The ligand structures were generated using the tool CORINA.[13] Three-dimensional optimizations of the ligand structures were selleck chem done and saved as ��.mol file��. Geometry optimizations of the ligands were performed according to the Hartree�CFock (HF) calculation method using ArgusLab 4.0.1 (Mark A. Thompson, Planaria Software LLC, Seattle, WA, USA, http://www.arguslab.com) software. The compounds included in the study are nimbin, azadiradione, azadirone, nimbolide, gedunin, salanin, vilasinin, behenic acid, meliantriol, quercetin, quercetrin, rutin, myricetrin, scopoletin, and azadirachtin. The bioactive compounds considered for the study are listed in Table 1. Table 1 Compounds of Azadirachta indica and their molecular structures Binding site predictionN Q-SiteFinder (http://www.bioinformatics.
leeds.ac.uk/qsitefinder) is used for binding site prediction.[14] It uses the interaction energy between the protein and a simple van der Waals probe to locate energetically favorable binding sites. Protein-ligand docking using ArgusLab 4.0.1 ArgusLab is an electronic structure program that is based on the quantum mechanics. It predicts the potential energies, molecular structures; geometry optimization of structure, vibration frequencies of coordinates of atoms, bond length, and bond angle. Cdk1_yeast protein was docked against the bioactive compounds from the leaves of neem tree using ArgusLab 4.0.1 (Mark A. Thompson, Planaria Software LLC, Seattle, WA, USA, http://www.arguslab.com).[15] The interaction was carried out to find the favorable binding geometries of the ligand with the protein.
Docking of the protein ligand complex was mainly targeted only to the predicted active site. Docking simulations were performed by selecting ��ArgusDock�� as the docking engine. The selected residues of the receptor were defined to be a part of the binding site. A spacing of 0.4 ? between the grid points was used and an exhaustive search was performed by enabling ��High precision�� Carfilzomib option in Docking precision menu, ��Dock�� was chosen as the calculation type, ��flexible�� for the ligand, and the ��AScore�� was used as the scoring function. A maximum of 150 poses were allowed to be analyzed; binding site box size was set to 20 �� 20 �� 20 ? so as to encompass the entire active site. The AScore function, with the parameters read from the AScore.prm file, was used to calculate the binding energies of the resulting docked structures. All the compounds in the dataset were docked into the active site of cdk1_yeast protein, using the same protocol. The docking poses saved for each compound were ranked according to their dock score function. The pose having the highest dock score was selected for further analysis.