In Silico Design and Molecular Docking Analysis of a Novel RNA Aptamer Targeting EGFR Extracellular Domain

Title: In Silico Design and Molecular Docking Analysis of a Novel RNA Aptamer Targeting EGFR Extracellular Domain for CRISPR/Cas9 Delivery Abstract & Project Overview: This study presents a targeted, non-viral gene therapy approach for non-small cell lung cancer (NSCLC) by utilizing an EGFR-targeting RNA aptamer functionalized onto ionizable lipid nanoparticles (Apt-LNP) for precise CRISPR/Cas9 delivery. Key Highlights & Updates in this Revision: 1. Computational & In Silico Validation: Detailed molecular docking analysis using HDOCK demonstrating high structural binding affinity (docking score: -338.22) between the RNA aptamer and the EGFR extracellular domain. 2. Formulation & Biophysical Characterization: Standardized molar ratios for LNP formulation (DLin-MC3-DMA:Cholesterol:DSPC:DSPE-PEG2000-Maleimide at 50:38.5:10:1.5) with comprehensive mathematical modeling for N/P ratio, encapsulation efficiency (EE%), and Pearson Correlation Coefficient (PCC). 3. Experimental Preclinical Protocols: Rigorously defined standardized in vitro cellular uptake and in vivo mouse model protocols (0.5 mg/kg systemic tail-vein administration over 3, 7, 14, and 28-day timeframes) for evaluating gene knockout efficiency (Indel %). 4. Data Scope Clarification: Full distinction between computational/in silico predictions and recommended standardized preclinical assay workflows. Keywords: CRISPR/Cas9, Aptamer, Lipid Nanoparticles (LNP), EGFR, Molecular Docking, Gene Therapy, Non-Small Cell Lung Cancer (NSCLC). Authors & Affiliation: Hosein Hoseini et al., Department of Cell and Molecular Biology, Faculty of Science, Payame Noor University, Lorestan, Iran.