Kaplan Elise, Chaloin Laurent, Guichou Jean-François, Berrou Kévin, Rahimova Rahila, Labesse Gilles, Lionne Corinne
Institut de Recherche en Infectiologie de Montpellier - IRIM, University of Montpellier, CNRS UMR 9004, 1919 route de Mende, 34293, Montpellier cedex 5, France.
Current address: University of Lyon, CNRS, UMR5086, Molecular Microbiology and Structural Biochemistry, IBCP, 7 Passage du Vercors, 69367, Lyon, France.
ChemMedChem. 2025 Apr 14;20(8):e202400842. doi: 10.1002/cmdc.202400842. Epub 2025 Jan 26.
Aminoglycoside-phosphotransferases (APHs) are a class of bacterial enzymes that mediate acquired resistance to aminoglycoside antibiotics. Here we report the identification of small molecules counteracting aminoglycoside resistance in Enterococcus casseliflavus. Molecular dynamics simulations were performed to identify an allosteric pocket in three APH enzymes belonging to 3' and 2'' subfamilies in which we then screened, in silico, 12,000 small molecules. From a subset of only 14 high-scored molecules tested in vitro, we identified a compound, named here EK3, able to non-competitively inhibit the APH(2'')-IVa, an enzyme mediating clinical gentamicin resistance. Structure-activity relationship (SAR) exploration of this hit compound allowed us to identify a molecule with improved enzymatic inhibition. By measuring bacterial sensitivity, we found that the three best compounds in this series restored bactericidal activity of various aminoglycosides, including gentamicin, without exhibiting toxicity to HeLa cells. This work not only provides a basis to fight aminoglycoside resistance but also highlights a proof-of-concept for the search of allosteric modulators by using in silico methods.
氨基糖苷磷酸转移酶（APHs）是一类细菌酶，可介导对氨基糖苷类抗生素的获得性耐药。在此，我们报告了在格氏肠球菌中鉴定出可对抗氨基糖苷耐药性的小分子。进行了分子动力学模拟，以在属于3'和2''亚家族的三种APH酶中鉴定一个变构口袋，然后我们在计算机上筛选了12000种小分子。从仅在体外测试的14种高分分子的子集中，我们鉴定出一种名为EK3的化合物，它能够非竞争性抑制APH(2'')-IVa，这是一种介导临床庆大霉素耐药性的酶。对这种命中化合物的构效关系（SAR）探索使我们能够鉴定出一种具有改善的酶抑制作用的分子。通过测量细菌敏感性，我们发现该系列中三种最佳化合物恢复了包括庆大霉素在内的各种氨基糖苷类药物的杀菌活性，而对HeLa细胞没有毒性。这项工作不仅为对抗氨基糖苷耐药性提供了基础，还突出了通过计算机方法寻找变构调节剂的概念验证。
