Comprehensive Bioinformatics Analysis Reveals Molecular Signatures and Potential Caloric Restriction Mimetics with Neuroprotective Effects: Validation in an In Vitro Stroke Model

Abstract

Caloric restriction (CR) is a dietary intervention that reduces calorie intake without inducing malnutrition, demonstrating lifespan-extending effects in preclinical studies and some human trials, along with potential benefits in ameliorating age-related ailments. Caloric restriction mimetics (CRMs) are compounds mimicking CR effects, offering a potential therapeutic avenue for age-related diseases. This study explores the potential protective effects of CR on the brain neocortex (GSE11291) and the identification of CRMs using integrative bioinformatics and systems biology approaches. Our findings indicate that long-term CR activates cellular pathways improving mitochondrial function, enhancing antioxidant capacity, and reducing inflammation, potentially providing neuroprotection. The key signaling pathways enriched in our study include PPAR, mTOR, FoxO, AMPK, and Notch signaling pathways, which are crucial regulators of metabolism, cellular stress response, neuroprotection, and longevity. We identify key signaling molecules and molecular mechanisms associated with CR, including transcription factors, kinase regulators, and microRNAs linked to differentially expressed genes. Furthermore, potential CRMs such as rapamycin, replicating CR-related health benefits, are identified. Additionally, machine learning models were developed to classify small molecules based on their CNS activity and anti-inflammatory properties. As a proof of concept, we have demonstrated the ischemic neuroprotective effects of two top-ranked candidate reference molecules (CRMs) using the oxygen–glucose deprivation (OGD) model, an established in vitro stroke model. However, further investigations are essential to fully elucidate the therapeutic potential of these CRMs. In summary, our study suggests that long-term CR entails protective mechanisms preserving and safeguarding neuronal function, potentially impacting the treatment of age-related neurological diseases. Moreover, our findings contribute to the identification of potential genes and regulatory molecules involved in CR, along with potential CRMs, providing a promising foundation for future research in the field of neurological disorder treatment.

Graphical Abstract