Comparative binding mechanisms of SND1 with MTDH and small-molecule inhibitors: insights from molecular dynamics simulations and free energy calculations

The protein–protein interaction (PPI) between metadherin (MTDH) and Staphylococcal nuclease domain-containing protein 1 (SND1) is a pivotal oncogenic driver in various cancers, yet the atomic-level details of their binding mechanism remain elusive, hindering targeted drug discovery. This study employs integrated computational approaches, including molecular dynamics (MD) simulations, binding free energy calculations, and residue interaction network analysis, to identify hotspot residues at the MTDH–SND1 interface and elucidate the binding mechanism. The results demonstrate that the MTDH–SND1 complex exhibits strong binding affinity, primarily driven by electrostatic and hydrophobic interactions. Structural stability analysis confirmed the complex's integrity during simulations, while dynamic cross-correlation and mutual information analyses revealed a key interaction region (R1) with correlated motions, which was further proved by contact probability analysis. Hydrogen bond analysis identified a stable network involving residues Arg239, Arg243, and Hie263, which were confirmed as hotspot residues by the alanine scanning mutagenesis method. Furthermore, the binding and interaction mechanisms between SND1 and 12 activity-known small molecule inhibitors were investigated and compared with that in the MTDH–SND1 complex. Energy decomposition highlighted that the conserved triad—Arg239, Arg243, and Hie263—is crucial across all systems. This work provides unprecedented atomic-level insights into the MTDH–SND1 interaction and offers a robust structural foundation for the rational design of high-affinity inhibitors against this oncogenic PPI.