Electron density analysis of CDK complexes using the AlteQ method.

Future Medicinal Chemistry
Hrvoje RimacVladimir Potemkin

Abstract

Background: A principle of complementarity is a well-established concept in chemistry and biology. This concept is based on the overlap of electron clouds of the molecules in question. Materials & methods: In this article, one such approach (an in-house developed quantum free-orbital AlteQ method) was used to evaluate the complementarity of 51 CDK-ligand complexes. Results: A significant universally applicable correlation (adjusted R2 = 0.9749; p < 2.2 × 10-16) relating the product of ligand and enzyme electron densities to the product of distances between the contacting atomic centers and the type of atoms involved in the interaction was found. Conclusion: The terms calculated in this article can provide a good basis for prognosis of bioactivity and scientifically based molecular docking.

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Citations

Dec 22, 2020·Journal of Biomolecular Structure & Dynamics·Vladislav NaumovichMagda H Abdellattif
Apr 3, 2021·Journal of Chemical Information and Modeling·Hrvoje RimacVladimir Potemkin
Apr 14, 2021·Future Medicinal Chemistry·Shivananda KandagallaMaria A Grishina
Jul 3, 2021·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Nadezhda PalkoVladimir Potemkin

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Methods Mentioned

BETA
x-ray diffraction

Software Mentioned

tidyverse
RColorBrewer
UCSF Chimera
hclust
RStudio
R
rgl
scatterplot3d
AlteQ

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