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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. These pharmacophores can be overlaid and superimposed using a pattern-matching based alignment algorithm 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.

Similar tools

Other software tools which help to model pharmacophores include:

• Molecular Operating Environment] (MOE) – by the Chemical Computing Group
• Phase – by Schrödinger
• Discovery Studio – by Accelrys
• SYBYL-X – by Tripos
• Pharao by Silicos-It

See also

• Comparison of software for molecular mechanics modeling

References

1. 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.
2. 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.
3. 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.
4. Molecular Operating Environment
5. Phase Archived 2013-05-14 at the Wayback Machine
6. Discovery Studio
7. SYBYL-X Archived 2010-10-19 at the Wayback Machine

Further reading

• 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.

• Medicinal chemistry
• Molecular modelling software