Schulz Michèle N, Fanghänel Jörg, Schäfer Martina, Badock Volker, Briem Hans, Boemer Ulf, Nguyen Duy, Husemann Manfred, Hillig Roman C
Bayer Schering Pharma AG, Global Drug Discovery, Berlin, Germany.
Acta Crystallogr D Biol Crystallogr. 2011 Mar;67(Pt 3):156-66. doi: 10.1107/S0907444910054144. Epub 2011 Feb 15.
A crystallographic fragment screen was carried out to identify starting points for the development of inhibitors of protein kinase Pim-1, a potential target for tumour therapy. All fragment hits identified via soaking in this study turned out to bind to the unusually hydrophobic pocket at the hinge region. The most potent fragments, two cinnamic acid derivatives (with a best IC(50) of 130 µM), additionally form a well defined hydrogen bond. The balance between hydrophobic and polar interactions makes these molecules good starting points for further optimization. Pim-2 inhibitors from a recently reported high-throughput screening campaign also feature a cinnamic acid moiety. Two of these Pim-2 inhibitors were synthesized, their potencies against Pim-1 were determined and their cocrystal structures were elucidated in order to determine to what degree the binding modes identified by fragment screening are conserved in optimized inhibitors. The structures show that the cinnamic acid moieties indeed adopt the same binding mode. Fragment screening thus correctly identified binding modes which are maintained when fragments are grown into larger and higher affinity inhibitors. The high-throughput screening-derived compound (E)-3-{3-[6-(4-aminocyclohexylamino)-pyrazin-2-yl]phenyl}acrylic acid (compound 1) is the most potent inhibitor of the cinnamic acid series for which the three-dimensional binding mode is known (IC(50) = 17 nM, K(d) = 28 nM). The structure reveals the molecular basis for the large gain in potency between the initial fragment hit and this optimized inhibitor.
开展了一项晶体片段筛选，以确定蛋白激酶Pim-1抑制剂开发的起始点，Pim-1是肿瘤治疗的一个潜在靶点。通过本研究中的浸泡法鉴定出的所有片段命中物结果都与铰链区异常疏水的口袋结合。最有效的片段，两种肉桂酸衍生物（最佳IC(50)为130 μM），还形成了明确的氢键。疏水和极性相互作用之间的平衡使这些分子成为进一步优化的良好起始点。最近报道的高通量筛选活动中的Pim-2抑制剂也具有肉桂酸部分。合成了其中两种Pim-2抑制剂，测定了它们对Pim-1的效力，并阐明了它们的共晶体结构，以确定片段筛选所确定的结合模式在优化抑制剂中保留的程度。结构表明肉桂酸部分确实采用相同的结合模式。因此，片段筛选正确地鉴定了结合模式，当片段生长为更大、亲和力更高的抑制剂时，这些结合模式得以维持。高通量筛选得到的化合物(E)-3-{3-[6-(4-氨基环己基氨基)-吡嗪-2-基]苯基}丙烯酸（化合物1）是已知三维结合模式的肉桂酸系列中最有效的抑制剂（IC(50)=17 nM，K(d)=28 nM）。该结构揭示了初始片段命中物与这种优化抑制剂之间效力大幅提高的分子基础。
