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  • 1
    Digitale Medien
    Digitale Medien
    Springer
    Journal of computer aided molecular design 14 (2000), S. 293-306 
    ISSN: 1573-4951
    Schlagwort(e): Connolly surface ; endothelin A ; HIV-reverse transcriptase ; holistic description ; molecular electrostatic potential ; PCA ; PLS
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Chemie und Pharmazie
    Notizen: Abstract The recently proposed MS-WHIM indices, a set of theoretical descriptors containing information about size, shape and electrostatic distribution of a molecule, have been further investigated. The main objectives of this work were: (i) to confirm the descriptive power of MS-WHIM in modelling specific biological interactions, (ii) to analyse the dependence of MS-WHIM on the type of atomic charges used for computing electrostatic potential and (iii) to compare the performances of MS-WHIM with those provided by other global 3D molecular descriptors. The spatial autocorrelation of atomic and molecular surface properties were selected for comparison purposes. WHIM-based and autocorrelation-based vectors were calculated for two molecular sets from the literature, namely a series of 18 HIV-1 reverse transcriptase inhibitors and a set of 36 sulphonamide endothelin inhibitors. PLS was adopted to derive statistical predictive models that were validated by means of cross-validation. The reported results confirmed that MS-WHIM indices are able to provide meaningful statistical correlations with biological activity. MS-WHIM descriptors are sensitive to the type of partial atomic charges applied and improved models were obtained using more accurate charges. Moreover for both the datasets, MS-WHIM results, in terms of fitting and predictive power of PLS models, were superior to those from autocorrelation. Finally, the strengths/weaknesses of global 3D-QSAR descriptors over local CoMFA-like methods, as well as the main differences between WHIM-based and autocorrelation-based vectors, are discussed.
    Materialart: Digitale Medien
    Bibliothek Standort Signatur Band/Heft/Jahr Verfügbarkeit
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  • 2
    ISSN: 1573-4951
    Schlagwort(e): CoMFA ; Holistic description ; Connolly surface ; PCA ; Experimental design ; PLS
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Chemie und Pharmazie
    Notizen: Abstract The recently proposed WHIM (Weighted Holistic Invariant Molecular) approach [Todeschini,R., Lasagni, M. and Marengo, E., J. Chemometrics, 8 (1994) 263] has been applied tomolecular surfaces to derive new 3D theoretical descriptors, called MS-WHIM. To test theirreliability, a 3D QSAR study has been performed on a series of steroids, comparing the MS-WHIM description to both the original WHIM indices and CoMFA fields. The analysis of thestatistical models obtained shows that MS-WHIM descriptors provide meaningful quantitativestructure–activity correlations. Thus, the results obtained agree well with thoseachieved using CoMFA fields. The concise number of indices, the ease of their calculationand their invariance to the coordinate system make MS-WHIM an attractive tool for 3DQSAR studies.
    Materialart: Digitale Medien
    Bibliothek Standort Signatur Band/Heft/Jahr Verfügbarkeit
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  • 3
    Digitale Medien
    Digitale Medien
    Springer
    International journal of peptide research and therapeutics 2 (1995), S. 161-164 
    ISSN: 1573-3904
    Schlagwort(e): Cyclised peptide ; Dioxopiperazine ; Thiazolidine ; NMR ; Computer modelling
    Quelle: Springer Online Journal Archives 1860-2000
    Thema: Chemie und Pharmazie
    Notizen: Summary Conformationally constrained peptidomimetics of the Lys-Pro sequence have been obtained using a new polycyclic structure. Bicyclic compounds containing a dioxopiperazine-thiazolidine fused ring have been synthesised starting from N-lysyl-4-ethoxycarbonylthiazolidine-2-carboxylic acid. The carboxyl group in either position 2 or 4 of the thiazolidine ring was reacted with the N-terminal amino group, giving different regioisomers. NMR and computer modelling were used to study the configuration of isomers and the lysine side-chain orientation with respect to the pseudoproline ring.
    Materialart: Digitale Medien
    Bibliothek Standort Signatur Band/Heft/Jahr Verfügbarkeit
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  • 4
    Digitale Medien
    Digitale Medien
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 1295-1311 
    ISSN: 0192-8651
    Schlagwort(e): cluster analysis ; SONHICA ; conformational analysis ; ITF1697 ; BQ123 ; molecular dynamics ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Quelle: Wiley InterScience Backfile Collection 1832-2000
    Thema: Chemie und Pharmazie , Informatik
    Notizen: We describe a new clustering program, SONHICA (Simple Optimized Non-HIerarchical Cluster Analysis), developed to analyze large data sets of molecular conformations. Unlike traditional clustering methods, SONHICA does not make use of an overall index, like a distance, to evaluate similarity between objects. Each descriptor variable is compared individually on the basis of a preset threshold value. This assures high control and sensitivity over the input variables. In addition, periodic and nonperiodic descriptors, such as dihedral angles and interatomic distances, can easily be used together. SONHICA generates clusters with the highest possible density and all pairs of objects within a cluster are similar. These features make SONHICA particularly suitable for the analysis of data sets which tend to form globular clusters. This method was applied to the analysis of a modified linear tetrapeptide, ITF1697, under investigation for its anti-ischemic properties, and a cyclic pentapeptide, BQ123, a potent antagonist of endothelin A. On the basis of the results presented here, SONHICA appears to be an interesting new tool in the field of the clustering methods applied to the analysis of molecular conformations. © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1295-1311, 1997
    Zusätzliches Material: 11 Ill.
    Materialart: Digitale Medien
    Bibliothek Standort Signatur Band/Heft/Jahr Verfügbarkeit
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