Peptide Bond Research Articles

Growth of dendritic CuS nanostructures for photoacoustic image guided Chemo-Photothermal therapy

Herein, we report a unique method for design and development of carboxyl enriched dendritic CuS nanostructures (CuS NSs) for photoacoustic image guided chemo-photothermal therapy. The dendritic network was grown on the surface of CuS nanoparticles via layer-by-layer assembly of amino acid. XRD and TEM studies established the formation of crystalline well-spherical nanosized hexagonal covellite (CuS) phase. The successful growth of dendritic structure was apparent from the rise in surface charge, hydrodynamic diameter and characteristic vibrational band intensity of peptide bonds. The developed different generations of dendritic CuS NSs (D0-CuS NSs, D1-CuS NSs, D2-CuS NSs and D3-CuS NSs) displayed wide-ranging absorption band in near infrared (NIR) zone and exhibited good photothermal heating efficacy upon irradiation of 980 nm laser light. From in-vitro cellular studies, it has been found that the NIR irradiation effectively enhanced the photothermal toxicity of D3-CuS NSs towards cancer cells. Moreover, these negatively charged water-dispersible D3-CuS NSs were conjugated with positively charged anticancer drug, doxorubicin hydrochloride (DOX) through electrostatic interaction. The DOX loaded D3-CuS NSs (DOX@D3-CuS NSs) revealed pH dependent drug release behaviour and their considerable uptake in breast cancer cells (MCF-7). Further, DOX@D3-CuS NSs exhibited a much higher toxicity towards cancer cells upon NIR light over individual counterparts suggesting their strong ability for chemo-photothermal therapy. Moreover, these biocompatible CuS NSs have shown excellent concentration dependent photoacoustic properties at pulse laser excitation (850 nm) and thus, they can be found potential application in chemo-photothermal therapy.

High Self‐Supporting Chitosan‐Based Hydrogel Ink for In Situ 3D Printed Diabetic Wound Dressing

AbstractCustomizable 3D‐printed biopolymer hydrogels, highly sought after for diabetic wound management, face challenges in clinical application due to weak physical crosslinking within their constituent inks. In this study, a novel chitosan‐based hydrogel ink with a dense yet reversible physical crosslinking network is subtly designed for the rapid in situ fabrication of personalized diabetic wound dressing. This robust network is established through multiple electrostatic and hydrogen bonding interactions between unique carboxymethyl chitosan and nanoclay, further reinforced by the introduction of amide bonds, which act as double hydrogen bond donors/acceptors. Benefiting from this network, the ink with low nanoclay content exhibits remarkable self‐supporting properties, enabling high‐fidelity, large‐scale, and complex 3D printability without additional processing, while substantially retaining its inherent rheological properties after autoclave sterilization and the incorporation of active components. Given these advantages, this multifunctional 3D printable hydrogel can be rapidly in situ constructed on diabetic wounds. Simultaneously, the 3D‐printed hydrogel demonstrates biodegradability, anti‐swelling, and appropriate mechanical properties, along with remarkable in vitro antibacterial and pro‐angiogenic capabilities, leading to effective diabetic wound healing in vivo. This work offers a new strategy for creating highly self‐supporting biopolymer inks and paves the way for developing advanced personalized wound dressings.

Relay C(sp3)-H bond trifluoromethylthiolation and amidation by visible light photoredox catalysis

Relay C(sp3)-H bond trifluoromethylthiolation and amidation by visible light photoredox catalysis

Investigation of photoinduced deterioration in shadow puppet artifacts collected from the National Shadow Pupperty Museum in Chengdu, China

Shadow puppet artifacts are a special type of cultural heritage made from animal skin, possessing significant cultural and artistic value. However, there is insufficient attention to the scientific preservation of these artifacts, and systematic research on their protection is lacking. In particular, light as an important factor and related conservation studies are weak. This study investigates the photoinduced deterioration of shadow puppet artifacts from the National Shadow Pupperty Museum in Chengdu collection. Based on the xenon arc lamp are a common method of light aging, the modern rawhide samples were aged by the xenon arc lamp to simulate photoinduced deterioration. After artificial light aging, the samples were stored in a stable environment (with temperature maintained at 22 ± 2 °C and relative humidity maintained at 50 ± 5%RH) for 150 days. It attempts to avoid further deterioration of the samples due to drastic cyclic changes in the environment. And continuously observe changes in characteristics during this process to verify the potential reversibility of photoinduced deterioration. Comprehensive assessments were conducted to gauge the extent of deterioration. In order to assess the deterioration, a series of analytical techniques were used. Moisture gain or loss was inferred from mass changes, and colorimetric measurements were measured using the CIELAB formula. Macroscopic and microscopic morphological damage was documented through camera, stereo microscope, and scanning electron microscope observations. Fourier transform infrared spectroscopy (FTIR) assessed amide bond degradation and moisture loss, while thermogravimetry/differential thermogravimetry (TG/DTG) evaluated collagen denaturation and thermal stability. The results indicated that prolonged light exposure caused significant deterioration, including color fading, moisture evaporation, and structural damage such as shrinkage and cracking. The findings indicate that light exposure is a crucial factor in the preservation of shadow puppet artifacts. Therefore, it is essential to implement careful management strategies in museum environments to ensure the protection of these artifacts.

Hybrids of Membrane-Translocating Antimicrobial Peptides Show Enhanced Activity through Membrane Permeabilization.

Antimicrobial peptides (AMPs) hold promise as useful tools to combat bacterial infection. Hybrid peptides, made by linking two independent AMPs together through peptide bonds, have the potential for enhancing antimicrobial activity. Here we explore hybrids created by combining two histone-derived antimicrobial peptides (HDAPs), BF2 and DesHDAP1, that each translocate across bacterial membranes. Our work represents the first systematic approach considering the activity and mechanism of hybrids made from two translocating AMPs. BF2/DesHDAP1 hybrids showed increased antimicrobial activity against both Gram-positive and Gram-negative bacteria compared with the parent peptides and no cytotoxicity against eukaryotic cells. Introducing amino acid linkers between the parent peptides did not further enhance the antibacterial activity. The increased antimicrobial activity comes from a mechanistic shift, as hybrid peptides show decreased translocation across bacterial cell membranes but increased membrane permeabilization compared to BF2 and DesHDAP1. These observations lay the groundwork for the further design of hybrid AMPs made from translocating peptides.

Cover Feature: From Meteorite to Life's Building Blocks: A possible Electrochemical Pathway to Amino Acids and Peptide Bonds (Chem. Eur. J. 57/2024)

Cover Feature: From Meteorite to Life's Building Blocks: A possible Electrochemical Pathway to Amino Acids and Peptide Bonds (Chem. Eur. J. 57/2024)

Characterization of glycylglycyltyrosine radical cations: Insights into β-radical formation and N–Cα peptide bond dissociation at the tyrosine residue

We investigated the dissociation and characterization of radical cations of glycylglycyltyrosine [GGY]•+, focusing on β-radical-induced N–Cα peptide bond cleavage reactions at the tyrosyl residue. By combining density functional theory (DFT) calculations with experimental studies utilizing low-energy collision-induced dissociation (CID) mass spectrometry and deuterium labeling on the two β-hydrogen atoms of the tyrosyl residue in [GGY]•+, we elucidated the intricacies of the β-radical structure and its origin. Unlike tryptophan-containing [GGW]•+, which forms canonical π-radical precursors, infrared multiphoton dissociation (IRMPD) spectroscopy results reveal that the β-radical [GGYβ•]+ isomerizes from the phenoxy-radical [GGYo•]+, with the radical localized on the β-carbon of the tyrosyl residue and the phenolic oxygen atom, respectively. The isomerization barriers from [GGYo•]+ to [GGYβ•]+ are <109 kJ mol−1.

Sequence-Similar Protein Domain Pairs With Structural or Topological Dissimilarity.

For a variety of applications, protein structures are clustered by sequence similarity, and sequence-redundant structures are disregarded. Sequence-similar chains are likely to have similar structures, but significant structural variation, as measured with RMSD, has been documented for sequence-similar chains and found usually to have a functional explanation. Moving two neighboring stretches of backbone through each other may change the chain topology and alter possible folding paths. The size of this motion is compatible to a variation in a flexible loop. We search and find domains with alternate chain topology in CATH4.2 sequence families relatively independent of sequence identity and of structural similarity as measured by RMSD. Structural, topological, and functional representative sets should therefore keep sequence-similar domains not just with structural variation but also with topological variation. We present BCAlign that finds Alignment and superposition of protein Backbone Curves by optimizing a user chosen convex combination of structural derivation and derivation between the structure-based sequence alignment and an input sequence alignment. Steric and topological obstructions from deforming a curve into an aligned curve are then found by a previously developed algorithm. For highly sequence-similar domains, sequence-based structural alignment better represents the chains motion and generally reveals larger structural and topological variation than structure-based does. Fold-switching protein pairs have been reported to be most frequent between X-ray and NMR structures and estimated to be underrepresented in the PDB as the alternate configuration is harder to resolve. Here we similarly find chain topology most frequently altered between X-ray and NMR structures.

Ultraviolet Irradiation Surface Treatment to Enhance the Bonding Strength of Polyamide-Based Carbon Fiber-Reinforced Thermoplastic Polymers.

Adhesive bonding is a suitable joining method to satisfy the increasing industrial demand for carbon fiber-reinforced polymers without the need for a machining process. However, thermoplastic-based carbon fiber-reinforced polymers have small adhesive strength with structural thermoset adhesives. In this study, an ultraviolet irradiation surface treatment was developed to improve the adhesive bonding strength for polyamide-based carbon fiber-reinforced polymer. The type of ultraviolet wavelength, irradiation distance and irradiation time were optimized. Surface treatment with simultaneous UV irradiation of 185 nm and 254 nm wavelength generated unbound N-H stretching that was capable of chemical bonding with epoxy adhesives through a photo-scission reaction of the amide bond of polyamide matrix. Therefore, ultraviolet irradiation treatment improved the wettability and functional groups of the polyamide-based carbon fiber-reinforced polymers for adhesive bonding. As a result, the adhesive strength of the polyamide-based carbon fiber-reinforced polymers was increased by more than 230%.

De novo protein design with a denoising diffusion network independent of pretrained structure prediction models.

The recent success of RFdiffusion, a method for protein structure design with a denoising diffusion probabilistic model, has relied on fine-tuning the RoseTTAFold structure prediction network for protein backbone denoising. Here, we introduce SCUBA-diffusion (SCUBA-D), a protein backbone denoising diffusion probabilistic model freshly trained by considering co-diffusion of sequence representation to enhance model regularization and adversarial losses to minimize data-out-of-distribution errors. While matching the performance of the pretrained RoseTTAFold-based RFdiffusion in generating experimentally realizable protein structures, SCUBA-D readily generates protein structures with not-yet-observed overall folds that are different from those predictable with RoseTTAFold. The accuracy of SCUBA-D was confirmed by the X-ray structures of 16 designed proteins and a protein complex, and by experiments validating designed heme-binding proteins and Ras-binding proteins. Our work shows that deep generative models of images or texts can be fruitfully extended to complex physical objects like protein structures by addressing outstanding issues such as the data-out-of-distribution errors.

Tissue derivatization for visualizing lactate and pyruvate in mouse testis tissues using matrix-assisted laser desorption/ionization-mass spectrometry imaging

Pyruvate and lactate are the final metabolites of the glycolytic system that are formed under oxygen-rich and anaerobic conditions, respectively. They play an important role in energy metabolism. Obtaining a tissue distribution image of pyruvate and lactate holds great significance in molecular biology because the glycolytic system plays an essential role in diseases, such as tumors and diabetes; microbial activities, such as alcohol production and lactic acid fermentation; and maintaining homeostasis in the gut environment. However, it is difficult to obtain images of the distribution of in vivo metabolites because of the low detection sensitivities of current methods. In this study, a novel derivatization method for pyruvate and lactate was developed using matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI) to detect pyruvate and lactate in vivo and obtain biodistribution images. We investigated derivatization methods using readily available 3-nitrophenylhydrazine (3NPH), the addition of which improves the sensitivity of pyruvate detection, and the distribution of pyruvate in mouse testes was successfully visualized. Furthermore, the distribution of lactate in the mouse testes could be visualized, and improved detection sensitivity for the main metabolites of the tricarboxylic acid cycle was demonstrated. This derivatization method can be used to detect carboxyl-containing metabolites, including pyruvate, via MALDI-MSI. Furthermore, 3NPH forms amide bonds with carbonyl, phosphate, and carboxyl groups, suggesting the possibility of visualizing its distribution in many metabolites.Graphical

Study on the adsorption process and kinetic, thermodynamic of bio-based waste cattle hair powder toward acidic complex dye.

In this paper, cattle hair waste (CHW) was collected and physically milled into different meshes of ultrafine cattle hair powder (UCHP). The reuse of CHW reaches the purpose of treating pollution with waste by using bio-base adsorbent. It was characterized by using scanning electron microscope-energy dispersive spectrometer (SEM-EDS), Fourier transform infrared (FT-IR) spectroscopy, X-ray photoelectron spectroscopy (XPS), thermogravimetric analysis (TGA), differential scanning calorimeter (DSC), and X-ray diffraction (XRD). The adsorption studies were carried out under different conditions of temperature, time, pH, concentration of dye solution, mesh size, and dosage of cattle hair powder, respectively. The pseudo-first and pseudo-secondary kinetics and intra-particle diffusion models were employed to analyze the adsorption kinetic. The Langmuir, Freundlich, and Temkin adsorption isotherm was used to analyze the adsorption isotherm. The results showed that the adsorption capacity of UCHP for acidic metal complex (Trupoxane Brown R6) dyes increased with the decreasing pH solution. The adsorption capacity of 200 mesh UCHP was 379.5mg.g-1 when the adsorption conditions were as follows: 100mL dye solution with the initial concentration of 1000mg·L-1, the dosage of adsorbent was 0.1g, the pH was 3 for 12h at 40°C. The kinetic model fitting results showed that the adsorption of dyes by UCHP conformed to the pseudo-second-order kinetic model. Adsorption thermodynamics study showed that the Langmuir model has the highest fitting result. The amino group contained on the surface of cattle hair powder and the amide bond contained in the molecular chain of peptide chain have better electrostatic adsorption binding force for acid metal complex dyes, and the binding between them is mainly electrostatic attraction. The experimental results show that the ultrafine powder has better adsorption property, which provides a high-value conversion way for recycling waste cattle hair.

From Meteorite to Life's Building Blocks: A possible Electrochemical Pathway to Amino Acids and Peptide Bonds.

This study explores the electrochemical properties of the carbonaceous Allende CV3 meteorite, focusing on its potential as a Fe-based catalyst derived from Mackinawite iron sulfide for electrocatalytic reactions facilitating nitrogen (N2) fixation into ammonia. Through comprehensive analysis, we not only monitored the evolution of key compounds such as CN-, sulfur/H2S, H2 and carbonyl compounds, but also identified potential reagent carriers, indicating significant implications for the Strecker synthesis of amino acids in space environments. Initial examination revealed the presence of polypeptides, notably sequences including dimer Ala-α-HO-Gly, pentamer Gly3-Ala2, and hexamer Gly4-(HO-Gly)2. These discoveries greatly enhance our understanding of astrobiological chemistry, offering valuable insights into prebiotic processes and the potential presence of life-building blocks throughout the universe.

Organophotocatalytic Selective Deuteration of Metabolically Labile Heteroatom Adjacent C-H Bonds via H/D Exchange with D2O.

We report a general approach for efficient deuteration of the metabolically labile α-C-H bonds of widespread amides and amines. Temporarily masking the secondary amine group as a carbamate allows an unprecedented photoredox hydrogen atom transfer-promoted α-carbamyl radical formation for efficient H/D exchange with D2O. The mild protocol delivers structurally diverse α-deuterated secondary amines including "privileged" piperidine and piperazine structures highly regioselectively with excellent levels of deuterium incorporation (≤100%). Furthermore, we successfully implemented the strategy for α-deuteration of amides, lactams, and ureas with high regioselectivity and high levels of D incorporation. Finally, the observed efficient deuteration of secondary alcohol moieties in late-stage modification of complex amine-containing pharmaceuticals allows for the development of a viable method for efficient α-deuteration of the important functionality.

From Catalysis of Evolution to Evolution of Catalysis.

ConspectusThe mystery of the origins of life is one of the most difficult yet intriguing challenges to which humanity has grappled. How did biopolymers emerge in the absence of enzymes (evolved biocatalysts), and how did long-lasting chemical evolution find a path to the highly selective complex biology that we observe today? In this paper, we discuss a chemical framework that explores the very roots of catalysis, demonstrating how standard catalytic activity based on chemical and physical principles can evolve into complex machineries. We provide several examples of how prebiotic catalysis by small molecules can be exploited to facilitate polymerization, which in biology has transformed the nature of catalysis. Thus, catalysis evolved, and evolution was catalyzed, during the transformation of prebiotic chemistry to biochemistry. Traditionally, a catalyst is defined as a substance that (i) speeds up a chemical reaction by lowering activation energy through different chemical mechanisms and (ii) is not consumed during the course of the reaction. However, considering prebiotic chemistry, which involved a highly diverse chemical space (i.e., high number of potential reactants and products) and constantly changing environment that lacked highly sophisticated catalytic machinery, we stress here that a more primitive, broader definition should be considered. Here, we consider a catalyst as any chemical species that lowers activation energy. We further discuss various demonstrations of how simple prebiotic molecules such as hydroxy acids and mercaptoacids promote the formation of peptide bonds via energetically favored exchange reactions. Even though the small molecules are partially regenerated and partially retained within the resulting oligomers, these prebiotic catalysts fulfill their primary role. Catalysis by metal ions and in complex chemical mixtures is also highlighted. We underline how chemical evolution is primarily dictated by kinetics rather than thermodynamics and demonstrate a novel concept to support this notion. Moreover, we propose a new perspective on the role of water in prebiotic catalysis. The role of water as simply a "medium" obscures its importance as an active participant in the chemistry of life, specifically as a very efficient catalyst and as a participant in many chemical transformations. Here we highlight the unusual contribution of water to increasing complexification over the course of chemical evolution. We discuss possible pathways by which prebiotic catalysis promoted chemical selection and complexification. Taken together, this Account draws a connection line between prebiotic catalysis and contemporary biocatalysis and demonstrates that the fundamental elements of chemical catalysis are embedded within today's biocatalysts. This Account illustrates how the evolution of catalysis was intertwined with chemical evolution from the very beginning.

A Structural Investigation of the Interaction between a GC-376-Based Peptidomimetic PROTAC and Its Precursor with the Viral Main Protease of Coxsackievirus B3

The conservation of the main protease in viral genomes, combined with the absence of a homologous protease in humans, makes this enzyme family an ideal target for developing broad-spectrum antiviral drugs with minimized host toxicity. GC-376, a peptidomimetic 3CL protease inhibitor, has shown significant efficacy against coronaviruses. Recently, a GC-376-based PROTAC was developed to target and induce the proteasome-mediated degradation of the dimeric SARS-CoV-2 3CLPro protein. Extending this approach, the current study investigates the application of the GC-376 PROTAC to the 3CPro protease of enteroviruses, specifically characterizing its interaction with CVB3 3CPro through X-ray crystallography, NMR (Nuclear Magnetic Resonance) and biochemical techniques. The crystal structure of CVB3 3CPro bound to the GC-376 PROTAC precursor was obtained at 1.9 Å resolution. The crystallographic data show that there are some changes between the binding of CVB3 3CPro and SARS-CoV-2 3CLPro, but the overall similarity is strong (RMSD on C-alpha 0.3 Å). The most notable variation is the orientation of the benzyloxycarbonyl group of GC-376 with the S4 subsite of the proteases. NMR backbone assignment of CVB3 3CPro bound and unbound to the GC-376 PROTAC precursor (80% and 97%, respectively) was obtained. This information complemented the investigation, by NMR, of the interaction of CVB3 3CPro with the GC-376 PROTAC, and its precursor allows us to define that the GC-376 PROTAC binds to CVB3 3CPro in a mode very similar to that of the precursor. The NMR relaxation data indicate that a quench of dynamics of a large part of the protein backbone involving the substrate-binding site and surrounding regions occurs upon GC-376 PROTAC precursor binding. This suggests that the substrate cavity, by sampling different backbone conformations in the absence of the substrate, is able to select the suitable one necessary to covalently bind the substrate, this being the latter reaction, which is the fundamental step required to functionally activate the enzymatic reaction. The inhibition activity assay showed inhibition potency in the micromolar range for GC-376 PROTAC and its precursor. Overall, we can conclude that the GC-376 PROTAC fits well within the binding sites of both proteases, demonstrating its potential as a broad-spectrum antiviral agent.

Arylacetamide deacetylase regulates hepatic iron homeostasis to protect against carbon tetrachloride-induced ferroptosis.

Arylacetamide deacetylase (AADAC) catalyzes the hydrolysis of small molecules containing ester and amide bonds. Recently, it has been reported that AADAC can suppress reactive oxygen species production in cancer cells. This study aimed to elucidate the possibility that AADAC protects against drug-induced liver injury accompanied by oxidative stress and to explore its molecular mechanisms. Intraperitoneal administration of carbon tetrachloride induced significantly more severe liver injury in Aadac knockout (KO) mice (plasma alanine aminotransferase level: 19,381 ± 10,578 U/L) than in wild-type (WT) mice (7219 ± 4729 U/L). More severe liver injury in Aadac KO mice was accompanied by higher hepatic malondialdehyde and antioxidant gene mRNA levels than those in WT mice. The increase in plasma alanine aminotransferase levels in Aadac KO mice was substantially suppressed by pretreatment with the ferroptosis inhibitors deferoxamine or ferrostatin-1, suggesting that Aadac deficiency increases susceptibility to ferroptosis. Immunoprecipitation followed by proteomic analysis revealed that AADAC interacts with ceruloplasmin (CP), which oxidizes ferrous iron to ferric iron. Hepatic CP activity was significantly lower in Aadac KO mice than that in WT mice, resulting in elevated hepatic ferrous iron levels in Aadac KO mice. Overexpression of human AADAC in Huh-7 cells significantly attenuated carbon tetrachloride-induced cytotoxicity by suppressing ferrous iron accumulation, suggesting that AADAC interacts with CP to suppress hepatic ferrous iron accumulation. The hepatoprotective role of Aadac in ferroptosis was also observed in mice with acetaminophen-induced liver injury. This study demonstrates a novel function of AADAC in protecting against ferroptosis induced by hepatotoxicants, carbon tetrachlorideand acetaminophen.

Innovative On-Resin and in Solution Peptidomimetics Synthesis via Metal-Free Photocatalytic Approach.

Nowadays, peptidomimetics are widely studied, being useful tools in drug discovery and medicinal chemistry. The coupling between a carboxylic acid with an amine to form a peptide bond is the most common reaction to obtain peptides/peptidomimetics. In this work, we have investigated an innovative metal-free photoredox-catalyzed carbamoylation to form peptidomimetics thanks to the reaction between dihydropyridines functionalized with amino acids (or peptide sequences) and differently functionalized imines. As the organic photocatalyst, we used 4CzIPN, a donor-acceptor cyanoarene vastly used in photoredox catalysis. By easily modulating the amino acid (or peptide sequence), which is directly attached to the dihydropyridine, we proposed this key-reaction as new valuable method to obtain peptidomimetics, in situ building the not-natural portion of the sequence. Moreover, we successfully employed this methodology in solid phase peptide synthesis, both inserting the new photoredox-generated amino acid at the end or in the middle of the sequence. Peptides with different lengths and secondary structures were prepared, proving the success of this approach, even in sterically hindered environment. Herein, to the best of our knowledge, we describe the first photocatalytic protocol which allows the building of the peptide backbone, with the possibility of simultaneously inserting a non-coded amino acid in the sequence.

Complementary Strategies for Installation of Thioimidates into Peptide Backbones.

Thioimidates are a precursor and synthetic branch point to access either thioamide or amidine isosteres of the native amide (peptide bond). Previous syntheses of thioimidate-containing peptides were prone to side reactivity and required slow, cumbersome steps that were difficult to monitor. We describe a more efficient approach to directly couple thioimidates onto the growing peptide chain. This work also outlines optimal conditions for thioimidate formation on solid support and identifies potential off-target sites for alkylation that impact the choice of protecting group.

Electrochemical Amide Bond Formation via Chemoselective Oxidation of Hemiaminals with Gold Electrocatalyst

Electrochemical Amide Bond Formation via Chemoselective Oxidation of Hemiaminals with Gold Electrocatalyst