Quantum chemical properties investigation and molecular docking analysis with DNA topoisomerase II of β-carboline indole alkaloids from Simaba guianensis: a combined experimental and theoretical DFT study

A theoretical and experimental DFT study of the vibrational, structural, and quantum properties of 9-methoxy-canthin-6-one (I) and 7-methoxy-(9H-β-carbolin-1-il)-(Z)-prop-2-enoic acid (II) alkaloids is presented using B3LYP exchange-correlation functional with 6-311G(2d,p) basis set. The theoretical geometry optimization data of both structures were compared with the X-ray data for a similar structure in the associated literature and a conformational study is presented for (II), providing a good comprehension of its conformers’ stability. In addition, natural bond orbitals (NBOs), HOMO-LUMO energy gap, mapped molecular electrostatic potential surface (MEPS) calculations, and first- and second-order hyperpolarizabilities were also performed at the same calculation level. The calculated UV spectra agreed well with the measured experimental data, with transitions assigned. Calculated HOMO/LUMO energy gaps revealed the excitation energy of the structures, justifying their stability and kinetics reaction. IR studies showed that for structure II the intramolecular hydrogen bond of the conformations and the intermolecular hydrogen bonds of the dimeric form influence the results and also revealed several characteristic vibrations for both structures. Molecular docking studies with DNA topoisomerase II-DNA complex showed binding free energies of − 8.4 and − 9.6 kcal/mol for II and I, respectively, while for amsacrine, used for the treatment of leukemia, the binding free energy ΔG presented a value of − 9.9 kcal/mol, showing a good binding affinity of alkaloid I.