Recently, an important topic of breast cancer had been published in 2013. In this report, estrogen receptor (ESR1) had defined the relation of hormone-cause breast cancer. The screening of traditional Chinese medicine (TCM) database has found the molecular compounds by simulating molecular docking and molecular dynamics to regulate ESR1. S-Allylmercaptocysteine and 5-hydroxy-L-tryptophan are selected according to the highest docking score than that of other TCM compounds and Raloxifene (control). The simulation from molecular dynamics is helpful in analyzing and detecting the protein-ligand interactions. After a comparing the control and the Apo form, then based on the docking poses, hydrophobic interactions, hydrogen bond and structure variations, this research postulates that S-allylmercaptocysteine may be more appropriate than other compounds for protein-ligand interaction.
There is an important topic of breast cancer that had been published in 2013. In this report, the estrogen receptor (ESR1) had defined the relation of breast cancer [
The breast cancer is a common cause of death in women and may originate either hormonally [
The ESR1 is a ligand-activated transcription factor that mediates the biological effects of the steroid hormone estrogen [
The Raloxifene is an FDA approval drug for reduction in the risk of breast cancer (
The computer-aided drug design (CADD) is an
The personalized medicine and biomedicine [
In this research, we screen a candidate compound against breast cancer from the TCM Database@Taiwan. The computational techniques of docking screening are used to select ligands prior to applying molecular simulation by molecular dynamics (MD) to investigate the variations in protein-ligand interactions that may contribute to the evaluation of the effects on ESR1 inhibition.
A total of 61,000 TCM compounds were downloaded from the TCM database (
The disorder region in protein plays an important role in drug design; thus we take the sequence to predict the disorder region by the Database of Protein Disorder (DisProt:
The LigandFit module [
The ligands of candidate complex must be reprepared before applying MD simulation by using SwissParam (
The disorder protein is defined as unstructured protein which makes the compounds dock to protein and stabilize the complex with difficultly while the docking site is a disorder region. The cited references [
The disorder and binding site detection. The blue curve in the figure is the disorder disposition of each amino acid, and the red lines are the important amino acids for docking site designed.
Ranking the result of molecular docking by docking score, the two top TCM compounds, and the control, were selected (Table
ESR1 basis PLP1, PLP2 and dock score sort screened top two from TCM database.
Name | Herb | -PLP1 | -PLP2 | Dock score |
---|---|---|---|---|
S-Allylmercaptocysteine |
|
49.96 | 49.61 | 182.706 |
5-Hydroxy-L-tryptophan |
|
66.74 | 63.42 | 177.541 |
Raloxifene core* | 77.09 | 83.51 | 63.907 |
The structure of control and the candidate compounds was selected after screening from the TCM database (Figure
The structure of control and candidate TCM compounds. (a) Raloxifene core, (b) S-allylmercaptocysteine, and (c) 5-hydroxy-L-tryptophan.
The docking poses of ligands. (a) The crystal structure of ESR1 and the docking site, (b) Raloxifene core, (c) S-allylmercaptocysteine, and (d) 5-hydroxy-L-tryptophan.
The hydrophobic interaction can be analyzed by Ligplus (Figure
Ligplot illustrates the protein-ligand interactions. (a) Raloxifene core, (b) S-allylmercaptocysteine, and (c) 5-hydroxy-L-tryptophan. The deep red color of the hydrophobic interactions presents a high frequency in all ligand interactions.
The RMSD and energy variation 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.
The RMSF focus on each residue was analyzed, and on the variation of the whole protein, including with the ligand interaction (Figure
The variation of RMSD focus on residue of protein. This figure compares the RMSF between apo and each ligand interaction.
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
The clustering is a result of the division of data into several groups based on RMSD variation; thus data in the same group will have the similar structure (position and composition) (Figure
The clustering for ESR1 in MD. (a) apo, (b) Raloxifene core, (c) S-allylmercaptocysteine, and (d) 5-hydroxy-L-tryptophan.
After the structure variation discussion is based on eigenvector and clustering, we should take focus on the structure variation during protein-ligand interaction (Figures
The variation of Raloxifene core and ESR1 complex in MD simulation. (a) H-bond variation, (b) structure variation. The (1)–(4) red color indicates the difference through MD.
S-Allylmercaptocysteine has high H bond occupancy in both Glu353 and Arg394, with the variation in 2 and 5 being more variable than the control (Figure
The variation of S-allylmercaptocysteine and ESR1 complex in MD simulation. (a) H-bond variation, (b) structure variation. The (1)–(6) red color indicates the difference through MD.
The variation of 5-hydroxy-L-tryptophan and ESR1 complex in MD simulation. (a) H-bond variation, (b) structure variation. The (1)–(4) red color indicates the difference through MD.
The 5-hydroxy-L-tryptophan complex interactions were recorded (Figure
From these variations found, we suggest Glu353 might be important in inhibition and Arg394 might make the force stronger based on the H bond and structure variation.
The pathway definition is according to the calculation of caver 3.0 to determine the inter-path protein path during MD simulation [
The pathway of ESR1 for compounds. (a) Unbound protein, (b) Raloxifene core, (c) S-allylmercaptocysteine, and (d) 5-hydroxy-L-tryptophan.
Based on the above discussion, we can find that the top two TCM compounds S-allylmercaptocysteine and 5-hydroxy-L-tryptophan can have effect on ESR1 against breast cancer. Glu353 might have important role in inhibition based on high H bond occupancy in MD. Finally, according to the discussion from docking, interaction, and variation, we suggest that S-allylmercaptocysteine might be the best compound to inhibit ESR1 against breast cancer, even better than the control.
The authors confirm that this paper’s content has no conflict of interests.
Tzu-Chieh Hung, Wen-Yuan Lee, and Kuen-Bao Chen contributed equally.
The research was supported by Grants from the National Science Council of Taiwan (NSC102-2325-B039-001, 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. Finally, our gratitude goes to Dr. Tim Williams, Asia University.