Principal component analysis on molecular descriptors as an alternative point of view in the search of new Hsp90 inhibitors.
Inhibiting a protein that regulates multiple signal transduction pathways in cancer cells is an attractive goal for cancer therapy. Heat shock protein 90 (Hsp90) is one of the most promising molecular targets for such an approach. In fact, Hsp90 is a ubiquitous molecular chaperone protein that is involved in folding, activating and assembling of many key mediators of signal transduction, cellular growth, differentiation, stress-response and apoptothic pathways. With the aim to analyze which molecular descriptors have the higher importance in the binding interactions of these classes, we first performed molecular docking experiments on the 187 Hsp90 inhibitors included in the BindingDB, a public database of measured binding affinities. Further, for each frozen conformation obtained from the docking, a set of 250 molecular descriptors was calculated, and the resulting Structure/Descriptors matrix was submitted to Principal Component Analysis. From the factor scores it emerged a good clusterization among similar compounds both in terms of structural class and activity spectrum, while examination of the loadings of the first two factors also allowed to study the classes of descriptors which mainly contribute to each one.
Lauria
Antonino
A
Dipartimento Farmacochimico, Tossicologico e Biologico, Università di Palermo, Via Archirafi 32, 90123 Palermo, Italy. lauria@unipa.it
Ippolito
Mario
M
Almerico
Anna Maria
AM
D001665:Binding Sites; D019295:Computational Biology; D003198:Computer Simulation; D016208:Databases, Factual; D004353:Drug Evaluation, Preclinical / Q000379:methods*; D018841:HSP90 Heat-Shock Proteins / Q000037:antagonists & inhibitors* / Q000378:metabolism; D007555:Isoxazoles / Q000737:chemistry / Q000494:pharmacology; D009284:Naphthols / Q000737:chemistry / Q000494:pharmacology; D025341:Principal Component Analysis; D011487:Protein Conformation; D011687:Purines / Q000737:chemistry / Q000494:pharmacology; D011720:Pyrazoles / Q000737:chemistry / Q000494:pharmacology; D013329:Structure-Activity Relationship
D018841:HSP90 Heat-Shock Proteins; D007555:Isoxazoles; D009284:Naphthols; D011687:Purines; D011720:Pyrazoles