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

systemic diseases through subgingival plaque and its
products. Therefore, timely treatment of periodontitis is
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of considerable importance to improve the quality of life
of patients with periodontitis. With the development of
bioinformatics, network pharmacology provides us with
a new entry point for research. Furthermore, molecular
docking and molecular dynamics are neoteric means of
new drug research and development, as they are cost-
effective, can save more time, and provide an accurate
possibility to identify new targeted drugs for periodontitis.
As a disease caused by microorganisms and mediated by
host inflammation, the treatment of periodontitis should
not only exert anti-inflammatory effects but also increase
the body’s immune regulation to promote the regeneration
Figure 2. Intersection targets of Epimedii herba (EH) and periodontitis. of periodontal tissue. TCM can not only inhibit the
6,26
Blue represents the target number for the active ingredients of EH, yellow
represents the target number for periodontitis, and the middle part inflammatory response but also control the elimination
represents the intersection targets of dental plaque (the initial factor of periodontitis) to kill
microorganisms and promote the body’s immune regulation
showed that the number of H-bonds gradually increased to achieve periodontal tissue regeneration. 27-29 EH, a TCM
after 10 ns, and the system tended to be stable, as depicted that has been used for several years worldwide, has recently
in Figure 8D. Solvent accessible surface area (SASA) is been proven to exert anti-inflammatory and immune-
another key factor of protein stabilization, which similarly regulating effects. 16,30 In this study, network pharmacology,
stabilized after 10 ns, as illustrated in Figure 8E. molecular docking, and molecular dynamics methods
were used to screen the pharmacological components
Molecular mechanics Poisson–Boltzmann surface of EH for the prevention and treatment of periodontitis,
area (MMPBSA) is one of the most common methods explore its molecular mechanism, and provide novel ideas
to estimate binding free energies, which can be used to for the clinical treatment of periodontitis.
accurately estimate the affinity of ligand–protein binding
and calculate the binding free energy generated by the OB and DL screening revealed 8-(3-methylbut-2-
docking of the ligand–protein complex. 23,24 The total enyl)-2-phenyl-chromone, 8-isopentenyl-kaempferol,
binding free energies of MMPBSA included GGAS and anhydroicaritin, chryseriol, DFV, kaempferol, luteolin,
GSOLV. The GGAS is composed of van der Waals force and quercetin, and Yinyanghuo C as the major active
electrostatic energy, which are −38.31 and −8.42 kcal/mol, ingredients of EH. According to the PPI network,
respectively. The GSOLV consists of a polar solvation AKT1, TNF, IL6, TP53, VEGFA, IL1B, CASP3, PTGS2,
energy of 30.99 kcal/mol and a non-polar solvation energy MMP9, and ESR1 were screened as the top 10 key
of −5.59 kcal/mol. Therefore, the total binding free energy targets, through which EH may play a vital role in
was 21.33 kcal/mol, indicating that the binding was periodontitis treatment. GO enrichment analysis
revealed that EH participated in the processes of cellular
relatively stable, as depicted in Figure 9A.
response to organic cyclic compounds, membrane raft,
During the binding process, the amino acid residues DNA-binding transcription factor binding, and other
participate in the formation of the binding site pocket. reaction processes. KEGG pathway enrichment analysis
The total contributing energy of the amino acid residues revealed that pathways related to cancer, lipid, and
was 7.67 kcal/mol, and LEU:346, MET:421, LEU:387, atherosclerosis as well as AGE–RAGE signaling pathways
MET:388, LEU:391, PHE:404, ILE:424, LEU:349, and in diabetic complications might be primarily involved
LEU:384 contributed significantly to the binding free in periodontitis treatment with EH. The results of
energies, as illustrated in Figure 9B. LEU:346 and MET:421 molecular docking and molecular dynamics simulation
contributed prominently with the binding energies of demonstrated that the active components of EH had
−2.69 and −2.20 kcal/mol, respectively. good binding ability to the key targets, suggesting that
EH plays a vital role in periodontitis treatment. These
4. Discussion methods also confirmed the predicted results of network
Periodontitis is a widespread disease worldwide that can pharmacology to a certain extent.
induce an inflammatory response and cause tooth loss, Regarding the anti-inflammatory effects of EH,
destruction of periodontal supporting tissues, and other previous studies have reported that icariin can alleviate

Volume 3 Issue 4 (2024) 6 doi: 10.36922/gpd.4427