计算分子生物学(英文) Pub Date : 2023-06-01 DOI: 10.4236/cmb.2023.132002

Elizabeth Cagle, Brent Lake, Anasua Banerjee, Jazmine Cuffee, Narendra Banerjee, Darla Gilmartin, Makaiyah Liverman, Shennel Brown, Erik Armstrong, Santanu Bhattacharya, Somiranjan Ghosh, Tanmoy Mandal, Hirendra Banerjee

{"title":"Analysis of Differential Gene Expression and Core Canonical Pathways Involved in the Epithelial to Mesenchymal Transition of Triple Negative Breast Cancer Cells by Ingenuity Pathway Analysis.","authors":"Elizabeth Cagle, Brent Lake, Anasua Banerjee, Jazmine Cuffee, Narendra Banerjee, Darla Gilmartin, Makaiyah Liverman, Shennel Brown, Erik Armstrong, Santanu Bhattacharya, Somiranjan Ghosh, Tanmoy Mandal, Hirendra Banerjee","doi":"10.4236/cmb.2023.132002","DOIUrl":"https://doi.org/10.4236/cmb.2023.132002","url":null,"abstract":"Triple Negative Breast Cancer (TNBC) is a malignant form of cancer with very high mortality and morbidity. Epithelial to Mesenchymal Transition (EMT) is the most common pathophysiological change observed in cancer cells of epithelial origin that promotes metastasis, drug resistance and cancer stem cell formation. Since the information regarding differential gene expression in TNBC cells and cell signaling events leading to EMT is limited, this investigation was done by comparing transcriptomic data generated by RNA isolation and sequencing of a EMT model TNBC cell line in comparison to regular TNBC cells. RNA sequencing and Ingenuity Pathway Software Analysis (IPA) of the transcriptomic data revealed several upregulated and downregulated gene expressions along with novel core canonical pathways including Sirtuin signaling, Oxidative Phosphorylation and Mitochondrial dysfunction events involved in EMT changes of the TNBC cells.","PeriodicalId":70839,"journal":{"name":"计算分子生物学(英文)","volume":"13 2","pages":"21-34"},"PeriodicalIF":0.0,"publicationDate":"2023-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10398793/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10318745","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

计算分子生物学(英文) Pub Date : 2020-09-01 DOI: 10.4236/cmb.2020.103004

Dipendra C Sengupta, Matthew D Hill, Kevin R Benton, Hirendra N Banerjee

引用次数: 0

Molecular Dynamics Simulations of DOPC Lipid Bilayers: The Effect of Lennard-Jones Parameters of Hydrocarbon Chains. DOPC脂质双层分子动力学模拟:碳氢链Lennard-Jones参数的影响。

计算分子生物学(英文) Pub Date : 2012-09-01 DOI: 10.4236/cmb.2012.23007

Anping Liu, Xiaoyang Qi

引用次数: 10

Role of Ligand Reorganization and Conformational Restraints on the Binding Free Energies of DAPY Non-Nucleoside Inhibitors to HIV Reverse Transcriptase. 配体重组和构象约束对DAPY非核苷类HIV逆转录酶抑制剂结合自由能的影响。

计算分子生物学(英文) Pub Date : 2012-03-01 DOI: 10.4236/cmb.2012.21002

Emilio Gallicchio

{"title":"Role of Ligand Reorganization and Conformational Restraints on the Binding Free Energies of DAPY Non-Nucleoside Inhibitors to HIV Reverse Transcriptase.","authors":"Emilio Gallicchio","doi":"10.4236/cmb.2012.21002","DOIUrl":"10.4236/cmb.2012.21002","url":null,"abstract":"The results of computer simulations of the binding of etravirine (TMC125) and rilpivirine (TMC278) to HIV reverse transcriptase are reported. It is confirmed that consistent binding free energy estimates are obtained with or without the application of torsional restraints when the free energies of imposing the restraints are taken into account. The restraints have a smaller influence on the thermodynamics and apparent kinetics of binding of TMC125 compared to the more flexible TMC278 inhibitor. The concept of the reorganization free energy of binding is useful to understand and categorize these effects. Contrary to expectations, the use of conformational restraints did not consistently enhance convergence of binding free energy estimates due to suppression of binding/unbinding pathways and due to the influence of rotational degrees of freedom not directly controlled by the restraints. Physical insights concerning the thermodynamic driving forces for binding and the role of \"jiggling\" and \"wiggling\" motion of the ligands are discussed. Based on these insights we conclude that an ideal inhibitor, if chemically realizable, would possess the electrostatic charge distribution of TMC125, so as to form strong interactions with the receptor, and the larger and more flexible substituents of TMC278, so as to minimize reorganization free energy penalties and the effects of resistance mutations, suitably modified, as in TMC125, so as to disfavor the formation of non-binding competent extended conformations when free in solution.","PeriodicalId":70839,"journal":{"name":"计算分子生物学(英文)","volume":"2 1","pages":"7-22"},"PeriodicalIF":0.0,"publicationDate":"2012-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3374582/pdf/nihms-368190.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"30697804","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

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