Males Alexandra, Raich Lluís, Williams Spencer J, Rovira Carme, Davies Gideon J
York Structural Biology Laboratory, Department of Chemistry, The University of York, York, YO10 5DD, UK.
Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica) and, Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08028, Barcelona, Spain.
Chembiochem. 2017 Aug 4;18(15):1496-1501. doi: 10.1002/cbic.201700166. Epub 2017 Jun 26.
The varied yet family-specific conformational pathways used by individual glycoside hydrolases (GHs) offer a tantalising prospect for the design of tightly binding and specific enzyme inhibitors. A cardinal example of a GH-family-specific inhibitor, and one that finds widespread practical use, is the natural product kifunensine, which is a low-nanomolar inhibitor that is selective for GH family 47 inverting α-mannosidases. Here we show, through quantum-mechanical approaches, that kifunensine is restrained to a "ring-flipped" C conformation with another accessible, but higher-energy, region around the B conformation. The conformations of kifunensine in complex with a range of GH47 enzymes-including an atomic-level resolution (1 Å) structure of kifunensine with Caulobacter sp. CkGH47 reported herein and with GH family 38 and 92 α-mannosidases-were mapped onto the kifunensine free-energy landscape. These studies revealed that kifunensine has the ability to mimic the product state of GH47 enzymes but cannot mimic any conformational states relevant to the reaction coordinate of mannosidases from other families.
单个糖苷水解酶（GHs）所采用的多样但具有家族特异性的构象途径为设计紧密结合且特异性的酶抑制剂提供了诱人的前景。GH家族特异性抑制剂的一个主要例子，也是一种得到广泛实际应用的抑制剂，是天然产物 kifunensine，它是一种低纳摩尔抑制剂，对GH家族47的转化α-甘露糖苷酶具有选择性。在此我们通过量子力学方法表明，kifunensine被限制在一种“环翻转”的C构象，同时在B构象周围还有另一个可及但能量更高的区域。kifunensine与一系列GH47酶形成复合物时的构象——包括本文报道的kifunensine与Caulobacter sp. CkGH47以及与GH家族38和92的α-甘露糖苷酶的原子水平分辨率（1 Å）结构——被映射到kifunensine的自由能景观上。这些研究表明，kifunensine能够模拟GH47酶的产物状态，但无法模拟与其他家族甘露糖苷酶反应坐标相关的任何构象状态。
