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      A user-friendly Matlab program and GUI for the pseudorotation analysis of saturated five-membered ring systems based on scalar coupling constants

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      1 , , 1 ,
      Chemistry Central Journal
      BioMed Central

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          Abstract

          Background

          The advent of combinatorial chemistry has revived the interest in five-membered heterocyclic rings as scaffolds in pharmaceutical research. They are also the target of modifications in nucleic acid chemistry. Hence, the characterization of their conformational features is of considerable interest. This can be accomplished from the analysis of the 3 J HH scalar coupling constants.

          Results

          A freely available program including an easy-to-use graphical user interface (GUI) has been developed for the calculation of five-membered ring conformations from scalar coupling constant data. A variety of operational modes and parameterizations can be selected by the user, and the coupling constants and electronegativity parameters can be defined interactively. Furthermore, the possibility of generating high-quality graphical output of the conformational space accessible to the molecule under study facilitates the interpretation of the results. These features are illustrated via the conformational analysis of two 4'-thio-2'-deoxynucleoside analogs. Results are discussed and compared with those obtained using the original PSEUROT program.

          Conclusion

          A user-friendly Matlab interface has been developed and tested. This should considerably improve the accessibility of this kind of calculations to the chemical community.

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          Most cited references51

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          Conformational analysis of the sugar ring in nucleosides and nucleotides. A new description using the concept of pseudorotation.

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            Combinatorial compound libraries for drug discovery: an ongoing challenge.

            Almost 20 years of combinatorial chemistry have emphasized the power of numbers, a key issue for drug discovery in the current genomic era, in which it has been estimated that there might be more than 10,000 potential targets for which it would be desirable to have small-molecule modulators. Combinatorial chemistry is best described as the industrialization of chemistry; the chemistry has not changed, just the way in which it is now carried out, which is principally by exploiting instrumentation and robotics coupled to the extensive use of computers to efficiently control the process and analyse the vast amounts of resulting data. Many researchers have contributed to the general concepts as well as to the technologies in present use. However, some interesting challenges still remain to be solved, and these are discussed here in the context of the application of combinatorial chemistry to drug discovery.
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              DNA analogues: from supramolecular principles to biological properties.

              Mainly driven by the needs of antisense research, a large number of oligonucleotide analogues have been prepared and evaluated over the last 15 years. Besides minor structural modifications of the building blocks of DNA and RNA itself, a considerable effort has been devoted to the de novo design of nucleoside analogues with improved binding properties. A particularly successful concept turned out to be that of conformational restriction. This review focuses on recent advances in this area and tries to summarize scope and limitations of this design principle.
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                Author and article information

                Journal
                Chem Cent J
                Chemistry Central Journal
                BioMed Central
                1752-153X
                2008
                24 October 2008
                : 2
                : 20
                Affiliations
                [1 ]NMR and Structure Analysis Unit, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
                Article
                1752-153X-2-20
                10.1186/1752-153X-2-20
                2634759
                18950513
                32188cf7-af06-450c-a609-ecfb3fa46e64
                Copyright © 2008 Hendrickx et al

                This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 9 July 2008
                : 24 October 2008
                Categories
                Software

                Chemistry
                Chemistry

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