Optimizing Open Source Tools for Protein Design, Characterization, and Docking in Alzheimer's Disease Drug Development

This study aims to establish a pipeline, or method, for the in-silico discovery of potential protein drugs to treat Alzheimer's Disease (AD). Specifically, this study focuses on the apolipoprotein E (ApoE) protein, the most significant genetic factor in regards to AD development. ApoE has been found to bind to the triggering receptor expressed on myeloid cells 2 (TREM2,) causing the pathogenesis of AD. ApoE has three isoforms, which bind to TREM2 RH47 in the following order: ApoE4 > ApoE3 (WT) > ApoE2. Knowing that a lower binding affinity results in a decrease in disease state, this study used these proteins to represent potential drugs to cure Alzheimer’s. The first step of the pipeline of this study was the in-silico design of the ApoE proteins isoforms. The resulting proteins were then put through the second phase and analyzed using molecular modeling, docking, and folding simulations available on accessible Open-Source tools such as PyMOL, AutoDock, GROMACS, Phyre2, and Clustal Omega. Next, their viability was tested through energy calculations and stability predictions in FoldX, ECEPPAK, and more. Last, protein docking simulation in ROSETTA, Autodock Vina, and HADDOCK evaluated binding efficiency to the TREM2 receptor. The findings indicate that the engineered proteins exhibited therapeutic potential by demonstrating reduced binding efficiency to the TREM2 receptor. To assess cost-effectiveness and accessibility, only open source, freely accessible programs were used on this computational pipeline. The results were optimistic, as the application of open-source tools for the analysis of protein design, characterization, and docking interactions were effective and yielded similar results, suggesting feasibility of developing cost-effective and accessible in-silico protein drugs targeting AD-related receptors. However, further experiments employing different software platforms are warranted to validate these findings.