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Computational Binding Analysis of Ethyl 3,3,5,5-Tetracyano-2-Hydroxy-2-Methyl-4,6-Diphenylcyclohexane-1-Carboxylate in Calf Thymus DNA

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Abstract

In the present paper, several computational binding analyses were performed on ethyl 3,3,5,5-tetracyano-2-hydroxy-2-methyl-4,6-diphenylcyclohexane-1-carboxylate which was newly synthesized by three-component condensation of benzaldehyde with ethyl acetoacetate and malononitrile in the presence of trichloroacetic acid, and the structure was finally proved by X-ray analysis. The visualization of molecular interaction was carried out through Hirshfeld surface analysis and ESP. The atomic charges, HOMO, LUMO, and electrostatic potential were also studied to explore the insight of the molecule deeper, and then, natural bonding orbitals (NBO) and non-linear optical properties (NLO) were calculated to reveal the interactions that happen to be between the filled and vacant orbitals. Afterwards, molecular docking studies predicted the compound binding mode fits in the minor groove of DNA and remained interacts via stable bonding as validated by molecular dynamics simulations. The binding energy estimation also affirmed domination van der Waals and electrostatic energies. Lastly, the compound was found as good drug-like molecule and had good pharmacokinetic profile with exception of toxic moieties.

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Authors and Affiliations

  1. Organic Chemistry Department, Baku State University, Z. Khalilov 23, Baku, AZ, 1148, Azerbaijan

    Malahat Kurbanova, Arzu Sadigova, Rizvan Askerov & Abel Magerramov

  2. Faculty of Chemistry, University of Warsaw, Warsaw, Poland

    Kandasamy Saravanan

  3. Department of Health and Biological Sciences, Abasyn University, Peshawar, 25000, Pakistan

    Sajjad Ahmad

  4. Department of Theoretical and Applied Chemistry, South Ural State University, Lenin prospect 76, Chelyabinsk, 454080, Russian Federation

    Youness El Bakri

Authors
  1. Malahat Kurbanova
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  2. Kandasamy Saravanan
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  3. Sajjad Ahmad
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  4. Arzu Sadigova
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  5. Rizvan Askerov
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  6. Abel Magerramov
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  7. Youness El Bakri
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Contributions

Malahat Kurbanova, Arzu Sadigova, and Abel Magerramov participated in the emergence of the synthesis. Rizvan Askerov contributed to X-ray analysis and Youness El Bakri, Kandasamy Saravanan, and Sajjad Ahmad took part in theoretical calculations.

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Correspondence to Malahat Kurbanova or Youness El Bakri.

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Kurbanova, M., Saravanan, K., Ahmad, S. et al. Computational Binding Analysis of Ethyl 3,3,5,5-Tetracyano-2-Hydroxy-2-Methyl-4,6-Diphenylcyclohexane-1-Carboxylate in Calf Thymus DNA. Appl Biochem Biotechnol 195, 5338–5354 (2023). https://doi.org/10.1007/s12010-022-03849-0

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