Department of Chemical, Materials and Industrial Production Engineering (DICMaPI), University of Naples Federico II, Piazzale V. Tecchio 80, 80125 Naples, Italy.
Institute of Biostructures and Bioimaging (IBB) - CNR, Via Mezzocannone 16, 80134 Naples, Italy.
Curr Med Chem. 2021;28(24):5004-5015. doi: 10.2174/0929867328666210201152326.
Nucleopeptides are chimeric compounds of biomedical importance carrying DNA nucleobases anchored to peptide backbones with the ascertained capacity to bind nucleic acids. However, their ability to interact with proteins involved in pathologies of social relevance is a feature that still requires investigation. The worrying situation currently observed worldwide for the COVID-19 pandemic urgently requires the research on novel anti-SARSCoV- 2 molecular weapons, whose discovery can be aided by in silico predictive studies.
The aim of this work is to explore by spectroscopic methods novel features of a thymine-bearing nucleopeptide based on L-diaminopropanoic acid, including conformational aspects as well as its ability to bind proteins, starting from bovine serum albumin (BSA) as a model protein. Moreover, in consideration of the importance of targeting viral proteins in the current fight against COVID-19, we evaluated in silico the interaction of the nucleopeptide with some of the most relevant coronavirus protein targets.
First, we investigated via circular dichroism (CD) the conformational behaviour of this thymine-bearing nucleopeptide with temperature: we observed CD spectral changes, particularly passing from 15 to 35 °C. Scanning Electron Microscopy (SEM) analysis of the nucleopeptide was also conducted on nucleopeptide solid samples. Additionally, CD binding and preliminary in silico investigations were performed with BSA as a model protein. Moreover, molecular dockings were run using as targets some of the main SARS-CoV-2 proteins.
The temperature-dependent CD behaviour reflected the three-dimensional rearrangement of the nucleopeptide at different temperatures, with higher exposure to the solvent of its chromophores at higher temperatures compared to a more stacked structure at a low temperature. SEM analysis of nucleopeptide samples in the solid-state showed a granular morphology, with a low roughness and some thread structures. Moreover, we found through spectroscopic studies that the modified peptide bound the albumin target by inducing significant changes to the protein secondary structure.
CD and preliminary in silico studies suggested that the nucleopeptide bound the BSA protein with high affinity according to different binding modes, as testified by binding energy scores lower than -11 kcal/mol. Interestingly, a predictive study performed on 3CLpro and other SARS-CoV-2 protein targets suggested the potential ability of the nucleopeptide to bind with good affinity the main protease of the virus and other relevant targets, including the RNAdependent RNA polymerase, especially when complexed with RNA, the papain-like protease, and the coronavirus helicase at the nucleic acid binding site.
核肽是一类具有重要生物医学意义的嵌合化合物，其 DNA 碱基锚定在肽骨架上，已被证实具有结合核酸的能力。然而，它们与涉及社会相关疾病的蛋白质相互作用的能力是一个仍需要研究的特征。目前，全球范围内对 COVID-19 大流行的担忧情况迫切需要研究新型抗 SARS-CoV-2 分子武器，其发现可以通过计算机预测研究来辅助。
本工作旨在通过光谱方法探索一种基于 L-二氨基丙氨酸的胸腺嘧啶核肽的新特性，包括构象方面以及与蛋白质结合的能力，以牛血清白蛋白（BSA）作为模型蛋白。此外，考虑到在当前抗击 COVID-19 的斗争中靶向病毒蛋白的重要性，我们还通过计算机预测研究评估了该核肽与一些最相关的冠状病毒蛋白靶标的相互作用。
首先，我们通过圆二色性（CD）研究了该胸腺嘧啶核肽的构象行为与温度的关系：我们观察到 CD 光谱的变化，特别是在 15 到 35°C 之间。还对核肽的固态样品进行了扫描电子显微镜（SEM）分析。此外，还进行了 CD 结合和初步的计算机预测研究，以 BSA 作为模型蛋白。此外，使用一些主要的 SARS-CoV-2 蛋白作为靶点进行了分子对接。
温度依赖性 CD 行为反映了核肽在不同温度下的三维重排，与低温时更堆叠的结构相比，其发色团在较高温度下更暴露于溶剂中。固态核肽样品的 SEM 分析显示出颗粒状形态，表面粗糙度低，存在一些线状结构。此外，通过光谱研究发现，修饰后的肽通过诱导蛋白质二级结构的显著变化与白蛋白靶标结合。
CD 和初步的计算机预测研究表明，核肽与 BSA 蛋白具有高亲和力，根据不同的结合模式，结合能评分低于-11 kcal/mol。有趣的是，对 3CLpro 和其他 SARS-CoV-2 蛋白靶标的预测研究表明，核肽具有与病毒主要蛋白酶和其他相关靶标（包括 RNA 依赖性 RNA 聚合酶）结合的潜在能力，特别是与 RNA 复合时，对木瓜蛋白酶样蛋白酶和冠状病毒解旋酶在核酸结合部位的结合具有良好的亲和力。
