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Year 2022, Volume: 8 Issue: 2, 6 - 30, 15.12.2022

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References

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A Combined 3D-QSAR, Pharmacophore Modelling, and Molecular Docking Study for Plastoquinone Analogues

Year 2022, Volume: 8 Issue: 2, 6 - 30, 15.12.2022

Abstract

In this study, a set consisting of 39 compounds that are in the literature and carrying Plastoquinone analogues was investigated. The 3D-QSAR study was performed using a field-based method and Partial Least Square (PLS) regression analysis. The generated 3D-QSAR model has sufficient statistical significance and acceptable prediction power with the regression correlation coefficient (r2) at 0.97 and q2 = 0.4. The pharmacophore modelling was carried out and a four-point model (AHHR_3) was generated. Molecular docking was performed with the selected 1IEP protein and the RMSD value for the position of the ligands docked at the two identified active sites was obtained as 0.3669 Å and 0.5535 Å. Docking analysis revealed that the ABQ16 is the best docked ligand with a DockScore of -9.55, followed by AQ2, AQ6 and ABQ11 with scores of -8.56, -8.2 and -7.64, respectively. It was seen that hydrophobic interactions are dominate and the TYR253 residue is responsible for the pi-pi interaction with the aromatic ring.

References

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  • Bayrak, N., Yıldırım, H., Yıldız, M., Radwan, M. O., Otsuka, M., Fujita, M., Tuyun, A. F., & Ciftci, H. I. (2019). Design, synthesis, and biological activity of Plastoquinone analogs as a new class of anticancer agents. Bioorganic Chemistry, 92, 103255. https://doi.org/10.1016/J.BIOORG.2019.103255
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  • Greenwood, J. R., Calkins, D., Sullivan, A. P., & Shelley, J. C. (2010). Towards the comprehensive, rapid, and accurate prediction of the favorable tautomeric states of drug-like molecules in aqueous solution. Journal of Computer-Aided Molecular Design, 24(6–7), 591–604. https://doi.org/10.1007/S10822-010-9349-1/FIGURES/6
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Primary Language English
Journal Section makaleler
Authors

Mehmet Çınar 0000-0002-0184-0082

Publication Date December 15, 2022
Published in Issue Year 2022 Volume: 8 Issue: 2

Cite

APA Çınar, M. (2022). A Combined 3D-QSAR, Pharmacophore Modelling, and Molecular Docking Study for Plastoquinone Analogues. Eastern Anatolian Journal of Science, 8(2), 6-30.
AMA Çınar M. A Combined 3D-QSAR, Pharmacophore Modelling, and Molecular Docking Study for Plastoquinone Analogues. Eastern Anatolian Journal of Science. December 2022;8(2):6-30.
Chicago Çınar, Mehmet. “A Combined 3D-QSAR, Pharmacophore Modelling, and Molecular Docking Study for Plastoquinone Analogues”. Eastern Anatolian Journal of Science 8, no. 2 (December 2022): 6-30.
EndNote Çınar M (December 1, 2022) A Combined 3D-QSAR, Pharmacophore Modelling, and Molecular Docking Study for Plastoquinone Analogues. Eastern Anatolian Journal of Science 8 2 6–30.
IEEE M. Çınar, “A Combined 3D-QSAR, Pharmacophore Modelling, and Molecular Docking Study for Plastoquinone Analogues”, Eastern Anatolian Journal of Science, vol. 8, no. 2, pp. 6–30, 2022.
ISNAD Çınar, Mehmet. “A Combined 3D-QSAR, Pharmacophore Modelling, and Molecular Docking Study for Plastoquinone Analogues”. Eastern Anatolian Journal of Science 8/2 (December 2022), 6-30.
JAMA Çınar M. A Combined 3D-QSAR, Pharmacophore Modelling, and Molecular Docking Study for Plastoquinone Analogues. Eastern Anatolian Journal of Science. 2022;8:6–30.
MLA Çınar, Mehmet. “A Combined 3D-QSAR, Pharmacophore Modelling, and Molecular Docking Study for Plastoquinone Analogues”. Eastern Anatolian Journal of Science, vol. 8, no. 2, 2022, pp. 6-30.
Vancouver Çınar M. A Combined 3D-QSAR, Pharmacophore Modelling, and Molecular Docking Study for Plastoquinone Analogues. Eastern Anatolian Journal of Science. 2022;8(2):6-30.