Characterization of crystal water molecules in a high-affinity inhibitor and hematopoietic prostaglandin D synthase complex by interaction energy studies
作者:Daisuke Takaya、Koji Inaka、Akifumi Omura、Kenji Takenuki、Masashi Kawanishi、Yukako Yabuki、Yukari Nakagawa、Keiko Tsuganezawa、Naoko Ogawa、Chiduru Watanabe、Teruki Honma、Kosuke Aritake、Yoshihiro Urade、Mikako Shirouzu、Akiko Tanaka
DOI:10.1016/j.bmc.2018.08.014
日期:2018.9
synthase (H-PGDS) is one of the two enzymes that catalyze prostaglandin D2 synthesis and a potential therapeutic target of allergic and inflammatory responses. To reveal key molecular interactions between a high-affinity ligand and H-PGDS, we designed and synthesized a potent new inhibitor (KD: 0.14 nM), determined the crystal structure in complex with human H-PGDS, and quantitatively analyzed the ligand–protein
造血前列腺素D合酶(H-PGDS)是催化前列腺素D 2合成的两种酶之一,并且是过敏和炎症反应的潜在治疗靶标。为了揭示高亲和力配体与H-PGDS之间的关键分子相互作用,我们设计并合成了一种有效的新抑制剂(K D:0.14 nM),测定与人类H-PGDS形成复合物的晶体结构,并通过片段分子轨道计算方法定量分析配体与蛋白质的相互作用。在空腔中,鉴定出10个水分子,相互作用能计算表明它们与空腔中的表面氨基酸稳定结合。其中,从深内腔到腔外围的6个水分子通过形成氢键相互作用直接促进了配体的结合。Arg12,Gly13,Gln36,Asp96,Trp104,Lys112和必需的辅因子谷胱甘肽也与配体具有很强的相互作用。通过与邻近的保守水分子形成氢键网络,Leu199与配体之间的强排斥性相互作用被抵消了。