Neckles Carla, Eltschkner Sandra, Cummings Jason E, Hirschbeck Maria, Daryaee Fereidoon, Bommineni Gopal R, Zhang Zhuo, Spagnuolo Lauren, Yu Weixuan, Davoodi Shabnam, Slayden Richard A, Kisker Caroline, Tonge Peter J
Institute for Chemical Biology and Drug Discovery, Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States.
Rudolf Virchow Center for Experimental Biomedicine, Institute for Structural Biology, University of Würzburg , D-97080 Würzburg, Germany.
Biochemistry. 2017 Apr 4;56(13):1865-1878. doi: 10.1021/acs.biochem.6b01048. Epub 2017 Mar 21.
There is growing awareness of the link between drug-target residence time and in vivo drug activity, and there are increasing efforts to determine the molecular factors that control the lifetime of a drug-target complex. Rational alterations in the drug-target residence time require knowledge of both the ground and transition states on the inhibition reaction coordinate, and we have determined the structure-kinetic relationship for 22 ethyl- or hexyl-substituted diphenyl ethers that are slow-binding inhibitors of bpFabI1, the enoyl-ACP reductase FabI1 from Burkholderia pseudomallei. Analysis of enzyme inhibition using a two-dimensional kinetic map demonstrates that the ethyl and hexyl diphenyl ethers fall into two distinct clusters. Modifications to the ethyl diphenyl ether B ring result in changes to both on and off rates, where residence times of up to ∼700 min (∼11 h) are achieved by either ground state stabilization (PT444) or transition state destabilization (slower on rate) (PT404). By contrast, modifications to the hexyl diphenyl ether B ring result in residence times of 300 min (∼5 h) through changes in only ground state stabilization (PT119). Structural analysis of nine enzyme:inhibitor complexes reveals that the variation in structure-kinetic relationships can be rationalized by structural rearrangements of bpFabI1 and subtle changes to the orientation of the inhibitor in the binding pocket. Finally, we demonstrate that three compounds with residence times on bpFabI1 from 118 min (∼2 h) to 670 min (∼11 h) have in vivo efficacy in an acute B. pseudomallei murine infection model using the virulent B. pseudomallei strain Bp400.
人们越来越意识到药物与靶点的驻留时间和体内药物活性之间的联系，并且正在加大力度确定控制药物 - 靶点复合物寿命的分子因素。合理改变药物与靶点的驻留时间需要了解抑制反应坐标上的基态和过渡态，我们已经确定了22种乙基或己基取代的二苯醚的结构 - 动力学关系，这些二苯醚是嗜麦芽窄食单胞菌的烯酰 - ACP还原酶FabI1（bpFabI1）的慢结合抑制剂。使用二维动力学图分析酶抑制作用表明，乙基和己基二苯醚分为两个不同的簇。对乙基二苯醚B环的修饰会导致结合和解离速率都发生变化，通过基态稳定（PT444）或过渡态去稳定（较慢的结合速率）（PT404）可实现长达约700分钟（约11小时）的驻留时间。相比之下，对己基二苯醚B环的修饰仅通过基态稳定的变化（PT119）导致300分钟（约5小时）的驻留时间。对9种酶 - 抑制剂复合物的结构分析表明，结构 - 动力学关系的变化可以通过bpFabI1的结构重排以及结合口袋中抑制剂方向的细微变化来解释。最后，我们证明，在使用强毒嗜麦芽窄食单胞菌菌株Bp400的急性嗜麦芽窄食单胞菌小鼠感染模型中，三种在bpFabI1上驻留时间从118分钟（约2小时）到670分钟（约11小时）的化合物具有体内疗效。
