Identification of potential RapJ hits as sporulation pathway inducer candidates in Bacillus coagulans via structure-based virtual screening and molecular dynamics simulation studies

by Selleckchem | Dec 01 2023

Background: The bacterium Bacillus coagulans has attracted interest because of its ability to produce spores and advantageous probiotic traits, such as facilitating food digestion in the intestine, managing some disorders, and controlling the symbiotic microbiota. Spore-forming probiotic bacteria are especially important in the probiotic industry compared to non-spore-forming bacteria due to their stability during production and high resistance to adverse factors such as stomach acid. When spore-forming bacteria are exposed to environmental stresses, they enter the sporulation pathway to survive. This pathway is activated by the final phosphorylation of the master regulator of spore response, Spo0A, and upon achieving the phosphorylation threshold. Spo0A is indirectly inhibited by some enzymes of the aspartate response regulator phosphatase (Rap) family, such as RapJ. RapJ is one of the most important Rap enzymes in the sporogenesis pathway, which is naturally inhibited by the pentapeptides.

Methods: This study used structure-based virtual screening and molecular dynamics (MD) simulation studies to find potential RapJ hits that could induce the sporulation pathway. The crystal structures of RapJ complexed with pentapeptide clearly elucidated their interactions with the enzyme active site.

Results: Based on the binding compartment, through molecular docking, MD simulation, hydrogen bonds, and binding-free energy calculations, a series of novel hits against RapJ named tandutinib, infigratinib, sitravatinib, linifanib, epertinib, surufatinib, and acarbose were identified. Among these compounds, acarbose obtained the highest score, especially in terms of the number of hydrogen bonds, which plays a major role in stabilizing RapJ-ligand complexes, and also according to the occupancy percentages of hydrogen bonds, its hydrogen bonds were more stable during the simulation time. Consequently, acarbose is probably the most suitable hit for RapJ enzyme. Notably, experimental validation is crucial to confirm the effectiveness of the selected ligands.

Comments:

The study you've described focuses on finding potential compounds that can induce the sporulation pathway in the bacterium Bacillus coagulans by inhibiting the RapJ enzyme. The sporulation pathway is vital for the survival of spore-forming probiotic bacteria under environmental stresses. The researchers used a combination of computational techniques, including structure-based virtual screening, molecular docking, molecular dynamics (MD) simulations, and binding-free energy calculations, to identify potential hits against the RapJ enzyme.

Based on their computational analyses, the researchers identified several novel compounds, including tandutinib, infigratinib, sitravatinib, linifanib, epertinib, surufatinib, and acarbose, as potential hits against RapJ. Among these compounds, acarbose showed the most promising results, particularly in terms of the number and stability of hydrogen bonds formed with the RapJ enzyme.

However, it's important to note that these findings are based on computational simulations and molecular modeling. Experimental validation is essential to confirm the effectiveness of these selected compounds in inhibiting RapJ enzyme activity and inducing the sporulation pathway in Bacillus coagulans. Further studies, including in vitro and in vivo experiments, are necessary to validate the potential of acarbose and other identified compounds as therapeutic agents for modulating the sporulation pathway in spore-forming probiotic bacteria.