Molecular Recognition of Tyrosine-Containing Polypeptides with Pseudopeptidic Cages Unraveled by Fluorescence and NMR Spectroscopies.

The molecular recognition of Tyr-containing peptide copolymers with pseudopeptidic cages has been studied using a combination of fluorescence and NMR spectroscopies. Fluorescence titrations rendered a reasonable estimation of the affinities, despite the presence of dynamic quenching masking the unambiguous detection of the supramolecular complexes. Regarding NMR, the effect of polypeptide (PP) binding on relaxation and diffusion parameters of the cages is much more reliable than the corresponding chemical shift perturbations. To that, purification of the commercial PPs is mandatory to obtain biopolymers with lower polydispersity. Thus, the relaxation/diffusion-filtered 1H spectra of the cages in the absence vs presence of the PPs represent a suitable setup for the fast detection of the noncovalent interactions. Additional key intermolecular NOE cross-peaks supported by molecular models allow the proposal of a structure of the supramolecular species, stabilized by the Tyr encapsulation within the cage cavity and additional attractive polar interactions between the side chains of cage and PP, thus defining a binding epitope with a potential for implementing sequence selectivity. Accordingly, the cages bearing positive/negative residues prefer to bind the peptides having complementary negative/positive side chains close to the target Tyr, suggesting an electrostatic contribution to the interaction. Overall, our results show that both techniques represent a powerful and complementary combination for studying cage-to-PP molecular recognition processes.

A Degenerate Metal-Templated Catalytic System with Redundant Functional Groups for the Asymmetric Aldol Reaction.

A degenerate zinc-templated catalytic system containing two bipyridine ligands with redundant functional groups for either enamine or hydrogen bond formation was applied to the asymmetric aldol reaction. This concept led to both a higher probability of reaction and rate acceleration. Thus, the catalyst loading could be decreased to a remarkable 2 mol % in what we think is a general approach.

Pseudopeptidic host adaptation in peptide recognition unveiled by ion mobility mass spectrometry.

Complexation of the glutamic-tyrosine-glutamic tripeptide (EYE) with a series of pseudopeptidic cages has been thoroughly investigated using different analytical techniques. The stoichiometry and affinities of the supramolecular host : guest complexes both in aqueous solution and in the gas-phase were obtained from a suitable combination of fluorescence spectroscopy, NMR, and mass spectrometry (MS) methods. The cages bearing basic groups (lysine, ornitine and histidine) display the tightest EYE binding in aqueous media following the order CyHis > CyLys > CyOrn, thus suggesting that Tyr side chain encapsulation is additionally modulated by the identity of the cage side chains and their ability to be engaged in polar interactions with the EYE peptide. Similarly, binding affinities estimated by MS methods clearly point towards a reduced affinity for the Cy cages with acidic pendant groups and a higher affinity of the CyHis cage over CyLys and CyOrn. Ion mobility spectrometry (IMS)-MS, assisted by molecular modelling, has been used to uncover the structural and conformational characteristics of the pseudopeptidic hosts and their supramolecular adducts with the EYE peptide. The cages display a collisional cross-section increase upon EYE inclusion that is associated with the expansion of the binding pocket of the cage cavity, thus constituting a unique example of conformational pseudopeptidic host adaptation to accommodate the inclusion of the guest.

An autonomous chemically fuelled small-molecule motor.

Molecular machines are among the most complex of all functional molecules and lie at the heart of nearly every biological process. A number of synthetic small-molecule machines have been developed, including molecular muscles, synthesizers, pumps, walkers, transporters and light-driven and electrically driven rotary motors. However, although biological molecular motors are powered by chemical gradients or the hydrolysis of adenosine triphosphate (ATP), so far there are no synthetic small-molecule motors that can operate autonomously using chemical energy (that is, the components move with net directionality as long as a chemical fuel is present). Here we describe a system in which a small molecular ring (macrocycle) is continuously transported directionally around a cyclic molecular track when powered by irreversible reactions of a chemical fuel, 9-fluorenylmethoxycarbonyl chloride. Key to the design is that the rate of reaction of this fuel with reactive sites on the cyclic track is faster when the macrocycle is far from the reactive site than when it is near to it. We find that a bulky pyridine-based catalyst promotes carbonate-forming reactions that ratchet the displacement of the macrocycle away from the reactive sites on the track. Under reaction conditions where both attachment and cleavage of the 9-fluorenylmethoxycarbonyl groups occur through different processes, and the cleavage reaction occurs at a rate independent of macrocycle location, net directional rotation of the molecular motor continues for as long as unreacted fuel remains. We anticipate that autonomous chemically fuelled molecular motors will find application as engines in molecular nanotechnology.

Evaluation of water-assisted UV-C light and its additive effect with peracetic acid for the inactivation of Listeria monocytogenes, Salmonella enterica and murine norovirus on whole and fresh-cut strawberries during shelf-life.

BACKGROUND: The purpose of the present study was to examine the inactivation of Salmonella enterica (50 µL; 109 CFU g-1 ), Listeria monocytogenes (50 µL; 109 CFU g-1 ), and murine norovirus (MNV-1; 50 µL; 107 50% tissue culture infectious dose (TCID50 ) mL-1 ) on whole and fresh-cut strawberries after 2 min disinfection treatments (water (H2 O), chlorine 200 mg L-1 (NaClO), water-assisted ultraviolet-C (UV-C) (WUV), and the combination WUV and 40 mg L-1 of PA (WUV + PA)) in a water tank (15 L) equipped with 4 UV-C lamps (17.2 W each), and after 7 days of cold storage (4 and 10 °C). For MNV-1, dry UV-C treatment (DUV) was also tested. For all UV-C treatments, an irradiation dose of 1.3 kJ m-2 was used. RESULTS: When strawberries were washed with WUV, L. monocytogenes and S. enterica were reduced by 2.8 and 2.2 log CFU g-1 , respectively. The addition of 40 mg L-1 of PA to WUV (WUV + PA) increased the reduction range of L. monocytogenes and S. enterica by 1.9 and 0.8 log, respectively. Regarding the wash water, no pathogens were recovered after the WUV + PA treatment (detection limit 50 CFU mL-1 ). Depending on storage conditions (7 days at 4 or 10 °C), reductions observed were 0.5 to 2.0 log for S. enterica and 0.5 to 3.0 log for L. monocytogenes. The reductions in MNV-1 titer after disinfection treatments ranged from 1.3 to 1.7 log. No significant differences between storage conditions were observed for MNV-1: titers did not decline or were reduced up to 0.3 log after 7 days of cold storage. CONCLUSION: The three-way action for disinfecting strawberries by UV-C irradiation and PA, plus the physical removal of the microorganisms by agitated water, are effective against foodborne pathogens on strawberries and water wash. During storage, WUV had a larger impact on the inactivation kinetics of S. enterica. Storage had little impact on MNV-1 inactivation. © 2022 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Modulation of Src Kinase Activity by Selective Substrate Recognition with Pseudopeptidic Cages.

The selective recognition of tyrosine residues in peptides is an appealing approach to inhibiting their tyrosine kinase (TK)-mediated phosphorylation. Herein, we describe pseudopeptidic cages that efficiently protect substrates from the action of the Src TK enzyme, precluding the corresponding Tyr phosphorylation. Fluorescence emission titrations show that the most efficient cage inhibitors strongly bind the peptide substrates with a very good correlation between the binding constant and the inhibitory potency. Structural insights and additional control experiments further support the proposed mechanism of selective supramolecular protection of the substrates. Moreover, the approach also works in a completely different kinase-substrate system. These results illustrate the potential of supramolecular complexes for the efficient and selective modulation of TK signaling.

Molecular cages for biological applications.

Artificial receptors able to recognise biologically relevant molecules or ions have gained interest in the chemical community because they offer a plethora of posibilities. Molecular cage compounds are polycyclic compounds with a cavity designed for the encapsulation of guest species. Once inside the host cavity, the substrate can be transported through membranes and protected from the action of enzymes or other reactive species, thus offering the possibility of interfering with biological systems. Commonly, enzymes have been an inspiration for chemists in the search and design of defined cavities for different purposes. However, the chemical preparation of molecular cages has struggled with many synthetic challenges but this effort is worthwhile as they are a very promising tool for many applications ranging from sensing, delivery, purification or even promotion of/prevention from chemical modifications. Since the early reports at the end of the 60s, this field has experienced a growing interest; this review summarises the progress in the preparation and study of cage-like compounds highlighting their importance in biological applications.

Introducing ergonomics requirements in the eco-design of energy-related products from users' behaviour approach.

Ergonomics has been a very important activity in the design process. However, ergonomics rarely includes the environmental requirements into the design of products. The article proposes and presents the Eco-Ergo model through its application to a real-world product, a washing machine, to allow designers and ergonomists to establish product design requirements in order to minimise environmental impacts related to user-product interaction during the use stage. This model uses a visual language of representation, Blueprinting-based, that helps designers explore problems they have not previously considered during the market research when a wide variety of products with different interaction elements is analysed. The application of this model allows direct efforts and attention on the user analysis phase in the most influential user's actions on the environmental performance of energy-related products during use, establishing ergonomics requirements related to users behaviour at the initial design phase. Practitioner summary: This study provides a proposal to incorporate ergonomics into the practice of eco-design through the use of human factors in the establishment of initial eco-design requirements. This blueprint-based model combines an empirical and theoretical approach, based on the product test developed by designers, ergonomists and environmentalists. Abbreviations: CO2: carbon dioxide; DBIM: design behaviour intervention model; DfSB: design for sustainable behaviour; DwI Method: design with intent method; LCA: life cycle assessment; LCD: liquid cristal display; MJ: megajoule; MTM: methods-time measurement; PSS: product-service system; RPM: revolutions per minute.

pH-Dependent Chloride Transport by Pseudopeptidic Cages for the Selective Killing of Cancer Cells in Acidic Microenvironments.

Acidic microenvironments in solid tumors are a hallmark of cancer. Inspired by that, we designed a family of pseudopeptidic cage-like anionophores displaying pH-dependent activity. When protonated, they efficiently bind chloride anions. They also transport chloride through lipid bilayers, with their anionophoric properties improving at acidic pH, suggesting an H+ /Cl- symport mechanism. NMR studies in DPC micelles demonstrate that the cages bind chloride within the lipid phase. The chloride affinity and the chloride-exchange rate with the aqueous bulk solution are improved when the pH is lowered. This increases cytotoxicity towards lung adenocarcinoma cells at the pH of the microenvironment of a solid tumor. These properties depend on the nature of the amino-acid side chains of the cages, which modulate their lipophilicity and interactions with the cell membrane. This paves the way towards using pH as a parameter to control the selectivity of cytotoxic ionophores as anticancer drugs.

A Dynamic Chemical Network for Cystinuria Diagnosis.

The study of molecular networks represents a conceptual revolution in chemistry. Building on previous knowledge and after understanding the rules of non-covalent interactions, the design of stimulus-responsive chemical systems is possible. Herein we report a new strategy, based on the reorganization of a dynamic chemical network that generates new fluorescent associations in the presence of cysteine or cystine. The binding and sensing units are encoded in the components that dynamically assemble and disassemble responding to external stimuli as a successful tool to detect both cysteine and cystine in aqueous media. Moreover, the dynamic sensing system works in human urine, as a prospective application for cystinuria diagnosis.

Unraveling the Multistimuli Responses of a Complex Dynamic System of Pseudopeptidic Macrocycles.

Dynamic combinatorial libraries (DCLs) are excellent benchmark models to study the stimuli-responsiveness of chemical networks. However, increasingly complex systems are difficult to analyze with simple data analysis methods, because many variables and connections must be considered for their full understanding. Here we propose the use of multivariate data analysis methods to bisect the evolution of a complex synthetic dynamic library of pseudopeptidic macrocycles, containing side chains with charges of different sign. Several stimuli (ionic strength, pH and the presence of a biogenic polyamine) were applied to the same dynamic chemical mixture, and the adaptation of the whole system was characterized by HPLC and analyzed with principal component analysis (PCA) and multivariate curve resolution-alternating least squares (MCR-ALS) methods. Both multivariate data analysis chemometric approaches are an excellent combination to extract both qualitative and semi-quantitative information about the adaptive process of the library upon the action of each stimulus. The resolution of the system with these chemometric tools proved to be especially useful when two inter-connected stimuli were combined in the same dynamic system. Our results demonstrate the utility of these two approaches for the analysis of complex dynamic chemical systems and open the way toward the application of these powerful tools in the emergent field of systems chemistry.

A copper-templated, bifunctional organocatalyst: a strongly cooperative dynamic system for the aldol reaction.

The study of novel metal-templated dynamic organocatalytic systems has led to the identification of CuSO4 as the most efficient template to assemble monofunctional prolinamide- and thiourea-modified pyridine ligands. The structural and electronic requirements to assemble an efficient catalyst have been disclosed: both pyridine ligands must bear a 1,3-substitution pattern, and the thiourea ligand serves as a reducing agent to copper(i) as well. Eventually, the cooperative effects achieved with such a simple system deliver high reaction rates and stereoselectivities at room temperature in the asymmetric aldol reaction, requiring only 1 mol% of copper salt.

Pseudopeptidic compounds for the generation of dynamic combinatorial libraries of chemically diverse macrocycles in aqueous media.

A straightforward four-step synthesis leads to the preparation of C2-symmetric dithiols containing a central aromatic core and amino acid side chains. These building blocks allow the preparation of dynamic covalent libraries of pseudopeptidic macrocycles in aqueous media that cover a broad range of polarities, functional groups and bulkiness mirroring the diversity found in natural peptides. The versatility of the generated dynamic libraries has been illustrated by the amplification of two different members from the same library upon the action of two biologically relevant templates.

Adaptive Correction from Virtually Complex Dynamic Libraries: The Role of Noncovalent Interactions in Structural Selection and Folding.

The hierarchical self-assembling of complex molecular systems is dictated by the chemical and structural information stored in their components. This information can be expressed through an adaptive process that determines the structurally fittest assembly under given environmental conditions. We have set up complex disulfide-based dynamic covalent libraries of chemically and topologically diverse pseudopeptidic compounds. We show how the reaction evolves from very complex mixtures at short reaction times to the almost exclusive formation of a major compound, through the establishment of intramolecular noncovalent interactions. Our experiments demonstrate that the systems evolve through error-check and error-correction processes. The nature of these interactions, the importance of the folding and the effects of the environment are also discussed.

Conformational promiscuity in triazolamers derived from quaternary amino acids mimics peptide behaviour.

1,4-Substituted triazole oligomers made from quaternary amino acid derivatives present a conformational behaviour with similarities to that of natural peptides. Twisted strand and zig-zag type conformations have both been obtained in the crystal state. In a solution signs of weakly ordered structures have been detected depending on the substituents and the solvents used.

Engineering the structure of an N-terminal ß-turn to maximize screw-sense preference in achiral helical peptide chains.

Oligomers of α-aminoisobutyric acid (Aib) are achiral peptides that typically adopt 310 helical conformations in which enantiomeric left- and right-handed conformers are, necessarily, equally populated. Incorporating a single protected chiral residue at the N-terminus of the peptide leads to induction of a screw-sense preference in the helical chain, which may be quantified (in the form of "helical excess") by NMR spectroscopy. Variation of this residue and its N-terminal protecting group leads to the conclusion that maximal levels of screw-sense preference are induced by bulky chiral tertiary amino acids carrying amide protecting groups or by chiral quaternary amino acids carrying carbamate protecting groups. Tertiary L-amino acids at the N-terminus of the oligomer induce a left-handed screw sense, while quaternary L-amino acids induce a right-handed screw sense. A screw-sense preference may also be induced from the second position of the chain, weakly by tertiary amino acids, and much more powerfully by quaternary amino acids. In this position, the L enantiomers of both families induce a right-handed screw sense. Maximal, and essentially quantitative, control is induced by an L-α-methylvaline residue at both positions 1 and 2 of the chain, carrying an N-terminal carbamate protecting group.

Foldamer-mediated remote stereocontrol: >1,60 asymmetric induction.

An N-terminal L-α-methylvaline dimer induces complete conformational control over the screw sense of an otherwise achiral helical peptide foldamer formed from the achiral quaternary amino acids Aib and Ac6 c. The persistent right-handed screw-sense preference of the helix enables remote reactive sites to fall under the influence of the terminal chiral residues, and permits diastereoselective reactions such as alkene hydrogenation or iminium ion addition to take place with 1,16-, 1,31-, 1,46- and even 1,61-asymmetric induction. Stereochemical information may be communicated in this way over distances of up to 4 nm.

Selection of a Probiotic for Its Potential for Developing a Synbiotic Peach and Grape Juice.

Due to recent interest in the potential of probiotics as health promoters and the impact of health and environmental concerns on eating habits, non-dairy probiotic food products are required. This study aimed to evaluate the viability of different probiotic microorganisms in peach and grape juice (PGJ) with or without the prebiotic inulin and their antimicrobial activity against the foodborne pathogen Listeria monocytogenes and the juice spoilage microorganism Saccharomyces cerevisiae. Firstly, the viability of seven probiotic strains was studied in PGJ with an initial concentration of 107 CFU/mL for 21 days at 4 °C and for 3 days at 37 °C. In parallel, the physicochemical effect, the antimicrobial effect and the lactic acid production in PGJ were evaluated. Secondly, the probiotic with the best viability results was selected to study its antimicrobial effect against L. monocytogenes and S. cerevisiae, as well as ethanol and acetaldehyde production by the latter. L. casei showed the highest viability and grew in both refrigerated and fermentation conditions (1 log), produced the greatest lactic acid (5.12 g/L) and demonstrated in vitro anti-Listeria activity. Although the addition of the prebiotic did not improve the viability, lactic acid production or anti-Listeria activity of the probiotics, under the conditions studied, the prebiotic potential of inulin, support the design of a synbiotic juice. Finally, although none of the probiotic, fermentation products, or postbiotics showed any antimicrobial activity against L. monocytogenes or S. cerevisiae, the addition of L. casei to the PGJ significantly reduced the production of S. cerevisiae metabolite ethanol (29%) and acetaldehyde (50%). L. casei might be a suitable probiotic to deliver a safe and functional PGJ, although further research should be carried out to determine the effect of the probiotic and fermentation on the nutritional profile of PGJ.

Environmental analysis of the logistics of agricultural products from roof top greenhouses in Mediterranean urban areas.

BACKGROUND: As urban populations increase so does the amount of food transported to cities worldwide, and innovative agro-urban systems are being developed to integrate agricultural production into buildings; for example, by using roof top greenhouses (RTGs). This paper aims to quantify and compare, through a life cycle assessment, the environmental impact of the current linear supply system with a RTG system by using a case study for the production of tomatoes. RESULTS: The main results indicate that a change from the current linear system to the RTG system could result in a reduction, per kilogram of tomatoes (the functional unit), in the range of 44.4-75.5% for the different impact categories analysed, and savings of up to 73.5% in energy requirements. These savings are associated with re-utilisation of packaging systems (55.4-85.2%), minimisation of transport requirements (7.6-15.6%) and reduction of the loss of product during transportation and retail stages (7.3-37%). CONCLUSIONS: The RTG may become a strategic factor in the design of low-carbon cities in Mediterranean areas. Short-term implementation in the city of Barcelona could result in savings of 66.1 tonnes of CO2 eq. ha(-1) when considering the global warming potential, and of 71.03 t ha(-1) when considering that the transformation from woodland to agricultural land is avoided.

Exploring the Nutritional Potential of Microalgae in the Formulation of Bakery Products.

Microalgae have positioned themselves as an innovative and sustainable source of bioactive compounds and high nutritional value. The selection of a suitable food carrier is important to ease its consumption, and to preserve bioactivity through food processing. The aim of this study was to assess the suitability of different microalgae in baked products. Crackers and grissini were produced following a specific formulation, with percentages ranging from 1.5 to 3.5% of flour substituted with Spirulina, Chlorella, and Tetraselmis dry biomass in the formulas. Physico-chemical, nutritional, and sensorial characterization was carried out. The incorporation of microalgae led to increased nutritional values, including antioxidant capacity (AOX), total phenolic content (TPC) and protein content with an amino acids' identification and quantification. Grissini with Chlorella at 3.5% and crackers with Spirulina at 1.5% levels, showed a higher overall acceptance within the panelists. For amino acid content, Spirulina crackers were shown to be rich in alanine, aspartate, and tryptophan, while Chlorella grissini stood out for being particularly rich in isoleucine, leucine, lysine, and valine. Thus, Spirulina and Chlorella could be a sustainable ingredient to formulate baked goods with an enhanced nutrimental matrix without altering their acceptability to consumers.