单分子拉动模拟可以区分活性与非活性酶抑制剂
Francesco Colizzi1, Remo Perozzo, Leonardo Scapozza
1Department of Pharmaceutical Sciences, University of Bologna, Via Belmeloro 6, I-40126 Bologna, Italy. francesco.colizzi@unibo.it
Journal of the American Chemical Society
|May 14, 2010
概括
这项研究引入了一种新的计算方法,将引导分子动力学 (SMD) 与对接相结合,以预测药物的疗效. 该方法成功地确定了Plasmodium falciparumβ-hydroxyacyl-ACP脱水酶 (PfFabZ) 的活性抑制剂,验证了其在药物设计中的潜力.
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.
- 药物发现 药物发现
背景情况:
- 配体-蛋白相互作用对于基于结构的药物设计至关重要.
- 传统的对接和分子动力学 (MD) 模拟在与生物数据一致的药物类似物排名方面存在局限性.
- 虫的β-hydroxyacyl-ACP脱水酶 (PfFabZ) 是抗疟疾药物开发的独特目标.
研究的目的:
- 开发和验证一种 in silico 方法来研究分子相互作用,并比较连接体-类似物结合特性.
- 通过将计算预测与实验验证相结合,确定pffabz的新型酶抑制剂.
- 建立一个强大的药物设计策略,基于方向分子动力学 (SMD) 力量概况.
主要方法:
- 使用了分子对接和引导分子动力学 (SMD) 模拟的组合.
- 开发了一种in silico方法来分析原子相互作用和结合亲和关系.
- 模拟了单分子拉动实验,使用SMD来生成用于化合物歧视的力概况.
主要成果:
- 从SMD衍生出来的力概况首次成功地将活性化合物与非活性化合物区分开来.
- 基于计算模型设计了一种新型化合物,并预测了它对PfFabZ的活性.
- 实验验证证证实了计算预测,证明了该方法的稳定性.
结论:
- 综合计算方法,特别是SMD,为理解联体蛋白识别和指导药物设计提供了强大的工具.
- 这种方法提高了预测和排名药物类型的能力,克服了传统技术的局限性.
- 对PfFabZ的成功申请突显了其在开发新的抗疟疾疗法和其他药物发现工作方面的潜力.
相关概念视频
Enzymes
Inside living organisms, enzymes act as catalysts for many biochemical reactions involved in cellular metabolism. The role of enzymes is to reduce the activation energies of biochemical reactions by forming complexes with its substrates. The lowering of activation energies favor an increase in the rates of biochemical reactions.
Enzyme deficiencies can often translate into life-threatening diseases. For example, a genetic abnormality resulting in the deficiency of the enzyme G6PD...
Enzyme deficiencies can often translate into life-threatening diseases. For example, a genetic abnormality resulting in the deficiency of the enzyme G6PD...
Enzyme Inhibition
Inhibitors are molecules that reduce enzyme activity by binding to the enzyme. In a normally functioning cell, enzymes are regulated by a variety of inhibitors. Drugs and other toxins can also inhibit enzymes. Some inhibitors bind to the enzyme’s active site, while others inhibit enzymatic activity by binding to other sites on the protein structure.
Induced-fit Model
Most chemical reactions in cells require enzymes—biological catalysts that speed up the reaction without being consumed or permanently changed. They reduce the activation energy needed to convert the reactants into products. Enzymes are proteins, that usually work by binding to a substrate—a reactant molecule that they act upon.
Enzymes exhibit substrate specificity, meaning that they can only bind to certain substrates. This is mainly determined by the shape and chemical characteristics of...
Enzymes exhibit substrate specificity, meaning that they can only bind to certain substrates. This is mainly determined by the shape and chemical characteristics of...


