Insights into biomolecular reactivity and structure for virus inactivation prediction

SARS-CoV-2及其变种等新病毒的出现和传播增加了评估消毒剂，包括氯和二氧化氯等化学氧化剂对病毒灭活效果的必要性。以培养为基础的方法是目前跟踪消毒前后感染性病毒水平的金标准方法。然而，许多病毒是不能培养的，或者太危险而不能培养，因此它们被化学氧化剂灭活的机制还不是很清楚。该项目的总体目标是调查和揭开病毒蛋白在氯和二氧化氯等化学氧化剂灭活病毒过程中发生的基本反应和结构变化。为了推进这一目标，首席调查员(PI)建议将高通量和高灵敏度的蛋白质组分析、结构分析和数据挖掘相结合，以检验以下假设：病毒被氧化剂灭活是由病毒蛋白质的衰变驱动的，病毒多肽的衰变速率常数是多肽序列中敏感氨基酸残基的溶剂可及性的函数。这一项目的成功完成将使社会受益，因为它建立了对病毒对消毒剂敏感性的机械理解，可以指导公众和自来水公司选择最有效的化学氧化剂和消毒剂剂量来灭活水传播的病毒，同时最大限度地减少有毒消毒副产品的形成。此外，还将通过学生教育和培训，包括指导布法罗大学的一名研究生，为社会带来更多好处。病毒颗粒由单个基因组分子组成，其周围包裹着蛋白质衣壳和/或脂膜。病毒基因组和蛋白质具有多种对病毒感染至关重要的生物功能。以前关于紫外线和化学氧化剂灭活病毒的研究表明，病毒生物大分子的降解，特别是基因组和蛋白质，对应于病毒感染性的丧失。然而，对化学氧化剂灭活病毒的机制的基本了解仍然难以捉摸。为了解决这一关键的知识鸿沟，该项目的首席研究员(PI)建议将高通量和高灵敏度的蛋白质组分析、结构分析和数据挖掘相结合，以调查和揭示化学消毒剂氧化病毒蛋白质的机制。这项研究的具体目标是：(1)表征化学氧化剂对病毒蛋白质的降解，并以氯和二氧化氯为模型消毒剂鉴定驱动病毒灭活的病毒多肽的结构特征；(2)评估氧化修饰和多肽裂解对病毒蛋白质构象变化的影响；以及(3)评估氧化剂分子对脂质的通透性对包膜水媒病毒灭活程度和灭活速度的影响。这项研究的成功完成有可能通过开发和验证一种新的模型来产生变革性的影响，该模型可以预测病毒用氧化剂处理时病毒蛋白质的衰退动力学，并有助于确定控制病毒易感性或对消毒剂的抵抗力的病毒蛋白质的生物分子特征。为了实施该项目的教育和外展活动，国际和平研究所计划将这项研究的结果纳入布法罗大学(UB)的本科生和研究生课程。此外，PI建议利用UB Louis Stokes Alliance for少数群体参与(LSAMP)暑期研究实习计划，从代表不足的群体中招聘两名本科生参与该项目。该奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

The emergence and spread of new viruses such as SARS-CoV-2 and its variants has heightened the need to assess the efficacy of virus inactivation by disinfectants including chemical oxidants such as chlorine and chlorine dioxide. Culture-based approaches are the current gold standard methods to track the levels of infective viruses before and after disinfection. However, many viruses are not culturable, or are too dangerous to be cultured, and thus their mechanisms of inactivation by chemical oxidants are not well understood. The overarching goal of this project is to investigate and unravel the fundamental reactions and structural changes of viral proteins that occur during virus inactivation by chemical oxidants such as chlorine and chlorine dioxide. To advance this goal, the Principal Investigator (PI) propose to integrate high-throughput and high-sensitivity proteomic analysis, structural analysis, and data mining to test the hypothesis that virus inactivation by oxidants is driven by the decay of viral proteins, and the decay rate constants of viral peptides is a function of solvent accessibility of susceptible amino acid residues in the peptide sequences. The successful completion of this project will benefit society through the development of a mechanistic understanding of virus susceptibility to disinfectants that could provide guidance to the public and water utilities regarding the selection of the most efficient chemical oxidants and disinfectant dosages to inactivate waterborne viruses while minimizing the formation of toxic disinfection byproducts. Additional benefits to society will be achieved through student education and training including the mentoring of a graduate student at the University at Buffalo.A virus particle consists of a single molecule of genome, which is surrounded by a protein capsid, and/or lipid envelope. The viral genome and proteins carry various biological functions that are essential for virus infection. Previous studies of virus inactivation by UV and chemical oxidants suggest that the degradation of viral biomacromolecules, particularly the genome and proteins, correspond to the loss of virus infectivity. However, a fundamental understanding of the mechanisms of virus inactivation by chemical oxidants has remained elusive. To address this critical knowledge gap, the Principal Investigator (PI) of this project proposes to integrate high-throughput and high-sensitivity proteomic analysis, structural analysis, and data mining to investigate and unravel the mechanisms of oxidation of viral proteins by chemical disinfectants. The specific objectives of the research are to: (1) Characterize viral protein degradation by chemical oxidants and identify structural features of viral peptides that drive virus inactivation using chlorine and chlorine dioxide as model disinfectants; (2) Evaluate the impacts of oxidative modifications and peptide cleavages on the conformational change of viral proteins; and (3) Evaluate the impacts of lipid permeability to oxidant molecules on the extents and rates of inactivation of enveloped waterborne viruses. The successful completion of this research has the potential for transformative impact through the development and validation of a new model that could predict the decay kinetics of viral proteins when viruses are treated by oxidants and help identify the biomolecular features of viral proteins that control virus susceptibility or resistance to disinfectants. To implement the education and outreach activities of the project, the PI plans to incorporate the findings from this research into undergraduate and graduate courses at the University at Buffalo (UB). In addition, the PI proposes to leverage the UB Louis Stokes Alliance for Minority Participation (LSAMP) Summer Research Internship Program to recruit two undergraduate students from underrepresented groups that will work on the project.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.