Molecular dynamics simulations suggest why the A2058G mutation in 23S RNA results in bacterial resistance against clindamycin

Abstract

Clindamycin, a lincosamide antibiotic, binds to 23S ribosomal RNA and inhibits protein synthesis. The A2058G mutation in 23S RNA results in bacterial resistance to clindamycin. To understand the influence of this mutation on short-range interactions of clindamycin with 23S RNA, we carried out full-atom molecular dynamics simulations of a ribosome fragment containing clindamycin binding site. We compared the dynamical behavior of this fragment simulated with and without the A2058G mutation. Molecular dynamics simulations suggest that clindamycin in the native ribosomal binding site is more internally flexible than in the A2058G mutant. Only in the native ribosome fragment did we observe intramolecular conformational change of clindamycin around its C7-N1-C10-C11 dihedral. In the mutant, G2058 makes more stable hydrogen bonds with clindamycin hindering its conformational freedom in the ribosome-bound state. Clindamycin binding site is located in the entrance to the tunnel through which the newly synthesized polypeptide leaves the ribosome. We observed that in the native ribosome fragment, clindamycin blocks the passage in the tunnel entrance, whereas in the mutated fragment the aperture is undisturbed due to a different mode of binding of clindamycin in the mutant. Restricted conformational freedom of clindamycin in a position not blocking the tunnel entrance in the A2058G mutant could explain the molecular mechanism of bacterial resistance against clindamycin occurring in this mutant.Electronic supplementary materialThe online version of this article (10.1007/s00894-018-3689-5) contains supplementary material, which is available to authorized users.

The outward shift of clarithromycin binding to the ribosome in mutantHelicobacter pyloristrains

“…Such derestriction of NPET was also observed in L22 mutations of Staphylococcus aureus , in interaction with erythromycin, using cryo‐electron microscopy maps 14 . Such an outward shift and derestriction of the NPET entrance have also been reported for the molecular dynamic simulation study of the interaction of clindamycin, a lincosamide–macrolide, with the mutant A2058G strain of E coli , where in addition to the lower tendency of drug binding, the binding to mutant conformations, is shifted 70 . Other supportive evidence comes from the molecular modeling research of telithromycin with A2058G mutant of 23S rRNA in Deinococcus radiodurans , which detected the antibiotic molecule distant from the position of G2058 and shifted toward the other side of the tunnel, to the vicinity of L22 71 .…”

Antimicrobial Susceptibility and Multilocus Sequence Typing ofListeria monocytogenesIsolated Over 11 Years from Food, Humans, and the Environment in Italy

“…Acquired resistance to both antimicrobials is a multistep process linked to the subsequent acquisition of multiple point mutations in core genes. In particular, clindamycin resistance was associated with methylation and mutations in the 23S rRNA (Kehrenberg et al, 2005;Poehlsgaard et al, 2005;Kulczycka-Mierzejewska et al, 2018). Ciprofloxacin resistance was associated to mutations in the quinolone resistance determining region of gyrA, overexpression of efflux pump gene llde and mutation in the fepR gene, and regulator of the efflux pump protein gene fepA in L. monocytogenes (Lampidis et al, 2002;Godreuil et al, 2003;Moreno et al, 2014;Jiang et al, 2018;Wilson et al, 2018).…”

Large-scale simulations of nucleoprotein complexes: ribosomes, nucleosomes, chromatin, chromosomes and CRISPR

“…Trylska and co-workers performed explicit solvent molecular dynamics simulations of decoding introducing various mutations, finding differences in the internal mobility of the A-site, as well as in ion and water density distributions inside the binding cleft, between the prokaryotic and mutated RNA [54]. They also examined the effect of A2058G on clindamycin activity [56]. In an important study, Trylska and co-workers used Brownian dynamics simulations to examine antibiotic binding to the 30S subunit, showing that electrostatic steering is not the sole factor directing the aminoglycosidic antibiotic toward the binding site on the 30S ribosomal subunit.…”