A microdroplet-accelerated Biginelli reaction: mechanisms and separation of isomers using IMS-MS

Electrospray ionization (ESI) combined with ion mobility spectrometry (IMS) and mass spectrometry (MS) techniques is used to examine the Biginelli reaction in an ensemble of ions generated from droplets.

Electrospray ionization (ESI) combined with ion mobility spectrometry (IMS) and mass spectrometry (MS) techniques is used to examine the Biginelli reaction in an ensemble of ions generated from droplets. We find evidence for rapid dihydropyrimidinone formation from condensation of ethyl acetoacetate, benzaldehyde, and urea on the very short timescales associated with the electrospray process (∼10 μs to ∼1.0 ms). Control bulk-solution reactions show no product formation even after several days. This implies that the in-droplet reaction rate is enhanced by an astonishing factor. Examination of the reaction conditions and characterization of the intermediates en route to product shows evidence for variations in the reaction mechanism. IMS separation shows that the Knoevenagel condensation intermediate from benzaldehyde and ethyl acetoacetate exists as both the cis- and trans-isomer, in a ∼5 to 1 ratio. We suggest that the dramatic acceleration arises because of increased reagent confinement as electrosprayed droplets shrink. The ability of IMS-MS to resolve intermediates (including isomers) provides a new means of understanding reaction pathways.

Structural insights reveal a recognition feature for tailoring hydrocarbon stapled-peptides against the eukaryotic translation initiation factor 4E protein

Stapled-peptides have emerged as an exciting class of molecules which can modulate protein-protein interactions. We have used a structure-guided approach to rationally develop a set of hydrocarbon stapled-peptides with high binding affinities and residence times against the oncogenic eukaryotic translation initiation factor 4E (eIF4E) protein. Crystal structures of these peptides in complex with eIF4E show that they form specific interactions with a region on the protein-binding interface of eIF4E which is distinct from the other well-established canonical interactions. This recognition element is a major molecular determinant underlying the improved binding kinetics of these peptides with eIF4E. The interactions were further exploited by designing features in the peptides to attenuate disorder and increase helicity which collectively resulted in the generation of a distinct class of hydrocarbon stapled-peptides targeting eIF4E. This study details new insights into the molecular basis of stapled-peptide: eIF4E interactions and their exploitation to enhance promising lead molecules for the development of stapled-peptide compounds for oncology.

Avoided emissions and conservation of scrub mangroves: potential for a Blue Carbon project in the Gulf of California, Mexico

Mangroves are considered ideal ecosystems for Blue Carbon projects. However, because of their short stature, some mangroves ('scrub' mangroves, less than 2 m) do not fulfil the current definition of 'forests', which makes them ineligible for emission reduction programmes such as REDD+. Short stature mangroves can be the dominant form of mangroves in arid and nutrient-poor landscapes, and emissions from their deforestation and degradation could be substantial. Here, we describe a Blue Carbon project in the Gulf of California, Mexico, to illustrate that projects that avoid emissions from deforestation and degradation could provide financial resources to protect mangroves that cannot be included in other emission reduction programmes. The goal of the project is to protect 16 058 ha of mangroves through conservation concessions from the Mexican Federal Government. The cumulative avoided emissions of the project are 2.84 million Mg CO₂ over 100 years, valued at $US 426 000 per year (US$15 per Mg CO₂ in the California market). The funds could be used for community-based projects that will improve mangrove management, such as surveillance, eradication of invasive species, rehabilitation after tropical storms and environmental education. The strong institutional support, secure financial status, community engagement and clear project boundaries provide favourable conditions to implement this Blue Carbon project. Financial resources from Blue Carbon projects, even in mangroves of short stature, can provide substantial resources to enhance community resilience and mangrove protection.

Functional changes in reef systems in warmer seas: Asymmetrical effects of altered grazing by a widespread crustacean mesograzer

Grazing is a pivotal function in many marine systems, conferring resilience to coral reefs by limiting algal overgrowth, but triggering phase shifts on temperate reefs. Thus, changes to consumption rates of grazing species in response to higher future temperatures may have broad ecological consequences. We measured how the consumption rates of a widespread mesograzer (the hermit crab Clibanarius virescens) responded to changing temperatures in the laboratory and applied these findings to model the spatial footprint on grazing animals throughout the Indo-Pacific region under climate change scenarios. We show that mean grazing capacity may increase in shallow coastal areas in the second half of the century. The effects are, however, asymmetrical, with tropical reefs predicted to experience slightly diminished grazing whilst reefs at higher latitudes will be grazed substantially more. Our findings suggest that assessments of the effects of climate change on reef ecosystems should consider how warming affects grazing performance when predicting wider ecological impacts.

Transanal endoscopic microsurgery as day surgery - a single-centre experience with 500 patients

AIM

Transanal endoscopic microsurgery (TEM) is the current treatment of choice for rectal adenomas and early rectal cancer. Postoperative admission to hospital is common but possibly unnecessary. Our objective was to analyse predictors and outcomes of TEM patients having same day discharge (TEM-D) compared with those who were admitted to hospital (TEM-A).

METHOD

At St Paul's Hospital (SPH), demographic, surgical, pathological and follow-up data have been collected prospectively since TEM was started in 2007. Trends in admission and readmission rates were analysed using the Cochran-Armitage trend test, and predictors of admission were analysed using univariate and multivariate logistic regressions.

RESULTS

Between 2007 and 2016, 500 patients were treated by TEM at SPH. The overall admission rate was 29% (145/500), but this decreased to 19% in the last 3 years of the study (P < 0.001). The readmission rate was 5.2% (n = 26/500) and did not change significantly over the study period (P = 0.30). Reasons for admission included the following: surgeon discretion/monitoring (35%), urinary retention (26%), haemorrhage (10%), breach of peritoneal cavity (7%), infection (7%) and other (15%). The most common reasons for readmission were haemorrhage (54%, n = 14), pain (19%, n = 5) and infection (12%, n = 3). Factors associated with admission were as follows: tumour height (OR 1.09, 1.02-1.17), prolonged operative time (OR 1.25, 1.14-1.37), unsutured surgical defect (OR 1.99, 1.22-3.25) and surgeon experience (OR 4.62, 2.75-7.77).

CONCLUSION

Outpatient TEM is safe and carries a low risk of readmission. In centres with an outpatient TEM strategy, predictors of hospital admission include proximal tumours, prolonged surgical time and open management of the surgical defect.

Estimating the footprint of pollution on coral reefs with models of species turnover

Ecological communities typically change along gradients of human impact, although it is difficult to estimate the footprint of impacts for diffuse threats such as pollution. We developed a joint model (i.e., one that includes multiple species and their interactions with each other and environmental covariates) of benthic habitats on lagoonal coral reefs and used it to infer change in benthic composition along a gradient of distance from logging operations. The model estimated both changes in abundances of benthic groups and their compositional turnover, a type of beta diversity. We used the model to predict the footprint of turbidity impacts from past and recent logging. Benthic communities far from logging were dominated by branching corals, whereas communities close to logging had higher cover of dead coral, massive corals, and soft sediment. Recent impacts were predicted to be small relative to the extensive impacts of past logging because recent logging has occurred far from lagoonal reefs. Our model can be used more generally to estimate the footprint of human impacts on ecosystems and evaluate the benefits of conservation actions for ecosystems.

Conformationally Regulated Peptide Bond Cleavage in Bradykinin

Ion mobility and mass spectrometry techniques are used to investigate the stabilities of different conformations of bradykinin (BK, Arg¹-Pro²-Pro³-Gly⁴-Phe⁵-Ser⁶-Pro⁷-Phe⁸-Arg⁹). At elevated solution temperatures, we observe a slow protonation reaction, i.e., [BK+2H]²⁺+H⁺ → [BK+3H]³⁺, that is regulated by trans → cis isomerization of Arg¹-Pro², resulting in the Arg¹- cis-Pro²- cis-Pro³-Gly⁴-Phe⁵-Ser⁶- cis-Pro⁷-Phe⁸-Arg⁹ (all- cis) configuration. Once formed, the all- cis [BK+3H]³⁺ spontaneously cleaves the bond between Pro²-Pro³ with perfect specificity, a bond that is biologically resistant to cleavage by any human enzyme. Temperature-dependent kinetics studies reveal details about the intrinsic peptide processing mechanism. We propose that nonenzymatic cleavage at Pro²-Pro³ occurs through multiple intermediates and is regulated by trans → cis isomerization of Arg¹-Pro². From this mechanism, we can extract transition state thermochemistry: Δ G^‡ = 94.8 ± 0.2 kJ·mol^-1, Δ H^‡ = 79.8 ± 0.2 kJ·mol^-1, and Δ S^‡ = -50.4 ± 1.7 J·mol^-1·K^-1 for the trans → cis protonation event; and, Δ G^‡ = 94.1 ± 9.2 kJ·mol^-1, Δ H^‡ = 107.3 ± 9.2 kJ·mol^-1, and Δ S^‡ = 44.4 ± 5.1 J·mol^-1·K^-1 for bond cleavage. Biological resistance to the most favored intrinsic processing pathway prevents formation of Pro³-Gly⁴-Phe⁵-Ser⁶- cis-Pro⁷-Phe⁸-Arg⁹ that is approximately an order of magnitude more antigenic than BK.

The MDM2/MDMX-p53 Antagonist PM2 Radiosensitizes Wild-Type p53 Tumors

Radiotherapy amplifies p53 expression in cancer cells with wild-type (wt) p53. Blocking the negative regulators MDM2 and MDMX stabilizes p53 and may therefore potentiate radiotherapy outcomes. In this study, we investigate the efficacy of the novel anti-MDM2/X stapled peptide PM2 alone and in combination with external gamma radiation in vitro and in vivo PM2 therapy combined with radiotherapy elicited synergistic therapeutic effects compared with monotherapy in cells with wt p53 in both in vitro and in vivo assays, whereas these effects did not manifest in p53 ^-/- cells. Biodistribution and autoradiography of ¹²⁵I-PM2 revealed high and retained uptake homogenously distributed throughout the tumor. In mice carrying wt p53 tumors, PM2 combined with radiotherapy significantly prolonged the median survival by 50%, whereas effects of PM2 therapy on mutant and p53 ^-/- tumors were negligible. PM2-dependent stabilization of p53 was confirmed with ex vivo immunohistochemistry. These data demonstrate the potential of the stapled peptide PM2 as a radiotherapy potentiator in vivo and suggest that clinical application of PM2 with radiotherapy in wt p53 cancers might improve tumor control.Significance: These findings contribute advances to cancer radiotherapy by using novel p53-reactivating stapled peptides as radiosensitizers in wild-type p53 cancers. Cancer Res; 78(17); 5084-93. ©2018 AACR.

Salvage TME following TEM: a possible indication for TaTME

BACKGROUND

Salvage surgery after transanal endoscopic microsurgery (TEM) has shown mixed results. Transanal total mesorectal excision (TaTME) might be advantageous in this population. The aim of this study was to assess the short-term oncologic and operative outcomes of salvage surgery after TEM, comparing TaTME to conventional salavge TME (sTME).

METHODS

Consecutive patients treated with salvage surgery after TEM were identified. Patients who underwent TaTME were compared to those who had conventional sTME. The primary outcome was the ability to perform an appropriate oncologic procedure defined by a composite outcome (negative distal margins, negative radial margins and complete or near complete mesorectum specimen).

RESULTS

During the study period, 41 patients had salvage surgery after TEM. Of those, 11 patients had TaTME while 30 patients had sTME. All patients in the TaTME group met the composite outcome of appropriate oncologic procedure compared to 76.7% for the conventional sTME group (p = 0.19). TaTME was associated with significantly higher rates of sphincter preservation (100 vs. 50%, p = 0.01), higher rates of laparoscopic surgery (100 vs. 23.3%, p < 0.001) and lower rates of conversion to open surgery (9.1 vs. 57%, p < 0.001). No difference was found in postoperative morbidity (36.3 vs. 36.7%, p = 0.77).

CONCLUSIONS

The present study demonstrates that for patients requiring salvage surgery after TEM, TaTME is associated with significantly higher rates of sphincter-sparing surgery when compared to conventional transabdominal TME while producing adequate short-term oncologic outcomes. Salvage surgery after TEM might be a clear indication for TaTME rather than conventional surgery.

Macrocyclic α helical peptide therapeutic modality: A perspective of learnings and challenges

Macrocyclic α-helical peptides have emerged as a compelling new therapeutic modality to tackle targets confined to the intracellular compartment. Within the scope of hydrocarbon-stapling there has been significant progress to date, including the first stapled α-helical peptide to enter into clinical trials. The principal design concept of stapled α-helical peptides is to mimic a cognate (protein) ligand relative to binding its target via an α-helical interface. However, it was the proclivity of such stapled α-helical peptides to exhibit cell permeability and proteolytic stability that underscored their promise as unique macrocyclic peptide drugs for intracellular targets. This perspective highlights key learnings as well as challenges in basic research with respect to structure-based design, innovative chemistry, cell permeability and proteolytic stability that are essential to fulfill the promise of stapled α-helical peptide drug development.

Proteome changes in the aging Drosophila melanogaster head

A combination of liquid chromatography, ion mobility spectrometry, mass spectrometry, and database searching techniques were used to characterize the proteomes of four biological replicates of adult Drosophila melanogaster heads at seven time points across their lifespans. Based on the detection of tryptic peptides, the identities of 1281 proteins were determined. An estimate of the abundance of each protein, based on the three most intense peptide ions, shows that the quantified species vary in concentration over a factor of ~10³. Compared to initial studies in the field of Drosophila proteomics, our current results show an eight-fold higher temporal protein coverage with increased quantitative accuracy. Across the lifespan, we observe a range of trends in the abundance of different proteins, including: an increase in abundance of proteins involved in oxidative phosphorylation, and the tricarboxylic acid cycle; a decrease in proteasomal proteins, as well as ribosomal proteins; and, many types of proteins, which remain relatively unchanged. For younger flies, proteomes are relatively similar within their age group. For older flies, proteome similarity decreases within their age group. These combined results illustrate a correlation between increasing age and decreasing proteostasis.

Structure-activity studies of Mdm2/Mdm4-binding stapled peptides comprising non-natural amino acids

As primary p53 antagonists, Mdm2 and the closely related Mdm4 are relevant cancer therapeutic targets. We have previously described a series of cell-permeable stapled peptides that bind to Mdm2 with high affinity, resulting in activation of the p53 tumour suppressor. Within this series, highest affinity was obtained by modification of an obligate tryptophan residue to the non-natural L-6-chlorotryptophan. To understand the structural basis for improved affinity we have solved the crystal structure of this stapled peptide (M011) bound to Mdm2 (residues 6–125) at 1.66 Å resolution. Surprisingly, near identity to the structure of a related peptide (M06) without the 6-chloro modification is observed. Further analysis of linear and stapled peptides comprising 6-Me-tryptophan provides mechanistic insight into dual Mdm2/Mdm4 antagonism and confirms L98 of Mdm4 as a mutable steric gate. The results also highlight a possible role of the flexible hinge region in determining Mdm2/Mdm4 plasticity.

Species traits and connectivity constrain stochastic community re-assembly

All communities may re-assemble after disturbance. Predictions for re-assembly outcomes are, however, rare. Here we model how fish communities in an extremely variable Australian desert river re-assemble following episodic floods and drying. We apply information entropy to quantify variability in re-assembly and the dichotomy between stochastic and deterministic community states. Species traits were the prime driver of community state: poor oxygen tolerance, low dispersal ability, and high fecundity constrain variation in re-assembly, shifting assemblages towards more stochastic states. In contrast, greater connectivity, while less influential than the measured traits, results in more deterministic states. Ecology has long recognised both the stochastic nature of some re-assembly trajectories and the role of evolutionary and bio-geographic processes. Our models explicitly test the addition of species traits and landscape linkages to improve predictions of community re-assembly, and will be useful in a range of different ecosystems.

Tracing the influence of land-use change on water quality and coral reefs using a Bayesian model

Coastal ecosystems can be degraded by poor water quality. Tracing the causes of poor water quality back to land-use change is necessary to target catchment management for coastal zone management. However, existing models for tracing the sources of pollution require extensive data-sets which are not available for many of the world’s coral reef regions that may have severe water quality issues. Here we develop a hierarchical Bayesian model that uses freely available satellite data to infer the connection between land-uses in catchments and water clarity in coastal oceans. We apply the model to estimate the influence of land-use change on water clarity in Fiji. We tested the model’s predictions against underwater surveys, finding that predictions of poor water quality are consistent with observations of high siltation and low coverage of sediment-sensitive coral genera. The model thus provides a means to link land-use change to declines in coastal water quality.

Managing consequences of climate-driven species redistribution requires integration of ecology, conservation and social science

Climate change is driving a pervasive global redistribution of the planet's species. Species redistribution poses new questions for the study of ecosystems, conservation science and human societies that require a coordinated and integrated approach. Here we review recent progress, key gaps and strategic directions in this nascent research area, emphasising emerging themes in species redistribution biology, the importance of understanding underlying drivers and the need to anticipate novel outcomes of changes in species ranges. We highlight that species redistribution has manifest implications across multiple temporal and spatial scales and from genes to ecosystems. Understanding range shifts from ecological, physiological, genetic and biogeographical perspectives is essential for informing changing paradigms in conservation science and for designing conservation strategies that incorporate changing population connectivity and advance adaptation to climate change. Species redistributions present challenges for human well-being, environmental management and sustainable development. By synthesising recent approaches, theories and tools, our review establishes an interdisciplinary foundation for the development of future research on species redistribution. Specifically, we demonstrate how ecological, conservation and social research on species redistribution can best be achieved by working across disciplinary boundaries to develop and implement solutions to climate change challenges. Future studies should therefore integrate existing and complementary scientific frameworks while incorporating social science and human-centred approaches. Finally, we emphasise that the best science will not be useful unless more scientists engage with managers, policy makers and the public to develop responsible and socially acceptable options for the global challenges arising from species redistributions.

Interactions among ecosystem stressors and their importance in conservation

Interactions between multiple ecosystem stressors are expected to jeopardize biological processes, functions and biodiversity. The scientific community has declared stressor interactions-notably synergies-a key issue for conservation and management. Here, we review ecological literature over the past four decades to evaluate trends in the reporting of ecological interactions (synergies, antagonisms and additive effects) and highlight the implications and importance to conservation. Despite increasing popularity, and ever-finer terminologies, we find that synergies are (still) not the most prevalent type of interaction, and that conservation practitioners need to appreciate and manage for all interaction outcomes, including antagonistic and additive effects. However, it will not be possible to identify the effect of every interaction on every organism's physiology and every ecosystem function because the number of stressors, and their potential interactions, are growing rapidly. Predicting the type of interactions may be possible in the near-future, using meta-analyses, conservation-oriented experiments and adaptive monitoring. Pending a general framework for predicting interactions, conservation management should enact interventions that are robust to uncertainty in interaction type and that continue to bolster biological resilience in a stressful world.

Water-Bridge Mediates Recognition of mRNA Cap in eIF4E

Ligand binding pockets in proteins contain water molecules, which play important roles in modulating protein-ligand interactions. Available crystallographic data for the 5' mRNA cap-binding pocket of the translation initiation factor protein eIF4E shows several structurally conserved waters, which also persist in molecular dynamics simulations. These waters engage an intricate hydrogen-bond network between the cap and protein. Two crystallographic waters in the cleft of the pocket show a high degree of conservation and bridge two residues, which are part of an evolutionarily conserved scaffold. This appears to be a preformed recognition module for the cap with the two structural waters facilitating an efficient interaction. This is also recapitulated in a new crystal structure of the apo protein. These findings open new windows for the design and screening of compounds targeting eIF4E.

Benzene Probes in Molecular Dynamics Simulations Reveal Novel Binding Sites for Ligand Design

Protein flexibility poses a major challenge in binding site identification. Several computational pocket detection methods that utilize small-molecule probes in molecular dynamics (MD) simulations have been developed to address this issue. Although they have proven hugely successful at reproducing experimental structural data, their ability to predict new binding sites that are yet to be identified and characterized has not been demonstrated. Here, we report the use of benzenes as probe molecules in ligand-mapping MD (LMMD) simulations to predict the existence of two novel binding sites on the surface of the oncoprotein MDM2. One of them was serendipitously confirmed by biophysical assays and X-ray crystallography to be important for the binding of a new family of hydrocarbon stapled peptides that were specifically designed to target the other putative site. These results highlight the predictive power of LMMD and suggest that predictions derived from LMMD simulations can serve as a reliable basis for the identification of novel ligand binding sites in structure-based drug design.