Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2025 May 31;21(5):1029-1033.
doi: 10.6026/973206300211029. eCollection 2025.

Petri Net modeling of thiamine diphosphate biosynthesis in Mycobacterium tuberculosis H37Rv

Mohd Asif Siddiqui  1 , Ravindra Kumar Jain  1 , Ashwani Kumar  1 , Dhanendra Kumar Rai  1 , Nikhil Chand  1 , Ritika Yadav  1 , Anu Chauhan  1 , Sarita Rana  1
Affiliations

Petri Net modeling of thiamine diphosphate biosynthesis in Mycobacterium tuberculosis H37Rv

Mohd Asif Siddiqui et al. Bioinformation. .

Abstract

Thiamine diphosphate (TPP) is essential cofactor in Mycobacterium tuberculosis 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.

Keywords: Mycobacterium tuberculosis; Petri nets; Thiamine biosynthesis; modelling; simulation.

PubMed Disclaimer

References

    1. Zhang X, et al. BMC Infectious Diseases. . 2023;23:680. - PMC - PubMed
    1. Sachan R.S.K, et al. ACS omega. . 2023;8:32244. - PMC - PubMed
    1. Hwang S, et al. BMC microbiology. . 2014;28:260. - PMC - PubMed
    1. Hardy S, Robillard P.N. Systems biology. . 2008;24:209. doi: 10.1093/bioinformatics/btm560. - DOI
    1. Koch I, et al. Modeling in Systems Biology: The Petri Net Approach. London: Springer; 2010. 74 pp.

LinkOut - more resources