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，提高了评估氯和二氧化氯等化学氧化剂等消毒剂灭活病毒效果的必要性。基于培养的方法是目前追踪消毒前后感染病毒水平的金标准方法。然而，许多病毒是不可培养的，或者是太危险而不能培养的，因此它们被化学氧化剂灭活的机制尚不清楚。该项目的总体目标是调查和揭示在化学氧化剂（如氯和二氧化氯）灭活病毒过程中发生的病毒蛋白质的基本反应和结构变化。为了推进这一目标，首席研究员（PI）提出将高通量和高灵敏度的蛋白质组学分析、结构分析和数据挖掘相结合，以验证氧化剂对病毒失活是由病毒蛋白质的衰变驱动的假设，以及病毒肽的衰变速率常数是肽序列中易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通过对病毒对消毒剂易感性的机制理解而造福社会，这将为公众和水务公司提供指导，以选择最有效的化学氧化剂和消毒剂剂量来灭活水传播病毒，同时最大限度地减少有毒消毒副产物的形成。通过学生教育和培训，包括在布法罗大学指导一名研究生，将为社会带来额外的好处。病毒颗粒由单个基因组分子组成，由蛋白质衣壳和/或脂质包膜包围。病毒基因组和蛋白质携带各种对病毒感染至关重要的生物学功能。先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的降解，与病毒传染性的丧失相对应。然而，对化学氧化剂灭活病毒的机制的基本理解仍然是难以捉摸的。为了解决这一关键的知识缺口，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学分析、结构分析和数据挖掘结合起来，研究和揭示化学消毒剂氧化病毒蛋白的机制。本研究的具体目标是：(1)表征化学氧化剂对病毒蛋白质的降解，并确定以氯和二氧化氯作为模型消毒剂驱动病毒灭活的病毒肽的结构特征；(2)评价氧化修饰和多肽裂解对病毒蛋白构象变化的影响；(3)评价脂质对氧化分子的渗透性对包膜水传播病毒灭活的程度和速率的影响。这项研究的成功完成具有变革性影响的潜力，通过开发和验证一个新模型，该模型可以预测病毒被氧化剂处理时病毒蛋白的衰变动力学，并有助于确定控制病毒对消毒剂易感性或抗性的病毒蛋白的生物分子特征。为了实施该项目的教育和推广活动，PI计划将这项研究的结果纳入布法罗大学（UB）的本科和研究生课程。此外，PI建议利用UB路易斯斯托克斯联盟少数民族参与（LSAMP）暑期研究实习计划，从代表性不足的群体招募两名本科生，将在该项目上工作。该奖项反映了美国国家科学基金会的法定使命，并通过使用基金会的知识价值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.