Rational cyclization-based minimization of entropy penalty upon the binding of Nrf2-derived linear peptides to Keap1: A new strategy to improve therapeutic peptide activity against sepsis
Rational cyclization-based minimization of entropy penalty upon the binding of Nrf2-derived linear peptides to Keap1: A new strategy to improve therapeutic peptide activity against sepsis
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DOI：
10.1016/j.bpc.2018.11.002
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发表时间：
2019-01-01
影响因子：
3.8
通讯作者：
Shen, Bin
中科院分区：
文献类型：
--
作者：
Chen, Ke;Huang, Liuliu;Shen, Bin
NRF2是脓毒症时先天免疫反应和生存的关键调节因子，它通过与E3泛素连接酶的Keapl接头蛋白结合而被结构性降解。分别来自Nrf2结合位点低亲和力基序和高亲和力基序的两个线状多肽DLG和ETG对Keap1中心孔(活性口袋)具有自结合亲和力，它们可以作为治疗性自抑制性多肽来破坏Nrf2 Keap1相互作用。分子动力学模拟和结合能分解表明，这两种多肽在非结合自由状态下具有很大的柔韧性和内在无序性，与Keap1结合时会产生相当大的熵惩罚。为了提高KEAP1与多肽的结合亲和力(或自由能ΔG)，我们在这里描述了一种合理的多肽环化策略，以最大限度地减少NRF2衍生的线性多肽与KEAP1结合时的不利熵惩罚(DELTA S)，而不是传统上增加有利的焓贡献(DELTA H)。晶体结构分析表明，与Keap1结合的DLG和ETG的天然活性构象分别折叠成U形和发夹构象，并利用它们的转头插入Keap1的中心孔中。这里，环化是通过在DLG U形或ETG发夹的两个臂上添加一个二硫键来设计的，它不会影响Keap1与多肽之间的直接分子间相互作用以及相互作用中的解溶效应，但可以有效地限制两个多肽在自由态下的构象灵活性和无序性，从而极大地减少了结合的熵惩罚。自由能计算和结合亲和力分析都证实，环化可以适度或显著地提高多肽与Keap1的结合能力，所设计的环肽的亲和力(解离常数K-d)比其线性环肽提高1.4-7.5倍。
Nrf2 is a critical regulator of innate immune response and survival during sepsis, which is constitutively degraded through binding to the Keapl adapter protein of E3 ubiquitin ligase. Two linear peptides DLG and ETG derived from, respectively, the low-affinity and high-affinity motifs of Nrf2 binding site exhibit self-binding affinity to Keap1 central hole (active pocket); they can be exploited as therapeutic self-inhibitory peptides to disrupt the Nrf2 Keap1 interaction. Molecular dynamics simulation and binding energetics decomposition reveal that the two peptides possess large flexibility and intrinsic disorder in unbound free state, and thus would incur a considerable entropy penalty upon binding to Keapl. In order to improve Keap1-peptide binding affinity (or free energy Delta G), instead of traditionally increasing favorable enthalpy contribution (Delta H) we herein describe a rational peptide cyclization strategy to minimize unfavorable entropy penalty (Delta S) upon the binding of Nrf2-derived linear peptides to Keap1. Crystal structure analysis impart that the native active conformations of DLG and ETG peptides bound with Keap1 are folded into U-shape and hairpin configurations, respectively, and adopt their turning head to insert into the central hole of Keap1. Here, cyclization is designed by adding a disulfide bond across the two arms of DLG U-shape or ETG hairpin, which would not influence the direct intermolecular interaction between Keap1 and peptide as well as desolvation effect involved in the interaction, but can effectively constrain the conformational flexibility and disorder of the two peptides in free state, thus largely minimizing entropy penalty upon the binding. Both free energy calculation and binding affinity assay substantiate that the cyclization, as might be expected, can moderately or considerably enhance peptide binding potency to Keap1, with affinity (dissociation constant K-d) increase by 1.4-7.5-fold for designed cyclic peptides relative to their linear counterparts.