Superstar Data Sheet

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  • SuperStar is a program for generating maps of interaction hotspots inprotein binding sites or around small molecules using crystallographicinformation about intermolecular interactions [1,2]. The interaction mapsthat SuperStar generates are therefore fully knowledge-based.

    SuperStar retrieves its data from IsoStar, the CCDCs knowledge base of intermolecularinteractions. IsoStar contains information about non-bonded interactions from both theCambridge Structural Database (CSD) and the Protein Data Bank (PDB).

    SuperStar features:

    Fast generation of maps (less than 1 minute per binding site) Use of either CSD or PDB data [3] Ability to predict metal coordination sites Built-in cavity detection that automatically selects appropriate residues Knowledge-based approach: all results can be traced back to experimentally observed

    geometries of interaction

    Application of parameterised Gaussian functions for speeding up calculations [4] Choice of 14 CSD probes and 6 PDB probes selected for diversity and data availability

    (including a water probe)

    Visualisation through 3D maps, Connolly surfaces, scatterplots, and pharmacophore fitting points Extensive validation on a test set of 305 protein-ligand complexes from the PDB [5] LogP-based hydrophobic correction for use with CSD dataRunning SuperStar:

    SuperStar is an additional option for all CSD System subscribers and is supported on UNIX (including Linux) operating systems

    Native and Tripos SYBYL interfaces are available Command-file driven interface is available for additional control and batch-processingOther CCDC products related to SuperStar:

    Relibase+ advanced searching of protein-ligand complexes GOLD/GoldMine protein-ligand docking and post-processing virtual screening results Cambridge Structural Database System, including Mogul and IsoStar click-of-a-button access

    to experimental information on conformations and intermolecular interactions

    References:[1] M. L. Verdonk, J. C. Cole, R. Taylor, J. Mol. Biol.,

    289, 1093-1108, 1999[2] M. L. Verdonk, J. C. Cole, P. Watson, V. Gillet, P.

    Willett, J. Mol. Biol., 307, 841-859, 2001[3] D. R. Boer, J. Kroon, J. C. Cole, B. Smith, M. L.

    Verdonk, J. Mol. Biol., 312, 275-287, 2001

    [4] J. W. M. Nissink, M. L. Verdonk, G. Klebe,J. Comput.Aided Mol. Des., 14, 787-803, 2000

    [5] J. W. M. Nissink, C. Murray, M. Hartshorn, M. L.Verdonk, J. C. Cole, R. Taylor, Proteins, 49, 457-471,2002

    Fig. 1: SuperStar CSD maps of 3CPA binding siteusing aromatic CH (blue) and C=O (yellow) probes.The ligand is glycyl-L-tyrosine.

    Fig. 3: Methyl carbon probe (blue) and unchargedNH nitrogen probe (red) maps for niacin (vitamin B3).

    Fig. 2: SuperStar CSD maps of 1A9U binding siteusing aromatic CH (blue) and C=O (yellow) probes.The ligand is a pyridinylimidazole.


    Predicting Intermolecular Interactions

    For further information, or to arrange a free evaluation, please contact Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, UK Tel: +44 1223 336408 Fax: +44 1223 336033 Email : Registered in England No. 2155347 Registered Charity No. 800579

    www.ccdc .uk

  • Fig. 6: SuperStar contour map ofan HIV protease binding site(1AAQ) using aromatic CH probe(red contour is at 1.5 propensitylevel, yellow contour at 2.5).The ligand is hydroxyethyleneisostere.

    Crystallographic data provide a rich source of information on non-bonded interactions for use in drugdesign and are available in abundance in the Cambridge Structural Database (CSD). Likewise, theProtein Data Bank (PDB) offers similar information at the macromolecular level, though usually at alower crystallographic resolution and with much lower diversity of functional groups.

    SuperStar uses such contact information to calculate its maps (Figures 1, 2, and 3). This is done by way of the intermediary IsoStar knowledge base [6]. IsoStar contains discrete contact information(Figure 4a), together with the necessary algorithms to convert this information to propensityinteraction maps. Propensity plots denote the likelihood of finding a given probe group at a certainposition in space. Contouring on propensity yields plots similar to the one shown in Figure 4b(propensity plot for hydroxyl groups in contact with an ester).

    PDB or CSD contact information can be used to compile maps, and available SuperStar probe groupscover hydrophilic and lipophilic interaction types.When predicting interactions for small molecules(e.g. for crystal structure prediction), CSD data can be used directly. Sophisticated correctionalgorithms [7] are used to transform CSD-based maps to a scale that is meaningful for protein bindingsites, if needed. This procedure takes into account hydrophobicity data for all regions of interest.

    Results can be displayed easily as contoured maps in current modelling packages (e.g. Tripos SYBYL,or Accelrys Insight). Pharmacophore points can be derived automatically, and can be used for databasesearches or QSAR [8].

    Figure 5 shows water-probe contour maps calculated both for a neuraminidase binding site, and forthe ligand in the bound orientation. The top water mediates a protein-protein contact, the bottomone a protein-ligand contact. Figure 6 displays a map for a lipophilic probe (aromatic CH carbon) foran HIV protease binding site, contoured on propensity. The hydrophobic pockets that accommodatethe side chains of the ligand can be clearly observed.

    An extensive validation of prediction of bound ligand groups in protein cavities by relevant SuperStarmaps (e.g. prediction of ligand alcohol groups by hydroxyl oxygen maps) has shown that success rates of prediction lie typically in the range 70-80% for solvent-inaccessible (buried) ligand moieties(60-70% when including less buried groups in the analysis too) [7].


    www.ccdc .uk

    Scientific Methodology

    For further information, or to arrange a free evaluation, please contact Cambridge Crystallographic Data Centre, 12 Union Road, Cambridge CB2 1EZ, UK Tel: +44 1223 336408 Fax: +44 1223 336033 Email : Registered in England No. 2155347 Registered Charity No. 800579

    References:[6] I. J. Bruno, J. C. Cole, J. P. M. Lommerse, R. S.

    Rowland, R. Taylor, M. L. Verdonk, J. Comput.-Aided.Mol. Design, 11, 525-537, 1997

    [7] J. W. M. Nissink, R. Taylor Org. Biomol. Chem., 2,3238-3249, 2004

    [8] M. Boehm, G. Klebe, J. Med. Chem., 45, 1585-1597,2002

    a bFig. 4: Scatterplot for hydroxyl groups interactingwith an ester moiety (a); propensity contourderived from this scatterplot (b)

    Fig. 5: Inhibitor zanamavir in neuraminidasebinding site (1A4G). Water probe maps for protein(red) and ligand (blue) highlight mediating watercontacts.