Development of Bio-Inspired Synthetic Metallopeptidases: Insight from Theoretical Studies

来自迈阿密大学的Rajeev Prabhakar教授将利用理论和计算化学技术推导肽水解的指导原则，并将其应用于开发高效的生物合成金属肽酶。选择性水解肽和蛋白质的极其稳定的肽或酰胺键（-(O=)C-NH-）在广泛的生物，生物技术和工业应用中起着关键作用。大量的实验数据表明，对金属离子或金属中心的配体（直接或间接）进行修饰可以显著改变肽水解的催化效率。方法是首先了解金属及其配体的单核和双核金属中心含酶及其现有的合成类似物在其功能中的作用。这些知识将用于修饰金属和配体，并与我们的合作者进行的实验严格结合，以设计下一代高效的合成金属肽酶。与天然酶和合成试剂相比，这些类似物具有以下优点：(1)价格便宜，可以回收利用；(2)体积较小，几乎没有空间限制；(3)可以在末端或内部切割蛋白质；(4)它们的性质可以针对特定应用进行调整，如蛋白质工程、蛋白质组学和治疗学。计算还将验证不同密度泛函理论（DFT）泛函、力场参数、混合量子力学（QM）和分子力学（MM）如QM/MM和QM/QM/MM方法以及机械和电子嵌入方案在含过渡金属配合物上的适用性。本项目开发的合成金属肽酶对社会的潜在优势包括节约能源、水和原料以及治疗，这对能源依赖、环境保护和健康至关重要。该项目还在培训方面产生了重大的广泛影响，并使当前和未来的研究生、本科生和高中学生全年参与其中。特别是，它将吸引来自社会经济和教育劣势家庭的有才华的学生来推进理论化学的研究。高中学生将通过迈阿密-戴德县公立学校的荣誉和行政实习计划（HEIP），美国化学学会（ACS）项目SEED（经济弱势群体暑期体验）和PI设计的一个名为“catch -高中计算和理论化学”的暑期研讨会参与研究。本科学生将通过美国国家科学基金会的支持和两门专业课程和一个暑期研究项目提供研究机会。

With this award from the Chemical Catalysis Program of the Chemistry Division, Professor Rajeev Prabhakar from the University of Miami will utilize theoretical and computational chemistry techniques to derive guiding principles of peptide hydrolysis and apply them for the development of efficient bio-inspired synthetic metallopeptidases. The selective hydrolysis of the extremely stable peptide or amide bond (-(O=)C-NH-) of peptides and proteins plays a critical role in a wide range of biological, biotechnological and industrial applications. A wealth of experimental data indicates that remarkable changes in catalytic efficiency can be attained in peptide hydrolysis with modifications in the metal ions or the ligands (direct and indirect) of the metal centers. The approach is to first understand the roles of metal(s) and ligands of mono- and binuclear metal center containing enzymes and their existing synthetic analogues in their functioning. This knowledge will then be used to modify metal(s) and ligands and rigorously integrated with experiments performed by our collaborators to design the next generation of efficient synthetic metallopeptidases. These analogues can offer the following advantages over natural enzymes and synthetic reagents: (1) they are inexpensive and may be recyclable, (2) being smaller in size they impose little or no steric constraints, (3) they can cleave proteins either terminally or internally, and (4) their properties can be tuned for specific applications such as protein engineering, proteomics and therapeutics. The calculations will also validate the applicability of different density functional theory (DFT) functionals, force field parameters, hybrid quantum mechanics(QM) and molecular mechanics (MM) such as QM/MM and QM/QM/MM methods and mechanical and electronic embedding schemes on the transition metal containing complexes. The potential advantages to society offered by the synthetic metallopeptidases developed in this project include energy, water and raw material conservation and therapeutics, which are critical to energy reliance, environmental protection and health. This project also has a significant broader impact in terms of training and involving current and future generations of students at the graduate, undergraduate and high school levels throughout the year. In particular, it will engage talented students from socio-economic and educationally disadvantaged families to advance research in theoretical chemistry. The high school students will be engaged in research through the Honors and Executive Internship Program (HEIP) of the Miami-Dade County Public Schools, the American Chemical Society's (ACS) Project SEED (Summer Experiences for the Economically Disadvantaged) and a summer workshop to be designed by the PI called CATCH-Computational and Theoretical Chemistry for High School. The undergraduate students will be provided research opportunities through NSF support and two specialized courses and a summer research program offered in the department.