探索由药物点中广泛的蛋白质形状变化驱动的神秘口袋形成的结构基础
Martijn P Bemelmans1,2, Alberto Borsatto2,3, Simone Marsili4
1Computer-Aided Drug Design, In Silico Discovery, Therapeutics Discovery, Johnson & Johnson Innovative Medicine, Turnhoutseweg 30, Beerse 2340, Belgium.
Journal of chemical theory and computation
|March 4, 2026
概括
对于药物发现至关重要的神秘口袋,来自复杂的蛋白质动态. 一种新的计算方法,SLICE,有助于探索这些动态,以确定新的药物标.
科学领域:
- 生物化学 生物化学
- 计算生物学 计算生物学
- 药物发现 药物发现 药物发现
背景情况:
- 密码口袋是药物发现中至关重要的短暂的全结合点.
- 它们的形成涉及显著的蛋白质构造变化,这给实验和计算识别带来了挑战.
- 了解这些口袋的动态是针对具有挑战性的制药蛋白的关键.
研究的目的:
- 研究动态药物点中神秘口袋形成的结构基础.
- 确定驱动加密口袋暴露的机制.
- 制定一个计算策略,以促进对加密口袋的探索.
主要方法:
- 利用基于模拟的方法研究PRMT5,PRMT6,SMARCA2,Abl1和PI3Kα中的神秘口袋形成.
- 分析了局部内分子接触在固功能蛋白质段中的作用.
- 开发并应用了SLICE (通过局部交互引导的符合性探索采样) 计算方法.
主要成果:
- 局部分子内接触的破坏导致了大规模的结构变化,导致了神秘口袋的形成.
- 简单的干扰,如探针或改变的溶剂相互作用不足以诱导口袋的形成.
- SLICE 方法有效地指导了围绕功能段的构造性采样.
- 该研究显示,高能障碍物参与形成可连接的神秘口袋.
结论:
- 神秘的口袋形成是由复杂的机制和高能障碍所支配的,简单的扰动不容易克服.
- SLICE计算方法增强了对蛋白质结构可塑性的理解和探索.
- 这种方法通过利用功能性蛋白质部分的动态来促进新药标的发现.
相关概念视频
Protein Organization
Overview
Protein Folding
Overview
Protein and Protein Structure
Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
A protein's shape is critical to its function. For example, an enzyme can...
A protein's shape is critical to its function. For example, an enzyme can...
Protein Folding
Overview
Protein Organization
Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence.
The primary structure of a protein is its amino acid sequence.
Protein Folding
Proteins are chains of amino acids linked together by peptide bonds. Upon synthesis, a protein folds into a three-dimensional conformation, critical to its biological function. Interactions between its constituent amino acids guide protein folding, and hence the protein structure is primarily dependent on its amino acid sequence.
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...
Protein Structure Is Critical to Its Biological Function
Proteins perform a wide range of biological functions such as catalyzing chemical reactions, providing...


