基于胺的抑制剂的形状变异性
1Department of Chemistry, Quantum Theory Project, 2328 New Physics Building, P.O. Box 118435, University of Florida, Gainesville, Florida 32611-8435, USA.
Journal of the American Chemical Society
|May 14, 2009
概括
先进的量子力学/分子力学 (QM/MM) 改进提高了对小分子如何与蛋白质结合的理解,这对于基于结构的药物设计和优化药物亲和力至关重要.
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:
- 确定与生物受体结合的小分子的结构对于基于结构的药物设计至关重要.
- 由于力场参数的限制,传统的X射线晶体学精细化方法可能对小分子缺乏准确性.
- 连接体构造可以在蛋白质结合时发生变化,影响受体亲和力.
研究的目的:
- 为了研究量子力学/分子力学 (QM/MM) 精细化对蛋白质/连接体复合物的有用性.
- 在蛋白质结合部位内的小分子准确建模方面克服传统精炼协议的局限性.
- 为了更深入地了解小分子结合模式和形状偏好.
主要方法:
- 开始使用基于QM/MM的X射线精细化程序.
- 精细化工作集中在蛋白质/抑制剂复合物的活性或结合部位上.
- 研究了胺衍生物作为模型抑制剂.
主要成果:
- 与传统方法相比,初始的QM/MM精制提供了对小分子结合的更深入的见解.
- 证明了QM/MM的能力,以解决小分子建模方面的缺陷,特别是在活跃地点.
- 基于精炼方案和活性场所环境,观察到对胺衍生物的可变形状偏好.
结论:
- 最初的QM/MM精细化是准确建模蛋白质-连接体相互作用的强大方法.
- 与传统的X射线精细化相比,这种方法提供了对连接体结合和构造性行为的卓越洞察力.
- 这些发现对于优化药物亲和力和推进基于结构的药物设计至关重要.
相关概念视频
¹H NMR of Conformationally Flexible Molecules: Temporal Resolution
At room temperature, the chair conformer of cyclohexane undergoes rapid ring flipping between two equivalent chair conformers at a rate of approximately 105 times per second. These two chair conformers are in equilibrium. The rapid ring flipping results in the interconversion of the axial proton to an equatorial proton and an equatorial to the axial proton. Such interconversions are too rapid and cannot be detected on the NMR timescale. Hence, the NMR spectrometer cannot distinguish between the...
¹H NMR of Conformationally Flexible Molecules: Variable-Temperature NMR
The axial and equatorial protons in cyclohexane can be distinguished by performing a variable-temperature NMR experiment. In this process, except for one proton, the remaining eleven protons are replaced by deuterium. The deuterium substitution avoids the possible peak splitting caused by the spin-spin coupling between the adjacent protons. The remaining proton flips between the axial and equatorial positions.
Directing and Steric Effects in Disubstituted Benzene Derivatives
When disubstituted benzenes undergo electrophilic substitution, the product distribution depends on the directing effect of both substituents. When the directing effects of both substituents reinforce each other, a single product is obtained. For example, bromination of p-nitrotoluene occurs ortho to the methyl group and meta to the nitro group, which is the same position, resulting in a single product. However, if the directing effects of the two groups oppose each other, the more strongly...
Stability of Substituted Cyclohexanes
This lesson discusses the stability of substituted cyclohexanes with a focus on energies of various conformers and the effect of 1,3-diaxial interactions.
The two chair conformations of cyclohexanes undergo rapid interconversion at room temperature. Both forms have identical energies and stabilities, each comprising equal amounts of the equilibrium mixture. Replacing a hydrogen atom with a functional group makes the two conformations energetically non-equivalent.
For example, in...
The two chair conformations of cyclohexanes undergo rapid interconversion at room temperature. Both forms have identical energies and stabilities, each comprising equal amounts of the equilibrium mixture. Replacing a hydrogen atom with a functional group makes the two conformations energetically non-equivalent.
For example, in...
Cooperative Allosteric Transitions
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...
Basicity of Heterocyclic Aromatic Amines
Heterocyclic amines, where the N atom is a part of an alicyclic system, are similar in basicity to alkylamines. Interestingly, the heterocyclic amine having a nitrogen atom as part of an aromatic ring has much less basicity than its corresponding alicyclic counterpart. For this reason, as presented in Figure 1, piperidine (pKb = 2.8) is significantly more basic than pyridine (pKb = 8.8).

