Conformational control in structure-based drug design

In structure-based drug design, the basic goal is to design molecules that fit complementarily to a given binding pocket. Since such computationally modeled molecules may not adopt the intended bound conformation outside the binding pocket, one challenge is to ensure that the designed ligands adopt similar low energy conformations both inside and outside of the binding pocket. Computational chemistry methods and conformational preferences of small molecules from PDB and Cambridge Structural Database (CSD) can be used to predict the bound structures of the designed molecules. Herein, we review applications of conformational control in structure-based drug design using selected examples from the recent medicinal chemistry literature. The main purpose is to highlight some intriguing conformational features that can be applied to other drug discovery programs.     

Modeling Healthcare Processes Using Commitments: An Empirical Evaluation

The two primary objectives of this paper are: (a) to demonstrate how Comma, a business modeling methodology based on commitments, can be applied in healthcare process modeling, and (b) to evaluate the effectiveness of such an approach in producing healthcare process models. We apply the Comma approach on a breast cancer diagnosis process adapted from an HHS committee report, and presents the results of an empirical study that compares Comma with a traditional approach based on the HL7 Messaging Standard (Traditional-HL7). Our empirical study involved 47 subjects, and two phases. In the first phase, we partitioned the subjects into two approximately equal groups. We gave each group the same requirements based on a process scenario for breast cancer diagnosis. Members of one group first applied Traditional-HL7 and then Comma whereas members of the second group first applied Comma and then Traditional-HL7—each on the above-mentioned requirements. Thus, each subject produced two models, each model being a set of UML Sequence Diagrams. In the second phase, we repartitioned the subjects into two groups with approximately equal distributions from both original groups. We developed exemplar Traditional-HL7 and Comma models; we gave one repartitioned group our Traditional-HL7 model and the other repartitioned group our Comma model. We provided the same changed set of requirements to all subjects and asked them to modify the provided exemplar model to satisfy the new requirements. We assessed solutions produced by subjects in both phases with respect to measures of flexibility, time, difficulty, objective quality, and subjective quality. Our study found that Comma is superior to Traditional-HL7 in flexibility and objective quality as validated via Student’s t-test to the 10% level of significance. Comma is a promising new approach for modeling healthcare processes. Further gains could be made through improved tooling and enhanced training of modeling personnel.     

Deriving phylogenetic trees from the similarity analysis of metabolic pathways

MOTIVATION: Comparative analysis of metabolic pathways in different genomes can give insights into the understanding of evolutionary and organizational relationships among species. This type of analysis allows one to measure the evolution of complete processes (with different functional roles) rather than the individual elements of a conventional analysis. We present a new technique for the phylogenetic analysis of metabolic pathways based on the topology of the underlying graphs. A distance measure between graphs is defined using the similarity between nodes of the graphs and the structural relationship between them. This distance measure is applied to the enzyme-enzyme relational graphs derived from metabolic pathways. Using this approach, pathways and group of pathways of different organisms are compared to each other and the resulting distance matrix is used to obtain a phylogenetic tree. RESULTS: We apply the method to the Citric Acid Cycle and the Glycolysis pathways of different groups of organisms, as well as to the Carbohydrate metabolic networks. Phylogenetic trees obtained from the experiments were close to existing phylogenies and revealed interesting relationships among organisms.     

Molecular Cloning and Nucleotide Sequence of the Gene for an Alkaline Protease from Bacillus circulans MTCC 7906

Bacillus circulans MTCC 7906, an extracellular alkaline protease producer was genetically characterized. B. circulans genomic DNA was isolated, oligonucleotide primers specific to alkaline protease gene of B. circulans were designed and its PCR amplification was done. The purified PCR product and pTrcHisA vector were subjected to restriction digestion with NcoI and HindIII and transformed into Escherichia coli DH5-α competent cells. The recombinant expression of alkaline protease gene studied by inducible expression and analysis by SDS-PAGE, established that the alkaline protease protein had an estimated molecular size of 46 kDa. Gene sequencing of the insert from selected recombinant clone showed it to be a 1329 bp gene encoding a protein of 442 amino acids. The sequence was blasted and aligned with known alkaline protease genes for comparison with their nucleotide and amino acid sequences. This identified major matches with three closely related subsp. of B. subtilis (B. subtilis subsp. subtilis strain 168, B. subtilis BSn5 and B. subtilis subsp. spizizenii strain W23). The insert also showed a number of substitutions (mutations) with other sp. of Bacillus which established that alkaline protease of B. circulans MTCC 7906 is a novel gene. The phylogenetic analysis of alkaline protease gene and its predicted amino acid sequences also validated that alkaline protease gene is a novel gene and the same has been accessioned in GenBank with accession number {"type":"entrez-nucleotide","attrs":{"text":"JN645176.1","term_id":"353260575","term_text":"JN645176.1"}}JN645176.1.     

Factors regulating copper uptake in free and immobilized cyanobacterium

The effect of population size, redox potential, exogenous ATP and complexing agents on Cu uptake by free and immobilized cyanobacteriumNostoc calcicola Bréb. has been studied. Cu uptake was regulated by the population size. In such comparisons, the immobilized cells had a greater longevity. Low pH conditions enhanced Cu uptake. Exogenous ATP (10 μmol/L) supplied to dark-grown free and immobilized cells did not support Cu uptake to the extent of light-grown cells. Experiments involving natural as well as synthetic complexing agents clearly established the superiority of soil extract and spent medium over EDTA (10 μmol/L), in sequestering Cu in free as well as immobilized cells.     

Silencing of Vlaro2 for chorismate synthase revealed that the phytopathogen Verticillium longisporum induces the cross-pathway control in the xylem

The first leaky auxotrophic mutant for aromatic amino acids of the near-diploid fungal plant pathogen Verticillium longisporum (VL) has been generated. VL enters its host Brassica napus through the roots and colonizes the xylem vessels. The xylem contains little nutrients including low concentrations of amino acids. We isolated the gene Vlaro2 encoding chorismate synthase by complementation of the corresponding yeast mutant strain. Chorismate synthase produces the first branch point intermediate of aromatic amino acid biosynthesis. A novel RNA-mediated gene silencing method reduced gene expression of both isogenes by 80% and resulted in a bradytrophic mutant, which is a leaky auxotroph due to impaired expression of chorismate synthase. In contrast to the wild type, silencing resulted in increased expression of the cross-pathway regulatory gene VlcpcA (similar to cpcA/GCN4) during saprotrophic life. The mutant fungus is still able to infect the host plant B. napus and the model Arabidopsis thaliana with reduced efficiency. VlcpcA expression is increased in planta in the mutant and the wild-type fungus. We assume that xylem colonization requires induction of the cross-pathway control, presumably because the fungus has to overcome imbalanced amino acid supply in the xylem.