1
|
Reveguk I, Simonson T. Classifying protein kinase conformations with machine learning. Protein Sci 2024; 33:e4918. [PMID: 38501429 PMCID: PMC10962494 DOI: 10.1002/pro.4918] [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: 07/26/2023] [Revised: 01/02/2024] [Accepted: 01/22/2024] [Indexed: 03/20/2024]
Abstract
Protein kinases are key actors of signaling networks and important drug targets. They cycle between active and inactive conformations, distinguished by a few elements within the catalytic domain. One is the activation loop, whose conserved DFG motif can occupy DFG-in, DFG-out, and some rarer conformations. Annotation and classification of the structural kinome are important, as different conformations can be targeted by different inhibitors and activators. Valuable resources exist; however, large-scale applications will benefit from increased automation and interpretability of structural annotation. Interpretable machine learning models are described for this purpose, based on ensembles of decision trees. To train them, a set of catalytic domain sequences and structures was collected, somewhat larger and more diverse than existing resources. The structures were clustered based on the DFG conformation and manually annotated. They were then used as training input. Two main models were constructed, which distinguished active/inactive and in/out/other DFG conformations. They considered initially 1692 structural variables, spanning the whole catalytic domain, then identified ("learned") a small subset that sufficed for accurate classification. The first model correctly labeled all but 3 of 3289 structures as active or inactive, while the second assigned the correct DFG label to all but 17 of 8826 structures. The most potent classifying variables were all related to well-known structural elements in or near the activation loop and their ranking gives insights into the conformational preferences. The models were used to automatically annotate 3850 kinase structures predicted recently with the Alphafold2 tool, showing that Alphafold2 reproduced the active/inactive but not the DFG-in proportions seen in the Protein Data Bank. We expect the models will be useful for understanding and engineering kinases.
Collapse
Affiliation(s)
- Ivan Reveguk
- Laboratoire de Biologie Structurale de la Cellule (CNRS UMR7654)Ecole PolytechniquePalaiseauFrance
| | - Thomas Simonson
- Laboratoire de Biologie Structurale de la Cellule (CNRS UMR7654)Ecole PolytechniquePalaiseauFrance
| |
Collapse
|
2
|
Basei FL, E Silva IR, Dias PRF, Ferezin CC, Peres de Oliveira A, Issayama LK, Moura LAR, da Silva FR, Kobarg J. The Mitochondrial Connection: The Nek Kinases' New Functional Axis in Mitochondrial Homeostasis. Cells 2024; 13:473. [PMID: 38534317 DOI: 10.3390/cells13060473] [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: 01/24/2024] [Revised: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 03/28/2024] Open
Abstract
Mitochondria provide energy for all cellular processes, including reactions associated with cell cycle progression, DNA damage repair, and cilia formation. Moreover, mitochondria participate in cell fate decisions between death and survival. Nek family members have already been implicated in DNA damage response, cilia formation, cell death, and cell cycle control. Here, we discuss the role of several Nek family members, namely Nek1, Nek4, Nek5, Nek6, and Nek10, which are not exclusively dedicated to cell cycle-related functions, in controlling mitochondrial functions. Specifically, we review the function of these Neks in mitochondrial respiration and dynamics, mtDNA maintenance, stress response, and cell death. Finally, we discuss the interplay of other cell cycle kinases in mitochondrial function and vice versa. Nek1, Nek5, and Nek6 are connected to the stress response, including ROS control, mtDNA repair, autophagy, and apoptosis. Nek4, in turn, seems to be related to mitochondrial dynamics, while Nek10 is involved with mitochondrial metabolism. Here, we propose that the participation of Neks in mitochondrial roles is a new functional axis for the Nek family.
Collapse
Affiliation(s)
- Fernanda L Basei
- Faculty of Pharmaceutical Sciences, University of Campinas, Campinas 13083-871, Brazil
| | - Ivan Rosa E Silva
- Faculty of Pharmaceutical Sciences, University of Campinas, Campinas 13083-871, Brazil
| | - Pedro R Firmino Dias
- Faculty of Pharmaceutical Sciences, University of Campinas, Campinas 13083-871, Brazil
| | - Camila C Ferezin
- Faculty of Pharmaceutical Sciences, University of Campinas, Campinas 13083-871, Brazil
| | | | - Luidy K Issayama
- Faculty of Pharmaceutical Sciences, University of Campinas, Campinas 13083-871, Brazil
| | - Livia A R Moura
- Faculty of Pharmaceutical Sciences, University of Campinas, Campinas 13083-871, Brazil
| | | | - Jörg Kobarg
- Faculty of Pharmaceutical Sciences, University of Campinas, Campinas 13083-871, Brazil
| |
Collapse
|
3
|
Mann JR, McKenna ED, Mawrie D, Papakis V, Alessandrini F, Anderson EN, Mayers R, Ball HE, Kaspi E, Lubinski K, Baron DM, Tellez L, Landers JE, Pandey UB, Kiskinis E. Loss of function of the ALS-associated NEK1 kinase disrupts microtubule homeostasis and nuclear import. SCIENCE ADVANCES 2023; 9:eadi5548. [PMID: 37585529 PMCID: PMC10431718 DOI: 10.1126/sciadv.adi5548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 07/17/2023] [Indexed: 08/18/2023]
Abstract
Loss-of-function variants in NIMA-related kinase 1 (NEK1) constitute a major genetic cause of amyotrophic lateral sclerosis (ALS), accounting for 2 to 3% of all cases. However, how NEK1 mutations cause motor neuron (MN) dysfunction is unknown. Using mass spectrometry analyses for NEK1 interactors and NEK1-dependent expression changes, we find functional enrichment for proteins involved in the microtubule cytoskeleton and nucleocytoplasmic transport. We show that α-tubulin and importin-β1, two key proteins involved in these processes, are phosphorylated by NEK1 in vitro. NEK1 is essential for motor control and survival in Drosophila models in vivo, while using several induced pluripotent stem cell (iPSC)-MN models, including NEK1 knockdown, kinase inhibition, and a patient mutation, we find evidence for disruptions in microtubule homeostasis and nuclear import. Notably, stabilizing microtubules with two distinct classes of drugs restored NEK1-dependent deficits in both pathways. The capacity of NEK1 to modulate these processes that are critically involved in ALS pathophysiology renders this kinase a formidable therapeutic candidate.
Collapse
Affiliation(s)
- Jacob R. Mann
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Elizabeth D. McKenna
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Darilang Mawrie
- Department of Pediatrics, Children’s Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - Vasileios Papakis
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Francesco Alessandrini
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Eric N. Anderson
- Department of Pediatrics, Children’s Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - Ryan Mayers
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Hannah E. Ball
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Evan Kaspi
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Katherine Lubinski
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Desiree M. Baron
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Liana Tellez
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - John E. Landers
- Department of Neurology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Udai B. Pandey
- Department of Pediatrics, Children’s Hospital of Pittsburgh, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - Evangelos Kiskinis
- The Ken & Ruth Davee Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
- Simpson Querrey Institute, Northwestern University, Chicago, IL 60611, USA
- Department of Neuroscience, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| |
Collapse
|
4
|
Bhoir S, De Benedetti A. Targeting Prostate Cancer, the 'Tousled Way'. Int J Mol Sci 2023; 24:11100. [PMID: 37446279 DOI: 10.3390/ijms241311100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/01/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
Androgen deprivation therapy (ADT) has been the mainstay of prostate cancer (PCa) treatment, with success in developing more effective inhibitors of androgen synthesis and antiandrogens in clinical practice. However, hormone deprivation and AR ablation have caused an increase in ADT-insensitive PCas associated with a poor prognosis. Resistance to ADT arises through various mechanisms, and most castration-resistant PCas still rely on the androgen axis, while others become truly androgen receptor (AR)-independent. Our research identified the human tousled-like kinase 1 (TLK1) as a crucial early mediator of PCa cell adaptation to ADT, promoting androgen-independent growth, inhibiting apoptosis, and facilitating cell motility and metastasis. Although explicit, the growing role of TLK1 biology in PCa has remained underrepresented and elusive. In this review, we aim to highlight the diverse functions of TLK1 in PCa, shed light on the molecular mechanisms underlying the transition from androgen-sensitive (AS) to an androgen-insensitive (AI) disease mediated by TLK1, and explore potential strategies to counteract this process. Targeting TLK1 and its associated signaling could prevent PCa progression to the incurable metastatic castration-resistant PCa (mCRPC) stage and provide a promising approach to treating PCa.
Collapse
Affiliation(s)
- Siddhant Bhoir
- Department of Biochemistry and Molecular Biology, LSU Health Shreveport, Shreveport, LA 71103, USA
| | - Arrigo De Benedetti
- Department of Biochemistry and Molecular Biology, LSU Health Shreveport, Shreveport, LA 71103, USA
| |
Collapse
|
5
|
Gregorczyk M, Pastore G, Muñoz I, Carroll T, Streubel J, Munro M, Lis P, Lange S, Lamoliatte F, Macartney T, Toth R, Brown F, Hastie J, Pereira G, Durocher D, Rouse J. Functional characterization of C21ORF2 association with the NEK1 kinase mutated in human in diseases. Life Sci Alliance 2023; 6:e202201740. [PMID: 37188479 PMCID: PMC10185812 DOI: 10.26508/lsa.202201740] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 05/17/2023] Open
Abstract
The NEK1 kinase controls ciliogenesis, mitosis, and DNA repair, and NEK1 mutations cause human diseases including axial spondylometaphyseal dysplasia and amyotrophic lateral sclerosis. C21ORF2 mutations cause a similar pattern of human diseases, suggesting close functional links with NEK1 Here, we report that endogenous NEK1 and C21ORF2 form a tight complex in human cells. A C21ORF2 interaction domain "CID" at the C-terminus of NEK1 is necessary for its association with C21ORF2 in cells, and pathogenic mutations in this region disrupt the complex. AlphaFold modelling predicts an extended binding interface between a leucine-rich repeat domain in C21ORF2 and the NEK1-CID, and our model may explain why pathogenic mutations perturb the complex. We show that NEK1 mutations that inhibit kinase activity or weaken its association with C21ORF2 severely compromise ciliogenesis, and that C21ORF2, like NEK1 is required for homologous recombination. These data enhance our understanding of how the NEK1 kinase is regulated, and they shed light on NEK1-C21ORF2-associated diseases.
Collapse
Affiliation(s)
- Mateusz Gregorczyk
- MRC Protein Phosphorylation and Ubiquitylation Unit, Wellcome Trust Biocentre, University of Dundee, Dundee, UK
| | - Graziana Pastore
- The Lunenfeld-Tannenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Ivan Muñoz
- MRC Protein Phosphorylation and Ubiquitylation Unit, Wellcome Trust Biocentre, University of Dundee, Dundee, UK
| | - Thomas Carroll
- MRC Protein Phosphorylation and Ubiquitylation Unit, Wellcome Trust Biocentre, University of Dundee, Dundee, UK
| | - Johanna Streubel
- German Cancer Research Centre (DKFZ), Centre for Organismal Studies, University of Heidelberg, Heidelberg, Germany
- DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Meagan Munro
- The Lunenfeld-Tannenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Pawel Lis
- MRC Protein Phosphorylation and Ubiquitylation Unit, Wellcome Trust Biocentre, University of Dundee, Dundee, UK
| | - Sven Lange
- MRC Protein Phosphorylation and Ubiquitylation Unit, Wellcome Trust Biocentre, University of Dundee, Dundee, UK
| | - Frederic Lamoliatte
- MRC Protein Phosphorylation and Ubiquitylation Unit, Wellcome Trust Biocentre, University of Dundee, Dundee, UK
| | - Thomas Macartney
- MRC Protein Phosphorylation and Ubiquitylation Unit, Wellcome Trust Biocentre, University of Dundee, Dundee, UK
| | - Rachel Toth
- MRC Protein Phosphorylation and Ubiquitylation Unit, Wellcome Trust Biocentre, University of Dundee, Dundee, UK
| | - Fiona Brown
- MRC Protein Phosphorylation and Ubiquitylation Unit, Wellcome Trust Biocentre, University of Dundee, Dundee, UK
| | - James Hastie
- MRC Protein Phosphorylation and Ubiquitylation Unit, Wellcome Trust Biocentre, University of Dundee, Dundee, UK
| | - Gislene Pereira
- German Cancer Research Centre (DKFZ), Centre for Organismal Studies, University of Heidelberg, Heidelberg, Germany
- DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Daniel Durocher
- The Lunenfeld-Tannenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - John Rouse
- MRC Protein Phosphorylation and Ubiquitylation Unit, Wellcome Trust Biocentre, University of Dundee, Dundee, UK
| |
Collapse
|
6
|
Zhang L, Zhang H, Du S, Song X, Hu D. In Vitro Transcriptional Response of Eimeria tenella to Toltrazuril Reveals That Oxidative Stress and Autophagy Contribute to Its Anticoccidial Effect. Int J Mol Sci 2023; 24:ijms24098370. [PMID: 37176073 PMCID: PMC10179680 DOI: 10.3390/ijms24098370] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/16/2023] [Accepted: 05/04/2023] [Indexed: 05/15/2023] Open
Abstract
Intestinal coccidiosis is a common parasitic disease in livestock, caused by the infection of Eimeria and Cystoisospora parasites, which results in great economic losses to animal husbandry. Triazine compounds, such as toltrazuril and diclazuril, are widely used in the treatment and chemoprophylaxis of coccidiosis. Unfortunately, widespread drug resistance has compromised their effectiveness. Most studies have focused on prophylaxis and therapeutics with toltrazuril in flocks, while a comprehensive understanding of how toltrazuril treatment alters the transcriptome of E. tenella remains unknown. In this study, merozoites of E. tenella were treated in vitro with 0.5 μg/mL toltrazuril for 0, 1, 2 and 4 h, respectively. The gene transcription profiles were then compared by high-throughput sequencing. Our results showed that protein hydrolysis genes were significantly upregulated after drug treatment, while cell cycle-related genes were significantly downregulated, suggesting that toltrazuril may affect parasite division. The expression of redox-related genes was upregulated and elevated levels of ROS and autophagosomes were detected in the parasite after toltrazuril treatment, suggesting that toltrazuril may cause oxidative stress to parasite cells and lead to its autophagy. Our results provide basic knowledge of the response of Eimeria genes to toltrazuril and further analysis of the identified transcriptional changes can provide useful information for a better understanding of the mechanism of action of toltrazuril against Eimeria.
Collapse
Affiliation(s)
- Lei Zhang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Hongtao Zhang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Shiqi Du
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Xingju Song
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning 530004, China
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Nanning 530004, China
| | - Dandan Hu
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
- Guangxi Zhuang Autonomous Region Engineering Research Center of Veterinary Biologics, Nanning 530004, China
- Guangxi Key Laboratory of Animal Breeding, Disease Control and Prevention, Nanning 530004, China
| |
Collapse
|
7
|
Giovannelli I, Higginbottom A, Kirby J, Azzouz M, Shaw PJ. Prospects for gene replacement therapies in amyotrophic lateral sclerosis. Nat Rev Neurol 2023; 19:39-52. [PMID: 36481799 DOI: 10.1038/s41582-022-00751-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/10/2022] [Indexed: 12/13/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a devastating and incurable neurodegenerative disease characterized by the progressive loss of upper and lower motor neurons. ALS causes death, usually within 2-5 years of diagnosis. Riluzole, the only drug currently approved in Europe for the treatment of this condition, offers only a modest benefit, increasing survival by 3 months on average. Recent advances in our understanding of causative or disease-modifying genetic variants and in the development of genetic therapy strategies present exciting new therapeutic opportunities for ALS. In addition, the approval of adeno-associated virus-mediated delivery of functional copies of the SMN1 gene to treat spinal muscular atrophy represents an important therapeutic milestone and demonstrates the potential of gene replacement therapies for motor neuron disorders. In this Review, we describe the current landscape of genetic therapies in ALS, highlighting achievements and critical challenges. In particular, we discuss opportunities for gene replacement therapy in subgroups of people with ALS, and we describe loss-of-function mutations that are known to contribute to the pathophysiology of ALS and could represent novel targets for gene replacement therapies.
Collapse
Affiliation(s)
- Ilaria Giovannelli
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Adrian Higginbottom
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Janine Kirby
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Mimoun Azzouz
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Pamela J Shaw
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK.
| |
Collapse
|
8
|
In Mitosis You Are Not: The NIMA Family of Kinases in Aspergillus, Yeast, and Mammals. Int J Mol Sci 2022; 23:ijms23074041. [PMID: 35409400 PMCID: PMC8999480 DOI: 10.3390/ijms23074041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 03/31/2022] [Accepted: 04/01/2022] [Indexed: 11/17/2022] Open
Abstract
The Never in mitosis gene A (NIMA) family of serine/threonine kinases is a diverse group of protein kinases implicated in a wide variety of cellular processes, including cilia regulation, microtubule dynamics, mitotic processes, cell growth, and DNA damage response. The founding member of this family was initially identified in Aspergillus and was found to play important roles in mitosis and cell division. The yeast family has one member each, Fin1p in fission yeast and Kin3p in budding yeast, also with functions in mitotic processes, but, overall, these are poorly studied kinases. The mammalian family, the main focus of this review, consists of 11 members named Nek1 to Nek11. With the exception of a few members, the functions of the mammalian Neks are poorly understood but appear to be quite diverse. Like the prototypical NIMA, many members appear to play important roles in mitosis and meiosis, but their functions in the cell go well beyond these well-established activities. In this review, we explore the roles of fungal and mammalian NIMA kinases and highlight the most recent findings in the field.
Collapse
|
9
|
CK1 Is a Druggable Regulator of Microtubule Dynamics and Microtubule-Associated Processes. Cancers (Basel) 2022; 14:cancers14051345. [PMID: 35267653 PMCID: PMC8909099 DOI: 10.3390/cancers14051345] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 02/25/2022] [Accepted: 03/03/2022] [Indexed: 02/05/2023] Open
Abstract
Protein kinases of the Casein Kinase 1 family play a vital role in the regulation of numerous cellular processes. Apart from functions associated with regulation of proliferation, differentiation, or apoptosis, localization of several Casein Kinase 1 isoforms to the centrosome and microtubule asters also implicates regulatory functions in microtubule dynamic processes. Being localized to the spindle apparatus during mitosis Casein Kinase 1 directly modulates microtubule dynamics by phosphorylation of tubulin isoforms. Additionally, site-specific phosphorylation of microtubule-associated proteins can be related to the maintenance of genomic stability but also microtubule stabilization/destabilization, e.g., by hyper-phosphorylation of microtubule-associated protein 1A and RITA1. Consequently, approaches interfering with Casein Kinase 1-mediated microtubule-specific functions might be exploited as therapeutic strategies for the treatment of cancer. Currently pursued strategies include the development of Casein Kinase 1 isoform-specific small molecule inhibitors and therapeutically useful peptides specifically inhibiting kinase-substrate interactions.
Collapse
|
10
|
Design, synthesis and biological evaluation of novel aminopyrazole- and 7-azaindole-based Nek1 inhibitors and their effects on zebrafish kidney development. Bioorg Med Chem Lett 2021; 53:128418. [PMID: 34715306 DOI: 10.1016/j.bmcl.2021.128418] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 10/15/2021] [Accepted: 10/19/2021] [Indexed: 01/17/2023]
Abstract
NIMA-related protein kinase Nek1 is crucially involved in cell cycle regulation, DNA repair and microtubule regulation and dysfunctions of Nek1 play key roles in amyotrophic lateral sclerosis (ALS), polycystic kidney disease (PKD) and several types of radiotherapy resistant cancer. Targeting of Nek1 could reveal a new class of radiosensitizing substances and provide useful tools to better understand the aforementioned diseases. In this report we explore substituted aminopyrazoles and 7-azaindoles as potent inhibitors for the Nek1 kinase domain and examine their effect on kidney organogenesis in Danio rerio.
Collapse
|
11
|
Martins MB, Perez AM, Bohr VA, Wilson DM, Kobarg J. NEK1 deficiency affects mitochondrial functions and the transcriptome of key DNA repair pathways. Mutagenesis 2021; 36:223-236. [PMID: 33740813 DOI: 10.1093/mutage/geab011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 03/17/2021] [Indexed: 12/16/2022] Open
Abstract
Previous studies have indicated important roles for NIMA-related kinase 1 (NEK1) in modulating DNA damage checkpoints and DNA repair capacity. To broadly assess the contributions of NEK1 to genotoxic stress and mitochondrial functions, we characterised several relevant phenotypes of NEK1 CRISPR knockout (KO) and wild-type (WT) HAP1 cells. Our studies revealed that NEK1 KO cells resulted in increased apoptosis and hypersensitivity to the alkylator methyl methanesulfonate, the radiomimetic bleomycin and UVC light, yet increased resistance to the crosslinker cisplatin. Mitochondrial functionalities were also altered in NEK1 KO cells, with phenotypes of reduced mitophagy, increased total mitochondria, elevated levels of reactive oxygen species, impaired complex I activity and higher amounts of mitochondrial DNA damage. RNA-seq transcriptome analysis coupled with quantitative real-time PCR studies comparing NEK1 KO cells with NEK1 overexpressing cells revealed that the expression of genes involved in DNA repair pathways, such as base excision repair, nucleotide excision repair and double-strand break repair, are altered in a way that might influence genotoxin resistance. Together, our studies underline and further support that NEK1 serves as a hub signalling kinase in response to DNA damage, modulating DNA repair capacity, mitochondrial activity and cell fate determination.
Collapse
Affiliation(s)
- Mariana Bonjiorno Martins
- Departamento de Bioquímica e de Biologia Tecidual, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Arina Marina Perez
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224-6825, USA
| | - Vilhelm A Bohr
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224-6825, USA
| | - David M Wilson
- Neurosciences Group, Biomedical Research Institute, Hasselt University, 3590 Diepenbeek, Belgium
| | - Jörg Kobarg
- Departamento de Bioquímica e de Biologia Tecidual, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil.,Faculdade de Ciências Farmacêuticas, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| |
Collapse
|
12
|
Baumann G, Meckel T, Böhm K, Shih YH, Dickhaut M, Reichardt T, Pilakowski J, Pehl U, Schmidt B. Illuminating a Dark Kinase: Structure-Guided Design, Synthesis, and Evaluation of a Potent Nek1 Inhibitor and Its Effects on the Embryonic Zebrafish Pronephros. J Med Chem 2021; 65:1265-1282. [DOI: 10.1021/acs.jmedchem.0c02118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Georg Baumann
- Clemens Schöpf−Institute of Organic Chemistry and Biochemistry, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Tobias Meckel
- Clemens Schöpf−Institute of Organic Chemistry and Biochemistry, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Kevin Böhm
- Clemens Schöpf−Institute of Organic Chemistry and Biochemistry, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Yung-Hsin Shih
- Clemens Schöpf−Institute of Organic Chemistry and Biochemistry, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Mirco Dickhaut
- Clemens Schöpf−Institute of Organic Chemistry and Biochemistry, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Torben Reichardt
- Clemens Schöpf−Institute of Organic Chemistry and Biochemistry, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Johannes Pilakowski
- Clemens Schöpf−Institute of Organic Chemistry and Biochemistry, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Ulrich Pehl
- Merck Healthcare KGaA, Biopharma R&D, Discovery and Development Technologies, 64293 Darmstadt, Germany
| | - Boris Schmidt
- Clemens Schöpf−Institute of Organic Chemistry and Biochemistry, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| |
Collapse
|
13
|
Pavan ICB, Peres de Oliveira A, Dias PRF, Basei FL, Issayama LK, Ferezin CDC, Silva FR, Rodrigues de Oliveira AL, Alves dos Reis Moura L, Martins MB, Simabuco FM, Kobarg J. On Broken Ne(c)ks and Broken DNA: The Role of Human NEKs in the DNA Damage Response. Cells 2021; 10:cells10030507. [PMID: 33673578 PMCID: PMC7997185 DOI: 10.3390/cells10030507] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/04/2021] [Accepted: 02/22/2021] [Indexed: 02/07/2023] Open
Abstract
NIMA-related kinases, or NEKs, are a family of Ser/Thr protein kinases involved in cell cycle and mitosis, centrosome disjunction, primary cilia functions, and DNA damage responses among other biological functional contexts in vertebrate cells. In human cells, there are 11 members, termed NEK1 to 11, and the research has mainly focused on exploring the more predominant roles of NEKs in mitosis regulation and cell cycle. A possible important role of NEKs in DNA damage response (DDR) first emerged for NEK1, but recent studies for most NEKs showed participation in DDR. A detailed analysis of the protein interactions, phosphorylation events, and studies of functional aspects of NEKs from the literature led us to propose a more general role of NEKs in DDR. In this review, we express that NEK1 is an activator of ataxia telangiectasia and Rad3-related (ATR), and its activation results in cell cycle arrest, guaranteeing DNA repair while activating specific repair pathways such as homology repair (HR) and DNA double-strand break (DSB) repair. For NEK2, 6, 8, 9, and 11, we found a role downstream of ATR and ataxia telangiectasia mutated (ATM) that results in cell cycle arrest, but details of possible activated repair pathways are still being investigated. NEK4 shows a connection to the regulation of the nonhomologous end-joining (NHEJ) repair of DNA DSBs, through recruitment of DNA-PK to DNA damage foci. NEK5 interacts with topoisomerase IIβ, and its knockdown results in the accumulation of damaged DNA. NEK7 has a regulatory role in the detection of oxidative damage to telomeric DNA. Finally, NEK10 has recently been shown to phosphorylate p53 at Y327, promoting cell cycle arrest after exposure to DNA damaging agents. In summary, this review highlights important discoveries of the ever-growing involvement of NEK kinases in the DDR pathways. A better understanding of these roles may open new diagnostic possibilities or pharmaceutical interventions regarding the chemo-sensitizing inhibition of NEKs in various forms of cancer and other diseases.
Collapse
Affiliation(s)
- Isadora Carolina Betim Pavan
- Graduate Program in “Ciências Farmacêuticas”, School of Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, State University of Campinas (UNICAMP), R. Cândido Portinari 200, Prédio 2, Campinas CEP 13083-871, Brazil; (I.C.B.P.); (A.P.d.O.); (P.R.F.D.); (F.L.B.); (L.K.I.); (F.R.S.); (A.L.R.d.O.); (L.A.d.R.M.); (M.B.M.)
| | - Andressa Peres de Oliveira
- Graduate Program in “Ciências Farmacêuticas”, School of Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, State University of Campinas (UNICAMP), R. Cândido Portinari 200, Prédio 2, Campinas CEP 13083-871, Brazil; (I.C.B.P.); (A.P.d.O.); (P.R.F.D.); (F.L.B.); (L.K.I.); (F.R.S.); (A.L.R.d.O.); (L.A.d.R.M.); (M.B.M.)
| | - Pedro Rafael Firmino Dias
- Graduate Program in “Ciências Farmacêuticas”, School of Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, State University of Campinas (UNICAMP), R. Cândido Portinari 200, Prédio 2, Campinas CEP 13083-871, Brazil; (I.C.B.P.); (A.P.d.O.); (P.R.F.D.); (F.L.B.); (L.K.I.); (F.R.S.); (A.L.R.d.O.); (L.A.d.R.M.); (M.B.M.)
| | - Fernanda Luisa Basei
- Graduate Program in “Ciências Farmacêuticas”, School of Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, State University of Campinas (UNICAMP), R. Cândido Portinari 200, Prédio 2, Campinas CEP 13083-871, Brazil; (I.C.B.P.); (A.P.d.O.); (P.R.F.D.); (F.L.B.); (L.K.I.); (F.R.S.); (A.L.R.d.O.); (L.A.d.R.M.); (M.B.M.)
| | - Luidy Kazuo Issayama
- Graduate Program in “Ciências Farmacêuticas”, School of Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, State University of Campinas (UNICAMP), R. Cândido Portinari 200, Prédio 2, Campinas CEP 13083-871, Brazil; (I.C.B.P.); (A.P.d.O.); (P.R.F.D.); (F.L.B.); (L.K.I.); (F.R.S.); (A.L.R.d.O.); (L.A.d.R.M.); (M.B.M.)
| | - Camila de Castro Ferezin
- Graduate Program in “Biologia Funcional e Molecular”, Department of Biochemistry and Tissue Biology, Institute of Biology, State University of Campinas (UNICAMP), Campinas 13083-857, Brazil;
| | - Fernando Riback Silva
- Graduate Program in “Ciências Farmacêuticas”, School of Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, State University of Campinas (UNICAMP), R. Cândido Portinari 200, Prédio 2, Campinas CEP 13083-871, Brazil; (I.C.B.P.); (A.P.d.O.); (P.R.F.D.); (F.L.B.); (L.K.I.); (F.R.S.); (A.L.R.d.O.); (L.A.d.R.M.); (M.B.M.)
| | - Ana Luisa Rodrigues de Oliveira
- Graduate Program in “Ciências Farmacêuticas”, School of Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, State University of Campinas (UNICAMP), R. Cândido Portinari 200, Prédio 2, Campinas CEP 13083-871, Brazil; (I.C.B.P.); (A.P.d.O.); (P.R.F.D.); (F.L.B.); (L.K.I.); (F.R.S.); (A.L.R.d.O.); (L.A.d.R.M.); (M.B.M.)
| | - Lívia Alves dos Reis Moura
- Graduate Program in “Ciências Farmacêuticas”, School of Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, State University of Campinas (UNICAMP), R. Cândido Portinari 200, Prédio 2, Campinas CEP 13083-871, Brazil; (I.C.B.P.); (A.P.d.O.); (P.R.F.D.); (F.L.B.); (L.K.I.); (F.R.S.); (A.L.R.d.O.); (L.A.d.R.M.); (M.B.M.)
| | - Mariana Bonjiorno Martins
- Graduate Program in “Ciências Farmacêuticas”, School of Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, State University of Campinas (UNICAMP), R. Cândido Portinari 200, Prédio 2, Campinas CEP 13083-871, Brazil; (I.C.B.P.); (A.P.d.O.); (P.R.F.D.); (F.L.B.); (L.K.I.); (F.R.S.); (A.L.R.d.O.); (L.A.d.R.M.); (M.B.M.)
- Graduate Program in “Biologia Funcional e Molecular”, Department of Biochemistry and Tissue Biology, Institute of Biology, State University of Campinas (UNICAMP), Campinas 13083-857, Brazil;
| | | | - Jörg Kobarg
- Graduate Program in “Ciências Farmacêuticas”, School of Pharmaceutical Sciences, Faculty of Pharmaceutical Sciences, State University of Campinas (UNICAMP), R. Cândido Portinari 200, Prédio 2, Campinas CEP 13083-871, Brazil; (I.C.B.P.); (A.P.d.O.); (P.R.F.D.); (F.L.B.); (L.K.I.); (F.R.S.); (A.L.R.d.O.); (L.A.d.R.M.); (M.B.M.)
- Graduate Program in “Biologia Funcional e Molecular”, Department of Biochemistry and Tissue Biology, Institute of Biology, State University of Campinas (UNICAMP), Campinas 13083-857, Brazil;
- Correspondence: ; Tel.: +55-19-3521-8143
| |
Collapse
|
14
|
Guo W, Vandoorne T, Steyaert J, Staats KA, Van Den Bosch L. The multifaceted role of kinases in amyotrophic lateral sclerosis: genetic, pathological and therapeutic implications. Brain 2021; 143:1651-1673. [PMID: 32206784 PMCID: PMC7296858 DOI: 10.1093/brain/awaa022] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 11/23/2019] [Accepted: 12/11/2019] [Indexed: 02/07/2023] Open
Abstract
Amyotrophic lateral sclerosis is the most common degenerative disorder of motor neurons in adults. As there is no cure, thousands of individuals who are alive at present will succumb to the disease. In recent years, numerous causative genes and risk factors for amyotrophic lateral sclerosis have been identified. Several of the recently identified genes encode kinases. In addition, the hypothesis that (de)phosphorylation processes drive the disease process resulting in selective motor neuron degeneration in different disease variants has been postulated. We re-evaluate the evidence for this hypothesis based on recent findings and discuss the multiple roles of kinases in amyotrophic lateral sclerosis pathogenesis. We propose that kinases could represent promising therapeutic targets. Mainly due to the comprehensive regulation of kinases, however, a better understanding of the disturbances in the kinome network in amyotrophic lateral sclerosis is needed to properly target specific kinases in the clinic.
Collapse
Affiliation(s)
- Wenting Guo
- KU Leuven-University of Leuven, Department of Neurosciences, Experimental Neurology, and Leuven Brain Institute (LBI), Leuven, Belgium.,VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, Leuven, Belgium.,KU Leuven-Stem Cell Institute (SCIL), Leuven, Belgium
| | - Tijs Vandoorne
- KU Leuven-University of Leuven, Department of Neurosciences, Experimental Neurology, and Leuven Brain Institute (LBI), Leuven, Belgium.,VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, Leuven, Belgium
| | - Jolien Steyaert
- KU Leuven-University of Leuven, Department of Neurosciences, Experimental Neurology, and Leuven Brain Institute (LBI), Leuven, Belgium.,VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, Leuven, Belgium
| | - Kim A Staats
- Department of Stem Cell Biology and Regenerative Medicine, University of Southern California, Los Angeles, California, USA
| | - Ludo Van Den Bosch
- KU Leuven-University of Leuven, Department of Neurosciences, Experimental Neurology, and Leuven Brain Institute (LBI), Leuven, Belgium.,VIB, Center for Brain & Disease Research, Laboratory of Neurobiology, Leuven, Belgium
| |
Collapse
|
15
|
Khalil MI, Ghosh I, Singh V, Chen J, Zhu H, De Benedetti A. NEK1 Phosphorylation of YAP Promotes Its Stabilization and Transcriptional Output. Cancers (Basel) 2020; 12:cancers12123666. [PMID: 33297404 PMCID: PMC7762262 DOI: 10.3390/cancers12123666] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 12/04/2020] [Accepted: 12/04/2020] [Indexed: 12/13/2022] Open
Abstract
Simple Summary We earlier described the involvement of the TLK1>NEK1>ATR>Chk1 axis as a key determinant of cell cycle arrest in androgen-dependent prostate cancer (PCa) cells after androgen deprivation. We now report that the TLK1>NEK1 axis is also involved in stabilization of yes-associated protein 1 (YAP1), the transcriptional co-activator in the Hippo pathway, presumably facilitating reprogramming of the cells toward castration-resistant PCa (CRPC). NEK1 interacts with YAP1 physically resulting in its phosphorylation of 6 residues, which enhance its stability and activity. Analyses of cancer Protein Atlas and TCGA expression panels revealed a link between activated NEK1 and YAP1 expression and several YAP transcription targets. Abstract Most prostate cancer (PCa) deaths result from progressive failure in standard androgen deprivation therapy (ADT), leading to metastatic castration-resistant PCa (mCRPC); however, the mechanism and key players leading to this are not fully understood. While studying the role of tousled-like kinase 1 (TLK1) and never in mitosis gene A (NIMA)-related kinase 1 (NEK1) in a DNA damage response (DDR)-mediated cell cycle arrest in LNCaP cells treated with bicalutamide, we uncovered that overexpression of wt-NEK1 resulted in a rapid conversion to androgen-independent (AI) growth, analogous to what has been observed when YAP1 is overexpressed. We now report that overexpression of wt-NEK1 results in accumulation of YAP1, suggesting the existence of a TLK1>NEK1>YAP1 axis that leads to adaptation to AI growth. Further, YAP1 is co-immunoprecipitated with NEK1. Importantly, NEK1 was able to phosphorylate YAP1 on six residues in vitro, which we believe are important for stabilization of the protein, possibly by increasing its interaction with transcriptional partners. In fact, knockout (KO) of NEK1 in NT1 PCa cells resulted in a parallel decrease of YAP1 level and reduced expression of typical YAP-regulated target genes. In terms of cancer potential implications, the expression of NEK1 and YAP1 proteins was found to be increased and correlated in several cancers. These include PCa stages according to Gleason score, head and neck squamous cell carcinoma, and glioblastoma, suggesting that this co-regulation is imparted by increased YAP1 stability when NEK1 is overexpressed or activated by TLK1, and not through transcriptional co-expression. We propose that the TLK1>NEK1>YAP1 axis is a key determinant for cancer progression, particularly during the process of androgen-sensitive to -independent conversion during progression to mCRPC.
Collapse
Affiliation(s)
- Md Imtiaz Khalil
- Department of Biochemistry and Molecular Biology, LSU Health Sciences Center, Shreveport, LA 71130, USA; (M.I.K.); (I.G.); (V.S.)
| | - Ishita Ghosh
- Department of Biochemistry and Molecular Biology, LSU Health Sciences Center, Shreveport, LA 71130, USA; (M.I.K.); (I.G.); (V.S.)
| | - Vibha Singh
- Department of Biochemistry and Molecular Biology, LSU Health Sciences Center, Shreveport, LA 71130, USA; (M.I.K.); (I.G.); (V.S.)
| | - Jing Chen
- Department of Molecular and Cellular Biochemistry and Proteomics Core, Center for Structural Biology, University of Kentucky, Lexington, KY 40506, USA; (J.C.); (H.Z.)
| | - Haining Zhu
- Department of Molecular and Cellular Biochemistry and Proteomics Core, Center for Structural Biology, University of Kentucky, Lexington, KY 40506, USA; (J.C.); (H.Z.)
| | - Arrigo De Benedetti
- Department of Biochemistry and Molecular Biology, LSU Health Sciences Center, Shreveport, LA 71130, USA; (M.I.K.); (I.G.); (V.S.)
- Correspondence: ; Tel.: +1-31-8675-5668
| |
Collapse
|
16
|
Dekel N, Eisenberg-Domovich Y, Karlas A, Meyer TF, Bracher F, Lebendiker M, Danieli T, Livnah O. Expression, purification and crystallization of CLK1 kinase - A potential target for antiviral therapy. Protein Expr Purif 2020; 176:105742. [PMID: 32866611 DOI: 10.1016/j.pep.2020.105742] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/03/2020] [Accepted: 08/26/2020] [Indexed: 12/15/2022]
Abstract
Cdc-like kinase 1 (CLK1) is a dual-specificity kinase capable of autophosphorylation on tyrosine residues and Ser/Thr phosphorylation of its substrates. CLK1 belongs to the CLK kinase family that regulates alternative splicing through phosphorylation of serine-arginine rich (SR) proteins. Recent studies have demonstrated that CLK1 has an important role in the replication of influenza A and chikungunya viruses. Furthermore, CLK1 was found to be relevant for the replication of HIV-1 and the West Nile virus, making CLK1 an interesting cellular candidate for the development of a host-directed antiviral therapy that might be efficient for treatment of newly emerging viruses. We describe here our attempts and detailed procedures to obtain the recombinant kinase domain of CLK1 in suitable amounts for crystallization in complex with specific inhibitors. The key solution for the reproducibility of crystals resides in devising and refining expression and purification protocols leading to homogeneous protein. Co-expression of CLK1 with λ-phosphatase and careful purification has yielded crystals of CLK1 complexed with the KH-CB19 inhibitor that diffracted to 1.65 Å. These results paved the path to the screening of more structures of CLK1 complexed compounds, leading to further optimization of their inhibitory activity. Moreover, since kinases are desired targets in numerous pathologies, the approach we report here, the co-expression of kinases with λ-phosphatase, previously used in other kinases, can be adopted as a general protocol in numerous kinase targets for obtaining reproducible and homogenic non-phosphorylated (inactive) forms suitable for biochemical and structural studies thus facilitating the development of novel inhibitors.
Collapse
Affiliation(s)
- Noa Dekel
- The Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Yael Eisenberg-Domovich
- The Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | | | - Thomas F Meyer
- Max Planck Institute for Infection Biology, Department of Molecular Biology, Charitéplatz 1, 10117, Berlin, Germany
| | - Franz Bracher
- Ludwig-Maximilians University, Department of Pharmacy-Center for Drug Research, Butenandstrasse 5-13, 81377, Munich, Germany
| | - Mario Lebendiker
- The Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Tsafi Danieli
- The Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Oded Livnah
- The Wolfson Centre for Applied Structural Biology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel; Department of Biological Chemistry, Alexander Silverman Institute of Life Sciences, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Israel.
| |
Collapse
|
17
|
Watanabe Y, Nakagawa T, Akiyama T, Nakagawa M, Suzuki N, Warita H, Aoki M, Nakayama K. An Amyotrophic Lateral Sclerosis-Associated Mutant of C21ORF2 Is Stabilized by NEK1-Mediated Hyperphosphorylation and the Inability to Bind FBXO3. iScience 2020; 23:101491. [PMID: 32891887 PMCID: PMC7481237 DOI: 10.1016/j.isci.2020.101491] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 07/18/2020] [Accepted: 08/19/2020] [Indexed: 11/21/2022] Open
Abstract
C21ORF2 and NEK1 have been identified as amyotrophic lateral sclerosis (ALS)-associated genes. Both genes are also mutated in certain ciliopathies, suggesting that they might contribute to the same signaling pathways. Here we show that FBXO3, the substrate receptor of an SCF ubiquitin ligase complex, binds and ubiquitylates C21ORF2, thereby targeting it for proteasomal degradation. C21ORF2 stabilizes the kinase NEK1, with the result that loss of FBXO3 stabilizes not only C21ORF2 but also NEK1. Conversely, NEK1-mediated phosphorylation stabilizes C21ORF2 by attenuating its interaction with FBXO3. We found that the ALS-associated V58L mutant of C21ORF2 is more susceptible to phosphorylation by NEK1, with the result that it is not ubiquitylated by FBXO3 and therefore accumulates together with NEK1. Expression of C21ORF2(V58L) in motor neurons induced from mouse embryonic stem cells impaired neurite outgrowth. We suggest that inhibition of NEK1 activity is a potential therapeutic approach to ALS associated with C21ORF2 mutation.
Collapse
Affiliation(s)
- Yasuaki Watanabe
- Department of Neurology, Graduate School of Medicine, Tohoku University, Sendai, Miyagi 980-8575, Japan; Division of Cell Proliferation, ART, Graduate School of Medicine, Tohoku University, Sendai, Miyagi 980-8575, Japan
| | - Tadashi Nakagawa
- Division of Cell Proliferation, ART, Graduate School of Medicine, Tohoku University, Sendai, Miyagi 980-8575, Japan
| | - Tetsuya Akiyama
- Department of Neurology, Graduate School of Medicine, Tohoku University, Sendai, Miyagi 980-8575, Japan
| | - Makiko Nakagawa
- Division of Cell Proliferation, ART, Graduate School of Medicine, Tohoku University, Sendai, Miyagi 980-8575, Japan
| | - Naoki Suzuki
- Department of Neurology, Graduate School of Medicine, Tohoku University, Sendai, Miyagi 980-8575, Japan
| | - Hitoshi Warita
- Department of Neurology, Graduate School of Medicine, Tohoku University, Sendai, Miyagi 980-8575, Japan
| | - Masashi Aoki
- Department of Neurology, Graduate School of Medicine, Tohoku University, Sendai, Miyagi 980-8575, Japan
| | - Keiko Nakayama
- Division of Cell Proliferation, ART, Graduate School of Medicine, Tohoku University, Sendai, Miyagi 980-8575, Japan.
| |
Collapse
|
18
|
Peres de Oliveira A, Kazuo Issayama L, Betim Pavan IC, Riback Silva F, Diniz Melo-Hanchuk T, Moreira Simabuco F, Kobarg J. Checking NEKs: Overcoming a Bottleneck in Human Diseases. Molecules 2020; 25:molecules25081778. [PMID: 32294979 PMCID: PMC7221840 DOI: 10.3390/molecules25081778] [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: 03/10/2020] [Revised: 04/02/2020] [Accepted: 04/09/2020] [Indexed: 12/12/2022] Open
Abstract
In previous years, several kinases, such as phosphoinositide 3-kinase (PI3K), mammalian target of rapamycin (mTOR), and extracellular-signal-regulated kinase (ERK), have been linked to important human diseases, although some kinase families remain neglected in terms of research, hiding their relevance to therapeutic approaches. Here, a review regarding the NEK family is presented, shedding light on important information related to NEKs and human diseases. NEKs are a large group of homologous kinases with related functions and structures that participate in several cellular processes such as the cell cycle, cell division, cilia formation, and the DNA damage response. The review of the literature points to the pivotal participation of NEKs in important human diseases, like different types of cancer, diabetes, ciliopathies and central nervous system related and inflammatory-related diseases. The different known regulatory molecular mechanisms specific to each NEK are also presented, relating to their involvement in different diseases. In addition, important information about NEKs remains to be elucidated and is highlighted in this review, showing the need for other studies and research regarding this kinase family. Therefore, the NEK family represents an important group of kinases with potential applications in the therapy of human diseases.
Collapse
Affiliation(s)
- Andressa Peres de Oliveira
- Instituto de Biologia, Departamento de Bioquímica e Biologia Tecidual, Universidade Estadual de Campinas, Campinas, São Paulo 13083-862, Brazil; (A.P.d.O.); (L.K.I.); (I.C.B.P.); (F.R.S.); (T.D.M.-H.)
| | - Luidy Kazuo Issayama
- Instituto de Biologia, Departamento de Bioquímica e Biologia Tecidual, Universidade Estadual de Campinas, Campinas, São Paulo 13083-862, Brazil; (A.P.d.O.); (L.K.I.); (I.C.B.P.); (F.R.S.); (T.D.M.-H.)
- Faculdade de Ciências Farmacêuticas, Universidade Estadual de Campinas, Campinas, São Paulo 13083-871, Brazil
| | - Isadora Carolina Betim Pavan
- Instituto de Biologia, Departamento de Bioquímica e Biologia Tecidual, Universidade Estadual de Campinas, Campinas, São Paulo 13083-862, Brazil; (A.P.d.O.); (L.K.I.); (I.C.B.P.); (F.R.S.); (T.D.M.-H.)
- Faculdade de Ciências Farmacêuticas, Universidade Estadual de Campinas, Campinas, São Paulo 13083-871, Brazil
- Laboratório Multidisciplinar em Alimentos e Saúde, Faculdade de Ciências Aplicadas, Universidade Estadual de Campinas, São Paulo 13484-350, Brazil;
| | - Fernando Riback Silva
- Instituto de Biologia, Departamento de Bioquímica e Biologia Tecidual, Universidade Estadual de Campinas, Campinas, São Paulo 13083-862, Brazil; (A.P.d.O.); (L.K.I.); (I.C.B.P.); (F.R.S.); (T.D.M.-H.)
- Faculdade de Ciências Farmacêuticas, Universidade Estadual de Campinas, Campinas, São Paulo 13083-871, Brazil
| | - Talita Diniz Melo-Hanchuk
- Instituto de Biologia, Departamento de Bioquímica e Biologia Tecidual, Universidade Estadual de Campinas, Campinas, São Paulo 13083-862, Brazil; (A.P.d.O.); (L.K.I.); (I.C.B.P.); (F.R.S.); (T.D.M.-H.)
- Faculdade de Ciências Farmacêuticas, Universidade Estadual de Campinas, Campinas, São Paulo 13083-871, Brazil
| | - Fernando Moreira Simabuco
- Laboratório Multidisciplinar em Alimentos e Saúde, Faculdade de Ciências Aplicadas, Universidade Estadual de Campinas, São Paulo 13484-350, Brazil;
| | - Jörg Kobarg
- Faculdade de Ciências Farmacêuticas, Universidade Estadual de Campinas, Campinas, São Paulo 13083-871, Brazil
- Correspondence: ; Tel.: +55-19-3521-8143
| |
Collapse
|
19
|
van de Kooij B, Creixell P, van Vlimmeren A, Joughin BA, Miller CJ, Haider N, Simpson CD, Linding R, Stambolic V, Turk BE, Yaffe MB. Comprehensive substrate specificity profiling of the human Nek kinome reveals unexpected signaling outputs. eLife 2019; 8:44635. [PMID: 31124786 PMCID: PMC6570481 DOI: 10.7554/elife.44635] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 05/13/2019] [Indexed: 12/25/2022] Open
Abstract
Human NimA-related kinases (Neks) have multiple mitotic and non-mitotic functions, but few substrates are known. We systematically determined the phosphorylation-site motifs for the entire Nek kinase family, except for Nek11. While all Nek kinases strongly select for hydrophobic residues in the −3 position, the family separates into four distinct groups based on specificity for a serine versus threonine phospho-acceptor, and preference for basic or acidic residues in other positions. Unlike Nek1-Nek9, Nek10 is a dual-specificity kinase that efficiently phosphorylates itself and peptide substrates on serine and tyrosine, and its activity is enhanced by tyrosine auto-phosphorylation. Nek10 dual-specificity depends on residues in the HRD+2 and APE-4 positions that are uncommon in either serine/threonine or tyrosine kinases. Finally, we show that the phosphorylation-site motifs for the mitotic kinases Nek6, Nek7 and Nek9 are essentially identical to that of their upstream activator Plk1, suggesting that Nek6/7/9 function as phospho-motif amplifiers of Plk1 signaling.
Collapse
Affiliation(s)
- Bert van de Kooij
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, United States.,MIT Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, United States
| | - Pau Creixell
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, United States.,MIT Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, United States
| | - Anne van Vlimmeren
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, United States.,MIT Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, United States
| | - Brian A Joughin
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, United States.,MIT Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, United States
| | - Chad J Miller
- Department of Pharmacology, Yale School of Medicine, New Haven, United States
| | - Nasir Haider
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Craig D Simpson
- Biotech Research and Innovation Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rune Linding
- Biotech Research and Innovation Center, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Vuk Stambolic
- Department of Medical Biophysics, University of Toronto, Toronto, Canada.,Princess Margaret Cancer Center, University Health Network, Toronto, Canada
| | - Benjamin E Turk
- Department of Pharmacology, Yale School of Medicine, New Haven, United States
| | - Michael B Yaffe
- Department of Biology, Massachusetts Institute of Technology, Cambridge, United States.,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States.,Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, United States.,MIT Center for Precision Cancer Medicine, Massachusetts Institute of Technology, Cambridge, United States.,Department of Surgery, Beth Israel Deaconess Medical Center, Divisions of Acute Care Surgery, Trauma, and Critical Care and Surgical Oncology, Harvard Medical School, Boston, United States
| |
Collapse
|
20
|
Melo-Hanchuk TD, Slepicka PF, Pelegrini AL, Menck CFM, Kobarg J. NEK5 interacts with topoisomerase IIβ and is involved in the DNA damage response induced by etoposide. J Cell Biochem 2019; 120:16853-16866. [PMID: 31090963 DOI: 10.1002/jcb.28943] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 04/16/2019] [Accepted: 04/18/2019] [Indexed: 02/06/2023]
Abstract
Cells are daily submitted to high levels of DNA lesions that trigger complex pathways and cellular responses by cell cycle arrest, apoptosis, alterations in transcriptional response, and the onset of DNA repair. Members of the NIMA-related kinase (NEK) family have been related to DNA damage response and repair and the first insight about NEK5 in this context is related to its role in centrosome separation resulting in defects in chromosome integrity. Here we investigate the potential correlation between NEK5 and the DNA damage repair index. The effect of NEK5 in double-strand breaks caused by etoposide was accessed by alkaline comet assay and revealed that NEK5-silenced cells are more sensitive to etoposide treatment. Topoisomerase IIβ (TOPIIβ) is a target of etoposide that leads to the production of DNA breaks. We demonstrate that NEK5 interacts with TOPIIβ, and the dynamics of this interaction is evaluated by proximity ligation assay. The complex NEK5/TOPIIβ is formed immediately after etoposide treatment. Taken together, the results of our study reveal that NEK5 depletion increases DNA damage and impairs proper DNA damage response, pointing out NEK5 as a potential kinase contributor to genomic stability.
Collapse
Affiliation(s)
- Talita Diniz Melo-Hanchuk
- Departamento de Bioquímica e Biologia Tecidual, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Priscila Ferreira Slepicka
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo, Brazil
| | - Alessandra Luiza Pelegrini
- Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | | | - Jörg Kobarg
- Departamento de Bioquímica e Biologia Tecidual, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil.,Faculdade de Ciências Farmacêuticas, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| |
Collapse
|
21
|
Vijayakumar UG, Milla V, Cynthia Stafford MY, Bjourson AJ, Duddy W, Duguez SMR. A Systematic Review of Suggested Molecular Strata, Biomarkers and Their Tissue Sources in ALS. Front Neurol 2019; 10:400. [PMID: 31139131 PMCID: PMC6527847 DOI: 10.3389/fneur.2019.00400] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 04/02/2019] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS), also known as motor neuron disease, is an incurable neurodegenerative condition, characterized by the loss of upper and lower motor neurons. It affects 1–1.8/100,000 individuals worldwide, and the number of cases is projected to increase as the population ages. Thus, there is an urgent need to identify both therapeutic targets and disease-specific biomarkers–biomarkers that would be useful to diagnose and stratify patients into different sub-groups for therapeutic strategies, as well as biomarkers to follow the efficacy of any treatment tested during clinical trials. There is a lack of knowledge about pathogenesis and many hypotheses. Numerous “omics” studies have been conducted on ALS in the past decade to identify a disease-signature in tissues and circulating biomarkers. The first goal of the present review was to group the molecular pathways that have been implicated in monogenic forms of ALS, to enable the description of patient strata corresponding to each pathway grouping. This strategy allowed us to suggest 14 strata, each potentially targetable by different pharmacological strategies. The second goal of this review was to identify diagnostic/prognostic biomarker candidates consistently observed across the literature. For this purpose, we explore previous biomarker-relevant “omics” studies of ALS and summarize their findings, focusing on potential circulating biomarker candidates. We systematically review 118 papers on biomarkers published during the last decade. Several candidate markers were consistently shared across the results of different studies in either cerebrospinal fluid (CSF) or blood (leukocyte or serum/plasma). Although these candidates still need to be validated in a systematic manner, we suggest the use of combinations of biomarkers that would likely reflect the “health status” of different tissues, including motor neuron health (e.g., pNFH and NF-L, cystatin C, Transthyretin), inflammation status (e.g., MCP-1, miR451), muscle health (miR-338-3p, miR-206) and metabolism (homocysteine, glutamate, cholesterol). In light of these studies and because ALS is increasingly perceived as a multi-system disease, the identification of a panel of biomarkers that accurately reflect features of pathology is a priority, not only for diagnostic purposes but also for prognostic or predictive applications.
Collapse
Affiliation(s)
- Udaya Geetha Vijayakumar
- Northern Ireland Center for Stratified Medicine, Biomedical Sciences Research Institute, Londonderry, United Kingdom
| | - Vanessa Milla
- Northern Ireland Center for Stratified Medicine, Biomedical Sciences Research Institute, Londonderry, United Kingdom
| | - Mei Yu Cynthia Stafford
- Northern Ireland Center for Stratified Medicine, Biomedical Sciences Research Institute, Londonderry, United Kingdom
| | - Anthony J Bjourson
- Northern Ireland Center for Stratified Medicine, Biomedical Sciences Research Institute, Londonderry, United Kingdom
| | - William Duddy
- Northern Ireland Center for Stratified Medicine, Biomedical Sciences Research Institute, Londonderry, United Kingdom
| | - Stephanie Marie-Rose Duguez
- Northern Ireland Center for Stratified Medicine, Biomedical Sciences Research Institute, Londonderry, United Kingdom
| |
Collapse
|
22
|
Fry AM, Bayliss R, Roig J. Mitotic Regulation by NEK Kinase Networks. Front Cell Dev Biol 2017; 5:102. [PMID: 29250521 PMCID: PMC5716973 DOI: 10.3389/fcell.2017.00102] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 11/17/2017] [Indexed: 12/24/2022] Open
Abstract
Genetic studies in yeast and Drosophila led to identification of cyclin-dependent kinases (CDKs), Polo-like kinases (PLKs) and Aurora kinases as essential regulators of mitosis. These enzymes have since been found in the majority of eukaryotes and their cell cycle-related functions characterized in great detail. However, genetic studies in another fungal species, Aspergillus nidulans, identified a distinct family of protein kinases, the NEKs, that are also widely conserved and have key roles in the cell cycle, but which remain less well studied. Nevertheless, it is now clear that multiple NEK family members act in networks to regulate specific events of mitosis, including centrosome separation, spindle assembly and cytokinesis. Here, we describe our current understanding of how the NEK kinases contribute to these processes, particularly through targeted phosphorylation of proteins associated with the microtubule cytoskeleton. We also present the latest findings on molecular events that control the activation state of the NEKs and how these are revealing novel modes of enzymatic regulation relevant not only to other kinases but also to pathological mechanisms of disease.
Collapse
Affiliation(s)
- Andrew M. Fry
- Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
| | - Richard Bayliss
- School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | - Joan Roig
- Institut de Biologia Molecular de Barcelona (IBMB-CSIC), Barcelona, Spain
| |
Collapse
|