Virtual screening of the SAMPL4 blinded HIV integrase inhibitors dataset

International audienceSeveral combinations of docking software and scoring functions were evaluated for their ability to predict the binding of a dataset of potential HIV integrase inhibitors. We found that different docking software were appropriate for each one of the three binding sites considered (LEDGF, Y3 and fragment sites), and the most suitable two docking protocols, involving Glide SP and Gold ChemScore, were selected using a training set of compounds identified from the structural data available. These protocols could successfully predict respectively 20.0% and 23.6% of the HIV integrase binders, all of them being present in the LEDGF site. When a different analysis of the results was carried out by removing all alternate isomers of binders from the set, our predictions were dramatically improved, with an overall ROC AUC of 0.73 and enrichment factor at 10% of 2.89 for the prediction obtained using Gold ChemScore. This study highlighted the ability of the selected docking protocols to correctly position in most cases the ortho-alkoxy-carboxylate core functional group of the ligands in the corresponding binding site, but also their difficulties to correctly rank the docking poses

Ligand Discovery for the Alanine-Serine-Cysteine Transporter (ASCT2, SLC1A5) from Homology Modeling and Virtual Screening

The Alanine-Serine-Cysteine transporter ASCT2 (SLC1A5) is a membrane protein that transports neutral amino acids into cells in exchange for outward movement of intracellular amino acids. ASCT2 is highly expressed in peripheral tissues such as the lung and intestines where it contributes to the homeostasis of intracellular concentrations of neutral amino acids. ASCT2 also plays an important role in the development of a variety of cancers such as melanoma by transporting amino acid nutrients such as glutamine into the proliferating tumors. Therefore, ASCT2 is a key drug target with potentially great pharmacological importance. Here, we identify seven ASCT2 ligands by computational modeling and experimental testing. In particular, we construct homology models based on crystallographic structures of the aspartate transporter Glt(Ph) in two different conformations. Optimization of the models\u27 binding sites for protein-ligand complementarity reveals new putative pockets that can be targeted via structure-based drug design. Virtual screening of drugs, metabolites, fragments-like, and lead-like molecules from the ZINC database, followed by experimental testing of 14 top hits with functional measurements using electrophysiological methods reveals seven ligands, including five activators and two inhibitors. For example, aminooxetane-3-carboxylate is a more efficient activator than any other known ASCT2 natural or unnatural substrate. Furthermore, two of the hits inhibited ASCT2 mediated glutamine uptake and proliferation of a melanoma cancer cell line. Our results improve our understanding of how substrate specificity is determined in amino acid transporters, as well as provide novel scaffolds for developing chemical tools targeting ASCT2, an emerging therapeutic target for cancer and neurological disorders

Du Mésolithique au Néolithique en Méditerranée occidentale: l’impact africain - MeNeMOIA

[EN] Between the 8th and 5th millennia BC, the human societies of the Western Mediterranean underwent several major changes. The first occurred during the 7th millennium with the appearance of the ‘Second Mesolithic’. It can be seen mainly in the material productions of these populations, in particular their stone tool industries, by a fundamental change in production, operating sequences and technical procedures. Deeper changes in the social organization of these societies are also perceptible, in particular through changes in rites and funeral practices. The precise origin of these changes escapes us at present, but they seem to occur initially in North Africa before spreading rapidly along the Mediterranean shores and reaching Western Europe. A second major upheaval took place a few centuries later, with the appearance of the Neolithic. In this extensive process, the southern shores of the Mediterranean should not be ignored. Recent data suggest that, during the 6th millennium before our era, human communities practicing hunting and gathering and having acquired ceramic technology, occupied parts of the Maghreb. Interactions with spheres of the Impresso / Cardial complex occurred in southern Italy and, at the other end, southern Spain. This seems to be indicated by some traits of the technical systems of the first Neolithic communities of Andalusia. These hypotheses should now be tested by close examination of timelines and technical systems which if confirmed may offer a possible alternative to the strictly European scenarios. The international program of research, MeNeMOIA, financed for 2016 and 2017, will attempt to estimate the importance of a North African impact on European societies of recent prehistory (Second Mesolithic, Early Neolithic), a scenario breaking with the traditional scenario which, since decolonization, has recognized in Europe only movements of east-west diffusion and completely ignored any that might indicate movement from the south northward (or from the north southward) on both shores of the western Mediterranean.[FR] Entre les viiie et ve millénaires avant notre ère, les sociétés humaines du Bassin occidental de la Méditerranée connaissent plusieurs évolutions majeures. La première d’entre elles se déroule durant le viie millénaire avec l’apparition du «Second Mésolithique». Elle se matérialise principalement dans les productions matérielles de ces populations, et notamment dans leurs industries lithiques par un bouleversement des modes de production, des séquences opératoires et des gestes techniques. Des évolutions plus profondes, dans l’organisation sociale même de ces sociétés, sont également sensibles, notamment au travers de l’évolution des rites et pratiques funéraires. L’origine précise de ces évolutions nous échappe encore actuellement, mais elles semblent se produire initialement en Afrique du Nord avant de diffuser ensuite le long des rivages méditerranéens de manière rapide, et gagner ensuite l’ensemble de l’Europe occidentale. Un second bouleversement majeur se déroule quelques siècles après le précédent, avec l’apparition du Néolithique. Dans ce vaste processus, les rives sud de la Méditerranée ne doivent pas être ignorées. De récentes données suggèrent en effet que, durant le vie millénaire avant notre ère, des communautés humaines pratiquant chasse et cueillette et ayant acquis la technologie céramique occupaient certaines parties du Maghreb. Des interactions avec les sphères du complexe Impresso / Cardial ont ainsi pu voir le jour dans le Sud italien et, à l’autre extrémité, dans le sud de l’Espagne. C’est d’ailleurs ce que semblent montrer certains caractères des systèmes techniques des premières communautés néolithiques d’Andalousie. Ces hypothèses qu’il faut désormais confirmer par la confrontation étroite des chronologies et des systèmes techniques offrent donc une alternative possible aux scénarios classiques strictement européens. Le programme international de recherche MeNeMOIA, financé par l’IDEX toulousain pour 2016 et 2017, va donc s’attacher à évaluer l’importance des impacts nord-africains sur les sociétés européennes de la Préhistoire récente (Second Mésolithique, Néolithique ancien), scénario rompant avec les schémas traditionnels qui, depuis la décolonisation, se cantonnent à ne reconnaitre en Europe que des mouvements de diffusion est-ouest et ignorent complètement ceux allant du sud vers le nord (ou du nord vers le sud) de part et d’autre du Bassin occidental de la Méditerranée.Peer Reviewe

Homology Modeling Informs Ligand Discovery for the Glutamine Transporter ASCT2

The Alanine-Serine-Cysteine transporter (SLC1A5, ASCT2), is a neutral amino acid exchanger involved in the intracellular homeostasis of amino acids in peripheral tissues. Given its role in supplying glutamine to rapidly proliferating cancer cells in several tumor types such as triple-negative breast cancer and melanoma, ASCT2 has been identified as a key drug target. Here we use a range of computational methods, including homology modeling and ligand docking, in combination with cell-based assays, to develop hypotheses for structure-function relationships in ASCT2. We perform a phylogenetic analysis of the SLC1 family and its prokaryotic homologs to develop a useful multiple sequence alignment for this protein family. We then generate homology models of ASCT2 in two different conformations, based on the human EAAT1 structures. Using ligand enrichment calculations, the ASCT2 models are then compared to crystal structures of various homologs for their utility in discovering ASCT2 inhibitors. We use virtual screening, cellular uptake and electrophysiology experiments to identify a non-amino acid ASCT2 inhibitor that is predicted to interact with the ASCT2 substrate binding site. Our results provide insights into the structural basis of substrate specificity in the SLC1 family, as well as a framework for the design of future selective and potent ASCT2 inhibitors as cancer therapeutics

A spontaneous mutation in MutL-Homolog 3 (HvMLH3) affects synapsis and crossover resolution in the barley desynaptic mutant des10

Although meiosis is evolutionarily conserved, many of the underlying mechanisms show species-specific differences. These are poorly understood in large genome plant species such as barley (Hordeum vulgare) where meiotic recombination is very heavily skewed to the ends of chromosomes. The characterization of mutant lines can help elucidate how recombination is controlled. We used a combination of genetic segregation analysis, cytogenetics, immunocytology and 3D imaging to genetically map and characterize the barley meiotic mutant DESYNAPTIC 10 (des10). We identified a spontaneous exonic deletion in the orthologue of MutL-Homolog 3 (HvMlh3) as the causal lesion. Compared with wild-type, des10 mutants exhibit reduced recombination and fewer chiasmata, resulting in the loss of obligate crossovers and leading to chromosome mis-segregation. Using 3D structured illumination microscopy (3D-SIM), we observed that normal synapsis progression was also disrupted in des10, a phenotype that was not evident with standard confocal microscopy and that has not been reported with Mlh3 knockout mutants in Arabidopsis. Our data provide new insights on the interplay between synapsis and recombination in barley and highlight the need for detailed studies of meiosis in nonmodel species. This study also confirms the importance of early stages of prophase I for the control of recombination in large genome cereals.Isabelle Colas, Malcolm Macaulay, James D. Higgins, Dylan Phillips, Abdellah Barakate ... Robbie Waugh ... et al

Dominant-negative mutations in human IL6ST underlie hyper-IgE syndrome

Autosomal dominant hyper-IgE syndrome (AD-HIES) is typically caused by dominant-negative (DN) STAT3 mutations. Patients suffer from cold staphylococcal lesions and mucocutaneous candidiasis, severe allergy, and skeletal abnormalities. We report 12 patients from 8 unrelated kindreds with AD-HIES due to DN IL6ST mutations. We identified seven different truncating mutations, one of which was recurrent. The mutant alleles encode GP130 receptors bearing the transmembrane domain but lacking both the recycling motif and all four STAT3-recruiting tyrosine residues. Upon overexpression, the mutant proteins accumulate at the cell surface and are loss of function and DN for cellular responses to IL-6, IL-11, LIF, and OSM. Moreover, the patients’ heterozygous leukocytes and fibroblasts respond poorly to IL-6 and IL-11. Consistently, patients with STAT3 and IL6ST mutations display infectious and allergic manifestations of IL-6R deficiency, and some of the skeletal abnormalities of IL-11R deficiency. DN STAT3 and IL6ST mutations thus appear to underlie clinical phenocopies through impairment of the IL-6 and IL-11 response pathways

Le gisement paléolithique multistratifié « les Bossats » à Ormesson (Seine-et-Marne, France) : palethnographie ou pâle ethnographie ? Une synthèse des huit premières années de fouille (2009-2016)

editorial reviewedÀ l'évidence, ces vingt dernières années ont vu en France, notamment, se développer en parallèle deux nouvelles façons de traiter le Paléolithique supérieur ancien qui ne sont pas antagonistes d'ailleurs. L'une consiste en une reprise des stratigraphies anciennes dans le Centre et le Sud-Ouest de la France plus spécifiquement et est associée à une meilleure redéfinition des entités culturelles par l'analyse détaillée des différentes composantes des systèmes techniques. L'autre s'efforce d'appliquer à cette période la démarche palethnographique, inféodée historiquement au Magdalénien du Bassin parisien. Il est vrai que peu de gisements autorisaient ce type d'approche, en raison d'une surface fouillée insuffisante ou d'un état de conservation médiocre, mais même lorsque les découvertes s'y prêtaient, le manque de temps et d'investissement freinait également toute velléité d'une étude approfondie des sites en question, qui aurait alors débouché sur une lecture palethnographique des lieux et des artefacts. À l'issue d'un PCR mené entre 1999 et 2005, nous pouvions ainsi légitimement nous demander si nous étions capables de jouer les ethnologues du passé pour le Paléolithique supérieur ancien dans le Bassin parisien. Les sites identifiés dans le cadre de ce programme de recherche étaient certes nombreux mais représentés surtout par des découvertes de surface, ils ne garantissaient pas un niveau d'analyse digne de ce qui a pu se faire depuis plus de 50 ans à Pincevent ou à Étiolles par exemple (Bodu et al., 2013). Il aura fallu attendre la découverte fortuite du gisement de plein-air d'Ormesson « les Bossats » (Seine-et-Marne, près de Nemours) au début des années 2000 pour que cette question trouve une réponse positive. Concernant, au départ, presqu'exclusivement des vestiges lithiques et osseux attribués au Gravettien, les premières fouilles menées en 2009 permirent d'identifier rapidement un second niveau d'occupation, d'attribution moustérienne. Les campagnes suivantes amenèrent à la découverte de cinq autres niveaux d'occupation paléolithiques, inégaux tant pour la surface couverte que pour l'état de conservation : un second niveau moustérien résultant vraisemblablement de palimpsestes, un ensemble châtelperronien, un autre solutréen, un quatrième badegoulien et enfin entre Châtelperronien et Gravettien, un foyer isolé sans vestiges archéologiques associés. Cette stratigraphie paléolithique de plein-air dilatée est le témoignage d'une forte occupation du lieu pendant près de 30 000 ans, ce qui s'explique notamment par la configuration particulière de la vallée à cet endroit. À la diversité chronologique des occupations préhistoriques répond une diversité des comportements économiques et techniques au sein des différentes sphères d'activités mais également des habitudes spatiales différentes. À l'issue des huit premières années de fouille (2009-2016), le site d'Ormesson « les Bossats » permet ainsi de développer une approche détaillée des comportements techniques, économiques, spatiaux de groupes culturels distincts ayant vécu durant 30 000 ans dans un cadre géomorphologique et plus globalement naturel, relativement identique. Dépassant le jeu de mot facile « palethnographie ou pâle ethnographie ? » à Ormesson « les Bossats », nous proposons ici quelques éléments de réponse

The Influence of Number and Timing of Pregnancies on Breast Cancer Risk for Women With BRCA1 or BRCA2 Mutations

International audienceBACKGROUND:Full-term pregnancy (FTP) is associated with a reduced breast cancer (BC) risk over time, but women are at increased BC risk in the immediate years following an FTP. No large prospective studies, however, have examined whether the number and timing of pregnancies are associated with BC risk for BRCA1 and BRCA2 mutation carriers.METHODS:Using weighted and time-varying Cox proportional hazards models, we investigated whether reproductive events are associated with BC risk for mutation carriers using a retrospective cohort (5707 BRCA1 and 3525 BRCA2 mutation carriers) and a prospective cohort (2276 BRCA1 and 1610 BRCA2 mutation carriers), separately for each cohort and the combined prospective and retrospective cohort.RESULTS:For BRCA1 mutation carriers, there was no overall association with parity compared with nulliparity (combined hazard ratio [HRc] = 0.99, 95% confidence interval [CI] = 0.83 to 1.18). Relative to being uniparous, an increased number of FTPs was associated with decreased BC risk (HRc = 0.79, 95% CI = 0.69 to 0.91; HRc = 0.70, 95% CI = 0.59 to 0.82; HRc = 0.50, 95% CI = 0.40 to 0.63, for 2, 3, and ≥4 FTPs, respectively, P trend < .0001) and increasing duration of breastfeeding was associated with decreased BC risk (combined cohort P trend = .0003). Relative to being nulliparous, uniparous BRCA1 mutation carriers were at increased BC risk in the prospective analysis (prospective hazard ration [HRp] = 1.69, 95% CI = 1.09 to 2.62). For BRCA2 mutation carriers, being parous was associated with a 30% increase in BC risk (HRc = 1.33, 95% CI = 1.05 to 1.69), and there was no apparent decrease in risk associated with multiparity except for having at least 4 FTPs vs. 1 FTP (HRc = 0.72, 95% CI = 0.54 to 0.98).CONCLUSIONS:These findings suggest differential associations with parity between BRCA1 and BRCA2 mutation carriers with higher risk for uniparous BRCA1 carriers and parous BRCA2 carriers