DNA methyltransferases 1 (DNMT1) has been looked as crucial targets against various types of cancers. MD simulations have advanced to a point where the atomic level information of biological macromolecule (protein or DNA-protein or protein-protein) can easily be advantageous to predict the functionality. In this study we utilize xanthomicrol and galloyl compounds to investigate potential compounds for the inhibition of DNMT1, and the results of these two compounds are compared with drug decitabine. Xanthomicrol and galloyl are found to dock successfully within the active site of DNMT1. A comparison of the inhibitory potential of screened xanthomicrol inhibited DNMT1 approximately is identical with those of their corresponding drugs, decitabine. The stability of the DNMT1 with the best docked xanthomicrol, were further analysed in molecular dynamics (MD) simulation and compared with those of the respective drugs namely decitabine which revealed stabilization of these complexes within 300 ns of simulation with better stability of DNMT1.
DNA methylation refers to the addition of a methyl group to one of the four bases that constitute the coding sequence of DNA. In humans, methylation is normally added only on the 5 position of the cytosine base in a post-DNA synthesis reaction catalyzed by one of several DNA methyltransferases. DNA methylation plays a key role in chromatin structure, suppression of the activity of endogenous parasitic sequences, and stable suppression of gene expression (epigenetic silencing), and a process normally is reserved for special situations such as the inactive X-chromosome and imprinted genes [
In this study we utilized computer-aided drug design (CADD) in this research in order to design potential lead drugs for AD therapy. CADD is an efficient approach for the rapid identification of potential lead compounds in target therapy and has been widely used in drug design including virus therapy, cancer therapy, treatment of sleeplessness, neuropathic therapy, weight loss therapy, diabetic treatment, inflammation treatment, erectile dysfunction treatment, and hair loss therapy [
At first 3D atomic coordinates of DNMT1 (ID: 2QRV) were obtained from the Protein Data bank [
The generated ligands were docked into the defined binding site on the DNMT1protein structure. Ligplot plus was used to analysis docking poses for H-bond and hydrophobic interactions.
Then molecular dynamics simulations were performed using the Gromacs 4.5.4 software, under G43a1 force field. Topology files and parameters of small compounds in protein-ligand complexes were generated for GROMACS simulation by SwissParam web server. The calculations were carried out using the crystallographic structure of domain DNMT1. The complex with the best position obtained from docking, was embedded into a box containing SPC216 model water. At first the entire system was minimized using the steepest descent followed by conjugate gradients algorithms, then the solvent and Na+, CL− were allowed to evolve using minimization and molecular dynamics at NVT ensemble for 500 ps and at NPT ensemble for 1000 ps at 100 K in which initial configuration of the structures was kept fixed. Finally in order to obtain equilibrium geometry at 300 K and 1 atm, 1 ns MD simulation run was performed at NPT ensemble. The time step for the simulation was 2 fs. Van der Waals and electrostatic forces cutoff were 14 Å and 12 Å respectively.
We used the Autodock (4.2) to select potent two compounds (Xanthomicrol and Galloyl) which have high affinity and almost equal with DNMT1 compared with Decitabine. The results of the docking score are listed in
The docking pose of Decitabine revealed two H-bonds with Phe238. For Galloyl, the docked ligand formed H-bonds with Thr 871, Val 873 and Thr 858. In the 2D diagram of docking poses by Ligplot (
Compound | Eb (kcal/mol) | Intermolecular Energy (kcal/mol) | Internal Energy (kcal/mol) | Torsional Energy (kcal/mol) | Unbounded External Energy (kcal/mol) |
---|---|---|---|---|---|
Decitabine | −3.84 | −5.33 | −0.45 | 1.49 | −0.45 |
Xanthomicrol | −5.83 | −7.32 | −1.59 | 1.49 | −1.59 |
Galloyl | −3.71 | −5.21 | −0.36 | 1.49 | −0.36 |
The stability of the DNMT1 during the simulation in the presence of Decitabine, Xanthomicrol and Galloyl was evaluated by the root mean square deviation (RMSD) and by monitoring its secondary structure elements during the simulations. As documented in
For total energy analysis, no significantly increased values were observed among all simulation times (
As DNMT1 have one hydrogen bond donor (OH) and one hydrogen bond acceptor (O), the probability to
form hydrogen bonds is rare. Number of H-bonds formed between DNMT1 and Decitabine, Xanthomicrol, and Galloyl compounds during a MD simulation was calculated. Of all these three cases, the number of H-bonds fluctuates between 1200 and 1280 (Figuar 5). A change in the number of hydrogen bonds in the simulation is approximately the same for all three compounds.
DNMT1 plays the key role in cell proliferation phase of all types of developing cancer. Conceptually, targeting DNMT1 will disrupt both DNA replication and transcription, thereby leading to inhibition of cell division and consequently stopping the growth of actively dividing cancerous cells. Therefore, any therapeutic approach targeted against DNA replication in cancerous cells will certainly be a key to the development of a novel anti-cancerous agent. Furthermore, long term use of synthetic drugs such as Decitabine has been reported to develop severe side effects. Therefore, for therapeutic applications, there is a need to identify more specific inhibitors of DNMT1, coming from natural sources, which are relatively safer in use with little or no side effects. In
view of these, in the present study, plant derived one hundred anti-cancerous has been selected and their pharmacokinetic properties are predicted through insilico analyses. Thus Xanthomicrol and Galloyl are selected. Furthermore, docking analyses reveal that Xanthomicrol inhibites DNMT1 more strongly, while Galloyl inhibites preferentially DNMT1 weaker than those of respective drugs, Decitabine outstanding. The results of best docked, Xanthomicrol, are further validated and compared with those of respective drugs namely Decitabine using molecular dynamics (MD) simulation. Thus, the present study makes a foundation for further investigations based on the experimental data (wet lab data) for therapeutic application of screened Plant Medicine in general and Xanthomicrol in particular.
This study was supported by Azad University, Shahrekord Branch, and the Young Research Club of Islamic Azad University, Shahrekord Branch, Shahrekord, Iran.