用于终点结合自由能量计算的连接物重组:识别 μ阿片类受体中芬太尼尔的首选位置
David D L Minh1, David A Cooper1, Bing Xie2
1Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616, United States.
Journal of chemical theory and computation
|January 13, 2025
概括
我们开发了一种新的计算方法,使用能量景观准确排列连接体结合姿势. 这种方法通过考虑连接体重组和相互作用来改善药物发现的预测.
科学领域:
- 计算化学是一种计算化学.
- 分子建模分子建模
- 药物发现 药物发现
背景情况:
- 准确预测连接体结合位置对于药物发现至关重要.
- 传统的方法,如平均相互作用能量可以模两可地排列姿势.
- 了解连接体重组自由能量是准确结合自由能量计算的关键.
研究的目的:
- 开发和验证一种新的计算方法来计算连接体重组自由能量.
- 应用这种方法来评估芬太尼衍生物在mu阿片类受体的结合作用.
- 为了证明该方法能够正确排序本地姿势而不是诱.
主要方法:
- 利用未结合和结合联体的能量景观来计算重组自由能量.
- 将该方法应用于现有模拟的芬太尼衍生物与mu阿片类受体结合.
- 分析了相互作用和连接体重组对结合自由能量的贡献.
主要成果:
- 开发的方法准确地排列了本地联结体在几何诱上的姿势.
- 发现相互作用和连接体重组对于姿势排名至关重要.
- 对 (3R,4S) - 洛芬坦尼尔相比 (3S,4R) - 洛芬坦尼尔的有利结合是由联体重组处罚解释的.
- 芬太尼的结合姿势主要是由相互作用驱动的.
结论:
- 这种新方法有效地计算了重组自由能量,用于终点绑定自由能量计算.
- 它为排名结合姿势提供了比平均相互作用能量显著的改进.
- 这种方法提供了有关联体结合亲和力和导向的分子驱动因素的宝贵见解.
- 该方法在计算上是高效的,并且广泛适用于其他具有约束力的自由能量研究.
更多相关视频
09:09Preparation and Delivery of Protein Microcrystals in Lipidic Cubic Phase for Serial Femtosecond Crystallography
Published on: September 20, 2016
11.4K
16:02Demonstration of the Sequence Alignment to Predict Across Species Susceptibility Tool for Rapid Assessment of Protein Conservation
Published on: February 10, 2023
2.6K
相关概念视频
Opioid Receptors: Overview
486
Opioid receptors, including the mu (μ, MOR), delta (δ, DOR), and kappa (κ, KOR) types, belong to the rhodopsin family of G protein-coupled receptors. These receptors are located throughout the central and peripheral nervous systems and in non-neuronal tissues such as macrophages and astrocytes. Opioid receptor ligands can be categorized into agonists or antagonists. Highly selective agonists include [d-Ala2, MePhe4, Gly(ol)5]-enkephalin or DAMGO for MOR, [D-Pen2,...
486
Drug-Receptor Interactions
4.8K
Drug-receptor interaction describes the binding of receptors by drugs, but not all drug-receptor interactions result in activation and tissue response. For instance, the binding of agonists activates the receptor to generate a cellular reaction, while antagonists bind to receptors without causing their activation.
Several parameters, such as the drug's affinity for its receptor and its efficacy, which is its ability to activate the receptor, determine the drug's effect on the tissue....
Several parameters, such as the drug's affinity for its receptor and its efficacy, which is its ability to activate the receptor, determine the drug's effect on the tissue....
4.8K
The Two-State Receptor Model
1.9K
The two-state receptor model explains a drug's interaction with receptors, such as G protein-coupled receptors and ligand-gated ion channels, to induce or inhibit a biological response. When no natural ligands are present, a receptor exists in an equilibrium of inactive (Ri) and active (Ra) conformations. The inactive form does not produce a response, while the active form generates a basal effect known as constitutive activity.
The binding affinity of a drug determines its interaction with...
The binding affinity of a drug determines its interaction with...
1.9K
GPCR Desensitization
5.8K
G protein-coupled receptor (GPCR) signaling plays a crucial role in cell functioning. GPCR desensitization is an equally essential process. It allows cells to respond to changing environments and regain sensitivity to new stimuli while preventing unnecessary stimulation when no longer needed. Prolonged exposure to stimuli leads to GPCR desensitization. It involves blocking the receptors from binding and activating additional G proteins. This inhibits activation of downstream effectors, thereby...
5.8K
The Equilibrium Binding Constant and Binding Strength
12.8K
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:
12.8K
Ligand-Gated Ion Channel Receptor: Gating Mechanism
2.1K
Ligand-gated ion channels are transmembrane proteins that play a vital role in intercellular communication and functions of the nervous system. They allow the influx of ions across the membrane once the neurotransmitter binds, allowing the subsequent transmission of electrical excitation across the neurons. Other ligand-gated ion channels, like the γ-aminobutyric acid (GABA) receptor, permit anions like chloride into the cells on the binding of the GABA molecule. Their entry into the cell...
2.1K
