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Crystal structure and computational analysis of 1,3-dioxo-2-phenyl-2,3-dihydro-1H-pyrrolo[3,4-c]quinoline 5-oxide, a caspase-3 inhibitor.

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Title: Crystal structure and computational analysis of 1,3-dioxo-2-phenyl-2,3-dihydro-1H-pyrrolo[3,4-c]quinoline 5-oxide, a caspase-3 inhibitor.
Authors: Thamotharan, Subbiah1 (AUTHOR) thamu@scbt.sastra.edu, Prasanna Kumari, Subramaniyan2 (AUTHOR), Selva Ganesan, Subramaniapillai2 (AUTHOR), Blacque, Olivier3 (AUTHOR), Venkatesan, Perumal4 (AUTHOR), Percino, M. Judith4 (AUTHOR)
Source: Structural Chemistry. Jun2026, Vol. 37 Issue 3, p1249-1264. 16p.
Subjects: Caspase inhibitors, Molecular docking, Heterocyclic compounds, Van der Waals forces, Molecular recognition, Intermolecular interactions, Molecular models, Crystal structure
Abstract: The crystal structure and noncovalent interaction profile of 1,3-dioxo-2-phenyl-2,3-dihydro-1H-pyrrolo[3,4-c]quinoline 5-oxide were investigated by single-crystal X-ray diffraction and computational methods. The compound crystallizes in the triclinic space group P-1 with two independent molecules in the asymmetric unit. Hirshfeld surface analysis and 2D fingerprint plots highlight the dominance of C–H···O, π–π stacking, and charge-assisted C–H···O⁻ interactions in the supramolecular assembly. CLP-PIXEL and generalized Kohn–Sham energy decomposition analysis (GKS-EDA) show that dispersion and electrostatic are the primary stabilizing forces, with excellent correlation (R²=0.986) between both methods. Topological analysis (QTAIM) confirms the closed-shell nature of the dominant contacts, including short H···H, C–H···O = C, and C = O···π interactions. The supramolecular organization is further characterized by columnar arrangements sustained through alternating dimeric motifs. Molecular docking indicates favourable binding of the title compound within the caspase-3 active site, mediated by hydrogen bonds, hydrophobic interactions, and π- π stacking with critical residues. Quantum chemical descriptors were computed and correlated with the predicted caspase-3 inhibition potential. [ABSTRACT FROM AUTHOR]
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Database: Engineering Source
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Abstract:The crystal structure and noncovalent interaction profile of 1,3-dioxo-2-phenyl-2,3-dihydro-1H-pyrrolo[3,4-c]quinoline 5-oxide were investigated by single-crystal X-ray diffraction and computational methods. The compound crystallizes in the triclinic space group P-1 with two independent molecules in the asymmetric unit. Hirshfeld surface analysis and 2D fingerprint plots highlight the dominance of C–H···O, π–π stacking, and charge-assisted C–H···O⁻ interactions in the supramolecular assembly. CLP-PIXEL and generalized Kohn–Sham energy decomposition analysis (GKS-EDA) show that dispersion and electrostatic are the primary stabilizing forces, with excellent correlation (R²=0.986) between both methods. Topological analysis (QTAIM) confirms the closed-shell nature of the dominant contacts, including short H···H, C–H···O = C, and C = O···π interactions. The supramolecular organization is further characterized by columnar arrangements sustained through alternating dimeric motifs. Molecular docking indicates favourable binding of the title compound within the caspase-3 active site, mediated by hydrogen bonds, hydrophobic interactions, and π- π stacking with critical residues. Quantum chemical descriptors were computed and correlated with the predicted caspase-3 inhibition potential. [ABSTRACT FROM AUTHOR]
ISSN:10400400
DOI:10.1007/s11224-025-02658-5