Structure-based optimization of 1H-imidazole-2-carboxamides as Axl kinase inhibitors utilizing a Mer mutant surrogate

Axl has been a target of interest in the oncology field for several years based on its role in various oncogenic processes. To date, no wild-type Axl crystal structure has been reported. Herein, we describe the structure-based optimization of a novel chemotype of Axl inhibitors, 1H-imidazole-2-carboxamide, using a mutated kinase homolog, Mer(I650M), as a crystallographic surrogate. Iterative optimization of the initial lead compound (1) led to compound (21), a selective and potent inhibitor of wild-type Axl. Compound (21) will serve as a useful compound for further in vivo studies.     

Divergence in male mating tactics between two populations of the soapberry bug: I. Guarding versus nonguarding

I compared male allocation to prolonged mate guarding versusnot guarding between two populations of the soapberry bug (Jaderahaematoloma) that differ in adult sex ratio: Oklahoma, USA (mean± SD adult sex ratio, 2.70 ± 0.95 males per female),and Florida, USA (1.09 ± 0.26 males per female). To predictthe reproductive performance of each mating tactic in each population,I collected data on search time per mating, time required forguarding to be effective, sperm competition, female rematingpropensity, and female resistance to guarding. Search time alonediffered significantly between the populations, being much greaterin Oklahoma (estimated as 26.2 h per mate) than in Florida (estimatedas 9.6 h per mate). For males in each region, these data wereused to model the costs and benefits of guarding for differentnumbers of oviposition bouts versus not guarding. The reproductiverate of nonguarders in Oklahoma is exceeded by that of guarderswho remain with a female for more than one oviposition bout,but in Florida, the reproductive rate of nonguarders is onlyexceeded by that of guarders who remain with a female for atleast three ovipositions. Consistent with the model, Oklahomamales in field arenas guarded more frequently than did Floridamales. However, nonguarding was common in both populations,and guarding durations were highly variable.     

Parental investment, sexual selection and sex ratios

Conventional sex roles imply caring females and competitive males. The evolution of sex role divergence is widely attributed to anisogamy initiating a self‐reinforcing process. The initial asymmetry in pre‐mating parental investment (eggs vs. sperm) is assumed to promote even greater divergence in post‐mating parental investment (parental care). But do we really understand the process? Trivers [Sexual Selection and the Descent of Man 1871–1971 (1972), Aldine Press, Chicago] introduced two arguments with a female and male perspective on whether to care for offspring that try to link pre‐mating and post‐mating investment. Here we review their merits and subsequent theoretical developments. The first argument is that females are more committed than males to providing care because they stand to lose a greater initial investment. This, however, commits the ‘Concorde Fallacy’ as optimal decisions should depend on future pay‐offs not past costs. Although the argument can be rephrased in terms of residual reproductive value when past investment affects future pay‐offs, it remains weak. The factors likely to change future pay‐offs seem to work against females providing more care than males. The second argument takes the reasonable premise that anisogamy produces a male‐biased operational sex ratio (OSR) leading to males competing for mates. Male care is then predicted to be less likely to evolve as it consumes resources that could otherwise be used to increase competitiveness. However, given each offspring has precisely two genetic parents (the Fisher condition), a biased OSR generates frequency‐dependent selection, analogous to Fisherian sex ratio selection, that favours increased parental investment by whichever sex faces more intense competition. Sex role divergence is therefore still an evolutionary conundrum. Here we review some possible solutions. Factors that promote conventional sex roles are sexual selection on males (but non‐random variance in male mating success must be high to override the Fisher condition), loss of paternity because of female multiple mating or group spawning and patterns of mortality that generate female‐biased adult sex ratios (ASR). We present an integrative model that shows how these factors interact to generate sex roles. We emphasize the need to distinguish between the ASR and the operational sex ratio (OSR). If mortality is higher when caring than competing this diminishes the likelihood of sex role divergence because this strongly limits the mating success of the earlier deserting sex. We illustrate this in a model where a change in relative mortality rates while caring and competing generates a shift from a mammalian type breeding system (female‐only care, male‐biased OSR and female‐biased ASR) to an avian type system (biparental care and a male‐biased OSR and ASR).     

Redesign of LAOBP to bind novel l‐amino acid ligands

Computational protein design is still a challenge for advancing structure‐function relationships. While recent advances in this field are promising, more information for genuine predictions is needed. Here, we discuss different approaches applied to install novel glutamine (Gln) binding into the Lysine/Arginine/Ornithine binding protein (LAOBP) from Salmonella typhimurium. We studied the ligand binding behavior of two mutants: a binding pocket grafting design based on a structural superposition of LAOBP to the Gln binding protein QBP from Escherichia coli and a design based on statistical coupled positions. The latter showed the ability to bind Gln even though the protein was not very stable. Comparison of both approaches highlighted a nonconservative shared point mutation between LAOBP_graft and LAOBP_sca. This context dependent L117K mutation in LAOBP turned out to be sufficient for introducing Gln binding, as confirmed by different experimental techniques. Moreover, the crystal structure of LAOBP_L117K in complex with its ligand is reported.     

Sequential Statistical Improvement of the Liquid Cultivation of Helicobacter pylori

Background: Colonization of the gastric mucosa by Helicobacter pylori is one of the most important causes of acute and chronic gastric pathologies in humans. Achieving the growth of H. pylori in liquid media is of great importance in the development of clinical studies. In this study, we developed a sequential optimization strategy based on statistical models to improve the conditions of liquid culture of H. pylori. Materials and Methods: Four statistical models were sequentially used. First, a Box‐Behnken design was used to select the best process conditions (shaking speed, inoculum concentration, and final volume of culture). Secondly, a general factorial design was used to evaluate the influence of adding gel blocks or gel beads (shape and composition). Then a D‐optimal reduce design was carried out to allow the selection of the most influential factors in increasing the cell concentration (culture media components). Finally, another Box‐Behnken design was used to optimize the concentration of the culture media components previously selected. Results: After 12 hours of liquid culture a concentration of 25 × 10⁸ cells per mL (9.4 log₁₀ cells per mL) of H. pylori was obtained, compared with a predicted 32 × 10⁸ (9.5 log₁₀ cells per mL), which means between 1 and 5 log₁₀ units higher than some previous reports. Conclusions: The sequential statistical approach increased the planktonic H. pylori cell culture. The final culture media and conditions were: Brain Heart Infusion, blood agarose (1.5% w/v), lamb’s blood (3.18% v/v), DENT (0.11% v/v), and Vitox (0.52% v/v) at 60 rpm and 37 °C with filtered CO₂ (5% v/v) bubbled directly into the culture media in a final volume of 76.22 mL.     

High levels of multiple paternity in a spermcast mating freshwater mussel

Multiple paternity is an important characteristic of the genetic mating system and common across a wide range of taxa. Multiple paternity can increase within‐population genotypic diversity, allowing selection to act on a wider spectre of genotypes, and potentially increasing effective population size. While the genetic mating system has been studied in many species with active mating behavior, little is known about multiple paternity in sessile species releasing gametes into the water. In freshwater mussels, males release sperm into the water, while eggs are retained and fertilized inside the female (spermcast mating). Mature parasitic glochidia are released into the water and attach to the gills of fish where they are encapsulated until settling in the bottom substrate. We used 15 microsatellite markers to detect multiple paternity in a wild population of the freshwater pearl mussel (Margaritifera margaritifera). We found multiple paternity in all clutches for which more than two offspring were genotyped, and numbers of sires were extremely high. Thirty‐two sires had contributed to the largest clutch (43 offspring sampled). This study provides the first evidence of multiple paternity in the freshwater pearl mussel, a species that has experienced dramatic declines across Europe. Previous studies on other species of freshwater mussels have detected much lower numbers of sires. Multiple paternity in freshwater pearl mussels may be central for maintaining genetic variability in small and fragmented populations and for their potential to recover after habitat restoration and may also be important in the evolutionary arms race with their fish host with a much shorter generation time.     

Competitive habitat utilization in the damselfly,Mnais nawai (Zygoptera: Calopterygidae) coexisting with a related species,Mnais pruinosa

Reproductive behaviors related to habitat utilization were studied in males of the damsefly,Mnais nawai, which has two male forms, territorial orange-winged males (nawai) and non-territorial pale-orange-winged males (sahoi), at the upper part of a mountain stream where they partiallycoexist with a related species,Mnais pruinosa, which also has two male forms, territorial orange-winged males (esakii) and non-territorial hyaline-winged males (strigata). These two species showed parapatric distribution; the lower part of the stream was occupied byM. nawai, and the upper part byM. pruinosa. In the present study, cross-matings occurred between bothMnais species, although normal intraspecific matings occurred more frequently than cross-matings. Territorial males of both species copulated with conspecific females that entered their territory and guarded the ovipositing females, probably to avoid sperm displacement resulting from subsequent copulations. Severe competition for oviposition sites by territorial males even occurred between the two species. On the other hand, non-territorial males of both species have alternative mating strategies (including several tactics such as sneaking, takeover and interception). The possible benefits from conflict among territorial males of both species is discussed.     

Evolutionary genetics and ecology of sperm-dependent parthenogenesis

Sperm-dependent (or pseudogamous) forms of parthenogenetic reproduction occur in a wide variety of animals. Inheritance is typically clonal and matroclinous (of female descent), but sperm are needed to initiate normal development. As opposed to true parthenogenesis (i.e., sperm-independent reproduction), pseudogamous parthenogenetic lineages must coexist with a ‘sperm donor’— e.g., males from a conspecific sexual lineage, conspecific hermaphrodites, or males from a closely related sexual species. Such sperm donors do not contribute genetically to the next generation. The parasitic nature of sperm-dependent parthenogenesis raises numerous ecological and evolutionary questions. How do they arise? What factors help stabilize coexistence between the pseudogamous parthenogens and their sperm donors (i.e., ‘sexual hosts’)? Why do males waste sperm on the asexual females? Why does true parthenogenesis not evolve in pseudogamous lineages and free them from their dependency on sperm donors? Does pseudogamous parthenogenesis provide compensatory benefits that outweigh the constraints of sperm-dependence? Herein, we consider some genetic, ecological, and geographical consequences of sperm-dependent parthenogenesis in animals.     

Mixture design of starchy substrates hydrolysis by an immobilized glucoamylase from Aspergillus brasiliensis

Starch has great importance in human diet, since it is a heteropolymer of plants, mainly found in roots, as potato, cassava and arrowroots. This carbohydrate is composed by a highly-branched chain: amylopectin; and a linear chain: amylose. The proportion between the chains varies according to the botanical source. Starch hydrolysis is catalyzed by enzymes of the amilolytic system, named amylases. Among the various enzymes of this system, the glucoamylases (EC 3.2.1.3 glucan 1,4-alpha-glucosidases) are the majority because they hydrolyze the glycosidic linkages at the end of starch chains releasing glucose monomers. In this work, a glucoamylase secreted in the culture medium, by the ascomycete Aspergillus brasiliensis, was immobilized in Dietilaminoetil Sepharose-Polyethylene Glycol (DEAE-PEG), since immobilized biocatalysts are more stable in long periods of hydrolysis, and can be recovered from the final product and reused for several cycles. Glucoamylase immobilization has shown great thermal stability improvement over the soluble enzyme, reaching 66% more activity after 6?h at 60?°C, and 68% of the activity after 10 hydrolysis cycles. A simplex centroid experimental mixture design was applied as a tool to characterize the affinity of the immobilized enzyme for different starchy substrates. In assays containing several proportions of amylose, amylopectin and starch, the glucoamylase from A. brasiliensis mainly hydrolyzed the amylopectin chains, showing to have preference by branched substrates.