LigandScout is computer software that allows creating three-dimensional (3D) pharmacophore models from structural data of macromolecule–ligand complexes, or from training and test sets of organic molecules. It incorporates a complete definition of 3D 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., predicting biological activity of novel human immunodeficiency virus (HIV) reverse transcriptase inhibitors.[3]
| Developer(s) | Inte:Ligand GmbH |
|---|---|
| Initial release | 2005 |
| Stable release | 4.4.3
/ January 21, 2020 |
| Operating system | Windows, Mac OS X, Linux |
| Platform | x86, x86-64 |
| Available in | English |
| Type | Molecular modelling and design |
| License | Proprietary commercial software |
| Website | www |
Similar tools
editOther software tools which help to model pharmacophores include:
- Molecular Operating Environment] (MOE) – by the Chemical Computing Group[4]
- Phase – by Schrödinger[5]
- Discovery Studio – by Accelrys[6]
- SYBYL-X – by Tripos[7]
- Pharao by Silicos-It[1]
See also
editReferences
edit- ^ Wolber G, Langer T (2005). "LigandScout: 3-D pharmacophores derived from protein-bound ligands and their use as virtual screening filters". J Chem Inf Model. 45 (1): 160–169. doi:10.1021/ci049885e. PMID 15667141.
- ^ Wolber G, Dornhofer AA, Langer T (2007). "Efficient overlay of small organic molecules using 3D pharmacophores". J Comput Aided Mol Des. 20 (12): 773–788. doi:10.1007/s10822-006-9078-7. PMID 17051340. S2CID 31986330.
- ^ Barreca ML, De Luca L, Iraci N, Rao A, Ferro S, Maga G, Chimirri A (2007). "Structure-based pharmacophore identification of new chemical scaffolds as non-nucleoside reverse transcriptase inhibitors". J Chem Inf Model. 47 (2): 557–562. doi:10.1021/ci600320q. PMID 17274611.
- ^ Molecular Operating Environment
- ^ Phase Archived 2013-05-14 at the Wayback Machine
- ^ Discovery Studio
- ^ SYBYL-X Archived 2010-10-19 at the Wayback Machine
Further reading
edit- Wolber G, Kosara R (30 October 2006). "Chapter 6: Pharmacophores from Macromolecular Complexes with LigandScout". Pharmacophores and Pharmacophore Searches. Wiley. ISBN 3-527-31250-1. Archived from the original on 2008-10-13.