Antioxidant properties of 34 alkaloids of natural origin: a density functional theory study.

The antioxidant properties of 34 plant alkaloids in gas phase, ethanol and water have been evaluated using density functional theory (DFT). The computations have been made according to three different single electron mechanisms: (1) H-atom transfer (HAT); (2) electron transfer followed by H transfer (SET-PT); and (3) sequential H-loss electron transfer (SPLET). As a result, the highest antioxidant activity was established for evodiamine.

Photophysics of 5,6,7,8-tetrahydrobiopterin on a femtosecond time-scale.

Pterins are naturally occurring compounds widespread in living organisms. 5,6,7,8-Tetrahydrobiopterin (HBip) is a cofactor of several key enzymes, including NO-synthases and phenylalanine hydroxylase, whereas tetrahydrocyanopterin is a photoreceptor molecule in cyanobacteria. In this regard, tetrahydropterins (Hpterins) photochemistry and photophysics have been attracting our attention.

Predicting fluorescence to singlet oxygen generation quantum yield ratio for BODIPY dyes using QSPR and machine learning.

Functional dyes that are capable of both bright fluorescence and efficient singlet oxygen generation are crucial for theranostic techniques, which integrate fluorescence imaging and photodynamic therapy (PDT). The development of new functional dyes for theranostics is often costly and time-consuming due to laborious synthesis and post-synthetic screening of large libraries of compounds. In this work, we describe machine learning methods suitable for simultaneous prediction of fluorescence and photosensitizing ability of heavy-atom-free boron dipyrromethene (BODIPY) compounds.

Interactions of coinage metal nanoclusters with low-molecular-weight biocompounds.

Nowadays, coinage metal nanoclusters (NCs) are largely presented in diagnostics, bioimaging, and biocatalysis due to their high biocompatibility, chemical stability, and sensitivity to surrounding biomolecules. Silver and gold NCs are usually characterized by intense luminescence and photostability, which is in great demand in the detection of organic compounds, ions, pH, temperature, etc. The experimental synthesis of metal NCs often occurs on biopolymer templates, mostly DNA and proteins.

Antioxidant properties of α-amino acids: a density functional theory viewpoint.

The antioxidant properties of 21 proteinogenic amino acids (AAs) and 3,4-dioxophenylanine (DOPA) have been studied in implicit water using density functional theory (DFT). All the calculations have been performed according to three oxidation mechanisms: (1) hydrogen-atom transfer (HAT); (2) single electron transfer followed by proton transfer (SET-PT); and (3) sequential proton-loss electron transfer (SPLET). As a result, five AAs with the highest antioxidant capacity have been established: DOPA, selenocysteine (Sec), tyrosine (Tyr), cysteine (Cys), and tryptophan (Trp).

Amino acid-stabilized luminescent gold clusters for sensing pterin and its analogues.

Pteridines are important low molecular weight biomarkers used in the diagnostics of inflammation, oxidative stress, phenylketonuria, cancer, In this experimental study, we present a simple and selective approach to determine pteridines (pterin, leucopterin and folic acid) and nucleobase guanine concentration using luminescent gold clusters stabilized by aromatic amino acids. We synthesized several new gold clusters (AA-Au NCs) stabilized by various aromatic amino acids - 3,4-dihydroxy-L-phenylalanine (DOPA), L-tryptophan (Trp), L-tyrosine (Tyr) and L-phenylalanine (Phe), emitting in the violet-green spectral range. Their luminescence appeared to be sensitive to the presence of pterin, leucopterin, folic acid and guanine depending on the stabilizing matrix.

Excited States in Single-Stranded and i-Motif DNA with Silver Ions.

We have studied the excited states and structural properties for the complexes of cytosine (dC) chains with silver ions (Ag) in a wide range of the Ag to DNA ratio () and pH conditions using circular dichroism, steady-state absorption, and fluorescence spectroscopy along with the ultrafast fluorescence upconversion technique. We also calculated vertical electronic transition energies and determined the nature of the corresponding excited states in some models of the cytosine-Ag complexes. We show that (dC) chains in the presence of silver ions form a duplex stabilized by C-Ag-C bonds.

Interactions of deprotonated phenylalanine with gold Clusters: Theoretical study with prospects for amino acid detection.

Nanomaterials are widely used nowadays in industry and medicine. The specific properties of gold nanoclusters (Au NCs) are chemical stability, low cytotoxicity, low photobleaching, high sensitivity to the molecular environment. This set of properties allows to use Au NCs as nanosensors in bioimaging and diagnostics.

Photosensitized isomerization of resveratrol: Evaluation of energy and electron transfer pathways.

Resveratrol (3,5,4'-trihydroxystilbene, RSV) is a natural stilbene synthetized as trans-isomer in plants exposed to oxidative stress. In order to understand the mechanism involved during photosensitized degradation of trans-resveratrol, steady-state and time-resolved experiments were performed and compared with quantum-chemical calculations using density functional theory (DFT). Pterin (Ptr), a well-known photosensitizer, under UV-A radiation induces the oxidation of several biomolecules mainly through electron-transfer mechanisms.

Tetrahydrobiopterin as a Trigger for Vitiligo: Phototransformation during UV Irradiation.

Vitiligo is a type of hypomelanosis. Tetrahydrobiopterin (HBip), the coenzyme of the initial stage of melanogenesis, appears to be a trigger for vitiligo. HBip is present in vitiligo in 3-5-fold excess and causes oxidative stress by triggering an autocatalytic cycle of excess hydrogen peroxide synthesis.

Rapid and selective colorimetric determination of L-DOPA in human serum with silver nanoparticles.

L-DOPA, or l-3,4-dihydroxyphenylalanine is an aromatic amino acid, which plays a significant role in human metabolism as a precursor of important neurotransmitters. We develop a fast and simple colorimetric method for the detection of L-DOPA in biological fluids. The method is based on the reduction of silver ions with L-DOPA and the subsequent formation of L-DOPA stabilized silver nanoparticles (Ag NPs).

Quantitative determination of albumin and immunoglobulin in human serum using gold nanoclusters.

In this experimental study, we developed a simple and selective approach to determine the concentrations of human serum albumin (HSA) and total amount of immunoglobulins (Ig) in real human serum (HS) sample using luminescent gold nanoclusters (Au NCs). In doing so, Au NCs were grown directly on the HS proteins without any sample pretreatment. We synthesized Au NCs on HSA and Ig and studied their photophysical properties.

Insights into Molecular Structure of Pterins Suitable for Biomedical Applications.

Pterins are an inseparable part of living organisms. Pterins participate in metabolic reactions mostly as tetrahydropterins. Dihydropterins are usually intermediates of these reactions, whereas oxidized pterins can be biomarkers of diseases.

Silver cluster interactions with Pterin: Complex structure, binding energies and spectroscopy.

Metal nanoclusters (NCs) are widely present today in biosensing, bioimaging, and diagnostics due to their small size, great biocompatibility, and sensitivity to the biomolecular environment. Silver (Ag) NCs often possess intense fluorescence, photostability, and low photobleaching, which is in high demand during the detection of organic molecules. Pterins are small compounds, which are used in medicine as biomarkers of oxidative stress, cardiovascular diseases, neurotransmitter synthesis, inflammation and immune system activation.

Silver Cluster Interactions with Tyrosine: Towards Amino Acid Detection.

Tyrosine (Tyr) is involved in the synthesis of neurotransmitters, catecholamines, thyroid hormones, etc. Multiple pathologies are associated with impaired Tyr metabolism. Silver nanoclusters (Ag NCs) can be applied for colorimetric, fluorescent, and surface-enhanced Raman spectroscopy (SERS) detection of Tyr.

UV Radiation in DNA Damage and Repair Involving DNA-Photolyases and Cryptochromes.

Prolonged exposure to ultraviolet radiation on human skin can lead to mutations in DNA, photoaging, suppression of the immune system, and other damage up to skin cancer (melanoma, basal cell, and squamous cell carcinoma). We reviewed the state of knowledge of the damaging action of UVB and UVA on DNA, and also the mechanisms of DNA repair with the participation of the DNA-photolyase enzyme or of the nucleotide excision repair (NER) system. In the course of evolution, most mammals lost the possibility of DNA photoreparation due to the disappearance of DNA photolyase genes, but they retained closely related cryptochromes that regulate the transcription of the NER system enzymes.

Quantitative Structure-Property Relationship Modelling for the Prediction of Singlet Oxygen Generation by Heavy-Atom-Free BODIPY Photosensitizers*.

Heavy-atom-free sensitizers forming long-living triplet excited states via the spin-orbit charge transfer intersystem crossing (SOCT-ISC) process have recently attracted attention due to their potential to replace costly transition metal complexes in photonic applications. The efficiency of SOCT-ISC in BODIPY donor-acceptor dyads, so far the most thoroughly investigated class of such sensitizers, can be finely tuned by structural modification. However, predicting the triplet state yields and reactive oxygen species (ROS) generation quantum yields for such compounds in a particular solvent is still very challenging due to a lack of established quantitative structure-property relationship (QSPR) models.

Autoxidation and photooxidation of tetrahydrobiopterin: a theoretical study.

Pterins are naturally occurring pigments and enzyme cofactors widespread in living organisms. Tetrahydrobiopterin (HBip) is a coenzyme of aromatic amino acid hydroxylases, NO-synthases, and alkylglycerol monooxygenases. This coenzyme is prone to oxidation in the presence of molecular oxygen, a so-called autoxidation.

Methods and Applications of In Silico Aptamer Design and Modeling.

Aptamers are nucleic acid analogues of antibodies with high affinity to different targets, such as cells, viruses, proteins, inorganic materials, and coenzymes. Empirical approaches allow the design of in vitro aptamers that bind particularly to a target molecule with high affinity and selectivity. Theoretical methods allow significant expansion of the possibilities of aptamer design.

Comparative study of gold and silver interactions with amino acids and nucleobases.

Metal nanoclusters (NCs) have gained much attention in the last decade. In solution, metal nanoclusters can be stabilized by proteins, and, thus, exhibit many advantages in biocatalysis, biosensing, and bioimaging. In spite of much progress in the synthesis of polypeptide-stabilized gold (Au) clusters, their structure, as well as amino acid-cluster and amino acid-Au interactions, remain poorly understood.

Nano-(Q)SAR for Cytotoxicity Prediction of Engineered Nanomaterials.

Although nanotechnology is a new and rapidly growing area of science, the impact of nanomaterials on living organisms is unknown in many aspects. In this regard, it is extremely important to perform toxicological tests, but complete characterization of all varying preparations is extremely laborious. The computational technique called quantitative structure-activity relationship, or QSAR, allows reducing the cost of time- and resource-consuming nanotoxicity tests.

Exciton Absorption and Luminescence in i-Motif DNA.

We have studied the excited-state dynamics for the i-motif form of cytosine chains (dC), using the ultrafast fluorescence up-conversion technique. We have also calculated vertical electronic transition energies and determined the nature of the corresponding excited states in a model tetramer i-motif structure. Quantum chemical calculations of the excitation spectrum of a tetramer i-motif structure predict a significant (0.

QSAR analysis of immune recognition for triazine herbicides based on immunoassay data for polyclonal and monoclonal antibodies.

A common task in the immunodetection of structurally close compounds is to analyze the selectivity of immune recognition; it is required to understand the regularities of immune recognition and to elucidate the basic structural elements which provide it. Triazines are compounds of particular interest for such research due to their high variability and the necessity of their monitoring to provide safety for agricultural products and foodstuffs. We evaluated the binding of 20 triazines with polyclonal (pAb) and monoclonal (mAb) antibodies obtained using atrazine as the immunogenic hapten.

Silver cluster-amino acid interactions: a quantum-chemical study.

Binding of silver ion (Ag) and two atomic neutral silver cluster (Ag) with a set of amino acids has been studied using Density Functional Theory (DFT) and ab initio MP2 method. We show that binding energy with Ag is higher for deprotonated anionic amino acids. Cysteine, aspartic acid, and tyrosine with deprotonated side chain exhibit the highest binding energy (G) values among all the amino acids: - 30.

Ciprofloxacin and Clinafloxacin Antibodies for an Immunoassay of Quinolones: Quantitative Structure⁻Activity Analysis of Cross-Reactivities.

A common problem in the immunodetection of structurally close compounds is understanding the regularities of immune recognition, and elucidating the basic structural elements that provide it. Correct identification of these elements would allow for select immunogens to obtain antibodies with either wide specificity to different representatives of a given chemical class (for class-specific immunoassays), or narrow specificity to a unique compound (mono-specific immunoassays). Fluoroquinolones (FQs; antibiotic contaminants of animal-derived foods) are of particular interest for such research.