蛋白质-蛋白质相互作用,或PPI,是每个生物活动的一部分,并与许多疾病有关,包括癌症,传染病,和神经系统疾病。因此,靶向PPI被认为是开发新药物的战略和重要方法.尽管如此,宽而平坦的接触界面使得难以找到小分子PP抑制剂。另一种策略是使用PPI相互作用基序作为设计基于肽的抑制剂的结构单元。在这里,我们设计了12-mer肽抑制剂来靶向p25诱导细胞周期蛋白依赖性激酶(Cdk5)的过度调节,PPI已被证明可以延续神经炎症,这是神经退行性疾病如阿尔茨海默病的主要因果关系之一,帕金森病,和额颞叶痴呆.我们从Cdk5/p25PP界面的相互作用基序中产生了5062500肽组合序列(PCS)的文库。将20个氨基酸分为6组,即,疏水性(脂肪族),芳香,基本的,酸性,独特,极性不带电,根据它们的理化性质。为了保留理想结合所需的相互作用基序,考虑了所有可能的肽序列取代的从头建模。一组过滤器,在支持向量机(SVM)算法的支持下,然后用于创建符合特定生物利用度的入围定制肽库,毒性,和治疗相关性,导致15PCS的精致图书馆。在后续建模研究之前,使用贪婪算法和粗粒度力场来预测肽结构和折叠。进行分子对接以估计相对结合亲和力,在热门歌曲中,与具有实验数据的已知肽抑制剂(模板肽)相比,对Pep15进行分子动力学模拟和结合自由能计算。有趣的是,通过我们的方案确定的肽,发现Pep15显示出比参考模板肽显着更高的结合亲和力(-48.10±0.23kcal/mol和-17.53±0.27kcal/mol,分别)。与模板肽相比,发现Pep15具有更紧凑和掩埋的表面积,更紧密的绑定景观,减少了构象变异性,导致Cdk5/p25复合物的结构和动力学稳定性增强。值得注意的是,发现两种肽抑制剂对Cdk5/p25二级结构的结构完整性影响最小。在这里,我们建议Pep15作为一种新的和潜在的破坏性肽药物,用于Cdk5/p25介导的神经退行性表型,需要进一步的临床研究.本报告的系统方案和发现将作为鉴定关键PPI界面反应残基的有价值的工具,类似物的设计,以及鉴定更有效的基于肽的PPI抑制剂。
Protein-protein interactions, or PPIs, are a part of every biological activity and have been linked to a number of diseases, including cancer, infectious diseases, and neurological disorders. As such, targeting PPIs is considered a strategic and vital approach in the development of new medications. Nonetheless, the wide and flat contact interface makes it difficult to find small-molecule PP inhibitors. An alternative strategy would be to use the PPI interaction motifs as building blocks for the design of peptide-based inhibitors. Herein, we designed 12-mer peptide inhibitors to target p25-inducing-cyclin-dependent kinase (Cdk5) hyperregulation, a PPI that has been shown to perpetuate neuroinflammation, which is one of the major causal implications of neurodegenerative disorders such as Alzheimer\'s disease, Parkinson\'s disease, and frontotemporal dementia. We generated a library of 5 062 500 peptide combination sequences (PCS) derived from the interaction motif of Cdk5/p25 PP interface. The 20 amino acids were differentiated into six groups, namely, hydrophobic (aliphatic), aromatic, basic, acidic, unique, and polar uncharged, on the basis of their physiochemical properties. To preserve the interaction motif necessary for ideal binding, de novo modeling of all possible peptide sequence substitutions was considered. A set of filters, backed by the Support Vector Machine (SVM) algorithm, was then used to create a shortlisted custom peptide library that met specific bioavailability, toxicity, and therapeutic relevance, leading to a refined library of 15 PCS. A greedy algorithm and coarse-grained force field were used to predict peptide structure and folding before subsequent modeling studies. Molecular docking was performed to estimate the relative binding affinities, and out of the top hits, Pep15 was subjected to molecular dynamics simulations and binding free-energy calculations in comparison to a known peptide inhibitor with experimental data (template peptide). Interestingly, the identified peptide through our protocol, Pep15, was found to show a significantly higher binding affinity than the reference template peptide (-48.10 ± 0.23 kcal/mol and -17.53 ± 0.27 kcal/mol, respectively). In comparison to the template peptide, Pep15 was found to possess a more compact and buried surface area, tighter binding landscape, and reduced conformational variability, leading to enhanced structural and kinetic stability of the Cdk5/p25 complex. Notably, both peptide inhibitors were found to have a minimal impact on the architectural integrity of the Cdk5/p25 secondary structure. Herein, we propose Pep15 as a novel and potentially disruptive peptide drug for Cdk5/p25-mediated neurodegenerative phenotypes that require further clinical investigation. The systematic protocol and findings of this report would serve as a valuable tool in the identification of critical PPI interface reactive residues, designing of analogs, and identification of more potent peptide-based PPI inhibitors.