1 and TTBK2 that highlight the unique cellular pathways and functional networks that each isoform is involved in. This data address an important gap in knowledge regarding the implications of targeting TTBK kinases and may prove valuable in the development of potential therapies for disease.
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Affiliation(s)
| | | | | | | | | | | | - Ru Wei
- Biogen, Cambridge, MA, 02134, USA
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13
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Turab Naqvi AA, Hasan GM, Hassan MI. Targeting Tau Hyperphosphorylation via Kinase Inhibition: Strategy to Address Alzheimer's Disease. Curr Top Med Chem 2021; 20:1059-1073. [PMID: 31903881 DOI: 10.2174/1568026620666200106125910] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/27/2019] [Accepted: 12/16/2019] [Indexed: 01/10/2023]
Abstract
Microtubule-associated protein tau is involved in the tubulin binding leading to microtubule stabilization in neuronal cells which is essential for stabilization of neuron cytoskeleton. The regulation of tau activity is accommodated by several kinases which phosphorylate tau protein on specific sites. In pathological conditions, abnormal activity of tau kinases such as glycogen synthase kinase-3 β (GSK3β), cyclin-dependent kinase 5 (CDK5), c-Jun N-terminal kinases (JNKs), extracellular signal-regulated kinase 1 and 2 (ERK1/2) and microtubule affinity regulating kinase (MARK) lead to tau hyperphosphorylation. Hyperphosphorylation of tau protein leads to aggregation of tau into paired helical filaments like structures which are major constituents of neurofibrillary tangles, a hallmark of Alzheimer's disease. In this review, we discuss various tau protein kinases and their association with tau hyperphosphorylation. We also discuss various strategies and the advancements made in the area of Alzheimer's disease drug development by designing effective and specific inhibitors for such kinases using traditional in vitro/in vivo methods and state of the art in silico techniques.
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Affiliation(s)
- Ahmad Abu Turab Naqvi
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi - 110025, India
| | - Gulam Mustafa Hasan
- Department of Biochemistry, College of Medicine, Prince Sattam Bin Abdulaziz University, P.O. Box 173, Al-Kharj - 11942, Saudi Arabia
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi - 110025, India
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14
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Brear P, Ball D, Stott K, D'Arcy S, Hyvönen M. Proposed Allosteric Inhibitors Bind to the ATP Site of CK2α. J Med Chem 2020; 63:12786-12798. [PMID: 33119282 DOI: 10.1021/acs.jmedchem.0c01173] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
CK2α is a ubiquitous, well-studied kinase that is a target for small-molecule inhibition, for treatment of cancers. While many different classes of adenosine 5'-triphosphate (ATP)-competitive inhibitors have been described for CK2α, they tend to suffer from significant off-target activity and new approaches are needed. A series of inhibitors of CK2α has recently been described as allosteric, acting at a previously unidentified binding site. Given the similarity of these inhibitors to known ATP-competitive inhibitors, we have investigated them further. In our thorough structural and biophysical analyses, we have found no evidence that these inhibitors bind to the proposed allosteric site. Rather, we report crystal structures, competitive isothermal titration calorimetry (ITC) and NMR, hydrogen-deuterium exchange (HDX) mass spectrometry, and chemoinformatic analyses that all point to these compounds binding in the ATP pocket. Comparisons of our results and experimental approach with the data presented in the original report suggest that the primary reason for the disparity is nonspecific inhibition by aggregation.
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Affiliation(s)
- Paul Brear
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, U.K
| | - Darby Ball
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Katherine Stott
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, U.K
| | - Sheena D'Arcy
- Department of Chemistry and Biochemistry, The University of Texas at Dallas, Richardson, Texas 75080, United States
| | - Marko Hyvönen
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, U.K
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15
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Palomo V, Nozal V, Rojas-Prats E, Gil C, Martinez A. Protein kinase inhibitors for amyotrophic lateral sclerosis therapy. Br J Pharmacol 2020; 178:1316-1335. [PMID: 32737989 DOI: 10.1111/bph.15221] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 07/03/2020] [Accepted: 07/25/2020] [Indexed: 12/14/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder that causes the progressive loss of motoneurons and, unfortunately, there is no effective treatment for this disease. Interconnecting multiple pathological mechanisms are involved in the neuropathology of this disease, including abnormal aggregation of proteins, neuroinflammation and dysregulation of the ubiquitin proteasome system. Such complex mechanisms, together with the lack of reliable animal models of the disease have hampered the development of drugs for this disease. Protein kinases, a key pharmacological target in several diseases, have been linked to ALS as they play a central role in the pathology of many diseases. Therefore several inhibitors are being currently trailed for clinical proof of concept in ALS patients. In this review, we examine the recent literature on protein kinase inhibitors currently in pharmaceutical development for this diseaseas future therapy for AS together with their involvement in the pathobiology of ALS. LINKED ARTICLES: This article is part of a themed issue on Neurochemistry in Japan. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v178.6/issuetoc.
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Affiliation(s)
- Valle Palomo
- Centro de Investigaciones Biológicas-CSIC, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto Carlos III, Madrid, Spain
| | - Vanesa Nozal
- Centro de Investigaciones Biológicas-CSIC, Madrid, Spain
| | | | - Carmen Gil
- Centro de Investigaciones Biológicas-CSIC, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto Carlos III, Madrid, Spain
| | - Ana Martinez
- Centro de Investigaciones Biológicas-CSIC, Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto Carlos III, Madrid, Spain
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16
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Marcotte DJ, Spilker KA, Wen D, Hesson T, Patterson TA, Kumar PR, Chodaparambil JV. The crystal structure of the catalytic domain of tau tubulin kinase 2 in complex with a small-molecule inhibitor. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS 2020; 76:103-108. [PMID: 32133995 DOI: 10.1107/s2053230x2000031x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/12/2020] [Indexed: 08/24/2023]
Abstract
Tau proteins play an important role in the proper assembly and function of neurons. Hyperphosphorylation of tau by kinases such as tau tubulin kinase (TTBK) has been hypothesized to cause the aggregation of tau and the formation of neurofibrillary tangles (NFTs) that lead to the destabilization of microtubules, thereby contributing to neurodegenerative diseases such as Alzheimer's disease (AD). There are two TTBK isoforms with highly homologous catalytic sites but with distinct tissue distributions, tau phosphorylation patterns and loss-of-function effects. Inhibition of TTBK1 reduces the levels of NFT formation involved in neurodegenerative diseases such as AD, whereas inhibition of TTBK2 may lead to the movement disorder spinocerebellar ataxia type 11 (SCA11). Hence, it is critical to obtain isoform-selective inhibitors. Structure-based drug design (SBDD) has been used to design highly potent and exquisitely selective inhibitors. While structures of TTBK1 have been reported in the literature, TTBK2 has evaded structural characterization. Here, the first crystal structure of the TTBK2 kinase domain is described. Furthermore, the crystal structure of human TTBK2 in complex with a small-molecule inhibitor has successfully been determined to elucidate the structural differences in protein conformations between the two TTBK isoforms that could aid in SBDD for the design of inhibitors that selectively target TTBK1 over TTBK2.
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Affiliation(s)
- Douglas J Marcotte
- Department of Biotherapeutics and Medicinal Sciences, Biogen, 115 Broadway, Cambridge, MA 02142, USA
| | - Kerri A Spilker
- Department of Biotherapeutics and Medicinal Sciences, Biogen, 115 Broadway, Cambridge, MA 02142, USA
| | - Dingyi Wen
- Department of Biotherapeutics and Medicinal Sciences, Biogen, 115 Broadway, Cambridge, MA 02142, USA
| | - Thomas Hesson
- Department of Biotherapeutics and Medicinal Sciences, Biogen, 115 Broadway, Cambridge, MA 02142, USA
| | - Thomas A Patterson
- Department of Biotherapeutics and Medicinal Sciences, Biogen, 115 Broadway, Cambridge, MA 02142, USA
| | - P Rajesh Kumar
- Department of Biotherapeutics and Medicinal Sciences, Biogen, 115 Broadway, Cambridge, MA 02142, USA
| | - Jayanth V Chodaparambil
- Department of Biotherapeutics and Medicinal Sciences, Biogen, 115 Broadway, Cambridge, MA 02142, USA
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17
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Taylor LM, McMillan PJ, Kraemer BC, Liachko NF. Tau tubulin kinases in proteinopathy. FEBS J 2019; 286:2434-2446. [PMID: 31034749 PMCID: PMC6936727 DOI: 10.1111/febs.14866] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 02/23/2019] [Accepted: 04/25/2019] [Indexed: 12/12/2022]
Abstract
A number of neurodegenerative diseases are characterized by deposition of abnormally phosphorylated tau or TDP-43 in disease-affected neurons. These diseases include Alzheimer's disease, frontotemporal lobar degeneration, and amyotrophic lateral sclerosis. No disease-modifying therapeutics is available to treat these disorders, and we have a limited understanding of the cellular and molecular factors integral to disease initiation or progression. Phosphorylated tau and TDP-43 are important markers of pathology in dementia disorders and directly contribute to tau- and TDP-43-related neurotoxicity and neurodegeneration. Here, we review the scope of tau and TDP-43 phosphorylation in neurodegenerative disease and discuss recent work demonstrating the kinases TTBK1 and TTBK2 phosphorylate both tau and TDP-43, promoting neurodegeneration.
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Affiliation(s)
- Laura M Taylor
- Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Pamela J McMillan
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, Washington, USA
| | - Brian C Kraemer
- Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, Washington, USA
- Geriatrics Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle, WA, USA
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - Nicole F Liachko
- Division of Gerontology and Geriatric Medicine, Department of Medicine, University of Washington, Seattle, WA, USA
- Geriatrics Research Education and Clinical Center, Veterans Affairs Puget Sound Health Care System, Seattle, WA, USA
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18
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Jana S, Singh SK. Identification of human tau-tubulin kinase 1 inhibitors: an integrated e-pharmacophore-based virtual screening and molecular dynamics simulation. J Biomol Struct Dyn 2019; 38:886-900. [DOI: 10.1080/07391102.2019.1590242] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Srabanti Jana
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
| | - Sushil Kumar Singh
- Pharmaceutical Chemistry Research Laboratory, Department of Pharmaceutical Engineering & Technology, Indian Institute of Technology (Banaras Hindu University), Varanasi, India
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19
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Palomo V, Tosat-Bitrian C, Nozal V, Nagaraj S, Martin-Requero A, Martinez A. TDP-43: A Key Therapeutic Target beyond Amyotrophic Lateral Sclerosis. ACS Chem Neurosci 2019; 10:1183-1196. [PMID: 30785719 DOI: 10.1021/acschemneuro.9b00026] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Accumulation of TDP-43 in the cytoplasm of diseased neurons is the pathological hallmark of frontotemporal dementia-TDP (FTLD-TDP) and amyotrophic lateral sclerosis (ALS), two diseases that lack efficacious medicine to prevent or to stop disease progression. The discovery of mutations in the TARDBP gene (encoding the nuclear protein known as TDP-43) in both FTLD and ALS patients provided evidence for a link between TDP-43 alterations and neurodegeneration. Our understanding of TDP-43 function has advanced profoundly in the past several years; however, its complete role and the molecular mechanisms that lead to disease are not fully understood. Here we summarize the recent studies of this protein, its relation to neurodegenerative diseases, and the therapeutic strategies for restoring its homeostasis with small molecules. Finally, we briefly discuss the available cellular and animal models that help to shed light on TDP-43 pathology and could serve as tools for the discovery of pharmacological agents for the treatment of TDP-43-related diseases.
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Affiliation(s)
- Valle Palomo
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto Carlos III, 28031 Madrid, Spain
| | | | - Vanesa Nozal
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Siranjeevi Nagaraj
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Angeles Martin-Requero
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto Carlos III, 28031 Madrid, Spain
| | - Ana Martinez
- Centro de Investigaciones Biológicas, CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto Carlos III, 28031 Madrid, Spain
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20
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Sonawane V, Mohd Siddique MU, Jadav SS, Sinha BN, Jayaprakash V, Chaudhuri B. Cink4T, a quinazolinone-based dual inhibitor of Cdk4 and tubulin polymerization, identified via ligand-based virtual screening, for efficient anticancer therapy. Eur J Med Chem 2019; 165:115-132. [PMID: 30665142 DOI: 10.1016/j.ejmech.2019.01.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 01/05/2019] [Accepted: 01/05/2019] [Indexed: 12/15/2022]
Abstract
Inhibition of cyclin dependent kinase 4 (Cdk4) prevents cancer cells from entering the early G0/G1 phase of the cell division cycle whereas inhibiting tubulin polymerization blocks cancer cells' ability to undergo mitosis (M) late in the cell cycle. We had reported earlier that two non-planar and relatively non-toxic fascaplysin derivatives, an indole and a tryptoline, inhibit Cdk4 with IC50 values of 6.2 and 10 μM, respectively. Serendipitously, we had also found that they inhibited tubulin polymerization. The molecules were efficacious in mouse tumor models. We have now identified Cink4T in a 59-compound quinazolinone library, designed on the basis of ligand-based virtual screening, as a compound that inhibits Cdk4 and tubulin. Its IC50 value for Cdk4 inhibition is 0.47 μM and >50 μM for inhibition of Cdk1, Cdk2, Cdk6, Cdk9. Cink4T inhibits tubulin polymerization with an IC50 of 0.6 μM. Molecular modelling studies on Cink4T with Cdk4 and tubulin crystal structures lend support to these observations. Cancer cell cycle analyses confirm that Cink4T blocks cells at both G0/G1 and M phases as it should if it were to inhibit both Cdk4 and tubulin polymerization. Our results show, for the very first time, that virtual screening can be used to design novel inhibitors that can potently block two crucial phases of the cell division cycle.
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Affiliation(s)
- Vinay Sonawane
- Leicester School of Pharmacy, De Montfort University, Leicester, LE1 9BH, UK
| | - Mohd Usman Mohd Siddique
- Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi, 835215, India
| | | | - Barij Nayan Sinha
- Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi, 835215, India
| | - Venkatesan Jayaprakash
- Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi, 835215, India.
| | - Bhabatosh Chaudhuri
- Leicester School of Pharmacy, De Montfort University, Leicester, LE1 9BH, UK.
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21
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Nozal V, Martinez A. Tau Tubulin Kinase 1 (TTBK1), a new player in the fight against neurodegenerative diseases. Eur J Med Chem 2019; 161:39-47. [DOI: 10.1016/j.ejmech.2018.10.030] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 10/09/2018] [Accepted: 10/12/2018] [Indexed: 10/28/2022]
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22
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Creixell P, Pandey JP, Palmeri A, Bhattacharyya M, Creixell M, Ranganathan R, Pincus D, Yaffe MB. Hierarchical Organization Endows the Kinase Domain with Regulatory Plasticity. Cell Syst 2018; 7:371-383.e4. [PMID: 30243563 DOI: 10.1016/j.cels.2018.08.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 06/24/2018] [Accepted: 08/13/2018] [Indexed: 02/08/2023]
Abstract
The functional diversity of kinases enables specificity in cellular signal transduction. Yet how more than 500 members of the human kinome specifically receive regulatory inputs and convey information to appropriate substrates-all while using the common signaling output of phosphorylation-remains enigmatic. Here, we perform statistical co-evolution analysis, mutational scanning, and quantitative live-cell assays to reveal a hierarchical organization of the kinase domain that facilitates the orthogonal evolution of regulatory inputs and substrate outputs while maintaining catalytic function. We find that three quasi-independent "sectors"-groups of evolutionarily coupled residues-represent functional units in the kinase domain that encode for catalytic activity, substrate specificity, and regulation. Sector positions impact both disease and pharmacology: the catalytic sector is significantly enriched for somatic cancer mutations, and residues in the regulatory sector interact with allosteric kinase inhibitors. We propose that this functional architecture endows the kinase domain with inherent regulatory plasticity.
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Affiliation(s)
- Pau Creixell
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Departments of Biology and Bioengineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Jai P Pandey
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | | | - Moitrayee Bhattacharyya
- Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Marc Creixell
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Departments of Biology and Bioengineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Rama Ranganathan
- Center for Physics of Evolving Systems, Department of Biochemistry and Molecular Biology, Institute for Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - David Pincus
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
| | - Michael B Yaffe
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Departments of Biology and Bioengineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Surgery, Beth Israel Deaconess Medical Center, Divisions of Acute Care Surgery, Trauma, and Critical Care and Surgical Oncology, Harvard Medical School, Boston 02215, USA.
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23
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Temperature-Sensitive Substrate and Product Binding Underlie Temperature-Compensated Phosphorylation in the Clock. Mol Cell 2017; 67:783-798.e20. [PMID: 28886336 DOI: 10.1016/j.molcel.2017.08.009] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 07/04/2017] [Accepted: 08/16/2017] [Indexed: 01/02/2023]
Abstract
Temperature compensation is a striking feature of the circadian clock. Here we investigate biochemical mechanisms underlying temperature-compensated, CKIδ-dependent multi-site phosphorylation in mammals. We identify two mechanisms for temperature-insensitive phosphorylation at higher temperature: lower substrate affinity to CKIδ-ATP complex and higher product affinity to CKIδ-ADP complex. Inhibitor screening of ADP-dependent phosphatase activity of CKIδ identified aurintricarboxylic acid (ATA) as a temperature-sensitive kinase activator. Docking simulation of ATA and mutagenesis experiment revealed K224D/K224E mutations in CKIδ that impaired product binding and temperature-compensated primed phosphorylation. Importantly, K224D mutation shortens behavioral circadian rhythms and changes the temperature dependency of SCN's circadian period. Interestingly, temperature-compensated phosphorylation was evolutionary conserved in yeast. Molecular dynamics simulation and X-ray crystallography demonstrate that an evolutionally conserved CKI-specific domain around K224 can provide a structural basis for temperature-sensitive substrate and product binding. Surprisingly, this domain can confer temperature compensation on a temperature-sensitive TTBK1. These findings suggest the temperature-sensitive substrate- and product-binding mechanisms underlie temperature compensation.
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24
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4-Carbonyl-2,6-dibenzylidenecyclohexanone derivatives as small molecule inhibitors of STAT3 signaling pathway. Bioorg Med Chem 2016; 24:6174-6182. [PMID: 27816267 DOI: 10.1016/j.bmc.2016.09.070] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 09/27/2016] [Accepted: 09/28/2016] [Indexed: 12/20/2022]
Abstract
Inhibition of STAT3 signaling pathway is proposed to be a promising strategy for cancer treatment. In this study, a series of 4-carbonyl-2,6-dibenzylidenecyclohexanone derivatives were prepared and evaluated as anticancer agents. The most potent compound 13r was discovered to exhibit antiproliferative activity against a broad rang of cancer cell lines and relatively low cytotoxicity against normal human cells. Besides, 13r effectively suppressed STAT3 expression as well as phosphorylation, and surface plasmon resonance analysis confirmed the direct interaction of 13r with STAT3. Docking simulation showed that 13r could inhibit STAT3 by targeting SH2 domain. This study provided evidence for these compounds to be further developed as antitumor agents through inhibition of the STAT3 pathway.
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25
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Schoop A, Dey F. On-rate based optimization of structure-kinetic relationship--surfing the kinetic map. DRUG DISCOVERY TODAY. TECHNOLOGIES 2015; 17:9-15. [PMID: 26724331 DOI: 10.1016/j.ddtec.2015.08.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Accepted: 08/24/2015] [Indexed: 05/16/2023]
Abstract
In the lead discovery process residence time has become an important parameter for the identification and characterization of the most efficacious compounds in vivo. To enable the success of compound optimization by medicinal chemistry toward a desired residence time the understanding of structure-kinetic relationship (SKR) is essential. This article reviews various approaches to monitor SKR and suggests using the on-rate as the key monitoring parameter. The literature is reviewed and examples of compound series with low variability as well as with significant changes in on-rates are highlighted. Furthermore, findings of kinetic on-rate changes are presented and potential underlying rationales are discussed.
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Affiliation(s)
- Andreas Schoop
- Proteros biostructures GmbH, Bunsenstrasse 7a, 82152 Martinsried, Germany.
| | - Fabian Dey
- Roche Pharmaceutical Research and Early Development, Small Molecule Research, Roche Innovation Center Basel, Grenzacherstrasse 124, 4070 Basel, Switzerland
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Morooka S, Hoshina M, Kii I, Okabe T, Kojima H, Inoue N, Okuno Y, Denawa M, Yoshida S, Fukuhara J, Ninomiya K, Ikura T, Furuya T, Nagano T, Noda K, Ishida S, Hosoya T, Ito N, Yoshimura N, Hagiwara M. Identification of a Dual Inhibitor of SRPK1 and CK2 That Attenuates Pathological Angiogenesis of Macular Degeneration in Mice. Mol Pharmacol 2015; 88:316-25. [PMID: 25993998 DOI: 10.1124/mol.114.097345] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 05/20/2015] [Indexed: 12/28/2022] Open
Abstract
Excessive angiogenesis contributes to numerous diseases, including cancer and blinding retinopathy. Antibodies against vascular endothelial growth factor (VEGF) have been approved and are widely used in clinical treatment. Our previous studies using SRPIN340, a small molecule inhibitor of SRPK1 (serine-arginine protein kinase 1), demonstrated that SRPK1 is a potential target for the development of antiangiogenic drugs. In this study, we solved the structure of SRPK1 bound to SRPIN340 by X-ray crystallography. Using pharmacophore docking models followed by in vitro kinase assays, we screened a large-scale chemical library, and thus identified a new inhibitor of SRPK1. This inhibitor, SRPIN803, prevented VEGF production more effectively than SRPIN340 owing to the dual inhibition of SRPK1 and CK2 (casein kinase 2). In a mouse model of age-related macular degeneration, topical administration of eye ointment containing SRPIN803 significantly inhibited choroidal neovascularization, suggesting a clinical potential of SRPIN803 as a topical ointment for ocular neovascularization. Thus SRPIN803 merits further investigation as a novel inhibitor of VEGF.
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Affiliation(s)
- Satoshi Morooka
- Department of Ophthalmology and Visual Sciences (S.M., N.Y.), Department of Anatomy and Developmental Biology (S.M., I.K., Ke.N., Ma.H.), and Medical Research Support Center (Y.O., M.D.), Graduate School of Medicine, Kyoto University, Kyoto, Japan; Laboratory of Structural Biology, Medical Research Institute (Mi.H., No.I., T.I.), and Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering (S.Y., T.H.), Tokyo Medical and Dental University, Tokyo, Japan; Open Innovation Center for Drug Discovery, The University of Tokyo, Tokyo, Japan (T.O., H.K., T.N.); PharmaDesign, Inc., Tokyo, Japan (Na.I., T.F.); and Department of Ophthalmology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan (J.F., Ko.N., S.I.)
| | - Mitsuteru Hoshina
- Department of Ophthalmology and Visual Sciences (S.M., N.Y.), Department of Anatomy and Developmental Biology (S.M., I.K., Ke.N., Ma.H.), and Medical Research Support Center (Y.O., M.D.), Graduate School of Medicine, Kyoto University, Kyoto, Japan; Laboratory of Structural Biology, Medical Research Institute (Mi.H., No.I., T.I.), and Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering (S.Y., T.H.), Tokyo Medical and Dental University, Tokyo, Japan; Open Innovation Center for Drug Discovery, The University of Tokyo, Tokyo, Japan (T.O., H.K., T.N.); PharmaDesign, Inc., Tokyo, Japan (Na.I., T.F.); and Department of Ophthalmology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan (J.F., Ko.N., S.I.)
| | - Isao Kii
- Department of Ophthalmology and Visual Sciences (S.M., N.Y.), Department of Anatomy and Developmental Biology (S.M., I.K., Ke.N., Ma.H.), and Medical Research Support Center (Y.O., M.D.), Graduate School of Medicine, Kyoto University, Kyoto, Japan; Laboratory of Structural Biology, Medical Research Institute (Mi.H., No.I., T.I.), and Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering (S.Y., T.H.), Tokyo Medical and Dental University, Tokyo, Japan; Open Innovation Center for Drug Discovery, The University of Tokyo, Tokyo, Japan (T.O., H.K., T.N.); PharmaDesign, Inc., Tokyo, Japan (Na.I., T.F.); and Department of Ophthalmology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan (J.F., Ko.N., S.I.)
| | - Takayoshi Okabe
- Department of Ophthalmology and Visual Sciences (S.M., N.Y.), Department of Anatomy and Developmental Biology (S.M., I.K., Ke.N., Ma.H.), and Medical Research Support Center (Y.O., M.D.), Graduate School of Medicine, Kyoto University, Kyoto, Japan; Laboratory of Structural Biology, Medical Research Institute (Mi.H., No.I., T.I.), and Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering (S.Y., T.H.), Tokyo Medical and Dental University, Tokyo, Japan; Open Innovation Center for Drug Discovery, The University of Tokyo, Tokyo, Japan (T.O., H.K., T.N.); PharmaDesign, Inc., Tokyo, Japan (Na.I., T.F.); and Department of Ophthalmology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan (J.F., Ko.N., S.I.)
| | - Hirotatsu Kojima
- Department of Ophthalmology and Visual Sciences (S.M., N.Y.), Department of Anatomy and Developmental Biology (S.M., I.K., Ke.N., Ma.H.), and Medical Research Support Center (Y.O., M.D.), Graduate School of Medicine, Kyoto University, Kyoto, Japan; Laboratory of Structural Biology, Medical Research Institute (Mi.H., No.I., T.I.), and Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering (S.Y., T.H.), Tokyo Medical and Dental University, Tokyo, Japan; Open Innovation Center for Drug Discovery, The University of Tokyo, Tokyo, Japan (T.O., H.K., T.N.); PharmaDesign, Inc., Tokyo, Japan (Na.I., T.F.); and Department of Ophthalmology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan (J.F., Ko.N., S.I.)
| | - Naoko Inoue
- Department of Ophthalmology and Visual Sciences (S.M., N.Y.), Department of Anatomy and Developmental Biology (S.M., I.K., Ke.N., Ma.H.), and Medical Research Support Center (Y.O., M.D.), Graduate School of Medicine, Kyoto University, Kyoto, Japan; Laboratory of Structural Biology, Medical Research Institute (Mi.H., No.I., T.I.), and Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering (S.Y., T.H.), Tokyo Medical and Dental University, Tokyo, Japan; Open Innovation Center for Drug Discovery, The University of Tokyo, Tokyo, Japan (T.O., H.K., T.N.); PharmaDesign, Inc., Tokyo, Japan (Na.I., T.F.); and Department of Ophthalmology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan (J.F., Ko.N., S.I.)
| | - Yukiko Okuno
- Department of Ophthalmology and Visual Sciences (S.M., N.Y.), Department of Anatomy and Developmental Biology (S.M., I.K., Ke.N., Ma.H.), and Medical Research Support Center (Y.O., M.D.), Graduate School of Medicine, Kyoto University, Kyoto, Japan; Laboratory of Structural Biology, Medical Research Institute (Mi.H., No.I., T.I.), and Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering (S.Y., T.H.), Tokyo Medical and Dental University, Tokyo, Japan; Open Innovation Center for Drug Discovery, The University of Tokyo, Tokyo, Japan (T.O., H.K., T.N.); PharmaDesign, Inc., Tokyo, Japan (Na.I., T.F.); and Department of Ophthalmology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan (J.F., Ko.N., S.I.)
| | - Masatsugu Denawa
- Department of Ophthalmology and Visual Sciences (S.M., N.Y.), Department of Anatomy and Developmental Biology (S.M., I.K., Ke.N., Ma.H.), and Medical Research Support Center (Y.O., M.D.), Graduate School of Medicine, Kyoto University, Kyoto, Japan; Laboratory of Structural Biology, Medical Research Institute (Mi.H., No.I., T.I.), and Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering (S.Y., T.H.), Tokyo Medical and Dental University, Tokyo, Japan; Open Innovation Center for Drug Discovery, The University of Tokyo, Tokyo, Japan (T.O., H.K., T.N.); PharmaDesign, Inc., Tokyo, Japan (Na.I., T.F.); and Department of Ophthalmology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan (J.F., Ko.N., S.I.)
| | - Suguru Yoshida
- Department of Ophthalmology and Visual Sciences (S.M., N.Y.), Department of Anatomy and Developmental Biology (S.M., I.K., Ke.N., Ma.H.), and Medical Research Support Center (Y.O., M.D.), Graduate School of Medicine, Kyoto University, Kyoto, Japan; Laboratory of Structural Biology, Medical Research Institute (Mi.H., No.I., T.I.), and Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering (S.Y., T.H.), Tokyo Medical and Dental University, Tokyo, Japan; Open Innovation Center for Drug Discovery, The University of Tokyo, Tokyo, Japan (T.O., H.K., T.N.); PharmaDesign, Inc., Tokyo, Japan (Na.I., T.F.); and Department of Ophthalmology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan (J.F., Ko.N., S.I.)
| | - Junichi Fukuhara
- Department of Ophthalmology and Visual Sciences (S.M., N.Y.), Department of Anatomy and Developmental Biology (S.M., I.K., Ke.N., Ma.H.), and Medical Research Support Center (Y.O., M.D.), Graduate School of Medicine, Kyoto University, Kyoto, Japan; Laboratory of Structural Biology, Medical Research Institute (Mi.H., No.I., T.I.), and Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering (S.Y., T.H.), Tokyo Medical and Dental University, Tokyo, Japan; Open Innovation Center for Drug Discovery, The University of Tokyo, Tokyo, Japan (T.O., H.K., T.N.); PharmaDesign, Inc., Tokyo, Japan (Na.I., T.F.); and Department of Ophthalmology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan (J.F., Ko.N., S.I.)
| | - Kensuke Ninomiya
- Department of Ophthalmology and Visual Sciences (S.M., N.Y.), Department of Anatomy and Developmental Biology (S.M., I.K., Ke.N., Ma.H.), and Medical Research Support Center (Y.O., M.D.), Graduate School of Medicine, Kyoto University, Kyoto, Japan; Laboratory of Structural Biology, Medical Research Institute (Mi.H., No.I., T.I.), and Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering (S.Y., T.H.), Tokyo Medical and Dental University, Tokyo, Japan; Open Innovation Center for Drug Discovery, The University of Tokyo, Tokyo, Japan (T.O., H.K., T.N.); PharmaDesign, Inc., Tokyo, Japan (Na.I., T.F.); and Department of Ophthalmology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan (J.F., Ko.N., S.I.)
| | - Teikichi Ikura
- Department of Ophthalmology and Visual Sciences (S.M., N.Y.), Department of Anatomy and Developmental Biology (S.M., I.K., Ke.N., Ma.H.), and Medical Research Support Center (Y.O., M.D.), Graduate School of Medicine, Kyoto University, Kyoto, Japan; Laboratory of Structural Biology, Medical Research Institute (Mi.H., No.I., T.I.), and Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering (S.Y., T.H.), Tokyo Medical and Dental University, Tokyo, Japan; Open Innovation Center for Drug Discovery, The University of Tokyo, Tokyo, Japan (T.O., H.K., T.N.); PharmaDesign, Inc., Tokyo, Japan (Na.I., T.F.); and Department of Ophthalmology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan (J.F., Ko.N., S.I.)
| | - Toshio Furuya
- Department of Ophthalmology and Visual Sciences (S.M., N.Y.), Department of Anatomy and Developmental Biology (S.M., I.K., Ke.N., Ma.H.), and Medical Research Support Center (Y.O., M.D.), Graduate School of Medicine, Kyoto University, Kyoto, Japan; Laboratory of Structural Biology, Medical Research Institute (Mi.H., No.I., T.I.), and Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering (S.Y., T.H.), Tokyo Medical and Dental University, Tokyo, Japan; Open Innovation Center for Drug Discovery, The University of Tokyo, Tokyo, Japan (T.O., H.K., T.N.); PharmaDesign, Inc., Tokyo, Japan (Na.I., T.F.); and Department of Ophthalmology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan (J.F., Ko.N., S.I.)
| | - Tetsuo Nagano
- Department of Ophthalmology and Visual Sciences (S.M., N.Y.), Department of Anatomy and Developmental Biology (S.M., I.K., Ke.N., Ma.H.), and Medical Research Support Center (Y.O., M.D.), Graduate School of Medicine, Kyoto University, Kyoto, Japan; Laboratory of Structural Biology, Medical Research Institute (Mi.H., No.I., T.I.), and Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering (S.Y., T.H.), Tokyo Medical and Dental University, Tokyo, Japan; Open Innovation Center for Drug Discovery, The University of Tokyo, Tokyo, Japan (T.O., H.K., T.N.); PharmaDesign, Inc., Tokyo, Japan (Na.I., T.F.); and Department of Ophthalmology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan (J.F., Ko.N., S.I.)
| | - Kousuke Noda
- Department of Ophthalmology and Visual Sciences (S.M., N.Y.), Department of Anatomy and Developmental Biology (S.M., I.K., Ke.N., Ma.H.), and Medical Research Support Center (Y.O., M.D.), Graduate School of Medicine, Kyoto University, Kyoto, Japan; Laboratory of Structural Biology, Medical Research Institute (Mi.H., No.I., T.I.), and Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering (S.Y., T.H.), Tokyo Medical and Dental University, Tokyo, Japan; Open Innovation Center for Drug Discovery, The University of Tokyo, Tokyo, Japan (T.O., H.K., T.N.); PharmaDesign, Inc., Tokyo, Japan (Na.I., T.F.); and Department of Ophthalmology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan (J.F., Ko.N., S.I.)
| | - Susumu Ishida
- Department of Ophthalmology and Visual Sciences (S.M., N.Y.), Department of Anatomy and Developmental Biology (S.M., I.K., Ke.N., Ma.H.), and Medical Research Support Center (Y.O., M.D.), Graduate School of Medicine, Kyoto University, Kyoto, Japan; Laboratory of Structural Biology, Medical Research Institute (Mi.H., No.I., T.I.), and Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering (S.Y., T.H.), Tokyo Medical and Dental University, Tokyo, Japan; Open Innovation Center for Drug Discovery, The University of Tokyo, Tokyo, Japan (T.O., H.K., T.N.); PharmaDesign, Inc., Tokyo, Japan (Na.I., T.F.); and Department of Ophthalmology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan (J.F., Ko.N., S.I.)
| | - Takamitsu Hosoya
- Department of Ophthalmology and Visual Sciences (S.M., N.Y.), Department of Anatomy and Developmental Biology (S.M., I.K., Ke.N., Ma.H.), and Medical Research Support Center (Y.O., M.D.), Graduate School of Medicine, Kyoto University, Kyoto, Japan; Laboratory of Structural Biology, Medical Research Institute (Mi.H., No.I., T.I.), and Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering (S.Y., T.H.), Tokyo Medical and Dental University, Tokyo, Japan; Open Innovation Center for Drug Discovery, The University of Tokyo, Tokyo, Japan (T.O., H.K., T.N.); PharmaDesign, Inc., Tokyo, Japan (Na.I., T.F.); and Department of Ophthalmology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan (J.F., Ko.N., S.I.)
| | - Nobutoshi Ito
- Department of Ophthalmology and Visual Sciences (S.M., N.Y.), Department of Anatomy and Developmental Biology (S.M., I.K., Ke.N., Ma.H.), and Medical Research Support Center (Y.O., M.D.), Graduate School of Medicine, Kyoto University, Kyoto, Japan; Laboratory of Structural Biology, Medical Research Institute (Mi.H., No.I., T.I.), and Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering (S.Y., T.H.), Tokyo Medical and Dental University, Tokyo, Japan; Open Innovation Center for Drug Discovery, The University of Tokyo, Tokyo, Japan (T.O., H.K., T.N.); PharmaDesign, Inc., Tokyo, Japan (Na.I., T.F.); and Department of Ophthalmology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan (J.F., Ko.N., S.I.)
| | - Nagahisa Yoshimura
- Department of Ophthalmology and Visual Sciences (S.M., N.Y.), Department of Anatomy and Developmental Biology (S.M., I.K., Ke.N., Ma.H.), and Medical Research Support Center (Y.O., M.D.), Graduate School of Medicine, Kyoto University, Kyoto, Japan; Laboratory of Structural Biology, Medical Research Institute (Mi.H., No.I., T.I.), and Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering (S.Y., T.H.), Tokyo Medical and Dental University, Tokyo, Japan; Open Innovation Center for Drug Discovery, The University of Tokyo, Tokyo, Japan (T.O., H.K., T.N.); PharmaDesign, Inc., Tokyo, Japan (Na.I., T.F.); and Department of Ophthalmology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan (J.F., Ko.N., S.I.)
| | - Masatoshi Hagiwara
- Department of Ophthalmology and Visual Sciences (S.M., N.Y.), Department of Anatomy and Developmental Biology (S.M., I.K., Ke.N., Ma.H.), and Medical Research Support Center (Y.O., M.D.), Graduate School of Medicine, Kyoto University, Kyoto, Japan; Laboratory of Structural Biology, Medical Research Institute (Mi.H., No.I., T.I.), and Laboratory of Chemical Bioscience, Institute of Biomaterials and Bioengineering (S.Y., T.H.), Tokyo Medical and Dental University, Tokyo, Japan; Open Innovation Center for Drug Discovery, The University of Tokyo, Tokyo, Japan (T.O., H.K., T.N.); PharmaDesign, Inc., Tokyo, Japan (Na.I., T.F.); and Department of Ophthalmology, Graduate School of Medicine, Hokkaido University, Sapporo, Japan (J.F., Ko.N., S.I.)
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TTBK2: a tau protein kinase beyond tau phosphorylation. BIOMED RESEARCH INTERNATIONAL 2015; 2015:575170. [PMID: 25950000 PMCID: PMC4407412 DOI: 10.1155/2015/575170] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2015] [Revised: 03/11/2015] [Accepted: 03/25/2015] [Indexed: 12/12/2022]
Abstract
Tau tubulin kinase 2 (TTBK2) is a kinase known to phosphorylate tau and tubulin. It has recently drawn much attention due to its involvement in multiple important cellular processes. Here, we review the current understanding of TTBK2, including its sequence, structure, binding sites, phosphorylation substrates, and cellular processes involved. TTBK2 possesses a casein kinase 1 (CK1) kinase domain followed by a ~900 amino acid segment, potentially responsible for its localization and substrate recruitment. It is known to bind to CEP164, a centriolar protein, and EB1, a microtubule plus-end tracking protein. In addition to autophosphorylation, known phosphorylation substrates of TTBK2 include tau, tubulin, CEP164, CEP97, and TDP-43, a neurodegeneration-associated protein. Mutations of TTBK2 are associated with spinocerebellar ataxia type 11. In addition, TTBK2 is essential for regulating the growth of axonemal microtubules in ciliogenesis. It also plays roles in resistance of cancer target therapies and in regulating glucose and GABA transport. Reported sites of TTBK2 localization include the centriole/basal body, the midbody, and possibly the mitotic spindles. Together, TTBK2 is a multifunctional kinase involved in important cellular processes and demands augmented efforts in investigating its functions.
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Abstract
Tau-tubulin kinase (TTBK) belongs to casein kinase superfamily and phosphorylates microtubule-associated protein tau and tubulin. TTBK has two isoforms, TTBK1 and TTBK2, which contain highly homologous catalytic domains but their non-catalytic domains are distinctly different. TTBK1 is expressed specifically in the central nervous system and is involved in phosphorylation and aggregation of tau. TTBK2 is ubiquitously expressed in multiple tissues and genetically linked to spinocerebellar ataxia type 11. TTBK1 directly phosphorylates tau protein, especially at Ser422, and also activates cycline-dependent kinase 5 in a unique mechanism. TTBK1 protein expression is significantly elevated in Alzheimer’s disease (AD) brains, and genetic variations of the TTBK1 gene are associated with late-onset Alzheimer’s disease in two cohorts of Chinese and Spanish populations. TTBK1 transgenic mice harboring the entire 55-kilobase genomic sequence of human TTBK1 show progression of tau accumulation, neuroinflammation, and neurodegeneration when crossed with tau mutant mice. Our recent study shows that there is a striking switch in mononuclear phagocyte and activation phenotypes in the anterior horn of the spinal cord from alternatively activated (M2-skewed) microglia in P301L tau mutant mice to pro-inflammatory (M1-skewed) infiltrating peripheral monocytes by crossing the tau mice with TTBK1 transgenic mice. TTBK1 is responsible for mediating M1-activated microglia-induced neurotoxicity, and its overexpression induces axonal degeneration in vitro. These studies suggest that TTBK1 is an important molecule for the inflammatory axonal degeneration, which may be relevant to the pathobiology of tauopathy including AD.
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Affiliation(s)
- Seiko Ikezu
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine Boston, MA, USA
| | - Tsuneya Ikezu
- Department of Pharmacology and Experimental Therapeutics, Boston University School of Medicine Boston, MA, USA ; Department of Neurology, Boston University School of Medicine Boston, MA, USA ; Alzheimer's Disease Center, Boston University School of Medicine Boston, MA, USA
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Kiefer SE, Chang CJ, Kimura SR, Gao M, Xie D, Zhang Y, Zhang G, Gill MB, Mastalerz H, Thompson LA, Cacace AM, Sheriff S. The structure of human tau-tubulin kinase 1 both in the apo form and in complex with an inhibitor. Acta Crystallogr F Struct Biol Commun 2014; 70:173-81. [PMID: 24637750 PMCID: PMC3936456 DOI: 10.1107/s2053230x14000144] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 01/03/2014] [Indexed: 11/10/2022] Open
Abstract
Tau-tubulin kinase 1 (TTBK1) is a dual-specificity (serine/threonine and tyrosine) kinase belonging to the casein kinase 1 superfamily. TTBK1 is a neuron-specific kinase that regulates tau phosphorylation. Hyperphosphorylation of tau is implicated in the pathogenesis of Alzheimer's disease. Two kinase-domain constructs of TTBK1 were expressed in a baculovirus-infected insect-cell system and purified. The purified TTBK1 kinase-domain proteins were crystallized using the hanging-drop vapor-diffusion method. X-ray diffraction data were collected and the structure of TTBK1 was determined by molecular replacement both as an apo structure and in complex with a kinase inhibitor.
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Affiliation(s)
- Susan E. Kiefer
- Molecular Discovery Technologies, Bristol-Myers Squibb Research and Development, PO Box 4000, Princeton, NJ 08543-4000, USA
| | - ChiehYing J. Chang
- Molecular Discovery Technologies, Bristol-Myers Squibb Research and Development, PO Box 4000, Princeton, NJ 08543-4000, USA
| | - S. Roy Kimura
- Molecular Discovery Technologies, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Mian Gao
- Molecular Discovery Technologies, Bristol-Myers Squibb Research and Development, PO Box 4000, Princeton, NJ 08543-4000, USA
| | - Dianlin Xie
- Molecular Discovery Technologies, Bristol-Myers Squibb Research and Development, PO Box 4000, Princeton, NJ 08543-4000, USA
| | - Yaqun Zhang
- Molecular Discovery Technologies, Bristol-Myers Squibb Research and Development, PO Box 4000, Princeton, NJ 08543-4000, USA
| | - Guifen Zhang
- Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Martin B. Gill
- Neuroscience Biology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Harold Mastalerz
- Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Lorin A. Thompson
- Discovery Chemistry, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Angela M. Cacace
- Neuroscience Biology, Bristol-Myers Squibb Research and Development, 5 Research Parkway, Wallingford, CT 06492, USA
| | - Steven Sheriff
- Molecular Discovery Technologies, Bristol-Myers Squibb Research and Development, PO Box 4000, Princeton, NJ 08543-4000, USA
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