Development of potent inhibitors of the coxsackievirus 3C protease

Coxsackievirus B3 (CVB3) 3C protease (3CP) plays essential roles in the viral replication cycle, and therefore, provides an attractive therapeutic target for treatment of human diseases caused by CVB3 infection. CVB3 3CP and human rhinovirus (HRV) 3CP have a high degree of amino acid sequence similarity. Comparative modeling of these two 3CPs revealed one prominent distinction; an Asn residue delineating the S2' pocket in HRV 3CP is replaced by a Tyr residue in CVB3 3CP. AG7088, a potent inhibitor of HRV 3CP, was modified by substitution of the ethyl group at the P2' position with various hydrophobic aromatic rings that are predicted to interact preferentially with the Tyr residue in the S2' pocket of CVB3 3CP. The resulting derivatives showed dramatically increased inhibitory activities against CVB3 3CP. In addition, one of the derivatives effectively inhibited the CVB3 proliferation in vitro.     

Endothelin and its receptor interactions: role of extracellular receptor domain and length of peptide ligands

Human endothelin B receptor and its domain-truncated forms were cloned and expressed in Pichia pastoris. Ligand binding studies with expressed proteins were carried out using biotinylated endothelins. Competitive binding and liposome incorporation studies showed that the extracellular region is essential for ligand binding and that longer peptides have higher affinity.     

E-Learning as a new tool in bioinformatics teaching

In recent years, virtual learning is growing rapidly. Universities, colleges, and secondary schools are now delivering training and education over the internet. Beside this, resources available over the WWW are huge and understanding the various techniques employed in the field of Bioinformatics is increasingly complex for students during implementation. Here, we discuss its importance in developing and delivering an educational system in Bioinformatics based on e-learning environment.     

Hybrid density functional theory with a specific reaction parameter: hydrogen abstraction reaction of difluoromethane by the hydroxyl radical

Accurate potential energy surfaces for the OH + CH2F2 --> H2O + CHF2 reaction are constructed using hybrid and hybrid meta density functional theory methods (mPW1PW91, B1B95, and mPW1B95) with specific reaction parameters in conjunction with the 6-31 + G(d,p) basis set. The accuracy of a surface is examined by comparing the calculated rate constants with the experimental ones. The rate constants are calculated over the temperature range 200-1,500 K using variational transition state theory with multidimensional tunneling contributions. The hybrid density functional theory methods with specific-reaction-parameter Hartree-Fock exchange contributions (39.2-41.0% for mPW1PW91, 41.0-42.2% for B1B95, and 44.9-46.3% for mPW1B95, respectively) provide accurate rate constants over an extended temperature range. The classical barrier height for the hydrogen abstraction reaction on these potential energy surfaces is determined to be 5.0-5.3 kcal mol(-1), and the best estimate value is 5.14 kcal mol(-1).     

Mass spectrometric characterization of isoform variants of peanut (Arachis hypogaea) stem lectin (SL-I)

Matrix assisted laser desorption/ionization–time-of-flight (MALDI–TOF) mass spectrometric (MS) analysis of purified Arachis hypogaea stem lectin (SL-I) and its tryptic digests suggested it to be an isoformic glucose/mannose binding lectin. Two-dimensional gel electrophoresis of SL-I indicated six isoforms (A1–A6), which were confirmed by Western blotting and MALDI–TOF MS analysis. Comparative analysis of peptide mass spectra of the isoforms matched with A. hypogaea lectins with three different accession numbers (Q43376_ARAHY, Q43377_ARAHY, Q70DJ5_ARAHY). Tandem mass spectrometric (MS/MS) analysis of tryptic peptides revealed these to be isoformic variants with altered amino acid sequences. Among the peptides, the peptide T12 showed major variation. The ¹⁹⁹Val–Ser–Tyr–Asn²⁰² sequence in peptide T12 of A1 and A2 was replaced by ¹⁹⁹Leu–Ser–His–Glu²⁰² in A3 and A4 (T12′) while in A5 and A6 this sequence was ¹⁹⁹Val–Ser–Tyr–Val²⁰² (T12″). Peptide T1 showed the presence of ¹⁰Asn in the isoforms A1–A5 while in A6 this amino acid was replaced by ¹⁰Lys (T1′). Overall amino acid sequence as identified by MS/MS showed a high degree of similarity between A1, A2 and among A3, A4, A5. Carbohydrate binding domain and adenine binding site seem to be conserved.     

CULTURE AND BIOCHEMICAL ANALYSIS OF A TEA ALGAL PATHOGEN,CEPHALEUROS PARASITICUS1

To assess the current situation regarding the incidence of red rust disease in tea plants, an extensive survey was conducted in southern Indian tea plantations covering different tea cultivars and agroclimatic zones. The results indicated that the incidence of disease was more severe in tea seedlings than clones in all the agroclimatic zones. On the other hand, a simple, reliable, and reproducible technique was standardized for culturing Cephaleuros parasiticus G. Karst. isolated from infected tea leaves. Ten isolates were obtained, of which two were screened based on growth rate and culture characters for further studies. Ten culture media were tested for the culturing of C. parasiticus in which Trebouxia and Bristol media were the best followed by George, Go algal, and tea leaf extract media. Variations between isolates (Valparai C. parasiticus field number 27 [VCP27], Munnar C. parasiticus field number 11 [MCP11], and University of Texas culture number 2412 [UTEX2412]) of C. parasiticus were studied based on the growth pattern, protein expression profile, and cellular constituents in the filaments. The quantitative estimation of cellular constituents showed that there was no significant difference in these constituents among isolates. The detection of amino acids in the filaments of C. parasiticus isolates showed 16 free forms and 11 bound forms. Amino acids in bound form were higher in all the isolates than in free form of amino acids. The three isolates of C. parasiticus were closely related, with bands lying between the molecular weight of 116 and 35 kDa.     

Lipase catalyzed synthesis of cinnamyl acetate via transesterification in non-aqueous medium

Cinnamyl acetate is used as flavor and fragrance ingredient in food and cosmetic industries. This work focuses on the synthesis of cinnamyl acetate via lipase catalyzed transesterification of cinnamyl alcohol with vinyl acetate in non-aqueous medium. Among the different immobilized lipases employed, Novozym 435 was found to be the best catalyst in toluene as solvent. The effects of various parameters were studied systematically. With a mole ratio of 1:2 of cinnamyl alcohol to vinyl acetate and 10 mg catalyst, 96% conversion was obtained in 1 h at 40 °C. The ternary complex mechanism with inhibition by cinnamyl alcohol was found to fit the data well. The kinetics of the reaction was studied by using non-linear regression analysis. Enzymatic synthesis of cinnamyl acetate is an efficient process vis-à-vis chemical catalysis.