Unveiling therapeutic biomarkers and druggable targets in ALS: An integrative microarray analysis, molecular docking, and structural dynamic studies

Deboral Eshak; Mohanapriya Arumugam

doi:10.1016/j.compbiolchem.2024.108211

Unveiling therapeutic biomarkers and druggable targets in ALS: An integrative microarray analysis, molecular docking, and structural dynamic studies

Comput Biol Chem. 2024 Sep 12:113:108211. doi: 10.1016/j.compbiolchem.2024.108211. Online ahead of print.

Authors

Deboral Eshak¹, Mohanapriya Arumugam²

Affiliations

¹ Department of Biotechnology, School of Bioscience and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014, India.
² Department of Biotechnology, School of Bioscience and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu 632014, India. Electronic address: mohanapriyaa@vit.ac.in.

PMID: 39299050
DOI: 10.1016/j.compbiolchem.2024.108211

Abstract

Amyotrophic lateral sclerosis (ALS), commonly known as Lou Gehrig's disease, is a debilitating neurodegenerative disorder characterized by the progressive degeneration of nerve cells in the brain and spinal cord. Despite extensive research, its precise etiology remains elusive, and early diagnosis is challenging due to the absence of specific tests. This study aimed to identify potential blood-based biomarkers for early ALS detection and monitoring using datasets from whole blood samples (GSE112680) and oligodendrocytes, astrocytes, and fibroblasts (GSE87385) obtained from the NCBI-GEO repository. Through bioinformatics analysis, including protein-protein interactions and molecular pathway analyses, we identified differentially expressed genes (DEGs) associated with ALS. Notably, ALS2, ADH7, ALDH8A1, ALDH3B1, ABHD2, ABHD17B, ABHD12, ABHD13, PGAM2, AURKB, ANAPC11, VAPA, UNC45B, and TNNT2 emerged as top-ranked DEGs, implicated in drug metabolism, protein depalmytilation, and the AKT/mTOR signaling pathways. Among these, AurKB established as a potential therapeutic biomarker with relevance to various neurological conditions. Consequently, AurKB was selected for identifying potential therapeutic molecules and utilized for in silico structural characterization studies. Exploration of the IMPATT database led to the discovery of a lead compound similar to Fostamatinib, currently used for AurKB. Initial molecular docking and MMGBSA-based binding energy analysis were followed by molecular dynamics simulation (MDS) and free energy landscape (FEL) analysis to validate the ligand's binding efficacy and understand dynamic processes within the biological system. The identified potential biomarkers and lead molecule provide novel insights into the correlation between blood cell transcripts and ALS pathology, paving the way for blood-based diagnostic tools for early ALS detection and ongoing disease monitoring.

Keywords: AURKB, Molecular dynamics simulation; Differentially expressed gene; Microarray; PCA based FEL analysis.