Tomašič Tihomir, Zubrienė Asta, Skok Žiga, Martini Riccardo, Pajk Stane, Sosič Izidor, Ilaš Janez, Matulis Daumantas, Bryant Sharon D
Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000 Ljubljana, Slovenia.
Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Saulėtekio 7, LT-10257 Vilnius, Lithuania.
Pharmaceuticals (Basel). 2021 Aug 10;14(8):789. doi: 10.3390/ph14080789.
DNA gyrase is an important target for the development of novel antibiotics. Although ATP-competitive DNA gyrase (GyrB) inhibitors are a well-studied class of antibacterial agents, there is currently no representative used in therapy, largely due to unwanted off-target activities. Selectivity of GyrB inhibitors against closely related human ATP-binding enzymes should be evaluated early in development to avoid off-target binding to homologous binding domains. To address this challenge, we developed selective 3D-pharmacophore models for GyrB, human topoisomerase IIα (TopoII), and the Hsp90 N-terminal domain (NTD) to be used in in silico activity profiling paradigms to identify molecules selective for GyrB over TopoII and Hsp90, as starting points for hit expansion and lead optimization. The models were used to profile highly active GyrB, TopoII, and Hsp90 inhibitors. Selected compounds were tested in in vitro assays. GyrB inhibitors and were inactive against TopoII and Hsp90, while and , potent Hsp90 inhibitors, displayed no inhibition of GyrB and TopoII, and TopoII inhibitors and were inactive at GyrB and Hsp90. The results provide a proof of concept for the use of target activity profiling methods to identify selective starting points for hit and lead identification.
DNA促旋酶是新型抗生素开发的重要靶点。尽管ATP竞争性DNA促旋酶（GyrB）抑制剂是一类经过充分研究的抗菌剂，但目前尚无用于治疗的代表性药物，这主要是由于存在不良的脱靶活性。GyrB抑制剂对密切相关的人类ATP结合酶的选择性应在开发早期进行评估，以避免脱靶结合到同源结合结构域。为应对这一挑战，我们开发了针对GyrB、人类拓扑异构酶IIα（TopoII）和热休克蛋白90 N端结构域（NTD）的选择性3D药效团模型，用于计算机模拟活性分析范式，以识别对GyrB比对TopoII和Hsp90更具选择性的分子，作为命中扩展和先导优化的起点。这些模型用于分析高活性的GyrB、TopoII和Hsp90抑制剂。对选定的化合物进行了体外试验。GyrB抑制剂 和 对TopoII和Hsp90无活性，而强效Hsp90抑制剂 和 对GyrB和TopoII无抑制作用，TopoII抑制剂 和 对GyrB和Hsp90无活性。结果为使用靶点活性分析方法来识别命中和先导物鉴定的选择性起点提供了概念验证。
