Recently, an important topic of liver tumorigenesis had been published in 2013. In this report, Ras and Rho had defined the relation of liver tumorigenesis. The traditional Chinese medicine (TCM) database has been screened for molecular compounds by simulating molecular docking and molecular dynamics to regulate Ras and liver tumorigenesis. Saussureamine C, S-allylmercaptocysteine, and Tryptophan are selected based on the highest docking score than other TCM compounds. The molecular dynamics are helpful in the analysis and detection of protein-ligand interactions. Based on the docking poses, hydrophobic interactions, and hydrogen bond variations, this research surmises are the main regions of important amino acids in Ras. In addition to the detection of TCM compound efficacy, we suggest Saussureamine C is better than the others for protein-ligand interaction.
Recently, an important topic of liver tumorigenesis had been published in 2013. In this report, Ras and Rho had defined the relation of liver tumorigenesis. Ras and Rho are an important target for liver tumorigenesis [
The liver tumorigenesis (or means hepatic carcinoma) is a serious disease in the world, especially in Asia. The main cause of liver tumorigenesis is virus (HBV or HCV) and abnormal eating and habits (smoke, drink, barbecue, raw food, fatigue, and staying up late). The cumulative burden decreases immunity and then makes liver tumorigenesis. The most cases of hepatic carcinoma are found too late to treat and there is no efficient drug that could prevent disease progression which then causes the patient’s death.
RAS (also called GTPase Kras) and Rho small GTPases are key molecular switches that control cell dynamics, cell growth, and tissue development through the signaling pathways. Previous references reported the inhibition of Ras for cancer treatment is viable [
Computer-aided drug design (CADD) is an
Recently, there are more attentions on personalized medicine and biomedicine [
In this study, we screen a possible lead compound against liver tumorigenesis from the TCM Database@Taiwan. We use the computational techniques of docking screening to select ligands. Finally, we apply molecular dynamics (MD) simulation to investigate variations from protein-ligand interactions that may contribute to the evaluation of the effect on Ras inhibition.
In this research, the molecular simulations platform was using Accelrys Discovery Studio 2.5 (DS 2.5). Amount of 61,000 TCM compounds was downloaded from the TCM database (
The disorder plays an important role in drug design; thus we take the sequence generated from Uniprot to predict the disorder region by the Database of Protein Disorder (DisProt:
Taking a comparison of the disorder regions and the docking sites could assess the protein-ligand interaction and drug efficacy.
The docking simulation applied on LigandFit module [
These ligands from candidate complex must be reprepared based on the reference force field [
The disorder protein is an unstructured protein. For this character, while the docking site is a disorder region, the compounds dock to protein and stabilize the complex with difficultly. In some cited references, [
The disorder and binding site detection. The blue curve in the top figure is the disorder disposition of each amino acid and the red lines are the residues of the important amino acids.
Ranking the result of molecular docking by docking score, the top three TCM compounds can be selected (Table
Scoring functions of the top three compounds and the inhibition of Ras.
Compounds | Herbs | -PLP1 | -PLP2 | Dock score |
---|---|---|---|---|
Saussureamine C |
|
35.6 | 35.37 | 196.626 |
S-Allylmercaptocysteine |
|
21.01 | 27.18 | 185.706 |
Tryptophan |
|
41.19 | 44.91 | 184.146 |
The structure of the candidate compounds is selected after screening from the TCM database (Figure
The structure of control and candidate TCM compounds. (a) Saussureamine C, (b) S-allylmercaptocysteine, and (c) Tryptophan.
The docking poses of ligands. (a) The crystal structure of Ras and Rho and the docking site: (b) Saussureamine C, (c) S-allylmercaptocysteine, and (d) Tryptophan.
The hydrophobic interaction can be analyzed by ligplot (Figure
Ligplot illustrates the protein-ligand interactions. (a) Saussureamine C, (b) S-allylmercaptocysteine, and (c) Tryptophan. The deep red color of the hydrophobic interactions indicates a high frequency in all ligand interactions.
The RMSD and total energy of a complex during MD simulation were recorded (Figure
Measures of the MD trajectories. (a) Complex RMSD, (b) ligand RMSD, and (c) the total energy.
We analyze RMSF which is the RMSD focus on each residue to detect the variation of protein while with ligand interaction (Figure
The variation of RMSD focus on residue of protein.
The reference-identified eigenvector was used to represent the protein variation [
The PCA-eigenvector between ligand and unbound protein. The projection to the first two PCA-eigenvectors as
After the structure variation discussion is based on eigenvector, we should focus on the structure variation during protein-ligand interaction (Figures
The variation of Saussureamine C and Ras complex in MD simulation. (a) H-bond variation and (b) structure variation. The (1)-(2) red color indicates the difference through MD.
Although the complex of S-allylmercaptocysteine and Ras has higher docking score and a lot of relation references, this complex is not stable. The Asp30 and Lys117 also present the important interaction in Figure
The variation of S-allylmercaptocysteine and Ras complex in MD simulation. (a) H-bond variation and (b) structure variation. The red color indicates the difference through MD.
The variation of Tryptophan and Ras complex in MD simulation. (a) H-bond variation and (b) structure variation. The (1)-(2) red color indicates the difference through MD.
The Tryptophan complex interactions were recorded (Figure
From these variations found, we suggest Saussureamine C could make the largest force on the inhibition of Ras.
Finally, the pathway definition which is based on the calculation of caver 3.0 to determine the interpath protein path during MD simulation [
The pathway of Ras for compounds. (a) Unbound protein, (b) Saussureamine C, (c) S-allylmercaptocysteine, and (d) Tryptophan.
Based on above discussion, we can find the top three TCM compounds Saussureamine C, S-allylmercaptocysteine, and Tryptophan can have an effect on Ras against liver tumorigenesis. Asp30 and Lys117 might present their effects on Ras when compounds bind or interact with protein. Even S-allylmercaptocysteine has a lot of references to identify the efficacy on this disease but the result of simulation indicates this compound may have more effect on the other protein then represent the regulation. Finally, according to the discussion from docking, interaction, and variation, we suggest Saussureamine C might be a best compound to inhibit Ras against liver tumorigenesis.
The authors declare that there is no conflict of interests regarding the publication of this paper.
Tzu-Chieh Hung, Wen-Yuan Lee, and Kuen-Bao Chen contributed equally to this paper.
The research was supported by Grants from the National Science Council of Taiwan (NSC102-2325-B039-001 and NSC102-2221-E-468-027-), Asia University (ASIA100-CMU-2, ASIA101-CMU-2, and 102-Asia-07), and China Medical University Hospital (DMR-103-058, DMR-103-001, and DMR-103-096). This study is also supported in part by Taiwan Department of Health Clinical Trial and Research Center of Excellence (DOH102-TD-B-111-004), Taiwan Department of Health Cancer Research Center of Excellence (MOHW103-TD-B-111-03), and CMU under the Aim for Top University Plan of the Ministry of Education, Taiwan.