Modification Of Peptides Research Articles

Peptide‐Hypervalent Iodine Reagent Chimeras: Enabling Peptide Functionalization and Macrocyclization**

AbstractHerein, we report a novel strategy for the modification of peptides based on the introduction of highly reactive hypervalent iodine reagents—ethynylbenziodoxolones (EBXs)—onto peptides. These peptide‐EBXs can be readily accessed, by both solution‐ and solid‐phase peptide synthesis (SPPS). They can be used to couple the peptide to other peptides or a protein through reaction with Cys, leading to thioalkynes in organic solvents and hypervalent iodine adducts in water buffer. Furthermore, a photocatalytic decarboxylative coupling to the C‐terminus of peptides was developed using an organic dye and was also successful in an intramolecular fashion, leading to macrocyclic peptides with unprecedented crosslinking. A rigid linear aryl alkyne linker was essential to achieve high affinity for Keap1 at the Nrf2 binding site with potential protein‐protein interaction inhibition.

Peptide-Hypervalent Iodine Reagent Chimeras: Enabling Peptide Functionalization and Macrocyclization.

Herein, we report a novel strategy for the modification of peptides based on the introduction of highly reactive hypervalent iodine reagents-ethynylbenziodoxolones (EBXs)-onto peptides. These peptide-EBXs can be readily accessed, by both solution- and solid-phase peptide synthesis (SPPS). They can be used to couple the peptide to other peptides or a protein through reaction with Cys, leading to thioalkynes in organic solvents and hypervalent iodine adducts in water buffer. Furthermore, a photocatalytic decarboxylative coupling to the C-terminus of peptides was developed using an organic dye and was also successful in an intramolecular fashion, leading to macrocyclic peptides with unprecedented crosslinking. A rigid linear aryl alkyne linker was essential to achieve high affinity for Keap1 at the Nrf2 binding site with potential protein-protein interaction inhibition.

Chemical Modification of Peptides and Proteins Using Spirooxindole Oxirane Derivatives

AbstractMethods for chemical modification of proteins and peptides at certain positions are required for the preparation of antibody‐drug conjugates, protein‐ or peptide‐biotin conjugates, and conjugates used as therapeutics or as tools in biomedical research. We have developed chemical modification methods that use spirooxindole oxirane derivatives for the synthesis of protein‐ and peptide‐conjugates. In most cases, the epoxide group of the spirooxindole oxirane derivatives reacted to form a covalent bond with certain histidine residues and/or the N‐terminal amino group of peptides and proteins. The modification reactions of various proteins resulted in the formation of proteins modified at only one or two positions.

Plant Mitochondrial-Targeted Gene Delivery by Peptide/DNA Micelles Quantitatively Surface-Modified with Mitochondrial Targeting and Membrane-Penetrating Peptides.

Plant mitochondria play essential roles in metabolism and respiration. Recently, there has been growing interest in mitochondrial transformation for developing crops with commercially valuable traits, such as resistance to environmental stress and shorter fallow periods. Mitochondrial targeting and cell membrane penetration functions are crucial for improving the gene delivery efficiency of mitochondrial transformation. Here, we developed a peptide-based carrier, referred to as Cytcox/KAibA-Mic, that contains multifunctional peptides for efficient transfection into plant mitochondria. We quantified the mitochondrial targeting and cell membrane-penetrating peptide modification rates to control their functions. The modification rates were easily determined from high-performance liquid chromatography chromatograms. Additionally, the gene carrier size remained constant even when the mitochondrial targeting peptide modification rate was altered. Using this gene carrier, we can quantitatively investigate the relationships between various peptide modifications and transfection efficiency and optimize the gene carrier conditions for mitochondrial transfection.

Self-Assembly of Organelle-Localized Neuropeptides Triggers Intrinsic Apoptosis against Breast Cancer.

Biosynthesis has become a diverse toolbox for the development of bioactive molecules and materials, particularly for enzyme-induced modification and assembly of peptides. However, intracellular spatiotemporal regulation of artificial biomolecular aggregates based on neuropeptide remains challenging. Here, we developed an enzyme responsive precursor (Y1 L-KGRR-FF-IR) based on the neuropeptide Y1 receptor ligand, which self-assembled into nanoscale assemblies in the lysosomes and subsequently had an appreciable destructive effect on the mitochondria and cytoskeleton, resulting in breast cancer cell apoptosis. More importantly, in vivo studies revealed that Y1 L-KGRR-FF-IR had a good therapeutic effect, reduced breast cancer tumor volume and generated excellent tracer efficacy in lung metastasis models. This study provides a novel strategy for stepwise targeting and precise regulation of tumor growth inhibition through functional neuropeptide Y-based artificial aggregates for intracellular spatiotemporal regulation. This article is protected by copyright. All rights reserved.

A Cysteine‐Directed Proximity‐Driven Crosslinking Method for Native Peptide Bicyclization

AbstractEfficient and site‐specific modification of native peptides and proteins is desirable for synthesizing antibody‐drug conjugates as well as for constructing chemically modified peptide libraries using genetically encoded platforms such as phage display. In particular, there is much interest in efficient multicyclization of native peptides due to the appeals of multicyclic peptides as therapeutics. However, conventional approaches for multicyclic peptide synthesis require orthogonal protecting groups or non‐proteinogenic clickable handles. Herein, we report a cysteine‐directed proximity‐driven strategy for the constructing bicyclic peptides from simple natural peptide precursors. This linear to bicycle transformation initiates with rapid cysteine labeling, which then triggers proximity‐driven amine‐selective cyclization. This bicyclization proceeds rapidly under physiologic conditions, yielding bicyclic peptides with a Cys‐Lys‐Cys, Lys‐Cys‐Lys or N‐terminus‐Cys‐Cys stapling pattern. We demonstrate the utility and power of this strategy by constructing bicyclic peptides fused to proteins as well as to the M13 phage, paving the way to phage display of novel bicyclic peptide libraries.

A Cysteine-Directed Proximity-Driven Crosslinking Method for Native Peptide Bicyclization.

Efficient and site-specific modification of native peptides and proteins is desirable for synthesizing antibody-drug conjugates as well as for constructing chemically modified peptide libraries using genetically encoded platforms such as phage display. In particular, there is much interest in efficient multicyclization of native peptides due to the appeals of multicyclic peptides as therapeutics. However, conventional approaches for multicyclic peptide synthesis require orthogonal protecting groups or non-proteinogenic clickable handles. Herein, we report a cysteine-directed proximity-driven strategy for the constructing bicyclic peptides from simple natural peptide precursors. This linear to bicycle transformation initiates with rapid cysteine labeling, which then triggers proximity-driven amine-selective cyclization. This bicyclization proceeds rapidly under physiologic conditions, yielding bicyclic peptides with a Cys-Lys-Cys, Lys-Cys-Lys or N-terminus-Cys-Cys stapling pattern. We demonstrate the utility and power of this strategy by constructing bicyclic peptides fused to proteins as well as to the M13 phage, paving the way to phage display of novel bicyclic peptide libraries.

A Dual Heat Shock Protein Down-Regulation Strategy Using PDA/Cu/ICG/R Controlled by NIR "Switch" Enhances Mild-Photothermal Therapy Effect.

The purpose of this study is to down-regulate heat shock proteins and improve the mild photothermal therapy (mild-PTT) effect of polydopamine (PDA) by preparing the nanosystem of Cu2+ and indocyanine green (ICG)-loaded PDA nanospheres with surface modification of integrin-targeted cyclic peptide (cRGD) (PDA/Cu/ICG/R), which can limit ATP synthesis through the double mitochondrial destruction pathway. In vitro and in vivo experiments using PDA/Cu/ICG/R irradiated with an NIR laser demonstrate that when NIR is "OFF," Cu2+ can undergo Fenton-like reaction in tumor cells, producing a large amount of hydroxyl radicals (·OH), which leads to oxidative stress in cells. This oxidative stress can cause mitochondrial oxidative phosphorylation dysfunction, resulting in limited ATP synthesis. When NIR is "ON," mild-PTT can accelerate Cu2+ to produce ·OH. Simultaneously, NIR can activate ICG to produce reactive oxygen species (ROS) storm, amplify intracellular oxidative stress, and continuously damage mitochondria. The biodegradability of PDA greatly reduces the risk of toxicity caused by long-term retention of PDA/Cu/ICG/R in organisms. Finally, the improvement of the mild-PTT effect of PDA is successfully achieved through the double mitochondrial destruction pathway of Cu2+ and ICG controlled by NIR "switch."

A Mild Synthesis of Aryl Triflates Enabling the Late-Stage Modification of Drug Analogs and Complex Peptides.

We report the discovery of a novel strategy to convert phenols into the corresponding aryl triflates using 1-methyl-3-((trifluoromethyl)sulfonyl)-1,3-dihydro-2H-benzo[d]imidazol-2-one in the presence of a fluoride source. This novel reagent can be handled without any precautions to exclude air or moisture making this method highly convenient. The reactions generally show very clean conversions within only a few minutes at room temperature. The mild conditions allow the so far unprecedented O-triflation of tyrosine in peptides bearing challenging side chains present for example in arginine and histidine including the late-stage triflation of complex bioactive peptides. We show how aryl triflates - an interesting but so far underutilized group - can be used to optimize physicochemical and in vitro properties of compound series in medicinal chemistry. We believe that this method is highly attractive for applications in peptide functionalization as well as automated and medicinal chemistry.

Teraryl Braces in Macrocycles: Synthesis and Conformational Landscape Remodeling of Peptides.

The three-dimensional structure of medium-sized cyclic peptides accounts for their biological activity and other important physiochemical properties. Despite significant advances in the past few decades, chemists' ability to fine-tune the structure, in particular, the backbone conformation, of short peptides made of canonical amino acids is still quite limited. Nature has shown that cross-linking the aromatic side chains of linear peptide precursors via enzyme catalysis can generate cyclophane-braced products with unusual structures and diverse activities. However, the biosynthetic path to these natural products is challenging to replicate in the synthetic laboratory using practical chemical modifications of peptides. Herein, we report a broadly applicable strategy to remodel the structure of homodetic peptides by cross-linking the aromatic side chains of Trp, His, and Tyr residues with various aryl linkers. The aryl linkers can be easily installed via copper-catalyzed double heteroatom-arylation reactions of peptides with aryl diiodides. These aromatic side chains and aryl linkers can be combined to form a large variety of assemblies of heteroatom-linked multi-aryl units. The assemblies can serve as tension-bearable multijoint braces to modulate the backbone conformation of peptides as an entry to previously inaccessible conformational space.

Tetrazole Diversification of Amino Acids and Peptides via Silver-Catalyzed Intermolecular Cycloaddition with Aryldiazonium Salts.

Selective structural modification of amino acids and peptides is a central strategy in organic chemistry, chemical biology but also in pharmacology and material science. In this context, the formation of tetrazole rings, known to possess significant therapeutic properties, would expand the chemical space of unnatural amino acids but has received less attention. In this study, we demonstrated that the classic unimolecular Wolff rearrangement of α-amino acid-derived diazoketones could be replaced by a faster intermolecular cycloaddition reaction with aryldiazonium salts under identical practical conditions. This strategy provides an efficient synthetic platform that could transform proteinogenic α-amino acids into a plethora of unprecedented tetrazole-decorated amino acid derivatives with preservation of the stereocenters. Density functional theory studies shed some light on the reaction mechanism and provided information regarding the origins of the chemo- and regioselectivity. Furthermore, this diazo-cycloaddition protocol was applied to construct tetrazole-modified peptidomimetics and drug-like amino acid derivatives.

Tetrazole Diversification of Amino Acids and Peptides via Silver‐Catalyzed Intermolecular Cycloaddition with Aryldiazonium Salts

AbstractSelective structural modification of amino acids and peptides is a central strategy in organic chemistry, chemical biology but also in pharmacology and material science. In this context, the formation of tetrazole rings, known to possess significant therapeutic properties, would expand the chemical space of unnatural amino acids but has received less attention. In this study, we demonstrated that the classic unimolecular Wolff rearrangement of α‐amino acid‐derived diazoketones could be replaced by a faster intermolecular cycloaddition reaction with aryldiazonium salts under identical practical conditions. This strategy provides an efficient synthetic platform that could transform proteinogenic α‐amino acids into a plethora of unprecedented tetrazole‐decorated amino acid derivatives with preservation of the stereocenters. Density functional theory studies shed some light on the reaction mechanism and provided information regarding the origins of the chemo‐ and regioselectivity. Furthermore, this diazo‐cycloaddition protocol was applied to construct tetrazole‐modified peptidomimetics and drug‐like amino acid derivatives.

Copper-catalyzed asymmetric C(sp3)-H cyanoalkylation of glycine derivatives and peptides

Alkylnitriles play important roles in many fields because of their unique electronic properties and structural characteristics. Incorporating cyanoalkyl with characteristic spectroscopy and reactivity properties into amino acids and peptides is of special interest for potential imaging and therapeutic purposes. Here, we report a copper-catalyzed asymmetric cyanoalkylation of C(sp3)-H. In the reactions, glycine derivatives can effectively couple with various cycloalkanone oxime esters with high enantioselectivities, and the reaction can be applied to the late-stage modification of peptides with good yields and excellent stereoselectivities, which is useful for modern peptide synthesis and drug discovery. The mechanistic studies show that the in situ formed copper complex by the coordination of glycine derivatives and chiral phosphine Cu catalyst can not only mediate the single electronic reduction of cycloalkanone oxime ester but also control the stereoselectivity of the cyanoalkylation reaction.

Photo-induced synthesis, stereochemistry and antitumor activity of natural cyclopeptide Hikiamide B analogs

Peptide cyclization has been recognized as capable of overcoming the shortcomings of linear peptides such as poor stability, short half-life, low selectivity and low affinity to receptors, and the modification of cyclic peptides to achieve specific activity requirements is receiving increasing attention. Hikiamide B is a cyclic pentadepsipeptide that can induce the expression of peroxisome-proliferator-activated receptor-γ (PPAR-γ). Considering that PPAR-γ can effectively regulate the expression of genes related to tumorigenesis, and is a potential tumor target, in this paper, we have prepared several Hikiamide B analogs by intramolecular photo-induced single-electron-transfer (SET) reaction to find novel antitumor drugs The stereochemistry and the in vitro antitumor activity against HepG-2 and HeLa cells were investigated. We found that the compound with stronger intramolecular hydrogen bonds (compound 2) than other compounds showed more promising antitumor activity, and the cyclic compounds present stronger bioactivity than that of their linear precursors. In vitro studies of apoptosis mechanisms and mitochondrial membrane potential following cyclopeptide 2 treat have shown that the cyclopeptide may induce apoptosis in tumor cells. Finally, in silico ADME analysis has shown the potential of compound 2 for practical application.

Predicting and Improving Insertions by Prime Editing

Predicting and Improving Insertions by Prime Editing

Bioorthogonal Fluoride-Responsive Azide and Alkynyl Pyridinium Click Cycloaddition in Vitro and in Live Cells.

The copper-free azide-alkyne cycloaddition was broadly applied in numerous research fields. Herein, we report a facile Cu-free click reaction utilizing fluoride-responsive azide and alkynyl pyridinium cycloaddition at ambient temperatures in aqueous media. The reactivity of alkynyl pyridinium was successfully masked by a silyl-protecting group at the alkyne group, and the deprotection could be readily achieved with the addition of F-, which renders the reactivity. The substrates were readily synthesized and proven to be stable at the bench. This bioorthogonal fluoride-responsive click reaction was then successfully employed in peptide modification, protein labeling, and cell imaging, suggesting its potential in various applications.

Targeting lactate metabolism and immune interaction in breast tumor via protease-triggered delivery.

Lactate is abundant in cancer tissues due to active glycolysis (aka Warburg effect) and mediates crosstalk between tumor cells and the immune microenvironment (TIME) to promote the progression of breast cancer. Quercetin (QU) is a potent monocarboxylate transporters (MCT) inhibitor, which can reduce lactate production and secretion of tumor cells. Doxorubicin (DOX) can induce immunogenic cell death (ICD), which promotes tumor-specific immune activation. Thus, we propose a combination therapy of QU&DOX to inhibit lactate metabolism and stimulate anti-tumor immunity. To enhance tumor-targeting efficiency, we developed a legumain-activatable liposome system (KC26-Lipo) with modification of KC26 peptide for co-delivery of QU&DOX for modulation of tumor metabolism and TIME in breast cancer. The KC26 peptide is a legumain-responsive, hairpin-structured cell-penetrating peptide (polyarginine) derivative. Legumain is a protease overexpressed in breast tumors, allowing selective activation of the KC26-Lipo to subsequently facilitate intra-tumoral and intracellular penetration. The KC26-Lipo effectively inhibited 4T1 breast cancer tumor growth through chemotherapy and anti-tumor immunity. Besides, inhibition of lactate metabolism suppressed the HIF-1α/VEGF pathway and angiogenesis and repolarized the tumor-associated macrophages (TAM). This work provides a promising breast cancer therapy strategy by regulating lactate metabolism and TIME.

Peptide‐Decorated Artificial Erythrocyte Microvesicles Endowed with Lymph Node Targeting Function for Drug Delivery (Adv. Therap. 6/2023)

In article number 2200236, Zhihong Zhang, Xiang Yu, and co-workers achieve the direct size conversion of erythrocyte-derived MVs (eMVs) via incubation with an ApoA-I mimetic peptide (R4F) capable of binding phospholipids. R4F peptide modification endows eMVs with SR-B1 receptor and lymph node targeting functions, providing an excellent drug delivery system for the targeted treatment of lymph node-associated diseases.

Proteome-Derived Peptide Libraries for Deep Specificity Profiling of N-terminal Modification Reagents.

Protein and peptide N termini are important targets for selective modification with chemoproteomics reagents and bioconjugation tools. The N-terminal ⍺-amine occurs only once in each polypeptide chain, making it an attractive target for protein bioconjugation. In cells, new N termini can be generated by proteolytic cleavage and captured by N-terminal modification reagents that enable proteome-wide identification of protease substrates through tandem mass spectrometry (LC-MS/MS). An understanding of the N-terminal sequence specificity of the modification reagents is critical for each of these applications. Proteome-derived peptide libraries in combination with LC-MS/MS are powerful tools for profiling the sequence specificity of N-terminal modification reagents. These libraries are highly diverse, and LC-MS/MS enables analysis of the modification efficiencies of tens of thousands of sequences in a single experiment. Proteome-derived peptide libraries are a powerful tool for profiling the sequence specificities of enzymatic and chemical peptide labeling reagents. Subtiligase, an enzymatic modification reagent, and 2-pyridinecarboxaldehyde (2PCA), a chemical modification reagent, are two reagents that have been developed for selective N-terminal peptide modification and can be studied using proteome-derived peptide libraries. This protocol outlines the steps for generating N-terminally diverse proteome-derived peptide libraries and for applying these libraries to profile the specificity of N-terminal modification reagents. Although we detail the steps for profiling the specificity of 2PCA and subtiligase in Escherichia coli and human cells, these protocols can easily be adapted to alternative proteome sources and other N-terminal peptide labeling reagents. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Generation of N-terminally diverse proteome-derived peptide libraries from E. coli Alternate Protocol: Generation of N-terminally diverse proteome-derived peptide libraries from human cells Basic Protocol 2: Characterizing the specificity of 2-pyridinecarboxaldehyde using proteome-derived peptide libraries Basic Protocol 3: Characterizing the specificity of subtiligase using proteome-derived peptide libraries.

Late-Stage, Stereoretentive, and Site-Selective Modification of Synthetic Peptides by Using Photoredox Catalysis.

Late-stage functionalisation is an attractive method to generate peptide analogues containing non-natural residues. It is shown that cysteine residues can be activated as Crich-type thioethers, either by alkylation of a synthetic cysteine-continuing peptide or by incorporation of a modified cysteine unit into solid phase or solution phase peptide synthesis. Photoredox catalysed reaction of the thioether generates an alanyl radical intermediate in a stereoretentive and site-selective manner, even in the presence of free cysteine residues. The radical can react with non-activated alkenes to form non-natural residues bearing aliphatic, hydrophobic units. A method to avoid unwanted alkylation of amine residues was identified and the process was applied to the functionalization of both linear and cyclic synthetic peptides.