从基于形状的片段合并和主动学习来广泛探索SARS-CoV-2宏观域的结构活动关系
Galen J Correy1, Moira Rachman2, Takaya Togo2
1Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94158.
bioRxiv : the preprint server for biology
|September 10, 2024
概括
研究人员开发了虚拟查工具FrankenROCS,以发现新型的SARS-CoV-2巨原体抑制剂. 这种方法确定了有前途的药物,可以改善病毒抑制疗法的膜透性.
科学领域:
- 生物化学 生物化学
- 药物发现 药物发现 药物发现
- 结构生物学 结构生物学
背景情况:
- 在非结构性蛋白3 (NSP3) 中的SARS-CoV-2宏观基因对病毒病原产生至关重要.
- 抑制这种宏观主体是对抗病毒感染的潜在治疗策略.
- 之前基于片段的药物发现工作产生了一种化合物,其优化挑战包括薄膜透性.
研究的目的:
- 开发和应用一个新的基于形状的虚拟选管道,FrankenROCS,用于识别宏域抑制剂.
- 克服以前化合物的局限性,并发现具有改进药物样性质的新抑制剂.
- 为了利用碎片X射线晶体结构以基于结构的药物发现.
主要方法:
- 开发FrankenROCS基于形状的虚拟选管道.
- 对Enamine HTS集合 (210万种化合物) 和Enamine REAL数据库 (22亿个分子) 的选.
- 将FrankenROCS与主动学习算法 (普森抽样) 集成,以实现高效的数据库搜索.
- 用X射线晶体学来确定已识别的抑制剂的结合模式.
主要成果:
- 最初的查发现了强大的宏基因抑制剂,最好的化合物显示IC50为130微米.
- 通过使用主动学习进行进一步的查,产生了IC50值高达220微米的抑制剂.
- 优化工作的结果是,同类产品的IC50值低于10微米.
- X射线结构揭示了抑制剂的多种结合姿势,突出了保存的化学特征,并为基于结构的设计提供了洞察力.
结论:
- 弗兰肯ROCS管道是一个可扩展和有效的方法,用于断片链接和识别新型宏观主体抑制剂.
- 新发现的类似物代表了具有增强膜透性的有前途的系列,适合进一步优化.
- 生成的结构数据为推进针对病毒点的基于结构的药物发现方法提供了宝贵的资源.
相关概念视频
Viral Structure
61.9K
Viruses are extraordinarily diverse in shape and size, but they all have several structural features in common. All viruses have a core that contains a DNA- or RNA-based genome. The core is surrounded by a protective coat of proteins called the capsid. The capsid is composed of subunits called capsomeres. The capsid and genome-containing core are together known as the nucleocapsid.
61.9K
Mechanisms of Membrane Domain Formation
3.0K
Different physical properties of lipids and proteins allow them to localize and form distinct islands or domains in the membrane. Some membrane domains are formed due to protein-protein interactions, whereas others are formed due to the presence of specific lipids such as sphingolipids and sterols—for example, large proteins, such as bacteriorhodopsin, aggregate and create distinct domains.
Another mechanism for membrane domain formation involves membrane proteins interacting with...
Another mechanism for membrane domain formation involves membrane proteins interacting with...
3.0K
Antibody Structure and Classes
852
Antibodies, also known as immunoglobulins, are produced by B cells in response to foreign substances, such as bacteria and viruses. These proteins are critical for recognizing and neutralizing these substances, protecting the body from potential harm.
The basic structure of an antibody consists of four protein chains: two identical heavy chains and two identical light chains. These chains are held together by disulfide bonds and other non-covalent interactions, forming a Y-shaped structure.
The basic structure of an antibody consists of four protein chains: two identical heavy chains and two identical light chains. These chains are held together by disulfide bonds and other non-covalent interactions, forming a Y-shaped structure.
852


