基于Synthon的策略利用分子相似性和蛋白质-连接体相互作用,以有效选超大化学库
Brian Medel-Lacruz1,2, Albert Herrero2, Fernando Martín2
1Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain and Department of Medicine and Life Sciences, Pompeu Fabra University (UPF), 08003 Barcelona, Spain.
Journal of chemical information and modeling
|April 28, 2025
概括
新的基于synthon的虚拟选 (VS) 方法,exaScreen和exaDock,有效地从庞大的化学图书馆中识别药物候选物. 与传统的VS技术相比,这些方法提供了显著的计算节约.
科学领域:
- 计算化学计算化学
- 药物发现 药物发现 药物发现
- 化学信息学 化学信息学
背景情况:
- 化学图书馆的指数增长给传统的虚拟选 (VS) 带来了可扩展性挑战.
- 基于synthon的方法提供了一个有前途的替代方案,通过专注于构建块而不是列举的分子.
研究的目的:
- 引入exaScreen和exaDock,这两种新的基于synthon的方法用于基于连接体和基于结构的VS.
- 为导航超大化学空间提供计算高效的策略.
主要方法:
- 在 exaScreen 中的 Synthon 选择使用 3D 疏水/疏模式和一个新的对齐协议.
- exaDock采用基于synthon的化合物的几何约束对接,用于绑定站点安置.
- 这两种方法都优先考虑synthons,而不是完全列出的库.
主要成果:
- 在识别活性化合物方面,exaScreen和exaDock的性能与传统的VS方法相美.
- 这些新的策略以显著降低计算成本实现这一目标.
- 这些方法在超大化学空间的虚拟选中是有效的.
结论:
- 基于Synthon的VS在庞大的化学图书馆中为药物发现提供了一个计算效率高的解决方案.
- exaScreen和exaDock为现代药物发现管道提供可扩展和有效的工具.
相关概念视频
Drug Discovery: Overview
7.1K
Drug discovery is a multifaceted process involving extensive screening, testing, and optimization of lead compounds to identify potential new drugs for therapeutic use. It combines several approaches, including screening large numbers of natural products, chemical modification of known active molecules, identification of new drug targets, and rational design based on biological mechanisms and drug-receptor structure. These approaches are carried out in both academic research laboratories and...
7.1K
Ligand Binding Sites
12.6K
Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
12.6K
Protein-protein Interfaces
12.4K
Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
12.4K


