Biotinylation and isolation of an RNA G-quadruplex based on its peroxidase-mimicking activity.

RNA G-quadruplexes (rG4s) are important RNA secondary structures considering their significance in regulating numerous cellular processes. Described herein is an rG4 detecting and isolation method, which exploits the complex of rG4 and hemin to mimic peroxidase. In the presence of biotin tyramide and hydrogen peroxide, rG4s can be selectively self-biotinylated and easily isolated from a complex RNA mixture using streptavidin magnetic beads.

Biomimetic and Biocatalytic Synthesis of Bruceol.

The first total synthesis of bruceol has been achieved using a biomimetic cascade cyclization initiated by a stereoselective Jacobsen-Katsuki epoxidation (and kinetic resolution) of racemic protobruceol-I. A bacterial cytochrome P450 monooxygenase was also found to catalyze the conversion of protobruceol-I into bruceol. The first full analysis of the NMR data of natural bruceol suggested that "isobruceol" was a previously unrecognized natural product also isolated from Philotheca brucei. This was confirmed by the re-isolation, synthesis, and X-ray analysis of isobruceol. In total, eight stereoisomers and structural isomers of bruceol have been synthesized in a highly divergent approach.

The deep-sea natural products, biogenic polyphosphate (Bio-PolyP) and biogenic silica (Bio-Silica), as biomimetic scaffolds for bone tissue engineering: fabrication of a morphogenetically-active polymer.

Bone defects in human, caused by fractures/nonunions or trauma, gain increasing impact and have become a medical challenge in the present-day aging population. Frequently, those fractures require surgical intervention which ideally relies on autografts or suboptimally on allografts. Therefore, it is pressing and likewise challenging to develop bone substitution materials to heal bone defects. During the differentiation of osteoblasts from their mesenchymal progenitor/stem cells and of osteoclasts from their hemopoietic precursor cells, a lineage-specific release of growth factors and a trans-lineage homeostatic cross-talk via signaling molecules take place. Hence, the major hurdle is to fabricate a template that is functioning in a way mimicking the morphogenetic, inductive role(s) of the native extracellular matrix. In the last few years, two naturally occurring polymers that are produced by deep-sea sponges, the biogenic polyphosphate (bio-polyP) and biogenic silica (bio-silica) have also been identified as promoting morphogenetic on both osteoblasts and osteoclasts. These polymers elicit cytokines that affect bone mineralization (hydroxyapatite formation). In this manner, bio-silica and bio-polyP cause an increased release of BMP-2, the key mediator activating the anabolic arm of the hydroxyapatite forming cells, and of RANKL. In addition, bio-polyP inhibits the progression of the pre-osteoclasts to functionally active osteoclasts. Based on these findings, new bioinspired strategies for the fabrication of bone biomimetic templates have been developed applying 3D-printing techniques. Finally, a strategy is outlined by which these two morphogenetically active polymers might be used to develop a novel functionally active polymer.

Biomimetic, Smart, and Multivalent Ligands for G-Quadruplex Isolation and Bioorthogonal Imaging.

G-quadruplexes (G4s) continue to gather wide attention in the field of chemical biology as their prevalence in the human genome and transcriptome strongly suggests that they play key regulatory roles in cell biology. G4-specific, cell-permeable small molecules (G4-ligands) innovatively permit the interrogation of cellular circuitries in order to assess to what extent G4s influence cell fate and functions. Here, we report on multivalent, biomimetic G4-ligands referred to as TASQs that enable both the isolation and visualization of G4s in human cells. Two biotinylated TASQs, BioTASQ and BioCyTASQ, are indeed efficient molecular tools to isolate G4s from mixtures of nucleic acids through simple affinity capture protocols and to image G4s in cells via a biotin/avidin pretargeted imaging system first applied here to G4s, found to be a reliable alternative to in situ click chemistry.

Biomimetic Affinity Ligands for Protein Purification.

The development of sophisticated molecular modeling software and new bioinformatic tools, as well as the emergence of data banks containing detailed information about a huge number of proteins, enabled the de novo intelligent design of synthetic affinity ligands. Such synthetic compounds can be tailored to mimic natural biological recognition motifs or to interact with key surface-exposed residues on target proteins, and are designated as "biomimetic ligands". A well-established methodology for generating biomimetic or synthetic affinity ligands integrates rational design with combinatorial solid-phase synthesis and screening, using the triazine scaffold and analogs of amino acid side chains to create molecular diversity.Triazine-based synthetic ligands are nontoxic, low-cost, and highly stable compounds that can replace advantageously natural biological ligands in the purification of proteins by affinity-based methodologies.

Modulatory properties of extracellular matrix glycosaminoglycans and proteoglycans on neural stem cells behavior: Highlights on regenerative potential and bioactivity.

Despite the poor regenerative capacity of the adult central nervous system (CNS) in mammals, two distinct regions, subventricular zone (SVZ) and the subgranular zone (SGZ), continue to generate new functional neurons throughout life which integrate into the pre-existing neuronal circuitry. This process is not fixed but highly modulated, revealing many intrinsic and extrinsic mechanisms by which this performance can be optimized for a given environment. The capacity for self-renewal, proliferation, migration, and multi-lineage potency of neural stem cells (NSCs) underlines the necessity of controlling stem cell fate. In this context, the native and local microenvironment plays a critical role, and the application of this highly organized architecture in the CNS has been considered as a fundamental concept in the generation of new effective therapeutic strategies in tissue engineering approaches. The brain extracellular matrix (ECM) is composed of biomacromolecules, including glycosaminoglycans, proteoglycans, and glycoproteins that provide various biological actions through biophysical and biochemical signaling pathways. Herein, we review predominantly the structure and function of the mentioned ECM composition and their regulatory impact on multiple and diversity of biological functions, including neural regeneration, survival, migration, differentiation, and final destiny of NSCs.

Mussel-Inspired Ag NPs Immobilized on Melamine Sponge for Reduction of 4-Nitrophenol, Antibacterial Applications and Its Superhydrophobic Derivative for Oil-Water Separation.

A functional material integrated with a variety of functions is highly desired in wastewater treatment. In this research, a mussel-inspired method of immobilizing silver nanoparticles on the skeleton of a melamine sponge is proposed and applied for water remediation. Ag NPs were reduced in situ and grown on a polydopamine-modified melamine sponge. The catalytic reduction of 4-nitrophenol (4-NP) in the presence of the obtained MS-PDA-Ag was evaluated, and the results demonstrated that the MS-PDA-Ag presented high catalytic reduction activity. In addition, the monolithic MS-PDA-Ag presents excellent reusability with no remarkable decrease in catalytic efficiency after multiple reuses. Owing to the immobilized Ag NPs, the MS-PDA-Ag can also effectively inhibit the growth of bacteria against both gram-positive and gram-negative species, making it possible for bacteria elimination in polluted water. To further explore the possibility of utilizing the MS-PDA-Ag for versatile applications, a superhydrophobic derivative (S-MS-PDA-Ag) was prepared by coating a low-surface-energy substance (octadecanethiol) on the surface of MS-PDA-Ag. The obtained S-MS-PDA-Ag presents the capacities of oil/organics adsorption and water repellence, which can separate the insoluble oil/organics from water. The melamine sponge immobilized with Ag NPs demonstrates prominent catalytic reduction of 4-NP, antibacterial activity and the superhydrophobic derivative presents the capacity of insoluble oil/organics separation from oil-water mixtures, exhibiting high potential in the remediation of polluted water.

Crotonpenoids A and B, Two Highly Modified Clerodane Diterpenoids with a Tricyclo[7.2.1.02,7]dodecane Core from Croton yanhuii: Isolation, Structural Elucidation, and Biomimetic Semisynthesis.

Crotonpenoids A (1) and B (2), two highly modified clerodane diterpenoids featuring a new 10-(butan-2-yl)-1,6,12-trimethyltricyclo[7.2.1.02,7]dodecane skeleton, were isolated from the leaves and twigs of Croton yanhuii. Their structures including the absolute configurations were determined by spectroscopic analysis, single-crystal X-ray diffraction, and biomimetic semisynthesis. Compounds 1 and 2 exhibited an agonistic effect on pregnane X receptor at 10 µM.

Antimicrobials offered from nature: Peroxidase-catalyzed systems and their mimics.

The control of antimicrobial resistance requires the development of novel antimicrobial alternatives and naturally occurring peroxidase-catalyzed systems may be of great value in this era of emerging antimicrobial resistance. In the peroxidase system, a peroxidase enzyme catalyzes the oxidation of a halide/pseudohalide, at the expense of hydrogen peroxide, to generate reactive products with broad antimicrobial properties. The appropriate use of peroxidase systems needs a better understanding of the identities and properties of the generated antimicrobial oxidants, specific targets in bacterial cells, their mode of action and the factors favoring or limiting their activity. Here, the ABCs (antibacterial activity, bacterial "backtalk" and cytotoxicity) of these systems and their mimics are discussed. Particular attention is paid to the concomitant use of thiocyanate and iodide dual substrates in peroxidase/peroxidase-free systems with implications on their antimicrobial activity. This review also provides a summary of actual applications of peroxidase systems as bio-preservatives in oral healthcare, milk industry, food/feed specialties and related products, mastitis and wound treatment; lastly, this review points to opportunities for further research and potential applications.

Functionalized polystyrene microspheres as Cryptosporidium surrogates.

Cryptosporidium, a waterborne protozoan pathogen that can cause gastrointestinal illness, is often found in surface waters that are used to supply drinking water. Filtration is a major process to remove Cryptosporidium in drinking water treatment. However, interactions between oocysts and filter media are still unclear and no satisfactory surrogates have been identified for quantifying their filtration removal in porous media. In the present study, polystyrene microsphere with a size, density, and shape similar to Cryptosporidium was modified with glycoprotein or synthesized biomolecules to mimic the surface properties of live Cryptosporidium oocyst. Deposition kinetics between live Cryptosporidium/modified microspheres and filter media were studied at the molecular scale using a quartz crystal microbalance with dissipation monitoring (QCM-D) and at the laboratory-scale using sand-packed columns. Both QCM-D and column experiments underlined the importance of Cryptosporidium surface charge and hydrophobicity on their attenuation and transport in porous media. As compared to live Cryptosporidium, glycopolymer and zwitterionic polymer co- odified polystyrene microspheres (later called copolymers-modified microspheres) represent comparable surface properties, adsorption kinetics on filter surfaces, and transport and deposition behaviors in filter columns; hence were selected as appropriate Cryptosporidium surrogates. This study improves our understanding on how surface characteristics impact Cryptosporidium transport behaviors in porous media and contributes to our capacity to evaluate the attenuation of Cryptosporidium in natural and engineered aquatic environments.

Biomimetic Separation of Transport and Matrix Functions in Lamellar Block Copolymer Channel-Based Membranes.

Cell membranes control mass, energy, and information flow to and from the cell. In the cell membrane a lipid bilayer serves as the barrier layer, with highly efficient molecular machines, membrane proteins, serving as the transport elements. In this way, highly specialized transport properties are achieved by these composite materials by segregating the matrix function from the transport function using different components. For example, cell membranes containing aquaporin proteins can transport ∼4 billion water molecules per second per aquaporin while rejecting all other molecules including salts, a feat unmatched by any synthetic system, while the impermeable lipid bilayer provides the barrier and matrix properties. True separation of functions between the matrix and the transport elements has been difficult to achieve in conventional solute separation synthetic membranes. In this study, we created membranes with distinct matrix and transport elements through designed coassembly of solvent-stable artificial (peptide-appended pillar[5]arene, PAP5) or natural (gramicidin A) model channels with block copolymers into lamellar multilayered membranes. Self-assembly of a lamellar structure from cross-linkable triblock copolymers was used as a scalable replacement for lipid bilayers, offering better stability and mechanical properties. By coassembly of channel molecules with block copolymers, we were able to synthesize nanofiltration membranes with sharp selectivity profiles as well as uncharged ion exchange membranes exhibiting ion selectivity. The developed method can be used for incorporation of different artificial and biological ion and water channels into synthetic polymer membranes. The strategy reported here could promote the construction of a range of channel-based membranes and sensors with desired properties, such as ion separations, stimuli responsiveness, and high sensitivity.

Development and characterization of a biomimetic coating for percutaneous devices.

Percutaneous osseointegrated prosthetics (POP), which consist of a metallic post attached to the bone that extends outward through the skin to connect to an external prosthesis, have become a clinically relevant option to replace the typical socket-residual limb connection. POP devices offer several advantages such as mechanical off-loading of soft tissues, direct force transfer to the musculoskeletal system, greater proprioception, and overall improvement in limb kinesis compared to a socket system. However, POP devices create several challenges including epidermal downgrowth, increased infection risk, and mechanical tearing at the skin-implant interface. To address these issues, biomimetic surfaces and coatings have been developed in an attempt to create an infection-free and cohesive interface between POP devices and skin. The fingernail is a prime example of a natural system with a skin interface that is both mechanically and biologically stable. Exploiting keratins' previously demonstrated tissue compatibility and creating a biomimetic coating for POP devices that can imitate the human fingernail, and demonstrating its ability to promote a stable interface with skin tissue is the goal of this work. Silane coupling aided in producing a coating on titanium substrates consisting of human keratin proteins. Several combinations of silane and keratin derivatives were investigated, and in general showed a nano-scale coating thickness that supported skin cell (i.e. fibroblast and keratinocyte) adhesion. Initial enzyme-mediated degradation resistance was also demonstrated, but the coatings appeared to degrade at long time periods. Importantly, keratinocytes showed a stable phenotype with no indication of wound healing-like activity. These data provide justification to further explore keratin biomaterials for POP coatings that may stabilize the implant-skin interface.

Stilbene oligomers from Parthenocissus laetevirens: isolation, biomimetic synthesis, absolute configuration, and implication of antioxidative defense system in the plant.

Five new stilbene oligomers, laetevirenol A-E (4-8), were isolated from Parthenocissus laetevirens, together with three known stilbene oligomers (2, 3, and 9). The structures of the new compounds were elucidated by spectroscopic analysis, including 1D and 2D NMR experiments. Afterward the absolute configurations were determined. Biomimetic transformations revealed a possible biogenetic route, where stilbene trimers were enzymatically synthesized for the first time. In addition, their antioxidant activities were evaluated by 1,1-diphenyl-2-picrylhydrazyl (DPPH) assay. The results showed that stilbene oligomers with an unusual phenanthrene moiety exhibited much stronger antioxidant activities. Thus, the photocatalyzed cyclization of stilbenes was supposed to be an antioxidant activity promoting transformation, which was hypothesized to play a role in the antioxidative defense system of the plant.

Preparation and characterization of carbonic anhydrase-conjugated liposomes for catalytic synthesis of calcium carbonate particles.

The biomimetic approach using immobilized enzymes is useful for the synthesis of structurally defined inorganic materials. In this work, carbonic anhydrase (CA) from bovine erythrocytes was covalently conjugated at 25°C to the liposomes composed of 15mol% 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine-N-(glutaryl) (NG-POPE), and the zwitterionic and anionic phospholipids with the same acyl chains as NG-POPE. For the conjugation, the carboxyl groups of liposomal NG-POPE were activated with 11mM 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) and 4.6mM N-hydroxysulfosuccinimide (sulfo-NHS). The carbonic anhydrase-conjugated liposomes (CALs) with the mean hydrodynamic diameter of 149nm showed the esterase activity corresponding to on average 5.5×102 free CA molecules per liposome. On the other hand, the intrinsic fluorescence and absorbance measurements consistently revealed that on average 1.4×103 CA molecules were conjugated to a liposome, suggesting that the molecular orientation of enzyme affected its activity. The formation of calcium carbonate particles was significantly accelerated by the CALs ([lipid]=50µ M) in the 0.3M Tris solution at 10-40°C with dissolved CO2 (≈17mM) and CaCl2 (46mM). The anionic CALs were adsorbed with calcium as revealed with the ζ-potential measurements. The CAL system offered the calcium-rich colloidal interface where the bicarbonate ions were catalytically produced by the liposome-conjugated CA molecules. The CALs also functioned in the external loop airlift bubble column operated with a model flue gas (10vol/vo% CO2), yielding partly agglomerated calcium carbonate particles as observed with the scanning electron microscopy (SEM).

Rhodomyrtials A and B, Two Meroterpenoids with a Triketone-Sesquiterpene-Triketone Skeleton from Rhodomyrtus tomentosa: Structural Elucidation and Biomimetic Synthesis.

Rhodomyrtials A and B (1 and 2), two unprecedented triketone-sesquiterpene-triketone adducts, along with five biogenetically related intermediates, rhodomentone A (3) and tomentodiones A-D (4-7), were isolated from the leaves of Rhodomyrtus tomentosa. Their structures and absolute configurations were determined by a combination of NMR spectroscopy, chemical conversion, and X-ray diffraction analysis. Compounds 1 and 2 were biomimetically synthesized via 5 and 4, respectively, rather than 3, revealing their key ordering of biosynthetic events and confirming their structural assignments. Compound 7 exhibited potent metastatic inhibitory activity against DLD-1 cells by suppressing the activation of matrix metalloproteinase (MMP)-2 and MMP-9.

A Cost-Effective Method to Assemble Biomimetic 3D Cell Culture Platforms.

METHODS: We utilized the hAM to provide the biological and the three dimensional (3D) topographic components of the prototype. The 3D nano-roughness of the hAM was characterized using surface electron microscopy and surface image analysis (ImageJ and SurfaceJ). We developed additional macro-scale and micro-scale versions of the platform which provided additional shear stress factors to simulate the fluid dynamics of the in vivo extracellular fluids. RESULTS: Three models of varying complexities of the prototype were assembled. A well-defined 3D surface modulation of the hAM in comparable to commercial 3D biomaterial culture substrates was achieved without complex fabrication and with significantly lower cost. Performance of the prototype was demonstrated through culture of primary human umbilical cord mononuclear blood cells (MNCs), human bone marrow mesenchymal stem cell line (hBMSC), and human breast cancer tissue. CONCLUSION: This study presents methods of assembling an integrated, flexible and low cost biomimetic cell culture platform for diverse cell culture applications.

Biomimetic surface modification with bolaamphiphilic archaeal tetraether lipids via liposome spreading.

Through investigations of the self-assembly behavior of three different tetraether lipids, the authors successfully established a solid supported, biomimetic tetraether lipid membrane via liposome spreading. These bolaamphiphilic lipids are the main compound in membranes of archaea, extremophile microorganisms, which underwent an enormous adaptation to extreme conditions in their natural environment with regard to temperature, pH, and high salt concentrations. Starting from a mathematical point of view, the authors calculated hydrophilic-lipophilic balance values for each lipid and recognized a wide difference in self-assembly potentials relying on size and hydrophilic properties of the lipid head groups. These results were in good accordance with data generated by lipid experiments at the air-water interface applying a Langmuir-Blodgett film balance so that the self-assembly potential of two different tetraether lipids was found to be sufficient to form stable liposomes in aqueous media. Liposomes composed of the main phospholipid of the archaea strain Sulfolobus acidocaldarius fused covalently on silanized glass substrates and formed a monomolecular lipid layer with upright standing molecules at film consistent thicknesses of approximately 5 nm determined by ellipsometry and atomic force microscopy. This work can be considered as a basic strategy to find optimized lipid properties in terms of liposome formation and spreading in water, and it is the first report about archaeal liposome fusing on surfaces to establish a solid supported lipid monolayer.

Identification and characterization of mimotopes of classical swine fever virus E2 glycoprotein using specific anti-E2 monoclonal antibodies.

Classical swine fever virus (CSFV) shares high nucleic acid and amino acid sequence homology with the other members of the pestivirus genus, namely bovine viral diarrhea virus and border disease virus. All three viruses are able to infect swine and generate cross reactive antibodies, which is problematic during differential diagnosis for classical swine fever (CSF). Toward the development of a new generation of CSF specific diagnostic tools, monoclonal antibodies specific for CSFV were mapped using phage display technology. Six mimotopes were identified, some of which were found to be antigenic and/or specific for CSF when used as coating antigens in an ELISA for the detection of CSF antibodies in swine serum. Two mimotopes in particular termed V2-2 and V7-1 recognized numerous strains of CSF antisera and bound fewer BVD and BD antisera compared to a commercial CSF antibody ELISA. These two mimotopes may be useful to the pestivirus field in the development of a highly specific CSF antibody ELISA as well as in the development of other potential diagnostic technologies.

Isolation of monobodies that bind specifically to the SH3 domain of the Fyn tyrosine protein kinase.

Fyn is a nonreceptor protein tyrosine kinase that belongs to a highly conserved kinase family, Src family kinases. Fyn plays an important role in inflammatory processes and neuronal functions. To generate a synthetic affinity reagent that can be used to probe Fyn, a phage-display library of fibronectin type III monobodies was affinity selected with the Src Homology 3 (SH3) domain of Fyn and three binders were isolated. One of the three binders, G9, is specific in binding to the SH3 domain of Fyn, but not to the other members of the Src family (i.e. Blk, Fgr, Hck, Lck, Lyn, Src and Yes), even though they share 51-81% amino acid identity. The other two bind principally to the Fyn SH3 domain, with some cross-reactivity to the Yes SH3 domain. The G9 binder has a dissociation constant of 166±6nM, as measured by isothermal titration calorimetry, and binds only to the Fyn SH3 domain out of 150 human SH3 domains examined in an array. Interestingly, although the G9 monobody lacks proline in its randomized BC and FG loops, it binds at the same site on the SH3 domain as proline-rich ligands, as revealed by competition assays. The G9 monobody, identified in this study, may be used as a highly selective probe for detecting and purifying cellular Fyn kinase.

The preparation of (-)-grandisine B from (+)-grandisine D; a biomimetic total synthesis or formation of an isolation artefact?

An efficient new alkyne-acetal cyclization procedure has been developed to prepare enantiopure indolizidine building blocks from l-proline and then applied to prepare the Elaeocarpus-derived alkaloids grandisine B and grandisine D in an efficient manner. However, evidence is presented which indicates that grandisine B does not occur naturally but is formed by reaction of grandisine D with ammonia during the extraction/purification process.