Structural Mimics Research Articles

Ruthenacyclic carbamoyl mimics of the [Fe]-hydrogenase active site: Derivatisation at the 4-position of the pyridinyl ring

The ruthenacyclic carbamoyl complexes [RuBr(2-NHC(O)C5H3N-4-R)(CO)2(MeCN)] in which the 4-position of the pyridinyl ring is derivatized, have been synthesized. These are ruthenium-based structural mimics of the natural [Fe]-hydrogenase metal cofactor. The derivative with R = H reacts with phosphine to form a disubstituted product [RuBr(2-NHC(O)C5H4N)(CO)(PPh2SPh)2].

Identification of Specific N6-Methyladenosine RNA Demethylase FTO Inhibitors by Single-Quantum-Dot-Based FRET Nanosensors.

The fat mass and obesity-associated enzyme (FTO) can catalyze the demethylation of N6-methyladenosine (m6A) residues in mRNA, regulates the cellular level of m6A modification, and plays a critical role in human obesity and cancers. Herein, we develop a single-quantum-dot (QD)-based fluorescence resonance energy transfer (FRET) sensor for the identification of specific FTO demethylase inhibitors. The FTO-mediated demethylation of m6A can induce the cleavage of demethylated DNA to generate the biotinylated DNA fragments, which may function as capture probes to assemble the Cy5-labeled reporter probes onto the QD surface, enabling the occurrence of FRET between the QD and Cy5. The presence of inhibitors can inhibit the FTO demethylation and consequently abolish FRET between the QD and Cy5. The inhibition effect of inhibitors upon FTO demethylation can be simply evaluated by monitoring the decrease of Cy5 counts. We use this nanosensor to screen several small-molecule inhibitors and identify diacerein as a highly selective inhibitor of FTO. Diacerein can inhibit the demethylation activity of endogenous FTO in HeLa cells. Interestingly, diacerein is neither a structural mimic of 2-oxoglutarate (2-OG) nor a chelator of metal ions, and it can selectively inhibit FTO demethylation by competitively binding the m6A-containing substrate.

Targeting TdT gene expression in Molt-4 cells by PNA-octaarginine conjugates

Peptide nucleic acid (PNA) is an amide based structural nucleic acid mimic with potential applications in gene therapeutic drug discovery. In the present study, we evaluated and compared the effects on gene expression, cell viability and apoptosis of two antisense PNA-d-octaarginine conjugates, targeting sequences at the AUG translation start site or the 5′-UTR of the TdT (terminal deoxynucleotidyl transferase) gene, as well as a sense oligomer corresponding to the 5′-UTR-antisense, in Molt-4 cells. The protein level of TdT was determined by flow cytometry, and qPCR was used for mRNA expression analysis. Mismatch PNAs were used as control to address the sequence/target spcifity of the biological effects. The results showed that treatment with the AUG- and to slightly lesser extent with the 5′-UTR-antisense PNAs reduced the TdT mRNA as wel as the protein level, whereas only very low effect was observed for the 5′-UTR-sense PNA. A parallel effect was observed on reduced cell survival and increased rate of apoptosis. Our findings suggest that antisense PNAs can inhibit expression of the TdT gene and induce apoptosis in Molt-4 cells.

Ruthenium‐Based Structural Mimics of the Cofactor of [Fe]‐Hydrogenase: Replacement of the Acyl Moiety with an N‐Heterocyclic Carbene

AbstractA synthetic route is reported towards ruthenium‐based structural mimics of the [Fe]‐hydrogenase metal cofactor in which the acyl moiety is replaced by an N‐heterocyclic carbene. It is observed that the pyridyl‐NHC ligand has a rather different trans influence from that of a simple NHC in their ruthenium derivatives. The basis for this difference is explored crystallographically and computationally, and it accounts for their different behaviour towards thiolation.

Replacement of the Cobalt Center of Vitamin B12 by Nickel: Nibalamin and Nibyric Acid Prepared from Metal-Free B12 Ligands Hydrogenobalamin and Hydrogenobyric Acid.

The (formal) replacement of Co in cobalamin (Cbl) by NiII generates nibalamin (Nibl), a new transition‐metal analogue of vitamin B12. Described here is Nibl, synthesized by incorporation of a NiII ion into the metal‐free B12 ligand hydrogenobalamin (Hbl), itself prepared from hydrogenobyric acid (Hby). The related NiII corrin nibyric acid (Niby) was similarly synthesized from Hby, the metal‐free cobyric acid ligand. The solution structures of Hbl, and Niby and Nibl, were characterized by spectroscopic studies. Hbl features two inner protons bound at N2 and N4 of the corrin ligand, as discovered in Hby. X‐ray analysis of Niby shows the structural adaptation of the corrin ligand to NiII ions and the coordination behavior of NiII. The diamagnetic Niby and Nibl, and corresponding isoelectronic CoI corrins, were deduced to be isostructural. Nibl is a structural mimic of four‐coordinate base‐off Cbls, as verified by its ability to act as a strong inhibitor of bacterial adenosyltransferase.

Replacement of the Cobalt Center of Vitamin B12 by Nickel: Nibalamin and Nibyric Acid Prepared from Metal‐Free B12 Ligands Hydrogenobalamin and Hydrogenobyric Acid

AbstractThe (formal) replacement of Co in cobalamin (Cbl) by NiII generates nibalamin (Nibl), a new transition‐metal analogue of vitamin B12. Described here is Nibl, synthesized by incorporation of a NiII ion into the metal‐free B12 ligand hydrogenobalamin (Hbl), itself prepared from hydrogenobyric acid (Hby). The related NiII corrin nibyric acid (Niby) was similarly synthesized from Hby, the metal‐free cobyric acid ligand. The solution structures of Hbl, and Niby and Nibl, were characterized by spectroscopic studies. Hbl features two inner protons bound at N2 and N4 of the corrin ligand, as discovered in Hby. X‐ray analysis of Niby shows the structural adaptation of the corrin ligand to NiII ions and the coordination behavior of NiII. The diamagnetic Niby and Nibl, and corresponding isoelectronic CoI corrins, were deduced to be isostructural. Nibl is a structural mimic of four‐coordinate base‐off Cbls, as verified by its ability to act as a strong inhibitor of bacterial adenosyltransferase.

Selenomelanin: An Abiotic Selenium Analogue of Pheomelanin.

Melanins are a family of heterogeneous biopolymers found ubiquitously across plant, animal, bacterial, and fungal kingdoms where they act variously as pigments and as radiation protection agents. There exist five multifunctional yet structurally and biosynthetically incompletely understood varieties of melanin: eumelanin, neuromelanin, pyomelanin, allomelanin, and pheomelanin. Although eumelanin and allomelanin have been the focus of most radiation protection studies to date, some research suggests that pheomelanin has a better absorption coefficient for X-rays than eumelanin. We reasoned that if a selenium enriched melanin existed, it would be a better X-ray protector than the sulfur-containing pheomelanin because the X-ray absorption coefficient is proportional to the fourth power of the atomic number (Z). Notably, selenium is an essential micronutrient, with the amino acid selenocysteine being genetically encoded in 25 natural human proteins. Therefore, we hypothesize that selenomelanin exists in nature, where it provides superior ionizing radiation protection to organisms compared to known melanins. Here we introduce this novel selenium analogue of pheomelanin through chemical and biosynthetic routes using selenocystine as a feedstock. The resulting selenomelanin is a structural mimic of pheomelanin. We found selenomelanin effectively prevented neonatal human epidermal keratinocytes (NHEK) from G2/M phase arrest under high-dose X-ray irradiation. Provocatively, this beneficial role of selenomelanin points to it as a sixth variety of yet to be discovered natural melanin.

820 Filling Injection of Platelet-rich Plasma Gel as A New Method to Treat En Coup de Sabre Scleroderma

Platelet-rich Plasma (PRP) plays an important role on the tissue regeneration process. A new preparatioin method of PRP provides an filling injection product which was named Platelet-rich Plasma Gel (PRPG) and could provied synergic effects on skin elasticity, dermal remodeling and re-vascularization. The aim of this pilot study was to assess the clinical benefit of PRPG filling injection on the treatment of en coup de sabre scleroderma. Five patients who were diagnosed under the confirmation of histopathology, and assessed by ultrasonography. Treatment was administered with PRP at a concentration 3.5 times above baseline. And under sterile condition, pre-seperated PRP was aspirated into several needle tubes, gradually heated in a dry bath machine, and prepare PRPG under the terminal temperature of 70 centigrade for 14 minutes. Under swelling anesthesia, subcutaneous tissue gaps were formed. Then PRPG was safely filled in these gaps without the risk of injection into the blood vessels. Therefore, a kind of structure mimic subcutaneous soft tissue was performed to slowly release cell and growth factors which enhance the regeneration effects on the remodeling of dermal tissue and reconstruction of vascular network. The subjective symptoms of pain and tightness were significantly relieved after at least one time of injecton. And after completion of 3 cycles of treatments at monthly intervals, objective lesions showed the improvement of skin elatisity, dermal thickness, subcutaneous tissue thickness and subcutaneous vascular network density. Even hair growth can be observed in those atrophy scalp filed. The main limitations of this study were the low number of cases, lack of a comparison group and the difficulty of identifying the exact role of each factor which would be studied in next clinical trial. However, PRPG is a good alternative of tissue filler substitution instead of hyaluronic acid and collagen, and represents a new and potentially regenerative treatment option for en coup de sabre scleroderma with minimal associated side effects.

Layer by layer assembly of a bio-inspired manganese cluster for electrocatalytic water oxidation

Mn12O12(O2CC6H3(NH2)2)16(H2O)4 (Mn12DA) is a structural mimic of the oxygen-evolving-complex in photosystem II. Herein we describe a method to integrate the Mn12DA with ITO electrodes using a layer-by-layer approach. Using (3-Aminopropyl)triethoxysilane, (APTES), glutaraldehyde, Mn12DA, and sodium cyanoborohydride as a mild reducing agent, five layers of the electrocatalysts with maximal electrocatalytic currents were obtained. The integration method limits the ligand self-oxidation and prevents the catalyst failure. Furthermore, the developed configuration enables efficient water oxidation electrocatalytic reaction at pH = 7, with an overpotential of 430 mV, a faradaic efficiency of 92% and a high turn-over-number.

Modulation of virus-induced NF-\u03baB signaling by NEMO coiled coil mimics

Protein-protein interactions featuring intricate binding epitopes remain challenging targets for synthetic inhibitors. Interactions of NEMO, a scaffolding protein central to NF-κB signaling, exemplify this challenge. Various regulators are known to interact with different coiled coil regions of NEMO, but the topological complexity of this protein has limited inhibitor design. We undertook a comprehensive effort to block the interaction between vFLIP, a Kaposi’s sarcoma herpesviral oncoprotein, and NEMO using small molecule screening and rational design. Our efforts reveal that a tertiary protein structure mimic of NEMO is necessary for potent inhibition. The rationally designed mimic engages vFLIP directly causing complex disruption, protein degradation and suppression of NF-κB signaling in primary effusion lymphoma (PEL). NEMO mimic treatment induces cell death and delays tumor growth in a PEL xenograft model. Our studies with this inhibitor reveal the critical nexus of signaling complex stability in the regulation of NF-κB by a viral oncoprotein.

Identifying socio-psychological constructs and beliefs underlying farmers’ intention to adopt on-farm silos

Brazil is one of the leading countries in production and exportation of grains. However, most grain production regions in Brazil do not have an adequate storage capacity, which result in losses for the grain supply chain. A possible solution to increase storage capacity is the adoption of on-farm silos. We used the Reasoned Action Approach as a framework to identify the impact of attitude, perceived norms, and perceived behavioral control on farmers’ intention to adopt on-farm silos and to identify the most important beliefs underlying their intentions to adopt it. A survey was conducted with 170 farmers in Brazil. Data was analyzed by means of Partial-Least-Square Structural Equation Modeling and MIMIC models. Results showed that attitude was the main determinant of intention, followed by perceived behavioral control and injunctive norms. Results also showed that “Sell grains at higher price”, “Have independence in relation to grain storage firms”, and “Have control over grain classification” are the most important beliefs that drive attitude; “Bank” is the most important belief that drive perceived norm; and “Have easy access to silos”, “Prioritize other investments”, and “Need skilled workers” are the most important beliefs that drive perceived behavioral control. These results revealed important implications to design public and private interventions aimed to stimulate the adoption of on-farm silos.

Primary lateral sclerosis: consensus diagnostic criteria

Primary lateral sclerosis (PLS) is a neurodegenerative disorder of the adult motor system. Characterised by a slowly progressive upper motor neuron syndrome, the diagnosis is clinical, after exclusion of structural,...

Synthetic Liposomal Mimics of Biological Viruses for the Study of Immune Responses to Infection and Vaccination.

Human viruses possess very complex supramolecular structures. Both icosahedral and enveloped viruses typically display an array of viral-encoded protein antigens at varied spatial densities on the viral particle surface. The viral nucleic acid genome, on the other hand, is encapsulated inside the viral particle. Although both the surface antigen and the interior nucleic acids could independently produce immunological responses, how B cells integrate these two types of signals and respond to a typical virus particle to initiate activation is not well understood at a molecular level. The study of these fundamental biological processes would benefit from the development of viral structural mimics that are well constructed to incorporate both quantitative and qualitative viral features for presentation to B cells. These novel tools would enable researchers to systematically dissect the underlying processes. Here we report the development of such particulate antigens based on liposomes engineered to display a model protein antigen, hen egg lysozyme (HEL). We developed methods to overexpress and purify various affinity mutants of HEL from E. coli. We conjugated the purified recombinant HEL proteins onto the surface of a virion-sized liposome in an orientation-specific manner at defined spatial densities and also encapsulated nucleic acid molecules into the interior of the liposome. Both the chemical conjugation of the HEL antigen on liposome surfaces and the encapsulation of nucleic acids were stable under physiologically relevant conditions. These liposomes elicited antigen-specific B-cell responses in vitro, which validate these supramolecular structures as a novel and effective approach to mimic and systematically isolate the role of essential viral features in directing the B-cell response to particulate antigens.

Bioinspired metal complexes for energy-related photocatalytic small molecule transformation.

Bioinspired transformation of small-molecules to energy-related feedstocks is an attractive research area to overcome both the environmental issues and the depletion of fossil fuels. The highly effective metalloenzymes in nature provide blueprints for the utilization of bioinspired metal complexes for artificial photosynthesis. Through simpler structural and functional mimics, the representative herein is the pivotal development of several critical small molecule conversions catalyzed by metal complexes, e.g., water oxidation, proton and CO2 reduction and organic chemical transformation of small molecules. Of great achievement is the establishment of bioinspired metal complexes as catalysts with high stability, specific selectivity and satisfactory efficiency to drive the multiple-electron and multiple-proton processes related to small molecule transformation. Also, potential opportunities and challenges for future development in these appealing areas are highlighted.

Probing the electronic and mechanistic roles of the μ4-sulfur atom in a synthetic CuZ model system.

Nitrous oxide (N2O) contributes significantly to ozone layer depletion and is a potent greenhouse agent, motivating interest in the chemical details of biological N2O fixation by nitrous oxide reductase (N2OR) during bacterial denitrification. In this study, we report a combined experimental/computational study of a synthetic [4Cu:1S] cluster supported by N-donor ligands that can be considered the closest structural and functional mimic of the CuZ catalytic site in N2OR reported to date. Quantitative N2 measurements during synthetic N2O reduction were used to determine reaction stoichiometry, which in turn was used as the basis for density functional theory (DFT) modeling of hypothetical reaction intermediates. The mechanism for N2O reduction emerging from this computational modeling involves cooperative activation of N2O across a Cu/S cluster edge. Direct interaction of the μ4-S ligand with the N2O substrate during coordination and N–O bond cleavage represents an unconventional mechanistic paradigm to be considered for the chemistry of CuZ and related metal–sulfur clusters. Consistent with hypothetical participation of the μ4-S unit in two-electron reduction of N2O, Cu K-edge and S K-edge X-ray absorption spectroscopy (XAS) reveal a high degree of participation by the μ4-S in redox changes, with approximately 21% S 3p contribution to the redox-active molecular orbital in the highly covalent [4Cu:1S] core, compared to approximately 14% Cu 3d contribution per copper. The XAS data included in this study represent the first spectroscopic interrogation of multiple redox levels of a [4Cu:1S] cluster and show high fidelity to the biological CuZ site.

Glycoside hydrolase stabilization of transition state charge: new directions for inhibitor design.

Carbasugars are structural mimics of naturally occurring carbohydrates that can interact with and inhibit enzymes involved in carbohydrate processing. In particular, carbasugars have attracted attention as inhibitors of glycoside hydrolases (GHs) and as therapeutic leads in several disease areas. However, it is unclear how the carbasugars are recognized and processed by GHs. Here, we report the synthesis of three carbasugar isotopologues and provide a detailed transition state (TS) analysis for the formation of the initial GH-carbasugar covalent intermediate, as well as for hydrolysis of this intermediate, using a combination of experimentally measured kinetic isotope effects and hybrid QM/MM calculations. We find that the α-galactosidase from Thermotoga maritima effectively stabilizes TS charge development on a remote C5-allylic center acting in concert with the reacting carbasugar, and catalysis proceeds via an exploded, or loose, SN2 transition state with no discrete enzyme-bound cationic intermediate. We conclude that, in complement to what we know about the TS structures of enzyme-natural substrate complexes, knowledge of the TS structures of enzymes reacting with non-natural carbasugar substrates shows that GHs can stabilize a wider range of positively charged TS structures than previously thought. Furthermore, this enhanced understanding will enable the design of new carbasugar GH transition state analogues to be used as, for example, chemical biology tools and pharmaceutical lead compounds.

Bent Into Shape: Folded Peptides to Mimic Protein Structure and Modulate Protein Function.

Protein secondary and tertiary structure mimics have served as model systems to probe biophysical parameters that guide protein folding and as attractive reagents to modulate protein interactions. Here we review contemporary methods to reproduce loop, helix, sheet and coiled-coil conformations in short peptides.

Design, construction, and biological testing of an implantable porous trilayer scaffold for repairing osteoarthritic cartilage

Various tissue engineering systems for cartilage repair have been designed and tested over the past two decades, leading to the development of many promising cartilage grafts. However, no one has yet succeeded in devising an optimal system to restore damaged articular cartilage. Here, the design, assembly, and biological testing of a porous, chitosan/collagen-based scaffold as an implant to repair damaged articular cartilage is reported. Its gradient composition and trilayer structure mimic variations in natural cartilage tissue. One of its layers includes hydroxyapatite, a bioactive component that facilitates the integration of growing tissue on local bone in the target area after scaffold implantation. The scaffold was evaluated for surface morphology; rheological performance (storage, loss, complex, and time-relaxation moduli at 1 kHz); physiological stability; in vitro activity and cytotoxicity (on a human chondrocyte C28 cell line); and in vivo performance (tissue growth and biodegradability), in a murine model of osteoarthritis. The scaffold was shown to be mechanically resistant and noncytotoxic, favored tissue growth in vivo, and remained stable for 35 days postimplantation in mice. These encouraging results highlight the potential of this porous chitosan/collagen scaffold for clinical applications in cartilage tissue engineering.

A Nanoparticle Platform for Improved Potency, Stability, and Adjuvanticity of Poly(I:C)

AbstractCancer immunotherapies and prophylactic vaccines against infectious diseases often exploit adjuvants such as toll‐like receptor agonists (TLRa) to drive potent and directed immune responses. Unfortunately, a promising class of TLRa based on nucleic acid derivatives is susceptible to degradation by nucleases, cause life‐threatening systemic toxicities, and is difficult to target to specific cell populations or tissues within the body. In this study a library of cationic polymeric nanoparticles (NP) is developed for encapsulation and delivery of the double‐stranded RNA structural mimic, poly(I:C) (pIC), to address these limitations. Using a combinatorial library screening approach, pIC/poly(β‐amino ester) (PBAE) NPs are identified that skew activation resulting in enhanced potency (13‐fold increase in type I interferon [IFN] production) and negligible toxicity. These highly potent adjuvant NPs increase the magnitude, duration, and affinity maturation of antigen‐specific antibodies following vaccination with a model subunit vaccine. This NP platform provides an opportunity to alter the immune response to pIC, creating a potent type I IFN‐producing adjuvant capable of driving stronger humoral responses to immunization and improving affinity maturation more than 14‐fold. This platform can be applied generally to develop more effective vaccines and immunotherapies.

Rational De Novo Design of a Cu Metalloenzyme for Superoxide Dismutation.

Superoxide dismutases (SODs) are highly efficient enzymes for superoxide dismutation and the first line of defense against oxidative stress. These metalloproteins contain a redox-active metal ion in their active site (Mn, Cu, Fe, Ni) with a tightly controlled reduction potential found in a close range around the optimal value of 0.36 V versus the normal hydrogen electrode (NHE). Rationally designed proteins with well-defined three-dimensional structures offer new opportunities for obtaining functional SOD mimics. Here, we explore four different copper-binding scaffolds: H3 (His3 ), H4 (His4 ), H2 DH (His3 Asp with two His and one Asp in the same plane) and H3 D (His3 Asp with three His in the same plane) by using the scaffold of the de novo protein GRα3 D. EPR and XAS analysis of the resulting copper complexes demonstrates that they are good CuII -bound structural mimics of Cu-only SODs. Furthermore, all the complexes exhibit SOD activity, though three orders of magnitude slower than the native enzyme, making them the first de novo copper SOD mimics.