Structure Guided Development of Novel Thymidine Mimetics Targeting Pseudomonas aeruginosa Thymidylate Kinase: From Hit to Lead Generation
Structure Guided Development of Novel Thymidine Mimetics Targeting Pseudomonas aeruginosa Thymidylate Kinase: From Hit to Lead Generation
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DOI：
10.1021/jm201349f
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发表时间：
2012-01-26
影响因子：
7.3
通讯作者：
Roush, William R.
中科院分区：
文献类型：
--
作者：
Choi, Jun Yong;Plummer, Mark S.;Roush, William R.
胸苷酸激酶（TMK）是一个潜在的化疗靶点，因为它直接参与DNA复制中一种重要成分胸苷三磷酸的合成。所有报道的TMK抑制剂都是胸苷类似物，由于细胞渗透性和对人TMK的脱靶活性，这可能阻碍它们作为有效治疗剂的发展。通过在铜绿假单胞菌TMK同源模型中分析胸苷或TP（5）A的结合模式，鉴定了对铜绿假单胞菌TMK（PaTMK）具有合理抑制效力的小分子命中物（1，IC 50 = 58 μ M）。将该命中物（1）与PaTMK共结晶，并使用计算机辅助设计方法（包括虚拟合成/筛选）合成了几种有效的PaTMK抑制剂（先导物，46、47、48和56，IC 50 = 100-200 nM），其用于指导抑制剂的设计。PaTMK中优化的前导序列的结合模式与其他细菌TMK的结合模式重叠，但不与人TMK重叠，人TMK与细菌酶具有很少的共同特征。因此，本文所述的优化的TMK抑制剂应该可用于开发靶向TMK而没有不期望的脱靶效应的抗菌剂。此外，抑制机制与LID环，它模仿的磷酸盐从ATP转移到dTMP的过程，提出了基于X-射线共晶结构，同源模型，和构效关系的结果。
Thymidylate kinase (TMK) is a potential chemotherapeutic target because it is directly involved in the synthesis of an essential component, thymidine triphosphate, in DNA replication. All reported TMK inhibitors are thymidine analogues, which might retard their development as potent therapeutics due to cell permeability and off-target activity against human TMK. A small molecule hit (1, IC50 = 58 mu M), which has reasonable inhibition potency against Pseudomonas aeruginosa TMK (PaTMK), was identified by the analysis of the binding mode of thymidine or TP(5)A in a PaTMK homology model. This hit (1) was cocrystallized with PaTMK, and several potent PaTMK inhibitors (leads, 46, 47, 48, and 56, IC50 = 100-200 nM) were synthesized using computer-aided design approaches including virtual synthesis/screening,, which was used to guide the design of inhibitors. The binding mode of the optimized leads in PaTMK overlaps with that of other bacterial TMKs but not with human TMK, which shares few common features with the bacterial enzymes. Therefore, the optimized TMK inhibitors described here should be useful for the development of antibacterial agents targeting TMK without undesired off-target effects. In addition, an inhibition mechanism associated with the LID loop, which mimics the process of phosphate transfer from ATP to dTMP, was proposed based on X-ray cocrystal structures, homology models, and structure-activity relationship results.