Local Mode Analysis: Decoding IR Spectra by Visualizing Molecular Details

In Vitro Anticancer Activity and Oxidative Stress Biomarkers Status Determined by Usnea barbata (L.) F.H. Wigg. Dry Extracts

Lichens represent an important resource for common traditional medicines due to their numerous metabolites that can exert diverse pharmacological activities including anticancer effects. To find new anticancer compounds with fewer side effects and low tumor resistance, a bioprospective study of Usnea barbata (L.) F.H. Wigg. (U. barbata), a lichen from the Călimani Mountains (Suceava county, Romania) was performed. The aim of this research was to investigate the anticancer potential, morphologic changes, wound healing property, clonogenesis, and oxidative stress biomarker status of four extracts of U. barbata in different solvents (methanol, ethanol, acetone, and ethyl acetate), and also of usnic acid (UA) as a positive control on the CAL-27 (ATCC^® CRL-2095™) oral squamous carcinoma (OSCC) cell line and V79 (ATCC^® CCL-93™) lung fibroblasts as normal cells. Using the MTT assay and according to IC₅₀ values, it was found that the most potent anticancer property was displayed by acetone and ethyl acetate extracts. All U. barbata extracts determined morphological modifications (losing adhesion capacity, membrane shrinkage, formation of abnormal cellular wrinkles, and vacuolization) with higher intensity in tumor cells than in normal ones. The most intense anti-migration effect was established in the acetone extract treatment. The clonogenic assay showed that some U. barbata extracts decreased the ability of cancer cells to form colonies compared to untreated cells, suggesting a potential anti-tumorigenic property of the tested extracts. Therefore, all the U. barbata extracts manifest anticancer activity of different intensity, based, at least partially, on an imbalance in antioxidant defense mechanisms, causing oxidative stress.

Anharmonic quantum nuclear densities from full dimensional vibrational eigenfunctions with application to protonated glycine

The interpretation of molecular vibrational spectroscopic signals in terms of atomic motion is essential to understand molecular mechanisms and for chemical characterization. The signals are usually assigned after harmonic normal mode analysis, even if molecular vibrations are known to be anharmonic. Here we obtain the quantum anharmonic vibrational eigenfunctions of the 11-atom protonated glycine molecule and we calculate the density distribution of its nuclei and its geometry parameters, for both the ground and the O-H stretch excited states, using our semiclassical method based on ab initio molecular dynamics trajectories. Our quantum mechanical results describe a molecule elongated and more flexible with respect to what previously thought. More importantly, our method is able to assign each spectral peak in vibrational spectroscopy by showing quantitatively how normal modes involving different functional groups cooperate to originate that spectroscopic signal. The method will possibly allow for a better rationalization of experimental spectroscopy.

Amide-imide tautomerization in the glutamine side chain in enzymatic and photochemical reactions in proteins

Amide-imide tautomerization presents a pervasive class of chemical transformations in organic chemistry of natural compounds. In this Perspective, we describe two distinctively different protein systems, in which the amide-imide tautomerization in the glutamine side chain takes place in enzymatic or photochemical reactions. First, hydrolysis of guanosine triphosphate (GTP) catalyzed by the Ras-GAP protein complex suggests the occurrence of the imide tautomer of glutamine in reaction intermediates. Second, photoexcitation of flavin-binding protein domains (BLUFs) initiates a chain of reactions in the chromophore-binding pocket, including amide-imide tautomerization of glutamine. Mechanisms of these reactions at the atomic level have been revealed in quantum mechanics/molecular mechanics (QM/MM) simulations. To reinforce conclusions on the critical role of amide-imide tautomerization of glutamine in these reactions we describe results of new quantum chemistry and QM/MM calculations for relevant molecular model systems. We reexamine results of the recent IR spectroscopy studies of BLUF domains, which provide experimental evidences of Gln tautomerization in proteins. We also propose to validate the glutamine-assisted mechanism of enzymatic GTP hydrolysis by using IR spectroscopy in a proper range of wavenumbers.

Monitoring transient events in infrared spectra using local mode analysis

Time-resolved Fourier transformed infrared (FTIR) spectroscopy of chemical reactions is highly sensitive to minimal spatiotemporal changes. Structural features are decoded and represented in a comprehensible manner by combining FTIR spectroscopy with biomolecular simulations. Local mode analysis (LMA) is a tool to connect molecular motion based on a quantum mechanics simulation with infrared (IR) spectral features and vice versa. Here, we present the python-based software tool of LMA and demonstrate the novel feature of LMA to extract transient structural details and identify the related IR spectra at the case example of malonaldehyde (MA). Deuterated MA exists in two almost equally populated tautomeric states separated by a low barrier for proton transfer so IR spectra represent a mixture of both states. By state-dependent LMA, we obtain pure spectra for each tautomeric state occurring within the quantum mechanics trajectory. By time-resolved LMA, we obtain a clear view of the transition between states in the spectrum. Through local mode decomposition and the band-pass filter, marker bands for each state are identified. Thus, LMA is beneficial to analyze the experimental spectra based on a mixture of states by determining the individual contributions to the spectrum and motion of each state.