CDK9（细胞周期蛋白依赖性激酶 9）在许多病理状况中发挥着重要作用，例如 HIV-1 感染和癌症。 CDK9 和细胞周期蛋白 T1 之间的相互作用对于维持激酶的活性状态至关重要。因此，针对这种蛋白质-蛋白质相互作用提供了一种有前途的抑制 CDK9 的策略。在本研究中，我们旨在设计和表征基于细胞周期蛋白 T1 与 CDK9 结合区域的突变肽库。使用Osprey软件，总共生成了7,776个突变肽。经过全面分析，三种肽，即 mp3 (RAADVEGQRKRRE)、mp20 (RAATVEGQRKRRE) 和 mp29 (RAADVEGQDKRRE)，被确定为有前途的抑制剂，它们具有高亲和力与 CDK9 结合的能力，并表现出较低的自由结合能。这些肽表现出良好的安全性并表现出有前途的动态行为。值得注意的是，我们的研究结果表明 mp3 和 mp29 肽与 CDK9 中的保守序列（残基 60-66）相互作用。此外，通过设计质粒载体pET28a（）中潜在肽的结构，我们已经能够为未来研究中在大肠杆菌表达系统中促进其重组生产过程铺平道路。预测表明过度表达后具有良好的溶解度，进一步支持了它们下游应用的潜力。虽然这些结果证明了设计的肽作为高亲和力 CDK9 阻断剂的前景，但仍需要进行额外的实验研究来验证其生物活性并评估其选择性。此类研究将为了解其治疗潜力提供有价值的见解，并为未来开发针对 CDK9-细胞周期蛋白 T1 复合物的肽抑制剂铺平道路。版权所有 © 2024 Taghizadeh、Taherishirazi、Niazi、Afsharifar 和 Moghadam。

CDK9 (cyclin-dependent kinase 9) plays a significant role in numerous pathological conditions, such as HIV-1 infection and cancer. The interaction between CDK9 and cyclin T1 is crucial for maintaining the kinase's active state. Therefore, targeting this protein-protein interaction offers a promising strategy for inhibiting CDK9. In this study, we aimed to design and characterize a library of mutant peptides based on the binding region of cyclin T1 to CDK9. Using Osprey software, a total of 7,776 mutant peptides were generated. After conducting a comprehensive analysis, three peptides, namely, mp3 (RAADVEGQRKRRE), mp20 (RAATVEGQRKRRE), and mp29 (RAADVEGQDKRRE), were identified as promising inhibitors that possess the ability to bind to CDK9 with high affinity and exhibit low free binding energy. These peptides exhibited favorable safety profiles and displayed promising dynamic behaviors. Notably, our findings revealed that the mp3 and mp29 peptides interacted with a conserved sequence in CDK9 (residues 60-66). In addition, by designing the structure of potential peptides in the plasmid vector pET28a (+), we have been able to pave the way for facilitating the process of their recombinant production in an Escherichia coli expression system in future studies. Predictions indicated good solubility upon overexpression, further supporting their potential for downstream applications. While these results demonstrate the promise of the designed peptides as blockers of CDK9 with high affinity, additional experimental studies are required to validate their biological activity and assess their selectivity. Such investigations will provide valuable insights into their therapeutic potential and pave the way for the future development of peptide-based inhibitors targeting the CDK9-cyclin T1 complex.Copyright © 2024 Taghizadeh, Taherishirazi, Niazi, Afsharifar and Moghadam.