Computational Identification and Prioritization of Novel Tankyrase 1 and 2 Inhibitor Candidates Through Structure-Based Design, ADMET Profiling, and Long-Timescale Molecular Dynamics

Triple-negative breast cancer (TNBC) remains one of the most aggressive breast cancer subtypes and is frequently associated with aberrant activation of the Wnt/β-catenin signaling pathway. Because tankyrase 1 and 2 (TNKS1/2) promote Wnt pathway activation through the regulation of AXIN stability, these enzymes represent attractive therapeutic targets for the development of novel anticancer agents. In this study, an integrated structure-based computational workflow was employed to identify new TNKS1/2 inhibitors. A library comprising known tankyrase inhibitors, structurally related analogues, and 1096 rationally designed compounds was evaluated through molecular docking, ADMET profiling, molecular dynamics simulations, and MM-PBSA binding free-energy calculations. The docking protocol was validated through redocking experiments, yielding RMSD values of 1.42 Å and 1.18 Å for TNKS1 and TNKS2, respectively. Affinity- and pharmacokinetic-based filtering identified three TNKS1 candidates and sixteen TNKS2 candidates, of which fifteen were selected for 300 ns MD simulations. For TNKS1, Output-37 and Output-44 demonstrated stable binding and favorable MM-PBSA free energies (−33.12 and −32.38 kcal/mol, respectively), comparable to the reference inhibitor OM-153. For TNKS2, Output-1036 emerged as a promising candidate, exhibiting a binding free energy of −44.62 kcal/mol, surpassing the co-crystallized ligand and being comparable to the reference inhibitor OM-153, while Output-1015 and Output-997 also displayed favorable energetic and conformational profiles. Interaction analyses revealed the conservation of key catalytic pocket recognition hotspots and stable interaction networks throughout the simulations. Collectively, these results identify Output-1036 as a promising TNKS2 inhibitor candidate and Output-37 and Output-44 as potential TNKS1-targeting scaffolds. However, further in vitro and in vivo studies are required to validate their biological activity and confirm their ability to modulate Wnt/β-catenin signaling in triple-negative breast cancer.