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G N S HS, Marise VLP, Rajalekshmi SG, Burri RR, Krishna Murthy TP. Articulating target-mining techniques to disinter Alzheimer's specific targets for drug repurposing. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2022; 222:106931. [PMID: 35724476 DOI: 10.1016/j.cmpb.2022.106931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 03/14/2022] [Accepted: 06/01/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND AND OBJECTIVES Alzheimer's Disease (AD), an extremely progressive neurodegenerative disorder is an amalgamation of numerous intricate pathological networks. This century old disease is still an unmet medical condition owing to the modest efficacy of existing therapeutic agents in antagonizing the multi-targeted pathological pathways underlying AD. Given the paucity in AD specific drugs, fabricating comprehensive research strategies to envision disease specific targets to channelize and expedite drug discovery are mandated. However, the dwindling approval rates and stringent regulatory constraints concerning the approval of a new chemical entity is daunting the pharmaceutical industries from effectuating de novo research. To bridge the existing gaps in AD drug research, a promising contemporary way out could be drug repurposing. This drug repurposing investigation is intended to envisage AD specific targets and create drug libraries pertinent to the shortlisted targets via a series of avant-garde bioinformatics and computational strategies. METHODS Transcriptomic analysis of three AD specific datasets viz., GSE122063, GSE15222 and GSE5281 revealed significant Differentially Expressed Genes (DEGs) and subsequent Protein-Protein Interactions (PPI) network analysis captured crucial AD targets. Later, homology model was constructed through I-TASSER for a shortlisted target protein which lacked X-ray crystallographic structure and the built protein model was validated by molecular dynamic simulations. Further, drug library was created for the shortlisted target based on structural and side effect similarity with respective standard drugs. Finally, molecular docking, binding energy calculations and molecular dynamics studies were carried out to unravel the interactions exhibited by drugs from the created library with amino acids in active binding pocket of RGS4. RESULTS SST and RGS4 were shortlisted as potentially significant AD specific targets, however, the less explored target RGS4 was considered for further sequential analysis. Homology model constructed for RGS4 displayed best quality when validated through Ramachandran plot and ERRAT plot. Subsequent docking and molecular dynamics studies showcased substantial affinity demonstrated by three drugs viz., Ziprasidone, Melfoquine and Metaxalone from the created drug libraries, towards RGS4. CONCLUSION This virtual analysis forecasted the repurposable potential of Ziprasidone, Melfoquine and Metaxalone against AD based on their affinity towards RGS4, a key AD-specific target.
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Affiliation(s)
- Hema Sree G N S
- Pharmacological Modelling and Simulation Centre, M. S. Ramaiah University of Applied Sciences, Bangalore, Karnataka 560094, India
| | - V Lakshmi Prasanna Marise
- Pharmacological Modelling and Simulation Centre, M. S. Ramaiah University of Applied Sciences, Bangalore, Karnataka 560094, India; Department of Pharmacy Practice, Faculty of Pharmacy, M. S. Ramaiah University of Applied Sciences, Bangalore, Karnataka 560094, India
| | - Saraswathy Ganesan Rajalekshmi
- Pharmacological Modelling and Simulation Centre, M. S. Ramaiah University of Applied Sciences, Bangalore, Karnataka 560094, India; Department of Pharmacy Practice, Faculty of Pharmacy, M. S. Ramaiah University of Applied Sciences, Bangalore, Karnataka 560094, India.
| | | | - T P Krishna Murthy
- Department of Biotechnology, M. S. Ramaiah Institute of Technology, Bangalore, Karnataka 560054, India
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G N S HS, Marise VLP, Satish KS, Yergolkar AV, Krishnamurthy M, Ganesan Rajalekshmi S, Radhika K, Burri RR. Untangling huge literature to disinter genetic underpinnings of Alzheimer's Disease: A systematic review and meta-analysis. Ageing Res Rev 2021; 71:101421. [PMID: 34371203 DOI: 10.1016/j.arr.2021.101421] [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: 03/21/2021] [Revised: 06/25/2021] [Accepted: 08/02/2021] [Indexed: 10/20/2022]
Abstract
Drug discovery for Alzheimer's Disease (AD) is channeled towards unravelling key disease specific drug targets/genes to predict promising therapeutic candidates. Though enormous literature on AD genetics is available, there exists dearth in data pertinent to drug targets and crucial pathological pathways intertwined in disease progression. Further, the research findings revealing genetic associations failed to demonstrate consistency across different studies. This scenario prompted us to initiate a systematic review and meta-analysis with an aim of unearthing significant genetic hallmarks of AD. Initially, a Boolean search strategy was developed to retrieve case-control studies from PubMed, Cochrane, ProQuest, Europe PMC, grey literature and HuGE navigator. Subsequently, certain inclusion and exclusion criteria were framed to shortlist the relevant studies. These studies were later critically appraised using New Castle Ottawa Scale and Q-Genie followed by data extraction. Later, meta-analysis was performed only for those Single Nucleotide Polymorphisms (SNPs) which were evaluated in at least two different ethnicities from two different reports. Among, 204,351 studies retrieved, 820 met our eligibility criteria and 117 were processed for systematic review after critical appraisal. Ultimately, meta-analysis was performed for 23 SNPs associated with 15 genes which revealed significant associations of rs3865444 (CD33), rs7561528 (BIN1) and rs1801133 (MTHFR) with AD risk.
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Revelation of Pivotal Genes Pertinent to Alzheimer's Pathogenesis: A Methodical Evaluation of 32 GEO Datasets. J Mol Neurosci 2021; 72:303-322. [PMID: 34668150 PMCID: PMC8526053 DOI: 10.1007/s12031-021-01919-2] [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: 08/20/2021] [Accepted: 09/18/2021] [Indexed: 11/26/2022]
Abstract
Alzheimer’s disease (AD), a dreadful neurodegenerative disorder that affects cognitive and behavioral function in geriatric populations, is characterized by the presence of amyloid deposits and neurofibrillary tangles in brain regions. The International D World Alzheimer Report2018 noted a global prevalence of 50 million AD cases and forecasted a threefold rise to 139 million by 2050. Although there exist numerous genetic association studies pertinent to AD in different ethnicities, critical genetic factors and signaling pathways underlying its pathogenesis remain ambiguous. This study was aimed to analyze the genetic data retrieved from 32 Gene Expression Omnibus datasets belonging to diverse ethnic cohorts in order to identify overlapping differentially expressed genes (DEGs). Stringent selection criteria were framed to shortlist appropriate datasets based on false discovery rate (FDR) p-value and log FC, and relevant details of upregulated and downregulated DEGs were retrieved. Among the 32 datasets, only six satisfied the selection criteria. The GEO2R tool was employed to retrieve significant DEGs. Nine common DEGs, i.e., SLC5A3, BDNF, SST, SERPINA3, RTN3, RGS4, NPTX, ENC1 and CRYM were found in more than 60% of the selected datasets. These DEGs were later subjected to protein–protein interaction analysis with 18 AD-specific literature-derived genes. Among the nine common DEGs, BDNF, SST, SERPINA3, RTN3 and RGS4 exhibited significant interactions with crucial proteins including BACE1, GRIN2B, APP, APOE, COMT, PSEN1, INS, NEP and MAPT. Functional enrichment analysis revealed involvement of these genes in trans-synaptic signaling, chemical transmission, PI3K pathway signaling, receptor–ligand activity and G protein signaling. These processes are interlinked with AD pathways.
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Babić Leko M, Nikolac Perković M, Klepac N, Švob Štrac D, Borovečki F, Pivac N, Hof PR, Šimić G. Relationships of Cerebrospinal Fluid Alzheimer's Disease Biomarkers and COMT, DBH, and MAOB Single Nucleotide Polymorphisms. J Alzheimers Dis 2021; 73:135-145. [PMID: 31771069 PMCID: PMC7029364 DOI: 10.3233/jad-190991] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The noradrenergic and dopaminergic systems are affected in Alzheimer’s disease (AD). Polymorphisms in genes encoding enzymes and proteins that are components of these systems can affect products of transcription and translation and lead to altered enzymatic activity and alterations in overall dopamine and noradrenaline levels. Catechol-O-methyltransferase (COMT) and monoamine oxidase B (MAOB) are the enzymes that regulate degradation of dopamine, while dopamine β-hydroxylase (DBH) is involved in synthesis of noradrenaline. COMT Val158Met (rs4680), DBH rs1611115 (also called –1021C/T or –970C/T), and MAOB rs1799836 (also called A644G) polymorphisms have been previously associated with AD. We assessed whether these polymorphisms are associated with cerebrospinal fluid (CSF) AD biomarkers including total tau (t-tau), phosphorylated tau proteins (p-tau181, p-tau199, and p-tau231), amyloid-β42 (Aβ42), and visinin-like protein 1 (VILIP-1) to test possible relationships of specific genotypes and pathological levels of CSF AD biomarkers. The study included 233 subjects: 115 AD, 53 mild cognitive impairment, 54 subjects with other primary causes of dementia, and 11 healthy controls. Significant decrease in Aβ42 levels was found in patients with GG compared to AG COMT Val158Met genotype, while t-tau and p-tau181 levels were increased in patients with AA compared to AG COMT Val158Met genotype. Aβ42 levels were also decreased in carriers of A allele in MAO-B rs1799836 polymorphism, while p-tau181 levels were increased in carriers of T allele in DBH rs1611115 polymorphism. These results indicate that COMT Val158Met, DBH rs1611115, and MAOB rs1799836 polymorphisms deserve further investigation as genetic markers of AD.
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Affiliation(s)
- Mirjana Babić Leko
- Department of Neuroscience, Croatian Institute for Brain Research, University of Zagreb Medical School, Zagreb, Croatia
| | | | - Nataša Klepac
- Department of Neurology, University Hospital Centre Zagreb, Zagreb, Croatia
| | | | - Fran Borovečki
- Department of Neurology, University Hospital Centre Zagreb, Zagreb, Croatia
| | - Nela Pivac
- Department of Molecular Medicine, Institute Ruđer Bošković, Zagreb, Croatia
| | - Patrick R Hof
- Nash Family Department of Neuroscience, Friedman Brain Institute, and Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Goran Šimić
- Department of Neuroscience, Croatian Institute for Brain Research, University of Zagreb Medical School, Zagreb, Croatia
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G. N. S HS, Ganesan Rajalekshmi S, Murahari M, Burri RR. Reappraisal of FDA approved drugs against Alzheimer’s disease based on differential gene expression and protein interaction network analysis: an in silico approach. J Biomol Struct Dyn 2019; 38:3972-3989. [DOI: 10.1080/07391102.2019.1671231] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Hema Sree G. N. S
- Pharmacological Modelling and Simulation Centre, M. S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India
| | - Saraswathy Ganesan Rajalekshmi
- Pharmacological Modelling and Simulation Centre, M. S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India
- Department of Pharmacy Practice, Faculty of Pharmacy, M. S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India
| | - Manikanta Murahari
- Pharmacological Modelling and Simulation Centre, M. S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, M. S. Ramaiah University of Applied Sciences, Bangalore, Karnataka, India
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Wang ZT, Zhong XL, Tan MS, Wang HF, Tan CC, Zhang W, Zheng ZJ, Kong LL, Tan L, Sun L. Association of lectin-like oxidized low density lipoprotein receptor 1 ( OLR1) polymorphisms with late-onset Alzheimer disease in Han Chinese. ANNALS OF TRANSLATIONAL MEDICINE 2018; 6:172. [PMID: 29951494 DOI: 10.21037/atm.2018.04.31] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Background Lectin-like oxidized low density lipoprotein receptor 1 (OLR1) locates within the area of chromosome 12p, which has been identified as the AD-susceptible region, and plays a role in lipid metabolism. Therefore, it has been suggested to be a good candidate gene for Alzheimer's disease (AD). Several SNPs within OLR1 have been reported to have association with AD among Caucasians. Methods We selected and genotyped three SNPs (rs1050283, rs1050286, rs17808009) in OLR1 to investigate its possible relationship with the onset of late-onset Alzheimer disease(LOAD) in 984 LOAD cases and 1,354 healthy controls among northern Han Chinese. Results No significant association was found between the OLR1 (rs1050283, rs1050286, rs17808009) polymorphisms and LOAD, even after adjustment for gender and age and stratification for apolipoprotein E (APOE) status. Conclusions Our study showed that the SNPs (rs1050283, rs1050286, rs17808009) located in the 3'UTR of OLR1 may not involve in the mechanism of LOAD in Han Chinese population.
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Affiliation(s)
- Zuo-Teng Wang
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, China
| | - Xiao-Ling Zhong
- Department of Neurology, Qingdao Central Hospital, Qingdao University, Qingdao 266042, China
| | - Meng-Shan Tan
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, China
| | - Hui-Fu Wang
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, China
| | - Chen-Chen Tan
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, China
| | - Wei Zhang
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, China
| | - Zhan-Jie Zheng
- Department of Geriatric, Qingdao Mental Health Center, Qingdao 266034, China
| | - Ling-Li Kong
- Department of Geriatric, Qingdao Mental Health Center, Qingdao 266034, China
| | - Lan Tan
- Department of Neurology, Qingdao Municipal Hospital, Qingdao University, Qingdao 266071, China
| | - Li Sun
- Department of Neurology, Qingdao Central Hospital, Qingdao University, Qingdao 266042, China
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Association between polymorphism of COMT gene (Val158Met) with Alzheimer's disease: An updated analysis. J Neurol Sci 2016; 361:250-5. [DOI: 10.1016/j.jns.2016.01.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 12/14/2015] [Accepted: 01/05/2016] [Indexed: 11/17/2022]
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Shibata N, Nagata T, Tagai K, Shinagawa S, Ohnuma T, Kawai E, Kasanuki K, Shimazaki H, Toda A, Tagata Y, Nakada T, Nakayama K, Yamada H, Arai H. Association between the catechol-O-methyltransferase polymorphism Val158Met and Alzheimer's disease in a Japanese population. Int J Geriatr Psychiatry 2015; 30:927-33. [PMID: 25491588 DOI: 10.1002/gps.4237] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 10/27/2014] [Indexed: 11/07/2022]
Abstract
OBJECTIVE Catechol-O-methyltransferase (COMT) plays an important role in dopamine degradation, which is associated with the pathophysiology of Alzheimer's disease (AD) and alcoholism. A functional COMT polymorphism, Val158Met (rs4680 G > A), affects the onset of AD and is associated with alcohol dependence through dopamine receptor sensitivity in the prefrontal cortex. METHODS The aim of this case-control study (398 cases and 149 controls) was to investigate whether Val158Met polymorphism influences the onset of AD stratified according to alcohol consumption and apolipoprotein E (APOE) status. We also used single photon-emission computed tomography (SPECT) to analyse 26 patients with AD with the polymorphism. RESULTS As a function of APOE status, the genotypic frequencies of rs4680 in patients with AD did not differ from those in controls. We detected a significant association between high alcohol consumption in patients with AD (HAC-AD group) and the polymorphism in genotypic and allelic frequencies. Logistic regression analyses demonstrated that the presence of the APOE genotype with rs4680 increased the risk for HAC-AD synergistically. Hyperperfusion in the right sub-lobar insula of patients with the G/G genotype was found compared with that of patients with the G/A genotype. SPECT studies showed a relationship between the polymorphism and compensatory reactions for dysfunctions of dopaminergic neurotransmission in AD pathophysiology. CONCLUSION Although genetic association between the polymorphism and the onset of AD in a Japanese population were not observed, the polymorphism affected the risk for HAC-AD.
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Affiliation(s)
- Nobuto Shibata
- Department of Psychiatry, Juntendo University School of Medicine, Tokyo, Japan
| | - Tomoyuki Nagata
- Department of Psychiatry, Jikei University School of Medicine, Tokyo, Japan.,Division of Molecular Genetics, Institute of DNA Medicine, Jikei University School of Medicine, Tokyo, Japan
| | - Kenji Tagai
- Department of Psychiatry, Jikei University School of Medicine, Tokyo, Japan
| | | | - Tohru Ohnuma
- Department of Psychiatry, Juntendo University School of Medicine, Tokyo, Japan
| | - Eri Kawai
- Department of Psychiatry, Juntendo University School of Medicine, Tokyo, Japan
| | - Koji Kasanuki
- Department of Psychiatry, Juntendo University School of Medicine, Tokyo, Japan
| | - Hiromi Shimazaki
- Department of Psychiatry, Juntendo University School of Medicine, Tokyo, Japan
| | - Aiko Toda
- Department of Psychiatry, Juntendo University School of Medicine, Tokyo, Japan
| | - Yuko Tagata
- Department of Psychiatry, Juntendo University School of Medicine, Tokyo, Japan
| | - Tomoko Nakada
- Department of Psychiatry, Juntendo University School of Medicine, Tokyo, Japan
| | - Kazuhiko Nakayama
- Department of Psychiatry, Jikei University School of Medicine, Tokyo, Japan
| | - Hisashi Yamada
- Division of Molecular Genetics, Institute of DNA Medicine, Jikei University School of Medicine, Tokyo, Japan
| | - Heii Arai
- Department of Psychiatry, Juntendo University School of Medicine, Tokyo, Japan
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Zhang G, Li YC, Xu HD, Liu X, Zhu J, Zhang F, Wang D, Wang Y, Jin C. Lack of association between COMT polymorphism rs4680 and risk of Alzheimer's disease in Asians: Evidence from a meta-analysis. Psychiatry Res 2015; 228:979-81. [PMID: 26026741 DOI: 10.1016/j.psychres.2015.04.037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Accepted: 04/27/2015] [Indexed: 10/23/2022]
Affiliation(s)
- Guofu Zhang
- Mental Health Institute of The Second Xiangya Hospital, Central South University, Changsha 410011, Hunan Province, PR China; Wuxi Mental Health Center of Nanjing Medical University, 156 Qian Rong Road, Wuxi 214151, Jiangsu Province, PR China
| | - Yong-Chun Li
- School of Pharmaceutical Science, Zhengzhou University, Zhengzhou 450001, Henan Province, PR China
| | - Hong-De Xu
- School of Pharmaceutical Science, Zhengzhou University, Zhengzhou 450001, Henan Province, PR China
| | - Xiaowei Liu
- Wuxi Mental Health Center of Nanjing Medical University, 156 Qian Rong Road, Wuxi 214151, Jiangsu Province, PR China
| | - Jianzhong Zhu
- Wuxi Mental Health Center of Nanjing Medical University, 156 Qian Rong Road, Wuxi 214151, Jiangsu Province, PR China
| | - Feng Zhang
- Wuxi Mental Health Center of Nanjing Medical University, 156 Qian Rong Road, Wuxi 214151, Jiangsu Province, PR China
| | - Degang Wang
- Wuxi Mental Health Center of Nanjing Medical University, 156 Qian Rong Road, Wuxi 214151, Jiangsu Province, PR China
| | - Ying Wang
- Wuxi Mental Health Center of Nanjing Medical University, 156 Qian Rong Road, Wuxi 214151, Jiangsu Province, PR China
| | - Chunhui Jin
- Wuxi Mental Health Center of Nanjing Medical University, 156 Qian Rong Road, Wuxi 214151, Jiangsu Province, PR China.
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COMT Val158Met and PPARγ Pro12Ala polymorphisms and susceptibility to Alzheimer’s disease: a meta-analysis. Neurol Sci 2014; 35:643-51. [DOI: 10.1007/s10072-014-1645-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 01/17/2014] [Indexed: 10/25/2022]
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