Diphenylene Iodonium as a Prominent Halogen Bond donor: The case of Human Monoamine Oxidase B.

Herein we have investigated the formation and interplay of several noncovalent interactions (NCIs) involved in the inhibition of human monoamine oxidase B (MAO B). Concretely, an inspection of the Protein Data Bank (PDB) revealed the formation of a halogen bond (HlgB) between a diphenylene iodonium (DPI) inhibitor and a water molecule present in the active site, in addition to a noncovalent network of interactions (e.g. lone pair-π, hydrogen bonding, OH-π, CH-π and π-stacking interactions) with surrounding protein residues. Several theoretical models were built to understand the strength and directionality features of the HlgB in addition to the interplay with other NCIs present in the active site of the enzyme. Besides, a computational study was carried out using DPI as HlgB donor and several electron rich molecules (CO, H2O, CH2O, HCN, pyridine, OCN-, SCN-, Cl- and Br-) as HlgB acceptors. The results were analyzed using several state-of-the-art computational tools. We expect that our results will be useful for those scientists working in the fields of rational drug design, chemical biology as well as supramolecular chemistry.

On the Importance of Halogen and Chalcogen Bonds in the Solid State of Nucleic Acids: A Combined Crystallographic and Theoretical Perspective.

In this work, intra- and intermolecular halogen and chalcogen bonds (HlgBs and ChBs, respectively) present in the solid state of nucleic acids (NAs) have been studied at the RI-MP2/def2-TZVP level of theory. To achieve this, a Protein Data Bank (PDB) survey was carried out, revealing a series of structures in which Br/I or S/Se/Te atoms belonging to nucleobases or pentose rings were involved in noncovalent interactions (NCIs) with electron-rich species. The energetics and directionality of these NCIs were rationalized through a computational study, which included the use of Molecular Electrostatic Potential (MEP) surfaces, the Quantum Theory of Atoms in Molecules (QTAIM), and Non Covalent Interaction plot (NCIplot) and Natural Bonding Orbital (NBO) techniques.

Tetrel bonds involving a CF3 group participate in protein-drug recognition: a combined crystallographic and computational study.

In this study, the ability of CF3 groups to bind to the electron-rich side chains and backbone groups of proteins has been investigated by combining a Protein Data Bank (PDB) survey and ab initio quantum mechanics calculations. More precisely, an inspection of the PDB involving organic ligands containing a CF3 group and electron-rich atoms (A = N, O and S) in the vicinity revealed 419 X-ray structures exhibiting CF3⋯A tetrel bonds (TtBs). In a posterior stage, those hits that exhibited the most relevant features in terms of directionality and intermolecular distance were selected for theoretical calculations at the RI-MP2/def2-TZVPD level of theory. Also, Hammett's regression plots of several TtB complexes involving meta- and para-substituted benzene derivatives were computed to shed light on the substituent effects. Moreover, the TtBs were characterized through several state-of-the-art computational techniques, such as the Quantum Theory of Atoms in Molecules (QTAIM) and Noncovalent Interactions plot (NCIplot) methodologies. We believe that the results gathered from our study will be useful for rational drug design and biological communities as well as for further expanding the role of this interaction to biomedical applications.

One-Pot Environmentally Friendly Synthesis of Nanomaterials Based on Phytate-Coated Fe3O4 Nanoparticles for Efficient Removal of the Radioactive Metal Ions 90Sr, 90Y and (UO2)2+ from Water.

We report the fast (three minutes) synthesis of green nanoparticles based on nanoparticles coated with the natural organic receptor phytate for the recognition and capture of 90Sr, 90Y, and (UO2)2+. The new material shows excellent retention for (UO2)2+, 97%; these values were 73% and 100% for 90Sr and 90Y, respectively. Recovery of the three radioactive metal ions occurs through a non-competitive process. The new hybrid material is harmless, easy to prepare, and immobilizes these radioactive contaminants in water with great efficiency.

Importance of Anion-π Interactions in RNA GAAA and GGAG Tetraloops: A Combined MD and QM Study.

In this study, we demonstrate that anion-π interactions (an attractive noncovalent force between electron deficient π-systems and anions) are involved in the stabilization of GAAA and GGAG RNA tetraloops. Using the single recognition particle (SRP)-RNA complexes as a case of study, we combined molecular dynamics (MD) and quantum mechanics (QM) calculations to shed light on the structural influence of phosphate-G anion-π interactions and hydrogen bonds (HBs) involving K+/Mg2+ water clusters. In addition, the RNA assemblies herein were further characterized by means of the "atoms in molecules" (AIM) and noncovalent interactions plot (NCIplot) methodologies. We believe the results derived from this study might be important in the fields of chemical biology (RNA folding and engineering) and supramolecular chemistry (anion-π interactions) as well as to further expand the current knowledge regarding RNA structural motifs.

Determination of Antioxidant Activity by Oxygen Radical Absorbance Capacity (ORAC-FL), Cellular Antioxidant Activity (CAA), Electrochemical and Microbiological Analyses of Silver Nanoparticles Using the Aqueous Leaf Extract of Solanum mammosum L.

PURPOSE: The importance of studying polyphenolic compounds as natural antioxidants has encouraged the search for new methods of analysis that are quick and simple. The synthesis of silver nanoparticles (AgNPs) using plant extracts has been presented as an alternative to determine the total polyphenolic content and its antioxidant activity. METHODS: In this study, aqueous leaf extract of Solanum mammosum, a species of plant endemic to South America, was used to produce AgNPs. The technique of oxygen radical absorption capacity using fluorescein (ORAC-FL) was used to measure antioxidant activity. The oxidation of the 2´,7´-dichlorodihydrofluorescein diacetate (DCFH2-DA) as fluorescent probe was used to measure cellular antioxidant activity (CAA). Electrochemical behavior was also examined using differential pulse voltammetry (DPV) and cyclic voltammetry (CV). Total polyphenolic content (TPH) was analyzed using the Folin-Ciocalteu method, and the major polyphenolic compound was analyzed by high performance liquid chromatography with diode array detector (HPLC/DAD). Finally, a microbial analysis was conducted using Escherichia coli and Bacillus sp. RESULTS: The average size of nanoparticles was 5.2 ± 2.3 nm measured by high-resolution transmission electron microscopy (HR-TEM). The antioxidant activity measured by ORAC-FL in the extract and nanoparticles were 3944 ± 112 and 637.5 ± 14.8 µM ET/g of sample, respectively. Cellular antioxidant activity was 14.7 ± 0.2 for the aqueous extract and 12.5 ± 0.2 for the nanoparticles. The electrochemical index (EI) was 402 µA/V for the extract and 324 µA/V for the nanoparticles. Total polyphenolic content was 826.6 ± 20.9 and 139.7 ± 20.9 mg EGA/100 g of sample. Gallic acid was the main polyphenolic compound present in the leaf extract. Microbiological analysis revealed that although leaf extract was not toxic for Escherichia coli and Bacillus sp., minor toxic activity for AgNPs was detected for both strains. CONCLUSION: It is concluded that the aqueous extract of the leaves of S. mammosum contains nontoxic antioxidant compounds capable of producing AgNPs. The methods using AgNPs can be used as a fast analytical tool to monitor the presence of water-soluble polyphenolic compounds from plant origin. Analysis and detection of new antioxidants from plant extracts may be potentially applicable in biomedicine.

Charge Assisted S/Se Chalcogen Bonds in SAM Riboswitches: A Combined PDB and ab Initio Study.

In this study, we provide experimental (Protein Data Bank (PDB) inspection) and theoretical (RI-MP2/def2-TZVP level of theory) evidence of the involvement of charge assisted chalcogen bonding (ChB) interactions in the recognition and folding mechanisms of S-adenosylmethionine (SAM) riboswitches. Concretely, an initial PDB search revealed several examples where ChBs between S-adenosyl methionine (SAM)/adenosyl selenomethionine (EEM) molecules and uracil (U) bases belonging to RNA take place. While these interactions are usually described as a merely Coulombic attraction between the positively charged S/Se group and RNA, theoretical calculations indicated that the σ holes of S and Se are involved. Moreover, computational models shed light on the strength and directionality properties of the interaction, which was also further characterized from a charge-density perspective using Bader's "Atoms in Molecules" (AIM) theory, Non-Covalent Interaction plot (NCIplot) visual index, and Natural Bonding Orbital (NBO) analyses. As far as our knowledge extends, this is the first time that ChBs in SAM-RNA complexes have been systematically analyzed, and we believe the results might be useful for scientists working in the field of RNA engineering and chemical biology as well as to increase the visibility of the interaction among the biological community.

Fertility and Iron Bioaccumulation in Drosophila melanogaster Fed with Magnetite Nanoparticles Using a Validated Method.

Research on nanomaterial exposure-related health risks is still quite limited; this includes standardizing methods for measuring metals in living organisms. Thus, this study validated an atomic absorption spectrophotometry method to determine fertility and bioaccumulated iron content in Drosophila melanogaster flies after feeding them magnetite nanoparticles (Fe3O4NPs) dosed in a culture medium (100, 250, 500, and 1000 mg kg-1). Some NPs were also coated with chitosan to compare iron assimilation. Considering both accuracy and precision, results showed the method was optimal for concentrations greater than 20 mg L-1. Recovery values were considered optimum within the 95-105% range. Regarding fertility, offspring for each coated and non-coated NPs concentration decreased in relation to the control group. Flies exposed to 100 mg L-1 of coated NPs presented the lowest fertility level and highest bioaccumulation factor. Despite an association between iron bioaccumulation and NPs concentration, the 500 mg L-1 dose of coated and non-coated NPs showed similar iron concentrations to those of the control group. Thus, Drosophila flies' fertility decreased after NPs exposure, while iron bioaccumulation was related to NPs concentration and coating. We determined this method can overcome sample limitations and biological matrix-associated heterogeneity, thus allowing for bioaccumulated iron detection regardless of exposure to coated or non-coated magnetite NPs, meaning this protocol could be applicable with any type of iron NPs.

Silver nanoparticles as a potential treatment against SARS-CoV-2: A review.

Several human coronaviruses (HCoVs) are distinguished by the ability to generate epidemics or pandemics, with their corresponding diseases characterized by severe respiratory illness, such as that which occurs in severe acute respiratory syndrome (SARS-CoV), Middle East respiratory syndrome (MERS-CoV), and, today, in SARS-CoV-2, an outbreak that has struck explosively and uncontrollably beginning in December 2019 and has claimed the lives of more than 1.9 M people worldwide as of January 2021. The development of vaccines has taken one year, which is why it is necessary to investigate whether some already-existing alternatives that have been successfully developed in recent years can mitigate the pandemic's advance. Silver nanoparticles (AgNPs) have proved effective in antiviral action. Thus, in this review, several in vitro and in vivo studies of the effect of AgNPs on viruses that cause respiratory diseases are analyzed and discussed to promote an understanding of the possible interaction of AgNPs with SARS-CoV-2. The study focuses on several in vivo toxicological studies of AgNPs and a dose extrapolation to humans to determine the chief avenue of exposure. It can be concluded that the use of AgNPs as a possible treatment for SARS-CoV-2 could be viable, based on comparing the virus' behavior to that of similar viruses in in vivo studies, and that the suggested route of administration in terms of least degree of adverse effects is inhalation. This article is categorized under: Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Therapeutic Approaches and Drug Discovery > Nanomedicine for Respiratory Disease Toxicology and Regulatory Issues in Nanomedicine > Toxicology of Nanomaterials.

Regium-π Bonds Are Involved in Protein-Gold Binding.

The regium-π interaction is an attractive noncovalent force between group 11 elements (Cu, Ag, and Au) acting as Lewis acids and aromatic surfaces. Herein, we report for the first time experimental (Protein Data Bank analysis) and theoretical (RI-MP2/def2-TZVP level of theory) evidence of regium-π bonds involving Au(I) and aromatic amino acids (Phe, Tyr, Trp, and His). These findings might be important in the field of drug design and for retrospectively understanding the role of gold in proteins.

Quantifying Intramolecular Halogen Bonds in Nucleic Acids: A Combined Protein Data Bank and Theoretical Study.

In this study, we report experimental (Protein Data Bank (PDB) search) and theoretical (RI-MP2/def2-TZVP level of theory) evidence of the nature, stability, and directionality properties of intramolecular halogen bonding interactions (HaBs) between 5-bromo/5-iodoracil bases and backbone phosphate groups in nucleic acids (NAs). A PDB survey revealed relevant examples where intramolecular HaBs are undertaken and serve as a structural source of stability in RNA and DNA molecules. In order to develop suitable energy predictors, we started this investigation by calculating the interaction energy values and both the potential V(r) and kinetic G(r) energy densities (using Bader's "atoms in molecules" theory) of several halogen bond complexes involving 5-bromo/5-iodoracil molecules and biologically relevant electron donors. Once the energy predictors based on V(r)/G(r) energy densities were developed, we analyzed the HaBs observed in the biological examples retrieved from the PDB search in order to estimate the strength of the interaction. As far as our knowledge extends, intramolecular halogen bonds in NAs have not been previously quantified in the literature using this methodology and may be of great importance in understanding their structural properties as well as in the construction of molecular materials with DNA and other biological macromolecules.

Halogenhalogen interactions in decahalo-closo-carboranes: CSD analysis and theoretical study.

The ability of decachloro, decabromo and decaiodo ortho, meta and para-closo-carboranes to establish "like-like" halogenhalogen interactions is evaluated in this study using the PBE0-D3/def2-TZVP level of theory. We have used three decahalocloso isomers (ortho-, meta-, and para-) and computed both homodimers and heterodimers. The resulting dimerization energies (B-XX-B) are moderately strong. Furthermore, we have used Bader's quantum theory of "atoms in molecules" (QTAIM) to characterize the type I/II halogenhalogen interactions described herein. Moreover, several examples retrieved from the Cambridge Structural Database (CSD) are also highlighted to show the ability of decahalo-closo-carboranes to participate in "like-like" halogen bonds.

Influence of the aromatic surface on the capacity of adsorption of VOCs by magnetite supported organic-inorganic hybrids.

It has been recently evidenced that hybrid magnetic nanomaterials based on perylene diimide (PDI) dopamine and iron oxide nanoparticles are useful for the adsorption and determination of volatile organic compounds (VOCs). However, NDI compounds are expensive and difficult to handle compared to smaller size diimides. Therefore, in this manuscript a combined experimental and theoretical investigation is reported including the analysis of the effect of changing the aromatic surface on the ability of these magnetite supported organic-inorganic hybrid nanoparticles (NPs) to adsorb several aromatic and non-aromatic VOCs. In particular, two new hybrid Fe3O4NPs are synthesized and characterized where the size of organic PDI dopamine linker is progressively reduced to naphthalene diimide (NDI) and pyromellitic diimide (PMDI). These materials were utilized to fill two sorbent tubes in series. Thermal desorption (TD) combined with capillary gas chromatography (GC)/flame detector (FID) was used to analyze both front and back tubes. Adsorption values (defined as % VOCs found in the front tube) were determined for a series of VOCs. The binding energies (DFT-D3 calculations) of VOC-Fe3O4NP complexes were also computed to correlate the electron-accepting ability of the arylene diimide (PDI, NDI or PMDI) with the adsorption capacity of the different tubes. The prepared hybrids can be easily separated magnetically and showed great reusability.