Computational simulation of interactions between SARS coronavirus spike mutants and host species-specific receptors

As a critical adaptive mechanism, amino acid replacements on the severe acute respiratory syndrome coronavirus (SARS-CoV) spike protein could alter the receptor-binding specificity of this envelope glycoprotein and in turn lead to the emergence or reemergence of this viral zoonosis. Based on the X-ray structures of SARS-CoV spike receptor-binding domain (RBD) in complex with its functional receptor (angiotensin-converting enzyme 2, ACE2), we perform computational simulations of interactions between three representative RBD mutants and four host species-specific receptors. The comparisons between computational predictions and experimental evidences validate our structural bioinformatics approaches. And the predictions further indicate that some viral prototypes might utilize the rat ACE2 while rats might serve as a vector or reservoir of SARS-CoV.     

Comparative study on the structural, optical, and electrochemical properties of bithiophene-fused benzo[c]phospholes

Three types of bithiophene-fused benzo[c]phospholes were successfully prepared by Ti(II)-mediated cyclization of the corresponding dialkynylated bithiophene derivatives as a key step. Each sigma(3)-phosphorus center of the benzo[c]phosphole subunits was readily transformed into sigma(4)-phosphorus center by Au coordination or oxygenation. In addition, the bithiophene subunit was functionalized at the alpha,alpha'-carbon atoms by Pd-catalyzed cross-coupling reactions with heteroarylmetals and by an S(N)Ar reaction with hexafluorobenzene. The experimentally observed results (NMR spectroscopy, X-ray analysis, UV/Vis absorption/fluorescence spectroscopy, and cyclic/differential-pulse voltammetry) have revealed that the structural, optical, and electrochemical properties of the bithiophene-fused benzo[c]phospholes vary considerably depending on the pi-conjugation modes at the bithiophene subunits and the substituents of the heterocyclopentadiene components. The appropriately ring-annulated sigma(3)-P derivatives and sigma(4)-P-AuCl complexes were found to emit fluorescence in the orange-red region, and the sigma(4)-P-oxo derivatives proved to undergo reversible one-electron reduction at -1.4 to -1.8 V (vs ferrocene/ferrocenium). These results indicate that the bithiophene-fused benzo[c]phospholes possess narrow HOMO-LUMO gaps and low-lying LUMOs, which was confirmed by density functional theory calculations of their model compounds. The time-of-flight measurement of an ITO/benzo[c]phosphole/Al device showed that the electron mobility in the P-oxo derivative is one-order higher than that in Alq(3) at low electric fields. The present study demonstrates that the arene-fused benzo[c]phosphole skeleton could be a highly promising platform for the construction of a new class of phosphole-based optoelectrochemical materials.     

Structural and binding study of modified siRNAs with the Argonaute 2 PAZ domain by NMR spectroscopy

By using high-resolution NMR spectroscopy, the structures of a natural short interfering RNA (siRNA) and of several altritol nucleic acid (ANA)-modified siRNAs were determined. The interaction of modified siRNAs with the PAZ domain of the Argonaute 2 protein of Drosophila melanogaster was also studied. The structures show that the modified siRNA duplexes (ANA/RNA) adopt a geometry very similar to the naturally occurring A-type siRNA duplex. All ribose residues, except for the 3' overhang, show 3'-endo conformation. The six-membered altritol sugar in ANA occurs in a chair conformation with the nucleobase in an axial position. In all siRNA duplexes, two overhanging nucleotides at the 3' end enhance the stability of the first neighboring base pair by a stacking interaction. The first overhanging nucleotide has a rather fixed position, whereas the second overhanging nucleotide shows larger flexibility. NMR binding studies of the PAZ domain with ANA-modified siRNAs demonstrate that modifications in the double-stranded region of the antisense strand have some small effects on the binding affinity as compared with the unmodified siRNA. Modification of the 3' overhang with thymidine (dTdT) residues shows a sixfold increase in the binding affinity compared with the unmodified siRNA (relative binding affinity of 17% compared with dTdT-modified overhang), whereas modification of the 3' overhang with ANA largely decreases the binding affinity.     

A DFT study of the interaction between microhydrated anions and naphthalendiimides

The characteristics of the interaction of anions with naphthalendiimides, the basic structural motif of a newly synthesized anion channel based on anion···π interactions, are studied by computational methods. Stable complexes are formed with bromide, chloride, fluoride or hydroxide anions, which exhibit strong anion···π interactions in the gas phase. Following the sequence of the polarizing power of the anions, hydroxide and fluoride complexes are the most strongly interacting. The presence of a small number of water molecules strongly affects the anion···π interactions, especially for hydroxide and fluoride complexes, so the differences in interaction strength among the anions drop significantly. The calculations suggest that a small number of water molecules can be crucial to reducing dehydration cost and contributing to stabilizing interactions with the naphthalendiimide units.     

Genetic and expression analysis of all non‐synonymous single nucleotide polymorphisms in the human deoxyribonuclease I‐like 1 and 2 genes

Members of the human DNase I family, DNase I‐like 1 and 2 (DNases 1L1 and 1L2), with physiological role(s) other than those of DNase I, possess three and one non‐synonymous SNPs in the genes, respectively. However, only limited population data are available, and the effect of these SNPs on the catalytic activity of the enzyme remains unknown. Genotyping of all the non‐synonymous SNPs was performed in three ethnic groups including six different populations using the PCR‐RFLP method newly developed. Asian and African groups including Japanese, Koreans, Ghanaians and Ovambos were typed as a single genotype at each SNP, but polymorphism at only SNP V122I in DNase 1L1 was found in Caucasian groups including Germans and Turks; thus a Caucasian‐specific allele was identified. The DNase 1L1 and 1L2 genes show relatively low genetic diversity with regard to these non‐synonymous SNPs. The level of activity derived from the V122I, Q170H and D227A substituted DNase 1L1 corresponding to SNPs was similar to that of the wild‐type, whereas replacement of the Asp residue at position 197 in the DNase 1L2 protein with Ala, corresponding to SNP D197A, reduced its activity greatly. Thus, SNP V122I in DNase 1L1 exhibiting polymorphism exerts no effect on the catalytic activity, and furthermore SNP D197A in DNase 1L2, affecting its catalytic activity, shows no polymorphism. These findings permit us to postulate that the non‐synonymous SNPs identified in the DNase 1L1 and 1L2 genes may exert no influence on the activity levels of DNases 1L1 and 1L2 in human populations.     

Ab initio study of chemical bond interactions between covalently functionalized carbon nanotubes via amide,ester and anhydride linkages

In this paper, we have investigated the chemical bond interactions between covalently functionalized zigzag (5,0) and (8,0) SWCNT–SWCNT via various covalent linkages. Side-to-side junctions connected via amide, ester and anhydride linkages were particularly studied. The geometries and energy of the forming reaction were investigated using first-principles density functional theory. Furthermore, the band structures and the total density of states (DOS) of the junctions have also been analyzed. Our results show that several promising structures could be obtained by using chemical connection strategy and particularly the junctions formed by coupling amino functionalized SWCNT and carboxylic acid functionalized SWCNT was more favorable.     

Rheological study of the pH-dependence of interactions between gelatin and anionic surfactants: flow behaviour and gelation

The interactions between gelatin and two anionic surfactants (sodium di-sec-butylnaphthalenesulfonate and sodium dodecylbenzenesulfonate, respectively) were investigated using rheological methods, charge and surface tension measurements. Upon the addition of surfactants, the viscosity of aqueous gelatin solutions increases at pH values higher than the isoelectric point (IEP) of the gelatin, provided that a distinct surfactant concentration is exceeded. The increase in viscosity depends on the structure of the hydrophobic moiety of the surfactant. Surface tension measurements suggest the formation of gelatin-surfactant-complexes. If the surfactant is added in high concentration, the viscosity does not further increase, and free micelles are formed in the solution. Directly at the IEP and at pH values below, the addition of surfactants leads to flocculation because of electrostatic interactions. At all surfactant concentrations, the flow behaviour was strictly Newtonian. As a model of the structure of the complex, a modified bead and necklace-model is suggested. This model proposes the nucleation of micelles at the hydrophobic gelatin regions (micellar surfactant-gelatin complexes). The number of micelle moieties per gelatin chain could be estimated to be about three. The complex stability is dependent on the extent of hydrophobic interaction.The gelation behaviour of gelatin is strongly affected by the addition of the surfactant. The ratio between the attainable linear storage and loss moduli,G andG, decreases strongly. Gelation is generally hindered, but the effect is stronger at pH values below the IEP than above.     

A molecular theory of inhomogeneous broadening,including the correlation between different transitions,in liquids and glasses

Summary We present a molecular theory of the energy distributions for the internal quantum states of a solute in a liquid or glassy solvent. We show that the energy distributions for different states are correlated in a way that depends on the solute-solvent interactions. We show how the theory can be modified easily to describe the transition-energy distributions for different pairs of states, which are of course related to inhomogeneously broadened absorption spectra. We also show that the distributions for different transitions are correlated, and describe how this correlation is measured by nonresonant fluorescence- and phosphorescence-line-narrowing and hole-burning experiments. The theory provides a microscopic framework within which to interpret different phenomenological models. For the case of a Lennard-Jones solute in a Lennard-Jones liquid solvent, we compare our theory to Monte Carlo simulation.     

Evaluation of binding performance of bioactive compounds against main protease and mutant model spike receptor binding domain of SARS-CoV-2: Docking,ADMET properties and molecular dynamics simulation study

Phytochemicals present in medicinal plants have a variety of biological activities that help to combat against diseases. As part of efforts to study the binding performance of different phytochemicals derived from different plants like Zingiber officinale, Citrus limon, Syzygiumaromaticum, Ocimum tenuiflorum and Curcumin. We have screened 424 molecules. The binding affinity as well as physicochemical properties of the thebaine, acacetin, indomethacin, crinamineacetate, (S)-1-Piperideine-6-carboxylate, levamisole, melatonin, nicotinicacid, curcumin, methotrimeprazine, omeprazole, and methaqualone phytocompounds were analyzed through computational study. From the molecular docking study we found that, LEU50, ASN72, PRO96, TYR154, GLY170, ALA193, ARG222, and MET274 residues of main protease play a crucial role in binding with ligands. The present study revealed a noticeable interaction of GLY446, SER477, GLY482, THR500 and LEU518 residues with mutant of spike receptor binding domain SARS-CoV-2 protein were observed. Finally, 100 ns molecular dynamics simulation were used to study their dynamic properties as well as conformational flexibility. Free energy landscape analysis was performed of the 6LU7- acacetin and 6Y2E-acacetin systems and spike RBD-acacetin system. From molecular docking study and molecular dynamics study revealed that, the compound acacetin shows promising inhibitor towards both main protease as well as mutant spike RBD of SARS-CoV-2 protein.     

Simultaneous determination of nitrite, nitrate, thiocyanate and uric acid in human saliva by capillary zone electrophoresis and its application to the study of daily variations

Simultaneous determination of nitrite (NO2-), nitrate (NO3-), thiocyanate (SCN-) and uric acid in human saliva was performed by capillary zone electrophoresis using a coated capillary with reversed electroosmotic flow (EOF), using a 100 mM sodium phosphate buffer at pH 6.5 as a running buffer. Saliva samples were deproteinized with acetonitrile and filtered through a membrane filter. The important advantages of the reported method are: simple operation, short analysis time, minimal sample pre-treatment and sample dilution. In order to evaluate the daily variations of the anionic components, the concentrations were determined in the human saliva of four healthy volunteers upon waking and at 2qh intervals during a day.     

Determinism and randomness in the evolution of introns and sine inserts in mouse and human mitochondrial solute carrier and cytokine receptor genes

In the homologous genes studied, the exons and introns alternated in the same order in mouse and human. We studied, in both species: corresponding short segments of introns, whole corresponding introns and complete homologous genes. We considered the total number of nucleotides and the number and orientation of the SINE inserts. Comparisons of mouse and human data series showed that at the level of individual relatively short segments of intronic sequences the stochastic variability prevails in the local structuring, but at higher levels of organization a deterministic component emerges, conserved in mouse and human during the divergent evolution, despite the ample re-editing of the intronic sequences and the fact that processes such as SINE spread had taken place in an independent way in the two species. Intron conservation is negatively correlated with the SINE occupancy, suggesting that virus inserts interfere with the conservation of the sequences inherited from the common ancestor.     

Toward a Consistent Interpretation of the QTAIM: Tortuous Link between Chemical Bonds,Interactions, and Bond/Line Paths

Currently, bonding analysis of molecules based on the Quantum Theory of Atoms in Molecules (QTAIM) is popular; however, “misinterpretations” of the QTAIM analysis are also very frequent. In this contribution the chemical relevance of the bond path as one of the key topological entities emerging from the QTAIM’s topological analysis of the one‐electron density is reconsidered. The role of nuclear vibrations on the topological analysis is investigated demonstrating that the bond paths are not indicators of chemical bonds. Also, it is argued that the detection of the bond paths is not necessary for the “interaction” to be present between two atoms in a molecule. The conceptual disentanglement of chemical bonds/interactions from the bonds paths, which are alternatively termed “line paths” in this contribution, dismisses many superficial inconsistencies. Such inconsistencies emerge from the presence/absence of the line paths in places of a molecule in which chemical intuition or alternative bonding analysis does not support the presence/absence of a chemical bond. Moreover, computational QTAIM studies have been performed on some “problematic” molecules, which were considered previously by other authors, and the role of nuclear vibrations on presence/absence of the line paths is studied demonstrating that a bonding pattern consistent with other theoretical schemes appears after a careful QTAIM analysis and a new “interpretation” of data is performed.     

Synthesis, X-ray diffraction and computational study of the crystal packing of polycyclic hydrocarbons featuring aromatic and perfluoroaromatic rings condensed in the same molecule: 1,2,3,4-tetrafluoronaphthalene, -anthracene and -phenanthrene

We have synthesised some planar polycyclic compounds, in which unsubstituted aromatic rings are condensed with perfluorinated aromatic rings, and have carried out a combined X-ray diffraction and computational study to analyse their self-recognition behaviour in crystalline phases. We compare our results with the parent hydrocarbons and with other compounds that have a variable degree of fluorination. Whereas the molecular planes in crystals of hydrocarbons with mono- or difluorinated aromatic rings or of perfluorinated compounds arrange themselves in V-shaped configurations, our present results show that perfluorinated rings tend to stack over unsubstituted rings even when these two moieties coexist in a condensed system, producing crystalline materials with parallel molecular layers with the arene-perfluoroarene recognition pattern. Our analysis shows that the packing energy of all these crystals is dispersion-dominated and that coulombic terms are selective rather than quantitatively predominant in crystals with arene-perfluoroarene interactions. No compelling proof of a special role of C-H...F interactions has been found.     

Fluorimetric study of the interaction between human serum albumin and quinolones-terbium complex and its application

A highly sensitive spectrofluorimetric method is proposed for determination of human serum albumin (HSA) and some quinolone drugs. Using quinolones-terbium (Tb3+) complex as a fluorescent probe, in the buffer solution of pH 7.8, HSA can remarkably enhance the fluorescence intensity of the quinolones-Tb3+ complex at 545 nm and the enhanced fluorescence intensity of Tb3+ ion is in proportion to the concentration of HSA and quinolone drugs. Optimum conditions for the determination of HSA were also investigated. The linear ranges and limits of detection are 8.0 x 10(-9) to 8.0 x 10(-8) mol L(-1), 4.20 x 10(-9) mol L(-1) (for HSA); 1.0 x 10(-6) to 4.0 x 10(-6) mol L(-1), 1.87 x 10(-8) mol L(-1) (for norfloxacin) and 1.0 x 10(-7) to 1.0 x 10(-6) mol L(-1), 4.82 x 10(-8) mol L(-1) (for enoxacine), respectively. This method is simple, practical and relatively free interference from coexisting substances, as well as much more sensitive than most of the existing assays.     

Crystallographic and first-principles density functional theory study on the structure,noncovalent interactions,and chemical reactivity of 1,5-benzodiazepin-2-ones derivatives

The present work arose out of a desire to fundamentally understand the molecular geometry, weak interactions, electron density delocalization, and chemical reactivity features of 1,5-benzodiazepines-containing family. Herein, a complete X-ray crystallographic study, supported by trustworthy sets of computational approaches, has been reported for two organic crystals. Quantifying intramolecular and intermolecular interactions by Hirshfeld-Becke surfaces analysis conjointly with noncovalent interaction-reduced density gradient topological study revealed that supramolecular assemblies are stabilized by N-H ^… O (inter) and O-H ^… N (intra) hydrogen bonds, Cg ^… Cg (π ^… π) and C-H(O) ^… π intercontacts, as well as Van der Waals interactions and steric effects. The long-range-corrected functional wB97XD, which uses Grimme's D2 dispersion model, seems to be just right for our systems. The quantum theory of atoms in molecules analysis confirms that both significant O1-H1…N1 and N2-H2A…O2 H-bonds are weak and electrostatic in nature. Furthermore, global reactivity indices computed via the conceptual density functional theory framework allows these molecules to be classified as moderate electrophiles and marginal nucleophiles. The active sites favorable for nucleophilic/electrophilic attacks were also predicted based on local Parr functions. Finally, a comparative evaluation on the aromaticity character and π-π stacking ability has been done for different (pseudo) rings.     

An in-silico approach to study the possible interactions of miRNA between human and SARS-CoV2

BackgroundThe progressive SARS-CoV2 outbreaks worldwide have evoked global investigation. Despite the numerousin-silico approaches, the virus-host relationship remains a serious concern. MicroRNAs are the small non-coding RNAs that help in regulating gene profiling. The current study utilized miRNA prediction tools along with the PANTHER classification system to demonstrate association and sequence similarities shared between miRNAs of SARS-CoV2 and human host.MethodAn in-silico approach was carried out using Vmir analyzer to predict miRNAs from SARS-CoV2 viral genomes. Predicted miRNAs from SARS-CoV2 viral genomes were used for effective hybridization sequence identification along the nucleotide similarities with human miRNAs from miRbase database. Further, it was proceeded to analyze the gene ontology using miRDB with PANTHER classification.ResultBased on the prediction and analysis, we have identified 22 potential miRNAs from five genomes of SARS-CoV2 linked with 12 human miRNAs. Analysis of human miRNAs hsa-mir-1267, hsa-mir-1-3p, hsa-mir-5683 were found shared between all the five viral SARS-CoV2 miRNAs. Further, PANTHER classification analyzed the gene-ontology being carried by these associations showed that 44 genes were involved in biological functions that includes genes specific for signaling pathway, immune complex generation, enzyme binding with effective role in the virus-host relationship.ConclusionOur analysis concludes that the genes identified in this study can be effective in analyzing the virus-host interaction. It also provides a new direction to understand viral pathogenesis with a probable new way to link, that can be used to understand and relate the miRNAs of the virus to the host conditions.     

The Balance between Hydrogen Bonds,Halogen Bonds,and Chalcogen Bonds in the Crystal Structures of a Series of 1,3,4-Chalcogenadiazoles

In order to explore how specific atom-to-atom replacements change the electrostatic potentials on 1,3,4-chalcogenadiazole derivatives, and to deliberately alter the balance between intermolecular interactions, four target molecules were synthesized and characterized. DFT calculations indicated that the atom-to-atom substitution of Br with I, and S with Se enhanced the σ-hole potentials, thus increasing the structure directing ability of halogen bonds and chalcogen bonds as compared to intermolecular hydrogen bonding. The delicate balance between these intermolecular forces was further underlined by the formation of two polymorphs of 5-(4-iodophenyl)-1,3,4-thiadiazol-2-amine; Form I displayed all three interactions while Form II only showed hydrogen and chalcogen bonding. The results emphasize that the deliberate alterations of the electrostatic potential on polarizable atoms can cause specific and deliberate changes to the main synthons and subsequent assemblies in the structures of this family of compounds.     

A theoretical study of the interactions between N,N-dimethylformamide and xylenes

The ab initio and density functional (DFT) methods were performed on binary systems of N,N-dimethylformamide (DMF) with xylenes (o-, or m-, or p-xylene), and seven stable configurations were obtained with no imaginary frequencies. To obtain the interaction energies of these complexes, single-point energy calculations with basis set superposition error (BSSE) correction were carried out at B3LYP/6-31G* and MP2/6-31G* levels. The structures, Chelpg (charges from electrostatic potentials using a grid-based method) charge distribution and bond characteristics of the mentioned complexes were calculated. The results indicated the presence of double C–H···O hydrogen bonds between DMF and xylenes in these complexes and the interaction energies of hydrogen bonding between DMF and xylene systems decreased in the following sequence: DMF–o-xylene: a1 > DMF–m-xylene: b1 > DMF–p-xylene: c1.