1–D Framework l-arginine zinc(II) units bridged by oxalate: synthesis,structure, properties,and theoretical studies

We synthesized a l-arginine containing Zn²⁺ complex and oxalate ions. {[Zn₂(l-Arg)₂(ox)₂]·8H₂O}_n (1) (l-Arg =l-arginine, ox = oxalate) crystallize in the monoclinic space group P2₁ with a = 8.979(2), b = 9.840(2) (Å), c = 18.509(3) (Å), β = 95.58(3) (Å), V = 1627.6(6) ų, and Z = 2. The zinc centers are six-coordinate via one l-arginine zwitterion and two bridging oxalates. The binuclear [Zn₂(l-Arg)₂(ox)₂] units are linked via oxalate and form 1-D “stair-like” linear chains. The complex was characterized using FT-IR, FT-Raman, UV–vis spectroscopy, and thermal analysis techniques, as well as DFT methods. Electronic bands above 31,000 cm^?1 originate in ^1,3A_u (n→π*) transitions within oxalate ions. Theoretical studies were performed for the model compound {[Zn(l-Arg)(Hox)₂]·4H₂O} using the fragment of the crystallographic structure of 1. The interaction energy (ΔE) values for l-arginine and two oxalate ions are comparable at -145 kcal mol^?1. Natural bond orbital (NBO) analysis of the electronic structure and bonding is also discussed.     

How many electrons form chemical bonds in the NgBeS (Ng = Ar,Kr, Xe) molecules? Topological study using the electron localisation function (ELF) and electron localisability indicator (ELI-D)

Nature of bonding in the NgBeS (Ng = Ar, Kr, Xe) molecules has been studied using topological analysis of ELF, ELI-D functions with the wave function approximated at the DFT (M062X, B3LYP + ZORA), MP2, CCSD and CASSCF level of calculations. Both Xe–Be and Be=S bonds display topological features typical for the covalent-dative bonding. The V₂(Xe) attractor characterising electron density, involved in interaction with the beryllium atom, is closer to the C(Be) core than to C(Xe). The population of the respective basin ranges between 1.59e (B3LYP + ZORA) and 1.83e (CCSD). The beryllium–sulphur bond is described by the bonding disynaptic basin V(Be,S) with the population between 3.22e (CASSCF) and 3.48e (M062X). The approximate weights for the Be–S and Be=S resonance forms are 0.3 and 0.7, respectively, in all molecules. Both the NgBe and BeS bonds are highly polarised with the values of the p _SBe and p _NgBe polarity indices (CCSD) of 0.8 and 0.9–1.0 for all studied molecules.     

Coevolution of information processing and topology in hierarchical adaptive random Boolean networks

Random Boolean Networks (RBNs) are frequently used for modeling complex systems driven by information processing, e.g. for gene regulatory networks (GRNs). Here we propose a hierarchical adaptive random Boolean Network (HARBN) as a system consisting of distinct adaptive RBNs (ARBNs) – subnetworks – connected by a set of permanent interlinks. We investigate mean node information, mean edge information as well as mean node degree. Information measures and internal subnetworks topology of HARBN coevolve and reach steady-states that are specific for a given network structure. The main natural feature of ARBNs, i.e. their adaptability, is preserved in HARBNs and they evolve towards critical configurations which is documented by power law distributions of network attractor lengths. The mean information processed by a single node or a single link increases with the number of interlinks added to the system. The mean length of network attractors and the mean steady-state connectivity possess minima for certain specific values of the quotient between the density of interlinks and the density of all links in networks. It means that the modular network displays extremal values of its observables when subnetworks are connected with a density a few times lower than a mean density of all links.     

Conformational indeterminism in protein misfolding: chiral amplification on amyloidogenic pathway of insulin

Unlike folding, protein aggregation is a multipathway, kinetically controlled process yielding different conformations of fibrils. The dynamics and determinism/indeterminism boundaries of misfolded conformations remain obscure. Here we show that, upon vortexing, insulin forms two distinct types of fibrils with opposite local chiral preferences, which manifest in the opposite twists of bound dye, thioflavin T. Occurrence of either type of fibrils in a test tube is only stochastically determined. By acting through an autocatalytic, "chiral amplification"-like mechanism, a random conformational fluctuation triggers conversion of the macroscopic amount of insulin into aggregates with uniformly biased chiral moieties, which bind and twist likewise the achiral dye. Although a convection-driven chiral amplification in achiral systems, which results in randomly distributed excesses of optically active forms, is known, observation of such a phenomenon in misfolded protein built of l-amino acids is unprecedented. The two optical variants of insulin fibrils show distinct morphologies and can propagate their chiral biases upon seeding to nonagitated insulin solutions. Our findings point to a new aspect of topological complexity of protein fibrils: a chiral feature of hierarchically assembled polypeptides, which is partly emancipated from the innate left-handedness of amino acids. Because altering chirality of a molecule changes dramatically its biological activity, the finding may have important ramifications in the context of the structural basis of "amyloid strains".     

Nucleoside-metallacarborane conjugates for base-specific metal labeling of DNA

A general approach to the synthesis of nucleoside conjugates between derivatives of thymidine (T), 2'-O-deoxycytidine (dC), 2'-O-deoxyadenosine (dA), and 2'-O-deoxyguanosine (dG), and metallacarborane complexes is described. Metallacarborane-nucleoside derivatives are prepared by reaction of the dioxane-metallacarborane adduct with a base-activated 3',5'-protected nucleoside. In the case of T and dG a mixture of regioisomers, which is easily separable by chromatographic methods, is obtained, thus yielding a series of modifications containing metallacarborane groups at the 2-O, 3-N, 4-O and 1-N, 2-N, 6-O locations, respectively; dC and dA are alkylated at the exo-amino function. The proposed methodology provides a route for the synthesis and study of nucleic acids modified with metallacarboranes at designated locations and a versatile approach to the incorporation of metals into DNA.     

High-performance thin-layer chromatography method for quantitative determination of oenothein B and quercetin glucuronide in aqueous extract of Epilobii angustifolii herba

A method was developed for separation and quantitative determination of oenothein B (OeB) and quercetin glucuronide (QG) in aqueous extract of Epilobii angustifolii herba by HPTLC-densitometry. The analyses were performed on HPTLC RP-18 WF(254) plates with 25% MeCN in water (+50mM H(3)PO(4)) as the mobile phase (distance of 8 cm) for OeB quantification and then with acetonitrile (distance of 4 cm) for QG quantification. OeB and QG were determined by densitometry at 270 and 350 nm, respectively. Their amounts were calculated using the regression equations of the calibration curves which were linear in a range of 1.14-2.28 microg spot(-1) for OeB and of 0.0768-0.6912 microg spot(-1) for QG. The amounts of OeB and QG in aqueous extract of Epilobii angustifolii herba measured by the method developed were 152.46+/-4.92 and 22.07+/-1.38 mg g(-1), respectively. The method was found to be relatively simple, specific, precise and accurate for the quality control of Epilobium angustifolium extracts.     

Ethyl Lauroyl Arginate,an Inherently Multicomponent Surfactant System

Ethyl lauroyl arginate (LAE) is an amino acid-based cationic surfactant with low toxicity and antimicrobial activity. It is widely used as a food preservative and component for food packaging. When stored, LAE decomposes by hydrolysis into surface-active components Nα-lauroyl–l-arginine (LAS) or dodecanoic (lauric) acid. There are only a limited number of reports considering the mechanism of surface activity of LAE. Thus, we analysed the surface tension isotherm of LAE with analytical standard purity in relation to LAE after prolonged storage. We used quantum mechanical density functional theory (DFT) computations to determine the preferred hydrolysis path and discuss the possibility of forming highly surface-active heterodimers, LAE-dodecanoate anion, or LAE-LAS. Applying molecular dynamics simulations, we determined the stability of those dimers linked by electrostatic interactions and hydrogen bonds. We used the adsorption model of surfactant mixtures to successfully describe the experimental surface tension isotherms. The real part surface dilational modulus determined by the oscillation drop method follows a diffusional transport mechanism. However, the nonlinear response of the surface tension could be observed for LAE concentration close to and above Critical Micelle Concentration (CMC). Nonlinearity originates from the presence of micelles and the reorganisation of the interfacial layer.     

l-Arginine Improves Solubility and ANTI SARS-CoV-2 Mpro Activity of Rutin but Not the Antiviral Activity in Cells

The COVID-19 pandemic outbreak prompts an urgent need for efficient therapeutics, and repurposing of known drugs has been extensively used in an attempt to get to anti-SARS-CoV-2 agents in the shortest possible time. The glycoside rutin shows manifold pharmacological activities and, despite its use being limited by its poor solubility in water, it is the active principle of many pharmaceutical preparations. We herein report our in silico and experimental investigations of rutin as a SARS-CoV-2 Mpro inhibitor and of its water solubility improvement obtained by mixing it with l-arginine. Tests of the rutin/l-arginine mixture in a cellular model of SARS-CoV-2 infection highlighted that the mixture still suffers from unfavorable pharmacokinetic properties, but nonetheless, the results of this study suggest that rutin might be a good starting point for hit optimization.