Developing Cyclopentadiene as a Reagent in Bioorthogonal Chemistry

项目总结/摘要 生物正交反应是能够改变和可视化生物过程的强大工具。 因此，将有机反应发展为生物正交反应的能力具有提高的潜力 生物医药尽管许多有机反应已经以生物正交的方式应用，但大多数反应都是在生物反应中进行的。 由于试剂的合成可及性、水溶性或化学稳定性差，或由于反应缓慢， 反应速率一个计算指导的合理设计方法将被用来提高效用和 基于环戊二烯的生物正交反应的可访问性，最终使其成为高效工具 用于生物系统中。 拟议研究的目标是开发基于环戊二烯的生物正交反应， 评价反应性和稳定性的计算机筛选程序。首先，最先进的计算 提供精确活化能的方法将用于评价环戊二烯的反应性 与已知的生物正交的2π环粘连蛋白。第二，计算得到具有合适反应的环戊二烯 将合成通过计算筛选的动力学（在室温下在水中k > 1 M-1 s-1）， 作为反应物进行实验评估。第三，这些环戊二烯的稳定性将在以下条件下评估： 生理条件。最后，从前三个目标中出现的环己烯将被用于一个 在细胞实验中检测活的人类细胞内DNA的新生生物合成。 这项工作将由麻省理工学院的Raines小组进行。雷恩斯小组解决了化学问题 和生物学三十年，并拥有所有必要的设施，进行计算，化学， 和生物学方面的研究。

PROJECT SUMMARY/ABSTRACT Bioorthogonal reactions are powerful tools capable of altering and visualizing biological processes. Accordingly, the ability to develop organic reactions into bioorthogonal reactions has the potential to advance biomedicine. Although a number of organic reactions have been applied in a bioorthogonal manner, most are limited by the poor synthetic accessibility, aqueous solubility, or chemical stability of reagents, or by slow reaction rates. A computationally guided rational design approach will be used to improve the utility and accessibility of cyclopentadiene-based bioorthogonal reactions, ultimately making them a highly efficient tool for applications in biological systems. The goal of the proposed research is to develop cyclopentadiene-based bioorthogonal reactions based upon an in silico screening procedure that evaluates reactivity and stability. First, state-of-the-art computational methods that provide accurate activation energies will be used to evaluate the reactivity of cyclopentadienes with known bioorthogonal 2π cycloaddends. Second, the cyclopentadienes calculated to have suitable reaction kinetics (k > 1 M–1s–1 at room temperature in water) by computational screening will be synthesized and evaluated experimentally as reactants. Third, the stability of these cyclopentadienes will be assessed under physiological conditions. Finally, the cyclopentadienes that emerge from the first three aims will be used in an in cellulo experiment to detect the nascent biosynthesis of DNA within living human cells. This work will be carried out in the Raines group at MIT. The Raines group has solved problems in chemistry and biology for three decades and has all of the facilities necessary to carry out the computational, chemical, and biological aspects of the proposed research.