A computational approach to the resonance Raman spectrum of doxorubicin in aqueous solution

Computational Insights into the Adsorption of Ligands on Gold Nanosurfaces

We study the adsorption process of model peptides, nucleobases, and selected standard ligands on gold through the development of a computational protocol based on fully atomistic classical molecular dynamics (MD) simulations combined with umbrella sampling techniques. The specific features of the interface components, namely, the molecule, the metallic substrate, and the solvent, are taken into account through different combinations of force fields (FFs), which are found to strongly affect the results, especially changing absolute and relative adsorption free energies and trends. Overall, noncovalent interactions drive the process along the adsorption pathways. Our findings also show that a suitable choice of the FF combinations can shed light on the affinity, position, orientation, and dynamic fluctuations of the target molecule with respect to the surface. The proposed protocol may help the understanding of the adsorption process at the microscopic level and may drive the in-silico design of biosensors for detection purposes.

UV-Resonance Raman Spectra of Systems in Complex Environments: A Multiscale Modeling Applied to Doxorubicin Intercalated into DNA

UV-Resonance Raman (RR) spectroscopy is a valuable tool to study the binding of drugs to biomolecular receptors. The extraction of information at the molecular level from experimental RR spectra is made much easier and more complete thanks to the use of computational approaches, specifically tuned to deal with the complexity of the supramolecular system. In this paper, we propose a protocol to simulate RR spectra of complex systems at different levels of sophistication, by exploiting a quantum mechanics/molecular mechanics (QM/MM) approach. The approach is challenged to investigate RR spectra of a widely used chemotherapy drug, doxorubicin (DOX) intercalated into a DNA double strand. The computed results show good agreement with experimental data, thus confirming the reliability of the computational protocol.

Absorption Properties of Large Complex Molecular Systems: The DFTB/Fluctuating Charge Approach

We report on the first formulation of a novel polarizable QM/MM approach, where the density functional tight binding (DFTB) is coupled to the fluctuating charge (FQ) force field. The resulting method (DFTB/FQ) is then extended to the linear response within the TD-DFTB framework and challenged to study absorption spectra of large condensed-phase systems.

Ring Vibrations to Sense Anionic Ibuprofen in Aqueous Solution as Revealed by Resonance Raman

We unravel the potentialities of resonance Raman spectroscopy to detect ibuprofen in diluted aqueous solutions. In particular, we exploit a fully polarizable quantum mechanics/molecular mechanics (QM/MM) methodology based on fluctuating charges coupled to molecular dynamics (MD) in order to take into account the dynamical aspects of the solvation phenomenon. Our findings, which are discussed in light of a natural bond orbital (NBO) analysis, reveal that a selective enhancement of the Raman signal due to the normal mode associated with the C-C stretching in the ring, νC=C, can be achieved by properly tuning the incident wavelength, thus facilitating the recognition of ibuprofen in water samples.

Development of a new electrochemical DNA biosensor based on Eu3+-doped NiO for determination of amsacrine as an anti-cancer drug: Electrochemical, spectroscopic and docking studies

The present research reported a new electrochemical biosensor based on ds-DNA/Eu³⁺ doped NiO/CPE to detect amsacrine. Therefore, UV-Vis spectrophotometry, docking, and differential pulse voltammetry (DPV) have been used to study the interactions between amsacrine and dsDNA. Then, experimental parameters affected DNA immobilization and interactions between amsacrine and ds-DNA have been optimized. Afterwards, guanine oxidation peak current of ds-DNA has been chosen as a signal to analyze amsacrine in a concentration ranging between 0.1 and 100.0 μM and finally, limit of detection (LOD) of 0.05 μM has been calculated at optimal condition. Ultimately, it was found that the suggested biosensor is able to determine amsacrine in human serum and urine samples successfully.

Are the Absorption Spectra of Doxorubicin Properly Described by Considering Different Tautomers?

The elucidation of the action of doxorubicin (DOX) has been considered a challenge for cancer therapy. Using theoretical approaches, we investigated the structure and electronic properties of DOX as a function of pH, which we thought likely to be related to the influence of its tautomers. Regarding the relative stabilities among the tautomers, the results obtained from PM6 were the most similar to those obtained from DFT. The theoretical absorption spectrum for each tautomeric species simply showed a single absorption peak located around 400 nm, in contrast to the experimental absorption spectra in the literature that showed four absorption bands. The experimental evidence was properly explained by considering four tautomeric conformers of DOX. The spectroscopic study of the deprotonated tautomers also suggested the presence of four deprotonated tautomers at more basic pH values. The spectrum at pH 10.08 can be explained by the presence of protonated and deprotonated doxorubicin species.

In vivo detection of changes in cutaneous carotenoids after chemotherapy using shifted excitation resonance Raman difference and fluorescence spectroscopy

BACKGROUND

Various cutaneous toxicities under chemotherapy indicate a local effect of chemotherapy by secretion after systemic application. Here, changes in the fluorescence and Raman spectral properties of the stratum corneum subsequent to intravenous chemotherapy were assessed.

METHODS

Twenty healthy subjects and 20 cancer patients undergoing chemotherapy were included. Measurement time points in cancer patients were before the first cycle of chemotherapy (T_base ) and immediately after intravenous application of the chemotherapy (T₁ ). Healthy subjects were measured once without any further intervention. Measurements were conducted using an individually manufactured system consisting of a handheld probe and a wavelength-tunable diode laser-based 488 nm SHG light source. Hereby, changes in both skin fluorescence and shifted excitation resonance Raman difference spectroscopy (SERRDS) carotenoid signals were assessed.

RESULTS

Healthy subjects showed significantly (P < .001) higher mean concentrations of carotenoids compared to cancer subjects at T_base . An increase in fluorescence intensity was detected in almost all patients after chemotherapy, especially after doxorubicin infusion. Furthermore, a decrease in the carotenoid concentration in the skin after chemotherapy was found.

CONCLUSION

The SERRDS based noninvasive detection can be used as an indirect quantitative assessment of fluorescent chemotherapeutics. The lower carotenoid SERRDS intensities at T_base might be due to cancerous diseases and co-medication.