Presentations

Activation of carbapenems in the active site of OXA-48

Kuznetsov M.E., Krivitskaya A.V.¹, Khrenova M.G.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: kuznetsovme@my.msu.ru

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

β-lactam antibiotics are widely used in medicine to combat pathogenic bacteria. These compounds act on the bacterial cell wall, inhibiting bacterial growth and reproduction. However, some bacteria have developed resistance to β-lactams by producing β-lactamases specific enzymes, which hydrolyze the antibiotics and prevent them to binding to the bacterial cell wall. The nucleophile in serine β-lactamases is the oxygen of the hydroxyl group of the catalytic serine residue. This atom attacks the carbonyl carbon in the β-lactam ring of substrate. This reaction leads to ring cleaving and inactivation of antibiotic. Nucleophilic attack is assisted by the activation of substrate in the active site. NH-groups of threonine and catalytic serine interact with carbonyl oxygen of substrate and polarize the C=O bond. Polarization of this bond makes the carbon atom more electrophilic. Interatomic distances in the oxyanion hole and distances of the nucleophilic attack can be utilized as a measure of interactions of the carbonyl group of the substrate with the active site of the enzyme.

In this study, the structural end electronic features of the OXA-48 complexes with meropenem and biapenem were considered. OXA-48 is a serine carbapenemase. Molecular dynamics simulation with QM/MM potentials were performed to analyze enzyme-substrate complexes. Distances of the nucleophilic attack and interatomic distances in the oxyanion hole were analyzed. This approach proved ineffective. Electron density-based criteria such as the Laplacian of electron density allows to classify structures as reactive and non-reactive. This method allowed to find differences between complexes with meropenem and meropenem. The proportion of reactive structures with meropenem was found to be lower compared to those with biapenem (86% vs 96%).

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. Krivitskaya, A.V.; Khrenova, M.G. Evolution of Ceftriaxone Resistance of Penicillin-Binding Proteins 2 Revealed by Molecular Modeling. // Int. J. Mol. Sci. 24(1), 176, 2023

• abstract in Russian (PDF)