Docking and Molecular Dynamics of the Natural Diterpenoid Dihydrotanshinone I in Human 15-PGDH Across Three Inhibitor-Bound Receptor Structures

<title>Abstract</title> <p> 15-hydroxyprostaglandin dehydrogenase (15-PGDH) is the enzyme that inactivates prostaglandin E2, and its inhibition raises prostaglandin E2 and rejuvenates aged skeletal muscle, which makes it an attractive target for age-related muscle decline. Although natural products are documented functional inhibitors of 15-PGDH, almost none has been characterized by structure-based docking, and the tanshinones of <italic>Salvia miltiorrhiza</italic> have not been examined against this enzyme. Here, dihydrotanshinone I, with panaxynol as a comparator, was docked into three experimentally determined 15-PGDH structures, the X-ray cocrystals 9PFL and 9PFM and the cryo-electron microscopy structure 8CVN, using a protocol validated for each receptor by redocking its own crystallographic inhibitor (heavy-atom RMSD 0.38 to 1.46 Angstrom). Dihydrotanshinone I docked favourably into the inhibitor pocket of all three structures, with best predicted docking affinities of − 8.94 to − 10.5 kcal/mol. In the X-ray structures, it formed a hydrogen bond with catalytic Ser138 and contacted Tyr151 and the lid-hinge residue Phe185, whereas in the cryo-electron microscopy structure it was anchored by Phe185 and Tyr217.Across fifteen independent random seeds the top pose was highly reproducible in every structure, with maximum pairwise RMSDs below 0.2 Angstrom, confirming that it is the dominant docking solution and not a seed-dependent artefact. The precise orientation was only partly conserved across the ensemble, so a single rigid binding mode is not established by docking alone. Triplicate 100 ns molecular dynamics simulations of all three complexes, nine trajectories in total, showed that the compound remained in continuous contact with the protein throughout every run and retained its contacts with the inhibitor-site residues, that Phe185 is contacted in essentially every frame while Lys155 is contacted in none, and that the three docked poses remained largely distinct under receptor flexibility, with one 8CVN replica of nine relocating toward the 9PFL pose. These three results were unchanged when recomputed across equilibration discard windows of 0 to 50 ns. Together the docking and the simulations identify dihydrotanshinone I as a reproducible, mechanistically plausible natural-compound candidate for the 15-PGDH inhibitor pocket. Predicted binding is reported as an estimate of binding potential and not as proven enzyme inhibition. </p>