Chemical structure and pharmacological data of hesperetin.
ADME describes the distribution of hesperetin inside the human body, which is needed to be considered while assessing the therapeutic efficacy of hesperetin against atherosclerosis (29). TCMSP database offered ADME-related 12 pharmacokinetic parameters, including molecular weight (MW), logarithm of the octanol-water partition coefficient (AlogP), hydrogen-bond donor (Hdon), hydrogen-bond acceptor (Hacc), oral bioavailability (OB%), Caco-2 permeability (Caco-2), blood brain barrier permeability (BBB), drug likeness (DL), fractional negative surface area (FASA), topological polar surface area (TPSA), rotatable bonds (RBN), and drug half-life (HL). The pharmacological properties of hesperetin have been investigated by referring to the TCMSP database (Table 1). Of note, the OB and DL, two crucial parameters for evaluating the druggability of hesperetin, were higher than the threshold value (“DL ≥ 0.18 and OB ≥ 30%”), suggesting that hesperetin is a druggable candidate.
Identification of hesperetin-atherosclerosis crossover targets
As described in the “Materials and methods” section, the 294 targets of hesperetin from Homo Sapiens were acquired from the PharmMapper database after removing the duplicates and non-human targets. Besides, 4346 targets associated with atherosclerosis were collected from the GeneCards database while a total of 383 targets were used for further investigation by filtering out low correlative targets (relevance score <6). Moreover, 53 hesperetin-atherosclerosis crossover targets were identified by the Venn diagram in the Bioinformatics website (Figure 2A). The gene names and gene symbols of the crossover targets have been listed (Table 2).
PPI network establishment
To explore the functional connections among these crossover targets, we constructed the PPI network of the crossover targets through employing the GeneMANIA database. Among the 53 targets and their interacting 20 proteins, 49.42% showed the co-expression characteristics, 10.05% had physical connections, 7.04% showed the characteristics of co-localization, and other connections, such as shared proteins, predicted interactions and genetic interactions have been quantified (Figure 3A). Furthermore, the crossover targets were subsequently sorted by “Degree value” in descending order residents in Cytoscape software (Table 3). Of note, as indicated by their degree value calculated by Cytoscape, Albumin, differing from HMG-CoA reductase, could be dug out for the further development of anti-atherosclerosis drugs.
GO and KEGG enrichment analysis
To systematically decipher the mode of action of hesperetin against atherosclerosis, GO and KEGG pathway enrichment analysis were carried out to identify the molecular functions, biological processes, cellular components, and cellular signaling pathways of these crossover targets. The KEGG pathway enrichment analysis suggested that the crossover targets are closely associated with the fluid shear stress and atherosclerosis pathway (hsa05418), AGE-RAGE signaling pathway in diabetic complications pathway (hsa04933), TNF signaling pathway (hsa04668), and insulin resistance pathway (hsa04931) in the top five pathways (Figure 4A). GO annotation revealed that the crossover targets were involved in lipid metabolism and inflammatory response, such as regulation of inflammatory response (GO:0006869) and lipid transport (GO:0050727) were included. Collectively, these crossover targets were highly associated with the pathogenesis of atherosclerosis.
Construction of the hesperetin-targets-pathway network
Based on the crossover targets and the corresponding pathways, an entire “hesperetin-targets-pathway” network was constructed using Cytoscape software. In general, this “hesperetin-targets-pathway” network has one compound and 53 targets, involving 58 cell signaling pathways, 112 nodes, and 412 edges. As presented in this network, the targets of hesperetin and its corresponding pathway were connected to obtain a visual view. For instance, hesperetin could regulate the fluid shear stress and atherosclerosis pathway (hsa05418) by interacting with its target including AKT2, RHOA, MAPK14, GSTM1, KDR, MMP2, MMP9, NOS3, MAPK8, SELE, and SRC, thereby ameliorating development and progression of atherosclerosis (Figure 5A).