ИСТИНА

L,D-transpeptidase 2 from Mycobacterium tuberculosis plays a key role in formation of the cell wall of the pathogen and catalyzes cross-linking of the growing peptidoglycan chains by non-classical 3-3 bonds (bonds between m-DAP residues in different peptidoglycan molecules) what causes its resistance to a broad spectrum of penicillins. Molecular modeling of L,D-transpeptidase 2 from Mycobacterium tuberculosis full-atom model interactions with the N- and C-terminal tetrapeptide fragments (N-Ac–L-Ala–γ-D-Glu–m-DAP–D-Ala) of the growing peptidoglycan chains was performed for the first time and has allowed to disclose peculiarities of their binding at formation of 3-3 cross-linkages as well as to build the full-atom model of L,D-transpeptidase 2 for screening and optimization of inhibitors’ structure [1]. Difficulty in determination of the substrate localization in the L,D-transpeptidase active site is complicated by the fact that binding of the two molecules of the same compound should be considered. One molecule should bind as an acyl donor what further leads to the formation of an acyl enzyme intermediate, whereas the other one should bind as a nucleophile what leads to the formation of an acyl enzyme-nucleophile complex followed by the acyl group transfer to the nucleophile and 3-3 cross-linking of peptidoglycan of the cell wall. Analysis of molecular dynamics simulations have shown that binding of N- and C-terminal fragments of the growing peptidoglycan chain in different tunnels is responsible for different steps of the catalytic mechanism at formation of non classical 3-3 cross-linkages in peptidoglycan. At binding of the substrate in the tunnel C a reactive enzyme-substrate complex is formed: the Sγ-atom of the catalytic Cys354 residue is in a distance (3.5–5.7 Å) favorable for nucleophilic attack of the C atom of carbonyl group of peptide bond m-DAP-D-Ala during the whole MD trajectory. At the same time orientation of the substrate molecule in the tunnel B well corresponds to the role of nucleophile at formation of 3-3 cross-linkage: a distance between the N-atom of the free amino group of m-DAP and the Sγ-atom of the catalytic Cys354 is in a range 3.2–6.8 Å. In order to simulate LdtMt2 interactions with β-lactam inhibitors capable of inactivating enzyme due to formation of stable acyl enzymes it is necessary to consider binding of the potential inhibitors in the tunnel C of the active site. This work was supported by the Russian Science Foundation (grant #15-14-00069) [1] S.M. Baldin, N.M. Misiura, V.K. Švedas, Building a Full-Atom Model of L,D-transpeptidase 2 from Mycobacterium tuberculosis for screening new inhibitors // Acta Naturae 2017, V. 9, № 1 (32), P.44-51.