Synthesis of a series of phenylacetic acid 1-β-O-acyl glucosides and comparison of their acyl migration and hydrolysis kinetics with the corresponding acyl glucuronides

We report the synthesis of the 1-β-O-acyl glucoside conjugates of phenylacetic acid (PAA), R- and S-α-methyl-PAA and α,α'-dimethyl-PAA, and measurement of their transacylation and hydrolysis reactivity by NMR methods. These are analogues of acyl glucuronides, the transacylation kinetics of which could be important in adverse drug effects. One aim of this work was to investigate whether, as previously postulated, the free carboxylate group of the acyl glucuronides plays a part in the mechanism of the internal acyl migration. In addition, such acyl glucosides are known to be endogenous biochemicals in their own right and investigation of their acyl migration propensities is novel. Our previously described selective acylation procedure has proved highly successful for 1-β-O-acyl glucuronide synthesis and when subsequently applied to 6-O-trityl glucose, it gave good yields and excellent anomeric selectivity. Mild acidolysis of the O-trityl intermediates gave the desired acyl glucosides in excellent yield with essentially complete β-selectivity. Measurement of the acyl glucoside transacylation kinetics by (1)H NMR spectroscopy, based simply on the disappearance of the 1-β-isomer in aqueous buffer at pH 7.4, showed marked differences depending on the degree of methyl substitution. Further kinetic modelling of the isomerisation and hydrolysis reactions of the acyl glucosides showed considerable differences in kinetics for the various isomeric reactions. Reactions involving the -CH(2)OH group, presumably via a 6-membered ring ortho-ester intermediate, are facile and the α-glucoside anomers are significantly more reactive than their β-counterparts. By comparison with degradation rates for the corresponding acyl glucuronides, it can be inferred that substitution of the carboxylate by -CH(2)OH in the acyl glucosides has a significant effect on acyl migration for those compounds, especially for rapidly transacylating molecules, and that thus the charged glucuronide carboxylate is a factor in the kinetics.     

Pseudo-Jahn-Teller effect as the origin of the exalted frequency of the b2u Kekulé mode in the 1(1)B2u excited state of benzene

In this paper we show that a pseudo-Jahn-Teller (PJT) coupling between the (1)A1g ground state and the (1)B2u excited states along the Kekulé mode of b2u symmetry is responsible for the surprisingly low frequency of this mode in the ground state and its remarkable upward shift of 261 cm(-1) upon excitation to the first (1)B2u excited state.     

miR-526b targets 3′ UTR of MMP1 mRNA

Regulation of matrix metalloproteinases (MMPs) is important for many physiological processes involving cancers, inflammation, tissue remodeling and skin aging. Here, we report the novel finding that the expression of MMP1 mRNA is downregulated by the overexpression of miR-526b which is a member of chromosome 19 microRNA cluster (C19MC). Our analysis using reporter constructs containing the 3′ untranslated region (3′ UTR) of MMP1 and its mutant form showed that the region from 377–383 in the 3′ UTR of MMP1 is critical for targeting by miR-526b. In addition, the expression pattern of miR-526b and MMP1 mRNA showed reverse relation between adult dermal and neonatal fibroblasts. We show for the first time that miR-526b, an miRNA belonging to C19MC, can target the 377–383 region of the MMP1 3′ UTR.     

Structure-based design of conformationally constrained cyclic peptidomimetics to target the MLL1-WDR5 protein–protein interaction as inhibitors of the MLL1 methyltransferase activity

We described herein structure-based design,synthesis and evaluation of conformationally constrained,cyclic peptidomimetics to block the MLL1-WDR5 protein–protein interaction as inhibitors of the MLL1 histone methyltransferase activity.Our study has yielded cyclic peptidomimetics with very high binding affinities to WDR5(Kivalues 1 nmol/L) and function as antagonists of the MLL1 histone methyltransferase activity.     

Exploring the effectiveness of the TSR-based protein 3-D structural comparison method for protein clustering,and structural motif identification and discovery of protein kinases,hydrolases, and SARS-CoV-2’s protein via the application of amino acid grouping

Development of protein 3-D structural comparison methods is essential for understanding protein functions. Some amino acids share structural similarities while others vary considerably. These structures determine the chemical and physical properties of amino acids. Grouping amino acids with similar structures potentially improves the ability to identify structurally conserved regions and increases the global structural similarity between proteins. We systematically studied the effects of amino acid grouping on the numbers of Specific/specific, Common/common, and statistically different keys to achieve a better understanding of protein structure relations. Common keys represent substructures found in all types of proteins and Specific keys represent substructures exclusively belonging to a certain type of proteins in a data set. Our results show that applying amino acid grouping to the Triangular Spatial Relationship (TSR)-based method, while computing structural similarity among proteins, improves the accuracy of protein clustering in certain cases. In addition, applying amino acid grouping facilitates the process of identification or discovery of conserved structural motifs. The results from the principal component analysis (PCA) demonstrate that applying amino acid grouping captures slightly more structural variation than when amino acid grouping is not used, indicating that amino acid grouping reduces structure diversity as predicted. The TSR-based method uniquely identifies and discovers binding sites for drugs or interacting proteins. The binding sites of nsp16 of SARS-CoV-2, SARS-CoV and MERS-CoV that we have defined will aid future antiviral drug design for improving therapeutic outcome. This approach for incorporating the amino acid grouping feature into our structural comparison method is promising and provides a deeper insight into understanding of structural relations of proteins.     

Theoretical prediction of the protein–protein interaction between Arabidopsis thaliana COP1 and UVR8

In plants, ultraviolet-B radiation (280–315 nm) regulates gene expression and plant morphology through the UV RESPONSE LOCUS 8 (UVR8) photoreceptor. The first signaling event after quantal absorbance is the interaction of the UVR8 C-terminus with the E3 ubiquitin ligase CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1). The nature of the interaction between these two proteins is hitherto unknown. A protein homology model of the Arabidopsis thaliana COP1 seven-bladed propeller WD40 repeat domain and de novo folds of the C-terminal 27 amino acid (amino acids 397–423) peptide of Arabidopsis UVR8 (UVR8^397?423) is herein reported. Using a theoretical computational docking protocol, the interaction between COP1 and UVR8 was predicted. A core motif was identified in UVR8^397?423 comprising adjacent hydrophobic residues V410 and P411 together with a charged residue D412, homologous to corresponding motifs in other COP1-binding proteins, such as ELONGATED HYPOCOTYL 5 (HY5), cryptochrome 1 (CRY1), and salt tolerance proteins STO/STH. The protein–protein interaction between the COP1 WD40 repeat domain and UVR8^397?423 reveals binding within a region of COP1 overlapping with the binding site for HY5 and the other COP1-interacting proteins. This study provides a framework for understanding docking between UVR8 and COP1, which in turn gives clues for experimental testing of UVR8/COP1 interaction.     

Computer-aided design and discovery of protein–protein interaction inhibitors as agents for anti-HIV therapy

Protein–protein interactions (PPI) are involved in most of the essential processes that occur in organisms. In recent years, PPI have become the object of increasing attention in drug discovery, particularly for anti-HIV drugs. Although the use of combinations of existing drugs, termed highly active antiretroviral therapy (HAART), has revolutionized the treatment of HIV/AIDS, problems with these agents, such as the rapid emergence of drug-resistant HIV-1 mutants and serious adverse effects, have highlighted the need for further discovery of new drugs and new targets. Numerous investigations have shown that PPI play a key role in the virus’s life cycle and that blocking or modulating them has a significant therapeutic potential. Here we summarize the recent progress in computer-aided design of PPI inhibitors, mainly focusing on the selection of the drug targets (HIV enzymes and virus entry machinery) and the utilization of peptides and small molecules to prevent a variety of protein–protein interactions (viral–viral or viral–host) that play a vital role in the progression of HIV infection.     

A study of the perturbations between the A1Σ+u and b3Πu states of Na2

The interaction between the A¹Σ⁺_u and b³Π_Ωu states of Na₂ is explored by resonantly exciting A states via A-X transitions and, after an adjustable delay time, photoionizing them. For long delays signals arise only from states with significant fractions of both A and b state character. Thus the regions where the interaction is important stand out clearly in the spectrum. Using this technique we have investigated perturbations of the A v' = 3, 7 and 8 states by the b v' = 10, 13 and 14 states.     

Screening and Identification of a Fungal β-Glucosidase and the Enzymatic Synthesis of Gentiooligosaccharide

After screening with 0.1% esculoside and 0.03% FeCl₃, we identified from rotten wood a fungal isolate HML0366 that produces high amount of β-glucosidase. Phenotypic and rDNA internal transcribed spacer sequence analyses indicated that the isolate belongs to Aspergillus oryzae. The β-glucosidase produced by HML0366 had an activity of 128 U/g. high performance liquid chromatography analysis also demonstrated a high transglycosylation activity of the crude enzyme. The β-glucosidase was stable between pH 4–10 at 60 °C. A gentiobiose yield of 30.86 g/L was achieved within 72 h of the enzymatic reaction at pH 5 and 55 °C using 50% glucose as the substrate. For the first time, we report here the isolation of an A. oryzae strain producing β-glucosidase with high hydrolytic activities. The crude enzyme has a high transglycosylation activity, which enables the enzymatic synthesis of gentiooligosaccharides.     

Design, synthesis and in vitro evaluation of a series thiazolidinediones analogs as PPAR modulators

A series of thiazolidinediones analogs,as PPAR modulators,were designed,synthesized and evaluated in vitro.     

Identification of sulfation sites of metabolites and prediction of the compounds’ biological effects

Characterizing the biological effects of metabolic transformations (or biotransformation) is one of the key steps in developing safe and effective pharmaceuticals. Sulfate conjugation, one of the major phase II biotransformations, is the focus of this study. While this biotransformation typically facilitates excretion of metabolites by making the compounds more water soluble, sulfation may also lead to bioactivation, producing carcinogenic products. The end result, excretion or bioactivation, depends on the structural features of the sulfation sites, so obtaining the structure of the sulfated metabolites is critically important. We describe herein a very simple, high-throughput procedure for using mass spectrometry to identify the structure—and thus the biological fate—of sulfated metabolites. We have chemically synthesized and analyzed libraries of compounds representing all the biologically relevant types of sulfation products, and using the mass spectral data, the structural features present in these analytes can be reliably determined, with a 97% success rate. This work represents the first example of a high-throughput analysis that can identify the structure of sulfated metabolites and predict their biological effects.     

Scoring protein–protein docked structures based on the balance and tightness of binding

One main issue in protein-protein docking is to filter or score the putative docked structures. Unlike many popular scoring functions that are based on geometric and energetic complementarity, we present a set of scoring functions that are based on the consideration of local balance and tightness of binding of the docked structures. These scoring functions include the force and moment acting on one component (ligand) imposed by the other (receptor) and the second order spatial derivatives of protein-protein interaction potential. The scoring functions were applied to the docked structures of 19 test targets including enzyme/inhibitor, antibody/antigen and other classes of protein complexes. The results indicate that these scoring functions are also discriminative for the near-native conformation. For some cases, such as antibody/antigen, they show more discriminative efficiency than some other scoring functions, such as desolvation free energy (deltaG(des)) based on pairwise atom-atom contact energy (ACE). The correlation analyses between present scoring functions and the energetic functions also show that there is no clear correlation between them; therefore, the present scoring functions are not essentially the same as energy functions.     

Walter Reppe Revival – Identification and Genesis of Copper Acetylides Cu2C2 as Active Species in Ethynylation Reactions

More than six decades after proposing copper acetylide, Cu₂C₂, as catalytically active species in ethynylation reactions by Walter Reppe, the explosive species have been experimentally identified and investigated during catalysis in detail now. Taking into account specific safety precautions, unequivocal qualitative characterization was achieved by Raman spectroscopy and X-ray powder diffraction of supported copper catalysts Cu/Bi/SiO₂ during and after activation and catalysis in comparison to bulk Cu₂C₂ materials. Quantification of Cu₂C₂ succeeded by thermal analysis and Raman spectroscopy. Its formation in aqueous suspension is studied starting from copper(II) oxide catalysts including dissolution, reduction and precipitation steps. Copper acetylide formation can be correlated with catalytic performance in the ethynylation of formaldehyde to 1,4-butynediol.     

Temperature dependence of the relaxation rate constants of the a 1Δg and b 1Σ +g states of oxygen isotopes

The relaxation rate constants of the low-lying electronic singlet states, a ¹Δ_g and b ¹Σ⁺_g , of gaseous natural O₂ and of the isotope ¹⁸O₂ were investigated as a function of temperature from 100 to 295 K. The measured increase of the rate constants with temperature is in good agreement with a theory of electronic-to-vibrational-translational energy transfer. The significant effects of the different electronic states and of the isotope masses on the absolute values of the relaxation rate constants, which range from 1.0× 10⁻²⁰ to 3.9× 10⁻¹⁷ s⁻¹ molecule⁻¹ cm³ at 295 K, are discussed.     

Evaluation of α-pyrones and pyrimidones as photoaffinity probes for affinity-based protein profiling

α-Pyrones and pyrimidones are common structural motifs in natural products and bioactive compounds. They also display photochemistry that generates high-energy intermediates that may be capable of protein reactivity. A library of pyrones and pyrimidones was synthesized, and their potential to act as photoaffinity probes for nondirected affinity-based protein profiling in several crude cell lysates was evaluated. Further "proof-of-principle" experiments demonstrate that a pyrimidone tag on an appropriate scaffold is equally capable of proteome labeling as a benzophenone.     

Oligomers of β2- and of β3-Homoproline: What are the Secondary Structures of β-Peptides Lacking H-Bonds?

To study the role of H-bonds in stabilizing β-peptidic secondary structures, we have synthesized β-oligopeptides (up to the octadecamer 12 ) consisting of β²- and β³-homoproline, i.e., β-peptides lacking amide protons. The enantiomer purity of the building block β²-homoproline (nipecotic acid, 4 ) was determined by HPLC analysis of the N-(2,4-dinitrophenyl) derivative 5 on a Chiralcel-OD column (cf. Fig. 2). The CD spectra of the all-(S)-β²- and all-(S)-β³-HPro-containing β-peptides display novel and intensive CD patterns which may be indicative of a secondary structure (cf. Fig. 3). It is noteworthy that a distinct CD pattern was observed with the β³-HPro derivatives containing as few as three residues ( 7a ). The crystal structure of a N-deprotected β³-HPro-tripeptide 7c is presented (cf. Figs. 4 and 5), and a model for the structure of β-peptides consisting of β³-HPro is discussed (cf. Figs. 6 and 7).     

Identification and Characterization of Monomeric,Volatile SiCl3NH2 as Product of the Reaction between SiCl4 and NH3: An Important Intermediate on the Way to Silicon Nitride?

We studied the reaction of SiCl(4) with NH(3) by mass spectrometry and IR spectroscopy. By means of mass spectrometry, SiCl(3)NH(2) was for the first time identified as an intermediate generated in significant amounts in the course of the reaction. In additional experiments, SiCl(3)NH(2) was formed as a stable gaseous product of the ammonolysis of SiCl(4), and the product was identified and characterized in detail by IR spectroscopic methods (gas phase and matrix isolation) in combination with quantum-chemical calculations. The calculations also gave access to important thermodynamical data.     

Evolution of the Texture and Structure of SiO2–Al2O3 Xerogels and Aerogels as a Function of the Si to Al Molar Ratio

SiO₂–Al₂O₃ aerogels and xerogels with a Si to Al molar ratio r _Si/Al varying from 0.25 to 20, were made by sol-gel process in acidic conditions at pH 2 and respectively dried by the CO₂ supercritical method and by solvent evaporation. The Al precursor was also chelated with ethylacetoacetate, which made it possible to study the structure and texture of such gels in conditions favorable to the formation of mixed Al–O–Si bonds. Nitrogen adsorption isotherms according to the Brunauer, Emmett and Teller method (BET), ²⁷Al magic angle spinning nuclear magnetic resonance (²⁷Al MAS-NMR), Fourier Transformed Infrared Spectroscopy (FTIR) and Infrared absorbance spectra after Temperature Programmed Desorption (TPD) of pyridine, showed that the Si–O infrared asymmetric stretching vibration and the Bronsted acidity relative to the Lewis acidity, depended on the ratio of Al^IV to Si atoms.     

Immune recognition of cytochrome c II. — The role of macrophages as modulators and not as antigen-presenting cells in immune response in vitro

C57BL mouse peritoneal macrophages sensitized with cytochrome c (cyt. c) in complete Freund adjuvant (CFA) in vivo were able to capture, internalize and reexpress horse cyt.c on their surface. The major portion of cyt.c captured came out of macrophages in 1 to 3 h, with molecular weight unmodified. Cyt.c could be partly cleaved into two fragments, with molecular masses of about 2-2.5 and 10 kD by external non-serine proteases. The dynamics of macrophage interactions with cyt.c coupled to fluorescent latex beads was also studied. Macrophages were shown not to present cyt.c in the immune response in vitro, but rather to modulate the response level. The activating substance was secreted into the culture fluid, while suppressive activity was mediated by the cells.