Dioscorea nipponica Makino: A comprehensive review of its chemical composition and pharmacology on chronic kidney disease

Integrating network pharmacology and experimental validation to decipher the pharmacological mechanism of DXXK in treating diabetic kidney injury

Diabetes mellitus (DM) is a chronic metabolic disease that is highly susceptible to kidney injury. Di'ao XinXueKang capsules (DXXK) is a novel Chinese herbal medicine that has been used in clinical trials for the therapy of DM and kidney disease, but the underlying pharmacological mechanism remains unclear. This study aims to integrate network pharmacology, molecular docking and in vivo experiments to explore the potential mechanisms of DXXK in the treatment of diabetic kidney injury. The chemical constituents of DXXK were extracted from the ETCM and Batman-TCM databases, and then evaluated for their pharmacological activity via the Swiss ADME platform. Multiple disease databases were searched and integrated for DM-related targets. Overlapping targets were then collected to construct a protein-protein interaction (PPI) network. KEGG and GO enrichment analyses were performed based on the Metascape database, and molecular docking was performed using AutoDock Vina software. The main components in DXXK were analyzed by HPLC. The results of network pharmacology and molecular docking were validated in an animal model of DM induced by the combination of a high-fat diet (HFD) and streptozotocin (STZ). We screened and obtained 7 ingredients and identified dioscin, protodioscin, and pseudoprotodioscin as the major components of DXXK by HPLC. A total of 2,216 DM-related pathogenic genes were obtained from DrugBank, GeneCards, OMIM, and DisGeNET databases. KEGG and GO enrichment analyses indicated that the TGF-beta signaling pathway is a critical pathway associated with DM therapy. Molecular docking revealed that the ingredients in DXXK bind to the pivotal targets TGFβ1, Smad2, and Smad3. In diabetic mice, we found that DXXK alleviated diabetic symptoms, lowered blood glucose, improved insulin tolerance, and modulated lipid metabolism. Furthermore, DXXK attenuated renal lesions and fibrosis by downregulating TGFβ1, Smad2, and Smad3. Collectively, our results suggest that DXXK has the potential to regulate glucolipid metabolism in DM, and it may serve as a viable therapeutic option for renoprotection by inhibiting of the TGF-β1/Smad2/3 pathway.

Intraspecific phylogeny and genomic resources development for an important medical plant Dioscorea nipponica, based on low-coverage whole genome sequencing data

Dioscorea nipponica Makino, a perennial twining herb with medicinal importance, has a disjunctive distribution in the Sino-Japanese Floristic Region. It has a long history in traditional Chinese medicine, with demonstrated efficacy against various health conditions. However, the limited genomic data and knowledge of genetic variation have hindered its comprehensive exploration, utilization and conservation. In this study, we undertook low-coverage whole genome sequencing of diverse D. nipponica accessions to develop both plastome (including whole plastome sequences, plastome-derived SSRs and plastome-divergent hotspots) and nuclear genomic resources (including polymorphic nuclear SSRs and single-copy nuclear genes), as well as elucidate the intraspecific phylogeny of this species. Our research revealed 639 plastome-derived SSRs and highlighted six key mutational hotspots (namely CDS ycf1, IGS trnL-rpl32, IGS trnE-trnT, IGS rps16-trnQ, Intron 1 of clpP, and Intron trnG) within these accessions. Besides, three IGS regions (i.e., ndhD-cssA, trnL-rpl32, trnD-trnY), and the intron rps16 were identified as potential markers for distinguishing D. nipponica from its closely related species. In parallel, we successfully developed 988 high-quality candidate polymorphic nuclear SSRs and identified 17 single-copy nuclear genes for D. nipponica, all of which empower us to conduct in-depth investigations into phylogenetics and population genetics of this species. Although our phylogenetic analyses, based on plastome sequences and single-copy nuclear genes revealed cytonuclear discordance within D. nipponica, both findings challenged the current subspecies classification. In summary, this study developed a wealth of genomic resources for D. nipponica and enhanced our understanding of the intraspecific phylogeny of this species, offering valuable insights that can be instrumental in the conservation and strategic utilization of this economically significant plant.