Withanolides and their target prediction
Based on the availability of structures of bioactives, 17 withanolides were chosen for the study. Among them, Withanolide Q was predicted to modulated the highest number of proteins i.e. 12 in which 5 were down-regulated (CHEK1, NR3C1, PRKCA, PROS1, ESR2) and 7 were up-regulated (TNFRSF1A, PLAT, RAC1, VDR, FKBP5, AR, GH1). The down-/up-regulated proteins of each compound are summarized in Table 1.
Prediction of druglikeness score and human intestinal absorptivity
Prediction of human intestinal absorptivity identified Withanolide E, Withanolide F, Somniferawithanolide, Withanolide Q, Withanolide M, Withanolide D, Withianoloide R, Withanolide I, Withanolide L, and Withanolide N to be absorbable from g.i.t (Figure 1). Further, druglikeness prediction identified Withanolide Q to possess the highest druglikeness score i.e. 0.75 (Figure 2).
Enrichment and network analysis
Enrichment analysis identified the prime modulation of Fluid shear stress and atherosclerosis with the highest number of gene sets i.e. 4 (CCL2, PLAT, RAC1, TNFRSF1A) at lowest false discovery rate i.e. 0.0012. The modulation of genes also identified the regulation of multiple pathways which are having direct/indirect relation with infectious/non-infectious diseases. Further, pathways related to the modulation of the immune system like TNF, Fc epsilon RI, p53, PI3K-Akt, IL-17, mTOR, NOD-like receptor, Chemokine, Rap1 and NF-kappa B signaling pathway and Cytokine-cytokine receptor interaction were also predicted (Table 2). Similarly, GO analysis identified the highest number of modulated genes i.e. 17 from membrane-bound organelle and cytoplasm as a cellular component, molecular function with 19 genes as binding, and stimulus respondent (19 genes) as biological processes (Figure 3). The network interaction of bioactives and modulated pathways with respective genes is represented in Figure 4.
Anti-viral PASS prediction of bioactives
All the bioactives were predicted as the anti-viral against Rhinovirus, six (Withanolide -D, -M, -N, -O, -P and -Q) for influenza, four (Withanolide-D, -O, -N, -Q,) and Withanolide Q against Hepatitis and HIV. Similarly, three bioactives (Withanolide -N, -O and -Q,) were predicted as undefined anti-viral agents (Figure 5).
In silico molecular docking
Withanolide G and Withanolide D were predicted to possess the highest binding affinity with PLpro with binding energy -8.9 kcal/mol; however, Withanolide G was predicted for the highest number of hydrogen bond interactions i.e. 6 by interacting with ARG167, GLN233, and TYR208. Similarly, Withanolide I was predicted for its highest hydrogen bond interactions i.e. 7 with ARG131, ASP289, THR199, LEU287, TYR239, ASN238 though it possessed -9.1 kcal/mol compared to Withanolide J (-9.3 kcal/mol). Likewise, Withanolide M was predicted to possess the highest binding affinity with spike protein by interacting with 4 hydrogen bond interactions with CYS566, THR525, LYS523. However, Withanolide H was predicted to interact with spike protein via 6 hydrogen bonds with ASN211, ASN185, THR254, SER67, THR94, ALA259 though it scored comparatively higher binding energy (-8.5 kcal/mol) compared to Withanolide H (Table 3). Figure 6 represents the interaction of lead hit based on binding energy with the respective protein.