Drug Repositioning as a Therapeutic Strategy against Streptococcus pneumoniae: Cell Membrane as Potential Target.

A collection of repurposing drugs (Prestwick Chemical Library) containing 1200 compounds was screened to investigate the drugs' antimicrobial effects against planktonic cultures of the respiratory pathogen Streptococcus pneumoniae. After four discrimination rounds, a set of seven compounds was finally selected, namely (i) clofilium tosylate; (ii) vanoxerine; (iii) mitoxantrone dihydrochloride; (iv) amiodarone hydrochloride; (v) tamoxifen citrate; (vi) terfenadine; and (vii) clomiphene citrate (Z, E). These molecules arrested pneumococcal growth in a liquid medium and induced a decrease in bacterial viability between 90.0% and 99.9% at 25 µM concentration, with minimal inhibitory concentrations (MICs) also in the micromolar range. Moreover, all compounds but mitoxantrone caused a remarkable increase in the permeability of the bacterial membrane and share a common, minimal chemical structure consisting of an aliphatic amine linked to a phenyl moiety via a short carbon/oxygen linker. These results open new possibilities to tackle pneumococcal disease through drug repositioning and provide clues for the design of novel membrane-targeted antimicrobials with a related chemical structure.

Driving the Active Site Incorporation in Zeolitic Materials via the Organic Structure-Directing Agent Through Development of H-Bonds with Hydroxyl Groups.

(1S,2S)-N-methyl-pseudoephedrine (MPS) was used as organic structure-directing agent (OSDA) for the synthesis of Mg-doped nanoporous aluminophosphates. This molecule displays a particular conformational behavior, where the presence of H-bond donor and acceptor groups provide a rigid conformational space with one asymmetric conformation preferentially occurring. MPS drives the crystallization of Mg-containing AFI materials. Characterization of these materials shows that the OSDA incorporate as protonated species, arranged as head-to-tail monomers. Combination of three-dimensional electron diffraction with high-resolution synchrotron powder X-ray diffraction allowed to locate both the Mg and the organic species. Interestingly, results showed that the spatial incorporation of Mg is driven by the hydroxyl groups of the organic cation through the development of H-bonds with negatively-charged MgO4 tetrahedra. This work demonstrates that H-bond forming groups can be used to drive the spatial incorporation of low-valent dopants within zeolitic frameworks, a highly desired aim in order to control their catalytic activity and selectivity.

GTM-3, an Extra-Large Pore Enantioselective Chiral Zeolitic Catalyst.

The development of chiral zeolitic catalysts possessing extra-large pores and endowed with the capability of enantioselectively processing bulky products represents one of the greatest challenges in chemistry. Here, we report the discovery of GTM-3, an enantio-enriched extra-large pore chiral zeolite material with -ITV framework structure, obtained using a simple enantiopure organic cation derived from the chiral pool, N,N-ethyl-methyl-pseudoephedrinium, as the chiral-inductor agent. We demonstrate the enantio-enrichment of GTM-3 in one of the two enantiomorphic polymorphs using the two enantiomers of the organic cation. Interestingly, we prove the ability of this zeolitic material to perform enantioselective catalytic operations with very large substrates, here exemplified by the catalytic epoxide aperture of the bulky trans-stilbene oxide with alcohols, yielding unprecedented product enantiomeric excesses up to 30%. Our discovery opens the way for the use of accessible chiral zeolitic materials for the catalytic asymmetric synthesis of chiral pharmaceutical compounds.

A combination of proton spin diffusion NMR and molecular simulations to probe supramolecular assemblies of organic molecules in nanoporous materials.

In this work we show the use of high-resolution 1H MAS NMR to distinguish between two kinds of aggregation states of (1R,2S)-ephedrine, a chiral organic structure directing agent, occluded within AFI-type microporous aluminophosphates. We investigate in particular the supramolecular assembly of the molecules through π⋯π type interactions of their aromatic rings when confined within the one-dimensional AFI channels. A series of high-resolution two-dimensional spin diffusion spectra combined with molecular simulations and DFT calculations allowed us to distinguish different aggregation states of ephedrine molecules and precisely estimate the distances between the aromatic rings and their closest protons inside the zeolite channels as a consequence of distinct proton spin diffusion profiles.

Choline-Functionalized Supramolecular Copolymers: Toward Antimicrobial Activity against Streptococcus pneumoniae.

Dynamic binding events are key to arrive at functionality in nature, and these events are often governed by electrostatic or hydrophobic interactions. Synthetic supramolecular polymers are promising candidates to obtain biomaterials that mimic this dynamicity. Here, we created four new functional monomers based on the benzene-1,3,5-tricarboxamide (BTA) motif. Choline or atropine groups were introduced to obtain functional monomers capable of competing with the cell wall of Streptococcus pneumoniae for binding of essential choline-binding proteins (CBPs). Atropine-functionalized monomers BTA-Atr and BTA-Atr3 were too hydrophobic to form homogeneous assemblies, while choline-functionalized monomers BTA-Chol and BTA-Chol3 were unable to form fibers due to charge repulsion. However, copolymerization of BTA-Chol3 with non-functionalized BTA-(OH)3 yielded dynamic fibers, similar to BTA-(OH)3. These copolymers showed an increased affinity toward CBPs compared to free choline due to multivalent effects. BTA-based supramolecular copolymers are therefore a versatile platform to design bioactive and dynamic supramolecular polymers with novel biotechnological properties.

Inter-hairpin linker sequences determine the structure of the ßß-solenoid fold: a "bottom-up" study of pneumococcal LytA choline-binding module.

The ßß-solenoid structures are part of many proteins involved in the recognition of bacterial cell wall. They are elongated polypeptides consisting of repeated ß-hairpins connected by linker sequences and disposed around a superhelical axis stabilised by short-range interactions. Among the most studied ßß-solenoids are those belonging to the family of choline-binding modules (CBMs) from the respiratory pathogen Streptococcus pneumoniae (pneumococcus) and its bacteriophages, and their properties have been employed to develop several biotechnological and biomedical tools. We have carried out a theoretical, spectroscopic and thermodynamic study of the ßß-solenoid structure of the CBM from the pneumococcal LytA autolysin using peptides of increasing length containing 1-3 repeats of this structure. Our results show that hints of native-like tertiary structure are only observed with a minimum of three ß-hairpins, corresponding to one turn of the solenoid superhelix, and identify the linker sequences between hairpins as the major directors of the solenoid folding. This study paves the way for the rational structural engineering of ßß-solenoids aimed to find novel applications.

From Residues to Added-Value Bacterial Biopolymers as Nanomaterials for Biomedical Applications.

Bacterial biopolymers are naturally occurring materials comprising a wide range of molecules with diverse chemical structures that can be produced from renewable sources following the principles of the circular economy. Over the last decades, they have gained substantial interest in the biomedical field as drug nanocarriers, implantable material coatings, and tissue-regeneration scaffolds or membranes due to their inherent biocompatibility, biodegradability into nonhazardous disintegration products, and their mechanical properties, which are similar to those of human tissues. The present review focuses upon three technologically advanced bacterial biopolymers, namely, bacterial cellulose (BC), polyhydroxyalkanoates (PHA), and γ-polyglutamic acid (PGA), as models of different carbon-backbone structures (polysaccharides, polyesters, and polyamides) produced by bacteria that are suitable for biomedical applications in nanoscale systems. This selection models evidence of the wide versatility of microorganisms to generate biopolymers by diverse metabolic strategies. We highlight the suitability for applied sustainable bioprocesses for the production of BC, PHA, and PGA based on renewable carbon sources and the singularity of each process driven by bacterial machinery. The inherent properties of each polymer can be fine-tuned by means of chemical and biotechnological approaches, such as metabolic engineering and peptide functionalization, to further expand their structural diversity and their applicability as nanomaterials in biomedicine.

Dissecting the Polyhydroxyalkanoate-Binding Domain of the PhaF Phasin: Rational Design of a Minimized Affinity Tag.

Phasin PhaF from Pseudomonas putida consists of a modular protein whose N-terminal domain (BioF) has been demonstrated to be responsible for binding to the polyhydroxyalkanoate (PHA) granule. BioF has been exploited for biotechnological purposes as an affinity tag in the functionalization of PHA beads with fusion proteins both in vivo and in vitro The structural model of this domain suggests an amphipathic α-helical conformation with the hydrophobic residues facing the PHA granule. In this work, we analyzed the mean hydrophobicity and the hydrophobic moment of the native BioF tag to rationally design shorter versions that maintain affinity for the granule. Hybrid proteins containing the green fluorescent protein (GFP) fused to the BioF derivatives were studied for in vivo localization on PHA, stability on the surface of the PHA granule against pH, temperature, and ionic strength, and their possible influence on PHA synthesis. Based on the results obtained, a minimized BioF tag for PHA functionalization has been proposed (MinP) that retains similar binding properties but possesses an attractive biotechnological potential derived from its reduced size. The MinP tag was further validated by analyzing the functionality and stability of the fusion proteins MinP-ß-galactosidase and MinP-CueO from Escherichia coliIMPORTANCE Polyhydroxyalkanoates (PHAs) are biocompatible, nontoxic, and biodegradable biopolymers with exceptional applications in the industrial and medical fields. The complex structure of the PHA granule can be exploited as a toolbox to display molecules of interest on their surface. Phasins, the most abundant group of proteins on the granule, have been employed as anchoring tags to obtain functionalized PHA beads for high-affinity bioseparation, enzyme immobilization, diagnostics, or cell targeting. Here, a shorter module based on the previously designed BioF tag has been demonstrated to maintain the affinity for the PHA granule, with higher stability and similar functionalization efficiency. The use of a 67% shorter peptide, which maintains the binding properties of the entire protein, constitutes an advantage for the immobilization of recombinant proteins on the PHA surface both in vitro and in vivo.

Searching for Antipneumococcal Targets: Choline-Binding Modules as Phagocytosis Enhancers.

Choline-binding proteins (CBPs) from Streptococcus pneumoniae comprise a family of modular polypeptides involved in essential events of this pathogen. They recognize the choline residues present in the teichoic and lipoteichoic acids of the cell wall using the so-called choline-binding modules (CBMs). The importance of CBPs in pneumococcal physiology points to them as novel targets to combat antimicrobial resistances shown by this organism. In this work we have tested the ability of exogenously added CBMs to act as CBP inhibitors by competing with the latter for the binding to the choline molecules in the bacterial surface. First, we carried out a thorough physicochemical characterization of three native CBMs, namely C-LytA, C-Cpl1, and C-CbpD, and assessed their affinity for choline and macromolecular, pneumococcal cell-wall mimics. The interaction with these substrates was evaluated by molecular modeling, analytical ultracentrifugation, surface plasmon resonance, and fluorescence and circular dichroism spectroscopies. Van't Hoff thermal analyses unveiled the existence of one noncanonical choline binding site in each of the C-Cpl1 and C-CbpD proteins, leading in total to 5 ligand-binding sites per dimer and 4 sites per monomer, respectively. Remarkably, the binding affinities of the CBMs do not directly correlate with their native oligomeric state or with the number of choline-binding sites, suggesting that choline recognition by these modules is a complex phenomenon. On the other hand, the exogenous addition of CBMs to pneumococcal planktonic cultures caused extensive cell-chaining probably as a consequence of the inhibition of CBP attachment to the cell wall. This was accompanied by bacterial aggregation and sedimentation, causing an enhancement of bacterial phagocytosis by peritoneal macrophages. In addition, the rational design of an oligomeric variant of a native CBM led to a substantial increase in its antibacterial activity by multivalency effects. These results suggest that CBMs might constitute promising nonlytic antimicrobial candidates based on the natural induction of the host defense system.

CLytA-DAAO, Free and Immobilized in Magnetic Nanoparticles, induces Cell Death in Human Cancer Cells.

D-amino acid oxidase (DAAO) catalyzes the oxidation of D-amino acids generating hydrogen peroxide, a potential producer of reactive oxygen species. In this study, we used a CLytA-DAAO chimera, both free and bound to magnetic nanoparticles, against colon carcinoma, pancreatic adenocarcinoma, and glioblastoma cell lines. We found that the enzyme induces cell death in most of the cell lines tested and its efficiency increases significantly when it is immobilized in nanoparticles. We also tested this enzyme therapy in non-tumor cells, and we found that there is not cell death induction, or it is significantly lower than in tumor cells. The mechanism triggering cell death is apparently a classical apoptosis pathway in the glioblastoma cell lines, while in colon and pancreatic carcinoma cell lines, CLytA-DAAO-induced cell death is a necrosis. Our results constitute a proof of concept that an enzymatic therapy, based on magnetic nanoparticles-delivering CLytA-DAAO, could constitute a useful therapy against cancer and besides it could be used as an enhancer of other treatments such as epigenetic therapy, radiotherapy, and treatments based on DNA repair.

Turncoat Polypeptides: We Adapt to Our Environment.

A common interpretation of Anfinsen's hypothesis states that one amino acid sequence should fold into a single, native, ordered state, or a highly similar set thereof, coinciding with the global minimum in the folding-energy landscape, which, in turn, is responsible for the function of the protein. However, this classical view is challenged by many proteins and peptide sequences, which can adopt exchangeable, significantly dissimilar conformations that even fulfill different biological roles. The similarities and differences of concepts related to these proteins, mainly chameleon sequences, metamorphic proteins, and switch peptides, which are all denoted herein "turncoat" polypeptides, are reviewed. As well as adding a twist to the conventional view of protein folding, the lack of structural definition adds clear versatility to the activity of proteins and can be used as a tool for protein design and further application in biotechnology and biomedicine.

Widening the antimicrobial spectrum of esters of bicyclic amines: In vitro effect on gram-positive Streptococcus pneumoniae and gram-negative non-typeable Haemophilus influenzae biofilms.

Antibiotic resistance is a global current threat of increasing importance. Moreover, biofilms represent a medical challenge since the inherent antibiotic resistance of their producers demands the use of high doses of antibiotics over prolonged periods. Frequently, these therapeutic measures fail, contributing to bacterial persistence, therefore demanding the development of novel antimicrobials. Esters of bicyclic amines (EBAs), which are strong inhibitors of Streptococcus pneumoniae growth, were initially designed as inhibitors of pneumococcal choline-binding proteins on the basis of their structural analogy to the choline residues in the cell wall. However, instead of mimicking the characteristic cell chaining phenotype caused by exogenously added choline on planktonic cultures of pneumococcal cells, EBAs showed an unexpected lytic activity. In this work we demonstrate that EBAs display a second, and even more important, function as cell membrane destabilizers. We then assayed the inhibitory and disintegrating activity of these molecules on pneumococcal biofilms. The selected compound (EBA 31) produced the highest effect on S. pneumoniae (encapsulated and non-encapsulated) biofilms at very low concentrations. EBA 31 was also effective on mixed biofilms of non-encapsulated S. pneumoniae plus non-typeable Haemophilus influenzae, two pathogens frequently forming a self-produced biofilm in the human nasopharynx. These results support the role of EBAs as a promising alternative for the development of novel, broad-range antimicrobial drugs encompassing both Gram-positive and Gram-negative pathogens.

Role of leucine zipper-like motifs in the oligomerization of Pseudomonas putida phasins.

BACKGROUND: Phasins are low molecular mass proteins that accumulate strongly in bacterial cells in response to the intracellular storage of polyhydroxyalkanoates (PHA). Although lacking catalytic activity, phasins are the major components of the surface of the PHA granules and could be potentially involved in the formation of a network-like protein layer surrounding the polyester inclusions. Structural models revealed phasins to possess coiled-coil regions that might be important in the establishment of protein-protein interactions. However, there is not experimental evidence of a coiled-coil mediated oligomerization in these proteins. METHODS: Structure prediction analyses were used to characterize the coiled-coil motifs of phasins PhaF and PhaI -produced by the model bacterium Pseudomonas putida KT2440-. Their oligomerization was evaluated by biolayer interferometry and the in vivo two-hybrid (BACTH) system. The interaction ability of a series of coiled-coil mutated derivatives was also measured. RESULTS: The formation of PhaF and PhaI complexes was detected. A predicted short leucine zipper-like coiled-coil (ZIP), containing "ideal" residues located within the hydrophobic core, was shown responsible for the oligomers stability. The substitution of key residues (leucines or valines) in PhaI ZIP (ZIPI) for alanine reduced by four fold the oligomerization efficiency. CONCLUSIONS: These results indicate that coiled-coil motifs are essential for phasin interactions. Correct oligomerization requires the formation of a stable hydrophobic interface between both phasins. GENERAL SIGNIFICANCE: Our findings elucidate the oligomerization motif of PhaF and PhaI. This motif is present in most phasins from PHA-accumulating bacteria and offers a potentially important target for modulating the PHA granules stability.

Comprehensive Study of the Enzymatic Catalysis of the Electrochemical Oxygen Reduction Reaction (ORR) by Immobilized Copper Efflux Oxidase (CueO) From Escherichia coli.

In recent years, enzymatic fuel cells have experienced a great development promoted by the availability of novel biological techniques that allow the access to a large number of enzymatic catalysts. One of the most important aspects in this area is the development of biocatalysts for the oxygen reduction reaction (ORR). Laccases from the group of enzymes called blue multi-cooper oxidases have received considerable attention because of their ability to catalyze the electrochemical oxygen reduction reaction to water when immobilized on metallic or carbonaceous electrode materials. In this paper we report a comprehensive study of the electrocatalytic activity of the enzyme Copper efflux oxidase (CueO) from Escherichia coli immobilized on different electrode materials. The influence of the electrode substrate employed for protein immobilization was evaluated using glassy carbon, gold or platinum electrodes. Gold and platinum electrodes were modified using different self-assembled monolayers (SAM) able to tune the electrostatic interaction between the protein and the substrate, depending on the nature of the terminal functional group in the SAM. The effects of protein immobilization time, electrode potential, solution pH and temperature, protein and O2 concentration have been carefully investigated. Finally, direct electron transfer (DET) was investigated in the presence of the following inhibitors: fluoride (F-), chloride (Cl-) and azide ( N3- ).

An enzymatic system for decolorization of wastewater dyes using immobilized CueO laccase-like multicopper oxidase on poly-3-hydroxybutyrate.

The presence of synthetic dyes in wastewaters generated by the textile industry constitutes a serious environmental and health problem that urges the scientific community on an appropriate action. As a proof-of-concept, we have developed a novel approach to design enzymatic bioreactors with the ability to decolorize dye solutions through the immobilization of the bacterial CueO laccase-like multicopper oxidase from Escherichia coli on polyhydroxybutyrate (PHB) beads by making use of the BioF affinity tag. The decolorization efficiency of the system was characterized by a series of parameters, namely maximum enzyme adsorption capacity, pH profile, kinetic constants, substrate range, temperature and bioreactor recycling. Depending on the tested dye, immobilization increased the catalytic activity of CueO by up to 40-fold with respect to the soluble enzyme, reaching decolorization efficiencies of 45-90%. Our results indicate that oxidase bioreactors based on polyhydroxyalkanoates are a promising alternative for the treatment of coloured industrial wastewaters.

Self-assembly of chiral (1R,2S)-ephedrine and (1S,2S)-pseudoephedrine into low-dimensional aluminophosphate materials driven by their amphiphilic nature.

In an attempt to promote the crystallization of chiral inorganic frameworks, we explore the ability of chiral (1R,2S)-ephedrine and its diastereoisomer (1S,2S)-pseudoephedrine to act as organic building blocks for the crystallization of hybrid organo-inorganic aluminophosphate frameworks in the presence of fluoride. These molecules were selected because of their particular molecular asymmetric structure, which enables a rich supramolecular chemistry and a potential chiral recognition phenomenon during crystallization. Up to four new low-dimensional materials have been produced, wherein the organic molecules form an organic bilayer in-between the inorganic networks. We analyze by molecular simulations the trend of these chiral molecules to form these types of framework, which is directly related to their amphiphilic nature that triggers a strong self-assembly through hydrophobic interactions between aromatic rings and hydrophilic interactions with the fluoro-aluminophosphate inorganic units. Such a self-assembly process is strongly dependent on the concentration of the organic molecules.

Roles of Amphipathicity and Hydrophobicity in the Micelle-Driven Structural Switch of a 14-mer Peptide Core from a Choline-Binding Repeat.

Choline-binding repeats (CBRs) are ubiquitous sequences with a ß-hairpin core that are found in the surface proteins of several microorganisms such as S. pneumoniae (pneumococcus). Previous studies on a 14-mer CBR sequence derived from the pneumoccal LytA autolysin (LytA239-252 peptide) have demonstrated a switch behaviour for this peptide, so that it acquires a stable, native-like ß-hairpin conformation in aqueous solution but is reversibly transformed into an amphipathic α-helix in the presence of detergent micelles. With the aim of understanding the factors responsible for this unusual ß-hairpin to α-helix transition, and to specifically assess the role of peptide hydrophobicity and helical amphipathicity in the process, we designed a series of LytA239-252 variants affecting these two parameters and studied their interaction with dodecylphosphocholine (DPC) micelles by solution NMR, circular dichroism and fluorescence spectroscopies. Our results indicate that stabilising cross-strand interactions become essential for ß-hairpin stability in the absence of optimal turn sequences. Moreover, both amphipathicity and hydrophobicity display comparable importance for helix stabilisation of CBR-derived peptides in micelles, indicating that these sequences represent a novel class of micelle/membrane-interacting peptides.

Poly-3-Hydroxybutyrate Functionalization with BioF-Tagged Recombinant Proteins.

Polyhydroxyalkanoates (PHAs) are biodegradable polyesters that accumulate in the cytoplasm of certain bacteria. One promising biotechnological application utilizes these biopolymers as supports for protein immobilization. Here, the PHA-binding domain of the Pseudomonas putida KT2440 PhaF phasin (BioF polypeptide) was investigated as an affinity tag for the in vitro functionalization of poly-3-hydroxybutyrate (PHB) particles with recombinant proteins, namely, full-length PhaF and two fusion proteins tagged to BioF (BioF-C-LytA and BioF-ß-galactosidase, containing the choline-binding module C-LytA and the ß-galactosidase enzyme, respectively). The protein-biopolyester interaction was strong and stable at a wide range of pHs and temperatures, and the bound protein was highly protected from self-degradation, while the binding strength could be modulated by coating with amphiphilic compounds. Finally, BioF-ß-galactosidase displayed very stable enzymatic activity after several continuous activity-plus-washing cycles when immobilized in a minibioreactor. Our results demonstrate the potentialities of PHA and the BioF tag for the construction of novel bioactive materials.IMPORTANCE Our results confirm the biotechnological potential of the BioF affinity tag as a versatile tool for functionalizing PHA supports with recombinant proteins, leading to novel bioactive materials. The wide substrate range of the BioF tag presumably enables protein immobilization in vitro of virtually all natural PHAs as well as blends, copolymers, or artificial chemically modified derivatives with novel physicochemical properties. Moreover, the strength of protein adsorption may be easily modulated by varying the coating of the support, providing new perspectives for the engineering of bioactive materials that require a tight control of protein loading.

Polyhydroxyalkanoate-associated phasins as phylogenetically heterogeneous, multipurpose proteins.

Polyhydroxyalkanoates (PHAs) are natural polyesters of increasing biotechnological importance that are synthesized by many prokaryotic organisms as carbon and energy storage compounds in limiting growth conditions. PHAs accumulate intracellularly in form of inclusion bodies that are covered with a proteinaceous surface layer (granule-associated proteins or GAPs) conforming a network-like surface of structural, metabolic and regulatory polypeptides, and configuring the PHA granules as complex and well-organized subcellular structures that have been designated as 'carbonosomes'. GAPs include several enzymes related to PHA metabolism (synthases, depolymerases and hydroxylases) together with the so-called phasins, an heterogeneous group of small-size proteins that cover most of the PHA granule and that are devoid of catalytic functions but nevertheless play an essential role in granule structure and PHA metabolism. Structurally, phasins are amphiphilic proteins that shield the hydrophobic polymer from the cytoplasm. Here, we summarize the characteristics of the different phasins identified so far from PHA producer organisms and highlight the diverse opportunities that they offer in the Biotechnology field.

Microbes go nano.

Walk on the small side. Nanotechnology meets Microbiology thanks to the high versatility of synthetic routes in microorganisms, leading to the production of nanoparticles of biotechnological and biomedical interest.