Peptide Amide Research Articles

A New Wave of Amide Bond Formations for Peptide Synthesis

The construction of peptidic amide bonds has become a daily laboratory practice by virtue of well-established ‘coupling reagents’. Nonetheless, inherent limitations connected to these classical coupling methods in terms of waste, safety and expense have yet to be conquered. Research efforts have been devoted to synthetic methods able to surpass these limitations. This short review focuses on the advances made in these ‘non-classical’ methods for amide bond formation with a specific application in peptide chemistry. It consists of two main sections: (i) novel carboxylic activation reagents, and (ii) carboxylic acid and amine surrogates.1 Introduction2 Alternative Carboxylic acid Activation Reagents3 Carboxylic Acid and Amine Surrogates4 Conclusion and Perspectives

Functional Implications of RFRP-3 in the Central Control of Daily and Seasonal Rhythms in Reproduction.

Adaptation of reproductive activity to environmental changes is essential for breeding success and offspring survival. In mammals, the reproductive system displays regular cycles of activation and inactivation which are synchronized with seasonal and/or daily rhythms in environmental factors, notably light intensity and duration. Thus, most species adapt their breeding activity along the year to ensure that birth and weaning of the offspring occur at a time when resources are optimal. Additionally, female reproductive activity is highest at the beginning of the active phase during the period of full oocyte maturation, in order to improve breeding success. In reproductive physiology, it is therefore fundamental to delineate how geophysical signals are integrated in the hypothalamo-pituitary-gonadal axis, notably by the neurons expressing gonadotropin releasing hormone (GnRH). Several neurochemicals have been reported to regulate GnRH neuronal activity, but recently two hypothalamic neuropeptides belonging to the superfamily of (Arg)(Phe)-amide peptides, RFRP-3 and kisspeptin, have emerged as critical for the integration of environmental cues within the reproductive axis. The goal of this review is to survey the current understanding of the role played by RFRP-3 in the temporal regulation of reproduction, and consider how its effect might combine with that of kisspeptin to improve the synchronization of reproduction to environmental challenges.

Short Peptides with Uncleavable Peptide Bond Mimetics as Photoactivatable Caspase-3 Inhibitors.

Chemical probes that covalently interact with proteases have found increasing use for the study of protease function and localization. The design and synthesis of such probes is still a bottleneck, as the strategies to target different families are highly diverse. We set out to design and synthesize chemical probes based on protease substrate specificity with inclusion of an uncleavable peptide bond mimic and a photocrosslinker for covalent modification of the protease target. With caspase-3 as a model target protease, we designed reduced amide and triazolo peptides as substrate mimetics, whose sequences can be conveniently constructed by modified solid phase peptide synthesis. We found that these probes inhibited the caspase-3 activity, but did not form a covalent bond. It turned out that the reduced amide mimics, upon irradiation with a benzophenone as photosensitizer, are oxidized and form low concentrations of peptide aldehydes, which then act as inhibitors of caspase-3. This type of photoactivation may be utilized in future photopharmacology experiments to form protease inhibitors at a precise time and location.

The role of methylation in the copper(ii) coordination properties of a His-containing decapeptide.

N-Methylation of the peptide amide bond has proven to be a powerful strategy to fine-tune the conformation and properties of peptides. In this context and for the first time, we show that N-methylation can also be used to control the copper(ii) coordination properties of peptides and stabilize at high pH values the copper(ii) species lacking amidate coordination. Namely, we have prepared a derivative of the O-Asp peptide where the copper(ii) coordinating amino acids, i.e. Asp and His residues, were N-methylated (ONMe-Asp). A combined study using potentiometric and spectroscopic (UV-Vis, CD, EPR and NMR) techniques indicates the formation of the wanted major species, [CuH(ONMe-Asp)]2+, where copper(ii) is bound to His4(Nε), His7(Nε), His9(Nε) and Asp2(COO-). With respect to the parent non-methylated O-Asp peptide, [CuH(ONMe-Asp)]2+ is stable at higher pH values but has lower affinity for copper(ii). Additionally, electrochemical studies reveal a Cu(ii) ⇌ Cu(i) redox process with a larger cathodic and anodic peak separation. Species containing copper(ii) coordinating amidates were not observed for this ONMe-Asp peptide.

A New Tool in the Quest for Biocompatible Phthalocyanines: Palladium Catalyzed Aminocarbonylation for Amide Substituted Phthalonitriles and Illustrative Phthalocyanines Thereof

The amide peptide bond type linkage is one of the most natural conjugations available, present in many biological synthons and pharmaceutical drugs. Hence, aiming the direct conjugation of potentially biologically active compounds to phthalocyanines, herein we disclose a new strategy for direct modulation of phthalonitriles, inspired by an attractive synthetic strategy for the preparation of carboxamides based on palladium-catalyzed aminocarbonylation of aryl halides in the presence of carbon monoxide (CO) which, to our knowledge, has never been used to prepare amide-substituted phthalonitriles, the natural precursors for the synthesis of phthalocyanines. Some examples of phthalocyanines prepared thereof are also reported, along with their full spectroscopic characterization and photophysical properties initial assessment.

Amide Bond Activation of Biological Molecules.

Amide bonds are the most prevalent structures found in organic molecules and various biomolecules such as peptides, proteins, DNA, and RNA. The unique feature of amide bonds is their ability to form resonating structures, thus, they are highly stable and adopt particular three-dimensional structures, which, in turn, are responsible for their functions. The main focus of this review article is to report the methodologies for the activation of the unactivated amide bonds present in biomolecules, which includes the enzymatic approach, metal complexes, and non-metal based methods. This article also discusses some of the applications of amide bond activation approaches in the sequencing of proteins and the synthesis of peptide acids, esters, amides, and thioesters.

NEUROPROTECTIVE ROLE OF ASCORBIC ACID: ANTIOXIDANT AND NON-ANTIOXIDANT FUNCTIONS

Ascorbic acid (AA) or Vitamin C is an important antioxidant which participates in numerous cellular functions. Although in human plasma its concentration is in micromolars but it reaches millimolar concentrations in most of the human tissues. The high ascorbate cellular concentrations are generated and maintained by a specific sodium-dependent Vitamin C transporter type 2 (SVCT2, member of Slc23 family). Metabolic processes recycle Vitamin C from its oxidized forms (ascorbate) inside the cells. AA concentration is highest in the neurons of the central nervous system (CNS) of mammals, and deletion of its transporter affects mice brain and overall survival. In the CNS, intracellular ascorbate serves several functions including antioxidant protection, peptide amidation, myelin formation, synaptic potentiation, and protection against glutamate toxicity. SVCT2 maintains neuronal ascorbate content in CNS which has relevance for neurodegenerative diseases such as Alzheimer’s, Parkinson’s, and Huntington’s disease. As ascorbate supplements decrease infarct size in ischemia-reperfusion injury and protect neurons from oxidative damage, it is a vital dietary antioxidant. The aim of this review is to assess the role of the SVCT2 in regulating neuronal ascorbate homeostasis in CNS and the extent to which ascorbate affects brain function as an antioxidant.

Molecular Basis for Autocatalytic Backbone N-Methylation in RiPP Natural Product Biosynthesis.

N-methylation of nucleic acids, proteins, and peptides is a chemical modification with significant impact on biological regulation. Despite the simplicity of the structural change, N-methylation can influence diverse functions including epigenetics, protein complex formation, and microtubule stability. While there are limited examples of N-methylation of the α-amino group of bacterial and eukaryotic proteins, there are no examples of catalysts that carry out post-translation methylation of backbone amides in proteins or peptides. Recent studies have identified enzymes that catalyze backbone N-methylation on a peptide substrate, a reaction with little biochemical precedent, in a family of ribosomally synthesized natural products produced in basidiomycetes. Here, we describe the crystal structures of Dendrothele bispora dbOphMA, a methyltransferase that catalyzes multiple N-methylations on the peptide backbone. We further carry out biochemical studies of this catalyst to determine the molecular details that promote this unusual chemical transformation. The structural and biochemical framework described here could facilitate biotechnological applications of catalysts for the rapid production of backbone N-methylated peptides.

Cis/trans isomerization of proline peptide bonds in the backbone of cyclic disulfide‐bridged peptides

AbstractPeptides are of interest as potential therapeutic agents, including cyclic disulfide‐bridged peptides because of their limited conformational flexibility and enhanced stability toward proteolysis. To further constrain the flexibility of the peptide backbone, the disulfide‐bridged rings often contain a proline residue, which also serves to facilitate the formation of reverse‐turn structures. However, the proline residue increases the conformational diversity because the tertiary amide peptide bond to proline can exist as significant populations of both the cis and trans isomers. To identify features that affect the distribution between the cis and trans isomers of proline peptide bonds in disulfide‐bridged peptide rings, we have characterized by 1H NMR the kinetics and equilibria of the cis/trans isomerization of the proline peptide bonds for the linear dithiol and cyclic disulfide‐bridged forms of three families of proline‐containing peptides: Ac‐Cys‐Pro‐[NH(CH2)nCO]‐Cys‐NH2, where n = 1‐4; Ac‐Cys‐Xaa‐Pro‐Cys‐NH2 and Ac‐Cys‐Pro‐Xaa‐Cys‐NH2, where Xaa is Gly, Ala and Val; and Ac‐Cys‐Pro‐His‐(Ala)n‐Cys‐NH2, where n = 0‐5. The peptide Ac‐Cys‐Pro‐(4‐AMBA)‐Cys‐NH2, where 4‐AMBA is 4‐aminomethylbenzoic acid, was also studied to determine the effect of a rigid aromatic ring in the peptide backbone on the conformational properties of the Cys‐Pro peptide bond. Equilibrium constants were determined for cis/trans isomerization from the relative intensities of resonances for the cis and trans isomers, and rate constants for cis‐to‐trans and trans‐to‐cis isomerization were determined by the magnetization transfer NMR method. The cis/trans equilibrium is a dynamic equilibrium, and the equilibrium constants vary widely due to the wide range of kinetic stabilities of the various cis and trans isomers.

Accelerated microfluidic native chemical ligation at difficult amino acids toward cyclic peptides

Cyclic peptide-based therapeutics have a promising growth forecast that justifies the development of microfluidic systems dedicated to their production, in phase with the actual transitioning toward continuous flow and microfluidic technologies for pharmaceutical production. The application of the most popular method for peptide cyclization in water, i.e., native chemical ligation, under microfluidic conditions is still unexplored. Herein, we report a general strategy for fast and efficient peptide cyclization using native chemical ligation under homogeneous microfluidic conditions. The strategy relies on a multistep sequence that concatenates the formation of highly reactive S-(2-((2-sulfanylethyl)amino)ethyl) peptidyl thioesters from stable peptide amide precursors with an intramolecular ligation step. With very fast ligation rates (<5 min), even for the most difficult junctions (including threonine, valine, isoleucine, or proline), this technology opens the door toward the scale-independent, expedient preparation of bioactive macrocyclic peptides.

Copper deficiency anemia: review article.

Copper is a crucial micronutrient needed by animals and humans for proper organ function and metabolic processes such as hemoglobin synthesis, as a neurotransmitter, for iron oxidation, cellular respiration, and antioxidant defense peptide amidation, and in the formation of pigments and connective tissue. Multiple factors, either hereditary or acquired, contribute to the increase in copper deficiency seen clinically over the past decades. The uptake of dietary copper into intestinal cells is via the Ctr1 transporter, located at the apical membrane aspect of intestinal cells and in most tissues. Copper is excreted from enterocytes into the blood via the Cu-ATPase, ATP7A, by trafficking the transporter towards the basolateral membrane. Zinc is another important micronutrient in animals and humans. Although zinc absorption may occur by direct interaction with the Ctr1 transporter, its absorption is slightly different. Copper deficiency affects physiologic systems such as bone marrow hematopoiesis, optic nerve function, and the nervous system in general. Detailed pathophysiology and its related diseases are explained in this manuscript. Diagnosis is made by measuring serum copper, serum ceruloplasmin, and 24-h urine copper levels. Copper deficiency anemia is treated with oral or intravenous copper replacement in the form of copper gluconate, copper sulfate, or copper chloride. Hematological manifestations are fully reversible with copper supplementation over a 4- to 12-week period. However, neurological manifestations are only partially reversible with copper supplementation.

Molecular Signature for Receptor Engagement in the Metabolic Peptide Hormone Amylin.

The pancreatic peptide hormone, amylin, plays a critical role in the control of appetite, and synergizes with other key metabolic hormones such as glucagon-like peptide 1 (GLP-1). There is opportunity to develop potent and long-acting analogues of amylin or hybrids between these and GLP-1 mimetics for treating obesity. To achieve this, interrogation of how the 37 amino acid amylin peptide engages with its complex receptor system is required. We synthesized an extensive library of peptides to profile the human amylin sequence, determining the role of its disulfide loop, amidated C-terminus and receptor "capture" and "activation" regions in receptor signaling. We profiled four signaling pathways with different ligands at multiple receptor subtypes, in addition to exploring selectivity determinants between related receptors. Distinct roles for peptide subregions in receptor binding and activation were identified, resulting in peptides with greater activity than the native sequence. Enhanced peptide activity was preserved in the brainstem, the major biological target for amylin. Interpretation of our data using full-length active receptor models supported by molecular dynamics, metadynamics, and supervised molecular dynamics simulations guided the synthesis of a potent dual agonist of GLP-1 and amylin receptors. The data offer new insights into the function of peptide amidation, how allostery drives peptide-receptor interactions, and provide a valuable resource for the development of novel amylin agonists for treating diabetes and obesity.

Quantification of live Lactobacillus acidophilus in mixed populations of live and killed by application of attenuated reflection Fourier transform infrared spectroscopy combined with chemometrics

Since culture-based methods are costly and time consuming, alternative methods are investigated for the quantification of probiotics in commercial products. In this work ATR- FTIR vibration spectroscopy was applied for the differentiation and quantification of live Lactobacillus (La 5) in mixed populations of live and killed La 5, in the absence and in the presence of enteric polymer Eudragit® L 100-55. Suspensions of live (La 5_L) and killed in acidic environment bacillus (La 5_K) were prepared and binary mixtures of different percentages were used to grow cell cultures for colony counting and spectral analysis. The increase in the number of colonies with added%La 5_L to the mixture was log-linear (r2 = 0.926). Differentiation of La 5_L from La 5_K was possible directly from the peak area at 1635 cm−1 (amides of proteins and peptides) and a linear relationship between%La 5_L and peak area in the range 0–95% was obtained. Application of partial least squares regression (PLSR) gave reasonable prediction of%La 5_L (RMSEp = 6.48) in binary mixtures of live and killed La 5 but poor prediction (RMSEp = 11.75) when polymer was added to the La 5 mixture. Application of artificial neural networks (ANNs) improved greatly the predictive ability for%La 5_L both in the absence and in the presence of polymer (RMSEp = 8.11 × 10−8 for La 5 only mixtures and RMSEp = 8.77 × 10−8 with added polymer) due to their ability to express in the calibration models more hidden spectral information than PLSR.

Recent progress using the Staudinger ligation for radiolabeling applications.

The increasing application of positron emission tomography and single-photon emission computer tomography in radiopharmacy and nuclear medicine has stimulated the development of a multitude of novel and versatile bioorthogonal conjugation techniques. Currently, there is particular interest in radiolabeling biologically active, high molecular weight compounds like peptides, proteins, or antibodies, but also for the labeling of small organic compounds. An enormous challenge in radiolabeling these biologically active molecules is that the introduction of radiohalogens like fluorine-18 as well as various radiometals proceeds under harsh conditions, which could destroy the biomolecule. The Staudinger ligation is one of the most powerful bioorthogonal conjugation techniques. The reaction proceeds over wide temperature and pH ranges; an amide (peptide) bond is formed as the ligation unit, which minimizes distortion of the structure; no isomers are obtained; and the reaction proceeds without any metal catalyst. Due to this adaptability, this robust ligation type is a perfect candidate with a high potential for various applications in the field of radiopharmacy for the labeling of biomolecules under mild conditions. This review summarizes recent research concerning the implementation of the Staudinger ligation for radiolabeling applications.

Nuclear factor-kappa B: Glucocorticoid-induced leucine zipper interface analogs suppress pathology in an Alzheimer's disease model

IntroductionGlucocorticoid-induced leucine zipper is a regulatory protein that sequesters activated nuclear factor-kappa B p65. Previously, we showed that rationally designed analogs of the p65-binding domain of glucocorticoid-induced leucine zipper, referred to as glucocorticoid-induced leucine zipper analogs (GAs), inhibited amyloid β–induced metabolic activity and inflammatory cytokines in mixed brain cell cultures. Here, we investigate the therapeutic efficacy of GA in an Alzheimer's disease model. MethodsGA and control peptides were synthesized covalently as peptide amides with the cell-penetrating agent. C57Bl/6J mice induced with lipopolysaccharide-mediated neuroinflammation (250 mg/kg i.p/day for six days) were treated on alternate days with GA-1, GA-2, or control peptides (25 mg/kg i.v). Brain tissues were assessed for gliosis, cytokines, and antiapoptotic factors. ResultsThe brain tissues of GA-1– and GA-2–treated mice exhibited significantly reduced gliosis, suppressed inflammatory cytokines, and elevated antiapoptotic factors. DiscussionThe antineuroinflammatory effects of GA suggest potential therapeutic application for Alzheimer's disease.

Downregulation of Deiodinase 3 is the earliest event in photoperiodic and photorefractory activation of the gonadotropic axis in seasonal hamsters

In seasonal rodents, reproduction is activated by a long photoperiod. Furthermore, maintaining an inhibitory short photoperiod for over 20 weeks triggers a spontaneous reactivation of the gonadotropic axis called photorefractoriness. Photoactivation is proposed to involve melatonin, hypothalamic thyroid hormones (TH) and (Arg) (Phe)-amide peptides. The mechanisms involved in photorefractoriness are so far unknown. We analyzed the dynamic changes in long photoperiod- and photorefractory-induced activation of reproduction in both Syrian and Djungarian hamsters to validate the current model of photoactivation and to uncover the mechanisms involved in photorefractoriness. We detected a conserved early inhibition of expression of the TH catabolizing enzyme deiodinase 3 (Dio3) in tanycytes, associated with a late decrease of the TH transporter MCT8. This suggests that an early peak of hypothalamic TH may be involved in both photoinduced and photorefractory reactivation. In photoactivation, Dio3 downregulation is followed by an upregulation of Dio2, which is not observed in photorefraction. The upregulation of (Arg) (Phe)-amides occurs several weeks after the initial Dio3 inhibition. In conclusion, we uncovered a so far unreported early inhibition of Dio3. This early downregulation of Dio3 is reinforced by an upregulation of Dio2 in photoactivated hamsters. In photorefractoriness, the Dio3 downregulation might be sufficient to reactivate the gonadotropic axis.

Thirteen decades of peptide synthesis: key developments in solid phase peptide synthesis and amide bond formation utilized in peptide ligation.

A historical overview of peptide chemistry from T. Curtius to E. Fischer to M. Bergmann and L. Zervas is first presented. Next, the fundamentals of peptide synthesis with a focus on solid phase peptide synthesis by R. B. Merrifield are described. Immobilization strategies to attach the first amino acid to the resin, coupling strategies in stepwise peptide chain elongation, and approaches to synthesize difficult peptide sequences are also shown. A brief comparison between tert-butyloxycarbonyl (Boc)/benzyl (Bzl) strategy and 9-fluorenylmethoxycarbonyl (Fmoc)/tert-butyl (t -Bu) strategy utilized in solid phase peptide synthesis is given with an emphasis on the latter. Finally, the review focuses on the discovery and development of peptide ligation and the latest advances in this field including native amide bond formation strategies, these include the native chemical ligation, α-ketoacid-hydroxylamine ligation, and serine/threonine ligation which are the most commonly used chemoselective ligation methods that provide amide bond at the ligation site. This review provides an overview of the literature concerning the most important advances in the chemical synthesis of proteins and peptides covering the period from 1882 to 2017.

Influence of Acyl Chain Saturation on the Membrane-Binding Activity of a Short Antimicrobial Peptide

Different bacterial types and their living environments can lead to different saturations in the chains of their membrane lipids. Such structural differences may influence the efficacy of antibiotics that target bacterial membranes. In this work, the effects of acyl chain saturation on the binding of an antimicrobial peptide G4 have been examined as a function of the packing density of lipid monolayers by combining external reflection Fourier transform infrared (ER-FTIR) spectroscopy and neutron reflection (NR) measurements. Langmuir monolayers were formed from 1,2-dipalmitoyl-sn-glycero-3-phospho-(1′-rac-glycerol) (DPPG) and 1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-(1′-rac-glycerol) (POPG), respectively, with the initial surface pressures controlled at 8 and 28 mN/m. A reduction in the order of the acyl chains associated with the increase in the layer thickness upon G4 binding was revealed from ER-FTIR spectroscopy, with peptide binding reaching equilibration faster in POPG than in DPPG monolayers. Whereas the dynamic DPPG-binding process displayed a steady increase in the amide I band area, the POPG-binding process showed little change in the amide area after the initial period. The peptide amide I area from ER-FTIR spectroscopy could be linearly correlated with the adsorbed G4 amount from NR, irrespective of time, initial pressure, or chain saturation, with clearly more peptide incorporated into the DPPG monolayer. Furthermore, NR revealed that although the peptide was associated with both POPG and DPPG lipid monolayers, it was more extensively distributed in the latter, showing that acyl chain saturation clearly promoted peptide binding and structural disruption.

Software-aided approach to investigate peptide structure and metabolic susceptibility of amide bonds in peptide drugs based on high resolution mass spectrometry.

Interest in using peptide molecules as therapeutic agents due to high selectivity and efficacy is increasing within the pharmaceutical industry. However, most peptide-derived drugs cannot be administered orally because of low bioavailability and instability in the gastrointestinal tract due to protease activity. Therefore, structural modifications peptides are required to improve their stability. For this purpose, several in-silico software tools have been developed such as PeptideCutter or PoPS, which aim to predict peptide cleavage sites for different proteases. Moreover, several databases exist where this information is collected and stored from public sources such as MEROPS and ExPASy ENZYME databases. These tools can help design a peptide drug with increased stability against proteolysis, though they are limited to natural amino acids or cannot process cyclic peptides, for example. We worked to develop a new methodology to analyze peptide structure and amide bond metabolic stability based on the peptide structure (linear/cyclic, natural/unnatural amino acids). This approach used liquid chromatography / high resolution, mass spectrometry to obtain the analytical data from in vitro incubations. We collected experimental data for a set (linear/cyclic, natural/unnatural amino acids) of fourteen peptide drugs and four substrate peptides incubated with different proteolytic media: trypsin, chymotrypsin, pepsin, pancreatic elastase, dipeptidyl peptidase-4 and neprilysin. Mass spectrometry data was analyzed to find metabolites and determine their structures, then all the results were stored in a chemically aware manner, which allows us to compute the peptide bond susceptibility by using a frequency analysis of the metabolic-liable bonds. In total 132 metabolites were found from the various in vitro conditions tested resulting in 77 distinct cleavage sites. The most frequent observed cleavage sites agreed with those reported in the literature. The main advantages of the developed approach are the abilities to elucidate metabolite structure of cyclic peptides and those containing unnatural amino acids, store processed information in a searchable format within a database leading to frequency analysis of the labile sites for the analyzed peptides. The presented algorithm may be useful to optimize peptide drug properties with regards to cleavage sites, stability, metabolism and degradation products in drug discovery.

A Major Step in Opening the Black Box of High-Molecular-Weight Dissolved Organic Nitrogen by Isotopic Labeling of Synechococcus and Multibond Two-Dimensional NMR.

Dissolved organic nitrogen (DON) comprises the largest pool of fixed N in the surface ocean, yet its composition has remained poorly constrained. Knowledge of the chemical composition of this nitrogen pool is crucial for understanding its biogeochemical function and reactivity in the environment. Previous work has suggested that high-molecular-weight (high-MW) DON exists only in two closely related forms, the secondary amides of peptides and of N-acetylated hexose sugars. Here, we demonstrate that the chemical structures of high-MW DON may be much more diverse than previously thought. We couple isotopic labeling of cyanobacterially derived dissolved organic matter with advanced two-dimensional NMR spectroscopy to open the "black box" of uncharacterized high-MW DON. Using multibond NMR correlations, we have identified novel N-methyl-containing amines and amides, primary amides, and novel N-acetylated sugars, which together account for nearly 50% of cyanobacterially derived high-MW DON. This study reveals unprecedented compositional details of the previously uncharacterized DON pool and outlines the means to further advance our understanding of this biogeochemically and globally important reservoir of organic nitrogen.