Identification of triosephosphate isomerase (TIM) genes from Microcystis (Cyanobacteria : Chroococcales) and theoretical analyses of the potential of cyanobacterial TIM as a target for designing specific inhibitors

The genes encoding triosephosphate isomerase (TIM) in three species of Microcystis (M. aeruginosa, M. viridis and M. wesenbergii) were investigated. Reverse transcriptase-polymerase chain reaction indicated that they were transcribed in the cells. Analyses showed that their DNA and deduced amino acid sequences were highly conserved between all the three species, only a single nonsynonymous substitution was seen at position 31, from an Asp in M. aeruginosa and M. viridis to Glu in M. wesenbergii. Sequence alignment of these with 12 other known cyanobacterial TIM sequences showed that all the cyanobacterial TIMs had a very high level of amino acid identity (over 50% between each two). Comparison of the cyanobacterial TIMs with other reported TIMs (from diverse lineages of the three Domains) showed that they possessed common active-site residues and sequence motifs. All cyanobacterial TIMs have two common cysteine residues (Cys127 and Cys176), and the Cys176 is almost cyanobacteria-specific with only one exception in Streptomyces coelicolor. Both secondary structure alignment and comparative modelling of Synechocystis sp. TIM showed that Cys176 was located at the hinge region of the flexible loop-6 and might therefore be critical to the movement of TIM's loop-6, which is important to the function of the enzyme. Thus, the cyanobacterial TIM-specific Cys176 may be a potential site for the discovery of suitable drugs against cyanobacteria, and such drugs may have utility in controlling water blooms due to cyanobacteria.

Comparison of steroid substrates and inhibitors of P-glycoprotein by 3D-QSAR analysis

Steroid derivatives show a complex interaction with P-glycoprotein (Pgp). To determine the essential structural requirements of a series of structurally related and functionally diverse steroids for Pgp-mediated transport or inhibition, a three-dimensional quantitative structure activity relationship study was performed by comparative similarity index analysis modeling. Twelve models have been explored to well correlate the physiochemical features with their biological functions with Pgp on basis of substrate and inhibitor datasets, in which the best predictive model for substrate gave cross-validated q(2) = 0.720, non-cross-validated r(2) = 0.998, standard error of estimate SEE = 0.012, F = 257.955, and the best predictive model for inhibitor gave q(2) = 0.536, r(2) = 0.950, SEE = 1.761 and F = 45.800. The predictive ability of all models was validated by a set of compounds that were not included in the training set. The physiochemical similarities and differences of steroids as Pgp substrate and inhibitor, respectively, were analyzed to be helpful in developing new steroid-like compounds. (C) 2004 Elsevier B.V. All rights reserved.

Weibull modulus for diverse strength due to sample-specificity

By sample specificity it is meant that specimens with the same nominal material parameters and tested under the same environmental conditions may exhibit different behavior with diversified strength. Such an effect has been widely observed in the testing of material failure and is usually attributed to the heterogeneity of material at the mesoscopic level. The degree with which mesoscopic heterogeneity affects macroscopic failure is still not clear. Recently, the problem has been examined by making use of statistical ensemble evolution of dynamical system and the mesoscopic stress re-distribution model (SRD). Sample specificity was observed for non-global mean stress field models, such as the duster mean field model, stress concentration at tip of microdamage, etc. Certain heterogeneity of microdamage could be sensitive to particular SRD leading to domino type of coalescence. Such an effect could start from the microdamage heterogeneity and then be magnified to other scale levels. This trans-scale sensitivity is the origin of sample specificity. The sample specificity leads to a failure probability Phi (N) with a transitional region 0 < (N) < 1, so that globally stable and catastrophic modes could co-exist. It is found that the scatter in strength can fit the Weibull distribution very well. Hence, the Weibull modulus is indicative of sample specificity. Numerical results obtained from the SRD for different non-global mean stress fields show that Weibull modulus increases with increasing sample span and influence region of microdamage.

Trypsin inhibitory loop is an excellent lead structure to design serine protease inhibitors and antimicrobial peptides

The disulfide-bridged hendecapeptide ( CWTKSIPPKPC) loop, derived from an amphibian skin peptide, is found to have strong trypsin inhibitory capability. This loop, called the trypsin inhibitory loop ( TIL), appears to be the smallest serine protease inhib

Antihemostatic molecules from saliva of blood-feeding arthropods

The ability to feed on vertebrate blood has evolved many times in various arthropod clades. Consequently, saliva of blood-feeding arthropods has proven to be a rich source of antihemostatic molecules. A variety of platelet aggregation inhibitors antagonize platelet responses to wound-generated signals, including ADP, thrombin, and collagen. Anticoagulants disrupt elements of both the intrinsic and extrinsic pathways. Vasodilators include nitrophorins (nitric oxide storage and transport heme proteins), a variety of peptides that mimic endogenous vasodilatory neuropeptides, and proteins that catabolize or sequester endogenous vasoconstrictors. Multiple salivary proteins may be directed against each component of hemostasis, resulting in both redundancy and in some cases cooperative interactions between antihemostatic proteins. The complexity and redundancy of saliva ensures an efficient blood meal for the arthropod, but it also provides a diverse array of novel antihemostatic molecules for the pharmacologist.

Two serine protease inhibitors from the skin secretions of the toad, Bombina microdeladigitora

Two serine protease inhibitors (named BMSI 1 and BMSI 2, respectively) were identified from the skin secretions of the toad, Bombina microdeladigitora. The cDNAs encoding BMSIs were cloned from a cDNA library prepared from the toad skin. The deduced complete amino acid sequences of BMSIs indicate that mature BMSI1 and BMSI2 are composed of 60 amino acids including 10 half-cystines to form 5 disulfide bridges. A FASTA search in the databanks revealed that BMSIs exhibit sequence similarity with other serine protease inhibitors from amphibians of the genus Bombina. BMSI1 potently inhibited trypsin and thrombin with a K(i) value of 0.02 mu M and 0.15 mu M, respectively. Sequence analysis revealed that all serine protease inhibitors from five amphibians of the genus Bombina share highly conserved primary structures. (c) 2007 Elsevier Inc. All rights reserved.

Evolutionary implications of multiple SINE insertions in an intronic region from diverse mammals

An analysis of the nuclear beta-fibrinogen intron 7 locus from 30 taxa representing 12 placental orders of mammals reveals the enriched occurrences of short interspersed clement (SINE) insertion events. Mammalian-wide interspersed repeats (MIRs) are present at orthologous sites of all examined species except those in the order Rodentia. The higher substitution rate in mouse and a rare MIR deletion from rat account for the absence of MIR in the rodents. A minimum of five lineage-specific SINE sequences are also found to have independently inserted into this intron in Carnivora, Artiodactyla and Lagomorpha. In the case of Carnivora, the unique amplification pattern of order-specific CAN SINE provides important evidence for the "pan-carnivore" hypothesis of this repeat element and reveals that the CAN SINE family may still be active today. Particularly interesting is the finding that all identified lineage-specific SINE elements show a strong tendency to insert within or in very close proximity to the preexisting MIRs for their efficient integrations, suggesting that the MIR clement is a hot spot for successive insertions of other SINEs. The unexpected MIR excision as a result of a random deletion in the rat intron locus and the non-random site targeting detected by this study indicate that SINEs actually have a greater insertional flexibility and regional specificity than had previously been recognized. Implications for SINE sequence evolution upon and following integration, as well as the fascinating interactions between retroposons and the host genomes are discussed.

Synthesis and biological evaluation of N-acetyl-beta-aryl-1,2-didehydroethylamines as new HIV-1 RT inhibitors in vitro

A variety of N-acetyl-o-aryl-1,2-didehydroethylamines were synthesized by direct reduction-acetylation of beta-aryl-nitroolefins and assayed as HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs) for the first time. Compound 7a exhibited a TI v

Efficient synthesis and utilization of phenyl-substituted heteroaromatic carboxylic acids as aryl diketo acid isosteres in the design of novel HIV-1 integrase inhibitors

Three new types of aryl diketo acid (ADK) isosteres were designed by conversion of the biologically labile 1,3-diketo unit into heteroaromatic motif such as isoxazole, isothiazole, or 1H-pyrazole to improve the physicochemical property of ADK-based HIV-1

Anti HIV-1 Agents 2. Discovery of Dibenzofurans as New HIV-1 Inhibitors In Vitro

Ten dibenzofurans were synthesized and evaluated as human immunodeficiency virus (HIV)-1 inhibitors in vitro for the first time. Among these compounds, compounds 1, 6, 7 and 8 demonstrated significant anti-HIV-1 activity. Especially compound 1 showed the

Anti Human Immunodeficiency Virus-1 (HIV-1) Agents 1. Discovery of Benzyl Phenyl Ethers as New HIV-1 Inhibitors in Vitro

Ten single benzyl phenyl ethers were synthesized and evaluated as human immunodeficiency virus-1 (HIV-1) inhibitors in vitro for the first time. Among these compounds, especially 4-nitrobenzyl phenyl ether (3h) exhibited the highest anti-HIV-1 activity wi

Anti Human Immunodeficiency Virus Type 1 (HIV-1) Agents 4. Discovery of 5,5 '-(p-Phenylenebisazo)-8-hydroxyquinoline Sulfonates as New HIV-1 Inhibitors in Vitro

To search for compounds with superior anti-human immunodeficiency virus type 1 (HIV-1) activity, ten 5,5'-(p-phenylenebisazo)-8-hydroxyquinoline sulfonates (4a-j) were synthesized and preliminarily evaluated as HIV-1 inhibitors in vitro for the first time. Some compounds demonstrated anti-HIV-1 activity, especially 5,5'-(p-phenylenebisazo)-8-hydroxyquinoline p-ethylbenzenesulfonate (4g) and 5,5'-(p-phenylenebisazo)-8-hydroxyquinoline p-chlorobenzenesulfonate (41) showed the more potent anti-HIV-1 activity with 50% effective concentration (EC50) values of 2.59 and 4.01 mu g/ml, and therapeutic index (TI) values of 31.77 and 24.51, respectively.