1,721,012 research outputs found
Preface [hot topic: Protein Crystallography in Drug Design (guest editor: Jonathan B. Cooper)]
No full texthe value of structure analysis of proteins in rational drug design is undisputed. The ability to visualize the three dimensional structure of a receptor or enzyme provides a unique view of the residues that make up the protein's ligand binding or catalytic site. The analysis of complexes with ligands or inhibitors provides many clues on the roles that these residues play in the functioning of the molecule. The information derived from this 'picture' can be used to design the next generation of inhibitors with improved complementarity to the ligand-binding site. Whilst many other considerations such as solubility, lipophilicity, chemical stability and bioavailability also 'shape' the drug design process, crystallography can assist in designing compounds which minimize the problems of resistance that arise, for example, when drugs are used to treat infections by viruses that undergo rapid mutation.In this volume, Elspeth Garman (Oxford) and Graeme Laver (Canberra) describe the impact which structural studies have had on the design of influenza drugs. Despite the fact that influenza is a disease which affects millions of people, sometimes with fatal consequences, there has not, until recently, been any drug effective against all strains and vaccines may be relatively or totally ineffective. Screening of many thousands of compounds by pharmaceutical companies has resulted in only two compounds, amantadine and rimantidine, which target the M2 ion channel on the virus and these drugs have major disadvantages. Knowledge of the crystal structure of influenza virus neuraminidase, on the other hand, has allowed the rational design of four “plug-drugs” which bind to the active site of flu neuraminidase and stop replication of the virus. Two of these compounds, Relenza and Tamiflu, are now being used world wide and, although effective when used properly, suffer from problems of delivery. They need to be given very soon after infection to be effective, they only inhibit the influenza virus and none of the other respiratory agents which cause flu-like symptoms, and they are very expensive.The review by Leo Brady and Gus Cameron (Bristol) details the application of protein crystallography and other structural techniques to identifying novel drug targets from plasmodia, the causative agent of malaria. The current use of structure-based design in developing effective drugs for plasmodial targets is discussed.The review by Steve Wood and Simon Kolstoe (Southampton) summarises the known properties of amyloid fibres and proteins found associated with them. The role of X-ray crystallography in analyzing the amyloid proteins themselves and proteins that protect the fibres is discussed. In addition the analysis of complexes with compounds that inhibit fibre formation and compounds that inhibit the processing enzymes will be covered. In the next article, Chris Dealwis and Jonathan Wall (Knoxville) describe structural approaches to combating the pathogenicity of amyloid disease characterised by the deposition of monoclonal free immunoglobulin light chain proteins (LC) as amyloid fibrils within vital organs. Finally, in the review by Leighton Coates (Southampton) and Dean Myles (Grenoble), the manifold benefits of atomic resolution X-ray diffraction analysis of proteins are described. The ability to locate hydrogen atoms of interest and thus define the protonation states of many side chains including the active site groups is potentially of enormous benefit to the drug design process. In addition, the ability to improve definition of disordered regions of the molecule, to analyse ligands which bind with poor occupancy and to study anisotropic movements within the molecule provides further important data. Recent developments in neutron data collection mean that complementary information on proton positions can be provided for an increasing number of proteins. There are several hundred Xray crystal structures that have been refined to or beyond atomic resolution in the protein databank. A number of these structures are of proteins that are currently targets for drug discovery and these are surveyed to illustrate the benefits of atomic resolution X-ray analysis
Aspartic proteinases in disease: A structural perspective
No full textThe aspartic proteinases are a family of enzymes involved in a number of important biological processes. In animals the enzyme renin has a hypertensive action through its role in the renin-angiotensin system. The retroviral aspartic proteinases, such as the HIV proteinase, are essential for maturation of the virus particle and inhibitors have a proven therapeutic record in the treatment of AIDS. The lysosomal aspartic proteinase cathepsin D has been implicated in tumorigenesis and the stomach enzyme pepsin, which plays a major physiological role in hydrolysis of acid-denatured proteins, is responsible for much of the tissue damage in peptic ulcer disease. Since aspartic proteinases also play major roles in amyloid disease, malaria and common fungal infections such as candidiasis, inhibitors to these enzymes are much sought after as potential therapeutic agents. In all aspartic proteinases, the catalytic aspartate residues are involved in an intricate arrangement of hydrogen bonds involving a solvent molecule which is presumed to be water. The catalytic mechanism is thought to involve nucleophilic attack of the active site water molecule on the scissile bond carbonyl generating a tetrahedral gem-diol intermediate. The design of inhibitors generally involves the use of short oligopeptides containing a transition state analogue which mimic this tetrahedral intermediate. The application of structure-based drug design to members of the aspartic proteinase family is the main subject of this review. <br/
A preliminary neutron Laue diffraction study of the aspartic proteinase endothiapepsin
No full textUntil now, no aspartic proteinase has been subjected to a successful neutron diffraction analysis, owing to the limited size of the crystals. However, the recent development of the neutron Laue technique at ILL and EMBL (Grenoble) has allowed the collection of data to 2.2 Å on a complex of endothiapepsin with a transition-state analogue. The objective is to define the positions of the protons at the active site by refinement using the neutron data. In line with work on serine proteinases, where neutron diffraction has provided some of the most definitive data on the catalytic mechanism, it is expected that this work will have a major significance for studies of the aspartic proteinase enzymes
Engineering of an intersubunit disulfide bridge in the iron-superoxide dismutase of Mycobacterium tuberculosis
No full textWith the aim of enhancing interactions involved in dimer formation, an intersubunit disulfide bridge was engineered in the superoxide dismutase enzyme of Mycobacterium tuberculosis. Ser-123 was chosen for mutation to cysteine since it resides at the dimer interface where the serine side chain interacts with the same residue in the opposite subunit. Gel electrophoresis and X-ray crystallographic studies of the expressed mutant confirmed formation of the disulfide bond under nonreducing conditions. However, the mutant protein was found to be less stable than the wild type as judged by susceptibility to denaturation in the presence of guanidine hydrochloride. Decreased stability probably results from formation of a disulfide bridge with a suboptimal torsion angle and exclusion of solvent molecules from the dimer interface.<br/
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Structure of Chlorobium vibrioforme 5-aminolaevulinic acid dehydratase complexed with a diacid inhibitor
No full textThe structure of Chlorobium vibrioforme 5-aminolaevulinic acid dehydratase (ALAD) complexed with the irreversible inhibitor 4,7-dioxosebacic acid has been solved. The inhibitor binds by forming Schiff-base linkages with lysines 200 and 253 at the active site. The structure reported here provides a definition of the interactions made by both of the substrate molecules (A-side and P-side substrates) with the C. vibrioforme ALAD and is compared and contrasted with structures of the same inhibitor bound to Escherichia coli and yeast ALAD. The structure suggests why 4,7-dioxosebacic acid is a better inhibitor of the zinc-dependent ALADs than of the zinc-independent ALADs
5-Aminolaevulinic acid dehydratase: metals, mutants and mechanism
No full text5-Aminolaevulinic acid dehydratase catalyses the formation of porphobilinogen from two molecules of 5-aminolaevulinic acid. The studies described highlight the importance of a bivalent metal ion and two active-site lysine residues for the functioning of 5-aminolaevulinic acid dehydratase. Dehydratases fall into two main categories: zinc-dependent enzymes and magnesium-dependent enzymes. Mutations that introduced zinc-binding ligands into a magnesium-dependent enzyme conferred an absolute requirement for zinc. Mutagenesis of lysine residues 247 and 195 in the Escherichia coli enzyme lead to dramatic effects on enzyme activity, with lysine 247 being absolutely essential. Mutation of either lysine 247 or 195 to cysteine, and treatment of the mutant enzyme with 2-bromethylamine, resulted in the recovery of substantial enzyme activity. The effects of the site-directed alkylating inhibitor, 5-chlorolaevulinic acid, and 4,7-dioxosebacic acid, a putative intermediate analogue, were investigated by X-ray crystallography. These inhibitors reacted with both active-site lysine residues. The role of these two lysine residues in the enzyme mechanism is discussed
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