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

通过分子动力学引导筛选和优化加速发现细胞活性 SARS-CoV-2 聚合酶抑制剂

• 批准号: 10238322
• 负责人: Jennifer E. Golden
• 金额: $ 44.25万
• 依托单位: UNIVERSITY OF WISCONSIN-MADISON
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-07-01 至 2024-06-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/10238322
• 关键词: 2019-nCoV; Active Sites; Address; Antiviral Agents; Binding; Biological Assay; COVID-19; COVID-19 assay; COVID-19 mortality; Cells; Collection; Communities; Complex; Computer Models; Crystallization; DNA-Directed RNA Polymerase; Development; Disease; Drug Kinetics; Economics; Education; Emergency Situation; Enzymes; Evaluation; FDA approved; Future; Genome; Health; Health education; High Performance Computing; Human; Injectable; K-18 conjugate; Laboratories; Lead; Ligands; Mediating; Methods; Modality; Molecular; Mutation; National Security; Natural Products; Nonstructural Protein; Outcome; Patients; Permeability; Pharmaceutical Chemistry; Pharmaceutical Preparations; Phosphorylation; Polymerase; Property; Proteins; Proteome; RNA Polymerase Inhibitor; RNA-Directed RNA Polymerase; Recovery; Research; Research Design; Research Methodology; Research Personnel; Resistance; Resources; SARS-CoV-2 inhibitor; Safety; Side; Site; Structure; Supercomputing; Therapeutic; Time; Vaccines; Validation; Viral; Virus; analog; base; design; drug discovery; efficacy evaluation; health economics; in silico; in vivo; inhibitor/antagonist; insight; lead optimization; mortality; mouse model; novel; nucleotide analog; pandemic disease; remdesivir; research clinical testing; scaffold; screening; small molecule; small molecule inhibitor; success; therapeutic target; viral RNA; virtual

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.

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2000万人死亡， 确诊的人类病例和730，000例COVID-19死亡，病例继续激增， 没有批准的疫苗或其他广泛可用的治疗方式来减轻 社区传播。该病毒不仅影响人类健康， 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提供 经审查的SARS-CoV-2病毒聚合酶小分子非核苷类抑制剂 酶将作为先导化合物用于未来的开发和临床评价 针对COVID-19疾病。 具体目的/前提：拟定目的旨在评价是否具有强效、细胞渗透性， SARS-CoV-2 RNA聚合酶的非核苷/核苷基抑制剂可以通过使用 一个完整的药物发现管道。具体来说，我们假设一个高效，动态的 计算机筛选方法将揭示出在抗病毒测定中将被验证的期望命中 以显示目标接合和细胞功效。此外，药物化学优化将 调整热门歌曲的活动和属性配置文件，使其适合在我们的 建立COVID-19 K18 hACE 2小鼠模型。 研究设计和方法：目标1将确定竞争性非核/侧SARS-CoV-2 使用有效的计算机模拟技术从策略性选择的化合物集合中获得RdRp抑制剂 筛选方法由Baudry和Smith博士开发和使用。点击率将被排名 通过结合能，并在Jonsson实验室中使用已建立的 细胞SARS-CoV-2检测，沿着验证活性位点抑制的二级检测， 病毒聚合酶黄金实验室将领导命中验证工作，并推进符合 目标2的标准。后一个目标将优先考虑和评估特定的支架， 药物化学优化（黄金实验室），由一级和二级测定指导， 计算模型和分层ADME和药代动力学分析，以优化化合物 适用于在Jonsson实验室进行的体内功效评估的活性谱。