Developing Broad-Spectrum Antivirals Targeting Coronavirus Replicase and Helicase

摘要 严重急性呼吸综合征冠状病毒2（SARS-CoV-2），COVID-19的病原体， 在美国有超过70万人死亡，在全球有超过480万人死亡。这场流行病真正的公共卫生， 经济和社会代价继续扩大。疫苗接种率不足，再加上不断的演变， 关注的SARS-CoV-2变体（VOC）在未接种疫苗和接种疫苗的人群中引发了COVID-19浪潮 组我们领导了两种COVID-19抗病毒疗法的IND临床前研究：FDA批准了 静脉注射药物remdesivir和口服抗病毒药物molnupiravir，目前处于3期临床试验。对于COVID- 19和未来新出现的CoV流行，我们需要多种口服广泛活性的抗病毒药物， 作用机制，以稳健地抑制病毒复制，并最大限度地减少门诊患者的耐药性。 在这里，在READDI-AC项目的项目2中，我们利用数十年的药物发现，药物化学， 生物化学，酶学和冠状病毒学专业知识，用于鉴定，验证，优化和 靶向保守的CoV RNA依赖性RNA的新型小分子抗病毒药物的临床前评价 聚合酶（RdRp，nsp 12）和解旋酶（Hel，nsp 13）。与READDI-AC核心实验室一起， 制药领导者武田和Chimerix，我们阐述了药物发现和开发的平台， 具体目的如下：1）鉴定和验证针对SARS-CoV-2 RdRp和解旋酶的小分子 活性和变构位点，使用多种互补方法进行发现（例如，基于片段的，DNA- 编码文库、小分子酶测定和基于细胞的抗病毒筛选）。由于RdRp是一种经过验证的药物， 早期发现工作优先考虑Hel。经过验证的生化检测和基于细胞的抗病毒检测 命中发现和迭代结构活性关系（SAR）研究，以改进和理解活性。 我们使用"Fleximer"药物化学从现有的核苷类似物（例如， Molnupiravir）和/或优化来自筛选工作的命中。最优秀的候选人将被评估和向下选择 基于原代培养系统中的抗病毒性能。2)药物化学将命中转化为线索， 迭代SAR研究。对于每种先导化合物，抗病毒活性的广度、作用机制和耐药性是 在生物化学和病毒学测定中确定。3)我们与行业合作伙伴合作，优化销售线索 用于在急性和慢性炎症的稳健模型中进行药代动力学、安全性和临床前疗效研究的候选药物， 慢性COVID-19疾病。我们目前手头有来自武田、Chimerix、Pardes和学术界的五个线索 在体内测试的合作者。项目2将提供全面的IND支持临床前数据包 成功的RdRp和Hel分子定位于人体试验。

ABSTRACT Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiologic agent of COVID-19 has caused over 700,000 deaths in the U.S. and over 4.8 million deaths worldwide. The pandemic’s true public health, economic and social cost continues to expand. Inadequate vaccination rates coupled with the perpetual evolution of SARS-CoV-2 variants of concern (VOCs) have fueled waves COVID-19 in unvaccinated and vaccinated groups. We led IND-enabling preclinical studies for two COVID-19 antiviral therapies: the FDA approved intravenous drug remdesivir and the oral antiviral, molnupiravir, which is now in Phase 3 clinical trial. For COVID- 19 and future emerging CoV epidemics, we need multiple oral broadly-active antivirals with disparate mechanisms of action to robustly inhibit virus replication and minimize the potential for resistance in outpatients. Here, in Project 2 of the READDI-AC program, we leverage decades of drug discovery, medicinal chemistry, biochemistry, enzymology and coronavirology expertise for the identification, validation, optimization and preclinical evaluation of novel small molecule antivirals targeting the conserved CoV RNA-dependent RNA polymerase (RdRp, nsp12) and helicase (Hel, nsp13). Together with the READDI-AC Core Labs and pharmaceutical leaders Takeda and Chimerix we articulate a platform for drug discovery and development in the following Specific Aims: 1) Identify and validate small molecules targeting SARS-CoV-2 RdRp and Helicase active and allosteric sites using multiple complementary approaches for discovery (e.g. fragment based, DNA- encoded library, small molecule enzymatic assay, and cell-based antiviral screens). As RdRp is a validated drug target, early discovery efforts prioritize Hel. Validated biochemical assays and cell-based antiviral assays drive hit discovery and iterative structure activity relationship (SAR) studies to improve upon and understand activity. We use “Fleximer” medicinal chemistry to generate new chemical matter from existing nucleoside analogs (e.g. Molnupiravir) and/or optimize hits from screening efforts. Top candidates will be evaluated and down selected based on antiviral performance in primary culture systems. 2) Medicinal chemistry transforms hits into leads in iterative SAR studies. For each lead, the breadth of antiviral activity, mechanism of action and resistance are determined in both biochemical and virologic assays. 3) We collaborate with industry partners to optimize leads into drug candidates for pharmacokinetic, safety and preclinical efficacy studies in robust models of acute and chronic COVID-19 disease. We have five leads currently in hand from Takeda, Chimerix, Pardes and academic collaborators for in vivo testing. Project 2 will provide a comprehensive IND-enabling preclinical data package for successful RdRp and Hel molecules positioning them for human trials.