‘Design,synthesis, and strategic use of small chemical probes toward identification of novel targets for drug development’

Chemical probes are essential tools used to study and modulate biological systems. Here, we describe some of the recent scientific advancement in the field of chemical biology, as well as how the advent of new technologies is redefining the criteria of ‘good’ chemical probes and influencing the discovery of valuable drug leads. In this review, we report selected examples of the usage of linkered and linker-free chemical probes for target identification, biological discovery, and general mechanistic understanding. We also discuss the promises of chemogenomics libraries in phenotypic screens, as well as the limitation of their usage to identify the modulation of new targets and biology.     

Discrimination between Functional and Non-functional Cellular Gag Complexes involved in HIV-1 Assembly

HIV-1 Gag and Gag-Pol are responsible for viral assembly and maturation and represent a major paradigm for enveloped virus assembly. Numerous intracellular Gag-containing complexes (GCCs) have been identified in cellular lysates using sucrose gradient ultracentrifugation. While these complexes are universally present in Gag-expressing cells, their roles in virus assembly are not well understood. Here we demonstrate that most GCC species are predominantly comprised of monomeric or dimeric Gag molecules bound to ribosomal complexes, and as such, are not on-pathway intermediates in HIV assembly. Rather, these GCCs represent a population of Gag that is not yet functionally committed for incorporation into a viable virion precursor. We hypothesize that these complexes act as a reservoir of monomeric Gag that can incorporate into assembling viruses, and serve to mitigate non-specific intracellular Gag oligomerization. We have identified a subset of large GCC complexes, comprising more than 20 Gag molecules, that may be equivalent to membrane-associated puncta previously shown to be bona fide assembling-virus intermediates. This work provides a clear rationale for the existence of diverse GCCs, and serves as the foundation for characterizing on-pathway intermediates early in virus assembly.     

Large-scale Identification of N-linked Intact Glycopeptides in Human Serum using HILIC Enrichment and Spectral Library Search

1. Download : Download high-res image (200KB)
2. Download : Download full-size image

Highlights

• •This study proposed a spectral library search method to accurately identify N-linked glycopeptides in human serum through LC-MS/MS with pMatchGlyco software.
• •The identification depth of serum N-linked intact glycopeptides and glycoproteins was increased by combination of acetonitrile precipitation, HILIC enrichment and high-pH RPLC fractionation.
• •22,677 unique serum N-linked intact glycopeptides corresponding to 526 N-linked glycoproteins were identified with N-glycosylation motif-specific FDR control.
• •This study revealed the great microheterogeneity of N-linked glycoproteins in serum.

     

Denitrification as a major regional nitrogen sink in subtropical forest catchments: Evidence from multi‐site dual nitrate isotopes

Increasing nitrogen (N) deposition in subtropical forests in south China causes N saturation, associated with significant nitrate (NO₃^?) leaching. Strong N attenuation may occur in groundwater discharge zones hydrologically connected to well‐drained hillslopes, as has been shown for the subtropical headwater catchment “TieShanPing”, where dual NO₃^? isotopes indicated that groundwater discharge zones act as an important N sink and hotspot for denitrification. Here, we present a regional study reporting inorganic N fluxes over two years together with dual NO₃^? isotope signatures obtained in two summer campaigns from seven forested catchments in China, representing a gradient in climate and atmospheric N input. In all catchments, fluxes of dissolved inorganic N indicated efficient conversion of NH₄⁺ to NO₃^? on well‐drained hillslopes, and subsequent interflow of NO₃^? over the argic B‐horizons to groundwater discharge zones. Depletion of ¹⁵N‐ and ¹⁸O–NO₃^? on hillslopes suggested nitrification as the main source of NO₃^?. In all catchments, except one of the northern sites, which had low N deposition rates, NO₃^? attenuation by denitrification occurred in groundwater discharge zones, as indicated by simultaneous ¹⁵N and ¹⁸O enrichment in residual NO₃^?. By contrast to the southern sites, the northern catchments lack continuous and well‐developed groundwater discharge zones, explaining less efficient N removal. Using a model based on ¹⁵NO₃^? signatures, we estimated denitrification fluxes from 2.4 to 21.7 kg N ha^?1 year^?1 for the southern sites, accounting for more than half of the observed N removal. Across the southern catchments, estimated denitrification scaled proportionally with N deposition. Together, this indicates that N removal by denitrification is an important component of the N budget of southern Chinese forests and that natural NO₃^? attenuation may increase with increasing N input, thus partly counteracting further aggravation of N contamination of surface waters in the region.     

Relationship between efficiency of nitrogen utilization and isotopic nitrogen fractionation in dairy cows: contribution of digestion v. metabolism?

Animal tissues are naturally ¹⁵N enriched relative to their diet and the extent of this difference (Δ¹⁵N_animal-diet) has been correlated to the efficiency of N assimilation in different species. The rationale is that transamination and deamination enzymes, involved in amino acid metabolism are likely to preferentially convert amino groups containing ¹⁴N over ¹⁵N. However, in ruminants the contribution of rumen bacterial metabolism relative to animal tissues metabolism to naturally enrich animal proteins in terms of ¹⁵N has been not assessed yet. The objective of this study was to assess the impact of rumen and digestion processes on the relationship between Δ¹⁵N_animal-diet and efficiency of N utilization for milk protein yield (milk N efficiency (MNE); milk N yield/N intake) as well as the relationship between the ¹⁵N natural abundance of rumen bacteria and the efficiency of N use at the rumen level. Solid- and liquid-associated rumen bacteria, duodenal digesta, feces and plasma proteins were obtained (n=16) from four lactating Holstein cows fed four different diets formulated at two metabolizable protein supplies (80% v. 110% of protein requirements) crossed by two different dietary energy source (diets rich in starch v. fiber). We measured the isotopic N fractionation between animal and diet (Δ¹⁵N_animal-diet) in these different body pools. The Δ¹⁵N_animal-diet was negatively correlated with MNE when measured in solid-associated rumen bacteria, duodenal digesta, feces and plasma proteins, with the strongest correlation found for the latter. However, our results showed a very weak ¹⁵N enrichment of duodenal digesta (Δ¹⁵N_{duodenal digesta-diet} mean value=0.42) compared with that observed in plasma proteins (Δ¹⁵N_{plasma protein-diet} mean value=2.41). These data support the idea that most of the isotopic N fractionation observed in ruminant proteins (Δ¹⁵N_{plasma protein-diet}) has a metabolic origin with very little direct impact of the overall digestion process on the existing relationship between Δ¹⁵N_{plasma protein-diet} and MNE. The ¹⁵N natural abundance of rumen bacteria was not related to either rumen N efficiency (microbial N/available N) or digestive N efficiency (metabolizable protein supply/CP intake), but showing a modest positive correlation with rumen ammonia concentration. When using diets not exceeding recommended protein levels, the contribution of rumen bacteria and digestion to the isotopic N fractionation between animal proteins and diet is low. In our conditions, most of the isotopic N fractionation (Δ¹⁵N_{plasma protein-diet}) could have a metabolic origin, but more studies are warranted to confirm this point with different diets and approaches.     

Content of trace elements and chromium speciation in Neem powder and tea infusions

Total concentrations of selected trace elements in Neem powder and in Neem tea were determined by inductively coupled plasma mass spectrometry (ICP-MS). The data revealed that despite high total concentrations of the potentially toxic elements Al and Ni in Neem powder, their amounts dissolved in Neem tea were low. Total concentrations of the other toxic elements Pb, As and Cd were also very low and do not represent a health hazard. In contrast, total concentrations of the essential elements Fe, Cu, Zn, Se Mo and Cr in Neem powder were high and also considerable in Neem tea. Consuming one cup of Neem tea (2 g per 200 mL of water) covers the recommended daily intakes for Cr and Se and represents an important source of Mo and Cu.Speciation analysis of Cr by high performance liquid chromatography (HPLC) coupled to ICP-MS with the use of enriched Cr isotopic tracers to follow species interconversions during the analytical procedure demonstrated that toxic Cr(VI) was not present either in Neem powder or in Neem tea. Its concentrations were below the limits of detection of the HPLC–ICP-MS procedure applied. The speciation analysis data confirmed that even Cr(VI) was added, it was rapidly reduced by the presence of antioxidants in Neem leaves. By the use of enriched Cr isotopic spike solutions it was also demonstrated that for obtaining reliable analytical data it is essential to apply the extraction procedures which prevent Cr species interconversions, or to correct for species transformation.     

Water pathways in wheat leaves. III. The passage of the mestome sheath and the function of the suberised lamellae

The fluorochrome sulphorhodamine G, when present in the transpiration stream in wheat leaves, passes rapidly out of the veins and produces fluorescence in the mesophyll and epidermal cell walls. The path of movement of the dye out of the tracherary elements and across the mestome sheath to the parenchyma sheath cells was followed by rapid freezing, freeze-subsitution, dry embedding in resin, sectioning and epifluorescence microscopy. The sulphorhodamine solution was visible in tracheary elements, and, where it had passed out of the tracheary elements, strongly fluorescent in some of the cell walls. The patterns of wall fluorescence are used to chart the movements of water from the xylem through some of the radial walls of mestome sheath cells near the xylem to the free space of the mesophyll. The suberised lamellae of the mestome sheath cells must form an incomplete barrier near the xylem to permit passage of the dye. A hypothesis is formulated that the function of the suberised lamellae is to keep separate the oppositely directed fluxes of water and assimilates through the sheath. It is further proposed that the function of pits in living cells is a similar insulation of the symplastic traffic from the wayward waters of the apoplast.     

Theoretical Proof and Empirical Confirmation of a Continuous Labeling Method Using Naturally ^13C-Depleted Carbon Dioxide

Continuous Isotope labeling and tracing is often needed to study the transformation, movement, and allocation of carbon in plant-soil systems. However, existing labeling methods have numerous limitations. The present study Introduces a new continuous labeling method using naturally ^13C-depleted CO2. We theoretically proved that a stable level of ^13C-CO2 abundance in a labeling chamber can be maintained by controlling the rate of CO2-free air Injection and the rate of ambient airflow with coupling of automatic control of CO2 concentration using a CO2 analyzer. The theoretical results were tested and confirmed in a 54 day experiment in a plant growth chamber. This new continuous labeling method avoids the use of radioactive ^14C or expensive ^13C-enrlched CO2 required by existing methods and therefore eliminates issues of radiation safety or unaffordable isotope cost, as well as creating new opportunities for short- or long-term labeling experiments under a controlled environment.     

Migratory connectivity in a declining bird species: using feather isotopes to inform demographic modelling

Aim Conservation programmes for endangered migratory species or populations require locating and evaluating breeding, stopover and wintering areas. We used multiple stable isotopes in two endangered European populations of wrynecks, Jynx torquilla L., to locate wintering regions and assess the degree of migratory connectivity between breeding and wintering populations. Location Switzerland and Germany. Methods We analysed stable nitrogen (δ¹⁵N), carbon (δ¹³C) and hydrogen (δD) isotopes from wing feathers from two populations of wrynecks to infer their wintering origins and to assess the strength of migratory connectivity. We tested whether variation in feather isotopic values within the Swiss population was affected by bird age and collection year and then considered differences in isotopic values between the two breeding populations. We used isotopic values of summer‐ and winter‐grown feathers to estimate seasonal distributions. Finally, we calculated a species‐specific δD discrimination factor between feathers and mean annual δD values to assign winter‐grown feathers to origin. Results Bird age and collection year caused substantial isotopic variation in winter‐grown feathers, which may be because of annually variable weather conditions, movements of birds among wintering sites and/or reflect asynchronous moulting or selection pressure. The large isotopic variance in winter‐grown feathers nevertheless suggested low migratory connectivity for each breeding population, with partially overlapping wintering regions for the two populations. Main conclusions Isotopic variance in winter‐grown feathers of two breeding populations of wrynecks and their geographical assignment point to defined, albeit overlapping, wintering areas, suggesting both leapfrog migration and low migratory connectivity. On this basis, integrative demographic models can be built looking at seasonal survival patterns with links to local environmental conditions on both breeding and wintering grounds, which may elucidate causes of declines in migratory bird species.     

Isotopic ecology ten years after a call for more laboratory experiments

About 10 years ago, reviews of the use of stable isotopes in animal ecology predicted explosive growth in this field and called for laboratory experiments to provide a mechanistic foundation to this growth. They identified four major areas of inquiry: (1) the dynamics of isotopic incorporation, (2) mixing models, (3) the problem of routing, and (4) trophic discrimination factors. Because these areas remain central to isotopic ecology, we use them as organising foci to review the experimental results that isotopic ecologists have collected in the intervening 10 years since the call for laboratory experiments. We also review the models that have been built to explain and organise experimental results in these areas.