In-silico study of Agaricus Bisporus on DNA damaging protein

Agaricus bisporus is belonging to family agaricaceae, which is widely acceptable and mostly cultivated among the all mushrooms. It has great nutritional values and it is rich in proteins, vitamins, carbohydrates, fibers, minerals and amino acids. It is effective in antimicrobial, anticancer, antidiabetic, antihypercholesterolemic, antihypertensive, hepatoprotective and antioxidant activities. As it is effective in anticancer property, we check the effects of chemical constituents of Agaricus Bisporus on DNA damaging protein which results its activity PARP inhibiting or vise-versa. We choose the molecular docking technique to check the effects of different chemical constituents of Agaricus Bisporus on DNA damaging protein. For that different PARP inhibitory drugs taken as the standard. We perform the molecular docking of the chemical constituents of Agaricus Bisporus, using 4UND protein with the help of PyRx software and BIOVIA Discovery studio software. Along with that PARP inhibitor drugs also run against the same protein. The results of molecular docking shows the some of the constituents of Agaricus Bisporus has better binding affinity than the standard taken PARP inhibitor drugs. The ergosterol shows the better binding affinity than the niraparib and rucaparib on the same proteins. On other hands the naringenin, quercetin, anthocyanin, folate and myricetin shows the better results than the rucaparib. That means the ergosterol shows the better results as PARP inhibitor than the niraparib and rucaparib.

Agaricus Bisporus is the mushroom is cultivated all over the world [01] in every ascetic except Antarctica [02]. It is most dominating and most cultivated in all over the mushroom [03,04]. It is rich in the proteins, carbohydrates, lipids, fibers, polyphenols, flavonoids, minerals, vitamins [05,06,07]. It also contains phenolic acids [08,09], fatty acids [10], flavonoids [11], essentials amino acid and non-essential amino acids [12]. Agaricus Bisporus is belonging to the to family agaricaceae [06]. It have been found effective in antimicrobial, anticancer, antidiabetic, antihypercholesterolemic, antihypertensive, hepatoprotective and antioxidant activities. [13] Apart from food and food beverages it has a role in perfumery, cosmetic industries and pharmaceutical industries [14]. As it has anticancer activity, we should perform the molecular docking on the chemical constituents of Agaricus Bisporus.
Molecular docking is the methodology that explores the responses of small molecules in the binding site of a targeted protein [15]. Molecular docking is a important tool in structural molecular biology and computer-assisted drug design. The goal of ligand-protein docking is to predict the binding of ligand with a protein of known three-dimensional structure [16]. Molecular docking is the computer-based approach for identification of bound conformation and prediction of binding affinity of ligands to protein [17].
The purpose of this study to know about the binding affinity of constituents of Agaricus Bisporus on the DNA damaging protein and compare with the standard PARP inhibitor drugs to check the binding affinity.

Materials-
PyRx is written in Python programming language and it can run on nearly any modern computer, from PC (personal computer) to supercomputer. This methods also work on Linux and Mac OS as well.

2.1.2] Input Files-
To start with structure-based virtual screening, structures of the target macromolecule and small molecules are needed as input files. For that there are different websites available where we can download these input files. We used PubChem website to get 3D structure of small molecules in the '.sdf' format which are chemical constituents of Agaricus Bisporus [20], and Protein Data Bank to get 3D structures of macromolecule that is protein in '.pdb' format [21].
i] For small molecules (ligands)- The chemical constituents of button mushroom i.e. ligands were downloaded from the PubChem site in 3d structure with the ".sdf" format. Open PubChem website and search their respective molecules and then click on download button, from that select 3D SDF: Save. In similar way we can downloaded all required molecules.
ii] For macromoleculeprotein is selected for molecular docking and it was downloaded from the protein data bank in ".pdb" format. Open RCSB PDB homepage and search our protein their with code 4UND and click on Download Files, and select PDB Format.
Here we selected PARP-1 i.e. '4UND' protein which are responsible for DNA damaging. It promotes the cancer growth and progression. For that different PARP inhibitors drugs are available in market; from that Olaparib, rucaparib, talazoparib and niraparib are taken as standard for molecular docking. Here we check that is chemical constituents of agaricus bisporus has binding with that protein and shows better results or not. Our hypothesis is that chemical constituents of Agaricus Bisporus may shows better results than the PARP-1 inhibitors drugs (rucaparib, talazoparib and niraparib) on 4UND protein.

A] Ligands-
The PDBQT file format suitable for docking for virtual screening in AutoDock Vina. For that input files can be used for virtual screening must be converted to PDBQT format by using open babel. 7. PyRx users can also export virtual screening results as CSV (Comma-Separated Values) or SDF files. This is useful for further analysis, filtering, or re-ranking of virtual screening results. From the docking results, it is shown that the binding affinity of ergosterol(-9.8 Kcal/mol) which is chemical constituent of Agaricus Bisporus is better than the rucaparib(-9.2 Kcal/mol) and equals to the niraparib(-9.8 Kcal/mol). Both niraparib and rucaparib are the standard PARP inhibitor drugs and the ergosterol shows the better binding affinity than them.

Results from docking-
Also, the naringenin, quercetin, anthocyanin and folate are the constituents which shows better binding affinity than the rucaparib; whereas the Myricetin shows the same binding affinity as rucaparib.  Rucaparib is an anti-cancer agent used to treat recurrent ovarian, fallopian tube, or peritoneal cancer [25,26]; and the Niraparib is a poly-ADP ribose polymerase inhibitor used to treat recurrent epithelial ovarian, fallopian tube, or primary peritoneal cancer responding to platinum-based chemotherapy [27,28].

Fig.2-2D & 3D images of standard PARP inhibitor drugs binding w ith 4UND protein
Ergosterol is useful in the cancer therapy as it inhibits the cancer growth [29]. Its also effective in breast cancer [30]. So, it has the anticancer activity. It may show the better results over the PARP inhibitor drugs on DNA damaging protein.

Conclusion :-
The analysis of molecular docking helps to examine and evaluate the binding of different  Pyridoxamine -5.6 Table 3 Remaining images of docking of chemical constituents of Agaricus Bisporus and 4UND protein: