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Singh VK, Thakur DC, Rajak N, Mishra A, Kumar A, Giri R, Garg N. The multi-protein targeting potential of bioactive syringin in inflammatory diseases: using molecular modelling and in-silico analysis of regulatory elements. J Biomol Struct Dyn 2023:1-12. [PMID: 37882327 DOI: 10.1080/07391102.2023.2273440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 10/14/2023] [Indexed: 10/27/2023]
Abstract
Inflammation plays a crucial role in the onset or progression of a variety of acute and chronic diseases. Non-steroidal anti-inflammatory drugs (NSAIDs) are the only available FDA-approved therapy. The therapeutic outcome of NSAIDs is still finite due to off-target effects and extreme side effects on other vital organs. Bioactive syringin has been manifested to hold anti-osteoporosis, cardiac hypertrophy, alter autophagy, anti-cancer, neuro-preventive effects, etc. However, its multi-protein targeting potential in inflammation mostly remains unexplored. In the present work, we have checked the multi-protein targeting potential of bioactive glycoside syringin in inflammatory diseases. Based on the binding score of protein-ligand complexes, glycoside syringin scored greater than -7 kcal/mol against 12 inflammatory proteins. Our molecular dynamic simulation study (200 ns) confirmed that bioactive syringin remained inside the binding cavity of inflammatory proteins (JAK1, TYK2, and COX1) in a stable conformation. Further, our co-expression analysis suggests that these genes play an essential role in multiple pathways and are regulated by multiple miRNAs. Our study demonstrates that bioactive glycoside syringin might be a multi-protein targeting potential against inflammatory diseases and could be further investigated utilizing different preclinical approaches.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Vipendra Kumar Singh
- School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, Mandi, India
| | - D C Thakur
- School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, Mandi, India
| | - Naina Rajak
- Faculty of Ayurveda, Department of Medicinal Chemistry, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Anand Mishra
- Molecular Plant Pathology Laboratory, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
| | - Ankur Kumar
- School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, Mandi, India
| | - Rajanish Giri
- School of Biosciences and Bioengineering, Indian Institute of Technology Mandi, Mandi, India
| | - Neha Garg
- Faculty of Ayurveda, Department of Medicinal Chemistry, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
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Liang XZ, Li R, Xu B, Luo D, Liu GB, Peng J, Li G. Systematic evaluation of the mechanisms of zoledronic acid based on network pharmacology. Comput Biol Chem 2019; 83:107097. [PMID: 31446368 DOI: 10.1016/j.compbiolchem.2019.107097] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 07/30/2019] [Accepted: 07/31/2019] [Indexed: 12/31/2022]
Abstract
Zoledronic acid (ZA) is an FDA-approved drug and a third-generation bisphosphonate (BPs). A systematic evaluation of the mechanisms of ZA has not previously been performed. In this study, validated targets of ZA were screened using PubChem, Herbal Ingredients' Targets Database (HIT), Binding Database (BindingDB), and ChemBank, and potential targets of ZA were identified based on structural characteristics of ligands and proteins. The candidate targets were then assessed using GeneMANIA, Gene Ontology (GO), and pathway analysis, and molecule-target-GO-pathway networks were visualized using Cytoscape. Nine validated targets and 26 potential targets were obtained. The networks generated via this analysis showed that the candidate targets were associated with cell proliferation and metabolism as well as other biological processes (BP) and pathways. In general, ZA appeared to play crucial roles in multiple functions, including metabolism, regulation of vascular smooth muscle cell proliferation, and chemical carcinogenesis; a great deal of additional research must be performed. Moreover, the current study showed that it is feasible to analyze the mechanisms of ZA via target prediction, which facilitates systematic pharmacological evaluation.
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Affiliation(s)
- Xue-Zhen Liang
- The First Clinical Medical School, Shandong University of Traditional Chinese Medicine, Shandong, 250355, China; Institute of Orthopedics, The General Hospital of PLA, Beijing, 100850, China
| | - Rui Li
- Institute of Orthopedics, The General Hospital of PLA, Beijing, 100850, China
| | - Bo Xu
- The First Clinical Medical School, Shandong University of Traditional Chinese Medicine, Shandong, 250355, China
| | - Di Luo
- The First Clinical Medical School, Shandong University of Traditional Chinese Medicine, Shandong, 250355, China
| | - Guang-Bo Liu
- Institute of Orthopedics, The General Hospital of PLA, Beijing, 100850, China
| | - Jiang Peng
- Institute of Orthopedics, The General Hospital of PLA, Beijing, 100850, China.
| | - Gang Li
- The First Clinical Medical School, Shandong University of Traditional Chinese Medicine, Shandong, 250355, China; Orthopaedic Microsurgery, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Shandong, 250014, China.
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Wang S, Lv Y, Wang Y, Du P, Tan W, Lammi MJ, Guo X. Network Analysis of Se-and Zn-related Proteins in the Serum Proteomics Expression Profile of the Endemic Dilated Cardiomyopathy Keshan Disease. Biol Trace Elem Res 2018; 183:40-48. [PMID: 28819918 DOI: 10.1007/s12011-017-1063-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 05/23/2017] [Indexed: 11/26/2022]
Abstract
Keshan disease (KD) is an endemic cardiomyopathy with high mortality. Selenium (Se) and zinc (Zn) deficiencies are closely related to KD. The molecular mechanism of KD pathogenesis is still unclear. There are only few studies on the interaction of trace elements and proteins associated with the pathogenesis of KD. In this study, isobaric tags for relative and absolute quantitation (iTRAQ)-coupled two-dimensional liquid chromatography tandem mass spectrometry (2DLC-MS/MS) technique analysis was used to analyze the differential expression of proteins from serum samples. Comparative Toxicogenomics Database (CTD) was used to screen Se- and Zn-associated proteins. Then, pathway and network analyses of Se- and Zn-associated proteins were constituted by Cytoscape ClueGO and GeneMANIA plugins. One hundred and five differentially expressed proteins were obtained by 2DLC-MS/MS, among them 19 Se- and 3 Zn-associated proteins. Fifty-two pathways were identified from ClueGO and 1 network from GeneMANIA analyses. The results showed that Se-associated proteins STAT3 and MAPK1 and Zn-associated proteins HIF1A and PARP1, the proteins involved in HIF-1 signaling pathway and apoptosis pathway, may play significant roles in the pathogenesis of KD. The approach of this study would be also beneficial for further dissecting molecular mechanism of other trace element-associated disease.
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Affiliation(s)
- Sen Wang
- School of Public Health, Health Science Center of Xi'an Jiaotong University, No. 76 Yanta West Road, Xi'an, Shaanxi, 710061, China
- Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, No. 76 Yanta West Road, Xi'an, Shaanxi, 710061, China
| | - Yanyan Lv
- Department of Rheumatology, Xi'an No.5 Hospital, Xi'an, Shaanxi, China
| | - Yingting Wang
- School of Public Health, Health Science Center of Xi'an Jiaotong University, No. 76 Yanta West Road, Xi'an, Shaanxi, 710061, China
- Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, No. 76 Yanta West Road, Xi'an, Shaanxi, 710061, China
| | - Peiru Du
- School of Public Health, Health Science Center of Xi'an Jiaotong University, No. 76 Yanta West Road, Xi'an, Shaanxi, 710061, China
- Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, No. 76 Yanta West Road, Xi'an, Shaanxi, 710061, China
| | - Wuhong Tan
- School of Public Health, Health Science Center of Xi'an Jiaotong University, No. 76 Yanta West Road, Xi'an, Shaanxi, 710061, China.
- Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, No. 76 Yanta West Road, Xi'an, Shaanxi, 710061, China.
| | - Mikko J Lammi
- School of Public Health, Health Science Center of Xi'an Jiaotong University, No. 76 Yanta West Road, Xi'an, Shaanxi, 710061, China.
- Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, No. 76 Yanta West Road, Xi'an, Shaanxi, 710061, China.
- Department of Integrative Medical Biology, University of Umeå, Umeå, Sweden.
| | - Xiong Guo
- School of Public Health, Health Science Center of Xi'an Jiaotong University, No. 76 Yanta West Road, Xi'an, Shaanxi, 710061, China
- Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, No. 76 Yanta West Road, Xi'an, Shaanxi, 710061, China
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Xu JH, Hu SL, Shen GD, Shen G. Tumor suppressor genes and their underlying interactions in paclitaxel resistance in cancer therapy. Cancer Cell Int 2016; 16:13. [PMID: 26900348 DOI: 10.1186/s12935-016-0290-9] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 02/12/2016] [Indexed: 01/01/2023] Open
Abstract
Objectives Paclitaxel (PTX) is frequently used in the clinical treatment of solid tumors. But the PTX-resistance is a great obstacle in cancer treatment. Exploration of the mechanisms of drug resistance suggests that tumor suppressor genes (TSGs) play a key role in the response of chemotherapeutic drugs. TSGs, a set of genes that are often inactivated in cancers, can regulate various biological processes. In this study, an overview of the contribution of TSGs to PTX resistance and their underlying relationship in cancers are reported by using GeneMANIA, a web-based tool for gene/protein function prediction. Methods Using PubMed online database and Google web site, the terms “paclitaxel resistance” or “taxol resistance” or “drug resistance” or “chemotherapy resistance”, and “cancer” or “carcinoma”, and “tumor suppressor genes” or “TSGs” or “negative regulated protein” or “antioncogenes” were searched and analyzed. GeneMANIA data base was used to predict gene/protein interactions and functions. Results We identified 22 TSGs involved in PTX resistance, including BRCA1, TP53, PTEN, APC, CDKN1A, CDKN2A, HIN-1, RASSF1, YAP, ING4, PLK2, FBW7, BLU, LZTS1, REST, FADD, PDCD4, TGFBI, ING1, Bax, PinX1 and hEx. The TSGs were found to have direct and indirect relationships with each other, and thus they could contribute to PTX resistance as a group. The varied expression status and regulation function of the TSGs on cell cycle in different cancers might play an important role in PTX resistance. Conclusion A further understanding of the roles of tumor suppressor genes in drug resistance is an important step to overcome chemotherapy tolerance. Tumor suppressor gene therapy targets the altered genes and signaling pathways and can be a new strategy to reverse chemotherapy resistance.
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Serrano JB, da Cruz E Silva OAB, Rebelo S. Lamina Associated Polypeptide 1 (LAP1) Interactome and Its Functional Features. Membranes (Basel) 2016; 6:membranes6010008. [PMID: 26784240 PMCID: PMC4812414 DOI: 10.3390/membranes6010008] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 01/05/2016] [Accepted: 01/06/2016] [Indexed: 12/26/2022]
Abstract
Lamina-associated polypeptide 1 (LAP1) is a type II transmembrane protein of the inner nuclear membrane encoded by the human gene TOR1AIP1. LAP1 is involved in maintaining the nuclear envelope structure and appears be involved in the positioning of lamins and chromatin. To date, LAP1’s precise function has not been fully elucidated but analysis of its interacting proteins will permit unraveling putative associations to specific cellular pathways and cellular processes. By assessing public databases it was possible to identify the LAP1 interactome, and this was curated. In total, 41 interactions were identified. Several functionally relevant proteins, such as TRF2, TERF2IP, RIF1, ATM, MAD2L1 and MAD2L1BP were identified and these support the putative functions proposed for LAP1. Furthermore, by making use of the Ingenuity Pathways Analysis tool and submitting the LAP1 interactors, the top two canonical pathways were “Telomerase signalling” and “Telomere Extension by Telomerase” and the top functions “Cell Morphology”, “Cellular Assembly and Organization” and “DNA Replication, Recombination, and Repair”. Once again, putative LAP1 functions are reinforced but novel functions are emerging.
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Affiliation(s)
- Joana B Serrano
- Neuroscience and Signalling Laboratory, Department of Medical Sciences, Institute of Biomedicine-iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal.
| | - Odete A B da Cruz E Silva
- Neuroscience and Signalling Laboratory, Department of Medical Sciences, Institute of Biomedicine-iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal.
| | - Sandra Rebelo
- Neuroscience and Signalling Laboratory, Department of Medical Sciences, Institute of Biomedicine-iBiMED, University of Aveiro, 3810-193 Aveiro, Portugal.
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Chaudhari HN, Kim SW, Yun JW. Gender-dimorphic regulation of DJ1 and its interactions with metabolic proteins in streptozotocin-induced diabetic rats. J Cell Mol Med 2015; 19:996-1009. [PMID: 25726699 PMCID: PMC4420602 DOI: 10.1111/jcmm.12490] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Accepted: 10/10/2014] [Indexed: 01/04/2023] Open
Abstract
Regulation of DJ1 is associated with a number of human diseases. To determine the involvement of DJ1 in progression of diabetes in a gender-dependent manner, we investigated its tissue-specific expression in streptozotocin (STZ)-induced diabetic male and female rats in this study. In animal experiments, females showed greater susceptibility towards developing diabetes because of lower insulin secretion and higher blood glucose levels as compared to male diabetic rats upon exposure to STZ. Immunoblotting confirmed sexually dimorphic regulation of DJ1 in various metabolic tissues such as the liver, pancreas and skeletal muscle. Immunofluorescence analysis revealed the location as well as reinforced the gender-dependent expression of DJ1 in hepatic tissue. Co-immunoprecipitation assay identified several interacting proteins with DJ1 whose functions were shown to be involved in various metabolic pathways viz. antioxidative and stress defence system, protein and methionine metabolism, nitrogen metabolism, urea metabolism, etc. Using GeneMANIA, a predictive web interface for gene functions, we showed for the first time that DJ1 may regulate T1DM via the JNK1 pathway, suggesting DJ1 interacts with other proteins from various metabolic pathways. We anticipate that the current data will provide insights into the aetiology of T1DM.
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Vied CM, Freudenberg F, Wang Y, Raposo AASF, Feng D, Nowakowski RS. A multi-resource data integration approach: identification of candidate genes regulating cell proliferation during neocortical development. Front Neurosci 2014; 8:257. [PMID: 25191221 PMCID: PMC4139594 DOI: 10.3389/fnins.2014.00257] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 08/01/2014] [Indexed: 11/17/2022] Open
Abstract
Neurons of the mammalian neocortex are produced by proliferating cells located in the ventricular zone (VZ) lining the lateral ventricles. This is a complex and sequential process, requiring precise control of cell cycle progression, fate commitment and differentiation. We have analyzed publicly available databases from mouse and human to identify candidate genes that are potentially involved in regulating early neocortical development and neurogenesis. We used a mouse in situ hybridization dataset (The Allen Institute for Brain Science) to identify 13 genes (Cdon, Celsr1, Dbi, E2f5, Eomes, Hmgn2, Neurog2, Notch1, Pcnt, Sox3, Ssrp1, Tead2, Tgif2) with high correlation of expression in the proliferating cells of the VZ of the neocortex at early stages of development (E15.5). We generated a similar human brain network using microarray and RNA-seq data (BrainSpan Atlas) and identified 407 genes with high expression in the developing human VZ and subventricular zone (SVZ) at 8–9 post-conception weeks. Seven of the human genes were also present in the mouse VZ network. The human and mouse networks were extended using available genetic and proteomic datasets through GeneMANIA. A gene ontology search of the mouse and human networks indicated that many of the genes are involved in the cell cycle, DNA replication, mitosis and transcriptional regulation. The reported involvement of Cdon, Celsr1, Dbi, Eomes, Neurog2, Notch1, Pcnt, Sox3, Tead2, and Tgif2 in neural development or diseases resulting from the disruption of neurogenesis validates these candidate genes. Taken together, our knowledge-based discovery method has validated the involvement of many genes already known to be involved in neocortical development and extended the potential number of genes by 100's, many of which are involved in functions related to cell proliferation but others of which are potential candidates for involvement in the regulation of neocortical development.
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Affiliation(s)
- Cynthia M Vied
- Department of Biomedical Sciences, College of Medicine, Florida State University Tallahassee, FL, USA
| | - Florian Freudenberg
- Department of Psychiatry, Psychosomatics and Psychotherapy, University Hospital of Frankfurt Frankfurt, Germany
| | - Yuting Wang
- NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore Singapore, Singapore
| | | | - David Feng
- Allen Institute for Brain Science Seattle, WA, USA
| | - Richard S Nowakowski
- Department of Biomedical Sciences, College of Medicine, Florida State University Tallahassee, FL, USA
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