Integrated computational modeling of chalcone-based inhibitors targeting carbonic anhydrase I and II: 3D-QSAR, molecular docking, and dynamics simulations

Carbonic anhydrase isoforms I and II (hCA-I and hCA-II) are metalloenzymes involved in essential physiological processes and represent relevant therapeutic targets for disorders such as glaucoma and osteoporosis. Chalcones have emerged as promising scaffolds for carbonic anhydrase inhibition; however, their structure–activity relationships, particularly for non-sulfonamide derivatives, remain insufficiently explored from a computational point of view. In this study, a dataset of 118 chalcone derivatives has been analyzed by using a three-dimensional quantitative structure-activity relationship (3D-QSAR) modeling, which comprises Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Similarity Index Analysis (CoMSIA). The developed models exhibited strong internal consistency and predictive capability for both isoforms. For hCA-I, steric, electrostatic, hydrophobic, and hydrogen bond acceptor fields has been identified as key contributors to inhibitory activity, whereas for hCA-II, hydrogen bond donor features played a more prominent role. Molecular docking and molecular dynamics simulations have been employed as complementary approaches to analyze ligand-protein interactions and binding stability. In addition, quantum chemical descriptors, derived from density functional theory, that have been integrated with the 3D-QSAR analysis, reveal a consistent correspondence between contour map features and the distribution of frontier molecular orbitals and molecular electrostatic potential. Furthermore, ADME-based pharmacokinetic properties of the proposed compounds have been evaluated to assess their potential drug-likeness. Based on the integrated computational analysis, six new chalcone derivatives, with predicted inhibitory activity in the nanomolar range, are proposed. Overall, this study provides a consistent physicochemical framework for understanding the inhibitory activity of chalcone derivatives and highlights key molecular features that may guide the modulation of activity across hCA-I and hCA-II isoforms.