Exploring the antibacterial activity of 1, 2 diaminoethane hexanedionic acid by spectroscopic, electronic, ELF, LOL, RDG analysis and molecular docking studies using DFT method

Vincy, C. Dabora; Tarika, J. D. Deephlin; Dexlin, X.D. Divya; Rathika, A.; Beaula, T. Joselin

doi:10.1016/j.molstruc.2021.131388

Cited by 53 publications

(11 citation statements)

References 39 publications

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“…RDG is regarded as a dimensionless quantity (r) which can be enumerated inculcating the density and its first derivative. [ 78 ] The picture represented implies that the distribution of electrons has become more uneven. When you go far away from the molecule, the RDG shows a highly positive value as the electron density falls off exponentially till it reaches zero.…”

Section: Resultsmentioning

confidence: 99%

Synthesis, spectral features, electronic structure studies, and molecular docking analysis of a Schiffbase (E)‐1‐(4‐chlorophenyl)‐N‐(nitrophenyl)methanimine from 4‐chloroaniline and 2‐nitrobenzaldehyde

Diya,

Unni,

Rajimon

et al. 2023

Vietnam Journal of Chemistry

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The compound (E)‐1‐(4‐chlorophenyl)‐N‐(nitrophenyl)methanimine was synthesised and characterised using techniques FTIR, UV‐Vis, NMR and it was compared with the experimental and simulated methods. The compound prepared was optimized using the DFT method employing the basis set B3LYP / cc‐pVDZ. The simulated spectra appeared to be in accordance with the experimental one. The HOMO‐LUMO orbitals and MEP are calculated with the same basis set; the study is chiefly forcasted to the biological activity of the synthesized compound. The wave function regards like localized orbital locator, electron localized function, average localized ionization energy and non‐covalent interaction are also examined as a means of theoretical evidence of the titled compound. The NBO calculations probe the intermolecular and intramolecular movement of charges, and additionally the molecule's stability. The ADMET properties are also considered for the compound with the assistance of Swiss ADMET online tool. The molecular docking analysis was accomplished against the protein (3RW9) of Spermidine dehydrogenase inhibitor employing the software Auto‐dock.

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Section: Resultsmentioning

confidence: 99%

Synthesis, spectral features, electronic structure studies, and molecular docking analysis of a Schiffbase (E)‐1‐(4‐chlorophenyl)‐N‐(nitrophenyl)methanimine from 4‐chloroaniline and 2‐nitrobenzaldehyde

Diya,

Unni,

Rajimon

et al. 2023

Vietnam Journal of Chemistry

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“…The ELF (electron localization function) and LOL (localized orbital locator) were studied to indicate how much of the domain's electrons are restricted to this area. 55,56,68 A LOL with a high value (>0.5) indicates the place where localized electrons dominate the electron density. Both the ELF and LOL reflect energy density functions in different forms, giving a similar analysis.…”

Section: Resultsmentioning

confidence: 99%

“…FMO theory was used to investigate the reaction features of ciprofloxacin, which assumes that the HOMO and LUMO molecular orbitals have critical roles in the electrophilic, nucleophilic, and radical reactions. 55,56 As seen in Fig. 4, the orbital distribution of ciprofloxacin suggests that the HOMO orbital is mainly concentrated around the piperazine ring.…”

Section: Quantum Chemical Structural Analysismentioning

confidence: 95%

Experimental study and quantum chemical calculation of free radical reactions in ciprofloxacin degradation during the UV/chlorine oxidation process

Yuan

Tang

et al. 2022

Environ. Sci.: Water Res. Technol.

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“…Antibacterial is a substance that can interfere with the growth or even kill bacteria by interfering the metabolism of harmful microbes [1]. Several microorganisms have been become resistance, one of them is Staphylococcus aureus (S. aureus).…”

Section: Introductionmentioning

confidence: 99%

Estimation of Hydrazone Derivative Compounds as Anti-Bacterial Agents Against Staphylococcus aureous Through Molecular Docking and Self Consisted Field

Frimayanti¹,

Octaviani²,

Wulandari³

et al. 2023

Trends Sci

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Molecular docking is an important computational method for drug design. It can be used to predict the binding interaction of receptor with the ligand. Hydrazone were reported as chemical compounds with =CH-N-NH group. In addition, hydrazone derivative compounds were also reported have various activities, such as antibacterial agents against Staphylococcus aureus. S. aureus is a very serious problem because this bacteria is increasingly resistant to various types of antibiotics (multidrug resistance). S. aureus is also having extraordinary adaptability thus, it can be resistant to many antibiotics. The purpose of this study is to predict whether the hydrazone compounds were active as anti-bacterial agents and also to ensure that the binding interaction is stable before and after docking calculation. Molecular docking research was conducted using the protein target 1N67 (PDB ID), which was derived from the crystallographic structure of hydrazone derivative chemicals. Four hydrazone derivative substances were docked to the protein in this investigation with grid boxes along x, y, and z radii of 67, 86 and 66, respectively. The positive control was chloramphenicol. Self-Consisted Field (SCF) was calculated using AM1 as basis set and molecular dynamic simulation was performed using CHARMM27 force field. The results showed that from 4 tested compounds, only compound 3 with the binding free energy of −6.535 kcal/mol was estimated as active agent against S. aureus. This compound showed very good potential to be an anti-bacterial with the lowest binding free energy value with the highest stability level. HIGHLIGHTS Due to in silico study such as molecular docking, molecular dynamic simulation is an important computational method for drug design. It can be used to predict the binding orientation of small molecule drug candidates to their protein targets. In addition, docking is also can be applied to predict small molecule affinity and activity. Thus, molecular docking has an important role in drug discovery and rational design The ligand interaction with the receptor was more stable due to the decreased binding free energy value The lowest binding free energy and lowest RMSD value of this molecule, which may presumably cause compound 3 to has better binding affinity compare to other compounds GRAPHICAL ABSTRACT

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Exploring the antibacterial activity of 1, 2 diaminoethane hexanedionic acid by spectroscopic, electronic, ELF, LOL, RDG analysis and molecular docking studies using DFT method

Cited by 53 publications

References 39 publications

Synthesis, spectral features, electronic structure studies, and molecular docking analysis of a Schiffbase (E)‐1‐(4‐chlorophenyl)‐N‐(nitrophenyl)methanimine from 4‐chloroaniline and 2‐nitrobenzaldehyde

Synthesis, spectral features, electronic structure studies, and molecular docking analysis of a Schiffbase (E)‐1‐(4‐chlorophenyl)‐N‐(nitrophenyl)methanimine from 4‐chloroaniline and 2‐nitrobenzaldehyde

Experimental study and quantum chemical calculation of free radical reactions in ciprofloxacin degradation during the UV/chlorine oxidation process

Estimation of Hydrazone Derivative Compounds as Anti-Bacterial Agents Against Staphylococcus aureous Through Molecular Docking and Self Consisted Field

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