Manuel Dauchez

The stimulating adventure of KRN 7000

Associated with the CD1d protein, KRN 7000, a potent synthetic α-galactosylceramide, is known to activate the invariant NKT immune cells. This stimulation then leads to the production of different cytokines modulating a T(H)1/T(H)2 immune response balance involved in protection against several pathologies such as autoimmune diseases and cancers. Various efforts have been made toward the synthesis of simple and more functionalized analogues in order to selectively induce T(H)1 or T(H)2-type cytokine production. Since the discovery of KRN 7000, structure-activity relationships, crystallographic and modelling studies have pointed to the potential of several GalCer analogues in term of selective bioactivity, and have highlighted interesting elements in order to better understand the recognition and activation mechanisms of immune iNKT cells. By presenting an up-to-date library of analogues, collecting recent breakthroughs done in crystallography and molecular modelling, and relating them to the available biological results, we hope that this review will highlight and help the scientific community in their KRN research.

Normal mode analysis as a prerequisite for drug design: Application to matrix metalloproteinases inhibitors

We demonstrate the utility of normal mode analysis in correctly predicting the binding modes of inhibitors in the active sites of matrix metalloproteinases (MMPs). We show the accuracy in predicting the positions of MMP‐3 inhibitors is strongly dependent on which structure is used as the target, especially when it has been energy minimized. This dependency can be overcome by using intermediate structures generated along one of the normal modes previously calculated for a given target. These results may be of prime importance for further in silico drug discovery.

Human thrombospondin's (TSP-1) C-terminal domain opens to interact with the CD-47 receptor: a molecular modeling study.

Thrombospondin-1 (TSP-1) interaction with the membranous receptor CD-47 involves the peptide RFYVVMWK (4N-1) located in its C-terminal domain. However, the available X-ray structure of TSP-1 describes this peptide as completely buried into a hydrophobic pocket, preventing any interaction. Where classical standard methods failed, an appropriate approach combining normal mode analysis and an adapted protocol of energy minimization identified the large amplitude motions responsible of the partial solvent exposure of 4N-1. In agreement, the obtained model of the open TSP-1 was further used for protein-protein docking experiments against a homology model generated for CD-47. Considering the multiple applications of the CD-47 receptor as a target, our results open new pharmacological perspectives for the design of TSP-1:CD-47 inhibitors and CD-47 antagonists. We also suggest a common opening mechanism for proteins sharing the same fold as TSP-1. This work also suggests the usefulness of our approach in other topics in which predictions of protein-protein interactions are of importance.

Elastin-Derived Peptides Are New Regulators of Insulin Resistance Development in Mice

Although it has long been established that the extracellular matrix acts as a mechanical support, its degradation products, which mainly accumulate during aging, have also been demonstrated to play an important role in cell physiology and the development of cardiovascular and metabolic diseases. In the current study, we show that elastin-derived peptides (EDPs) may be involved in the development of insulin resistance (IRES) in mice. In chow-fed mice, acute or chronic intravenous injections of EDPs induced hyperglycemic effects associated with glucose uptake reduction and IRES in skeletal muscle, liver, and adipose tissue. Based on in vivo, in vitro, and in silico approaches, we propose that this IRES is due to interaction between the insulin receptor (IR) and the neuraminidase-1 subunit of the elastin receptor complex triggered by EDPs. This interplay was correlated with decreased sialic acid levels on the β-chain of the IR and reduction of IR signaling. In conclusion, this is the first study to demonstrate that EDPs, which mainly accumulate with aging, may be involved in the insidious development of IRES.

Interaction between the elastin peptide VGVAPG and human elastin binding protein

Background: The interaction of the peptide VGVAPG with the elastin binding protein is critically involved in aneurysm progression. Results: A molecular model of this interaction is proposed and explored using a site-directed mutagenesis strategy. Conclusion: Three residues, Leu-103, Arg-107, and Glu-137, of elastin binding protein are critical players in this interaction. Significance: Our data now allow the design of antagonists of VGVAPG. The elastin binding protein (EBP), a spliced variant of lysosomal β-galactosidase, is the primary receptor of elastin peptides that have been linked to emphysema, aneurysm and cancer progression. The sequences recognized by EBP share the XGXXPG consensus pattern found in numerous matrix proteins, notably in elastin where the VGVAPG motif is repeated. To delineate the elastin binding site of human EBP, we built a homology model of this protein and docked VGVAPG on its surface. Analysis of this model suggested that Gln-97 and Asp-98 were required for interaction with VGVAPG because they contribute to the definition of a pocket thought to represent the elastin binding site of EBP. Additionally, we proposed that Leu-103, Arg-107, and Glu-137 were essential residues because they could interact with VGVAPG itself. Site-directed mutagenesis experiments at these key positions validated our model. This work therefore provides the first structural data concerning the interaction of the VGVAPG with its cognate receptor. The present structural data should now allow the development of EBP-specific antagonists.

A crucial role for Lyn in TIMP-1 erythroid cell survival signalling pathway

TIMP‐1, a well‐known MMP inhibitor, displays other biological activities such as cell survival, proliferation and differentiation in hematopoietic cells. In this report, we investigated the role of the Src‐related kinase Lyn in TIMP‐1 induced UT‐7 erythroleukemic cell survival. We showed that (i) tyrosine 507 of Lyn was dephosphorylated and Lyn kinase activity enhanced by TIMP‐1, (ii) Lyn silencing suppressed TIMP‐1 anti‐apoptotic activity and (iii) Lyn was activated upstream the JAK2/PI 3‐kinase/Akt pathway. Our data suggest a novel role for Lyn in erythroid cell survival.

Inverse docking method for new proteins targets identification

A framework to perform inverse docking was developed.Different strategies to distribute the docking procedure were implemented.Validation with experimental complex have been done.A docking test of one ligand versus 100 proteins was performed.A better conformational sampling is processed than current methods. Molecular docking is a widely used computational technique that allows studying structure-based interactions complexes between biological objects at the molecular scale. The purpose of the current work is to develop a set of tools that allows performing inverse docking, i.e., to test at a large scale a chemical ligand on a large dataset of proteins, which has several applications on the field of drug research. We developed different strategies to parallelize/distribute the docking procedure, as a way to efficiently exploit the computational performance of multi-core and multi-machine (cluster) environments. The experiments conducted to compare these different strategies encourage the search for decomposing strategies since it improves the execution of inverse docking.

Parallel strategies for an inverse docking method

Molecular docking is a widely used computational technique that allows studying structure-based interactions complexes between biological objects at the molecular scale. The purpose of the current work is to develop a set of tools that allows performing inverse docking, i.e., to test at a large scale a chemical ligand on a large dataset of proteins, which has several applications on the field of drug research. We developed different strategies to parallelize/distribute the docking procedure, as a way to efficiently exploit the computational performance of multi-core and multi-machine (cluster) environments. The experiments conducted to compare these different strategies encourage the search for decomposing strategies as a way to improve the execution of inverse docking.

Ab initio calculations of polyhedra liquid water

Ab initio calculations have been performed using the 6-31G* basis set for different structures of water clusters (H2O)n, n=1–10, 15. When increasing the number of water molecules, it appears that for n > 5, we observe a transition from planar to threedimensional structures. All the different clusters present many stable geometries that are all very close in energy. To be sure that a minimum of the energy potential surface has been reached, vibrational frequencies for both (H2O)n and (D2O)n were calculated. When n increases, the O–O distance is always decreasing. From this study, we deduced that in the temperature range � 10 to 100 � C, the most abundant clusters in liquid water at density 1 g/ml contain more than five water molecules. # 2003 Elsevier Science Ltd. All rights reserved.

Conformation-dependent binding of a Tetrastatin peptide to α v β 3 integrin decreases melanoma progression through FAK/PI 3 K/Akt pathway inhibition

Tetrastatin, a 230 amino acid sequence from collagen IV, was previously demonstrated to inhibit melanoma progression. In the present paper, we identified the minimal active sequence (QKISRCQVCVKYS: QS-13) that reproduced the anti-tumor effects of whole Tetrastatin in vivo and in vitro on melanoma cell proliferation, migration and invasion. We demonstrated that QS-13 binds to SK-MEL-28 melanoma cells through the αvβ3 integrin using blocking antibody and β3 integrin subunit siRNAs strategies. Relevant QS-13 conformations were extracted from molecular dynamics simulations and their interactions with αVβ3 integrin were analyzed by docking experiments to determine the binding areas and the QS-13 amino acids crucial for the binding. The in silico results were confirmed by in vitro experiments. Indeed, QS-13 binding to SK-MEL-28 was dependent on the presence of a disulfide-bound as shown by mass spectroscopy and the binding site on αVβ3 was located in close vicinity to the RGD binding site. QS-13 binding inhibits the FAK/PI3K/Akt pathway, a transduction pathway that is largely involved in tumor cell proliferation and migration. Taken together, our results demonstrate that the QS-13 peptide binds αvβ3 integrin in a conformation-dependent manner and is a potent antitumor agent that could target cancer cells through αVβ3.