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bioRxiv · 10.1101/2025.07.09.663866

Thermodynamics and unbinding kinetics of A22 at multiple actin binding sites revealed by enhanced sampling simulations

Kumar, A.·Pramanik, D.
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Abstract

The cytoskeletal protein plays a major role in various cellular processes. Understanding the interactions of small molecules with cytoskeletal protein therefore might help in the development of therapeutics. Employing combined molecular docking, all-atom molecular dynamics (MD) and infrequent well-tempered metadynamics (iWT-MetaD) we studied bacterial inhibitor A22 and actin protein interaction. Five probable A22 binding sites (S1-S5) were observed in actin and unbiased MD simulations of 100 ns - 500 ns showed structural stability at these sites. Interaction analyses showed A22 to mostly forms transient interactions except at sites S4 and S5 where long-lives interactions were present. Enhanced sampling simulations quantitatively estimated ligand dissociation free energy ({Delta}G) [~] - 2 kcal/mol to - 3.5 kcal/mol for sites S1-S4 with residence times [~] {micro}s to ms. For site S5, we observed the highest binding affinity ({Delta}G [~] - 6.05 {+/-} 0.48 kcal/mol) and longest residence time [~] 0.75 sec. Analyses of the dissociation trajectories predict multiple dissociation pathways for A22 and found key gatekeeper residues at specific-sites facilitating ligand dissociation. Comparison of A22 with other known inhibitors suggest that A22 binds actin with relatively lower affinity, however, exhibits site-specific unbinding kinetics. Thus, our study provides a detailed mechanistic overview of A22-actin interaction, its various binding modes, and unbinding kinetics. It also shows the importance and usage of infrequent metadynamics in exploring rare events like ligand-protein interaction. Deeper insights gained from this study expands our understanding of cytoskeletal ligand dynamics. These knowledges will be paramount in designing drug targeting cytoskeletal protein actin. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=72 SRC="FIGDIR/small/663866v2_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@dea318org.highwire.dtl.DTLVardef@a592a4org.highwire.dtl.DTLVardef@3e8df1org.highwire.dtl.DTLVardef@d8dddb_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG

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Kumar, A., Pramanik, D.. 2025-07-12. Thermodynamics and unbinding kinetics of A22 at multiple actin binding sites revealed by enhanced sampling simulations. https://doi.org/10.1101/2025.07.09.663866

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