Page 86 - GPD-3-4

Gene & Protein in Disease A prediction on how Epimedii herba treat periodontitis

Cytoscape3.7.0. Nodes represented the ingredients and module was used to connect the key active ingredients of EH
targets in the network, and the interactions between them to the processed protein to perform molecular docking. The
were represented by edges. Then, the key ingredients were higher the negative CDocker interaction energy (−CIE) value
selected in the network based on the “degree” value. of the docking, the more stable the docking system between
the chemical ingredients and protein receptors.
2.5. Construction of a protein–protein interaction
(PPI) network 2.8. Molecular dynamics
The intersection targets of EH and periodontitis were Gromacs-2022.04GPU was used to perform molecular
input into the STRING platform (https://string-db.org), dynamics simulations between the active ingredient
after which the tab control of “Multiple Proteins” was and target protein with the best bonding ability in the
selected, and “Homo Sapiens” was chosen as the organism molecular docking results. The ATB website (http://atb.
to construct the PPI network. Next, the obtained network uq.edu.au/) was used to convert the active ingredient files
was imported into Cytoscape 3.7.0 for further analysis. into the molecular structure and topology files; the built-in
The top 10 core targets were calculated using “CytoHubba” commands in Gromacs-2022.04GPU were used to convert
with the highest maximal clique centrality score. the protein files into the molecular structure files. Then,
using the TIP3P model as water molecules, chloride, and
2.6. Gene functional pathway enrichment analysis sodium ions were added to the system to leave the system

When the intersection targets were imported into the at a normal saline concentration. The topology files of the
Metascape database (http://metascape.org/), the species chemical components were prepared using the PDB-2gmx
was selected as “H. Sapiens” for GO and KEGG enrichment module, and the receptor proteins were subjected to the
analyses. GO is an internationally standardized system for latest charmm36-jul2022 force field. After optimizing the
the classification of gene functions, which can be divided energy of the system, the temperature should be maintained
into cellular components (CC), molecular functions (MF), at 36.85°C, and the pressure should be maintained at 1 atm
and biological processes (BP). KEGG analysis provides within a simulation period of 50 ns.
more insights into the biological functions of genes. We 3. Results
next selected the top 20 items of BP, MF, and CC and the
top 20 results of KEGG enrichment analysis to construct 3.1. Collection of the active compounds and targets
a histogram and bubble diagram using the Weishengxin of EH
website (http://www.bioinformatics.com.cn/). Based on TCMSP, 23 effective active ingredients of EH
were obtained, as shown in Table 1. A total of 199 targets
2.7. Molecular docking
related to the active ingredients of EH were obtained.
The 3D structure files of the key active ingredients and
targets were input into Discovery Studio 2019 for molecular 3.2. Acquisition of periodontitis-related targets
docking. The PDB IDs of related proteins were 4EJN(AKT1), Two periodontitis-related datasets were obtained from the
7KP9(TNF), 1ALU(IL6), 6BFT(VEGFA), 1RHM(CASP3), GEO database, namely, GSE10334 and GSE16134, which
2OW1(MMP9), and 3OS8(ESR1). Protein preparation contained 183 and 241 samples, respectively. Both datasets
was performed, wherein the “Clean Protein” and “Prepare covered the gingival tissues of patients with periodontitis
Protein” modules were used to delete redundant protein and healthy people. Figure 1 shows the volcano map
conformation and water molecules, and target proteins were and heatmap of differential genes in periodontitis. After
hydrogenated simultaneously. Then, the protein’s ligand deleting duplicate gene targets, 3291 periodontitis-related
position was selected as the active binding site. After deleting targets were obtained from GeneCards, DrugBank, TTD,
the original ligand and exposing the active binding pocket, CTD, and GEO databases.
the active site was defined as a receptor in the docking
system. Next, hydrogenation and energy optimization were 3.3. Screening of the intersection targets of EH and
also performed on the key effective ingredient. Then, the periodontitis
CDocker module was used to connect the original ligand to By constructing a Venn diagram, 137 intersection targets
the active pocket and calculate the root mean square deviation were obtained, as depicted in Figure 2.
(RMSD) of the molecular conformations. RMSD values of
<2.0 Å indicate that the molecular conformation obtained by 3.4. Construction of the EH ingredient–target
docking can reduce the ligand and receptor binding affinity, interaction network
thereby confirming the rationality of the selected docking The EH ingredient–target interaction network (Figure 3)
methods and parameter settings. Finally, the CDocker consisted of 219 nodes and 439 edges. Each pathway

Volume 3 Issue 4 (2024) 3 doi: 10.36922/gpd.4427