DFT studies on vibrational and electronic spectra, HOMO–LUMO, MEP, HOMA, NBO and molecular docking analysis of benzyl-3-N-(2,4,5-trimethoxyphenylmethylene)hydrazinecarbodithioate

Mumit, Mohammad Abdul; Pal, Tarun Kumar; Alam, Ashraful; Islam, M. A. A. A. A.; Paul, Subrata; Sheikh, Chanmiya

doi:10.1016/j.molstruc.2020.128715

Cited by 242 publications

(76 citation statements)

References 47 publications

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“…The determination of the MEP region is the best ﬁt for identifying sites for intra- and inter-molecular interactions ( Figure 7 ). 33 Red/yellow regions indicate negative electrostatic potentials and the blue region shows positive, and green color designates neutral potential region.…”

Section: Resultsmentioning

confidence: 99%

In silico Molecular Docking, DFT Analysis and ADMET Studies of Carbazole Alkaloid and Coumarins from Roots of Clausena anisata: A Potent Inhibitor for Quorum Sensing

Eswaramoorthy¹,

Hailekiros²,

Sabir³

et al. 2021

AABC

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Introduction In modern drug design, in silico methods are largely used to understand drug-receptor interactions and quantum chemical properties. In the present study, a computational de novo design approach was used to confirm mode of binding for antibacterial activity, elucidating quantum chemical properties and ADMET-drug-likeness of carbazole alkaloid ( 1 ) and three coumarins ( 2 – 4 ) isolated from roots of Clausena anisata . Methods Docking studies were performed with DNA-Gyrase (6F86) and LasR binding domain (2UV0) employing a flexible ligand docking approach using AutoDock Vina. SwissADME prediction and toxicological predictions were performed by ADMET. The optimized structures and molecular electrostatic potential surface of the isolated compounds were predicted by DFT analysis using B3LYP/6-31G basis levels. Results and Discussion The docking results revealed that compound 3 showed better docking scores against both DNA gyrase B and LasR binding domain compared with ciprofloxacin with potential as an inhibitor of bacterial DNA gyrase and quorum sensing LasR binding domain. The SwissADME prediction results showed that all the isolated compounds ( 1–4 ) satisfy Lipinski’s rule of five with zero violations. Toxicological prediction results suggested that all compounds and ciprofloxacin are non-hepatotoxic, non-carcinogenic, non-irritant, immunogenic, and non-cytotoxic. The DFT analysis results revealed that compound 3 has large electronegativity (χeV), global softness (σ eV −1 ), global electrophilicity (ωeV), and mutagenicity value closer to ciprofloxacin (with LD 50 value of 480 mg/kg) suggesting better bioactivity and chemical reactivity with considerable intra-molecular charge transfer between electron-donor to electron-acceptor groups. Conclusion Overall, compound 3 may serve as a lead molecule that could be developed into a potent E. coli DNA gyrase B inhibitor and efficient inhibitor for quorum sensing auto-inducer LasR binding domain of Pseudomonas aeruginosa .

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Section: Resultsmentioning

confidence: 99%

In silico Molecular Docking, DFT Analysis and ADMET Studies of Carbazole Alkaloid and Coumarins from Roots of Clausena anisata: A Potent Inhibitor for Quorum Sensing

Eswaramoorthy¹,

Hailekiros²,

Sabir³

et al. 2021

AABC

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“…NBO resulted in conjugative and hyperconjugative interactions. According to the second-order perturbation theory, the electrons moving from filled NBO donor (n) to empty NBO acceptor (m) will produce the stable energy E (2) [22]:…”

Section: Natural Bond Orbital Analysis (Nbo)mentioning

confidence: 99%

Antioxidant of Trans-Resveratrol: A Comparison between OH and CH Groups Based on Thermodynamic Views

Thi

2020

Journal of Chemistry

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Trans-resveratrol establishes the planarity in its structure which makes it an interesting compound in both experimental and theoretical examinations. The current study, using the density functional method (DFT), attempts to compare the antioxidative capacities between hydroxyl (OH) and aromatic methine (CH) groups of this molecule. Becke’s exchange-correlation B3LYP functional together with 6-311++G(d, p) basis set was used to reveal the effects of structural geometry and electronic feature on the antioxidative results of OH and CH groups. The antioxidative action of trans-resveratrol has followed the HAT mechanism in gas, but the SPLET pathway in liquids. OH bond breaking is easier than CH bond disruption. 4-OH bond breaking induces the lowest BDE values of 74.4–77.9 kcal/mol in gas, acetone, methanol, and water, as well as the lowest PA values of 37.2–46.2 kcal/mol in acetone, methanol, and water. From the kinetic view, 4-OH is also an active center to capture laboratory radical DPPH, ROS radicals HOO• and CH3O•, and RNS radical •NO2.

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“…Sub-shells as seen in Table S6. The NBO analysis of the investigated mycotoxins is carried out to predict the delocalization patterns of electron density from the principal occupied Lewis-type orbitals to unoccupied non-Lewis-type orbitals (from the bonding orbitals to anti-bonding orbitals) [ 31 , 41 , 42 ].…”

Section: Resultsmentioning

confidence: 99%

Investigation on electronic structure, vibrational spectra, NBO analysis, and molecular docking studies of aflatoxins and selected emerging mycotoxins against wild-type androgen receptor

Agwupuye

Neji

Louis

et al. 2021

Heliyon

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The geometry, frontier molecular orbitals (FMOs), vibrational, NBO analysis, and molecular docking simulations of aflatoxins (B1, B2, M1, M2, G1, G2), zearalenone (ZEA) emodin (EMO), alternariol (AOH), alternariol monoethyl ether (AMME), and tenuazonic acid (TeA) mycotoxins have been extensively theoretically studied and discussed based on quantum density functional theory calculations using Gaussian 16 software package. The theoretical computation for the geometry optimization, NBOs, and the molecular docking interaction was conducted using Density Functional Theory with B3LYP/6-31+G(d,p), NBO program, and AutoDock Vina tools respectively. Charge delocalization patterns and second-order perturbation energies of the most interacting natural bond orbitals (NBOs) of these mycotoxins have also been computed and predicted. Interestingly, among the mycotoxins investigated, aflatoxin G1 is seen to give the strongest stabilization energy while Zearalenone shows the highest tendency to accept electron(s) and emodin, an emerging mycotoxin gave the best binding pose within the androgen receptor pocket with a mean binding affinity of -7.40 kcal/mol.

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DFT studies on vibrational and electronic spectra, HOMO–LUMO, MEP, HOMA, NBO and molecular docking analysis of benzyl-3-N-(2,4,5-trimethoxyphenylmethylene)hydrazinecarbodithioate

Cited by 242 publications

References 47 publications

In silico Molecular Docking, DFT Analysis and ADMET Studies of Carbazole Alkaloid and Coumarins from Roots of Clausena anisata: A Potent Inhibitor for Quorum Sensing

In silico Molecular Docking, DFT Analysis and ADMET Studies of Carbazole Alkaloid and Coumarins from Roots of Clausena anisata: A Potent Inhibitor for Quorum Sensing

Antioxidant of Trans-Resveratrol: A Comparison between OH and CH Groups Based on Thermodynamic Views

Investigation on electronic structure, vibrational spectra, NBO analysis, and molecular docking studies of aflatoxins and selected emerging mycotoxins against wild-type androgen receptor

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