MSD International, 8 Biomedical Grove, #04-01/05 Neuros Building, Singapore 138665, Singapore.
p53Lab, Agency for Science, Technology and Research (A*STAR), 8A Biomedical Grove, #06-04/05 Neuros/Immunos, Singapore 138648, Singapore.
Molecules. 2019 Jun 20;24(12):2292. doi: 10.3390/molecules24122292.
Stapled α-helical peptides represent an emerging superclass of macrocyclic molecules with drug-like properties, including high-affinity target binding, protease resistance, and membrane permeability. As a model system for probing the chemical space available for optimizing these properties, we focused on dual Mdm2/MdmX antagonist stapled peptides related to the p53 N-terminus. Specifically, we first generated a library of ATSP-7041 (Chang et al., 2013) analogs iteratively modified by L-Ala and D-amino acids. Single L-Ala substitutions beyond the Mdm2/(X) binding interfacial residues (i.e., Phe, Trp, and Cba) had minimal effects on target binding, α-helical content, and cellular activity. Similar binding affinities and cellular activities were noted at non-interfacial positions when the template residues were substituted with their d-amino acid counterparts, despite the fact that d-amino acid residues typically 'break' right-handed α-helices. d-amino acid substitutions at the interfacial residues Phe and Cba resulted in the expected decreases in binding affinity and cellular activity. Surprisingly, substitution at the remaining interfacial position with its d-amino acid equivalent (i.e., Trp to d-Trp) was fully tolerated, both in terms of its binding affinity and cellular activity. An X-ray structure of the d-Trp-modified peptide was determined and revealed that the indole side chain was able to interact optimally with its Mdm2 binding site by a slight global re-orientation of the stapled peptide. To further investigate the comparative effects of d-amino acid substitutions we used linear analogs of ATSP-7041, where we replaced the stapling amino acids by Aib (i.e., 8 to Aib and 5 to Aib) to retain the helix-inducing properties of α-methylation. The resultant analog sequence Ac-Leu-Thr-Phe-Aib-Glu-Tyr-Trp-Gln-Leu-Cba-Aib-Ser-Ala-Ala-NH exhibited high-affinity target binding (Mdm2 K = 43 nM) and significant α-helicity in circular dichroism studies. Relative to this linear ATSP-7041 analog, several d-amino acid substitutions at Mdm2(X) non-binding residues (e.g., d-Glu, d-Gln, and d-Leu) demonstrated decreased binding and α-helicity. Importantly, circular dichroism (CD) spectroscopy showed that although helicity was indeed disrupted by d-amino acids in linear versions of our template sequence, stapled molecules tolerated these residues well. Further studies on stapled peptides incorporating N-methylated amino acids, l-Pro, or Gly substitutions showed that despite some positional dependence, these helix-breaking residues were also generally tolerated in terms of secondary structure, binding affinity, and cellular activity. Overall, macrocyclization by hydrocarbon stapling appears to overcome the destabilization of α-helicity by helix breaking residues and, in the specific case of d-Trp-modification, a highly potent ATSP-7041 analog (Mdm2 K = 30 nM; cellular EC = 600 nM) was identified. Our findings provide incentive for future studies to expand the chemical diversity of macrocyclic α-helical peptides (e.g., d-amino acid modifications) to explore their biophysical properties and cellular permeability. Indeed, using the library of 50 peptides generated in this study, a good correlation between cellular permeability and lipophilicity was observed.
订书钉 α-螺旋肽代表了一类新兴的大环分子,具有类似药物的特性,包括与靶标高亲和力结合、抗蛋白酶和膜通透性。作为探索这些特性可优化的化学空间的模型系统,我们专注于与 p53 N 端相关的双重 Mdm2/MdmX 拮抗剂订书钉肽。具体来说,我们首先通过 L-丙氨酸和 D-氨基酸迭代生成了 ATSP-7041(Chang 等人,2013)类似物的文库。在 Mdm2/(X)结合界面残基(即 Phe、Trp 和 Cba)之外进行单个 L-丙氨酸取代对靶标结合、α-螺旋含量和细胞活性几乎没有影响。当模板残基被其 D-氨基酸对应物取代时,在非界面位置也注意到相似的结合亲和力和细胞活性,尽管 D-氨基酸残基通常“破坏”右手α-螺旋。在界面残基 Phe 和 Cba 处进行 D-氨基酸取代会导致结合亲和力和细胞活性预期下降。令人惊讶的是,在剩余的界面位置用其 D-氨基酸等效物(即 Trp 至 d-Trp)进行取代,在结合亲和力和细胞活性方面均完全耐受。对 d-Trp 修饰肽的 X 射线结构进行了测定,结果表明吲哚侧链通过订书钉肽的轻微整体重定向能够与 Mdm2 结合位点最佳相互作用。为了进一步研究 D-氨基酸取代的比较效果,我们使用了 ATSP-7041 的线性类似物,其中我们用 Aib(即 8 位到 Aib 和 5 位到 Aib)取代订书钉氨基酸以保留α-甲基化的诱导螺旋特性。所得类似物序列 Ac-Leu-Thr-Phe-Aib-Glu-Tyr-Trp-Gln-Leu-Cba-Aib-Ser-Ala-Ala-NH 表现出与靶标高亲和力结合(Mdm2 K = 43 nM)和圆二色性研究中的显著α-螺旋性。与这种线性 ATSP-7041 类似物相比,在 Mdm2(X)非结合残基(例如,d-Glu、d-Gln 和 d-Leu)处进行几个 D-氨基酸取代会导致结合和α-螺旋性降低。重要的是,圆二色性(CD)光谱表明,尽管我们模板序列的线性版本中的 D-氨基酸确实破坏了螺旋性,但订书钉分子很好地耐受了这些残基。进一步研究包含 N-甲基化氨基酸、l-Pro 或 Gly 取代的订书钉肽表明,尽管存在一些位置依赖性,但这些破坏螺旋的残基在二级结构、结合亲和力和细胞活性方面通常也能耐受。总体而言,通过烃订书钉进行大环化似乎克服了由螺旋破坏残基引起的α-螺旋不稳定性,并且在 d-Trp 修饰的特定情况下,鉴定出了非常有效的 ATSP-7041 类似物(Mdm2 K = 30 nM;细胞 EC = 600 nM)。我们的发现为未来进一步研究扩展大环α-螺旋肽的化学多样性(例如,D-氨基酸修饰)提供了动力,以探索它们的生物物理特性和细胞通透性。事实上,使用本研究中生成的 50 个肽文库,可以观察到细胞通透性和疏水性之间的良好相关性。