ArticleJournal of molecular modeling2025
Exploring the potential of vanadium(IV) complex in autophagy activation: structural modifications, NMR calculations, and novel interactions with PI3Kγ.
Article in Journal of molecular modeling, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
contextThe modulation of autophagy - inhibition or induction - has emerged as a promising strategy in cancer treatment, offering significant advantages over conventional chemotherapy. Previously, we demonstrated that the vanadium complex [VO(oda)(phen)] inhibits autophagy by activating the phosphoinositide 3-kinase gamma (PI3Kγ) protein. Given the therapeutic potential of autophagy modulation, we proposed structural modifications to this complex to achieve the opposite effect: autophagy activation by preventing PI3Kγ activation. In this context, this study aimed to perform structural modifications on the vanadium complex to elucidate and discuss new conformational implications and its role in the autophagic machinery. The AMBER force field (FF) was adapted for the modified vanadium complex (mVC), yielding excellent results in molecular dynamics (MD) simulations in vacuum, protein, and aqueous environments. The structural modifications successfully disrupted the interaction between [VO(oda)(phen)] and PI3Kγ, previously identified as a key factor in PI3Kγ activation. Consequently, PI3Kγ deactivation leads to a shift in the autophagy signaling pathway, promoting autophagy activation. Additionally, NMR calculations were performed to explore a novel role for mVC, broadening its potential applications.
methodsMD simulations were conducted at 800 ns using the AMBER program, while Molegro Virtual Docker (MVD) was employed for docking simulations. Optimization calculations (B3LYP/def2-TZVP and LANL2DZ ECP for V) and NMR calculations (PBE/IGLO-II and Wachters + f for V) were performed using Gaussian 09. The key frames from the MD simulations were selected using the OWSCA algorithm. Ligand and protein performance were evaluated through RMSD, RMSF, and hydrogen bond analyses, applying cutoff distances of 3.5 Å and 30°.
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