描述 PROTAC 系统与终点绑定自由能量计算的合作效应
Kexin Xu1, Zhe Wang2,3, Sutong Xiang1
1Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009 Jiangsu, P. R. China.
Journal of chemical information and modeling
|October 3, 2024
概括
计算方法现在可以预测蛋白质溶解向金马 (PROTACs) 的合作性. 分子力学/一般化天生的表面积 (MM/GBSA) 有效地表征了 PROTAC 系统中的稳定和效应.
科学领域:
- 生物化学 生物化学
- 计算化学计算化学
- 药物发现 药物发现 药物发现
背景情况:
- 化向基马体 (PROTACs) 通过接近E3无素连接酶来诱导向蛋白质的降解.
- 合作性对于降解效率至关重要,但在设计上具有挑战性.
- 开发可靠的计算方法用于PROTAC设计具有显著的兴趣.
研究的目的:
- 调查终点绑定自由能源计算的可行性,以描述PROTAC系统的合作性.
- 为此目的评估分子力学/Poisson-Boltzmann (一般化-Born) 表面积 (MM/PB(GB) SA) 方法.
主要方法:
- 使用的分子力学/Poisson-Boltzmann (一般化-Born) 表面积 (MM/PB) 计算.
- 进行了分子动力学模拟 (50-100 ns).
- 在PROTAC三元复合体内分析了稳定和效应.
主要成果:
- MM/GBSA对PROTAC的合作效应表现出了良好的预测能力.
- 实现了Pearson相关系数 (rp) >0.5用于稳定和>0.6用于效应.
- 通过长时间的分子动力学调整和低介电常数 (εin = 1) 观察到最佳性能.
结论:
- MM/GBSA 是一种可行的计算策略,用于描述 PROTAC 系统的合作性.
- 这种方法促进了新型PROTAC分子的合理设计.
- 这些发现支持使用计算方法来优化PROTAC药物开发.
相关概念视频
Cooperative Binding of Transcription Regulators
7.4K
Transcriptional regulators bind to specific cis-regulatory sequences in the DNA to regulate gene transcription. These cis-regulatory sequences are very short, usually less than ten nucleotide pairs in length. The short length means that there is a high probability of the exact same sequence randomly occurring throughout the genome. Since regulators can also bind to groups of similar sequences, this further increases the chances of random binding. Transcriptional regulators form...
7.4K
Cooperative Binding of Transcription Regulators
2.6K
No description available
2.6K
Calculating Standard Free Energy Changes
25.6K
The free energy change for a reaction that occurs under the standard conditions of 1 bar pressure and at 298 K is called the standard free energy change. Since free energy is a state function, its value depends only on the conditions of the initial and final states of the system. A convenient and common approach to the calculation of free energy changes for physical and chemical reactions is by use of widely available compilations of standard state thermodynamic data. One method involves the...
25.6K
Nuclear Binding Energy
14.8K
The difference between the calculated and experimentally measured masses is known as the mass defect of the atom. In the case of helium-4, the mass defect indicates a “loss” in mass of 4.0331 amu – 4.0026 amu = 0.0305 amu. The loss in mass accompanying the formation of an atom from protons, neutrons, and electrons is due to the conversion of that mass into energy that is evolved as the atom forms. The nuclear binding energy is the energy produced when the atoms’ nucleons are bound...
14.8K
Cooperative Allosteric Transitions
8.8K
Cooperative allosteric transitions can occur in multimeric proteins, where each subunit of the protein has its own ligand-binding site. When a ligand binds to any of these subunits, it triggers a conformational change that affects the binding sites in the other subunits; this can change the affinity of the other sites for their respective ligands. The ability of the protein to change the shape of its binding site is attributed to the presence of a mix of flexible and stable segments in the...
8.8K
Cooperative Allosteric Transitions
3.1K
No description available
3.1K


