1
|
Panchal NK, Mohanty S, Prince SE. Computational insights into NIMA-related kinase 6: unraveling mutational effects on structure and function. Mol Cell Biochem 2023:10.1007/s11010-023-04910-0. [PMID: 38117419 DOI: 10.1007/s11010-023-04910-0] [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: 09/09/2023] [Accepted: 11/25/2023] [Indexed: 12/21/2023]
Abstract
The NEK6 (NIMA-related kinase 6) serine/threonine kinase is a pivotal player in a multitude of cellular processes, including the regulation of the cell cycle and the response to DNA damage. Its significance extends to disease pathogenesis, as changes in NEK6 activity have been linked to the development of cancer. Non-synonymous single nucleotide polymorphisms (nsSNPs) in NEK6 have been linked to cancer as they alter the protein's native structure and function. The association between NEK6 activity and cancer development has prompted researchers to explore the effects of genetic variations within the NEK6 gene. Therefore, we utilized advanced computational tools to analyze 155 high-confidence nsSNPs in the NEK6 gene. From this analysis, 21 nsSNPs were identified as potentially harmful, raising concerns about their impact on NEK6 activity and cancer risk. These 21 mutations were then examined for structural alterations, and eight of nsSNPs (I51M, V76A, I134N, Y152D, R171Q, V186G, L237R, and C285S) were found to destabilize the protein. Among the destabilizing mutations screened, a specific mutation, R171Q, stood out due to its conserved nature. To understand its impact on the protein and conformation, all-atom molecular dynamics simulations (MDS) for 100 ns were performed for both Wildtype NEK6 (WT-NEK6) and R171Q. The simulations revealed that the R171Q variant was unstable and led to significant conformational changes in NEK6. This study provides valuable insights into NEK6 dysfunction caused by single amino acid alterations, offering a novel understanding of the molecular mechanisms underlying NEK6-related cancer progression.
Collapse
Affiliation(s)
- Nagesh Kishan Panchal
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, 632 014, India
| | - Shruti Mohanty
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, 632014, India
| | - Sabina Evan Prince
- Department of Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, 632 014, India.
| |
Collapse
|
2
|
Nguyen K, Boehling J, Tran MN, Cheng T, Rivera A, Collins-Burow BM, Lee SB, Drewry DH, Burow ME. NEK Family Review and Correlations with Patient Survival Outcomes in Various Cancer Types. Cancers (Basel) 2023; 15:cancers15072067. [PMID: 37046733 PMCID: PMC10093199 DOI: 10.3390/cancers15072067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 03/22/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023] Open
Abstract
The Never in Mitosis Gene A (NIMA)–related kinases (NEKs) are a group of serine/threonine kinases that are involved in a wide array of cellular processes including cell cycle regulation, DNA damage repair response (DDR), apoptosis, and microtubule organization. Recent studies have identified the involvement of NEK family members in various diseases such as autoimmune disorders, malignancies, and developmental defects. Despite the existing literature exemplifying the importance of the NEK family of kinases, this family of protein kinases remains understudied. This report seeks to provide a foundation for investigating the role of different NEKs in malignancies. We do this by evaluating the 11 NEK family kinase gene expression associations with patients’ overall survival (OS) from various cancers using the Kaplan–Meier Online Tool (KMPlotter) to correlate the relationship between mRNA expression of NEK1-11 in various cancers and patient survival. Furthermore, we use the Catalog of Somatic Mutations in Cancer (COSMIC) database to identify NEK family mutations in cancers of different tissues. Overall, the data suggest that the NEK family has varying associations with patient survival in different cancers with tumor-suppressive and tumor-promoting effects being tissue-dependent.
Collapse
|
3
|
Panchal NK, Mohanty S, Prince SE. NIMA-related kinase-6 (NEK6) as an executable target in cancer. CLINICAL & TRANSLATIONAL ONCOLOGY : OFFICIAL PUBLICATION OF THE FEDERATION OF SPANISH ONCOLOGY SOCIETIES AND OF THE NATIONAL CANCER INSTITUTE OF MEXICO 2023; 25:66-77. [PMID: 36074296 DOI: 10.1007/s12094-022-02926-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 08/09/2022] [Indexed: 01/07/2023]
Abstract
Cancer is a disease that develops when cells begin to divide uncontrollably and spreads to other parts of the body. Proliferation and invasion of cancerous cells are generally known to be influenced by cell cycle-related proteins in human malignancies. Therefore, in this review, we have emphasized on the serine/threonine kinase named NEK6. NEK6 is been deliberated to play a critical role in mitosis progression that includes mitotic spindle formation, metaphase to anaphase transition, and centrosome separation. Moreover, it has a mechanistic role in DNA repair and can cause apoptosis when inhibited. Past studies have connected NEK6 protein expression to cancer cell senescence. Besides, there are reports relating NEK6 to a range of malignancies including breast, lung, ovarian, prostate, kidney, liver, and others. Given its significance, this review attempts to describe the structural and functional aspects of NEK6 in various cellular processes, as well as how it is linked to different forms of cancer. Lastly, we have accentuated, on some of the plausible inhibitors that have been explored against NEK6 overexpression.
Collapse
Affiliation(s)
- Nagesh Kishan Panchal
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, 632014, India
| | - Shruti Mohanty
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, 632014, India
| | - Sabina Evan Prince
- Department of Biomedical Sciences, School of Biosciences and Technology, Vellore Institute of Technology, Vellore, 632014, India.
| |
Collapse
|
4
|
Identification of potent inhibitors of NEK7 protein using a comprehensive computational approach. Sci Rep 2022; 12:6404. [PMID: 35436996 PMCID: PMC9016071 DOI: 10.1038/s41598-022-10253-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 04/01/2022] [Indexed: 02/07/2023] Open
Abstract
NIMA related Kinases (NEK7) plays an important role in spindle assembly and mitotic division of the cell. Over expression of NEK7 leads to the progression of different cancers and associated malignancies. It is becoming the next wave of targets for the development of selective and potent anti-cancerous agents. The current study is the first comprehensive computational approach to identify potent inhibitors of NEK7 protein. For this purpose, previously identified anti-inflammatory compound i.e., Phenylcarbamoylpiperidine-1,2,4-triazole amide derivatives by our own group were selected for their anti-cancer potential via detailed Computational studies. Initially, the density functional theory (DFT) calculations were carried out using Gaussian 09 software which provided information about the compounds' stability and reactivity. Furthermore, Autodock suite and Molecular Operating Environment (MOE) software’s were used to dock the ligand database into the active pocket of the NEK7 protein. Both software performances were compared in terms of sampling power and scoring power. During the analysis, Autodock results were found to be more reproducible, implying that this software outperforms the MOE. The majority of the compounds, including M7, and M12 showed excellent binding energies and formed stable protein–ligand complexes with docking scores of − 29.66 kJ/mol and − 31.38 kJ/mol, respectively. The results were validated by molecular dynamics simulation studies where the stability and conformational transformation of the best protein–ligand complex were justified on the basis of RMSD and RMSF trajectory analysis. The drug likeness properties and toxicity profile of all compounds were determined by ADMETlab 2.0. Furthermore, the anticancer potential of the potent compounds were confirmed by cell viability (MTT) assay. This study suggested that selected compounds can be further investigated at molecular level and evaluated for cancer treatment and associated malignancies.
Collapse
|
5
|
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
|
6
|
Wang XJ, Li S, Fang J, Yan ZJ, Luo GC. LncRNA FAM13A-AS1 Promotes Renal Carcinoma Tumorigenesis Through Sponging miR-141-3p to Upregulate NEK6 Expression. Front Mol Biosci 2022; 9:738711. [PMID: 35402517 PMCID: PMC8984162 DOI: 10.3389/fmolb.2022.738711] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 03/03/2022] [Indexed: 11/13/2022] Open
Abstract
Long non-coding RNAs are a diverse catalog of RNAs that have been implicated in various aspects of tumorigenesis. Emerging evidence indicates that they play crucial roles in tumor growth, disease progression, and drug resistance. However, the clinical significance of lncRNAs in tumor behavior prediction and disease prognosis as well as the underlying mechanism in renal cell carcinoma (RCC) remains elusive. By analyzing the gene expression profiles of 539 RCC patients from the TCGA cohort and 40 RCC patients from an independent cohort, we identified FAM13A-AS1, a poorly studied lncRNA, upregulated in RCC patients. Knockdown experiments revealed that FAM13A-AS1 promotes cell proliferation, migration, and invasion by interacting with miR-141-3p. FAM13A-AS1 regulates the expression of NEK6 by decoying miR-141-3p. In addition, there was a strong positive correlation between the expression of FAM13A-AS1 and NEK6 in RCC patients. In summary, our results demonstrate the oncogenic role of FAM13A-AS1 in RCC and suggest that it promotes tumorigenesis by upregulating the expression of NEK6 by competitively binding to miR-141-3p.
Collapse
Affiliation(s)
- Xin Jun Wang
- Department of Urology, Zhongshan Hospital Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- The Third Clinical Medical College, Fujian Medical University, Fuzhou, China
| | - Si Li
- Department of Urology, Zhongshan Hospital Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- The Third Clinical Medical College, Fujian Medical University, Fuzhou, China
| | - Jiang Fang
- Department of Urology, Zhongshan Hospital Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- The Third Clinical Medical College, Fujian Medical University, Fuzhou, China
| | - Zhi Jian Yan
- Department of Urology, Zhongshan Hospital Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- The Third Clinical Medical College, Fujian Medical University, Fuzhou, China
| | - Guang Cheng Luo
- Department of Urology, Zhongshan Hospital Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- The Third Clinical Medical College, Fujian Medical University, Fuzhou, China
- *Correspondence: Guang Cheng Luo,
| |
Collapse
|
7
|
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
|
8
|
RBBP6 interactome: RBBP6 isoform 3/DWNN and Nek6 interaction is critical for cell cycle regulation and may play a role in carcinogenesis. INFORMATICS IN MEDICINE UNLOCKED 2021. [DOI: 10.1016/j.imu.2021.100522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
|
9
|
Liu G, Chen X, Wang Q, Yuan L. NEK7: a potential therapy target for NLRP3-related diseases. Biosci Trends 2020; 14:74-82. [PMID: 32295992 DOI: 10.5582/bst.2020.01029] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
NLRP3 inflammasome plays an essential role in innate immunity, yet the activation mechanism of NLRP3 inflammasome is not clear. In human or animal models, inappropriate NLRP3 inflammasome activation is implicated in many NLRP3-related diseases, such as tumors, inflammatory diseases and autoimmune diseases. Until now, a great number of inhibitors have been used to disturb the related signaling pathways, such as IL-1β blockade, IL-18 blockade and caspase-1 inhibitors. Unfortunately, most of these inhibitors just disturb the signaling pathways after the activation of NLRP3 inflammasome. Inhibitors that directly regulate NLRP3 to abolish the inflammation response may be more effective. NEK7 is a multifunctional kinase affecting centrosome duplication, mitochondrial regulation, intracellular protein transport, DNA repair and mitotic spindle assembly. Researchers have made significant observations on the regulation of gene transcription or protein expression of the NLRP3 inflammasome signaling pathway by NEK7. Those signaling pathways include ROS signaling, potassium efflux, lysosomal destabilization, and NF-κB signaling. Furthermore, NEK7 has been proved to be involved in many NLRP3-related diseases in humans or in animal models. Inhibitors focused on NEK7 may regulate NLRP3 to abolish the inflammation response and NEK7 may be a potential therapeutic target for NLRP3-related diseases.
Collapse
Affiliation(s)
- Ganglei Liu
- Department of Geriatrics Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xueliang Chen
- Department of Geriatrics Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qianqian Wang
- Department of Oncology, The Affiliated Zhuzhou Hospital of Xiangya Medical College, Central South University, Zhuzhou, Hunan, China
| | - Lianwen Yuan
- Department of Geriatrics Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| |
Collapse
|
10
|
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
|
11
|
De Donato M, Righino B, Filippetti F, Battaglia A, Petrillo M, Pirolli D, Scambia G, De Rosa MC, Gallo D. Identification and antitumor activity of a novel inhibitor of the NIMA-related kinase NEK6. Sci Rep 2018; 8:16047. [PMID: 30375481 PMCID: PMC6207720 DOI: 10.1038/s41598-018-34471-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 10/12/2018] [Indexed: 12/29/2022] Open
Abstract
The NIMA (never in mitosis, gene A)-related kinase-6 (NEK6), which is implicated in cell cycle control and plays significant roles in tumorigenesis, is an attractive target for the development of novel anti-cancer drugs. Here we describe the discovery of a potent ATP site-directed inhibitor of NEK6 identified by virtual screening, adopting both structure- and ligand-based techniques. Using a homology-built model of NEK6 as well as the pharmacophoric features of known NEK6 inhibitors we identified novel binding scaffolds. Twenty-five compounds from the top ranking hits were subjected to in vitro kinase assays. The best compound, i.e. compound 8 ((5Z)-2-hydroxy-4-methyl-6-oxo-5-[(5-phenylfuran-2-yl)methylidene]-5,6-dihydropyridine-3-carbonitrile), was able to inhibit NEK6 with low micromolar IC50 value, also displaying antiproliferative activity against a panel of human cancer cell lines. Our results suggest that the identified inhibitor can be used as lead candidate for the development of novel anti-cancer agents, thus opening the possibility of new therapeutic strategies.
Collapse
Affiliation(s)
- Marta De Donato
- Institute of Obstetrics and Gynecology, Università Cattolica del Sacro Cuore, Rome, Italy.,Department of Woman and Child Health, Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - Benedetta Righino
- Institute of Biochemistry and Clinical Biochemistry - Università Cattolica del Sacro Cuore, Rome, Italy
| | - Flavia Filippetti
- Institute of Obstetrics and Gynecology, Università Cattolica del Sacro Cuore, Rome, Italy.,Department of Woman and Child Health, Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - Alessandra Battaglia
- Institute of Obstetrics and Gynecology, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Marco Petrillo
- Institute of Obstetrics and Gynecology, Università Cattolica del Sacro Cuore, Rome, Italy.,Gynecologic and Obstetric Clinic, Department of Clinical and Experimental Medicine, University of Sassari, Sassari, Italy
| | - Davide Pirolli
- Institute of Chemistry of Molecular Recognition (ICRM) - CNR, Rome, Italy
| | - Giovanni Scambia
- Institute of Obstetrics and Gynecology, Università Cattolica del Sacro Cuore, Rome, Italy.,Department of Woman and Child Health, Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | | | - Daniela Gallo
- Institute of Obstetrics and Gynecology, Università Cattolica del Sacro Cuore, Rome, Italy.,Department of Woman and Child Health, Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| |
Collapse
|
12
|
Tan R, Nakajima S, Wang Q, Sun H, Xue J, Wu J, Hellwig S, Zeng X, Yates NA, Smithgall TE, Lei M, Jiang Y, Levine AS, Su B, Lan L. Nek7 Protects Telomeres from Oxidative DNA Damage by Phosphorylation and Stabilization of TRF1. Mol Cell 2017; 65:818-831.e5. [PMID: 28216227 PMCID: PMC5924698 DOI: 10.1016/j.molcel.2017.01.015] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 11/26/2016] [Accepted: 01/05/2017] [Indexed: 11/24/2022]
Abstract
Telomeric repeat binding factor 1 (TRF1) is essential to the maintenance of telomere chromatin structure and integrity. However, how telomere integrity is maintained, especially in response to damage, remains poorly understood. Here, we identify Nek7, a member of the Never in Mitosis Gene A (NIMA) kinase family, as a regulator of telomere integrity. Nek7 is recruited to telomeres and stabilizes TRF1 at telomeres after damage in an ATM activation-dependent manner. Nek7 deficiency leads to telomere aberrations, long-lasting γH2AX and 53BP1 foci, and augmented cell death upon oxidative telomeric DNA damage. Mechanistically, Nek7 interacts with and phosphorylates TRF1 on Ser114, which prevents TRF1 from binding to Fbx4, an Skp1-Cul1-F box E3 ligase subunit, thereby alleviating proteasomal degradation of TRF1, leading to a stable association of TRF1 with Tin2 to form a shelterin complex. Our data reveal a mechanism of efficient protection of telomeres from damage through Nek7-dependent stabilization of TRF1.
Collapse
Affiliation(s)
- Rong Tan
- Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, China; University of Pittsburgh Cancer Institute, University of Pittsburgh School of Medicine, 5117 Centre Avenue, Pittsburgh, PA 15213, USA; Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Bridgeside Point II, 450 Technology Drive, Pittsburgh, PA 15219, USA; Shanghai Institute of Immunology, Shanghai JiaoTong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, China
| | - Satoshi Nakajima
- University of Pittsburgh Cancer Institute, University of Pittsburgh School of Medicine, 5117 Centre Avenue, Pittsburgh, PA 15213, USA; Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Bridgeside Point II, 450 Technology Drive, Pittsburgh, PA 15219, USA
| | - Qun Wang
- Shanghai Institute of Immunology, Shanghai JiaoTong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, China
| | - Hongxiang Sun
- Shanghai Institute of Immunology, Shanghai JiaoTong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, China
| | - Jing Xue
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Jian Wu
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Sabine Hellwig
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Bridgeside Point II, 450 Technology Drive, Pittsburgh, PA 15219, USA
| | - Xuemei Zeng
- Biomedical Mass Spectrometry Center, University of Pittsburgh Schools of the Health Sciences, 3501 Fifth Avenue, 9th Floor Biomedical Science Tower III, Pittsburgh, PA 15261, USA
| | - Nathan A Yates
- University of Pittsburgh Cancer Institute, University of Pittsburgh School of Medicine, 5117 Centre Avenue, Pittsburgh, PA 15213, USA; Biomedical Mass Spectrometry Center, University of Pittsburgh Schools of the Health Sciences, 3501 Fifth Avenue, 9th Floor Biomedical Science Tower III, Pittsburgh, PA 15261, USA; Department of Cell Biology, University of Pittsburgh School of Medicine, 3500 Terrace Street, S362 Biomedical Science Tower S, Pittsburgh, PA 15261, USA
| | - Thomas E Smithgall
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Bridgeside Point II, 450 Technology Drive, Pittsburgh, PA 15219, USA
| | - Ming Lei
- Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai 200031, China
| | - Yu Jiang
- Department of Pharmacology and Chemical Biology, University of Pittsburgh School of Medicine, W1058 Thomas E. Starzl Biomedical Science Tower, Pittsburgh, PA 15261, USA
| | - Arthur S Levine
- University of Pittsburgh Cancer Institute, University of Pittsburgh School of Medicine, 5117 Centre Avenue, Pittsburgh, PA 15213, USA; Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Bridgeside Point II, 450 Technology Drive, Pittsburgh, PA 15219, USA
| | - Bing Su
- Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, China; Shanghai Institute of Immunology, Shanghai JiaoTong University School of Medicine, 280 South Chongqing Road, Shanghai 200025, China; Department of Immunobiology and the Vascular Biology and Therapeutics Program, Yale School of Medicine, 10 Amistad Street, PO Box 208011, New Haven, CT 06520, USA.
| | - Li Lan
- University of Pittsburgh Cancer Institute, University of Pittsburgh School of Medicine, 5117 Centre Avenue, Pittsburgh, PA 15213, USA; Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Bridgeside Point II, 450 Technology Drive, Pittsburgh, PA 15219, USA.
| |
Collapse
|
13
|
Lažetić V, Fay DS. Conserved Ankyrin Repeat Proteins and Their NIMA Kinase Partners Regulate Extracellular Matrix Remodeling and Intracellular Trafficking in Caenorhabditis elegans. Genetics 2017; 205:273-293. [PMID: 27799278 PMCID: PMC5223508 DOI: 10.1534/genetics.116.194464] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 10/28/2016] [Indexed: 12/27/2022] Open
Abstract
Molting is an essential developmental process in nematodes during which the epidermal apical extracellular matrix, the cuticle, is remodeled to accommodate further growth. Using genetic approaches, we identified a requirement for three conserved ankyrin repeat-rich proteins, MLT-2/ANKS6, MLT-3/ANKS3, and MLT-4/INVS, in Caenorhabditis elegans molting. Loss of mlt function resulted in severe defects in the ability of larvae to shed old cuticle and led to developmental arrest. Genetic analyses demonstrated that MLT proteins functionally cooperate with the conserved NIMA kinase family members NEKL-2/NEK8 and NEKL-3/NEK6/NEK7 to promote cuticle shedding. MLT and NEKL proteins were specifically required within the hyp7 epidermal syncytium, and fluorescently tagged mlt and nekl alleles were expressed in puncta within this tissue. Expression studies further showed that NEKL-2-MLT-2-MLT-4 and NEKL-3-MLT-3 colocalize within largely distinct assemblies of apical foci. MLT-2 and MLT-4 were required for the normal accumulation of NEKL-2 at the hyp7-seam cell boundary, and loss of mlt-2 caused abnormal nuclear accumulation of NEKL-2 Correspondingly, MLT-3, which bound directly to NEKL-3, prevented NEKL-3 nuclear localization, supporting the model that MLT proteins may serve as molecular scaffolds for NEKL kinases. Our studies additionally showed that the NEKL-MLT network regulates early steps in clathrin-mediated endocytosis at the apical surface of hyp7, which may in part account for molting defects observed in nekl and mlt mutants. This study has thus identified a conserved NEKL-MLT protein network that regulates remodeling of the apical extracellular matrix and intracellular trafficking, functions that may be conserved across species.
Collapse
Affiliation(s)
- Vladimir Lažetić
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, Wyoming 82071
| | - David S Fay
- Department of Molecular Biology, College of Agriculture and Natural Resources, University of Wyoming, Laramie, Wyoming 82071
| |
Collapse
|
14
|
Moraes EC, Meirelles GV, Honorato RV, de Souza TDACB, de Souza EE, Murakami MT, de Oliveira PSL, Kobarg J. Kinase inhibitor profile for human nek1, nek6, and nek7 and analysis of the structural basis for inhibitor specificity. Molecules 2015; 20:1176-91. [PMID: 25591119 PMCID: PMC6272266 DOI: 10.3390/molecules20011176] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 01/05/2015] [Indexed: 12/11/2022] Open
Abstract
Human Neks are a conserved protein kinase family related to cell cycle progression and cell division and are considered potential drug targets for the treatment of cancer and other pathologies. We screened the activation loop mutant kinases hNek1 and hNek2, wild-type hNek7, and five hNek6 variants in different activation/phosphorylation statesand compared them against 85 compounds using thermal shift denaturation. We identified three compounds with significant Tm shifts: JNK Inhibitor II for hNek1(Δ262-1258)-(T162A), Isogranulatimide for hNek6(S206A), andGSK-3 Inhibitor XIII for hNek7wt. Each one of these compounds was also validated by reducing the kinases activity by at least 25%. The binding sites for these compounds were identified by in silico docking at the ATP-binding site of the respective hNeks. Potential inhibitors were first screened by thermal shift assays, had their efficiency tested by a kinase assay, and were finally analyzed by molecular docking. Our findings corroborate the idea of ATP-competitive inhibition for hNek1 and hNek6 and suggest a novel non-competitive inhibition for hNek7 in regard to GSK-3 Inhibitor XIII. Our results demonstrate that our approach is useful for finding promising general and specific hNekscandidate inhibitors, which may also function as scaffolds to design more potent and selective inhibitors.
Collapse
Affiliation(s)
- Eduardo Cruz Moraes
- LaboratórioNacional de Biociências, Centro Nacional de PesquisaemEnergia e Materiais, Campinas, 13083-970 SP, Brazil.
| | - Gabriela Vaz Meirelles
- LaboratórioNacional de Biociências, Centro Nacional de PesquisaemEnergia e Materiais, Campinas, 13083-970 SP, Brazil.
| | - Rodrigo Vargas Honorato
- LaboratórioNacional de Biociências, Centro Nacional de PesquisaemEnergia e Materiais, Campinas, 13083-970 SP, Brazil.
| | | | - Edmarcia Elisa de Souza
- LaboratórioNacional de Biociências, Centro Nacional de PesquisaemEnergia e Materiais, Campinas, 13083-970 SP, Brazil.
| | - Mario Tyago Murakami
- LaboratórioNacional de Biociências, Centro Nacional de PesquisaemEnergia e Materiais, Campinas, 13083-970 SP, Brazil.
| | | | - Jörg Kobarg
- Programa de Pós-graduação em Biologia Funcional e Molecular, Departamento de Bioquímica e BiologiaTecidual, Instituto de Biologia, UniversidadeEstadual de Campinas, Campinas, 13083-862 SP, Brazil.
| |
Collapse
|
15
|
de Souza EE, Meirelles GV, Godoy BB, Perez AM, Smetana JHC, Doxsey SJ, McComb ME, Costello CE, Whelan SA, Kobarg J. Characterization of the human NEK7 interactome suggests catalytic and regulatory properties distinct from those of NEK6. J Proteome Res 2014; 13:4074-90. [PMID: 25093993 PMCID: PMC4156247 DOI: 10.1021/pr500437x] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Human NEK7 is a regulator of cell division and plays an important role in growth and survival of mammalian cells. Human NEK6 and NEK7 are closely related, consisting of a conserved C-terminal catalytic domain and a nonconserved and disordered N-terminal regulatory domain, crucial to mediate the interactions with their respective proteins. Here, in order to better understand NEK7 cellular functions, we characterize the NEK7 interactome by two screening approaches: one using a yeast two-hybrid system and the other based on immunoprecipitation followed by mass spectrometry analysis. These approaches led to the identification of 61 NEK7 interactors that contribute to a variety of biological processes, including cell division. Combining additional interaction and phosphorylation assays from yeast two-hybrid screens, we validated CC2D1A, TUBB2B, MNAT1, and NEK9 proteins as potential NEK7 interactors and substrates. Notably, endogenous RGS2, TUBB, MNAT1, NEK9, and PLEKHA8 localized with NEK7 at key sites throughout the cell cycle, especially during mitosis and cytokinesis. Furthermore, we obtained evidence that the closely related kinases NEK6 and NEK7 do not share common interactors, with the exception of NEK9, and display different modes of protein interaction, depending on their N- and C-terminal regions, in distinct fashions. In summary, our work shows for the first time a comprehensive NEK7 interactome that, combined with functional in vitro and in vivo assays, suggests that NEK7 is a multifunctional kinase acting in different cellular processes in concert with cell division signaling and independently of NEK6.
Collapse
Affiliation(s)
- Edmarcia Elisa de Souza
- Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais , Campinas, São Paulo, Brazil
| | | | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Parker M, Zhu X, Stubbe J. Bacillus subtilis class Ib ribonucleotide reductase: high activity and dynamic subunit interactions. Biochemistry 2014; 53:766-76. [PMID: 24401092 PMCID: PMC3985883 DOI: 10.1021/bi401056e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2013] [Revised: 11/22/2013] [Indexed: 11/29/2022]
Abstract
The class Ib ribonucleotide reductase (RNR) isolated from Bacillus subtilis was recently purified as a 1:1 ratio of NrdE (α) and NrdF (β) subunits and determined to have a dimanganic-tyrosyl radical (Mn(III)2-Y·) cofactor. The activity of this RNR and the one reconstituted from recombinantly expressed NrdE and reconstituted Mn(III)2-Y· NrdF using dithiothreitol as the reductant, however, was low (160 nmol min(-1) mg(-1)). The apparent tight affinity between the two subunits, distinct from all class Ia RNRs, suggested that B. subtilis RNR might be the protein that yields to the elusive X-ray crystallographic characterization of an "active" RNR complex. We now report our efforts to optimize the activity of B. subtilis RNR by (1) isolation of NrdF with a homogeneous cofactor, and (2) identification and purification of the endogenous reductant(s). Goal one was achieved using anion exchange chromatography to separate apo-/mismetalated-NrdFs from Mn(III)2-Y· NrdF, yielding enzyme containing 4 Mn and 1 Y·/β2. Goal two was achieved by cloning, expressing, and purifying TrxA (thioredoxin), YosR (a glutaredoxin-like thioredoxin), and TrxB (thioredoxin reductase). The success of both goals increased the specific activity to ~1250 nmol min(-1) mg(-1) using a 1:1 mixture of NrdE:Mn(III)2-Y· NrdF and either TrxA or YosR and TrxB. The quaternary structures of NrdE, NrdF, and NrdE:NrdF (1:1) were characterized by size exclusion chromatography and analytical ultracentrifugation. At physiological concentrations (~1 μM), NrdE is a monomer (α) and Mn(III)2-Y· NrdF is a dimer (β2). A 1:1 mixture of NrdE:NrdF, however, is composed of a complex mixture of structures in contrast to expectations.
Collapse
Affiliation(s)
- Mackenzie
J. Parker
- Departments of Chemistry and Biology, Massachusetts
Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Xuling Zhu
- Departments of Chemistry and Biology, Massachusetts
Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - JoAnne Stubbe
- Departments of Chemistry and Biology, Massachusetts
Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| |
Collapse
|
17
|
Discovery of novel inhibitors for Nek6 protein through homology model assisted structure based virtual screening and molecular docking approaches. ScientificWorldJournal 2014; 2014:967873. [PMID: 24587765 PMCID: PMC3920677 DOI: 10.1155/2014/967873] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2013] [Accepted: 11/13/2013] [Indexed: 01/24/2023] Open
Abstract
Nek6 is a member of the NIMA (never in mitosis, gene A)-related serine/threonine kinase family that plays an important role in the initiation of mitotic cell cycle progression. This work is an attempt to emphasize the structural and functional relationship of Nek6 protein based on homology modeling and binding pocket analysis. The three-dimensional structure of Nek6 was constructed by molecular modeling studies and the best model was further assessed by PROCHECK, ProSA, and ERRAT plot in order to analyze the quality and consistency of generated model. The overall quality of computed model showed 87.4% amino acid residues under the favored region. A 3 ns molecular dynamics simulation confirmed that the structure was reliable and stable. Two lead compounds (Binding database ID: 15666, 18602) were retrieved through structure-based virtual screening and induced fit docking approaches as novel Nek6 inhibitors. Hence, we concluded that the potential compounds may act as new leads for Nek6 inhibitors designing.
Collapse
|
18
|
Li L, Sase A, Patil S, Sunyer B, Höger H, Smalla KH, Stork O, Lubec G. Distinct set of kinases induced after retrieval of spatial memory discriminate memory modulation processes in the mouse hippocampus. Hippocampus 2013; 23:672-83. [PMID: 23536525 DOI: 10.1002/hipo.22127] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2013] [Indexed: 12/15/2022]
Abstract
Protein phosphorylation and dephosphorylation events play a key role in memory formation and various protein kinases and phosphatases have been firmly associated with memory performance. Here, we determined expression changes of protein kinases and phosphatases following retrieval of spatial memory in CD1 mice in a Morris Water Maze task, using antibody microarrays and confirmatory Western blot. Comparing changes following single and consecutive retrieval, we identified stably and differentially expressed kinases, some of which have never been implicated before in memory functions. On the basis of these findings we define a small signaling network associated with spatial memory retrieval. Moreover, we describe differential regulation and correlation of expression levels with behavioral performance of polo-like kinase 1. Together with its recently observed genetic association to autism-spectrum disorders our data suggest a role of this kinase in balancing preservation and flexibility of learned behavior.
Collapse
Affiliation(s)
- Lin Li
- Department of Pediatrics, Medical University of Vienna, Vienna, Austria
| | | | | | | | | | | | | | | |
Collapse
|