A rhodanine derivative as a potential antibacterial and anticancer agent: Crystal structure, spectral characterization, DFT calculations, Hirshfeld surface analysis, in silico molecular docking and ADMET studies

A novel rhodanine derivative, namely 5-(4-dimethylaminobenzylidene) rhodanine C12H12N2OS2 , was successfully crystallized from condensation route and characterized by NMR, FT-IR, UV-Vis spectral meth-ods as well as single-crystal X-ray diffraction. This rhodanine derivate crystallizes in the monoclinic P21/c space group, with the cell parameters: a = 3.93590(10), b = 11.2480(3), c = 26.6703(7) A and beta = 93.8530(10) degrees. The molecular structure displays intra-(C - S middotmiddotmiddotH) and intermolecular ( N - HmiddotmiddotmiddotO) hydrogen-bonding interactions. Micro-spectroscopy performed on single-crystals of the studied com-pound revealed the first absorption transition at 2.25 eV, and a well-structured luminescence peaked at 2.01 eV (0.15 eV broad). Density functional theory (DFT) calculations allowed the structure optimiza-tion, the electronic properties, the IR-vibrational modes and frequencies as well as the 1 H and 13 C NMR chemical shifts' calculation. Furthermore, time-dependent DFT (TD-DFT) calculations were performed for the vertical transition energies. Hirshfeld surface analysis (HSA) showed the presence of non-conventional C-H middotmiddotmiddotH-C, C-H middotmiddotmiddotn-and n-middotmiddotmiddotlp interactions and n--n-stacking. The anti-cancer and anti-bacterial activities of the studied compound towards the Polo-like kinase PLK1 and the Escherichia coli MurB enzymes were in silico evaluated by performing molecular docking simulations. The results suggest that the molecule can significantly inhibit the enzymes' active sites. Additionally, the physicochemical and pharmacokinetic characteristics of the molecule were evaluated through absorption, distribution, metabolism, excretion and toxicity (ADMET) analysis, and the results ensure its good drug-likeness properties.(c) 2023 Elsevier B.V. All rights reserved.

Automated summary

A novel rhodanine derivative was synthesized and characterized by various spectroscopic methods. The compound crystallizes in the monoclinic P21/c space group with intra- and intermolecular hydrogen-bonding interactions. Optical properties were determined by absorption and luminescence spectroscopy, while DFT calculations provided insights into the molecular structure and electronic properties. Molecular docking simulations predicted significant inhibition of enzyme activity, and ADMET analysis confirmed drug-likeness properties.