Structure based design of novel 6,5 heterobicyclic mitogen-activated protein kinase kinase (MEK) inhibitors leading to the discovery of imidazo[1,5-a] pyrazine G-479

Use of the tools of SBDD including crystallography led to the discovery of novel and potent 6,5 heterobicyclic MEKi’s [J. Med. Chem. 2012, 55, 4594]. The core change from a 5,6 heterobicycle to a 6,5 heterobicycle was driven by the desire for increased structural diversity and aided by the co-crystal structure of G-925 [J. Med. Chem. 2012, 55, 4594]. The key design feature was the shift of the attachment of the five-membered heterocyclic ring towards the B ring while maintaining the key hydroxamate and anilino pharamcophoric elements in a remarkably similar position as in G-925. From modelling, changing the connection point of the five membered ring heterocycle placed the H-bond accepting nitrogen within a good distance and angle to the Ser212 [J. Med. Chem. 2012, 55, 4594]. The resulting novel 6,5 benzoisothiazole MEKi G-155 exhibited improved potency versus aza-benzofurans G-925 and G-963 but was a potent inhibitor of cytochrome P450’s 2C9 and 2C19. Lowering the log D by switching to the more polar imidazo[1,5-a] pyridine core significantly diminished 2C9/2C19 inhibition while retaining potency. The imidazo[1,5-a] pyridine G-868 exhibited increased potency versus the starting point for this work (aza-benzofuran G-925) leading to deprioritization of the azabenzofurans. The 6,5-imidazo[1,5-a] pyridine scaffold was further diversified by incorporating a nitrogen at the 7 position to give the imidazo[1,5-a] pyrazine scaffold. The introduction of the C7 nitrogen was driven by the desire to improve metabolic stability by blocking metabolism at the C7 and C8 positions (particularly the HLM stability). It was found that improving on G-868 (later renamed GDC-0623) required combining C7 nitrogen with a diol hydroxamate to give G-479. G-479 with polarity distributed throughout the molecule was improved over G-868 in many aspects.     

Tropical ant communities are in long-term equilibrium

Communities change with time. Studying long-term change in community structure permits deeper understanding of community dynamics, and allows us to forecast community responses to perturbations at local (e.g. fire, secondary succession) and global (e.g. desertification, global warming) spatial scales. Monitoring efforts exploring the temporal dynamics of indicator taxa are therefore a critical part of conservation agendas. Here, the temporal dynamics of the Otongachi leaf litter ant community, occurring in a cloud forest in coastal Ecuador, were explored. By sampling this community six times over eleven years, I assessed how the ant fauna caught by Winkler traps (more diverse and cryptic fauna) and caught by pitfall traps (larger, more mobile fauna) changed over time. The Otongachi leaf litter ant community was dynamic. Although species richness in the community remained constant, temporal turnover of species was high: on average, 51% of the ant species in Winkler traps, and 56% of those in pitfall traps, were replaced with other ant species from one year to the other. Shifts in the rank abundance of species in the community were also large across the eleven years and, on average, shifts in the rank abundance of species collected by Winkler traps doubled those occurring in pitfall traps from one census to the other. In spite of these trends, the Otongachi ant fauna showed no (Winkler) or weak (pitfall) evidence of directional change (towards a new community). Thus, this tropical ant community can be divided in two community compartments. The Winkler compartment composed by a more diverse and cryptic ant fauna appears to be resilient and stable in time. The pitfall compartment composed by larger and more mobile ants may be prone to respond to disturbance. This study suggests that 1) species appearing/disappearing from a site may be rather the rule, difficult to separate from responses to ecological stress. 2) Conclusions made in short-term studies, or studies comparing two (e.g. before and after) snapshots of a community, should thus be revisited. Finally, 3) the ant fauna caught by pitfall traps (a rather simple and cheap survey method) is the most likely community compartment to indicate ecological perturbation. This study adds to the growing evidence that using ants as ecological indicators should incorporate long-term temporal dynamics.     

How does the cumulative impacts approach support Maritime Spatial Planning?

Maritime Spatial Planning (MSP) needs to incorporate spatial information on human impacts. As human activities and uses increase in marine and coastal waters around the world, pressures in ecosystems are also increasing, leading to multiple adverse effects on different species and habitats. The European Directive on MSP aims to achieve an integrated approach to marine governance, whilst securing and maintaining the healthy status of marine and coastal waters, in accordance with the Marine Strategy Framework Directive. The latter requires Member States to develop assessments not only on pressures and impacts, but also on the state of the marine environment and then take measures towards reaching a Good Environmental Status by 2020.The Portuguese Maritime Spatial Plan – Plano de Ordenamento do Espaço Marítimo (POEM) was developed between 2009 and 2012. In 2014 a law establishing the Basis for the Spatial Planning and Management of the National Maritime Space was enacted and in 2015 the framework for the elaboration of a new national Maritime Spatial Plan, named Situation Plan, was established. Portugal will face, in the next five years, the challenge of planning and managing its marine space, whilst promoting its sustainable use and protection.This study adapted a cumulative effects assessment model to understand how the impacts from multiple threats affect the marine and coastal ecosystems and, how this information can be used to improve the management process. Information was gathered on intensity and distribution of activities and uses for the Portuguese continental subdivision marine area, quantified and mapped their cumulative impacts in marine ecosystems, and overlapped with the POEM. Results show that impacts are spreading from the coast up to the Contiguous Zone. Higher scores appear in Transitional and Coastal Waters in the north (Viana do Castelo/Figueira da Foz), centre (Peniche/Setúbal) and south (Lagos/Faro). In some areas with higher ranks, statutes of nature conservation are already in place, but potential activities may still occur on top of existing ones. This study shows that the adapted model is a helpful tool to clarify ocean planning, identify areas of potential conflicts among users and support the decision making process.     

Target identification of covalently binding drugs by activity-based protein profiling (ABPP)

The characterization of the target proteins of drug molecules has become an important goal in understanding its mode of action and origin of side effects due to off-target binding. This is especially important for covalently binding drugs usually containing electrophilic moieties, which potentially can react with nucleophilic residues found in many proteins. This review gives a comprehensive overview of the use of activity-based protein profiling (ABPP) as an efficient tool for the target identification of covalently binding drugs.     

Identifying fern gametophytes using DNA sequences

Identification of fern gametophytes is generally hampered by low morphological complexity. Here we explore an alternative: DNA‐based identification. We obtained a plastid rbcL sequence from a sterile gametophyte of unknown origin (cultivated for more than 30 years) and employed blast to determine its affinities. Using this approach, we identified the gametophyte as Osmunda regalis. To evaluate the robustness of this determination, and the usefulness of rbcL in differentiating among species, we conducted a phylogenetic analysis of osmundaceous fern sequences. Based on our results, it is evident that DNA‐based identification has considerable potential in exploring the ecology of fern gametophytes.     

Population-level cure of colorectal cancer in Malta: An analysis of patients diagnosed between 1995 and 2004

AimThe aim of this study was to estimate the population-level ‘cure’ of Maltese colorectal cancer patients diagnosed between 1995 and 2004, and to estimate the median survival time for the ‘uncured’ patients.Methods and study populationAnalysis was conducted on 1470 cases registered by the Malta National Cancer Register between 1995 and 2004 and followed up to end of 2010. The mean age of the patients was 66.4 (95%CI 65.8–67.1), and the number of men and women were equal. Background mortality for 1995–2010 was extracted from publicly available life tables. A mixture model with Weibull survival distribution and identity link was used to model ‘cure’.ResultsThe overall ‘cured’ proportion for the patients diagnosed in 1995–1999 was 45.3% (95%CI 40.2–50.5) while the ‘cured’ proportion for the patients diagnosed in 2000–2004 was 52.3% (95%CI 47.2–57.5). Median survival time for the ‘uncured’ patients increased in the second calendar period from 1.25 years (95%CI 1.04–1.45) to 1.42 years (95%CI 1.15–1.76).ConclusionIn Malta, as in the rest of Europe, improvements have been made in short- and long-term survival over the 15-year period under study. To continue this improvement, differences by age that still persist must be investigated and efforts focused to reduce any gaps between Malta and other European countries.     

Biogeography and diversification of colletid bees (Hymenoptera: Colletidae): emerging patterns from the southern end of the world

Aim The evolutionary history of bees is presumed to extend back in time to the Early Cretaceous. Among all major clades of bees, Colletidae has been a prime example of an ancient group whose Gondwanan origin probably precedes the complete break‐up of Africa, Antarctica, Australia and South America, because modern lineages of this family occur primarily in southern continents. In this paper, we aim to study the temporal and spatial diversification of colletid bees to better understand the processes that have resulted in the present southern disjunctions. Location Southern continents. Methods We assembled a dataset comprising four nuclear genes of a broad sample of Colletidae. We used Bayesian inference analyses to estimate the phylogenetic tree topology and divergence times. Biogeographical relationships were investigated using event‐based analytical methods: a Bayesian approach to dispersal–vicariance analysis, a likelihood‐based dispersal–extinction–cladogenesis model and a Bayesian model. We also used lineage through time analyses to explore the tempo of radiations of Colletidae and their context in the biogeographical history of these bees. Results Initial diversification of Colletidae took place at the Late Cretaceous (≥ 70 Ma). Several (6–14) lineage exchanges between Australia and South America via Antarctica during the Late Cretaceous and Eocene epochs could explain the disjunctions observed between colletid lineages today. All biogeographical methods consistently indicated that there were multiple lineage exchanges between South America and Australia, and these approaches were valuable in exploring the degree of uncertainty inherent in the ancestral reconstructions. Biogeographical and dating results preclude an explanation of Scrapterinae in Africa as a result of vicariance, so one dispersal event is assumed to explain the disjunction in relation to Euryglossinae. The net diversification rate was found to be highest in the recent history of colletid evolution. Main conclusions The biogeography and macroevolutionary history of colletid bees can be explained by a combination of Cenozoic vicariance and palaeoclimatic changes during the Neogene. The austral connection and posterior break‐up of South America, Antarctica and Australia resulted in a pattern of disjunct sister lineages. Increased biome aridification coupled with floristic diversification in the southern continents during the Neogene may have contributed to the high rates of cladogenesis in these bees in the last 25–30 million years.     

Geometric morphometric analysis of the effect of temperature on wing size and shape in Aedes albopictus

Wing geometry helps to identify mosquito species, even cryptic ones. On the other hand, temperature has a well‐known effect on insect metric properties. Can such effects blur the taxonomic signal embedded in the wing? Two strains of Aedes albopictus (laboratory and field strain) were examined under three different rearing temperatures (26, 30 and 33 °C) using landmark‐ and outline‐based morphometric approaches. The wings of each experimental line were compared with Aedes aegypti. Both approaches indicated similar associations between wing size and temperature. For the laboratory strain, the wing size significantly decreased as the temperature increased. For the field strain, the largest wings were observed at the intermediate temperature. The two morphometric approaches describing shape showed different sensibilities to temperature. For both strains and sexes, the landmark‐based approach disclosed significant wing shape changes with temperature changes. The outline‐based approach showed lesser effects, detecting significant changes only in laboratory females and in field males. Despite the size and shape changes induced by temperature, the two strains of Ae. albopictus were always distinguished from Ae. aegypti. The present study confirms the lability of size. However, it also suggests that, despite environmentally‐induced variation, the architecture of the wing still provides a strong taxonomic signal.     

Parietal lobe variation in cercopithecid endocasts

In extant primates, the posterior parietal cortex is involved in visuospatial integration, attention, and eye‐hand coordination, which are crucial functions for foraging and feeding behaviors. Paleoneurology studies brain evolution through the analysis of endocasts, that is molds of the inner surface of the braincase. These may preserve imprints of cortical structures, such as sulci, which might be of interest for locating the boundaries of major cortical regions. Old World monkeys (Cercopithecidae) represent an interesting zoological group for evolutionary studies, because of their diverse ecologies and locomotor behaviors. In this study, we quantify parietal lobe variation within the cercopithecid family, in a sample of 30 endocasts including 11 genera and 17 species, by combining landmark‐based and landmark‐free geometric morphometric analyses. More specifically, we quantitatively assess variation of the parietal proportions based on landmarks placed on reliable anatomical references and of parietal lobe surface morphology through deformation‐based methods. The main feature associated with the cercopithecid endocranial variation regards the inverse proportions of parietal and occipital lobes, with colobines, Theropithecus, and Papio displaying relatively larger parietal lobes and smaller occipital lobes compared with cercopithecins. The parietal surface is anteroposteriorly longer and mediolaterally flatter in colobines, while longitudinally shorter but laterally bulging in baboons. Large parietal lobes in colobines and baboons are likely to be independent evolutionary traits, and not necessarily associated with analogous functions or morphogenetic mechanisms.