Kutchukian Peter S, Yang Jae Shick, Verdine Gregory L, Shakhnovich Eugene I
Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA.
J Am Chem Soc. 2009 Apr 8;131(13):4622-7. doi: 10.1021/ja805037p.
Recent work has shown that the incorporation of an all-hydrocarbon "staple" into peptides can greatly increase their alpha-helix propensity, leading to an improvement in pharmaceutical properties such as proteolytic stability, receptor affinity, and cell permeability. Stapled peptides thus show promise as a new class of drugs capable of accessing intractable targets such as those that engage in intracellular protein-protein interactions. The extent of alpha-helix stabilization provided by stapling has proven to be substantially context dependent, requiring cumbersome screening to identify the optimal site for staple incorporation. In certain cases, a staple encompassing one turn of the helix (attached at residues i and i+4) furnishes greater helix stabilization than one encompassing two turns (i,i+7 staple), which runs counter to expectation based on polymer theory. These findings highlight the need for a more thorough understanding of the forces that underlie helix stabilization by hydrocarbon staples. Here we report all-atom Monte Carlo folding simulations comparing unmodified peptides derived from RNase A and BID BH3 with various i,i+4 and i,i+7 stapled versions thereof. The results of these simulations were found to be in quantitative agreement with experimentally determined helix propensities. We also discovered that staples can stabilize quasi-stable decoy conformations, and that the removal of these states plays a major role in determining the helix stability of stapled peptides. Finally, we critically investigate why our method works, exposing the underlying physical forces that stabilize stapled peptides.
近期研究表明，将全碳“订书钉”引入肽中可显著提高其α-螺旋倾向，从而改善诸如蛋白水解稳定性、受体亲和力和细胞通透性等药物性质。因此，订书钉肽有望成为一类新型药物，能够作用于难以攻克的靶点，比如那些参与细胞内蛋白质-蛋白质相互作用的靶点。事实证明，订书钉提供的α-螺旋稳定性程度很大程度上取决于具体情况，需要进行繁琐的筛选以确定订书钉引入的最佳位点。在某些情况下，包含一圈螺旋的订书钉（连接在i和i + 4位残基处）比包含两圈螺旋的订书钉（i，i + 7订书钉）能提供更大的螺旋稳定性，这与基于聚合物理论的预期相反。这些发现凸显了更深入了解烃类订书钉稳定螺旋背后作用力的必要性。在此，我们报告了全原子蒙特卡罗折叠模拟，比较了源自核糖核酸酶A和BID BH3的未修饰肽及其各种i，i + 4和i，i + 7订书钉修饰版本。这些模拟结果与实验测定的螺旋倾向在定量上一致。我们还发现订书钉可以稳定准稳定的诱饵构象，并且去除这些状态在确定订书钉肽的螺旋稳定性中起主要作用。最后，我们深入研究了我们的方法为何有效，揭示了稳定订书钉肽的潜在物理力。
