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Quelques images dans la gamme protéine-ligand qui donnent une idée (non exhaustive, non chronologique) de la production dans le domaine. En bas de page, les références bibliographiques correspondantes.

Docking poses of Ferutinin in ERa binding cavities

Ferutinine arrimée dans deux conformations d'un récepteur nuléaire (ERa)
Docking poses of Ferutinin in ERa binding cavities. Ferutinin (FRT, green) docking poses are shown in 1G50 (A, chain A, ERa, brown, closed cavity) and 1XPC (B, chain A, ERa, purple, opened cavity) structures, including the corresponding co-crystallized ligands EST (gold, agonist) and AIT (purple, antagonist). The clipping planes of aligned structures are the same, and set using lateral chains of GLU 353 and ARG394 (left), PHE 404 is also shown (left-up).
Thèse Rémi SAFI, Université Paul Sabatier - Université Libanaise, 2015.

GEQ and THT in InhA binding site

Susbtrat (THT) et inhibiteur (GEQ) cristallographiés dans InhA
Superimposition of GEQ (blue) and substrate analog (purple) molecules in the InhA binding site (PDB IDs respectively 1P44 and 1BVR). Coloring according the kd Hydrophobicity scale for each amino acid from dodger blue to the most hydrophilic, to white, to orange red for the most hydrophobic.
Thèse Aurélien Cholet, Université Paul Sabatier, 2015.

Arrimage stéréospécifique de dérivés amphiphiles à longues chaînes
Superposition of the corresponding crystallographic structures (gray) with lowest energy docked poses (green) of C16-d-erythro-ceramide. The orientation and protein surface (orange) clipping show the placement of the lipid polar heads at the left of the binding site cavity of CERT (CERamide Transfer protein).
Thèse Cécile Santos, Université Paul Sabatier, 2015.

Poses (dérivés d'alcaloïdes marins) après arrimage dans une kinase
Clipped (UCSF Chimera) view of ATP-binding pocket of Chk1 (structure 1NVSa) including SB-218078 ligand (sand, mesh surface) and best poses of compounds 4 (light blue), 5 (purple) and 2 (light pink).

Dérivés du GEQ basés sur un fragment succinimide
Superimposition of crystallographic conformation of GEQ (carbons in green stick representation) and simulated by docking binding mode of 11b (carbons in violet stick representation) in the binding groove of InhA (1P44 PDB entry, chain A). Degree of residue flexibility (side chains of residues around the site, backbone) was applied in docking procedure. Residues Phe149, Tyr158 and Met161 colored in magenta (docked protein structure) and green (1P44 protein structure).
Thèse Tétiana Matviiuk, Université Paul Sabatier, 2014.

Dérivés du triclosan engagés dans le 'minor portal' de InhA
Hypothetical binding mode of compounds 8PS (cyan) and 18 (magenta) in the active site of InhA enzyme (PDB ID 2B37) obtained by molecular docking. Cocrystallised cofactor NAD+ and 8PS are coloured in green and white respectively; the molecular surface of protein is coloured using a hydrophobic scale and rendered using UCSF Chimera. Tyr158 residue is coloured (white for 2B37 native state) in a final conformation obtained after docking. The same calculation protocol was used in both cases and the docking of 8PS shows an agreement in reproducing crystallography (RMSD = 0.94 Å) without displacing Tyr158.

Modes de liaison de sondes lipidiques fluorescentes
Putative conformations of probe A (n = 14) in which the NBD group is found outside CERT cavity (2E3N, blue). These docking poses (extracted from the 50 higher Molegro’s rerank scores) are typical of conformations that reproduce the conformation of hydroxyl and amido groups of a ceramide (right part of the site) with a good accuracy. The C16-ceramide (pink) crystallographic conformation (2E3O) is shown for reference.
Thèse Stéphanie Combemale, Université Paul Sabatier, 2010.

Inhibiteur bisubstrat arrimé dans une histone acétyltransférase (p300)
Binding mode of best compound. Model clipping of PDB structure 3BIY with continuum electrostatics coloring of molecular surface, and compound 3 after docking (35,36). The figure shows occupancy of cavities P1 and P2 by long chain (n = 5) and Boc moieties, respectively, at right of the (yellow) overlapping loop (upper clipping plane).
Thèse Franciane Ho-A-Kwie, Université Paul Sabatier, 2009.

Informations complémentaires

La plupart des images comportant des surfaces moléculaires ont été générées avec le logiciel [UCSF Chimera].
  • Hemisynthesis, Antitumoral Effect, and Molecular Docking Studies of Ferutinin and Its Analogues. Safi R, Rodriguez F, Hilal G, Diab-Assaf M, Diab Y, El-Sabban M, Najjar F, Delfourne E. Chem Biol Drug Des. (2016) 87(3):382-97.
  • Design, synthesis and evaluation of new GEQ derivatives as inhibitors of InhA enzyme and Mycobacterium tuberculosis growth. Chollet A, Mori G, Menendez C, Rodriguez F, Fabing I, Pasca MR, Madacki J, Korduláková J, Constant P, Quémard A, Bernardes-Génisson V, Lherbet C, Baltas M. Eur J Med Chem. (2015) 28;101:218-35.
  • Identification of Novel CERT Ligands as Potential Ceramide Trafficking Inhibitors. Santos C, Rodriguez F, Garcia V, Moravčikova D, Berkeš D, Daïch A, Levade T, Baudoin-Dehoux C, Ballereau S, Génisson Y. ChemBioChem (2014) 15: 2522 – 2528.
  • Design of granulatimide and isogranulatimide analogues as potential Chk1 inhibitors: Study of amino-platforms for their synthesis. Lavrard H, Rodriguez F, Delfourne D. Bioorg. Med. Chem. (2014) 22:4961–4967.
  • A biologically relevant ceramide fluorescent probe to assess the binding of potential ligands to the CERT transfer protein. Combemale S, Santos C, Rodriguez F, Garcia V, Galaup C, Frongia C, Lobjois V, Levade T, Baudoin-Dehoux C, Ballereau S, Génisson Y. RSC Adv. (2013) 3, 18970–18984.
  • Design, chemical synthesis of 3-(9H-fluoren-9-yl)pyrrolidine-2,5-dione derivatives and biological activity against enoyl-ACP reductase (InhA) and Mycobacterium tuberculosis. Matviiuk T, Rodriguez F, Saffon N, Mallet-Ladeira S, Gorichko M, Jesus Lopes Ribeiro AL, Pasca MR, Lherbet C, Voitenko Z, Baltas M. Eur. J. Med. Chem. (2013) 70, 37-48.
  • Chemical synthesis and biological evaluation of triazole derivatives as inhibitors of InhA and antituberculosis agents. Menendez C, Chollet A, Rodriguez F, Inard C, Pasca MR, Lherbet C, Baltas M. Eur. J. Med. Chem. (2012) 52, 275-283.
  • New potent bisubstrate inhibitors of histone acetyltransferase p300: design, synthesis and biological evaluation. Kwie FH, Briet M, Soupaya D, Hoffmann P, Maturano M, Rodriguez F, Blonski C, Lherbet C, Baudoin-Dehoux C. Chem Biol Drug Des. (2011) 77(1):86-92.

Date de mise à jour 8 août 2016

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