Jordi Rodrigo

Comparative Evaluation of Eight Docking Tools for Docking and Virtual Screening Accuracy

Eight docking programs (DOCK, FLEXX, FRED, GLIDE, GOLD, SLIDE, SURFLEX, and QXP) that can be used for either single‐ligand docking or database screening have been compared for their propensity to recover the X‐ray pose of 100 small‐molecular‐weight ligands, and for their capacity to discriminate known inhibitors of an enzyme (thymidine kinase) from randomly chosen “drug‐like” molecules. Interestingly, both properties are found to be correlated, since the tools showing the best docking accuracy (GLIDE, GOLD, and SURFLEX) are also the most successful in ranking known inhibitors in a virtual screening experiment. Moreover, the current study pinpoints some physicochemical descriptors of either the ligand or its cognate protein‐binding site that generally lead to docking/scoring inaccuracies. Proteins 2004.

A Chemogenomic Analysis of the Transmembrane Binding Cavity of Human G-Protein-Coupled Receptors

The amino acid sequences of 369 human nonolfactory G‐protein‐coupled receptors (GPCRs) have been aligned at the seven transmembrane domain (TM) and used to extract the nature of 30 critical residues supposed—from the X‐ray structure of bovine rhodopsin bound to retinal—to line the TM binding cavity of ground‐state receptors. Interestingly, the clustering of human GPCRs from these 30 residues mirrors the recently described phylogenetic tree of full‐sequence human GPCRs (Fredriksson et al., Mol Pharmacol 2003;63:1256–1272 ) with few exceptions. A TM cavity could be found for all investigated GPCRs with physicochemical properties matching that of their cognate ligands. The current approach allows a very fast comparison of most human GPCRs from the focused perspective of the predicted TM cavity and permits to easily detect key residues that drive ligand selectivity or promiscuity. Proteins 2006.

Overlapping binding sites drive allosteric agonism and positive cooperativity in type 4 metabotropic glutamate receptors

Type 4 metabotropic glutamate (mGlu4) receptors are emerging targets for the treatment of various disorders. Accordingly, numerous mGlu4‐positive allosteric modulators (PAMs) have been identified, some of which also display agonist activity. To identify the structural bases for their allosteric action, we explored the relationship between the binding pockets of mGlu4 PAMs with different chemical scaffolds and their functional properties. By use of innovative mGlu4 biosensors and second‐messenger assays, we show that all PAMs enhance agonist action on the receptor through different degrees of allosteric agonism and positive cooperativity. For example, whereas VU0155041 and VU0415374 display equivalent efficacies [log(τB) = 1.15 ± 0.38 and 1.25 ± 0.44, respectively], they increase the ability of l‐AP4 to stabilize the active conformation of the receptor by 4 and 39 times, respectively. Modeling and docking studies identify 2 overlapping binding pockets as follows: a first site homologous to the pocket of natural agonists of class A GPCRs linked to allosteric agonism and a second one pointing toward a site topographically homologous to the Na+ binding pocket of class A GPCRs, occupied by PAMs exhibiting the strongest cooperativity. These results reveal that intrinsic efficacy and cooperativity of mGlu4 PAMs are correlated with their binding mode, and vice versa, integrating structural and functional knowledge from different GPCR classes.—Rovira, X., Malhaire, F., Scholler, P., Rodrigo, J., Gonzalez‐Bulnes, P., Llebaria, A., Pin, J.P., Giraldo, J., Goudet, C., Overlapping binding sites drive allosteric agonism and positive cooperativity in type 4 metabotropic glutamate receptors. FASEB J. 29, 116–130 (2015). www.fasebj.org

B-ring-modified isocombretastatin A-4 analogues endowed with interesting anticancer activities.

A novel class of isocombretastatin A‐4 (isoCA‐4) analogues with modifications at the 3′‐position of the B‐ring by replacement with C‐linked substituents was studied. Exploration of the structure–activity relationships of theses analogues led to the identification of several compounds that exhibit excellent antiproliferative activities in the nanomolar concentration range against H1299, MDA‐MB231, HCT116, and K562 cancer cell lines; they also inhibit tubulin polymerization with potency similar to that of isoCA‐4. 1,1‐Diarylethylenes 8 and 17, respectively with (E)‐propen‐3‐ol and propyn‐3‐ol substituents at the 3′‐position of the B‐ring, proved to be the most active in this series. Both compounds led to the arrest of various cancer cell lines at the G2/M phase of the cell cycle and strongly induced apoptosis. Docking of compounds 8 and 17 in the colchicine binding site indicated that their C3′ substituents guide the positioning of the B‐ring in a manner different from that observed for isoCA‐4.

Identification and structure-activity relationship of 8-hydroxy-quinoline-7-carboxylic acid derivatives as inhibitors of Pim-1 kinase.

Pim-1 kinase is a cytoplasmic serine/threonine kinase that controls programmed cell death by phosphorylating substrates that regulate both apoptosis and cellular metabolism. A series of 2-styrylquinolines and quinoline-2-carboxamides has been identified as potent inhibitors of the Pim-1 kinase. The 8-hydroxy-quinoline 7-carboxylic acid moiety appeared to be a crucial pharmacophore for activity. Molecular modeling indicated that interaction of this scaffold with Asp186 and Lys67 residues within the ATP-binding pocket might be responsible for the kinase inhibitory potency.

Design, synthesis and anticancer properties of 5-arylbenzoxepins as conformationally restricted isocombretastatin A-4 analogs

A series of novel benzoxepins 6 was designed and prepared as rigid-isoCA-4 analogs according to a convergent strategy using the coupling of N-tosylhydrazones with aryl iodides under palladium catalysis. The most potent compound 6b, having the greatest resemblance to CA-4 and isoCA-4 displayed antiproliferative activity at nanomolar concentrations against various cancer cell lines and inhibited tubulin assembly at a micromolar range. In addition, benzoxepin 6b led to the arrest of HCT116, K562, H1299 and MDA-MB231 cancer cell lines in the G2/M phase of the cell cycle, and strongly induced apoptosis at low concentrations. Docking studies demonstrated that benzoxepin 6b adopt an orientation similar to that of isoCA-4 at the colchicine binding site on β-tubulin.

Rapid synthesis of 4-arylchromenes from ortho-substituted alkynols: A versatile access to restricted isocombretastatin A-4 analogues as antitumor agents

Potent anticancer 4-arylchromene agents 6, as restricted isoCA-4 analogues, were prepared with excellent yields by a rapid and versatile synthetic pathway. First, in the presence of PTSA in EtOH, a variety of arylalkynols 9 were transformed into substituted 4-chromanones 10 in a one pot procedure which include regioselective arylalkynols hydration, alcohol etherification, MOM-cleavage, and cyclization. Further palladium coupling reactions, using aryl halides and N-tosylhydrazones 11 gave access to a small library of functionalized 4-arylchromenes 6 with good yields. From this series of 4-arylchromenes, we have identified compound 6s which inhibit tubulin assembly at a micromolar level and demonstrate a remarkable nanomolar level of cytotoxicity against four human cancer cell lines. Docking studies showed that isoCA-4 and its restricted chromene analogue 6s adopt a similar positioning in the colchicine binding-site of tubulin.

Pyridazine derivatives. Part 27: A joint theoretical and experimental approach to the synthesis of 6-phenyl-4,5-disubstituted-3(2H)-pyridazinones ☆

Abstract A theoretical study of the structures of a series of 5-substituted-6-phenyl-3(2H)-pyridazinones has been carried out using quantum-mechanical calculations. This study indicates a significant effect of the nature of the substituent at the 5-position on the reactivity of this system. The results have also been confirmed by means of 1H NMR measurements. The outcome of this work has guided the development of novel and efficient synthetic pathways to obtain pharmacologically useful 6-phenyl-4,5-substituted-3(2H)-pyridazinones.

α- and β-hydrazino acid-based pseudopeptides inhibit the chymotrypsin-like activity of the eukaryotic 20S proteasome

We describe the synthesis of a library of new pseudopeptides and their inhibitory activity of the rabbit 20S proteasome chymotrypsin-like (ChT-L) activity. We replaced a natural α-amino acid by an α- or a β-hydrazino acid and obtained inhibitors of proteasome up to a submicromolar range (0.7 μM for molecule 24b). Structural variations influenced the inhibition of the ChT-L activity. Models of inhibitor/20S proteasome complexes corroborated the inhibition efficacies obtained by kinetic studies.

Subtlety of the Structure-Affinity and Structure—Efficacy Relationships around a Nonpeptide Oxytocin Receptor Agonist

Very few nonpeptide oxytocin agonists have currently been reported, and none of them seem suitable for the in vivo investigation of the oxytocin mediated functions. In an attempt to rationalize the design of better tools, we have systematically studied the structural determinants of the affinity and efficacy of representative ligands of the V(1a), V(2), and OT receptor subtypes. Despite apparently obvious similarity between the ligand structures on one hand, and between the receptor subtypes on the other hand, the binding affinity and the functional activity profiles of truncated and hybrid ligands highlight the subtlety of ligand-receptor interactions for obtaining nonpeptide OT receptor agonists.