Peptide Bond Research Articles

Bioisosteres at C9 of 2-Deoxy-2,3-didehydro-N-acetyl Neuraminic Acid Identify Selective Inhibitors of NEU3.

Human neuraminidases play critical roles in many physiological and pathological processes. Humans have four isoenzymes of NEU, making selective inhibitors important tools to investigate the function of individual isoenzymes. A typical scaffold for NEU inhibitors is 2-deoxy-2,3-didehydro-N-acetylneuraminic acid (DANA) where C9 modifications can be critical for potency and selectivity against human NEU. To design improved DANA analogues, we generated a library of compounds with either a short alkyl chain or a biphenyl substituent linked to the C9 position through one of six amide bioisosteres. Bioisostere linkers included triazole, urea, thiourea, carbamate, thiocarbamate, and sulfonamide groups. Within this library, we identified a C9 biphenyl carbamate derivative (963) that showed high selectivity and potency for NEU3 (Ki = 0.12 ± 0.01 μM). In contrast, NEU1 and NEU4 isoenzymes preferred amide and triazole linkers, respectively. Finally, analogues with urea, sulfonamide, and amide linkers showed enhanced inhibitory activity for a bacterial NEU, NanI from Clostridium perfringens.

Encapsulation of octadecane through crosslinking of cellulose nanofibrils at the interface of Pickering emulsion: Effect of ionic strength on cellulose assembly and capsule shell properties

Emulsion interfacial polymerization is a versatile approach for the encapsulation of organic phase-change materials to improve their stability and prevent their elution and leakage. Herein, we report the successful octadecane encapsulation by the preparation of Pickering emulsions stabilized with carboxylated cellulose nanofibrils (CNF) at various ionic strengths of the dispersive medium. The stable capsule shells were obtained through the formation of amide bonds in the reaction with polymeric isocyanate dissolved in the oil phase. The addition of 5–200 mM NaCl resulted in different adsorption behaviors of carboxylated CNF, which led to an increase in capsule shell thickness (up to 530 nm), improved octadecane encapsulation efficiency (up to 78 %) and thermal stability, as well as reduced elution in organic medium with increasing ionic strength. The study presents a new strategy for the encapsulation of phase-change materials by surfactant-free emulsion interfacial polymerization into containers with defined and adjustable properties.

Structure-Activity Relationship of Oxacyclo- and Triazolo-Containing Respiratory Syncytial Virus Polymerase Inhibitors.

Despite the availability of medicines preventing respiratory syncytial virus (RSV) infection, post-exposure treatment options are needed for addressing patient's needs. RSV non-nucleoside polymerase inhibitors (NNI) have emerged as a promising asset for which our group previously disclosed JNJ-8003 with potent in vitro antiviral activity and pronounced in vivo efficacy. In this work, a structural-guided design to modify the linker vector of JNJ-8003 resulted in the identification of 2-oxacyclo pyridine-containing derivatives whose various ring closing strategies are described. In addition, bioisosteric replacement of an amide bond with triazole retained potency, and cryo-electron microscopy (cryo-EM) confirmed binding in the capping domain. Subsequent NMR conformational analysis suggested a correlation between the potency and conformations. Our efforts have fulfilled the aim of identifying linker modifications with maintained biological activity while enriching structural diversity and allowing modulations of other parameters.

The conformational properties of alamethicin in ethanol studied by NMR.

Alamethicin, a peptide consisted of 20 amino acid residues, has been known to function as an antibiotic. The peptides self-associate in biological membranes, form an ion channel, and then induce cell death by leaking intracellular contents through a transmembrane pore of an ion channel. We investigated conformation and its thermal stability of alamethicin-A6 and -U6 in ethanol using proton nuclear magnetic resonance (NMR) spectroscopy; alamethicin-A6 and -U6 have the amino acid sequences of UPUAUAQUVUGLUPVUUQQO and UPUAUUQUVUGLUPVUUQQO, respectively, where U and O represent α-aminoisobutyric acid and phenylalaninol, respectively. As indicated by the under bars in the sequences, only the residue 6 differs between the alamethicins. We show that the alamethicins in ethanol form helix conformation in the region of the residues 2-11 and a non-regular conformation in the regions of the N- and C-termini, and that the helices are maintained up to 66°C at least. Conformations in the region of the residues 12-18 of the alamethicins, however, are not well identified due to the lack of NMR data. In addition, we demonstrate that the amide proton chemical shift temperature coefficients' method, which is known as an indicator for intramolecular hydrogen bonds in peptides and proteins in aqueous solutions, can be also applied to the alamethicins in ethanol. Further, we show that the conformation around the C-terminus of alamethicin-A6 is restrained by intramolecular hydrogen bonds, whereas that of alamethicin-U6 is either restrained or unrestrained by intramolecular hydrogen bonds; the alamethicin-U6 molecules having the restrained and unrestrained conformations coexist in ethanol. We discuss the two types of conformations using a model chain consisting of particles linked by rigid bonds called as the free jointed chain.

Design, synthesis and anti-HBV activity study of novel HBV capsid assembly modulators

Capsid assembly modulators (CAMs) have the potential to cure chronic hepatitis B, as demonstrated in clinical trials. Lead compounds NVR3-778 and 5a were found to exist in normal and flipped conformations through induced fit docking. Therefore, we designed and synthesized series I and II compounds by interchanging the amide and sulfonamide bonds of 5a to modify both the tolerance region and solvent-opening region. Among them, compound 4a (EC50 = 0.24 ± 0.10 μM, CC50 > 100 μM) exhibited potent anti-HBV activity with low toxicity, surpassing the lead compounds NVR3-778 (EC50 = 0.29 ± 0.03 μM, CC50 = 20.78 ± 2.29 μM) and 5a (EC50 = 0.50 ± 0.07 μM, CC50 = 48.16 ± 9.15 μM) in HepAD38 cells. Additionally, compared with the lead compound, 4a displayed a stronger inhibitory effect on HBV capsid protein assembly. Molecular dynamics (MD) simulations confirmed that the normal conformation of 4a had relatively stable conformation at different frames of binding modes. Furthermore, 4a showed better metabolic stability in human plasma than positive control drugs. Therefore, compound 4a could be further structurally modified as a potent lead compound.

Structure-based molecular characterization of a putative aspartic proteinase from Bacteroides fragilis

Bacteroides fragilis resides in mammals and human intestines and secrete series of proteins and molecules outside that cause various diseases such as colon cancer and chronic colitis in the host. B. fragilis has been shown to produce numerous proteins to the infected cell surface which are involved in host colonization, microbial interactions, and pathogenicity. Among secreted proteins, a B. fragilis toxin (BFT) is a metalloprotease and disintegrates the epithelial cell layer and causes colon cancers. Except the BFT, information of secreted proteases from B. fragilis is limited and no structure is available. Aspartic proteinase cleaves a peptide bond using two aspartate residues in a catalytic site in acidic conditions, pH ranges from 3 to 6. Aspartic proteinase have been characterized mostly from eukaryotes and retroviruses but rare from bacteria including B. fragilis. A putative aspartic proteinase is identified from the B. fragilis genome and prepared recombinantly as a Bacteroides aspartic proteinase (BAPtase). The crystal structure of BAPtase was determined at 2.6 Å. Structure-based comparative and endopeptidase analyses demonstrated that BAPtase presents a two-domain structure and is a functional aspartic proteinase in unusually weak basic pHs, which would propose to be a critical in bacterial pathogenesis and in host immunity. Our observations on the distinct structural and catalytic properties of BAPtase would benefit the future development of B. fragilis-specific drugs or preventatives.

A sensitive benzothiazole fluorescent probe for the detection of γ-glutamyl transpeptidase activity and its application.

A sensitive benzothiazole fluorescent probe (PBZO) for the detection of γ-glutamyl transpeptidase (GGT) activity was developed. Based on the enzymatic hydrolysis of peptide bonds by glutamyl transpeptidase, it can be specifically recognized by PBZO. The PBZO has a good linear relationship with different gradients of GGT activity at the emission wavelength of 560 nm, the Stokes shift reached 215 nm, and the detection limit of GGT activity is 0.1644 U/ml. With the increase of GGT concentration in the probe solution, the color of the solution gradually changed from orange to dark yellow under the 365 nm UV lamp. The same color change was also observed on the probe test paper. In addition, there is a linear relationship between the GGT activity and the R-value of the probe solution. More importantly, the probe has a good recovery rate in serum. Therefore, this probe can be used as a convenient tool for detecting GGT activity.

Accurate Structure Prediction for Cyclic Peptides Containing Proline Residues with High-Temperature Molecular Dynamics.

Cyclic peptides (CPs) are emerging as promising drug candidates. Numerous natural CPs and their analogs are effective therapeutics against various diseases. Notably, many of them contain peptidyl cis-prolyl bonds. Due to the high rotational barrier of peptide bonds, conventional molecular dynamics simulations struggle to effectively sample the cis/trans-isomerization of peptide bonds. Previous studies have highlighted the high accuracy of the residue-specific force field (RSFF) and the high sampling efficiency of high-temperature molecular dynamics (high-T MD). Herein, we propose a protocol that combines high-T MD with RSFF2C and a recently developed reweighting method based on probability densities for accurate structure prediction of proline-containing CPs. Our method successfully predicted 19 out of 23 CPs with the backbone rmsd < 1.0 Å compared to X-ray structures. Furthermore, we performed high-T MD and density reweighting on the sunflower trypsin inhibitor (SFTI-1)/trypsin complex to demonstrate its applicability in studying CP-complexes containing cis-prolines. Our results show that the conformation of SFTI-1 in aqueous solution is consistent with its bound conformation, potentially facilitating its binding.

Pilot screening of potential matrikines resulting from collagen breakages through ionizing radiation

Little is known regarding radiation-induced matrikines and the possible degradation of extracellular matrix following therapeutic irradiation. The goal of this study was to determine if irradiation can cut collagen proteins at specific sites, inducing potentially biologically active peptides against cartilage cells. Chondrocytes cultured as 3D models were evaluated for extracellular matrix production. Bystander molecules were analyzed in vitro in the conditioned medium of X-irradiated chondrocytes. Preferential breakage sites were analyzed in collagen polypeptide by mass spectrometry and resulting peptides were tested against chondrocytes. 3D models of chondrocytes displayed a light extracellular matrix able to maintain the structure. Irradiated and bystander chondrocytes showed a surprising radiation sensitivity at low doses, characteristic of the presence of bystander factors, particularly following 0.1 Gy. The glycine-proline peptidic bond was observed as a preferential cleavage site and a possible weakness of the collagen polypeptide after irradiation. From the 46 collagen peptides analyzed against chondrocytes culture, 20 peptides induced a reduction of viability and 5 peptides induced an increase of viability at the highest concentration between 0.1 and 1 µg/ml. We conclude that irradiation promoted a site-specific degradation of collagen. The potentially resulting peptides induce negative or positive regulations of chondrocyte growth. Taken together, these results suggest that ionizing radiation causes a degradation of cartilage proteins, leading to a functional unbalance of cartilage homeostasis after exposure, contributing to cartilage dysfunction.

An Infrared Nanospectroscopy Technique for the Study of Electric-Field-Induced Molecular Dynamics.

Static electric fields play a considerable role in a variety of molecular nanosystems as diverse as single-molecule junctions, molecules supporting electrostatic catalysis, and biological cell membranes incorporating proteins. External electric fields can be applied to nanoscale samples with a conductive atomic force microscopy (AFM) probe in contact mode, but typically, no structural information is retrieved. Here we combine photothermal expansion infrared (IR) nanospectroscopy with electrostatic AFM probes to measure nanometric volumes where the IR field enhancement and the static electric field overlap spatially. We leverage the vibrational Stark effect in the polymer poly(methyl methacrylate) for calibrating the local electric field strength. In the relevant case of membrane protein bacteriorhodopsin, we observe electric-field-induced changes of the protein backbone conformation and residue protonation state. The proposed technique also has the potential to measure DC currents and IR spectra simultaneously, insofar enabling the monitoring of the possible interplay between charge transport and other effects.

Novel Bifunctional Amidase Catalyzing the Degradation of Propanil and Aryloxyphenoxypropionate Herbicides in Rhodococcus sp. C-1.

Propanil residues can contaminate habitats where microbial degradation is predominant. In this study, an efficient propanil-degrading strain C-1 was isolated from paddy and identified as Rhodococcus sp. It can completely degrade 10 μg/L-150 mg/L propanil within 0.33-10 h via the hydrolysis of the amide bond, forming 3,4-dichloroaniline. A novel bifunctional amidase, PamC, was identified in strain C-1. PamC can catalyze the hydrolysis of the amide bond of propanil to produce 3,4-dichloroaniline as well as the hydrolysis of the ester bonds of aryloxyphenoxypropionate herbicides (APPHs, clodinafop-propargyl, cyhalofop-butyl, fenoxaprop-p-ethyl, fluazifop-p-butyl, haloxyfop-p-methyl, and quizalofop-p-ethyl) to form aryloxyphenoxypropionic acids. Molecular docking and site-directed mutagenesis confirmed that the catalytic triad Lys82-Ser157-Ser181 was the active center for PamC to hydrolyze propanil and cyhalofop-butyl. This study presents a novel bifunctional amidase with capabilities for both amide and ester bond hydrolysis and enhances our understanding of the molecular mechanisms underlying the degradation of propanil and APPHs.

Insights into Peptidyl-Prolyl cis-trans Isomerases from Clinically Important Protozoans: From Structure to Potential Biotechnological Applications.

Peptidyl-prolyl cis/trans isomerases (PPIases) are present in a wide variety of microorganisms, including protozoan parasites such as Trypanosoma cruzi, Trypanosoma brucei, Trichomonas vaginalis, Leishmania major, Leishmania donovani, Plasmodium falciparum, Plasmodium vivax, Entamoeba histolytica, Giardia intestinalis, Cryptosporidium parvum, and Cryptosporidium hominis, all of which cause important neglected diseases. PPIases are classified as cyclophilins, FKBPs, or parvulins and play crucial roles in catalyzing the cis-trans isomerization of the peptide bond preceding a proline residue. This activity assists in correct protein folding. However, experimentally, the biological structure-function characterization of PPIases from these protozoan parasites has been poorly addressed. The recombinant production of these enzymes is highly relevant for this ongoing research. Thus, this review explores the structural diversity, functions, recombinant production, activity, and inhibition of protozoan PPIases. We also highlight their potential as biotechnological tools for the in vitro refolding of other recombinant proteins from these parasites. These applications are invaluable for the development of diagnostic and therapeutic tools.

A dual-mode electrochemical biosensor based on GO-Fe3O4 doped PEDOT nanocomposite for the ultrasensitive assay of microRNA

MicroRNA, as a distinctive biomarker, plays a crucial role in the early prognosis and diagnosis of numerous severe diseases. However, due to its inherent properties such as low abundance, small size, and high sequence similarity, the sensitive and accurate detection of microRNA remains a major challenge. Herein, a dual-mode electrochemical biosensing platform was developed for microRNA detection, based on poly(3,4-ethylenedioxythiophene) (PEDOT) doped with graphene oxide-Fe3O4 (GO-Fe3O4) nanocomposite. The GO-Fe3O4/PEDOT composite demonstrated a porous microstructure, outstanding conductivity, and robust catalytic activity towards nitrite. It was electrodeposited onto the electrode surface in a one-step process using the cyclic voltammetry method (CV). The microRNA biosensor was obtained by anchoring DNA with amino groups to the GO-Fe3O4/PEDOT layer through the formation of amide bonds. The designed dual-mode microRNA biosensor demonstrated a broad linear range spanning from 10−15 M to 10−6 M, with low detection limits of 5.18 × 10−15 M and 7.36 × 10−15 M when using chronocoulometry (CC) and amperometric i-t curve (i-t) modes, respectively. Furthermore, a dual-mode electrochemical biosensor has been successfully developed and utilized for the detection of microRNA in human serum, demonstrating its potential for precise and sensitive microRNA detection and its practical application value in clinical medicine.

Eudragit-maleimide as total denture base material: Proof of concept for a promising mucoadhesive strategy

AimTo develop an Eudragit S100-2(aminoethyl) maleimide (ES100-AEMal) conjugate as total denture base material candidate and to prove mucoadhesive properties. Methods2-(N-aminoethyl) maleimide (AEMal) was attached to Eudragit S100 (ES100) backbone via amide bond formation resulting in ES100-AEMal. After characterization of the product via nuclear magnetic resonance, infrared spectroscopy, and quantification of attached maleimide groups by a quantification assay kit, safety was assessed following the 3-(4,5-dimethylthiazolyl-2)-2,5-diphenyltetrazolium bromide assay towards Caco-2 cells and fibroblasts. In addition, membrane damage was tested using human erythrocytes. Mucoadhesive properties were examined on gingiva in terms of rheometry and detachment time. ResultsThe successfully synthesized conjugate ES100-AEMal presented a 15 % degree of modification and no toxicity or membrane damage could be observed after one day of incubation. Mucoadhesiveness exhibited 239.91-fold, 490.6-fold and 24.15-fold increase in elastic modulus, viscous modulus, and dynamic viscosity, respectively. Furthermore, detachment time was enhanced 47.5-fold. ConclusionES100-AEMal demonstrated enhancement in gingival mucoadhesiveness maintaining biocompatibility.

Quantum Cascade Laser Infrared Spectroscopy for Glycan Analysis of Glycoprotein Solutions.

Glycans are oligosaccharides attached to proteins or lipids and affect their functions, such as drug efficacy, structural contribution, metabolism, immunogenicity, and molecular recognition. Conventional glycosylation analysis has relied on destructive, slow, system-sensitive methods, including enzymatic reactions, chromatography, fluorescence labeling, and mass spectrometry. Herein, we propose quantum cascade laser (QCL) infrared (IR) spectroscopy as a rapid, nondestructive method to quantify glycans and their monosaccharide composition. Previously, we demonstrated high-sensitivity IR spectroscopy of protein solution using solvent absorption compensation (SAC) and double-beam modulation (DBM) techniques. However, the SAC-DBM approach suffered a limited frequency scanning range (<400 cm-1) due to the light dispersion by acousto-optic modulators (AOMs). Here, we implemented a mirror-based double-pass AOM in the SAC-DBM scheme and successfully extended the frequency range to (970 to 1840 cm-1), which encompasses the vibrational fingerprint of biomolecules. The extended frequency range allowed the simultaneous observation of monosaccharide ring bands (1000 to 1200 cm-1) and protein amide bands (1500 to 1700 cm-1). We compared the IR spectra of six glycoproteins and two nonglycosylated proteins with the results from intact mass spectrometry. The IR absorbance ratios of the ring band to the amide band of glycoproteins in solutions showed a linear correlation with the ratios of glycan to protein backbone masses. Furthermore, a multivariate analysis produced monosaccharide compositions consistent with the reported database for the glycoproteins, and the monosaccharide compositions were used to improve the predictability of the glycan-protein mass ratio from the IR-absorbance ratio. This nondestructive, high-sensitivity QCL-IR spectroscopy could be used as a standard method to monitor batch-to-batch comparability during drug manufacturing and quantify the glycosylation and monosaccharide composition of new glycoproteins and other glycosylated biosystems.

Highly thermally conductive and flexible nanocomposites prepared by integrating 1D/2D polyethyleneimine-modified boron nitride

Thermally conductive composites rely on efficient heat transfer networks. Here, we employ polyethyleneimine to modify 1D boron nitride nanotubes (BNNTs) and 2D boron nitride nanosheets (BNNSs) to improve their dispersion while enhancing the interfacial interaction between them and the matrix through amide bonds, hydrogen bonds, and Lewis acid-base interactions, thereby reducing interfacial thermal resistance. Moreover, the introduction of 1D BNNTs bridges 2D BNNSs, boosting the thermal conductivity network. This resulted in an enhanced thermal conductivity of the composite film by 17.8 %, reaching 28.71 W/(m·K) at a 30 wt% filler content. Coupled with satisfactory mechanical strength and thermal stability, this heat dissipation capability is highly valuable for applications.

The Utilization Of Field Snails Into Soy Sauce Ingredients Enzymatically Regardless Of The Physical Quality

Rice soy sauce is a thick liquid made from snail meat juice . Soy sauce can be made in 2 ways, namely, traditionally/fermentation and by adding enzymes. Making soy sauce does not require a particular type of snail . In this research, we will study the use of rice snails to make rice snail sauce enzymatically. The aim of this research is to determine the effect of adding crushed pineapple tubers and fermentation time on the physical, chemical and organoleptic quality of the rice snail soy sauce produced. Proteolytic enzymes can break down and decompose proteins. Bromelain proteolytic enzymes can break down protein molecules into amino acids, enzymes that hydrolyze peptide bonds in the middle. This research used a completely randomized design (CRD) with a factorial pattern with 2 factors and 3 replications. The first factor was the addition of crushed pineapple tubers (10%), (15%), and (20%) and the second factor was the fermentation time (5.7 and 9 days). The results of this research show that when increasing the number of workers from 4 to 6 people, variable costs increase, but the number of rice snails produced increases , therefore the cost per bottle produced (marginal variable coast) decreases. The tendency to increase productivity often occurs when companies initiate production expansion. T et fire This is not the case if the company continues to expand production by continuing to increase the workforce employed.

Ubiquitin-derived artificial binding proteins targeting oncofetal fibronectin reveal scaffold plasticity by β-strand slippage

Affilin proteins, artificial binding proteins based on the ubiquitin scaffold, have been generated by directed protein evolution to yield de-novo variants that bind the extra-domain B (EDB) of oncofetal fibronectin, an established marker of tumor neovasculature. The crystal structures of two EDB-specific Affilin variants reveal a striking structural plasticity of the ubiquitin scaffold, characterised by β-strand slippage, leading to different negative register shifts of the β5 strands. This process recruits amino acid residues from β5 towards the N-terminus to an adjacent loop region and subsequent residues into β5, respectively, remodeling the binding interface and leading to target specificity and affinity. Protein backbone alterations resulting from β-strand register shifts, as seen in the ubiquitin fold, can pose additional challenges to protein engineering as structural evidence of these events is still limited and they are difficult to predict. However, they can surface under the selection pressure of directed evolution and suggest that backbone plasticity allowing β-strand slippages can increase structural diversity, enhancing the evolutionary potential of a protein scaffold.

A Fluorescent Probe for the Detection of γ‐Glutamyl Transpeptidase Activity and its Application in Garlic

AbstractA fluorescent probe (probe 1) was developed for detection the activity of γ‐glutamyl transpeptidase (GGT). Probe 1 could recognize GGT by the enzymatic hydrolysis of peptide bond by GGT. There has a linear relationship between the fluorescence intensity of probe 1 at 416 nm and the activity of GGT, and the detection limit of GGT activity was 0.0796 U/mL. And the color of the probe solution gradually changed from light blue to bright yellow with the increase of GGT activity under 365 nm ultraviolet light. Importantly, the activity of GGT was linearly related to the photo of the probe solution with B/(R+G) value. Probe 1 could detect GGT activity by smartphone without professional equipment. Furthermore, the probe has been successfully applied to detect of GGT activity in garlic.

General instability of dipeptides in concentrated sulfuric acid as relevant for the Venus cloud habitability

Recent renewed interest in the possibility of life in the acidic clouds of Venus has led to new studies on organic chemistry in concentrated sulfuric acid. We have previously found that the majority of amino acids are stable in the range of Venus’ cloud sulfuric acid concentrations (81% and 98% w/w, the rest being water). The natural next question is whether dipeptides, as precursors to larger peptides and proteins, could be stable in this environment. We investigated the reactivity of the peptide bond using 20 homodipeptides and find that the majority of them undergo solvolysis within a few weeks, at both sulfuric acid concentrations. Notably, a few exceptions exist. HH and GG dipeptides are stable in 98% w/w sulfuric acid for at least 4 months, while II, LL, VV, PP, RR and KK resist hydrolysis in 81% w/w sulfuric acid for at least 5 weeks. Moreover, the breakdown process of the dipeptides studied in 98% w/w concentrated sulfuric acid is different from the standard acid-catalyzed hydrolysis that releases monomeric amino acids. Despite a few exceptions at a single concentration, no homodipeptides have demonstrated stability across both acid concentrations studied. This indicates that any hypothetical life on Venus would likely require a functional substitute for the peptide bond that can maintain stability throughout the range of sulfuric acid concentrations present.