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Taxonomic group: bacteria / Proteobacteria (Phylum: Proteobacteria)
Associated disease: infection due to Escherichia coli [ICD11: XN6P4

]

NCBI PubMed ID: 35215321
Publication DOI: 10.3390/ph15020209
Journal NLM ID: 101238453
Publisher: Basel, Switzerland: MDPI
Correspondence: G. Widmalm <goran.widmalm

su.se>
Institutions: Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University, Stockholm, Sweden, Department of Medical, Surgical and Experimental Sciences, University of Sassari, Via Muroni, 23A, 07100 Sassari, Italy, Department of Chemistry, University of Natural Resources and Life Sciences-Vienna, 1190 Vienna, Austria

Glucosyl transferase I (WaaG) in E. coli catalyzes the transfer of an alpha-d-glucosyl group to the inner core of the lipopolysaccharide (LPS) and plays an important role in the biogenesis of the outer membrane. If its activity could be inhibited, the integrity of the outer membrane would be compromised and the bacterium would be susceptible to antibiotics that are normally prevented from entering the cell. Herein, three libraries of molecules (A, B and C) were docked in the binding pocket of WaaG, utilizing the docking binding affinity as a filter to select fragment-based compounds for further investigations. From the results of the docking procedure, a selection of compounds was investigated by molecular dynamics (MD) simulations to obtain binding free energy (BFE) and KD values for ligands as an evaluation for the binding to WaaG. Derivatives of 1,3-thiazoles (A7 and A4) from library A and 1,3,4-thiadiazole (B33) from library B displayed a promising profile of BFE, with KD < mM, viz., 0.11, 0.62 and 0.04 mM, respectively. Further root-mean-square-deviation (RMSD), electrostatic/van der Waals contribution to the binding and H-bond interactions displayed a favorable profile for ligands A4 and B33. Mannose and/or heptose-containing disaccharides C1-C4, representing sub-structures of the inner core of the LPS, were also investigated by MD simulations, and compound C42- showed a calculated KD = 0.4 µM. In the presence of UDP-Glc2-, the best-docked pose of disaccharide C42- is proximate to the glucose-binding site of WaaG. A study of the variation in angle and distance was performed on the different portions of WaaG (N-, the C- domains and the hinge region). The Spearman correlation coefficient between the two variables was close to unity, where both variables increase in the same way, suggesting a conformational rearrangement of the protein during the MD simulation, revealing molecular motions of the enzyme that may be part of the catalytic cycle. Selected compounds were also analyzed by Saturation Transfer Difference (STD) NMR experiments. STD effects were notable for the 1,3-thiazole derivatives A4, A8 and A15 with the apo form of the protein as well as in the presence of UDP for A4.

molecular dynamics, NMR spectroscopy, molecular docking, binding free energy

Structure type: oligomer
Location inside paper: Fig. 1
Compound class: core oligosaccharide
Contained glycoepitopes: IEDB_130650,IEDB_130659,IEDB_130670,IEDB_131186,IEDB_133751,IEDB_135394,IEDB_135818,IEDB_136906,IEDB_137340,IEDB_137472,IEDB_140088,IEDB_141794,IEDB_141807,IEDB_142488,IEDB_144998,IEDB_146664,IEDB_150908,IEDB_151528,IEDB_151531,IEDB_190606,IEDB_2189047,IEDB_226811,IEDB_983931,SB_192,SB_7

Methods: MD simulations, STD NMR, binding assays, molecular docking, binding free energy calculation
3D data: 3D data

NCBI Taxonomy refs (TaxIDs): 562
Show glycosyltransferases

There is only one chemically distinct structure:

[1*][1*]N[C@H]1[C@@H](OP(=O)(O)O)O[C@H](CO[C@@H]2O[C@H](CO[C@]3(C(=O)O)C[C@@H](O[C@]4(C(=O)O)C[C@@H](O)[C@@H](O)[C@@H]([C@H](O)CO)O4)[C@@H](O[C@H]4O[C@H]([C@@H](O)CO)[C@@H](OP(=O)(O)O)[C@H](O[C@H]5O[C@H]([C@@H](O)CO[C@H]6O[C@H]([C@@H](O)CO)[C@@H](O)[C@H](O)[C@@H]6O)[C@@H](OP(=O)(O)O)[C@H](O[C@H]6O[C@H](CO)[C@@H](O)[C@H](O[C@H]7O[C@H](CO)[C@@H](O)[C@H](O[C@@H]8O[C@H](CO)[C@@H](O)[C@H](O)[C@H]8O)[C@H]7O[C@H]7O[C@H](CO)[C@H](O)[C@H](O)[C@H]7O[C@H]7O[C@H](CO)[C@H](O)[C@H](O)[C@H]7O)[C@H]6O)[C@@H]5O)[C@@H]4O)[C@@H]([C@H](O)CO)O3)[C@@H](OP(=O)(O)O)[C@H](O[1*])[C@H]2N[1*])[C@@H](O)[C@@H]1O

SVG MW SMILES 3D mol Ionize

R1 = LIP