扩展PROXIMAL以预测人类肠道微生物群中的化合物的降解途径
Francesco Balzerani1, Telmo Blasco1, Sergio Pérez-Burillo1
1University of Navarra, Tecnun School of Engineering, Manuel de Lardizábal 13, 20018, San Sebastián, Spain.
NPJ systems biology and applications
|May 27, 2024
概括
通过改进多步反应处理和电荷跟踪,PROXIMAL2增强了酶乱交预测,比以前的代谢网络分析方法提供了更高的准确性.
科学领域:
- 代谢工程是代谢工程.
- 计算生物学 计算生物学
- 酶学 是一种酶学.
背景情况:
- 了解细胞代谢对于许多生物来说至关重要,但不完整.
- 酶乱交,酶催化非注释反应的能力,为发现提供了一个有希望的途径.
- 计算方法对于有效地探索酶乱交是必不可少的.
研究的目的:
- 开发一个改进的计算管道,PROXIMAL2,用于预测酶乱交.
- 克服现有方法的局限性,例如依赖特定数据库和处理复杂反应的不足.
- 增强新型代谢途径的预测,特别是肠道微生物群中的化合物降解.
主要方法:
- 开发PROXIMAL2,一种用于酶乱交分析的新型计算管道.
- PROXIMAL2 包含了多步反应的精确处理和电荷的跟踪.
- 将PROXIMAL2与原来的PROXIMAL算法和RetroPath RL进行比较,使用KEGG反应和化合物降解预测.
主要成果:
- 与PROXIMAL相比,PROXIMAL2在从基板中回收注释产品的准确性明显更高.
- 应用PROXIMAL2来预测人类肠道微生物群中的化合物降解产生了相关的见解.
- 与RetroPath RL的比较显示了重叠和互补的预测,突出了新的研究途径.
结论:
- PROXIMAL2代表了对酶乱交的计算预测的重大进步.
- 管道处理多步骤反应和电荷的能力改善了代谢网络的重建.
- 这些发现为微生物新陈代谢,营养和酶功能的预测开辟了新的研究方向.
相关概念视频
Oxidation of Phenols to Quinones
3.0K
In the presence of oxidizing agents, phenols are oxidized to quinones. Quinones can be easily reduced back to phenols using mild reducing agents. The electron-donating hydroxyl group enhances the reactivity of the aromatic ring, enabling oxidation of the ring even in the absence of an α hydrogen.
o-hydroxy phenols are oxidized to o-quinones and p-hydroxy phenols to p-quinones. Such redox reactions involve the transfer of two electrons and two protons. The reversible redox...
o-hydroxy phenols are oxidized to o-quinones and p-hydroxy phenols to p-quinones. Such redox reactions involve the transfer of two electrons and two protons. The reversible redox...
3.0K
Phase I Reactions: Oxidation of Aliphatic and Aromatic Carbon-Containing Systems
187
Phase I biotransformation reactions are integral to drug metabolism, predominantly involving oxidative, reductive, and hydrolytic transformations. Chief among these are oxidative reactions, which enhance the hydrophilicity of xenobiotics and introduce polar functional groups to facilitate their elimination from the body.
Oxidation reactions are fundamental in aromatic carbon-containing systems. An example is the hydroxylation of phenobarbital, a process that transforms it into...
Oxidation reactions are fundamental in aromatic carbon-containing systems. An example is the hydroxylation of phenobarbital, a process that transforms it into...
187
Phase I Oxidative Reactions: Overview
264
Phase I biotransformation, or functionalization, is a crucial chemical process that converts drugs and other xenobiotics into more water-soluble forms, facilitating expulsion from the body. It involves oxidative, reductive, and hydrolytic reactions that add or unveil polar functional groups on lipophilic substrates. Key players in phase I reactions are the mixed-function oxidases. Situated in liver cell microsomes, these enzymes predominantly carry out drug metabolism. They require molecular...
264
Drug Metabolism: Phase II Reactions
3.8K
Phase II reactions are essential for the detoxification and elimination of drugs from the body. These reactions involve the conjugation of parent drugs or their phase I metabolites with endogenous molecules, resulting in more hydrophilic drug conjugates. The primary conjugation reactions in this phase are sulfation and glucuronidation. Both sulfation and glucuronidation typically produce biologically inactive metabolites. However, in some cases involving prodrugs, active metabolites may be...
3.8K
Bioremediation
18.3K
Bioremediation is the use of prokaryotes, fungi, or plants to remove pollutants from the environment. This process has been used to remove harmful toxins in groundwater as a byproduct of agricultural run-off and also to clean up oil spills.
18.3K
Drug Metabolism: Phase I Reactions
3.2K
A phase I reaction is a biochemical process that introduces a functionally reactive polar group to a substance. This transformation predominantly occurs in the liver, facilitated by the cytochrome P450 system of hemoproteins situated in the lipophilic endoplasmic reticulum of cells. The metabolite generated through this process can have varying polarities. If it is sufficiently polar, it can be easily excreted in the urine due to its water compatibility. However, if the metabolite is nonpolar,...
3.2K


