ChemGPS-NP is a principal component analysis (PCA) based global space map or a chemical global positioning system.
ChemGPS-NP has eight principal components (dimensions) describing physical-chemical properties for a reference set of compounds. The basic interpretation of the first four dimensions of ChemGPS-NP is: Size increases in the positive direction of principal component one (PC1); compounds are increasingly aromatic in the positive direction of PC2; lipophilic compounds are situated in the positive direction of PC3; and predominantly polar compounds are located in the negative PC3 direction; compounds are increasingly flexible in the PC4 positive direction and more rigid in its negative direction. Compounds of interest or under study are positioned onto this map using interpolation in terms of (PCA) score prediction. The properties of the compounds together with trends and groupings can easily be interpreted from the resulting projections.
ChemGPS-NP is tuned for exploration of the regions of chemical space most likely to enclose compounds with biologically relevant functions and activities. Large libraries can for instance be compared without positions changing as new structures are included. For instance known inhibitors of a certain target can first be positioned on the map and possible active regions of space can be discovered. Full libraries can then be positioned on the map and selection of candidates to continue with can be selected from the active region.
In the ChemGPS-NP we set-up employed since 2019, alvaDesc is used as the descriptor engine providing input for subsequent positioning in ChemGPS-NP physical-chemical property space via PCA score prediction by SIMCA-Q.
For more information about ChemGPS-NP, read the original publication:
Larsson J, Gottfries J, Muresan S, Backlund A. ChemGPS-NP: tuned for navigation in biologically relevant chemical space. J Nat Prod. 2007;70(5):789-794.