Merget Benjamin, Sotriffer Christoph A
Institute of Pharmacy and Food Chemistry, University of Würzburg, Am Hubland, D-97074, Würzburg, Germany.
PLoS One. 2015 May 21;10(5):e0127009. doi: 10.1371/journal.pone.0127009. eCollection 2015.
An important kinetic parameter for drug efficacy is the residence time of a compound at a drug target, which is related to the dissociation rate constant koff. For the essential antimycobacterial target InhA, this parameter is most likely governed by the ordering of the flexible substrate binding loop (SBL). Whereas the diphenyl ether inhibitors 6PP and triclosan (TCL) do not show loop ordering and thus, no slow-binding inhibition and high koff values, the slightly modified PT70 leads to an ordered loop and a residence time of 24 minutes. To assess the structural differences of the complexes from a dynamic point of view, molecular dynamics (MD) simulations with a total sampling time of 3.0 µs were performed for three ligand-bound and two ligand-free (perturbed) InhA systems. The individual simulations show comparable conformational features with respect to both the binding pocket and the SBL, allowing to define five recurring conformational families. Based on their different occurrence frequencies in the simulated systems, the conformational preferences could be linked to structural differences of the respective ligands to reveal important determinants of residence time. The most abundant conformation besides the stable EI* state is characterized by a shift of Ile202 and Val203 toward the hydrophobic pocket of InhA. The analyses revealed potential directions for avoiding this conformational change and, thus, hindering rapid dissociation: (1) an anchor group in 2'-position of the B-ring for scaffold stabilization, (2) proper occupation of the hydrophobic pocket, and (3) the introduction of a barricade substituent in 5'-position of the diphenyl ether B-ring.
药物疗效的一个重要动力学参数是化合物在药物靶点的停留时间，它与解离速率常数koff相关。对于必需的抗分枝杆菌靶点InhA，这个参数很可能由柔性底物结合环（SBL）的排序决定。而二苯醚抑制剂6PP和三氯生（TCL）不会使环发生排序，因此，不会出现慢结合抑制和高koff值，稍微修饰的PT70会导致环有序排列，停留时间为24分钟。为了从动力学角度评估复合物的结构差异，对三个配体结合和两个无配体（受干扰）的InhA系统进行了总采样时间为3.0微秒的分子动力学（MD）模拟。单独的模拟显示，结合口袋和SBL的构象特征具有可比性，从而可以定义五个重复出现的构象家族。根据它们在模拟系统中的不同出现频率，构象偏好可以与各自配体的结构差异联系起来，以揭示停留时间的重要决定因素。除了稳定的EI*状态外，最丰富的构象的特征是Ile202和Val203向InhA的疏水口袋移动。分析揭示了避免这种构象变化从而阻碍快速解离的潜在方向：（1）在B环的2'-位有一个锚定基团以稳定支架，（2）适当占据疏水口袋，以及（3）在二苯醚B环的5'-位引入一个屏障取代基。
