RAPID: Undergraduate Research in Modeling and Computation for Discovery of Molecular Probes for SARS-CoV-2 Proteins

RAPID：发现 SARS-CoV-2 蛋白分子探针的建模和计算本科生研究

• 批准号: 2031778
• 负责人: Mary Jo Ondrechen
• 金额: $ 7.28万
• 依托单位: Northeastern University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2020
• 资助国家: 美国
• 起止时间: 2020-05-01 至 2023-04-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2031778&HistoricalAwards=false
• 关键词: RAPID; Undergraduate; Research; Modeling; Computation

This REU Site award to Northeastern University, located in Boston, MA, will support the training of six students for 10 weeks during the summer of 2020. Because of the ongoing COVID-19 pandemic and the recommendation to maintain social distancing, students will virtually contribute to computational research projects focused on COVID-19. The Northeastern University REU Site will recruit a total of six students, primarily from colleges with limited research opportunities or who are from an under-represented group, to be trained in the program. Students will learn how research is conducted and many will present the results of their work at future scientific conferences. Assessment of the program will be done through the online SALG URSSA tool. Students will be tracked after the program in order to determine their career paths. The primary focus of this undergraduate research program will be for the students to learn about and use computational techniques that will be applied to urgent research questions surrounding the functions and control mechanisms of the SARS-CoV-2 proteins. Each student will be trained in some of the following skills: molecular modeling, ligand docking, molecular dynamics simulations, biomolecular electrostatics, and quantum mechanical electronic structure calculations. Students will analyze SARS-CoV-2 proteins and screen libraries of small molecules that can bind to and control these proteins. They will be mentored by three faculty members and six graduate students from the departments of Chemistry and Chemical Biology and Bioengineering at Northeastern University. They will contribute critical new knowledge about how the viral proteins function and how their function may be modulated. The students will also receive professional development training in areas such as research ethics, scientific writing, the graduate school application process, and resume writing. Participants will be selected by the PIs, based on applications consisting of college transcripts, personal statements, and letters of reference. Preference will be given to students who were accepted by another REU program that was subsequently cancelled because of the pandemic. More information about the program is available by contacting PI Dr. Mary Jo Ondrechen ([e-mail]) or co-PIs Dr. Steven Lopez ([e-mail]) and Dr. Mona Minkara ([e-mail]).This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

该REU网站奖授予位于马萨诸塞州波士顿的东北大学，将在2020年夏季支持对六名学生进行为期10周的培训。由于COVID-19大流行正在进行，以及保持社交距离的建议，学生们实际上将为以COVID-19为重点的计算研究项目做出贡献。东北大学REU网站将招募总共六名学生，主要来自研究机会有限的大学或来自代表性不足的群体，以接受该计划的培训。学生将学习如何进行研究，许多人将在未来的科学会议上展示他们的工作成果。该计划的评估将通过在线SALG URSSA工具进行。课程结束后，将对学生进行跟踪，以确定他们的职业道路。这个本科研究项目的主要重点是让学生学习和使用计算技术，这些技术将应用于围绕SARS-CoV-2蛋白的功能和控制机制的紧急研究问题。每个学生都将接受以下技能方面的培训：分子建模、配体对接、分子动力学模拟、生物分子静电学和量子力学电子结构计算。学生们将分析SARS-CoV-2蛋白质，并筛选可以结合和控制这些蛋白质的小分子文库。他们将由东北大学化学与化学生物与生物工程系的三名教员和六名研究生指导。他们将对病毒蛋白如何发挥作用以及如何调节其功能提供重要的新知识。学生们还将在研究伦理、科学写作、研究生申请流程和简历写作等领域接受专业发展培训。参与者将由pi根据由大学成绩单、个人陈述和推荐信组成的申请来选择。被另一个REU项目录取的学生将优先考虑，该项目随后因流感大流行而取消。有关该计划的更多信息，请联系PI Mary Jo Ondrechen博士（[e-mail]）或共同PI Steven Lopez博士（[e-mail]）和Mona Minkara博士（[e-mail]）。该奖项反映了美国国家科学基金会的法定使命，并通过基金会的智力价值和更广泛的影响审查标准进行评估，认为值得支持。

项目成果

Identification and characterization of alternative sites and molecular probes for SARS-CoV-2 target proteins.

• DOI: 10.3389/fchem.2022.1017394
• 发表时间: 2022
• 期刊: Frontiers in chemistry
• 影响因子: 5.5

Machine-Learning Photodynamics Simulations Uncover the Role of Substituent Effects on the Photochemical Formation of Cubanes

• DOI: 10.1021/jacs.1c07725
• 发表时间: 2021-12-08
• 期刊: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
• 影响因子: 15
• 作者: Li, Jingbai;Stein, Rachel;Lopez, Steven A.
• 通讯作者: Lopez, Steven A.

A Theoretical Stereoselectivity Model of Photochemical Denitrogenations of Diazoalkanes Toward Strained 1,3-Dihalogenated Bicyclobutanes

重氮烷光化学脱氮对应变 1,3-二卤双环丁烷的立体选择性理论模型

• DOI: 10.1021/acs.joc.0c02905
• 发表时间: 2021
• 期刊: The Journal of Organic Chemistry
• 作者: Li, Jingbai;Stein, Rachel;Lopez, Steven A.
• 通讯作者: Lopez, Steven A.