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Purushothaman K, Sivasankar E, Krishnamoorthy M, Karunakaran K, Muniyan R. Computational identification of potential tau tubulin kinase 1 (TTBK1) inhibitors: a structural analog approach. In Silico Pharmacol 2024; 12:66. [PMID: 39050776 PMCID: PMC11264489 DOI: 10.1007/s40203-024-00242-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 07/14/2024] [Indexed: 07/27/2024] Open
Abstract
Abnormal deposition or aggregation of protein alpha-synuclein and tau in the brain leads to neurodegenerative disorders. Excessive hyperphosphorylation of tau protein and aggregations destroys the microtubule structure resulting in neurofibrillary tangles in neurons and affecting cytoskeleton structure, mitochondrial axonal transport, and loss of synapses in neuronal cells. Tau tubulin kinase 1 (TTBK1), a specific neuronal kinase is a potential therapeutic target for neurodegenerative disorders as it is involved in hyperphosphorylation and aggregation of tau protein. TTBK inhibitors are now the subject of intense study, but limited numbers are found. Hence, this study involves structure-based virtual screening of TTBK1 inhibitor analogs to obtain efficient compounds targeting the TTBK1 using docking, molecular dynamics simulation and protein-ligand interaction profile. The initial analogs set containing 3884 compounds was subjected to Lipinski rule and the non-violated compounds were selected. Docking analysis was done on 2772 compounds through Autodock vina and Autodock 4.2. Data Warrior and SwissADME was utilized to filter the toxic compounds. The stability and protein-ligand interaction of the docked complex was analyzed through Gromacs and VMD. Molecular simulation results such as RMSD, Rg, and hydrogen bond interaction along with pharmacokinetic properties showed CID70794974 as the potential hit targeting TTBKl prompting the need for further experimental investigation to evaluate their potential therapeutic efficacy in Alzheimer's disease. Graphical Abstract Supplementary Information The online version contains supplementary material available at 10.1007/s40203-024-00242-z.
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Affiliation(s)
- Kaathambari Purushothaman
- School of BioSciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014 India
| | - Esaimozhi Sivasankar
- School of BioSciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014 India
| | - Monika Krishnamoorthy
- School of BioSciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014 India
| | - Keerthana Karunakaran
- School of BioSciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014 India
| | - Rajiniraja Muniyan
- School of BioSciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014 India
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Hendriks WJAJ, van Cruchten RTP, Pulido R. Hereditable variants of classical protein tyrosine phosphatase genes: Will they prove innocent or guilty? Front Cell Dev Biol 2023; 10:1051311. [PMID: 36755664 PMCID: PMC9900141 DOI: 10.3389/fcell.2022.1051311] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 12/28/2022] [Indexed: 01/24/2023] Open
Abstract
Protein tyrosine phosphatases, together with protein tyrosine kinases, control many molecular signaling steps that control life at cellular and organismal levels. Impairing alterations in the genes encoding the involved proteins is expected to profoundly affect the quality of life-if compatible with life at all. Here, we review the current knowledge on the effects of germline variants that have been reported for genes encoding a subset of the protein tyrosine phosphatase superfamily; that of the thirty seven classical members. The conclusion must be that the newest genome research tools produced an avalanche of data that suggest 'guilt by association' for individual genes to specific disorders. Future research should face the challenge to investigate these accusations thoroughly and convincingly, to reach a mature genotype-phenotype map for this intriguing protein family.
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Affiliation(s)
- Wiljan J. A. J. Hendriks
- Department of Cell Biology, Radboud University Medical Centre, Nijmegen, The Netherlands,*Correspondence: Wiljan J. A. J. Hendriks,
| | | | - Rafael Pulido
- Biomarkers in Cancer Unit, Biocruces Bizkaia Health Research Institute, Barakaldo, Spain,Ikerbasque, Basque Foundation for Science, Bilbao, Spain
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Fatima A, Abdullah U, Farooq M, Mang Y, Mehrjouy MM, Asif M, Ali Z, Tommerup N, Baig SM. Rare Pathogenic Variants in Genes Implicated in Glutamatergic Neurotransmission Pathway Segregate with Schizophrenia in Pakistani Families. Genes (Basel) 2021; 12:1899. [PMID: 34946848 PMCID: PMC8700876 DOI: 10.3390/genes12121899] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 11/14/2021] [Accepted: 11/16/2021] [Indexed: 01/02/2023] Open
Abstract
Schizophrenia is a disabling neuropsychiatric disorder of adulthood onset with high heritability. Worldwide collaborations have identified an association of ~270 common loci, with small individual effects and hence weak clinical implications. The recent technological feasibility of exome sequencing enables the identification of rare variants of high penetrance that refine previous findings and improve risk assessment and prognosis. We recruited two multiplex Pakistani families, having 11 patients and 19 unaffected individuals in three generations. We performed genome-wide SNP genotyping, next-generation mate pairing and whole-exome sequencing of selected members to unveil genetic components. Candidate variants were screened in unrelated cohorts of 508 cases, 300 controls and fifteen families (with 51 affected and 47 unaffected individuals) of Pakistani origin. The structural impact of substituted residues was assessed through in silico modeling using iTASSER. In one family, we identified a rare novel microduplication (5q14.1_q14.2) encompassing critical genes involved in glutamate signaling, such as CMYA5, HOMER and RasGRF2. The second family segregates two ultra-rare, predicted pathogenic variants in the GRIN2A (NM_001134407.3: c.3505C>T, (p.R1169W) and in the NRG3 NM_001010848.4: c.1951G>A, (p.E651K). These genes encode for parts of AMPA and NMDA receptors of glutamatergic neurotransmission, respectively, and the variants are predicted to compromise protein function by destabilizing their structures. The variants were absent in the aforementioned cohorts. Our findings suggest that rare, highly penetrant variants of genes involved in glutamatergic neurotransmission are contributing to the etiology of schizophrenia in these families. It also highlights that genetic investigations of multiplex, multigenerational families could be a powerful approach to identify rare genetic variants involved in complex disorders.
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Affiliation(s)
- Ambrin Fatima
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad 38000, Pakistan; (A.F.); (U.A.); (M.A.)
- Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark; (Y.M.); (M.M.M.); (Z.A.); (N.T.)
- Department of Biological and Biomedical Sciences, The Aga Khan University, Karachi 74800, Pakistan
| | - Uzma Abdullah
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad 38000, Pakistan; (A.F.); (U.A.); (M.A.)
- Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark; (Y.M.); (M.M.M.); (Z.A.); (N.T.)
- University Institute of Biochemistry and Biotechnology (UIBB), PMAS-Arid Agriculture University Rawalpindi, Rawalpindi 46000, Pakistan
| | - Muhammad Farooq
- Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark; (Y.M.); (M.M.M.); (Z.A.); (N.T.)
- Department of Biotechnology, Institute of Biochemistry, Biotechnology and Bioinformatics (IBBB), The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
- Department of Bioinformatics, Institute of Biochemistry, Biotechnology and Bioinformatics (IBBB), The Islamia University of Bahawalpur, Bahawalpur 63100, Pakistan
| | - Yuan Mang
- Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark; (Y.M.); (M.M.M.); (Z.A.); (N.T.)
| | - Mana M. Mehrjouy
- Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark; (Y.M.); (M.M.M.); (Z.A.); (N.T.)
| | - Maria Asif
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad 38000, Pakistan; (A.F.); (U.A.); (M.A.)
- Cologne Center for Genomics (CCG), University of Cologne, 50931 Cologne, Germany
| | - Zafar Ali
- Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark; (Y.M.); (M.M.M.); (Z.A.); (N.T.)
- Centre for Biotechnology and Microbiology, University of Swat, Mingora 19130, Pakistan
| | - Niels Tommerup
- Department of Cellular and Molecular Medicine, University of Copenhagen, 2200 Copenhagen, Denmark; (Y.M.); (M.M.M.); (Z.A.); (N.T.)
| | - Shahid M. Baig
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad 38000, Pakistan; (A.F.); (U.A.); (M.A.)
- Department of Biological and Biomedical Sciences, The Aga Khan University, Karachi 74800, Pakistan
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Igeta H, Watanabe Y, Morikawa R, Ikeda M, Otsuka I, Hoya S, Koizumi M, Egawa J, Hishimoto A, Iwata N, Someya T. Rare compound heterozygous missense SPATA7 variations and risk of schizophrenia; whole-exome sequencing in a consanguineous family with affected siblings, follow-up sequencing and a case-control study. Neuropsychiatr Dis Treat 2019; 15:2353-2363. [PMID: 31695380 PMCID: PMC6707433 DOI: 10.2147/ndt.s218773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 07/23/2019] [Indexed: 12/14/2022] Open
Abstract
PURPOSE Whole-exome sequencing (WES) of multiplex families is a promising strategy for identifying causative variations for common diseases. To identify rare recessive risk variations for schizophrenia, we performed a WES study in a consanguineous family with affected siblings. We then performed follow-up sequencing of SPATA7 in schizophrenia-affected families. In addition, we performed a case-control study to investigate association between SPATA7 variations and schizophrenia. PATIENTS AND METHODS WES was performed on two affected siblings and their unaffected parents, who were second cousins, of a multiplex schizophrenia family. Subsequently, we sequenced the coding region of SPATA7, a potential risk gene identified by the WES analysis, in 142 affected offspring from 137 families for whom parental DNA samples were available. We further tested rare recessive SPATA7 variations, identified by WES and sequencing, for associations with schizophrenia in 2,756 patients and 2,646 controls. RESULTS Our WES analysis identified rare compound heterozygous missense SPATA7 variations, p.Asp134Gly and p.Ile332Thr, in both affected siblings. Sequencing SPATA7 coding regions from 137 families identified no rare recessive variations in affected offspring. In the case-control study, we did not detect the rare compound heterozygous SPATA7 missense variations in patients or controls. CONCLUSION Our data does not support the role of the rare compound heterozygous SPATA7 missense variations p.Asp134Gly and p.Ile332Thr in conferring a substantial risk of schizophrenia.
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Affiliation(s)
- Hirofumi Igeta
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Yuichiro Watanabe
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Ryo Morikawa
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Masashi Ikeda
- Department of Psychiatry, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Ikuo Otsuka
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Satoshi Hoya
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Masataka Koizumi
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Jun Egawa
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
| | - Akitoyo Hishimoto
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Hyogo, Japan
| | - Nakao Iwata
- Department of Psychiatry, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| | - Toshiyuki Someya
- Department of Psychiatry, Niigata University Graduate School of Medical and Dental Sciences, Niigata, Japan
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