title: Virtual screening on an α-helix to β-strand switchable region of the FGFR2 extracellular domain revealed positive and negative modulators.
abstract: The secondary structure of some protein segments may vary between α-helix and β-strand. To predict these switchable segments, we have developed an algorithm, Switch-P, based solely on the protein sequence. This algorithm was used on the extracellular parts of FGF receptors. For FGFR2, it predicted that β4 and β5 strands of the third Ig-like domain were highly switchable. These two strands possess a high number of somatic mutations associated with cancer. Analysis of PDB structures of FGF receptors confirmed the switchability prediction for β5. We thus evaluated if compound-driven α-helix/β-strand switching of β5 could modulate FGFR2 signaling. We performed the virtual screening of a library containing 1.4 million of chemical compounds with two models of the third Ig-like domain of FGFR2 showing different secondary structures for β5, and we selected 32 compounds. Experimental testing using proliferation assays with FGF7-stimulated SNU-16 cells and a FGFR2-dependent Erk1/2 phosphorylation assay with FGFR2-transfected L6 cells, revealed activators and inhibitors of FGFR2. Our method for the identification of switchable proteinic regions, associated with our virtual screening approach, provides an opportunity to discover new generation of drugs with under-explored mechanism of action.
authors.affiliation: Exploratory Unit, Sanofi-Aventis Research and Development, 195 Route d'Espagne, 31036, Toulouse, France.
authors.forename: Constantino
authors.initials: C
authors.lastname: Diaz
authors.forename: Herbert
authors.initials: H
authors.lastname: Corentin
authors.forename: Vermat
authors.initials: V
authors.lastname: Thierry
authors.forename: Alcouffe
authors.initials: A
authors.lastname: Chantal
authors.forename: Bozec
authors.initials: B
authors.lastname: Tanguy
authors.forename: Sibrac
authors.initials: S
authors.lastname: David
authors.forename: Herbert
authors.initials: H
authors.lastname: Jean-Marc
authors.forename: Ferrara
authors.initials: F
authors.lastname: Pascual
authors.forename: Bono
authors.initials: B
authors.lastname: Françoise
authors.forename: Ferran
authors.initials: F
authors.lastname: Edgardo
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D002460:Cell Line / Q000187:drug effects; D049109:Cell Proliferation / Q000187:drug effects; D003198:Computer Simulation; D004353:Drug Evaluation, Preclinical / Q000379:methods*; D006801:Humans; D046609:Libraries, Digital; D019950:Mitogen-Activated Protein Kinase 1 / Q000378:metabolism; D048052:Mitogen-Activated Protein Kinase 3 / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009154:Mutation; D009369:Neoplasms / Q000235:genetics; D010766:Phosphorylation / Q000187:drug effects; D017434:Protein Structure, Tertiary; D051381:Rats; D051497:Receptor, Fibroblast Growth Factor, Type 2 / Q000235:genetics / Q000378:metabolism; D017468:Receptors, Fibroblast Growth Factor / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D017386:Sequence Homology, Amino Acid; D015398:Signal Transduction / Q000187:drug effects
chemical_list: D017468:Receptors, Fibroblast Growth Factor; C496353:FGFR2 protein, human; C496356:Fgfr2 protein, rat; D051497:Receptor, Fibroblast Growth Factor, Type 2; D019950:Mitogen-Activated Protein Kinase 1; D048052:Mitogen-Activated Protein Kinase 3
keywords: allosteric modulation; ambivalence; bioinformatics; disease; drug discovery; mutation; protein structure; receptor function; secondary structure; virtual screening