Novel Allosteric Sites on Ras for Lead Generation
Novel Allosteric Sites on Ras for Lead Generation
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DOI：
10.1371/journal.pone.0025711
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发表时间：
2011-10-25
期刊：
影响因子：
3.7
通讯作者：
Gorfe, Alemayehu A.
中科院分区：
文献类型：
--
作者：
Grant, Barry J.;Lukman, Suryani;Gorfe, Alemayehu A.
RAS活性异常是多种癌症和发育性疾病的标志。不幸的是，开发有效的小分子RAS抑制剂的传统努力取得的成功有限。我们开发了一种新的多水平计算方法来发现以前未表征的变构位点的潜在抑制剂。我们的方法结合了生物信息学分析、先进的分子模拟、整体对接和潜在抑制剂的初步实验测试。分子动力学模拟强调了核苷酸结合开关区与末端区域(包括环7和螺旋5)的保守变构耦合。生物信息学方法发现了靠近这些区域和构象响应开关区附近的新的瞬时小分子结合口袋。通过锌和NCI化合物文库的整体对接选择用于这些口袋的候选粘结剂。最后，基于细胞的分析证实了我们的假设，即所选择的结合剂可以抑制RAS的下游信号活性。因此，我们认为预测的变构中心是开发和优化新药的可行靶点。
Aberrant Ras activity is a hallmark of diverse cancers and developmental diseases. Unfortunately, conventional efforts to develop effective small molecule Ras inhibitors have met with limited success. We have developed a novel multi-level computational approach to discover potential inhibitors of previously uncharacterized allosteric sites. Our approach couples bioinformatics analysis, advanced molecular simulations, ensemble docking and initial experimental testing of potential inhibitors. Molecular dynamics simulation highlighted conserved allosteric coupling of the nucleotide-binding switch region with distal regions, including loop 7 and helix 5. Bioinformatics methods identified novel transient small molecule binding pockets close to these regions and in the vicinity of the conformationally responsive switch region. Candidate binders for these pockets were selected through ensemble docking of ZINC and NCI compound libraries. Finally, cell-based assays confirmed our hypothesis that the chosen binders can inhibit the downstream signaling activity of Ras. We thus propose that the predicted allosteric sites are viable targets for the development and optimization of new drugs.