It is observed in Table?3 that this scaled FTIR bands of the CCPEHP have a close relationship between experimental frequencies [47]. Targeting the 3CLpro protease of the corona computer virus consisting of structural and nonstructural polyproteins could constitute a valid approach for the treatment of COVID-19 potential drug design. One of the structures CNT2 inhibitor-1 of 3CLpro like protease protein was downloaded (PDBID: 6LU7, 2.16??) from Protein Data Lender (PDB) (http://www.rcsb.org), in 3D format [33]. Preparation for simulation and simulation processes of COVID-19 3CLpro/Mpro structure and ligand were carried out by AutoDock Tools 1.5.6, MG Tools of AutoDock Vina program and Discovery Studio 2020 Client (Dassault Systemes BIOVIA) [34,35]. In protein preparation, the missing residues were first checked and there Mouse monoclonal to DKK3 were no missing residues of the viral protein. Chain A, one of two chains of main protein, was selected and the binding affinity of this chain was performed with our potential drug candidate molecule. Water molecules and hetero atoms were deleted from the COVID-19 CNT2 inhibitor-1 main protease, then Kollman charges and polar hydrogen atoms were added to the target protein (chain A) and saved with AutoDock Tools in pdbqt format [10,36]. Autodock vina algorithm with the most appropriate configurations (exhaustiveness= 8, binding modes= 9, energy difference= 3?kcal/mol, feasible with x, y, and z coordinate) parameters is used in simulation studies [34,37]. Default settings were used in the other parameters. The grid box value and intermolecular interactions of the ligand-protein complex were visualized with the Discovery studio 2020 client program. Hydrophobic gap coordinates of the binding site were used in the docking of N3 (as control) and fungal metabolites. The active site of the amino acid was calculated as sized (30?? x 30?? x 30??) and centered (?10.71?? x 12.41?? x 68.83??). (Default grid spacing= 0.375??) [38]. In order to prepare the ligand for docking, the CIF data obtained from the X-ray crystal structure [39] was converted to mol2 format. The partial charge and torsion angels were changed and saved in pdbqt format with AutoDock Tools. Before CNT2 inhibitor-1 the simulation, the individual pdbqt formats and docking parameters of the drug candidate compound and COVID-19 main protease were combined into a single .txt file and the complexation process was completed through the AutoDock Vina software. 3.?Results and discussion 3.1. X-ray data collection and structure refinement The structure was solved using SHELXT [40] and then refined by full-matrix least-squares refinements on using the SHELXL [41] in Olex2 Software Package [42]. Crystallographic data and refinement details of the data collection for CCPEHP are tabulated in Table?1 . Geometrical calculations and crystal structure validations were performed using Platon software [43]. Mercury software [44] was used for visualization of the cif file. Additional crystallographic data with CCDC reference number 2 2,068,456 for CCPEHP has been deposited within the Cambridge Crystallographic Data Center with the asymmetric unit made up of two CCPEHP molecules. The structure exhibited chlorophenyl subunit with the chloropyridine moieties lying nearly in the same plane with the tilt angles 2.34 and 14.44, which matches well with the computationally optimized geometries, for two molecules in the asymmetric unit, and these values are comparable to those observed in 2-2-[1-(4-nitrophenyl)ethylidene]hydrazinylpyridine [CSD Ref Code: MEMQIH] [45]. In the solid state of CCPEHP, the poor hydrogen bonds (C11???Cl27?=?3.636(4) ? as D???A) between the CH of pyridine ring and chloride moiety connected two molecules in the asymmetric unit. As shown in Fig.?2 b, the major intermolecular interactions governing the crystal packing are identified as weak CH???N hydrogen bonding contacts (C3???N3?=?3.397(5) ?, C14???N8?=?3.522(4) ?, C25???N11?=?3.661(4) ?), and these interactions lead a 1D hydrogen-bonded tubular CNT2 inhibitor-1 architecture (Fig.?2c) along the vibrations found in pyridine and chlorophenyl rings and hydrazone group were tried to be investigated. The scaled and unscaled calculated vibrational modes and intensities of FTIR with CNT2 inhibitor-1 their PED and observed FTIR and FTRaman bands are reported in Table?3 . It is observed in Table?3 that this scaled FTIR bands of the CCPEHP have a close relationship between experimental frequencies [47]. The CCPEHP molecule has 29 atoms. All vibration modes are assigned thanks to the graphical interface GaussView 6.0.