Presentations

Molecular modeling of GES-type enzymes

Tatarnikova D.A., Krivitskaia A.V.¹

Lomonosov Moscow State University, Faculty of Chemistry, Department of Physical Chemistry, Russia, 119234, Moscow, Leninskie Gory 1, Phone: (495)939-20-35, E-mail: daria.tatarnikova@chemistry.msu.ru

¹Research Center of Biotechnology RAS, Russia, 119071, Moscow, Leninsky Prospekt 33/2

The GES-type extended-spectrum β lactamases (ESBLs) hydrolyze penicillins and cephalosporins avidly. A special feature of these enzymes is point mutations leading to the expansion of their spectrum of activity to carbapenems. Thus, the Gly170Asn and Gly170Ser mutations increase carbapenemase activity and decrease monobactams activity. The Glu104Lys mutation is responsible for increased activity against cephalosporins and decreased against carbapenems. These mutations are located mainly in the active site, in a Ω loop. This loop contains the Glu166 residue, which plays an important role in the reaction mechanism. The reaction mechanism consists of a nucleophilic attack of serine on the β-lactam ring of the antibiotic, which leads to the formation of an acyl-enzyme complex. Then acyl-enzyme complex is hydrolyzed using a water molecule and the Glu166 residue.

In this work, a molecular dynamics (MD) study of the enzymes GES-1 (Gly170), GES-2 (Asp170) and GES-5 (Ser170) was carried out with classical potentials for analyzing the Ω loop mobility and with QM/MM potentials to explain the difference in catalytic activity with the antibiotic cefotaxime. The obtained MD trajectories were analyzed by the UMAP, PCA and SRV methods using the EnGens software package [1], also by the dynamic network analysis (DNA). The analysis showed that amino acid mutations affect the Ω-loop mobility. The nucleophilic attack distances and distances forming the oxyanion hole were analyzed from QM/MM MD trajectories. As well as Laplacian maps of the electron density were constructed. GES-5 was shown to exhibit the least activity against cefotaxime, while the activity of GES-1 and GES-2 was similar, which is consistent with experimental data [2].

This work was supported by the Russian Science Foundation (project №19-73-20032). We acknowledge the use of supercomputer resources of the Joint Supercomputer Center of the Russian Academy of Sciences and the equipment of the shared research facilities of HPC computing resources at Lomonosov Moscow State University.

References

1. Conev A. et al. EnGens: a computational framework for generation and analysis of representative protein conformational ensembles // Briefings in Bioinformatics vol. 24, № 4, 2023. P. bbad242.

2. Kotsakis S.D. et al. Comparative Biochemical and Computational Study of the Role of Naturally Occurring Mutations at Ambler Positions 104 and 170 in GES β-Lactamases // Antimicrob Agents Chemother vol 54, № 11, 2010. P. 4864–4871.

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