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All Journal Journal of Molecular Docking
Maya Georgieva
Medical University – Sofia
Medicine & Pharmacology

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Suitable Docking Protocol for the Design of Novel Coumarin Derivatives with Selective MAO-B Effects Emilio Viktorov Mateev; Iva Valkova; Maya Georgieva; Alexander Zlatkov
Journal of Molecular Docking Vol 1 No 1 (2021): Journal of Molecular Docking
Publisher : Institute for Research and Community Services Universitas Muhammadiyah Palangkaraya

Show Abstract | Download Original | Original Source | Check in Google Scholar | Full PDF (355.214 KB) | DOI: 10.33084/jmd.v1i1.2357

Abstract

Recently, the application of molecular docking is drastically increasing due to the rapid growth of resolved crystallographic receptors with co-crystallized ligands. However, the inability of docking softwares to correctly score the occurred interactions between ligands and receptors is still a relevant issue. This study examined the Pearson’s correlation coefficient between the experimental monoamine oxidase-B (MAO-B) inhibitory activity of 44 novel coumarins and the obtained GOLD 5.3 docking scores. Subsequently, optimization of the docking protocol was carried out to achieve the best possible pairwise correlation. Numerous modifications in the docking settings such as alteration in the scoring functions, size of the grid space, presence of active waters, and side-chain flexibility were conducted. Furthermore, ensemble docking simulations into two superimposed complexes were performed. The model was validated with a test set. A significant Pearson’s correlation coefficient of 0.8217 was obtained for the latter. In the final stage of our work, we observed the major interactions between the top-scored ligands and the active site of 1S3B.
Co-Authors Alexander Zlatkov Emilio Viktorov Mateev Iva Valkova