Determination of 3D structure and molecular interaction for mir-135b and its silencer as Triple Negative Breast Cancer (TNBC) biomarkers

Abstract

Triple Negative Breast Cancer (TNBC) is considered as the most dangerous breast cancer type in women and the most difficult to be medicated due to its unresponsive nature towards drug treatments. However, as transcriptomics studies are becoming more advanced, the research on non-coding (nc)RNAs like miRNA and siRNA is being considered as a more feasible approach to deal with TNBC. The mir-135b, a newly found miRNA that has a role in the molecular mechanism of TNBC, is studied mainly for its function as a possible biomarker and a drug candidate. The molecular interaction and structures are still unknown and determining them is the objective of this research. This research utilizes the RNAComposer webservice for 3D RNA structure prediction and the AutoDockTool for molecular docking to determine their interaction. The result shows satisfactory illustration of mir-135b and its siRNA structures with feasible bindings between them. It is shown that the bindings are strong enough to maintain silencing of the gene. However, the molecular docking result shows reversible interaction based on the binding energy meaning its biomarker potential requires combination with other special drug delivery systems. It could be inferred that the siRNAs have potential to be developed in the wet laboratory settings.

A Computational Design of siRNA in SARS-CoV-2 Spike Glycoprotein Gene and Its Binding Capability toward mRNA

“…The procedure was inspired by the previously developed pipeline for RNA-RNA molecular simulation [38][39]. Specific parameters were added, as mentioned in the subsections below, if necessary.…”