Modeling of binding modes and inhibition mechanism of some natural ligands of farnesyl transferase using molecular docking.
Several natural inhibitors of farnesyl transferase have been reported in the literature: some compounds are competitive with farnesyl pyrophosphate (FPP), whereas other ones are competitive with Ras proteins, even though it is usually hard to highlight their inhibition mechanism, which is still unknown for several natural compounds. The aim of this work is to show that the molecular docking analysis can be successfully used to underline the inhibition mechanism of these natural compounds. First, the selected compounds were subjected to a detailed docking analysis, by means of BioDock, a program able to reveal the most likely binding mode for each ligand. By comparing these results with the binding sites for the natural substrates, earlier determined, it was possible to highlight the site specificity and the inhibition mechanism of the selected compounds. In addition, it is possible to relate the binding mode of these molecules with their lipole values, which is appreciably less for peptidomimetics than for FPP mimetic and reveals a straightforward method to predict and to understand the inhibition mechanism of these natural derivatives.
Pedretti
Alessandro
A
Istituto di Chimica Farmaceutica e Tossicologica, University of Milan, Viale Abruzzi 42, I-20131 Milan, Italy.
Villa
Luigi
L
Vistoli
Giulio
G
D019883:Alkyl and Aryl Transferases / Q000737:chemistry* / Q000378:metabolism*; D020816:Amino Acid Motifs; D000730:Androstadienes / Q000737:chemistry; D000935:Antifungal Agents / Q000494:pharmacology; D001120:Arginine / Q000737:chemistry; D001665:Binding Sites; D019086:Bridged Bicyclo Compounds, Heterocyclic / Q000737:chemistry; D002867:Chromones / Q000494:pharmacology; D003198:Computer Simulation; D018360:Crystallography, X-Ray; D004791:Enzyme Inhibitors / Q000494:pharmacology; D051231:Farnesyltranstransferase; D005227:Fatty Acids / Q000737:chemistry; D005650:Fumarates / Q000737:chemistry; D006576:Heterocyclic Compounds, 4 or More Rings / Q000494:pharmacology; D020128:Inhibitory Concentration 50; D007783:Lactones / Q000494:pharmacology; D007810:Lanosterol / Q000031:analogs & derivatives* / Q000737:chemistry; D008024:Ligands; D008956:Models, Chemical; D008958:Models, Molecular; D015233:Models, Statistical; D010082:Oxepins / Q000494:pharmacology; D011485:Protein Binding; D012717:Sesquiterpenes; D012984:Software; D014233:Tricarboxylic Acids / Q000737:chemistry; D015032:Zinc / Q000737:chemistry; D018631:ras Proteins / Q000378:metabolism
D000730:Androstadienes; D000935:Antifungal Agents; D019086:Bridged Bicyclo Compounds, Heterocyclic; D002867:Chromones; D004791:Enzyme Inhibitors; D005227:Fatty Acids; D005650:Fumarates; D006576:Heterocyclic Compounds, 4 or More Rings; D007783:Lactones; D008024:Ligands; D010082:Oxepins; D012717:Sesquiterpenes; D014233:Tricarboxylic Acids; C100395:andrastin A; C452822:artemidolide; C115583:clavaric acid; C101437:schizostatin; C075117:squalestatin 1; C452821:fusidienol; D007810:Lanosterol; D001120:Arginine; D019883:Alkyl and Aryl Transferases; D051231:Farnesyltranstransferase; D018631:ras Proteins; D015032:Zinc