Targeting SARS-CoV-2 PLpro for COVID-19 treatment

摘要 由新型严重急性呼吸系统综合征冠状病毒2型引起的COVID-19大流行 （SARS-CoV-2）给人类带来了深刻的社会经济挑战。抗病毒剂 阻断SARS-CoV-2病毒复制，补充疫苗接种，迫切需要停止 目前的流行病，并避免潜在的未来爆发。木瓜蛋白酶样蛋白酶（PLpro）， 一种调节病毒复制和宿主免疫感应的必需半胱氨酸蛋白酶， 有希望的抗SARS-CoV-2的抗病毒靶点。然而，快速发展的有效PLpro 抑制剂已经被活性位点上有限的可药物相互作用所阻碍， 具有甘氨酸识别的P1和P2位点。为了应对这些挑战，我们调查了 使用结构导向设计和X射线， 结晶学这些努力导致了一系列基于2-苯基噻吩的抑制剂， 纳摩尔效力。晶体结构显示，这些有效的SARS-CoV-2 PLpro抑制剂 与一个新的配体结合位点，“BL 2沟”，导致更慢的解离速率，改善 结合亲和力，和低微摩尔抗病毒效力在SARS-CoV-2感染的人类细胞。 此外，这些抑制剂显示出良好的微粒体稳定性和体内暴露后， 腹膜内（IP）施用。基于这些令人鼓舞的初步数据，我们建议在 本项目旨在进一步优化和开发这些新型PLpro抑制剂，以实现体内抗病毒 功效我们提出：目的1）优化我们的铅PLpro抑制剂，以提高效力和药物- 使用结构导向设计的相似性质;目的2）评估和分类PLpro抑制剂 基于生化、ADME和抗病毒试验;目的3）评估top 抑制剂并建立体内抗病毒功效。研究的完成将导致小 适合作为治疗SARS-CoV-2的候选药物开发的分子。

ABSTRACT The COVID-19 pandemic, caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has caused profound socioeconomic challenges for humankind. Antiviral agents blocking SARS-CoV-2 viral replication that complement vaccination are urgently needed to stop the current pandemic and to avoid potential future outbreaks. The papain-like protease (PLpro), an essential cysteine protease that regulates viral replication and host immune sensing, is a promising antiviral target against SARS-CoV-2. However, the rapid development of potent PLpro inhibitors has been hindered by limited draggable interactions at the active site due to restricted P1 and P2 sites with glycine recognition. To address these challenges, we have investigated novel, druggable binding sites, distal to the active site, using structure-guided design and X-ray crystallography. These efforts led to a series of 2-phenylthiophene-based inhibitors with low nanomolar potency. Crystal structures revealed that these potent SARS-CoV-2 PLpro inhibitors engage with a novel ligand-binding site, the “BL2 groove”, leading to slower off-rates, improved binding affinities, and low micromolar antiviral potency in SARS-CoV-2-infected human cells. Moreover, these inhibitors showed good microsomal stability and in vivo exposure after intraperitoneal (IP) administration. Building on these encouraging preliminary data, we propose in this project to further optimize and develop these novel PLpro inhibitors to achieve in vivo antiviral efficacy. We propose: Aim 1) to optimize our lead PLpro inhibitors for improved potency and drug- likeness properties using structure-guided design; Aim 2) to evaluate and triage PLpro inhibitors based on biochemical, ADME, and antiviral assays; Aim 3) to assess the PK/PD profile of top inhibitors and to establish in vivo antiviral efficacy. Completion of the research will lead to small molecules suitable for development as drug candidates to treat SARS-CoV-2.