Exploring the structure, binding mode, flexibility and toxicity nature for Sinefungin molecule: a theoretical approach

Bangaru, Sathya; Saravanan, Muthupandian; Srinivasan, M.; Prasath, M.; Perumalsamy, Ramasamy

doi:10.1007/s11164-022-04714-9

Cited by 8 publications

(4 citation statements)

References 27 publications

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“…The protein molecule was modi ed using the AutoDockTools to include hydrogen atoms and kollman charges, and it was then saved in the pdbqt format [21]. A grid box was created with an equal number of grid points (50,50,50) using grid space 0.375, and it was stored as a gpf le (grid parameter le) in order to study the binding modes of the protein molecule. Molecular docking was carried out using the Lamarckian genetic algorithm (LGA) with a maximum of 25,00,000 energy assessments, 27,000 generations, and 150 population size, and the results were stored in a dpf le (docking parameter le) [22].…”

Section: Molecular Docking Analysismentioning

confidence: 99%

“…Molecular orbital theory explains the electronic structure and reactivity of molecules quite successfully using these orbitals. By utilizing the HOMO-LUMO orbitals and the energy difference between them, the electronic properties of molecules such as chemical softness (S), chemical hardness (η), ionization potential (I), electron a nity (A), spherical electrophilicity (ω) and spherical electronegativity (χ) can be illuminated [49,50].…”

Section: Vibrational Spectral Analysismentioning

confidence: 99%

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Spectroscopic, DFT investigation and active site analysis of 2,2-diphenyl-1,3-propanediol against estrogen receptor EPR gamma

Bayrakdar,

Magudeeswaran,

Manivannan

et al. 2024

Res Chem Intermed

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The compound 2,2-Diphenyl-1,3-Propanediol (22D13P) is very useful in the development of biologicalbased plastic materials. The FT-IR, 13 C and 1 H-NMR spectra of 22D13P molecule was recorded theoretically as well as compared with experimental results. The fundamental vibrational modes were assigned based on potential energy distribution% (PED%) analysis. The stabilization energy and charge distributions of 22D13P molecule were obtained with the help of natural bond orbital (NBO) analysis. In addition, the electronic properties of 22D13P molecule were analyzed via highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO). The drug-likeness properties of 22D13P molecule were studied. Furthermore, molecular docking was used to examine the interactions between the 22D13P molecule and 6I65 receptor from estrogen-related receptor (ER) family. The molecular dynamics simulation analysis showed that 22D13P molecule can be a potential inhibitor for breast cancer treatment.

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Section: Molecular Docking Analysismentioning

confidence: 99%

Section: Vibrational Spectral Analysismentioning

confidence: 99%

Spectroscopic, DFT investigation and active site analysis of 2,2-diphenyl-1,3-propanediol against estrogen receptor EPR gamma

Bayrakdar,

Magudeeswaran,

Manivannan

et al. 2024

Res Chem Intermed

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“…4. The energy gap is the difference in energy between the HOMO and LUMO orbitals, softmolecules have smaller band gap energy, while hard molecules have greater band gap energy [31][32][33][34][35][36]. The Ononin (4.239eV for gas phase and 4.227eV for active site) and Corylin (4.009eV for gas phase and 4.005eV for active site) molecules have small energy gap, therefore the molecules fall under soft molecule category.…”

Section: Global Reactivity Descriptorsmentioning

confidence: 99%

Probing the Ononin and Corylin molecules against anti-influenza H1N1 A virus: a detailed active site analysis

Bangaru¹,

Thamotharan²,

Srinivasan³

et al. 2023

Res Chem Intermed

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Ononin and Corylin drug molecules exhibit antiviral effects against the H1N1 in uenza A virus, with IC 50 values of30%at 200 µM and > 115 µM, respectively.The drug molecules Ononin and Corylin obey the Lipinski's rule of ve. Ononin and Corylin's ADMET properties indicate that the molecules can be exploited as an oral drug due to high solubility nature. The combined approach of computational methods such as molecular docking, molecular dynamics simulation and binding free calculations was used as a tool to achieve the drug-receptor intermolecular interactions, molecular electrostatic potential, conformational and energetic stability for Ononin and Corylin with H1N1 NA enzyme. The NBO, global and local reactivity descriptors were computed to nd the stabilization energy, chemical reactivity, kinetic stability and toxicity nature for Ononin and Corylin molecules. As a consequence, the Ononin and Corylin molecules has good biological activity and could be used as a probable treatment against the H1N1 in uenza A virus.

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Section: Vibrational Spectral Analysismentioning

confidence: 99%

Spectroscopic and an active site analysis of 2,2-diphenyl-1,3- propanediol as antitumor and inflammatory potential

Bayrakdar,

Magudeeswaran,

Manivannan

et al. 2023

Preprint

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The compound 2,2-Diphenyl-1,3-Propanediol (22D13P) is very useful in the development of biological-based plastic materials. The FT-IR, 13C and 1H-NMR spectra of 22D13P molecule was recorded theoretically as well as compared with experimental results. The fundamental vibrational modes were assigned based on potential energy distribution% (PED%) analysis. The stabilization energy and charge distributions of 22D13P molecule were obtained with the help of natural bond orbital (NBO) analysis. In addition, the electronic properties of 22D13P molecule were analyzed via highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO). The drug-likeness properties of 22D13P molecule were studied. Furthermore, molecular docking was used to examine the interactions between the 22D13P molecule and 6I65 receptor from estrogen-related receptor (ER) family. The molecular dynamics simulation analysis showed that 22D13P molecule can be a potential inhibitor for breast cancer treatment.

show abstract

Exploring the structure, binding mode, flexibility and toxicity nature for Sinefungin molecule: a theoretical approach

Cited by 8 publications

References 27 publications

Spectroscopic, DFT investigation and active site analysis of 2,2-diphenyl-1,3-propanediol against estrogen receptor EPR gamma

Spectroscopic, DFT investigation and active site analysis of 2,2-diphenyl-1,3-propanediol against estrogen receptor EPR gamma

Probing the Ononin and Corylin molecules against anti-influenza H1N1 A virus: a detailed active site analysis

Spectroscopic and an active site analysis of 2,2-diphenyl-1,3- propanediol as antitumor and inflammatory potential

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