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Ghamsari PA, Samadizadeh M, Mirzaei M. Halogenated derivatives of cytidine: Structural analysis and binding affinity. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2020. [DOI: 10.1142/s0219633620500339] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Cytidine is a well-known inhibitor of DNA methyltransferase (MTN) enzyme for preventing cancer cells growth. Based on therapeutic benefits, it could be considered as a “lead compound” to be optimized through structural modification for arising better binding affinity in this case. Halogenated derivatives of cytidine were investigated in this work to examine structural and biological features employing in silico approach. To this aim, geometries of the original cytidine and four of its halogenated derivatives were minimized to prepare ligands for interacting with MTN enzyme target in molecular docking simulations. The results for singular ligand structures introduced I-cytidine as an optimized lead compound for contributing to proper interactions with MTN enzyme; the trend was confirmed by molecular docking simulations. As a final remark, I-cytidine could be considered as better ligand for complexation with the MTN enzyme in comparison with the original cytidine.
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Affiliation(s)
- Parnia Abyar Ghamsari
- Department of Chemistry, Central Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Marjaneh Samadizadeh
- Department of Chemistry, Central Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Mahmoud Mirzaei
- Biosensor Research Center, School of Advanced Technologies in Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
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Zavadil JA, Herzig MCS, Hildreth K, Foroushani A, Boswell W, Walter R, Reddick R, White H, Zare H, Walter CA. C3HeB/FeJ Mice mimic many aspects of gene expression and pathobiological features of human hepatocellular carcinoma. Mol Carcinog 2018; 58:309-320. [PMID: 30365185 DOI: 10.1002/mc.22929] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 10/23/2018] [Indexed: 12/18/2022]
Abstract
Hepatocellular carcinoma (HCC) remains a deadly cancer, underscoring the need for relevant preclinical models. Male C3HeB/FeJ mice model spontaneous HCC with some hepatocarcinogenesis susceptibility loci corresponding to syntenic regions of human chromosomes altered in HCC. We tested other properties of C3HeB/FeJ tumors for similarity to human HCC. C3HeB/FeJ tumors were grossly visible at 4 months of age, with prevalence and size increasing until about 11 months of age. Histologic features shared with human HCC include hepatosteatosis, tumor progression from dysplasia to poorly differentiated, vascular invasion, and trabecular, oncocytic, vacuolar, and clear cell variants. More tumor cells displayed cytoplasmic APE1 staining versus normal liver. Ultrasound effectively detected and monitored tumors, with 85.7% sensitivity. Over 5000 genes were differentially expressed based on the GSE62232 and GSE63898 human HCC datasets. Of these, 158 and 198 genes, respectively, were also differentially expressed in C3HeB/FeJ. Common cancer pathways, cell cycle, p53 signaling and other molecular aspects, were shared between human and mouse differentially expressed genes. We established eigengenes that distinguish HCC from normal liver in the C3HeB/FeJ model and a subset of human HCC. These features extend the relevance and improve the utility of the C3HeB/FeJ line for HCC studies.
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Affiliation(s)
- Jessica A Zavadil
- Department of Cell Systems & Anatomy, University of Texas Health Science Center, San Antonio, Texas
| | - Maryanne C S Herzig
- Department of Cell Systems & Anatomy, University of Texas Health Science Center, San Antonio, Texas
| | - Kim Hildreth
- Department of Cell Systems & Anatomy, University of Texas Health Science Center, San Antonio, Texas
| | - Amir Foroushani
- Department of Computer Science, Texas State University, San Marcos, Texas
| | - William Boswell
- Chemistry & Biochemistry Department, Texas State University, San Marcos, Texas
| | - Ronald Walter
- Chemistry & Biochemistry Department, Texas State University, San Marcos, Texas
| | - Robert Reddick
- Pathology Department, University of Texas Health Science Center, San Antonio, Texas
| | - Hugh White
- Radiology Department, University of Texas Health Science Center, San Antonio, Texas.,Radiology Department, Audie L. Murphy Memorial Veterans Affairs Hospital, San Antonio, Texas
| | - Habil Zare
- Department of Cell Systems & Anatomy, University of Texas Health Science Center, San Antonio, Texas
| | - Christi A Walter
- Department of Cell Systems & Anatomy, University of Texas Health Science Center, San Antonio, Texas
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Visualization of chemical modifications in the human 80S ribosome structure. Nature 2017; 551:472-477. [PMID: 29143818 DOI: 10.1038/nature24482] [Citation(s) in RCA: 226] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 10/03/2017] [Indexed: 12/18/2022]
Abstract
Chemical modifications of human ribosomal RNA (rRNA) are introduced during biogenesis and have been implicated in the dysregulation of protein synthesis, as is found in cancer and other diseases. However, their role in this phenomenon is unknown. Here we visualize more than 130 individual rRNA modifications in the three-dimensional structure of the human ribosome, explaining their structural and functional roles. In addition to a small number of universally conserved sites, we identify many eukaryote- or human-specific modifications and unique sites that form an extended shell in comparison to bacterial ribosomes, and which stabilize the RNA. Several of the modifications are associated with the binding sites of three ribosome-targeting antibiotics, or are associated with degenerate states in cancer, such as keto alkylations on nucleotide bases reminiscent of specialized ribosomes. This high-resolution structure of the human 80S ribosome paves the way towards understanding the role of epigenetic rRNA modifications in human diseases and suggests new possibilities for designing selective inhibitors and therapeutic drugs.
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