Structure-Guided Repurposing of SARS-CoV-2 Compounds Identifies Putative Inhibitors of Mpox Viral Enzymes

<title>Abstract</title> <p>Mpox remains a therapeutically underserved orthopoxvirus infection, and clinical evidence reinforces the need for antivirals acting through mechanisms distinct from tecovirimat. This study investigated whether a SARS-CoV-2 antiviral chemical library could be repurposed against three structurally characterised Mpox targets: the core protease, VP39 mRNA cap methyltransferase and poxin nuclease. A hierarchical workflow integrating high-throughput and precision docking, interaction profiling, and molecular mechanics generalised Born surface area rescoring was applied across the three targets. Top-scoring core protease and VP39 complexes were further evaluated using 100 ns molecular dynamics simulations and pharmacokinetic prediction. Redocking reproduced the crystallographic poses with root-mean-square deviations of 1.46, 0.79 and 1.83 Å for the core protease, VP39 and poxin complexes, respectively. For Mpox protease inhibitors, J08_67 showed the most favourable static binding free energy (− 37.03 kcal/mol) and the most balanced predicted pharmacokinetic profile, whereas J02_11 demonstrated lower ligand displacement than the reference complex and an 85% persistent Lys126 hydrogen bond. J08_51 emerged as the principal VP39 candidate, retaining a favourable post-simulation binding energy (− 68.38 ± 10.25 kcal/mol) and sustained interactions with Asp95 and Arg114. For poxin, J02_14 showed the most coherent non-native energetic profile, although it remained weaker than the co-crystallised ligand and was not evaluated dynamically. These findings demonstrate that cross-viral chemical-space repurposing can generate target-specific Mpox lead hypotheses and that integrating solvation, ligand strain and dynamic stability improves prioritisation beyond docking scores. The identified candidates warrant biochemical validation and medicinal-chemistry optimisation.</p>