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HIV-1 IN is a pertinent target for the development of AIDS chemotherapy. The first IN-specific inhibitor approved for the treatment of HIV/AIDS, RAL, was designed to block the ST reaction. We characterized the structural and conformational features of RAL and its recognition by putative HIV-1 targets - the unbound IN, the vDNA, and the IN•vDNA complex - mimicking the IN states over the integration process. RAL binding to the targets was studied by performing an extensive sampling of the inhibitor conformational landscape and by using four different docking algorithms: Glide, Autodock, VINA, and SurFlex. The obtained data evidenced that: (i) a large binding pocket delineated by the active site and an extended loop in the unbound IN accommodates RAL in distinct conformational states all lacking specific interactions with the target; (ii) a well-defined cavity formed by the active site, the vDNA, and the shortened loop in the IN•vDNA complex provide a more optimized inhibitor binding site in which RAL chelates Mg(2+) cations; (iii) a specific recognition between RAL and the unpaired cytosine of the processed DNA is governed by a pair of strong H-bonds similar to those observed in DNA base pair G-C. The identified RAL pose at the cleaved vDNA shed light on a putative step of RAL inhibition mechanism. This modeling study indicates that the inhibition process may include as a first step RAL recognition by the processed vDNA bound to a transient intermediate IN state, and thus provides a potentially promising route to the design of IN inhibitors with improved affinity and selectivity.

Most antiretroviral medical treatments were developed and tested principally on HIV-1 B nonrecombinant strain, which represents less than 10% of the worldwide HIV-1-infected population. HIV-1 circulating recombinant form CRF02_AG is prevalent in West Africa and is becoming more frequent in other countries. Previous studies suggested that the HIV-1 polymorphisms might be associated to variable susceptibility to antiretrovirals. This study is pointed to compare the susceptibility to integrase (IN) inhibitors of HIV-1 subtype CRF02_AG IN respectively to HIV-1 B. Structural models of B and CRF02_AG HIV-1 INs as unbound enzymes and in complex with the DNA substrate were built by homology modeling. IN inhibitors—raltegravir (RAL), elvitegravir (ELV) and L731,988—were docked onto the models, and their binding affinity for both HIV-1 B and CRF02_AG INs was compared. CRF02_AG INs were cloned and expressed from plasma of integrase strand transfer inhibitor (INSTI)-naïve infected patients. Ourin silicoandin vitrostudies showed that the sequence variations between the INs of CRF02_AG and B strains did not lead to any notable difference in the structural features of the enzyme and did not impact the susceptibility to the IN inhibitors. The binding modes and affinities of INSTI inhibitors to B and CRF02_AG INs were found to be similar. Although previous studies suggested that several naturally occurring variations of CRF02_AG IN might alter either IN/vDNA interactions or INSTIs binding, our study demonstrate that these variations do affect neither IN activity nor its susceptibility to INSTIs.

The type III receptor tyrosine kinase (RTK) KIT plays a crucial role in the transmission of cellular signals through phosphorylation events that are associated with a switching of the protein conformation between inactive and active states. D816V KIT mutation is associated with various pathologies including mastocytosis and cancers. D816V-mutated KIT is constitutively active, and resistant to treatment with the anti-cancer drug Imatinib. To elucidate the activating molecular mechanism of this mutation, we applied a multi-approach procedure combining molecular dynamics (MD) simulations, normal modes analysis (NMA) and binding site prediction. Multiple 50-ns MD simulations of wild-type KIT and its mutant D816V were recorded using the inactive auto-inhibited structure of the protein, characteristic of type III RTKs. Computed free energy differences enabled us to quantify the impact of D816V on protein stability in the inactive state. We evidenced a local structural alteration of the activation loop (A-loop) upon mutation, and a long-range structural re-organization of the juxta-membrane region (JMR) followed by a weakening of the interaction network with the kinase domain. A thorough normal mode analysis of several MD conformations led to a plausible molecular rationale to propose that JMR is able to depart its auto-inhibitory position more easily in the mutant than in wild-type KIT and is thus able to promote kinase mutant dimerization without the need for extra-cellular ligand binding. Pocket detection at the surface of NMA-displaced conformations finally revealed that detachment of JMR from the kinase domain in the mutant was sufficient to open an access to the catalytic and substrate binding sites., Author Summary Protein kinases are involved in a huge amount of cellular processes through phosphorylation, a crucial mechanism in cell signaling, and their misregulation often results in disease. The deactivation of protein tyrosine kinases (PTKs) or their oncogenic activation arises from mutations which affect the protein primary structure and the configuration of the enzymatic site apparently by stabilizing the activation loop (A-loop) extended conformation. Particularly, mutation D816V of receptor tyrosine kinase (RTK) KIT, found in patients with pediatric mastocytosis, acute leukemia or germ cell tumors, can be considered as the archetype of mutation inducing a displacement of the population equilibrium toward the active conformation. We present a comprehensive computational study of the activating mechanism(s) of this mutation. Our multi-approach in silico procedure evidenced a local alteration of the A-loop structure, and a long-range structural re-organization of the juxta-membrane region (JMR) followed by a weakening of the interaction network with the kinase domain. Our results provided a plausible conception of how the observed departure of JMR from kinase domain in the mutant promotes kinase mutant dimerization without requiring extra-cellular ligand binding. The pocket profiles we obtained suggested putative allosteric binding sites that could be targeted by ligands/modulators that trap the mutated enzyme.

While searching for new HIV integrase inhibitors we discovered that some ethyl malonate amides (EMA) are active against this enzyme. Surprisingly, the main function can only very rarely be found among the reported drug candidates. We synthesised a series of compounds in order to establish and analyse the structure–activity relationship. The similarity to the important classes of HIV integrase inhibitors as well as the synthetic availability of the different targets including this pharmacophore makes EMA compounds an interesting object of investigations.

Racemic as well as optically pure 1,1′-binaphthyl-substituted α-aminoisobutyric acid (Bin), a new chiral atropoisomeric α,α-disubstituted glycine, and its biphenyl analogue (Bip), have been prepared by bis-alkylation of a glycine tert-butyl ester Schiff base. The free aminoacids Bin and Bip, as well as their C-and/or N-protected derivatives have been obtained. X-ray analysis of H-Bip-OtBu and H-(S)Bin-OH is presented.

The synthesis and structural characterization of the novel [MnIII,IV2O2(N,Nbispicen)2](ClO4)3·CH3CN complex employing the tetradentate ligand N,Nbispicen = N,N-bis(2-pyridylmethyl)-1,2-diaminoethane are reported. Magnetic properties were determined and show that the ground state is a spin doublet. This can be quantitatively interpreted by antiferromagnetic coupling between a Mn(III) high spin and a Mn(IV) (J = −316 cm−1). The 16 line solution EPR spectrum exhibits an unusual splitting in the low field resonances. The following rhombic tensors were needed to simulate the EPR spectrum: |A1x|= 160 10−4 cm−1, |A1y| = 144 10−4 cm−1, |A1z|= 109 10−4 cm−1, |A2x|= 69 10−4 cm−1, |A2y| = 72 10−4 cm−1, |A2z| = 75 10−4 cm−1, gx = 2.001, gy = 1.996, gz = 1.984. The classical ligand field theory of local [gIII] and [gIV] tensors implemented with the first order perturbation theory to describe the properties of the pair does not result in a satisfying description of the [g1/2] tensor unless a large reduction in the spin-orbit constant is invoked. A simplified version of second-order perturbation theory leads to effects in qualitative agreement with experiment but weak as expected from the large |J| value. The magnitude of these effects depends, however, on the anisotropy effects on each Mn ion. It is suggested that determination of the anisotropy of the magnetic properties of the monomeric Mn(III) and Mn(IV) moieties would be a valuable goal for a future study of these mixed valent dimanganese-di-μ-oxo complexes. The complex exhibits two quasi-reversible waves in the cyclic voltammogram, one at E1/2 = 0.18 V vs SCE for the III/IV █ III/III couple and the other at E1/2 = 0.98 V vs SCE for the III/IV █ IV/IV couple. The UV-Vis spectra of the three redox states have been recorded spectroelectrochemically.

Several new ortho bridged biphenyls mimicking the structure of (−)-rhazinilam were synthesized and evaluated as cytotoxic compounds and as inhibitors of microtubules disassembly. These included azadibenzo[a,c]cyclononene derivatives having an ester, urea or carbamate function present in the 9-membered ring linking the two phenyl moieties. The compound bearing a carbamate function instead of the amide group of rhazinilam interacts better with tubulin than (−) rhazinilam.

Strand-transfer inhibitors, of which raltegravir, elvitegravir and S/GSK1349572, is a new class of antiretrovirals that inhibit HIV integrase-catalyzed insertion of the HIV-1 genome into cell chromosomes. The results of clinical trials were very encouraging regarding their viral efficiency and tolerance. However resistance mutations were identified in patients failing to respond to treatment with these inhibitors, involving primary mutations as well as numerous secondary mutations. This review focuses on recent advanced computational studies that have highlighted the contribution of those residues subject to primary mutations and the role of conformational flexibility of the enzyme in binding to strand-transfer inhibitors.

Raltegravir (MK-0518) is clinically used against viruses resistant to other antiretroviral compounds. However, it has been reported that Raltegravir induces integrase (IN) resistance very soon after the administration of the drug. Some residues in the protein seem to be preferentially targeted: E92Q, N155H, and the double mutant G140S/Q148H. It was demonstrated that most of these mutations altered both 3'-processing and strand transfer activities of IN. In this report, we addressed for the first time by real time PCR the kinetics of the integrase mutants as well their resistance towards Raltegravir. Furthermore, we characterised the activities of the recombinant proteins. Our data highly suggest that the resistance towards Raltegravir is due to the mutation Q148H. This mutation results in a slower replication kinetic which is compensate by the G140S mutation. These data explain why only the double mutant G140S/Q148H is observed in clinical trials as one of the most prevalent profile of raltegravir resistance. Two patients receiving raltegravir as part as their regimen were followed. After a viral load decrease, these patients harbored virological failure and selection of raltegravir resistance mutations in the integrase gene (N155H for patient 1 and G140S + Q148H for patient 2). At failure, patients harbouring viruses with these raltegravir mutations showed HIV viral load rebound corresponding to baseline values.

Received 9 October 2008; returned 21 November 2008; revised 12 December 2008; accepted 8 January 2009 Objectives: Raltegravir is the first approved inhibitor of HIV-1 integrase (IN). In most patients, raltegravir failure is associated with mutations in the IN gene, through two different genetic pathways: 155 (N155H) or 148 (Q148K/R/H). The objective of this study was to characterize the dynamics of HIV-1 quasispecies variant populations in patients who failed to respond to raltegravir treatment. Patients and methods: Bulk genotyping and clonal analysis were performed during the follow-up of 10 patients who failed to respond to raltegravir treatment. Results: Treatment failed through the 155 pathway in six patients and through the 148 pathway in two patients; two further patients switched from the 155 to the 148 pathway. In the two patients switching from the 155 to the 148 pathway, clonal analysis showed that Q148R/H and N155H mutations were present on different strands, suggesting that these two pathways are independent. This was consistent with our finding that each genetic profile was associated with different secondary mutations. We observed a greater variability among quasispecies associated with the 155 pathway, and IC50 determinations showed that the fold resistance to raltegravir, relative to wild-type, was 10 for the N155H mutant and 50 for the G140S1Q148H mutant. Conclusions: Clonal analysis strongly suggests that the two main genetic pathways, 155 and 148, involved in the development of resistance to raltegravir are independent and exclusive. Moreover, the switch of the resistance profile from 155 to 148 may be related to the higher level of resistance to raltegravir conferred by the 148 pathway and also to the higher instability of the 155 pathway.

International audience; Virologic failure during treatment with raltegravir, the first effective drug targeting HIV integrase, is associated with two exclusive pathways involving either Q148H/R/K, G140S/A or N155H mutations. We carried out a detailed analysis of the molecular and structural effects of these mutations. We observed no topological change in the integrase core domain, with conservation of a newly identified V-shaped hairpin containing the Q148 residue, in particular. In contrast, the mutations greatly altered the specificity of DNA recognition by integrase. The native residues displayed a clear preference for adenine, whereas the mutant residues strongly favored pyrimidines. Raltegravir may bind to N155 and/or Q148 residues as an adenine bioisoster. This may account for the selected mutations impairing raltegravir binding while allowing alternative DNA recognition by integrase. This study opens up new opportunities for the design of integrase inhibitors active against raltegravir-resistant viruses. Copyright Cop. 2009 John Wiley and Sons, Ltd. Supporting information may be found in the online version of this article.

Geometrical parameters of covalently bonded organic azides have been analysed using X-ray structural data retrieved from the Cambridge Structural Database. The RNNN fragment geometry shows some important general features: (i) a preference for a trans C s configuration; (ii) bending of the N—N—N unit; (iii) substantially different N—N bond lengths in the azide group. Electron-density redistribution within the covalently bonded azide group (relative to that in the isolated azide anion) promotes the capacity of the terminal azide N atom to form hydrogen bonds.

International audience; HIV-1 integrase is one of the three essential enzyme required for viral replication and has a great potential as a novel target for anti-HIV drugs. The sequence variability of the entire integrase (IN) was examined in HIV-1 subtype B and CRF02-AG antiretroviral na? infected patients for the presence of naturally occurring polymorphisms IN gene sequences and protein structures from both subtypes were compared. The phylogenetic analysis showed a total concordance between the 3 pol gene sequences for patients identified as subtype B whereas 3% of patients identified as CRF02-AG showed a mixture of subtypes. The analysis of IN aa sequences showed that 13 positions (K/R14, V/I31, L/I101, T/V112, T/A124, T/A125, G/N134, I/V135, K/T136, V/I201, T/S206, L/I234, and S/G283) differed between subtypes B and CRF02-AG. As observed in the 3D model of the preintegration complex, these differences may impact the functional property of IN. The fact that most variations were grouped suggests that some of them are linked together through compensatory mechanisms. This comparison allowed us to identify several variations of amino acids in HIV-1 IN subtype CRF02-AG that could have a putative impact on anti-integrase sensitivity. In particular, the region formed by Thr125, Thr124, Val31 contains at least one residue, T125, which variation has been involved in eliciting resistance to the naphtyridine carboxamide L870,810 IN inhibitor. In conclusion, virological response to anti-integrase should be studied carefully, according to the subtype, in clinical trials.

Catechol and beta-ketoenol are important pharmacophores of HIV-1 integrase (IN) inhibitors. We investigated their recognition of the divalent metals, Mg and Mn, and of hydrogen bond donors (HBD) and acceptors (HBA). We used data retrieved from the Cambridge Structural Database (CSD), applying a 3-D structure-based, in silico-driven approach. We found that both biophores were stabilized by intramolecular H-bonding (IHB), which was weak in catechols and very strong in beta-ketoenols. Catechols tended to recognize environmental HBD and HBA, demonstrating their ability to make use of both hydroxyl groups to form multiple, strong intermolecular H-bonds. In contrast, beta-ketoenols stabilized by strong IHB inefficiently formed intermolecular H-bonds. beta-Ketoenolate chelated both Mg and Mn ions much more efficiently than dioxolene, which was highly selective for Mn cations. The significant differences in the ability of these two pharmacophores to bind HBD and HBA and in their ability to chelate Mg and Mn have important consequences for competitive inhibitor binding and selectivity for metals and integrase DNA-binding sites.

Two manganese complexes, (py2(NMe)2)MnIICl2 (1) and [(py2(NMe)2)MnIIIF2]+ (2), are here described with the macrocyclic ligand py2(NMe)2 (py2(NMe)2 = N,N'-dimethyl-2,11-diaza[3,3](2,6)pyridinophane). For both, the crystal structure is reported. The UV-visible spectrum of 2 exhibits a very broad near-infrared (NIR) band corresponding to the transition between the two e(g)-type orbitals split by the Jahn-Teller effect. A negative D value of ca. -4 cm(-1) was estimated by high-field and high-frequency electron paramagnetic resonance (HF-EPR) spectroscopy, which was consistent with symmetry considerations. Density functional theory (DFT) calculations on 2 support the 5B1 electronic ground state predicted from the X-ray structure. Moreover, to explain the large value of the D parameter, a spin triplet first excited spin state was postulated to occur at low energy. This was confirmed by the DFT calculations.

Context : Germline mutations in genes involved in the hypoxia sensing pathway (VHL, PHD2/EGLN1, HIF2A/EPAS1) predispose patients to erythrocytosis associated with normal or high serum erythropoietin level. The more frequent mutation, VHL-R200W (R200W), has been identified in homozygous carriers with a congenital erythrocytosis named Chuvash polycythemia. Survival in the Chuvash patients was found to be reduced compared to control groups due to higher rates of arterial and venous thromboses, and to haemorrhagic events. Noteworthily, a characteristic of these patients and their parents, heterozygous for the mutation, is the total absence of tumor development as the opposite of heterozygous carriers of other VHL mutations. Indeed, VHL is a tumor suppressor gene and heterozygous carriers of VHLmutations have von Hippel-Lindau disease and are at high risk of multiple tumors (e.g. CNS hemangioblastomas, pheochromocytoma, renal cell carcinoma). The absence of tumor development in patients with congenital erythrocytosis remained unexplained. The R200W mutation is transmitted within a 340-kilobases haplotype inherited 14,000 to 62,000 years ago from a single founder event. The absence of tumor development in patients carrying the R200W mutation raised the possibility of the presence of a protective element within this core haplotype. Objective: The purpose of this study was to determine the mechanisms underlying the absence of tumor development in patients carrying the R200W mutation, healthy (heterozygous carriers) or with congenital erythrocytosis (homozygous). Methods: We report here one particular family carring a heterozygous R200W mutation associated, for the first time, with a typical von Hippel-Lindau disease (with pheochromocytoma, hemangioblastoma and renal cell carcinoma) (Olswang et al., 1998). We performed a comprehensive study with genotyping, phenotypic analysis, structural modeling, functional and transcriptomic studies of the R200W mutant in comparison to classical mutants involved in von Hippel-Lindau disease. For the first time, the use of inducible expression vectors encoding untagged VHL in the functional studies allowed the observation of very subtle effects. Results: We show that the R200W mutation alone is definitely not associated with the von Hippel Lindau disease because this particular family actually carries another pathogenic mutation, VHL-R161Q, on the same VHL allele, and the double mutated allele segregates with disease. Our genotyping showed that the doubled mutations lies on the Chuvash core haplotype transmitted with the R200W mutation. We can thus conclude that this haplotype does not contain any protective elements against cancer development and that the VHLmutations are, by themselves, predominantly responsible for manifestations of the von Hippel-Lindau disease. Functional studies demonstrate that the function of the R200W mutation is close to the wild type protein and the severity of disease manifestations observed in VHL syndrome is perfectly correlated with a gradient of pVHL dysfunction in hypoxia signaling pathways. Conclusion: We show that the R200W mutation associated with congenital erythrocytosis is at the bottom of an oncogenic gradient. These results validate for the first time in humans the recently proposed “continuum” model of tumor suppression, which differs from the classical Knudson’s two-hit model and implies that subtle gene dosage-sensitivity may underlie tumor predisposition. This model may be of major importance in our understanding of tumor risk in patients with erythrocytosis carrying germline mutations in other genes belonging the HIF pathway. Indeed, in rare cases, PHD2 and HIF2A pathogenic mutations also predispose patients to pheochromocytomas or paragangliomas development. Disclosures No relevant conflicts of interest to declare.

2-C- and 3-C-[(2′-chloro)pyrid-5′-yl]-hex-5-enopyranosides were synthesized from 4,6-O-benzylidene acetals in three steps. By treatment with mercury or palladium salts, the corresponding cyclohexanones could be obtained. The stereochemistry of these reactions was highly dependent on the substitution pattern of the starting material and the nature and concentration of the catalyst.

2-C- and 3-C-[(2′-chloro)pyrid-5′-yl]-hex-5-enopyranosides were synthesized from 4,6-O-benzylidene acetals in three steps. By treatment with mercury or palladium salts, the corresponding cyclohexanones could be obtained. The stereochemistry of these reactions was highly dependent on the substitution pattern of the starting material and the nature and concentration of the catalyst.

Novel (−)- and (+)-rhazinilam derivatives substituted on the D-ring (compounds 3 , 4 , 5 and 6 ) have been prepared from (+)-vincadifformine 7 and (−)-tabersonine and evaluated against the disassembly of microtubules into tubulin. Along with this study, a reproducible ‘one pot’ semisynthesis of (−)-rhazinilam 1 from (+)-1,2-didehydroaspidospermidine 2 was performed allowing the easy preparation of these new compounds.

The study of hydrogen bonding and anion-cation interactions allows us to understand how molecules self-recognize and self- organize and to gain insight into the relationship between molecular and supramolecular crystal structures.

Abstract 823 Background: Despite extensive knowledge of the molecular defects causing β-thalassemia major (TM), less is known about the mechanisms responsible of the ineffective erythropoiesis. This latter is characterized by accelerated erythroid differentiation, apoptosis and maturation arrest at the polychromatophilic stage. It explains, at least in part, the profound anemia observed in this disease. Although it has been proposed that both the precipitation of unmatched globin chains as well as the accumulation of unbound iron could lead to oxidative stress and subsequent hemolysis, the mechanism by which apoptosis and maturation arrest are induced remains unclear. Hypothesis: We have previously demonstrated that normal human erythroid cell maturation requires the transcription factor GATA-1 and an transient activation of caspase-3 at the basophilic stage (Zermati Y, J Exp Med 2001). Although GATA-1 is a capsase-3 target, we have shown that it was protected during erythroid maturation by the nucleus translocation of heat shock protein 70 (Hsp70) at the onset of caspase-3 activation (Ribeil JA, Nature 2007). Hsp70 is an universally highly conserved protein chaperone involved in the regulation of protein folding and in the prevention of damaging aggregates formation (Hart HU, Nature 2011). We hypothesized that, in addition to AHSP the cognate chaperone of α-globin chains, Hsp70 could also serve as a secondary chaperone in case of excess of free α-globin chains or aggregates to reduce their toxicity. As a result, this interaction could be detrimental by preventing the nuclear localization of Hsp70 leading to the degradation of GATA-1, maturation arrest and apoptosis in TM erythroid mature cells. Results: During erythroid maturation of CD34+ derived from TM peripheral blood (n=8) or bone marrow (n=3), we have first shown by confocal microscopy that, in contrast to CD34+ from healthy donor (n=10), Hsp70 nuclear translocation did not occur at the late stage of maturation. As a result, GATA-1 was poorly expressed, end stage erythroid maturation was arrested and apoptosis occurred. Hsp70/α-globin complexes were evidenced by confocal analysis in cytosol (specific co-localization), by immunoprecipitation of lysed differentiated erythroid TM cells in liquid culture, and by yeast two-hydrid experiments. In order to better characterize this interaction, we have demonstrated by molecular modeling, docking and molecular dynamic simulation (3D models of the human full-length Hsp701-701generated by homology modeling from crystallographic structures) that α-globin bounds to a highly electronegative cavity formed by NBD, SBD and LID (3 major domains of Hsp70). The Hsp70/α-globin complex is characterized by extensive protein-protein interactions stabilized by multiple hydrogen bonds that we have accurately characterized. Then, to demonstrate the pathological role of the Hsp70 cytosolic sequestration, by lentivirus transfection of TM CD34+ cells, we have expressed a nucleus-targeted mutant of Hsp70 and a wtHsp70 (overexpressing Hsp70). As expected, both lentivirus increased nuclear Hsp70 expression and rescued GATA-1 expression. They also increased TM erythroid cell maturation (more mature cells -acidophils and reticulocytes- than in control transfected cells -21.5% vs 11,8%, p Conclusion: Our data indicate that, cytosolic Hsp70 sequestration by α-globin chains prevents its nuclear localization and is a key mechanism of the ineffective erythropoiesis observed in β-TM patients. In order to increase nuclear Hsp70 translocation, developing drugs or small molecules that could increase Hsp70 expression or better disrupt the Hsp70/α-globin complex could be a novel approach of targeted therapies to improve erythropoiesis in TM. Disclosures: Leboulch: bluebird bio: Consultancy, Equity Ownership, Membership on an entity's Board of Directors or advisory committees, Patents & Royalties, Research Funding.

International audience; BACKGROUND: Sarcomas are rare mesenchymal malignancies whose pathogenesis is poorly understood; both environmental and genetic risk factors could contribute to their aetiology.METHODS AND RESULTS: We performed whole-exome sequencing (WES) in a familial aggregation of three individuals affected with soft-tissue sarcoma (STS) without TP53 mutation (Li-Fraumeni-like, LFL) and found a shared pathogenic mutation in CDKN2A tumour suppressor gene. We searched for individuals with sarcoma among 474 melanoma-prone families with a CDKN2A-/+ genotype and for CDKN2A mutations in 190 TP53-negative LFL families where the index case was a sarcoma. Including the initial family, eight independent sarcoma cases carried a germline mutation in the CDKN2A/p16INK4A gene. In five out of seven formalin-fixed paraffin-embedded sarcomas, heterozygosity was lost at germline CDKN2A mutations sites demonstrating complete loss of function. As sarcomas are rare in CDKN2A/p16INK4A carriers, we searched in constitutional WES of nine carriers for potential modifying rare variants and identified three in platelet-derived growth factor receptor (PDGFRA) gene. Molecular modelling showed that two never-described variants could impact the PDGFRA extracellular domain structure.CONCLUSION: Germline mutations in CDKN2A/P16INK4A, a gene known to predispose to hereditary melanoma, pancreatic cancer and tobacco-related cancers, account also for a subset of hereditary sarcoma. In addition, we identified PDGFRA as a candidate modifier gene

By using the recently proposed biphenyl-based, Cα-tetrasubstituted, cyclic, axially chiral α-amino acid Bip we synthesised by solution methods a large set of model peptides, including the homo-oligomer series, to the pentamer level. All of the peptides were fully characterised and their preferred conformation was assessed in solution by means of a FT-IR absorption and 1H NMR study. Results of X-ray diffraction analyses of two Bip derivatives and a terminally protected tripeptide with the sequence –Gly–Bip–Gly– are also presented. Our findings indicate that Bip tends to support β-turn and 310-helical structures, although in short peptides the fully-extended (C5) conformation would also be populated to some extent.

International audience; Three new complexes, [Fe(LN4H2)Cl2]+, [Fe(LN4H2)(Cat)]+, and [Fe(LN4H2)(DBC)]+, were synthesized by using the tetradentate macrocyclic ligand LN4H2 (where LN4H2, Cat, and DBC stand for 2,11-diaza[3,3](2,6) pyridinophane, catecholate, and 3,5-di-tert-butylcatecholate, respectively). The structure of [Fe(LN4H2)Cl2]+ was determined by X-ray diffraction. It crystallizes in the monoclinic space group C2/c with a = 9.613(1), b = 11.589(1), c = 14.063(2) Å, ß=110.20(2)°, V = 1541.9(3) Å3 and Z = 4. These complexes were found to catalyze the oxidation of catechol groups using O2. This was performed in various organic solvents at 20 °C. The reaction rates were measured for the stoichiometric complexes [Fe(LN4H2)(Cat)]+ and [Fe(LN4H2)(DBC)]+. It was found that despite the relatively high energy of the ligand-to-metal charge transfer O(DBC or Cat)?FeIII, their activity was comparable to that of the fast TPA systems [TPA indicates tris(2-pyridylmethyl)amine]. The oxidation products of DBCH2 have been studied. It has then been shown that the LN4H2 systems catalyse by means of both intra- and extradiol cleavage of catechol groups. The existence of multiple reactive pathways can account for the fast reactivity observed.

Molecular dynamics (MD) simulations can produce nowadays huge amount of data using high-throughput CPU/GPU clusters. However, in addition not to consider the kinetic aspect of the data, the routine use of MD simulations for a study of real macromolecules present some drawbacks. The RMSD approach remains too vague for the description of local equilibrium, whereas classical clustering methods can provide artifacts: the both points of view share a limited exploitation of the information held by the MD data regarding the dynamics of the underlying process. We will present here a work towards the dynamics modelling of such trajectories, and we will show to what extend they can me described as resulting from an SDE, or better, a Langevin equation. Furthermore, we present a new method addressing the detection of local equilibrium, the κ-segmentation algorithm, allowing to detect and quantidy local equilibrium, while avoiding the detection of artifacts, and thusly, making up for the downsides of the quoted methods.; Les ressources informatiques actuelles (CPU/GPU) permettent de générer une grande quantité de trajectoires de simulation de la dynamique moléculaire (DM). Cependant, en plus de ne pas toujours tirer profit du contenu dynamique des trajectoires, les méthodes d'analyse actuelles visant à extraire de l'information pertinente au regard des macromolécules étudiées présentent certaines lacunes. Si la RMSD manque de finesse quant à la description des phénomènes d'équilibrations locaux, les méthodes de clustering sont sujettes à la détection d'artefacts: ces deux méthodes ont par ailleurs en commun une exploitation limitée de l'information dynamique que contiennent les trajectoires. Nous présentons au court de ce travail une façon d'aborder la question de la modélisation des trajectoires observées, et nous verrons dans quelles mesures celles-ci peuvent être modélisées par une EDS, ou mieux, une équation de Langevin. Nous développons également une méthode de segmentation des trajectoires, appelée κ-segmentation, permettant la détection et la quantification d'équilibres locaux tout en évitant la détection d'artefacts, comblant ainsi les déficiences des méthodes citées.

Molecular dynamics (MD) simulations can produce nowadays huge amount of data using high-throughput CPU/GPU clusters. However, in addition not to consider the kinetic aspect of the data, the routine use of MD simulations for a study of real macromolecules present some drawbacks. The RMSD approach remains too vague for the description of local equilibrium, whereas classical clustering methods can provide artifacts: the both points of view share a limited exploitation of the information held by the MD data regarding the dynamics of the underlying process. We will present here a work towards the dynamics modelling of such trajectories, and we will show to what extend they can me described as resulting from an SDE, or better, a Langevin equation. Furthermore, we present a new method addressing the detection of local equilibrium, the κ-segmentation algorithm, allowing to detect and quantidy local equilibrium, while avoiding the detection of artifacts, and thusly, making up for the downsides of the quoted methods., Les ressources informatiques actuelles (CPU/GPU) permettent de générer une grande quantité de trajectoires de simulation de la dynamique moléculaire (DM). Cependant, en plus de ne pas toujours tirer profit du contenu dynamique des trajectoires, les méthodes d'analyse actuelles visant à extraire de l'information pertinente au regard des macromolécules étudiées présentent certaines lacunes. Si la RMSD manque de finesse quant à la description des phénomènes d'équilibrations locaux, les méthodes de clustering sont sujettes à la détection d'artefacts: ces deux méthodes ont par ailleurs en commun une exploitation limitée de l'information dynamique que contiennent les trajectoires. Nous présentons au court de ce travail une façon d'aborder la question de la modélisation des trajectoires observées, et nous verrons dans quelles mesures celles-ci peuvent être modélisées par une EDS, ou mieux, une équation de Langevin. Nous développons également une méthode de segmentation des trajectoires, appelée κ-segmentation, permettant la détection et la quantification d'équilibres locaux tout en évitant la détection d'artefacts, comblant ainsi les déficiences des méthodes citées.

VKORC1 is an endoplasmic reticulum membrane-resident enzyme, responsible for vitamin K epoxide reduction to vitamin K quinone that activates coagulation factors synthesis. VKORC1 is thus a prominent target of vitamin K agonists (VKAs) in anticoagulant therapies. However, some VKORC1 mutations lead to physiological dysregulation and/or VKAs resistance. No VKORC1 structural data is available, and postulated topological models are based on biochemical and biophysical experimental observations frequently contradicting. Topology of VKORC1 and involvement of cysteines residues (highly conserved in VKORs) in the protein enzymatic mechanism remain unclear. We built an in silico 3D model of the wild-type human VKORC1 (hVKORC1WT) at the atomistic scale. Molecular dynamics simulations of the protein model, carrying all the cysteines residues in their oxidized form (SH), were used for identification of cysteines residues which may plausibly form disulfide bridges. We thus described hVKORC1WT metastable conformations depicting the functionally relevant states of protein. Study of the vitamin K (in epoxide and in reduced forms) recognition by the predicted conformations of hVKORC1WT revealed their reciprocal selectivity. The hVKORC1WT conformations targeted by each vitamin K form were established and their role in the reduction mechanism of this molecule was explained. Using our results, we postulated the comprehensive enzymatic mechanism of hVKORC1WT and we proposed the 3D structure as the VKAs target. Interactions between the predicted target - hVKORC1WT active state - and three different VKAs were characterized. The obtained affinities (free binding energy) were in good correlation with in vivo measured inhibition constants (Ki), thus validating our theoretical predictions. Our protocol developed for hVKORC1WT is suitable for a study of its mutants. Description of the enzymatic mechanisms of mutated hVKORC1 will lead to understanding of the modified reductase activity or/and to explaining of its resistance to VKAs. Such data are crucial for the development of novel strategies in the design of a new generation of inhibitors overcoming VKAs resistance. Our concept and the established in silico protocol can be extended to analysis of mammalian VKORs and other oxidoreductases family proteins., VKORC1 est une enzyme membranaire du réticulum endoplasmique, responsable de la réduction de la vitamine K époxyde en vitamine K quinone, activant la synthèse des facteurs de coagulation. VKORC1 constitue ainsi une cible thérapeutique privilégiée des anticoagulants de type anti-vitamine K (AVKs). Cependant, certaines mutations de VKORC1 induisent une dérégulation physiologique et/ou une résistance aux AVKs. En l’absence de données structurales, plusieurs modèles topologiques de VKORC1 ont été proposés à partir des données biochimiques et biophysiques, fréquemment contradictoires. La topologie de VKORC1 ainsi que l'implication des résidus de cystéine (strictement conservés chez toutes les VKORs) dans le mécanisme enzymatique de la protéine restent incertaines. Nous avons construit, par des méthodes in silico, un modèle 3D de la VKORC1 humaine sauvage (hVKORC1WT) à l'échelle atomique. Des simulations de dynamique moléculaire de la protéine, en considérant tous les résidus de cystéine sous leur forme oxydée (SH), nous ont permis d'identifier les résidus de cystéine les plus susceptibles de former des ponts disulfures. Nous avons par conséquent décrit les conformations métastables de hVKORC1WT mimant les états fonctionnels de la protéine. L’étude de la reconnaissance des formes époxyde et réduites de la vitamine K par les conformations prédites de hVKORC1WT a mis en évidence leur sélectivité réciproque. Les conformations de hVKORC1WT ciblées par chaque forme de la vitamine K et leur rôle dans le mécanisme de réduction de la molécule ont ainsi été caractérisés. Nous avons postulé à partir de ces résultats le mécanisme enzymatique détaillé de hVKORC1WT et proposé la structure-cible des AVKs. Les interactions entre la cible prédite - hVKORC1WT à l'état actif - et trois AVKs différents ont été décrites en termes d’énergie libre de liaison. Ces résultats ont été corrélés avec les constantes d'inhibition mesurées in vivo, validant nos prédictions théoriques. Notre protocole, développé pour hVKORC1WT, est applicable aux formes mutées de l’enzyme. Il permettra la description des mécanismes modifiant l'activité réductase de hVKORC1 et/ou provoquant une résistance aux AVKs. Cette description ouvre la voie à la conception d'une nouvelle génération d'inhibiteurs surmontant les résistances aux AVKs. Notre concept et le protocole établi pour l’étude de hVKORC1 peuvent être étendus à l'analyse des VKORs mammaliennes et aux autres enzymes de la famille des oxydoréductases.

The receptors tyrosine kinase (RTKs) CSF-1R and KIT are important mediators of signal transduction. Their normal function is altered by gain-of-function mutations associated with cancer diseases. A secondary effect of the mutations is the alteration of receptors’ sensitivity imatinib, employed in cancer treatment. Our goals in this thesis consist of (i) study the structural and dynamical effects induced by the D802V mutation in CSF-1R; (ii) characterize imatinib’s affinity to the wild-type (WT) and mutant forms of KIT (V560G, S628N and D816V) and CSF-1R (D802V). By means of molecular dynamics (MD) simulations, we have shown that the D802V mutation disrupts the allosteric communication between the activation loop and the auto-inhibitory juxtamembrane (JMR) domain. However, this rupture is not sufficient to induce the JMR’s departure. The subtle effect of this mutation in CSF-1R was associated with differences in the primary sequence between CSF-1R and KIT in the JMR region. The affinity of imatinib to the different targets was estimated by docking, DM and binding energy calculations. The electrostatic interactions showed to be the main force driving the resistance, with mutations D802/816V being the most deleterious in energy contribution. As a general conclusion, we have established that the D802V mutation in CSF-1R does not provoke the same structural effects as its equivalent in KIT. In addition, the study of both receptors in their WT and mutant forms complexed with imatinib indicate that the conformational changes induced by the mutations allied to the electrostatic interactions with the ligand could explain the resistance phenomena., Les récepteurs tyrosine kinase (RTKs) CSF-1R et KIT sont médiateurs importants de la signalisation cellulaire. Leur fonction basale est altérée par des mutations associées à divers types de cancer. Ces mutations modifient également leur sensibilité à l’imatinib, utilisé en clinique dans le traitement des cancers. Dans cette thèse, nos objectifs sont (i) étudier les effets structuraux et dynamiques induits par la mutation D802V chez CSF-1R; (ii) caractériser l’affinité de l’imatinib aux formes sauvages (WT) et mutés de KIT (V560G, S628N et D816V) et CSF-1R (D802V). Par simulations de Dynamique Moléculaire (DM), nous avons montré que la mutation D802V interrompt la communication allostérique entre la boucle d’activation et le domaine auto-inhibiteur juxtamembranaire (JMR). Néanmoins, cette rupture n’est pas suffisante pour induire le départ du JMR. L’effet subtil de la mutation chez CSF-1R a été attribué aux différences de séquence primaire entre KIT et CSF-1R dans la région du JMR. L’affinité de l’imatinib aux différentes cibles a été calculée par simulations de docking, DM et calculs d’énergie de liaison. Les interactions électrostatiques constituent la force motrice de la résistance, les mutations D802/816V étant les plus délétères en termes d’énergie. Comme conclusion générale, nous avons établi que la mutation D802V chez CSF-1R n’entraine pas les mêmes effets structuraux provoqués par la mutation D816V chez KIT. En outre, l’étude des deux récepteurs dans leurs formes WT et mutés complexés avec l’imatinib indiquent que le changement structural induit par les mutations associé aux interactions électrostatiques avec le ligand expliqueraient le phénomène de résistance.

STAT5 is a protein involved in normal cell signalling that is crucial for transformation, survival and resistance to tyrosine kinase inhibitors of tumour cells. The constitutive phosphorylation activates STAT5 and is related to oncogenic proteins like the hybrid protein BCR/ABL1 (chronic myeloid leukaemia) or mutated KIT receptor (mastocytosis). The pharmacologic inhibition of STAT5 is thus a major therapeutic concern in several malignant pathologies. We performed the first modelling and molecular dynamics simulations of the main cellular species of STAT5: the cytoplasmic phosphorylated or unphosphorylated monomer, and the phosphorylated dimer bound to DNA. We characterized the dynamical properties and the intramolecular allosteric network of the monomers. The generated results show structural and dynamic variations linked to the primary sequence changes between the two STAT5 isoforms and/or to the phosphate group. Two pockets were characterized at the surface of STAT5. Their location at close proximity of allosteric communication pathways suggests new putative inhibition sites to modulate STAT5 functions. We also described the hydrogen bonds network between the monomers of the dimeric species and the recognition of the DNA. We identified key residues at the interfaces, allowing us to better understand the effects of clinically relevant STAT5 mutations observed in malignancies., STAT5 est une protéine de la signalisation cellulaire normale, qui peut jouer un rôle important dans la transformation, la survie et à la résistance aux inhibiteurs de tyrosine kinase des cellules tumorales. Son activation constitutive par phosphorylation est liée à la présence de protéines oncogéniques comme la protéine de fusion BCR/ABL1 (leucémie myéloïde chronique) ou de formes mutées de KIT (mastocytoses), par exemple. L’inhibition pharmacologique de STAT5 constitue donc un enjeu thérapeutique majeur pour plusieurs pathologies malignes. Nous avons réalisé la première modélisation et les simulations de dynamique moléculaire des principales formes de STAT5 : la forme monomérique cytoplasmique phosphorylée ou non, et la forme dimérique phosphorylée et liée à l’ADN. Nous avons caractérisé les propriétés dynamiques et le réseau allostérique intramoléculaire des monomères de STAT5. Les résultats générés montrent des variations structurales et dynamiques liées à la différence de séquence primaire des isoformes de STAT5 et/ou à la présence du groupement phosphate. Deux poches à la surface des protéines ont également été caractérisées. Leur localisation à proximité de voies de communication allostériques suggère que ces poches pourraient constituer des sites de modulation des fonctions de STAT5. Nous avons également caractérisé les liaisons hydrogènes entre les monomères constituant les dimères de STAT5 et leur reconnaissance de l’ADN. En outre, nous avons identifié des résidus clés aux interfaces entre les entités moléculaires, nous permettant de mieux comprendre les effets de mutations de STAT5 observées en clinique dans certaines pathologies malignes.

The HIV-1 integrase catalyzes the integration of HIV-1 viral DNA (vDNA) into the host cell chromosome in a process, which is essential for viral replication through two independent reactions, 3’-processing (3’-P) and strand transfer (ST), catalyzed by IN. Deciphering the structural determinants of the interaction between integrase and its substrates and the kinetics of this interaction sheds light on the importance of inhibitors targeting the pre-integration IN•vDNA complex. This approach led to the identification of raltegravir (RAL) and elvitegravir (ELV), which turned out to be highly efficient inhibitors of ST. RAL, formerly known under the code MK-0518, is a new anti-HIV drug that obtained clinical approval in the United States under the name IsentressTM on October 12, 2007. ELV is still in clinical trials. However, these compounds nevertheless encounter resistance phenomenon. To date, no experimental data characterizing the RAL structure, structure of the HIV-1 IN and/or interactions of RAL with its targets, has been reported.First, we characterized the structural and conformational properties of RAL in different states ‒ the gas phase, in water solution and the solid state. Second, a detailed study allowed characterisation the RAL recognition by the viral targets ‒ IN and the vDNA, before and after the 3'-P. We found that RAL shows a broad spectrum of conformations and configurations in isolated state and/or associated with the target(s). The best docking poses and scores confirmed that the model representing IN•vDNA complex is a biologically relevant target of RAL. This result is consistent with the commonly accepted mechanism of RAL inhibition.Based on the docking results we suggested that the inhibition process may include, as a first step, the RAL recognition by the processed vDNA bound to a transient intermediate IN state. RAL coupled to vDNA shows an outside orientation of all oxygen atoms, excellent putative chelating agents of Mg2+ cations, which could facilitate the insertion of RAL into the active site. The conformational flexibility of RAL further allows the accommodation/adaptation of the inhibitor in a relatively large binding pocket of IN•vDNA pre-integration complex thus producing various RAL conformation. We believe that such variety of the RAL conformations contributing alternatively to the enzyme residue recognition may impact the selection of the clinically observed alternative resistance pathways to the drug.We also studied the recognition of the HIV-1 IN inhibitors from two different strains, B and CRF02_AG. Our in silico study showed that the sequence variations between CRF02_AG and B strains did not lead to any notable difference in the structural features of the enzyme and did not impact the susceptibility to the IN inhibitors. Our analysis of the resistance mutations effects showed that structure of the wild-type enzyme and mutants is almost identical. However, the resistance mutations significantly altered the specificity of the viral DNA recognition by IN.We performed molecular dynamics simulations of the native and mutated IN with a point mutation R228A localized in the C-terminal domain. The study of targets flexibility opens a very promising way, not only in terms of fundamental research, but also for the application of our concepts to the development of new generations of inhibitors targeting IN., L'intégrase (IN) rétrovirale est responsable de l’intégration de l'ADN viral du VIH-1dans l’ADN cellulaire, processus indispensable à la réplication virale. Ce processus se déroule en deux étapes indépendantes, le 3’-processing et le transfert de brins, catalysées par l’IN. La compréhension des interactions entre l’IN et l’ADN viral et de la cinétique de formation des complexes pré-intégratifs a permis l’identification du raltégravir (RAL) et de l’elvitégravir (ELV) qui se sont avérés être des inhibiteurs très efficaces de la réplication virale. Le RAL, auparavant désigné sous le code MK-0518, est un nouveau médicament anti-VIH qui a obtenu son autorisation de commercialisation aux Etats-Unis sous le nom de IsentressTM le 12 octobre 2007. Le ELV est toujours en essais cliniques. Toutefois, comme on l'observe pour d'autres antirétroviraux, ces composés n’échappent cependant pas aux phénomènes de résistance. Des mutations de résistance spécifiques au RAL ont ainsi été identifiées chez des patients. À ce jour, aucune donnée expérimentale caractérisant la structure de l’IN du VIH-1, la structure au RAL et/ou les interactions du RAL avec sa cible n'a été rapporté.Premièrement, nous avons caractérisé les propriétés structurales et conformationnelles du RAL dans des états différents, en phase gazeuse, en solution dans l'eau et à l'état solide. Une etude détaillée a permis de caracteriser la reconnaissance du RAL par des cibles virals, l’IN et l’ADN viral avant et après la réaction de 3’-processing. Nous avons trouvé que le RAL adopte un large spectre de conformations et configurations dans des états isolés et/ou liés avec le(s) cible(s). Les meilleures score et poses de docking confirment que le modèle représentant le complexe IN•vADN est la cible biologiquement pertinente du RAL. Ce résultat est cohérent avec le mécanisme d'inhibition du RAL communément admise. Nous avons suggéré que le processus d'inhibition peut comprendre dans un premier temps la reconnaissance du RAL par l'ADN viral clivé et lié à un état intermédiaire de l’IN. Le RAL couplé à l’ADN viral montre une orientation à l'extérieur de tous les atomes d'oxygène, d'excellents agents putatifs pour capturer de cations Mg2+, ce qui pourrait faciliter l'insertion du RAL dans le site actif. La flexibilité conformationnelle du RAL permet l'adaptation de l'inhibiteur dans une poche relativement grande de du complexe IN•vADN, permettant la production de diverses conformations du RAL. Nous croyons que cette diversité des conformations du RAL contribue à la reconnaissance de résidus enzymatiques et peut influer sur le choix des voies alternatives de résistance au RAL observées cliniquement.Nous avons étudié également la reconnaissance par l’IN des inhibiteurs du VIH appartenant à différents souches, B et CRF02_AG. Nous avons montré que la structure de l’IN des deux souches est quasi-identique. Le docking du RAL et de deux autres inhibiteurs de transfert de brins (ELV et L731_988) sur chaque modèle montre que leur reconnaissance par deux différentes souches cibles est identique.Notre analyse des effets moléculaires et structuraux des mutations de résistance sur la structure de l’IN a montré que les structures de l’enzyme sauvage et mutante sont aussi quasiidentique.Par contre, les mutations modifient considérablement la spécificité de reconnaissance de l'ADN par l'IN.Nous avons effectué la simulation de dynamique moléculaire (MD) de l’IN sauvage et mutant, avec une mutation ponctuelle R228A localisée dans le domaine C-terminale. Notre étude de la flexibilité de l’IN et du complexe IN•ADN par la dynamique moléculaire ouvre une voie très prometteuse non seulement sur le plan de la recherche fondamentale mais aussi pour l'application de nos concepts au développement de nouvelles générations d'inhibiteurs ciblant l'IN.