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Docking Linear Ligands to Glucose Oxidase

Department of Physical Chemistry, Faculty of Pharmacy, Collegium Medicum, Nicolaus Copernicus University, Kurpińskiego 5, 85-096 Bydgoszcz, Poland
Symmetry 2019, 11(7), 901; https://doi.org/10.3390/sym11070901
Received: 12 June 2019 / Revised: 28 June 2019 / Accepted: 8 July 2019 / Published: 10 July 2019
(This article belongs to the Special Issue Applied Designs in Chemical Structures with High Symmetry)
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Abstract

GOX (3QVR), glucose oxidase, is an oxidoreductase enzyme, which has found many applications in biotechnology and modern diagnostics with typical assays including biosensors useful in the determination of free glucose in body fluids. PEI (polyethylenimines) are polymer molecules made up of amine groups and two aliphatic carbons, which are cyclically repeated. PEI are transfection reagents which, using positively charged units, bind well to anionic DNA residues. During the studies on GOX, PEI were used both in their linear and branched structures. Rhombellanes, RBL, are structures decorated with rhombs/squares. The aim of the paper is to study the interactions of two kinds of linear ligands: PEIs (Polyethylenimines) and CHRs (ethers of Hexahydroxy-cyclohexane) with the glucose oxidase enzyme, GOX (3QVR). To understand the structure-activity relationship between the GOX enzyme and the linear ligands PEI and CHR, two steps of docking simulation were performed; mapping the whole area of the 3QVR enzyme and docking on the first and second surface of the enzyme, separately. The studied ligands interacted with amino acids of GOX inside the protein and on its surface, with stronger and shorter bonds inside of the protein. However, long chain ligands can only interact with amino acids on the external protein surface. After the study, two domains of the enzyme were clearly evidenced; the external surface domain more easily creates interactions with ligands, particularly with CHR ligands. View Full-Text
Keywords: PEI; CHR; 3QVR; Glucose oxidase; docking PEI; CHR; 3QVR; Glucose oxidase; docking
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Szefler, B. Docking Linear Ligands to Glucose Oxidase. Symmetry 2019, 11, 901.

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