A Small Nonrule of 3 Compatible Fragment Library Provides High Hit Rate of Endothiapepsin Crystal Structures with Various Fragment Chemotypes
A Small Nonrule of 3 Compatible Fragment Library Provides High Hit Rate of Endothiapepsin Crystal Structures with Various Fragment Chemotypes
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DOI：
10.1021/jm200642w
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发表时间：
2011-11-24
影响因子：
7.3
通讯作者：
Klebe, Gerhard
中科院分区：
文献类型：
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作者：
Koester, Helene;Craan, Tobias;Klebe, Gerhard
类药物分子由Lipinski的5法则定义，为了表征片段阈值，它们从5减少到3 （Astex的3法则）。它们被用于组装片段库，提供者使用它们来选择商业提供的片段。我们质疑这些规则是否过于严格，以至于候选片段库显示出足够的空间进行化学后续生长和合并修饰，因为化学转化需要适当的官能团。通常这些基团表现出氢键供体/受体的性质，并为优化化学提供切入点。因此，我们设计了一个片段库（364个条目），没有严格应用3规则。为了初步筛选内硫肽结合，我们在1mm处对荧光底物进行了生化裂解试验。“命中”被定义为抑制酶至少40%。建议注射55次，然后将其浸泡在内硫肽晶体中。可以确定11种晶体结构，覆盖了具有不同结合模式的片段：(i)直接与催化二偶体天冬氨酸结合，（ii）水介导的与天冬氨酸结合，（iii）与二偶体不直接相互作用。它们占据不同的特异性口袋。11个碎片中只有4个符合3的规则。对这一规则的限制将使片段命中的化学型数量大大减少。
Drug like molecules are defined by Lipinski's rule of 5, to characterize fragment thresholds, they have been reduced from 5 to 3 (Astex's rule of 3). They are applied to assemble fragment libraries, and providers use them to select fragments for commercial offer. We question whether these rules are too stringent to compose fragment libraries with candidates exhibiting sufficient room for chemical subsequent growing and merging modifications as appropriate functional groups for chemical transformations are required. Usually these groups exhibit properties as hydrogen bond donors/acceptors and provide entry points for optimization chemistry. We therefore designed a fragment library (364 entries) without strictly applying the rule of 3. For initial screening for endothiapepsin binding, we performed a biochemical cleavage assay of a fluorogenic substrate at 1 mM. "Hits" were defined to inhibit the enzyme by at least 40%. Fifty-five hits were suggested and subsequently soaked into endothiapepsin crystals. Eleven crystal structures could be determined covering fragments with diverse binding modes: (i) direct binding to the catalytic dyad aspartates, (ii) water-mediated binding to the aspartates, (iii) no direct interaction with the dyad. They occupy different specificity pockets. Only 4 of the 11 fragments are consistent with the rule of 3. Restriction to this rule would have limited the fragment hits to a strongly reduced variety of chemotypes.