Introduction: Grapes (Vitis vinifera) one of the world's agricultural and produced fruits, grape seed extract has Protects against toxic reproductive agents.(1)
Grapes contain significant amounts of the carotenoid antioxidant lycopene. In men who are deficient in the carotenoid lycopene, this antioxidant can increase sperm motility and count. The carotenoid lycopene is important for healthy sperm, and men who are deficient in it usually suffer from fertility problems. Grapes contain significant amounts of the carotenoid antioxidant lycopene. In men who are deficient in the carotenoid lycopene, this antioxidant can increase sperm motility and count. The carotenoid lycopene is important for healthy sperm.
punica granatum L (pomegranate) plant is a small shrub and is one of the oldest fruit plants. which can be used as a medicinal plant. It has been used for generations to treat ulcers, diarrhea and male infertility.(2)
Serine/threonine-protein kinase component of the chromosomal passenger complex (CPC), a complex that acts as a key regulator of mitosis. The CPC complex has essential functions at the centromere in ensuring correct chromosome alignment and segregation and is required for chromatin-induced microtubule stabilization and spindle assembly. Also plays a role in meiosis and more particularly in spermatogenesis. Has redundant cellular functions with AURKB and can rescue an AURKB knockdown. Like AURKB, AURKC phosphorylates histone H3 at 'Ser-10' and 'Ser-28'. AURKC phosphorylates the CPC complex subunits BIRC5/survivin and INCENP leading to increased AURKC activity .(3)
Herbal medicines, as a treatment method, have received a great deal of attention. In this study, we investigated the effect of grape seed extract and punica granatum L on Aurora Kinase C protein by molecular docking method.
Methods: In this descriptive-analytical project, we first downloaded the most suitable three-dimensional structure Of Aurora Kinase C protein in terms of resolution and number of suitable chains from the uniprot site in pdb format. We see some specifications of this protein below. Chain A was selected for the docking process because it is larger than the other chains and has the most amino acids.
Released: 2019-05-15
Then, protein chains were examined using Chimera software. The most suitable chain in the protein was selected separately, which had more amino acids than other chains and the largest chain was the protein. Through this software, molecules were selected. We removed water and all solvents from these chains and hydrogen ions and charge bar were added to these chains and finally saved in pdb format. In the next step, we downloaded the structure of Aurora Kinase C drug from Pubcheem site in SDF format.
The information about grape seed extract drug was as follows:
Exudate from seeds of the grape plant Vitis vinifera, composed of oils and secondary plant metabolites (BIOFLAVONOIDS and polyphenols) credited with important medicinal properties.(4)
Molecular formula: C32H30O11
The information about punica granatum L drug was as follows:
Ellagic acid is an organic heterotetracyclic compound resulting from the formal dimerisation of gallic acid by oxidative aromatic coupling with intramolecular lactonisation of both carboxylic acid groups of the resulting biaryl. It is found in many fruits and vegetables, including raspberries, strawberries, cranberries, and pomegranates. It has a role as an antioxidant, a food additive, a plant metabolite, an EC 5.99.1.2 (DNA topoisomerase) inhibitor, an EC 5.99.1.3 [DNA topoisomerase (ATP-hydrolysing)] inhibitor, an EC 1.14.18.1 (tyrosinase) inhibitor, an EC 2.3.1.5 (arylamine N-acetyltransferase) inhibitor, an EC 2.4.1.1 (glycogen phosphorylase) inhibitor, an EC 2.5.1.18 (glutathione transferase) inhibitor, an EC 2.7.1.127 (inositol-trisphosphate 3-kinase) inhibitor, an EC 2.7.1.151 (inositol-polyphosphate multikinase) inhibitor, an EC 2.7.4.6 (nucleoside-diphosphate kinase) inhibitor, a skin lightening agent, a fungal metabolite, an EC 2.7.7.7 (DNA-directed DNA polymerase) inhibitor and a geroprotector. It is an organic heterotetracyclic compound, a cyclic ketone, a lactone, a member of catechols and a polyphenol. It derives from a gallic acid.(5)
Molecular formula: C14H6O8
To perform the docking process, pyrx software was used. In this software, after importing the protein as a receptor and the drug as a ligand, we obtained the binding site through the Deepsite site, the specifications of which were as follows:
exhaustiveness = 8
center_x= 35.1554
center_y= 4.7732
center_z= 19.2287
size_x = 25.0
size_y = 25.0
size_z = 25.0
Results: After performing molecular docking separately for grape seed extract and punica granatum L, the results were as shown in the table below.
The result of grape seed extract docking
grape seed extract Binding Affinity(kcal/mol) RMSD lower bound RMSD upper bound
Conformation 1 -6.9 0 0
Conformation2 -6.8 2.414 4.307
Conformation 3 -6.5 1.546 2.071
The result of punica granatum L docking
punica granatum L Binding Affinity(kcal/mol) RMSD lower bound RMSD upper bound
Conformation 1 -6.0 0 0
Conformation2 -6.0 0.105 6.183
Conformation 3 -5.9 2.519 5.889
Conclusion: According to Docking results, it can be concluded that grape seed extract can bind well with Aurora Kinase C protein with good negative binding energy. Proper orientation of drug within protein according to RMSD = 0 in pyrx method is another reason for this is
Keywords: grape seed extract , punica granatum L , Aurora Kinase C protein