## 3 Results
### Target-Based Virtual Screening Using AutoDock  
Traditional Chinese medicines (TCMs) areused in the treatment of several diseases. The polyphenols possess activities that inhibit the adhesion of the osteoclast to the bone matrix, affect the proton transportation relevant to a less acidic environment, and inhibit the degrading enzymes, which should be considered multitarget candidates. All 108 selected compounds were docked into the active site of three targets: Cathepsin K, V-ATPase, and \(\alpha_{\mathrm{V}}\beta_{3}\) integrin receptor. The binding energies of docked compounds were presented in terms of AutoDock score. A set of docking scores toward the individual enzyme showed no difference among groups in a range of \(-3.0\) to \(-14.5\) kcal/mol. The validations of the docking set were made by redocking the native ligands, and the rmsd tolerance of native ligands was less than \(2.0\) A. Considering the binding affinities of compounds against the individual target, the top 20 docked scores of compounds are depicted in Figure 3. Kushenol F was used as a positive control for Cathepsin K with a dock score of \(-8.3\) kcal/mol. According to the result, rutin exhibited the highest binding affinity at \(-13.75\) kcal/mol, followed by icarin, kaempferirtin, acetoside, and salivalic acid with the binding affinities of \(-11.93\), \(-11.35\), \(-11.23\), and \(-11.22\) kcal/mol, respectively. Figure 2: The input genes present in the different box styles such as ellipse for Cathepsin K, triangle for integrin receptor, and round rectangle for V-ATPase. Nodes represent protein, and edges represent interactions. (**a**) The gene expression in bone tissues are mapped to the node color; nodes with high expression are colored dark blue, while those of low expression are colored gray. The blue gradient is used to define the location of genes in bone tissue. A total of 25 enriched modes with PPI enrichment \(p\)-value of \(<\)1.0 \(\times\) 10\({}^{-16}\). (**b**) The most significant genes from the PPI network (node color: yellow indicates the Cathepsin K gene, green indicates the V-ATPase genes, and red indicates the \(\alpha_{\mathrm{V}}\beta_{3}\) integrin genes). As a docking result of V-ATPase, the compounds were docked into the binding site of ATP (or ADP), as mentioned in the Material and Method section. Diphylllin was used as a positive control for V-ATPase [46] with a dock score of \(-8.56\) kcal/mol. Among the top five candidates, kaempferirtin showed the highest binding affinity of \(-14.00\) kcal/mol toward V-ATPase, followed by rutin, sagittatoside A, and icarini with the binding affinities of \(-13.91\), \(-13.67\), and \(-13.26\) kcal/mol, respectively. The top 20 binding energies of compounds bound to an active site of \(\alpha_{\rm V}\beta_{3}\) integrin receptor are presented in Figure 3. A binding site is defined according to the location of the native ligand. Artemisinin was used as a positive control for \(\alpha_{\rm V}\beta_{3}\) integrin receptor [47] with a dock score of \(-6.41\) kcal/mol. The docking result indicated that rutin exhibited the strongest binding affinity of \(-13.76\) kcal/mol toward an integrin receptor, followed by sagittatoside A, icarini, kaempferirtin, and oleuprein with the binding affinities of \(-12.93\), \(-11.76\), \(-11.57\), and \(-11.21\) kcal/mol, respectively. We rearranged and combined these three docking results from Cathepsin K, V-ATPase, and \(\alpha_{\rm V}\beta_{3}\) integrin receptor. The top 20 energy-based compounds were visualized in a heatmap plot (Figure 3). The cells with high binding score were given a steel blue color, whereas those of a low binding score were shown in white color. Further, these data sets were normalized and illustrated in the scatter plot. Each point represented the mean normalized score of an individual compound toward three targets, called the z-score. We  
Figure 3: The binding energies of phytochemicals.