推断与AlphaFold预测结构的分子抑制功效
Pedro F Oliveira1, Rita C Guedes2, Andre O Falcao3
1Lasige, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal.
Scientific reports
|April 8, 2024
概括
这项研究引入了一种新的机器学习方法,集成AlphaFold蛋白质结构,用于预测药物向相互作用,包括新向. 该方法表现出与现有技术相当的性能,为药物发现提供了可扩展的解决方案.
科学领域:
- 计算化学是一种计算化学.
- 结构生物学是结构生物学.
- 机器学习在药物发现中的作用
背景情况:
- 在形药物发现方法中,经常难以预测新型或未经评估的蛋白质标的相互作用.
- 当目标结构未知或目标新时,基于连接体的方法是有限的.
研究的目的:
- 开发一种机器学习模型,将从预测的蛋白质结构 (AlphaFold 2) 中集成3D结构信息,以改善药物向相互作用预测.
- 为了能够准确地预测以前未经测试的分子和蛋白质标,包括孤儿标.
主要方法:
- 从AlphaFold 2预测的结构中提取3D结构蛋白指纹.
- 蛋白质结构指纹与连接体结构数据的整合.
- 训练一个单一的机器学习模型来捕捉蛋白质化学关系.
- 使用144个人类G蛋白合受体 (GPCR) 和超过14万个抑制常数 (Ki) 的数据集进行验证.
主要成果:
- 拟议的方法显示性能与最先进的基于联体的方法相美.
- 在一个单独的测试组中,该模型对73%的目标正确预测了相互作用,解释差异在22%的案例中>0.50.
- 使用预测的蛋白质结构构建的模型与使用实验确定结构的模型相比,没有显示任何统计差异.
结论:
- 蛋白质化学测量方法有效地利用预测的蛋白质结构数据用于药物查.
- 这种方法提供了一种简单,可扩展的方法来预测蛋白质分子相互作用,即使是孤儿目标.
- 整合结构数据可以提高机器学习模型在药物发现中的预测能力.
相关概念视频
The Equilibrium Binding Constant and Binding Strength
12.9K
The equilibrium binding constant (Kb) quantifies the strength of a protein-ligand interaction. Kb can be calculated as follows when the reaction is at equilibrium:
12.9K
Conserved Binding Sites
4.2K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
4.2K
Ligand Binding and Linkage
4.8K
Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked. In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence...
4.8K
Protein-protein Interfaces
12.5K
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...
12.5K
Ligand Binding Sites
12.8K
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...
12.8K
Allosteric Proteins-ATCase
5.7K
Binding sites linkages can regulate a protein's function. For example, enzyme activity is often regulated through a feedback mechanism where the end product of the biochemical process serves as an inhibitor.
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis...
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis...
5.7K


