H37Rv中硫胺素二磷酸生物合成的Petri网建模
Petri Net modeling of thiamine diphosphate biosynthesis in H37Rv.
作者信息
Siddiqui Mohd Asif, Jain Ravindra Kumar, Kumar Ashwani, Rai Dhanendra Kumar, Chand Nikhil, Yadav Ritika, Chauhan Anu, Rana Sarita
机构信息
Department of Biotechnology, Swami Vivekanand Subharti University, Subhartipuram, NH-58, Delhi-Haridwar Bypass Road, Meerut-250005, India.
出版信息
Bioinformation. 2025 May 31;21(5):1029-1033. doi: 10.6026/973206300211029. eCollection 2025.
Thiamine diphosphate (TPP) is essential cofactor in H37Rv metabolism, making its biosynthesis pathway a key target for therapy. Therefore, it is of interest to describe a Petri net-based model of the TPP biosynthesis super-pathway, developed using curated MetaCyc data and simulated with Snoopy software. The model integrates three biosynthetic branches and maps key enzymes (ThiC, ThiD, ThiE, ThiF, ThiG, ThiS) along with their gene identifiers. The simulation of token flow revealed the pathway's dynamics, highlighting critical regulatory nodes. This computational approach provides insights into TPP biosynthesis and serves as a basis for drug design targeting tuberculosis.
硫胺素二磷酸（TPP）是H37Rv代谢中必不可少的辅因子，使其生物合成途径成为治疗的关键靶点。因此，描述一个基于Petri网的TPP生物合成超级途径模型很有意义，该模型使用经过整理的MetaCyc数据开发，并使用Snoopy软件进行模拟。该模型整合了三个生物合成分支，并绘制了关键酶（ThiC、ThiD、ThiE、ThiF、ThiG、ThiS）及其基因标识符。令牌流模拟揭示了该途径的动态变化，突出了关键调控节点。这种计算方法为TPP生物合成提供了见解，并为针对结核病的药物设计奠定了基础。
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