LigandScout

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LigandScout is a software tool that allows to model 3D pharmacophore models from structural data of macromolecule/ligand complexes. It incorporates a complete definition of three-dimensional chemical features (such as hydrogen bond donors, acceptors, lipophilic areas, positively and negatively ionizable chemical groups) that describe the interaction of a bound small organic molecule (ligand) and the surrounding binding site of the macromolecule[1]. These pharmacophores can be overlaid and superimposed using a pattern-matching based alignment algorithm[2] that is solely based on pharmacophoric feature points instead of chemical structure. From such an overlay, shared features can be interpolated to create a so-called "shared-feature pharmacophore" that shares all common interactions of several binding sites/ligands or extended to create a so-called "merged-feature" pharmacophore. The software has been successfully used to predict new lead structures in drug design, e.g. for the prediction of biological activity of novel HIV reverse transcriptase inhibitors[3].

Other software tools which help to model pharmacophore include MOE, by the Chemical Computing Group, Phase by Schroedinger, Discovery Studio by Accelrys, and others.

[edit] References

  1. ^ Wolber, G.; Langer, T.; LigandScout: 3-D pharmacophores derived from protein-bound ligands and their use as virtual screening filters J. Chem. Inf. Model; 2005; 45(1); 160-169. DOI: 10.1021/ci049885e
  2. ^ Wolber, G.; Dornhofer, A. A.; Langer, T.; Efficient overlay of small organic molecules using 3D pharmacophores J. Comput. Aided Mol. Des.; 2007; 20(12); 773-788. DOI: 10.1007/s10822-006-9078-7
  3. ^ Barreca, M. L.; De Luca, L.; Iraci, N.; Rao, A.; Ferro, S.; Maga, G.; Chimirri, A; Structure-Based Pharmacophore Identification of New Chemical Scaffolds as Non-Nucleoside Reverse Transcriptase Inhibitors J. Chem. Inf. Model; 2007; 47(2); 557-562. DOI: 10.1021/ci600320q

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