Accelerated discovery of cell-active SARS-CoV-2 polymerase inhibitors via molecular dynamic guided screening and optimization

项目摘要 意义：SARS-CoV-2病毒在全球范围内的传播已导致超过2000万人 新冠肺炎确诊人间病例和730,000人死亡，病例继续激增 目前还没有广泛可用的疫苗或其他治疗方法来缓解 社区传播。这种病毒不仅影响了人类的健康，而且还威胁到 国家安全、经济稳定和教育。 广泛的、长期的目标：本提案中描述的研究目标将 SARS-CoV-2病毒聚合酶小分子非核苷类抑制剂的筛选 将作为未来开发和临床评估的先导化合物的酶 瞄准新冠肺炎疾病。 具体目标/前提：建议的目标旨在评估是否有效、细胞透过性、 非核/侧基的SARS-CoV-2RNA聚合酶抑制剂可以用以下方法发现 一个综合的药物发现流水线。具体地说，我们假设一个高效、动态的 计算机筛选方法将显示所需的命中率，这些命中率将在抗病毒检测中得到验证 以显示目标参与度和细胞效能。进一步，药物化学优化将 调整HITS的活动和属性配置文件，使其适合在我们的 建立新冠肺炎K18 hACE2小鼠模型。 研究设计和方法：目标1将识别具有竞争力的非核型/侧翼SARS-CoV-2 RdRp抑制剂来自战略选择的化合物集合，使用高效的硅胶 Baudry和Smith博士开发和使用的筛查方法。点击率将进行排名 通过结合能并选择在Jonsson的实验室中使用已建立的 细胞SARS-CoV-2检测，以及验证活性部位抑制的二次检测 病毒聚合酶。金牌实验室将领导HIT验证工作，并推动符合以下条件的HIT 为目标2定义的标准。后一个目标将通过以下方式确定特定支架的优先顺序并进行评估 药物化学优化(金实验室)，以一次和二次分析为指导， 计算模型和分级ADME和药代动力学分析，以提炼化合物 适合于在Jonsson实验室进行体内疗效评估的活动配置文件。

Project Summary Significance: Worldwide spread of the SARS-CoV-2 virus has resulted in over 20 million confirmed human cases and 730,000 deaths from COVID-19, and cases continue to surge as there is no approved vaccine or other therapeutic modality broadly available to mitigate community spread. The virus has not only impacted human health but has also threatened national security, economic stability, and education. Broad, long term objectives: The research objectives described in this proposal will afford vetted, small molecule non-nucleoside-based inhibitors of the SARS-CoV-2 viral polymerase enzyme that will serve as lead compounds for future development and clinical evaluation targeting COVID-19 disease. Specific Aims/premise: The proposed aims are constructed to evaluate if potent, cell permeable, non-nucleot/side-based inhibitors of the SARS-CoV-2 RNA polymerase can be discovered using an integrated drug discovery pipeline. Specifically, we hypothesize that a highly efficient, dynamic computational screening method will reveal desirable hits that will be validated in antiviral assays to show target engagement and cellular efficacy. Further, medicinal chemistry optimization will tune the activity and property profiles of hits to make them suitable for evaluation in our established COVID-19 K18 hACE2 mouse models. Research design and methods: Aim 1 will identify competitive non-nucleot/side SARS-CoV-2 RdRp inhibitors from a strategically chosen compound collection using an efficient in silico screening approach developed and employed by Drs. Baudry and Smith. The hits will be ranked by binding energies and selected for confirmatory activity in the Jonsson’s lab using established cellular SARS-CoV-2 assays, along with secondary assays that validate active site inhibition of the viral polymerase. The Golden lab will lead hit validation efforts and advance hits that meet defined criteria to Aim 2. The latter aim will prioritize and evaluate specific scaffolds by medicinal chemistry optimization (Golden lab), guided by the primary and secondary assays, computational models and tiered ADME and pharmacokinetic analyses, to refine compound activity profiles that are suitable for in vivo efficacy assessments performed in the Jonsson lab.