Secondary Metabolites from the Red Macroalga Sphaerococcus coronopifolius as Hit Candidates of Helicobacter pylori Purine Nucleoside Phosphorylase

Abstract Helicobacter pylori is a major human pathogen associated with gastric cancer and a growing global public health concern due to increasing antimicrobial resistance. As H. pylori lacks de novo purine biosynthesis and relies entirely on purine salvage for nucleotide production, purine nucleoside phosphorylase represents a rational antibacterial target. Natural products remain a valuable and largely underexplored source of structurally diverse scaffolds for the discovery of novel enzyme inhibitors, with marine organisms representing a rich yet underexploited source of such bioactive metabolites; however, the pharmacological exploration of this enzyme from natural sources remains limited. In this context, six terpenoids, including five brominated diterpenes, isolated from the red macroalga Sphaerococcus coronopifolius were screened against recombinant H. pylori PNP using a target-based biochemical approach. Two of the six compounds tested, bromosphaerol and sphaerodactylomelol, showed reproducible inhibitory activity at 30 μM, reducing H. pylori PNP activity by 46.04 ± 4.70% and 39.39 ± 8.24%, respectively. Molecular docking predicted binding of both compounds within the active-site purine-binding region, with hydrophobic contacts involving Phe159 and Leu206. Hydrogen bonds were predicted with the backbone carbonyl of Ile178 for bromosphaerol and of Phe159 for sphaerodactylomelol. Molecular dynamics simulations (200 ns, three independent replicates per system) showed that both ligands remained stably accommodated within the predicted active-site binding pocket across all six monomers of the hexameric assembly, while root mean square deviation (RMSD) and root mean square fluctuation (RMSF) analyses indicated that the enzyme retained its global structural integrity throughout the simulations. Bromosphaerol exhibited a lower RMSD than the conformationally flexible sphaerodactylomelol, reflecting differences in ligand dynamics within the binding pocket. Taken together, these findings provide initial biochemical evidence that S. coronopifolius represents a source of secondary metabolites capable of interacting with H. pylori PNP, and nominate bromosphaerol and sphaerodactylomelol as preliminary hits for future concentration–response characterization.