Identification of Novel Candidate Targets for Fascaplysin through <i>in silico</i> and <i>in vivo</i> Analyses of Shared Targets among Structurally Similar Compounds

Background The discovery of new drug targets is a critical and challenging aspect of drug development. Fascaplysin, a marine natural product, has shown potential in various biological applications, but identifying suitable protein targets for such compounds remains a complex task. Objectives This study aims to identify new candidate protein targets for fascaplysin by analyzing the expected targets of structural analogs, utilizing both molecular docking analysis for prediction and in vivo experiments for validation. Materials and Methods We utilized a public database to classify structurally similar analogs to fascaplysin into four groups based on their scaffold structures. The predicted protein targets were organized by scaffold structure and assessed for potential binding with fascaplysin through molecular docking analysis. In adult zebrafish, we employed quantitative polymerase chain reaction (qPCR) to detect expression changes in downstream signaling genes of the selected candidate targets, providing a predictive measure of interaction and biological effect. Results: A total of 93 common targets were identified across all groups, categorized based on protein characteristics. The molecular binding affinities between fascaplysin and 37 selected candidates, comprising 14 kinases and 23 receptors, were quantified. Molecular docking analyses highlighted MAPK8, MAP2K1, ERBB2, and JAK3 as novel drug target candidates. In adult zebrafish, fascaplysin modulated expression changes in downstream genes of these targets. This indicates the applicability of fascaplysin in treating diseases associated with these targets, revealing promising therapeutic potential. Conclusion: The in silico analysis method used in this study provides an efficient and cost-effective way to identify protein target candidates for drugs, using structural similarities and molecular docking to make the target validation process in drug development faster and easier. Integration of in vivo observations in adult zebrafish, specifically the modulation of downstream gene expression of candidate targets, complements in silico findings, enhancing the reliability of target identification. These results not only identify specific targets for fascaplysin but also establish a flexible framework that can be applied to other compounds, potentially expediting the drug discovery process.