QSAR study was performed by using negative logarithm of experimental LC50 (ppm) [pLC50 = –log (LC50)] as dependent variable and 2D descriptors (Table 5 ) as independent variables. ChemDraw Ultra 7.0 software was used for drawing 2D structures of compounds which were converted to mol structures. To describe several features of molecular structure 239 2D descriptors were taken and composed of structural, thermodynamic, electronic and spatial descriptors, e.g., element count, atomic valence connectivity index (chiV), refractivity, estate number, chain path count, retention index (chi), path cluster, semi-empirical path count, molecular cluster, topological index, molecular weight, and logP. The various descriptors were calculated by energy minimization and geometry optimization through batch energy minimization method using Merck Molecular Force Field (MMFF) by taking RMS gradient (0.01), number of cycles (max. 1,000) and distance dependent dielectric (1). Various Baumann alignment-independent (AI) descriptors were also calculated. All computational activities were performed by using Vlife MDS QSAR plus 4.6 software in ASUS VivoBook (windows 10 OS and Intel Core i5).
Chemdraw ultra 7
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ChemDraw Ultra 7.0 is a software application for creating and editing chemical structures and diagrams. It provides a range of tools and features for visualizing and manipulating chemical compounds and related data.
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Lab products found in correlation
6 protocols using chemdraw ultra 7
1
2D Molecular Descriptors for QSAR
2
Molecular Docking and Binding Analysis of Lopinavir/Ritonavir
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The orientation of lopinavir/ritonavir in the target proteins’ active site was assessed through MOE web-based. We carried out the data analysis by ChemDraw Ultra 7.0 to draw the structure of lopinavir/ritonavir, which was then subjected to energy minimization by MOE. The crystal structure of proteins was obtained from the RCSB Protein Data Bank. The GBVI/WSA dG scoring method was utilized to evaluate the concluding scores [20 (link),21 (link)]. The GBVI/WSA dG scoring method was used to investigate the concluding scores, and the binding free energy of the ligand was estimated from a presented pose. The inhibition constant (Ki) was calculated based on the binding free energy estimated using the GBVI/WSA dG scoring function, according to the equation [∆G = RTLn(Ki)], where T represents the temperature in Kelvin and R is the gas constant. Finally, the pKi was calculated from the binding free energy values at a fixed temperature of 298 K using the equation [log Ki = pKi].
3
Computer-Aided Molecular Structure Analysis
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The chemical structures of the derivatives (fig. 1 ) were drawn using ChemDraw Ultra 7.0 and energy minimization of derivatives was achieved with Chem3D Pro of ChemOffice suit for taking energy of each molecule up to its lowest energy state (highest stability). 3D structure of phenytoin (CID: 1775) was retrieved from PubChem compound database at NCBI.
4
Structural Modeling and Docking of MsrA Protein
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Homology modelling was used to predict the tertiary structure of the MsrA protein. The protein sequence was submitted to the online protein structure homology-modelling website [33 ], and then homologous proteins with high sequence homology were searched in the database for each amino acid sequence. Using these proteins with known crystal structures as templates, a three-dimensional (3D) structure model of the target protein was constructed. The protein with the highest homology was selected to construct the 3D structure of the target protein, which was saved in PDB file format for subsequent molecular docking. For ligand preparation, the structure of luteolin was drawn using ChemDraw Ultra 7.0, energy-minimized in Chem3D Ultra 7.0 and saved as a PDB file. AutoDock is a suite of tools used to predict interactions between small molecules (ligands) and proteins of known 3D structure based on the properties (polar atoms and bond rotations) of the ligand and the binding site of the protein [34 (link)]. AutoDock 4.2 was used for the molecular docking of luteolin and MsrA protein.
5
Molecular Docking of Novel Antibacterial Compounds
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Docking studies37 (link) were achieved on the new synthesized molecules 2–9a towards S. aureus tyrosyl-tRNA synthetase. The 3D structure of the target (PDB ID: 1JIJ ) was retrieved from the Protein Data Bank (PDB).38 (link) The 2D structures of the ligand molecules were sketched using ChemDraw Ultra 7.0, then converted to 3D structures using OpenBabel GUI tool.39 Before performing the docking approach, the 3D files of the ligand molecules and target were subjected to energy minimization by using AMBER Force Field40 (link) in Open Babel and CHARMm Force Field41 (link) in Discovery Studio 3.5, respectively, to obtain more stable confirmations. The molecular docking approach was performed by PyRx software tool.25 The 2D orientations of the docked molecules with the enzyme were generated by Discovery Studio visualizer software. Finally, the pharmacokinetics and ADMET properties of molecules were anticipated using AdmetSAR, SwissADME, and mol inspiration tools.
6
Molecular Docking of Synthesized Compounds
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The molecular docking of synthesized compounds was conducted using Autodock Vina software (Trott and Olson, 2010 (link)). The 2D structure of compounds was sketched using ChemDraw Ultra 7.0 software and converted into 3D using OpenBabel 3.0.0 software (O'Boyle et al., 2011 ). The hydrogen atoms of protein and ligands were added by Autodock Tools and saved in PDBQT format. The auto grid tool was utilized for arrangement affiliation of grid maps and contained 1.00 Å spacing with box dimensions of 20 X × 20 Y × 20 Z Å and centers of 76.160 X × 71.016 Y × 71.999 Z Å. The docking grid box was centered to cover residues within the active site (ASP29 and ASP56) in the protein structure. The interactions of hydrophobicity and hydrogen bonds between the docked compounds and protein were investigated utilizing the Discovery Studio 2019 software, and have been furthermore visualized and analyzed in PyMOL and UCSF Chimera 1.14 in 3D structure.
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