Fluorogenic tagging of peptides via Cys residues using thiol-specific vinyl sulfone affinity tags

Fluorescent tagging of Cys-containing peptides is presented herein. The procedure follows a two-step sequential reaction scheme using thiol specific bifunctional chemical reporters and fluorogenic labels. Vinyl-sulfone bearing chemical reporters have been synthesized and demonstrated to selectively modify cysteine under physiological conditions in the presence of other nucleophilic amino acids. Bifunctional chemical reporters decorated with a terminal alkyne moiety, suitable for modification with azide containing fluorogenic labels were also synthesized. Such fluorogenic (turn on) labels in combination with these new vinyl-sulfone tags can be used generally in fluorescent modulation schemes of thiol-bearing biomolecules.     

Discovery of bound and unbound waters in crystalline amino acids revealed by thermal analysis

The thermal analytical study of most hydrophobic and hydrophilic D/L amino acids reveals significant hydropathy index correlation between the presence of water and crystalline amino acids. The TG derivative mass profiles for arginine and lysine (hydrophilic acids) at various time intervals of atmospheric exposure, show two distinct peaks, one between 50 and 60°C (unbound water), and one close to 100°C (bound-like water). The DSC heat-cool profiles for lysine and arginine confirmed the presence of these multiple waters with two heats of vaporization. The absence of these patterns from the TG and DSC for cysteine and phenylalanine (hydrophobic acids) further supports the conclusions.     

Biochemical Characterization of an Arginine 2,3‐Aminomutase with Dual Substrate Specificity

The radical S‐adenosylmethionine (SAM) aminomutases represent an important pathway for the biosynthesis of β‐amino acids. In this study, we report biochemical characterization of BlsG involved in blasticidin S biosynthesis as a radical SAM arginine 2,3‐aminomutase. We showed that BlsG acts on both L‐arginine and L‐lysine with comparable catalytic efficiencies. Similar dual substrate specificity was also observed for the lysine 2,3‐aminomutase from Escherichia coli (LAM_EC). The catalytic efficiency of LAM_EC is similar to that of BlsG, but is significantly lower than that of the enzyme from Clostridium subterminale (LAM_CS), which acts only on L‐lysine rather than on L‐arginine. Moreover, we showed that enzymes can be grouped into two major phylogenetic clades, each corresponding to a certain C3 stereochemistry of the β‐amino acid product. Our study expands the radical SAM aminomutase members and provides insights into enzyme evolution, supporting a trade‐off between substrate promiscuity and catalytic efficiency.     

Calix[4]pyrrole-TCBQ assembly: a signal magnifier of TCBQ for colorimetric determining amino acids and amines

The interaction and colorimetric sensing properties of the calix[4]pyrrole-TCBQ charge-transfer complex with amino acids and amines in CHCl₃/EtOH/H₂O were investigated using UV/vis spectroscopic techniques. The obvious spectral and visual changes of the complex solution in the presence of basic amino acids (namely, lysine, arginine, and histidine) and aliphatic amines were observed, and the calix[4]pyrrole-TCBQ supramolecular assembly, like a ‘signal magnifier’, markedly improves sensing sensitivity and selectivity of TCBQ for amino acids and amines.     

Chemoselective deacylation of functionalized esters catalyzed by dioxomolybdenum dichloride

Among five different oxidometallic species and two Lewis acids investigated, MoO₂Cl₂ shows the best catalytic and chemoselective activity for the deacylation of esters in methanol at ambient or elevated temperature. Both high efficiency and chemoselectivity were achieved for substrates bearing different ether or ester groups. Acylated mono and disaccharides can also be selectively deacetylated in good yields, leading to useful carbohydrate templates for further synthetic manipulations.     

Prediction for understanding the effectiveness of antiviral peptides

The low efficacy of current antivirals in conjunction with the resistance of viruses against existing antiviral drugs has resulted in the demand for the development of novel antiviral agents. Antiviral peptides (AVPs) are those bioactive peptides having virucidal activity and they can be developed into promising antiviral drugs. They are shorter length peptides having the ability to cease the progression of viral infections. The use of antiviral peptides in therapeutics has recently attracted the attention of the research community. The development and identification of AVPs is imperative for the discovery of novel therapeutics for viral infections. In the present work, a meta classifier (stacking) based approach is implemented for the prediction of IC₅₀ (half maximal inhibitory concentration) and pIC₅₀ (negative log of half maximal inhibitory concentration) values. The best prediction model with evolutionary information and local alignment scores as features achieved a correlation coefficient values of 0.670 and 0.753 on the training and testing sets respectively for IC₅₀. Further, the prediction of pIC₅₀ reached a correlation coefficient value of 0.797 and 0.789 for training and testing sets respectively. For the development of machine learning models involved in the prediction of IC₅₀, the use of pIC₅₀ over IC₅₀ is recommended as the target variable. Further on a systematic comparison of AVPs with high IC₅₀ values and Low IC₅₀ values, it is revealed that higher mean charge and tiny amino acids are preferred and higher length and consecutive hydrophilic amino acids are avoided in the former.     

Electrochromatographic enantioseparation using chiral ligand exchange monolithic sol-gel column

This paper describes the development of a monolithic sol-gel column modified with l-hydroxyproline as a ligand exchange chiral stationary phase. It has been demonstrated that the monolithic chiral stationary phase can be used for the enantioseparation of dansyl amino acids, free amino acids, hydroxy acids, and dipeptides by capillary electrochromatography and micro-liquid chromatography. The recommended mobile phase was acetonitrile/0.50 mM Cu(Ac)₂-50 mM NH₄Ac (7:3) adjusted to pH 6.5. The characteristics of the monolithic column using hydroxyproline as chiral selector in CEC have been discussed.     

Synthesis,Biological Evaluation,and Molecular Docking Studies of Novel Pyrazolo[3,4‐d]pyrimidines as Potential Telomerase Inhibitors

Series of novel pyrazolo[3,4‐d]pyrimidines as potential telomerase inhibitors were synthesized. Results of the antitumor assay indicated that compounds 4b , 5a – b , 13b , c , and 14a , b exhibited the most potent activity (IC₅₀ from 39 to 43 μM) against Ehrlich ascites carcinoma cells (EAC). Also, the newly synthesized compounds were examined for telomerase inhibition by the known a TRAP assay. The results showed that compound 13c has remarkable inhibition activity with IC₅₀ value of 30 μM. On the other hand, computational studies were performed to the titled compounds to get insight in their degree of recognition with the conserved amino acids of the telomerase enzyme active site (code: 3DU6) as promising lead in the cancer cure era.     

Sensing Properties of NH2-MIL-101 Series for Specific Amino Acids via Turn-On Fluorescence

Metal–organic frameworks (MOFs) have been demonstrated to be desired candidates for sensing definite species owing to their tunable composition, framework structure and functionality. In this work, the NH₂-MIL-101 series was utilized for sensing specific amino acids. The results show that cysteine (Cys) can significantly enhance the fluorescence emission of NH₂-MIL-101-Fe suspended in water, while NH₂-MIL-101-Al exhibits the ability to sense lysine (Lys), arginine (Arg) and histidine (His) in aqueous media via turn-on fluorescence emission. Titration experiments ensure that NH₂-MIL-101-Fe and NH₂-MIL-101-Al can selectively and quantitatively detect these amino acids. The sensing mechanism was examined and discussed. The results of this study show that the metal centers in MOFs are crucial for sensing specific amino acids.     

Studies on the Chemical Modification of the Essential Groups of <Emphasis Type="Italic">N</Emphasis>-Acetyl-β-<Emphasis Type="SmallCaps">d</Emphasis>-Glucosaminidase from Viscera of Green Crab (<Emphasis Type="Italic">Scylla Serrata</Emphasis>)

The chemical modification of N-acetyl-β-d-glucosaminidase (EC3.2.1.30) from viscera of green crab (Scylla serrata) has been first studied. The modification of indole groups of tryptophan of the enzyme by N-bromosuccinimide can lead to complete inactivation, accompanying the absorption decreasing at 275 nm and the fluorescence intensity quenching at 338 nm, indicating that tryptophan is essential residue to the enzyme. The modification of histidine residue, the carboxyl groups, and lysine residue inactivates the enzyme completely or incompletely. The results show that imidazole groups of histidine residue or sulfhydryl residues, the carboxyl groups of acidic amino acid, amino groups of lysine residue, and indole groups of tryptophan were essential for the catalytic activity of enzyme, while the results demonstrate that the disulfide bonds and the carbamidine groups of arginine residues are not essential to the enzyme’s function.     

Chemoenzymatic Syntheses of Sialylated Oligosaccharides Containing C5‐Modified Neuraminic Acids for Dual Inhibition of Hemagglutinins and Neuraminidases

A fast chemoenzymatic synthesis of sialylated oligosaccharides containing C5‐modified neuraminic acids is reported. Analogues of GM₃ and GM₂ ganglioside saccharidic portions where the acetyl group of NeuNAc has been replaced by a phenylacetyl (PhAc) or a propanoyl (Prop) moiety have been efficiently prepared with metabolically engineered E. coli bacteria. GM₃ analogues were either obtained by chemoselective modification of biosynthetic N‐acetyl‐sialyllactoside (GM₃NAc) or by direct bacterial synthesis using C5‐modified neuraminic acid precursors. The latter strategy proved to be very versatile as it led to an efficient synthesis of GM₂ analogues. These glycomimetics were assessed against hemagglutinins and sialidases. In particular, the GM₃NPhAc displayed a binding affinity for Maackia amurensis agglutinin (MAA) similar to that of GM₃NAc, while being resistant to hydrolysis by Vibrio cholerae (VC) neuraminidase. A preliminary study with influenza viruses also confirmed a selective inhibition of N1 neuraminidase by GM₃NPhAc, suggesting potential developments for the detection of flu viruses and for fighting them.     

Chemoselective Acylation of Nucleosides

Acylated nucleoside analogues play an important role in medicinal chemistry and are extremely useful precursors to various other nucleoside analogues. However, chemoselective acylation of nucleosides usually requires several protection and deprotection steps due to the competing nucleophilicity of hydroxy and amino groups. In contrast, direct protecting-group-free chemoselective acylation of nucleosides is a preferred strategy due to lower cost and fewer overall synthetic steps. Herein, a simple and efficient chemoselective acylation of nucleosides and nucleotides under mild reaction conditions, giving either O- or N-acylated products respectively with excellent chemoselectivity is reported.     

Gas-Phase Binding of Noncovalent Complexes Between α-cyclodextrin and Amino Acids Investigated by Mass Spectrometry

Noncovalent complexes between cyclodextrins and small molecules have been extensively studied recently because of their widespread application in the pharmaceutical industry for chiral and molecular recognition. To date, gas phase noncovalent binding affinities between α-cyclodextrin and amino acids have not been widely investigated. In this study, gas-phase binding of noncovalent complexes between α-CD and amino acids was investigated by electrospray ionization mass spectrometry (ESI-MS), demonstrating the formation of 1:1 stoichiometric noncovalent complexes. The binding of the complexes were further confirmed by collision-induced dissociation by tandem mass spectrometry. Mass spectrometric titrations between α-cyclodextrin and phenylalanine, glutamic acid, and arginine were performed to provide binding constants (lgK_a) as references for competitive ESI-MS. Calibration curves for the complexes of α-cyclodextrin with phenylalanine, glutamic acid, and arginine were plotted. Through competitive ESI-MS, the lgK_a for the complexes of α-CD with aspartic acid, lysine, proline, glycine, alanine, asparagine, cystine, glutamine, histidine, leucine, isoleucine, methionine, serine, threonine, and valine were measured directly. By comparison, it is seen that the measured binding constants for the complexes of α-cyclodextrin with basic amino acids such as arginine and lysine are lower than those for most complexes of neutral amino acids. The chiral selectivity of α-cyclodextrin for L- and D-isomers of methionine, threonine, asparagine, and phenylalanine determined by ESI-MS revealed its application as a chiral selector.     

Purification and Side Chain Selective Chemical Modifications of Glutamate Dehydrogenase from Bacillus subtilis Natto

Glutamate dehydrogenase (GDH) from Bacillus subtilis natto was purified to apparent homogeneity by ammonium sulfate precipitation, ion-exchange chromatography, size exclusion chromatography, and hydroxyapatite (HA) affinity chromatography. The GDH was purified 34-fold, with a yield of 41 % of total activity and a specific activity of 34.29 U/mg proteins. The molecular weight (M_r) of was measured at 47 kDa with sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) and 264 kDa with high-performance liquid chromatography (HPLC). The optimum pH and temperature for the deammoniation reaction were measured to be 7.5 and 30 °C, respectively. The active-site amino acid residues of GDH were investigated by chemical modification. The compounds 2,4,6-trinitrobenzenesulfonic acid (TNBS), phenylglyoxal (PG), and phenylmethanesulfonyl fluoride (PMSF) were used to modify lysine, arginine, and serine active site residues, respectively. After treatment with modifying reagents at concentrations of 1 mM, GDH activity fell to 10.7 % with TNBS, 83.3 % with PG, and 12.8 % with PMSF. However, with substrate protection, there was almost no loss in GDH activity following treatment with any modifying reagent. The kinetic parameters K _m and V _max were determined in each case. K _m values for native GDH, 50 % TNBS-inactivated GDH, and 50 % PMSF-inactivated GDH were 0.037, 0.104, and 0.017 mM, respectively. V _max values were 0.048, 0.022, and 0.031 mM/s, respectively. These results suggest that the active site contains one or more lysine residues that play a role in substrate binding and one or more serine residues that may maintain the enzyme conformation. However, arginine residues played less of a role in the activity of GDH.     

Some distinguishing tests for α-amino acids and a specific spot test for lysine

Tests are described for differentiation between neutral, basic, and acidic amino acids based on the formation of nickel dimethylglyoxime precipitate from an equilibrium mixture containing Ni²⁺, dimethylglyoxime and Ni²⁺, dimethylglyoxime-glycine. A highly sensitive and specific test for lysine is described, based on the formation of nickel dimethylglyoxime precipitate in a drop of the equilibrium mixture, by the reaction of the volatile amino aldehyde, produced by the oxidative deamination-decarboxylation of lysine. Other basic amino acids, i.e., arginine and histidine do not interfere, and the test can be applied for lysine in a mixture with other amino acids.     

Discovery of new inhibitor for the protein arginine deiminase type 4 (PAD4) by rational design of α-enolase-derived peptides

Rheumatoid arthritis (RA) is an inflammatory autoimmune disease affecting about 0.24 % of the world population. Protein arginine deiminase type 4 (PAD4) is believed to be responsible for the occurrence of RA by catalyzing citrullination of proteins. The citrullinated proteins act as autoantigens by stimulating an immune response. Citrullinated α-enolase has been identified as one of the autoantigens for RA. Hence, α-enolase serves as a suitable template for design of potential peptide inhibitors against PAD4. The binding affinity of α-enolase-derived peptides and PAD4 was virtually determined using PatchDock and HADDOCK docking programs. Synthesis of the designed peptides was performed using a solid phase peptide synthesis method. The inhibitory potential of each peptide was determined experimentally by PAD4 inhibition assay and IC₅₀ measurement. PAD4 assay data show that the N-P2 peptide is the most favourable substrate among all peptides. Further modification of N-P2 by changing the Arg residue to canavanine [P2 (Cav)] rendered it an inhibitor against PAD4 by reducing the PAD4 activity to 35 % with IC₅₀ 1.39 mM. We conclude that P2 (Cav) is a potential inhibitor against PAD4 and can serve as a starting point for the development of even more potent inhibitors.     

Thermochemical Aspects of the Conversion of the Gaseous System CO2-N2-H2O into a Solid Mixture of Amino Acids

Conversion of the gaseous mixture CO₂(g)+N₂(g)+H₂O(g) to a solid amino acid condensate in an electric discharge plasma has high efficiency of the energy transfer from the different plasma components into chemical processes. The basic activation process is activation of the N₂ metastable electronic state, followed by formation of NCO* and ON-NCO free-radicals and generation of many reactive radicals. These radicals help to overcome the high activation energy of thermal dissociation of N₂ to N (950 kJ=9.846 eV). The major product is a statistical polycondensate containing the amino acids: arginine, lysine, histidine, methionine, glycine, alanine, serine and aspartic acid. This information was obtained by comparing the IR spectra of the products with reference IR absorption spectra of pure components. Identification of the individual amino acids in the solid product was performed by HPLC, when samples were dissolved using 6 M HCl applied at 100°C for 24 h. Properties of the condensate were estimated using thermogravimetric analysis. Small amounts of oxamidato complexes and oligo pyrrole structures are formed on the electrode surface giving the surface catalytic properties. The gas cleaning process has practical applicability (production of useful fertilizers, reduction of the CO₂ concentration in the atmosphere) and may also contribute to explanation of the origin of life on Earth. This revised version was published online in August 2006 with corrections to the Cover Date.     

Polyisoprenylated acylphloroglucinols and a polyisoprenylated tetracyclic xanthone from the bark of Calophyllum thorelii

Two new polyisoprenylated acylphloroglucinols, thoreliones A and B, and a new polyisoprenylated tetracyclic xanthone, oxy-thorelione A, together with twelve known compounds, were isolated from the bark of Calophyllum thorelii. The new structures were determined using spectroscopic methods and chemical modification. The major compound thorelione A (1) showed moderate cytotoxic activity against MCF-7, HeLa and NCI-H460 cells with IC₅₀ values of 7.4, 9.3 and 10.6 μg/mL, respectively, using the sulforhodamine B assay.     

Chemoselective Reduction of Tertiary Amides under Thermal Control: Formation of either Aldehydes or Amines

The chemoselective reduction of amides in the presence of other more reactive reducible functional groups is a highly challenging transformation, and successful examples thereof are most valuable in synthetic organic chemistry. Only a limited number of systems have demonstrated the chemoselective reduction of amides over ketones. Until now, the aldehyde functionality has not been shown to be compatible in any catalytic reduction protocol. Described herein is a [Mo(CO)₆]‐catalyzed protocol with an unprecedented chemoselectivity and allows for the reduction of amides in the presence of aldehydes and imines. Furthermore, the system proved to be tunable by variation of the temperature, which enabled for either C?O or C?N bond cleavage that ultimately led to the isolation of both amines and aldehydes, respectively, in high chemical yields.