Developing Cyclopentadiene as a Reagent in Bioorthogonal Chemistry

项目摘要/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，将有机反应发展成生物正交反应的能力有可能取得进展。 生物医学。尽管一些有机反应已经以生物正交的方式应用，但大多数都是 受试剂的合成可及性、水溶度或化学稳定性差的限制，或受反应缓慢的限制 反应速度。将使用计算指导的理性设计方法来提高实用性和 基于环戊二烯的生物正交反应的可及性，最终使其成为一种高效的工具 在生物系统中的应用。 本研究的目标是开发基于环戊二烯的生物正交反应。 一种用于评估反应性和稳定性的计算机筛选程序。第一，最先进的计算技术 提供准确活化能的方法将用于评价环戊二烯的反应性。 具有已知的生物正交环加成物2π。其次，计算出的环戊二烯具有合适的反应 将通过计算筛选合成动力学(k&gt；1M-1s-1在室温水中)并 经实验评估为反应物。第三，这些环戊二烯的稳定性将根据以下条件进行评估 生理条件。最后，从前三个目标中产生的环戊二烯将用于 在细胞实验中检测活着的人类细胞中DNA的新生生物合成。 这项工作将在麻省理工学院的雷恩斯小组中进行。雷恩斯小组已经解决了化学方面的问题 已经有三十年的历史了，并且拥有进行计算、化学、 和生物学方面的拟议研究。

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.