Dataset on Insilco Evaluation; Antibacterial Activities of Synthesis of (2,6-diethylphenyl)- 5-oxopyrrolidine Derivatives
Description
With the rise of antibacterial resistance, researchers develop new strategies to combat resistance and also design drug-like compound that possess stronger antibacterial properties. 2-Pyrrolidine is known for its biological properties and this led researchers to explore and synthesize functionalized 2-pyrrolidinone derivatives. The antibacterial effect of functionalised synthesis of (2,6-diethylphenyl)- 5-oxopyrrolidine was examined. Basis set of 6-6-31G* and B3LYP with Density functional theory was used in optimising the functionalised synthesised compound of 2-Pyrrolidine. Discovery studio software was used in preparing the protein downloaded from the protein data bank Cytolysin A (ClyA) and SleL (4PHQ,4S3J {PDB ID}) (4PHQ,4S3J {PDB ID}) whose source organism is Escherichia coli and Bacillus cereus respectively for docking. Already optimized molecular compounds were subjected to molecular docking to obtain the calculated binding affinity of each derivative of 2 oxopyrrolidine and the active site off the receptor. Autodock Tool was also employed to locate the site of binding of the target protein Autodock vina for the docking calculations. After all the above steps were taken, discovery studio was used to visualise in 2D the interaction between the ligand and the receptor. The calculated molecular descriptors obtained from optimized studied compounds are highest occupied molecular orbital energy (EHOMO), lowest unoccupied molecular orbital energy (ELUMO), polarizability, dipole moment, hydrogen bond acceptor, energy band gap, area, volume, polar surface area, Log P, hydrogen bond donor. These molecular descriptors reveals some of the antibacterial activities of 1-(2,6-diethylphenyl)-5-oxopyrrolidine derivatives and binding affinity shows the compounds ability to inhibit Cytolysin A (ClyA) and SleL whose source organism is Escherichia coli and Bacillus cereus. Compound 8- 12 posses’ higher inhibition of S1el (Bacillus cereus) compared to the reference drug Ampicillin.
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Optimization Two dimensional structures of the molecular compounds were obtained using CHEMDRAW ultra version 12.0 [1] and the molecular compound was subjected to optimization using Spartan’14. Density functional theory with B3LYP and 6-31G was used as the basis set.[2] Molecular compounds were subjected to optimization to obtain descriptors and properties that best describe antibacterial activities of derivatives of 2-pyrrolidinone derivative. Docking Already optimized molecular compounds were subjected to molecular docking to obtain the calculated binding affinity of each derivative of 2-pyrrolidinone derivative. Molecular docking facilitates and observes non-bonding interaction that exists amongst the complexes. Discovery studio software was used in preparing the protein downloaded from the protein data bank Cytolysin A (ClyA) and SleL (4PHQ,4S3J {PDB ID}) (4PHQ,4S3J {PDB ID}) whose source organism is Escherichia coli and Bacillus cereus respectively for docking. This is done by cleaning and treating the protein, removing unwanted compounds that are attached to the protein. Autodock Tool was also employed to locate the site of binding of the target protein, also used to convert the receptor and ligand from protein data bank file (pdb) to protein data bank partial charge(q) and atom type(t) (pdb.qt) format. [3] Autodock vina for the docking calculations. After all the above steps were taken, Discovery studio was used to visualise in 2D the interaction between the ligand and the receptor.