Exploring phytochemical candidates against nephrolithiasis via similarity searching, network pharmacology, and...

Nephrolithiasis (kidney stones) affects nearly 13 % of the global population, with a high recurrence rate posing significant challenges. Current remedies often fail to prevent recurrence, necessitating new therapeutic approaches. This study explores phytochemicals with potential protective effects against nephrolithiasis using similarity searching, network pharmacology, and molecular docking methods. Six anti-nephrolithiatic parent molecules were identified through a literature review. Structural similarity searches yielded 67 related compounds, which were screened using Lipinski' s rule of five, along with ADME (absorption, distribution, metabolism, excretion) parameters and toxicity profiles, and subsequently compared with standard drugs. The standard drug offered poor results; therefore, we aimed to overcome this limitation by searching for phytochemicals with favorable ADMET properties. Shortlisted compounds and nephrolithiasis-related targets were analyzed using Swiss Target Prediction and GeneCards. Hub genes were identified via Cytoscape' s Cytohubba plugin and subjected to Gene Ontology (GO) and KEGG pathway analysis. Molecular docking evaluated the binding of phytochemical ligands to disease proteins. Five phytochemicals namely 4- 4-Vinylguaiacol, anethole, isoeugenol, nadolol, and silibinin, were identified as potential candidates. Network pharmacology revealed 191 common targets between these compounds and nephrolithiasis. GO analysis highlighted key biological processes (response to organic substances, chemical stimuli), cellular components (nuclear lumen, nucleoplasm), and molecular functions (enzyme binding, catalytic activity). KEGG pathway analysis identified pathways in cancer, hepatitis B, and Kaposi sarcoma-associated herpesvirus infection as relevant to nephrolithiasis. Molecular docking demonstrated strong binding affinities between the shortlisted phytochemicals and disease targets. The multi-level screening and molecular docking findings highlight 4-Vinylguaiacol, anethole, isoeugenol, nadolol, and silibinin as promising therapeutic agents for nephrolithiasis. Among these, silibinin was tested for the in-vitro cytotoxicity assay based on the docking score. Importantly, in vitro validation using NRK-52E cells confirmed nephroprotective efficacy of silibinin. While calcium oxalate crystal exposure significantly reduced cell viability to below 50 %, co-treatment with silibinin improved cell survival to approximately 70 %, underscoring its potential to mitigate oxalate-induced cytotoxicity. Further experimental studies are required to validate these findings.