Development of Bio-inspired Synthetic Metallohydrolases Based on Theoretical Insights

基于理论洞察力的仿生合成金属水解酶的发展通过与水反应，打破多肽(小蛋白)和其他生物重要分子中的化学键是很重要的。这种被称为水解的反应在广泛的生物、生物技术和工业应用中起着至关重要的作用。大自然设计了一种被称为金属水解酶的高度专业化的酶来实现这些反应。然而，大多数天然酶只能在特定条件下发挥作用。开发高效、环保和经济的模拟天然酶的分子是非常可取的。它们的设计和合成是一个具有挑战性的研究课题，需要跨学科的合作。在这个项目中，迈阿密大学的Prabhakar教授正在发展对水解的基本理解，并将其应用于合成金属水解酶的设计。这项研究将这些过程中涉及的基本化学反应与潜在的生物、生物技术和工业应用联系起来。普拉巴卡尔博士还为高中和本科阶段的少数群体成员提供教育和研究机会。这些外展活动包括迈阿密-戴德县公立学校的荣誉和高管实习计划(HEIP)、美国化学协会的SEED项目(为经济困难的人提供暑期体验)、夏季讲习班(CATCH：高中计算和理论化学)和高中研究通讯(HRN)。此外，本科生正在通过两门专业课和一个暑期研究项目进行研究。在化学系化学催化项目的资助下，迈阿密大学的Rajeev Prabhakar教授正在推导肽(-(O=)C-NH-)和磷酸酯((O=)(RO)(RO)(P-O-R))水解的指导原则，以开发高效的仿生合成金属水解酶。与天然酶相比，这些类似物可能具有以下优点：(1)价格低廉，可回收利用；(2)体积更小，空间限制很少或没有空间限制；(3)特定功能可调。然而，它们的发展所需的关键结构和机械信息不能通过现有的实验技术轻易获得。本研究将分子动力学、量子力学(QM)和混合量子力学/分子力学(QM/MM)等几种最新的理论和计算化学技术与实验相结合，首先推导出多肽和磷酸酯水解的指导原理，然后将其应用于设计廉价、环保、高效、特异和催化的类似物。这些计算也验证了不同的密度泛函理论(DFT)泛函、力场参数以及混合QM/MM和QM/QM/MM方法对金属水解酶及其合成类似物的机械和电子嵌入方案的适用性。为了支持该项目的更广泛影响，Prabhakar博士正在通过迈阿密-戴德县公立学校的荣誉和高管实习计划(HEIP)、美国化学协会的SEED项目(面向经济弱势群体的暑期体验)、名为CATCH-计算和理论化学的高中暑期讲习班和高中研究通讯(HRN)，积极培训和吸引来自社会经济和教育困难家庭的当代和未来一代研究生、本科生和高中生。这些本科生参与了由国家科学基金会和迈阿密大学现有的暑期项目和专业课程支持的研究。

Development of Bio-inspired Synthetic Metallohydrolases Based on Theoretical Insights The breaking of chemical bonds in peptides (small proteins) and other biologically-important molecules by reaction with water is important. This reaction, known as hydrolysis, plays a critical role in a wide range of biological, biotechnological, and industrial applications. Nature has devised highly specialized enzymes known as metallohydrolases to enable these reactions. However, most of the natural enzymes work only under specific conditions. The development of efficient, environmentally-friendly, and economical molecules that mimic the natural enzymes is highly desirable. Their design and synthesis is challenging topic of research that requires interdisciplinary cooperation. In this project, Professor Prabhakar, University of Miami, is developing a fundamental understanding of hydrolysis and applying it to the design of synthetic metallohydrolases. This research links the basic chemical reactions involved in these processes to potential biological, biotechnological, and industrial applications. Dr. Prabhakar is also providing educational and research opportunities to members of minority groups at the high school and undergraduate levels. These outreach activities include the Honors and Executive Internship Program (HEIP) of the Miami-Dade County Public Schools, the American Chemical Society's Project SEED (Summer Experiences for the Economically Disadvantaged), a summer workshop (CATCH: Computational and Theoretical Chemistry for High School) and a High School Research Newsletter (HRN). Additionally, undergraduate students are conducting research through two specialized courses and a summer research program. With funding from the Chemical Catalysis Program of the Chemistry Division, Professor Rajeev Prabhakar of the University of Miami is deriving guiding principles of peptide (-(O=)C-NH-) and phosphoester ((O=)(RO)(RO)(P-O-R)) hydrolysis for the development of efficient bio-inspired synthetic metallohydrolases. These analogues are likely to offer the following advantages over natural enzymes: (1) inexpensive and recyclable, (2) smaller in size with little or no steric constraints, and (3) tunable for specific functions. However, the critical structural and mechanistic information required for their development cannot be readily obtained through existing experimental techniques. In this research, several state-of-the-art theoretical and computational chemistry techniques involving molecular dynamics, quantum mechanics (QM) and hybrid quantum mechanics/molecular mechanics (QM/MM) are integrated with experiments to first derive the guiding principles of peptide and phosphoester hydrolysis and then apply them to design inexpensive, environment friendly, efficient, specific, and catalytic analogues. These calculations are also validating the applicability of different Density Functional Theory (DFT) functionals, force field parameters, and hybrid QM/MM and QM/QM/MM methods with mechanical and electronic embedding schemes on metallohydrolases and their synthetic analogues. In support of the broader impacts of the project, Dr. Prabhakar is actively training and engaging current and future generations of students at the graduate, undergraduate and high school levels from socio-economically- and educationally-disadvantaged families through the Honors and Executive Internship Program (HEIP) of Miami-Dade County Public Schools, the American Chemical Society's Project SEED (Summer Experiences for the Economically Disadvantaged), a summer workshop called CATCH-Computational and Theoretical Chemistry for High School and a High School Research Newsletter (HRN). The undergraduate students are involved in research supported by the NSF and an existing summer program and specialized courses at the University of Miami.