Molecular modeling strategy for detailing the primary mechanism of action of copanlisib to PI3K: combined ligand-based and target-based approach

AbstractSince dysregulation of the phosphatidylinositol 3-kinase (PI3K) signaling pathway is associated with the pathogenesis of cancer, inflammation, and autoimmunity, PI3K has emerged as an attractive target for drug development. Although copanlisib is the first pan-PI3K inhibitor to be approved for clinical use, the precise mechanism by which it acts on PI3K has not been fully elucidated. To reveal the binding mechanisms and structure-activity relationship between PI3K and copanlisib, a comprehensive modeling approach that combines 3D-quantitative structure-activity relationship (3D-QSAR), pharmacophore model, and molecular dynamics (MD) simulation was utilized. Initially, the structure-activity relationship of copanlisib and its derivatives were explored by constructing a 3D-QSAR. Then, the key chemical characteristics were identified by building common feature pharmacophore models. Finally, MD simulations were performed to elucidate the important interactions between copanlisib and different PI3K subtypes, and highlight the key residues for tight-binding inhibitors. The present study uncovered the principal mechanism of copanlisib’s action on PI3K at the theoretical level, and these findings might provide guidance for the rational design of pan-PI3K inhibitors.Communicated by Ramaswamy H. SarmaKeywords: PI3K inhibitorcopanlisib3D-QSARpharmacophoremolecular dynamics simulation Disclosure statementNo potential conflict of interest was reported by the author(s).Additional informationFundingThe study was supported by the National Natural Science Foundation of China [No. 21807049, 82001711], the Fundamental Research Funds for the Central Universities [JUSRP51703A], the University-Industry Cooperation Research Project in Jiangsu [No. BY2020432], the Natural Science Foundation of Jiangsu Province [BK20201137], Foundation of Wuxi Municipal Health Commission [Q202007, HB2020035].