Amino acid sequence and D/L-configuration determination methods for D-amino acid-containing peptides in living organisms

D-amino acid-containing peptides with biological activities have been isolated from invertebrates and amphibians, and partial racemization of amino acid residues in mammalian peptides associated with aging and diseases have been discussed. Here, we review the amino acid configuration determination methods in these peptides and recent progress of simultaneous determination method for sequence and configuration of amino acid residues. The applicability of C-terminus sequence analysis and mass spectrometry to configuration determination of amino acids is also discussed.     

Fabrication of Chiral Materials via Self‐Assembly and Biomineralization of Peptides

With different scales of chirality, chiral materials have various particular properties and potential applications in many fields. Peptides are the fundamental building units of biological systems, and a variety of ordered functional nanostructures are produced through self‐assembly and biomineralization of peptides in nature. This Personal Account describes chiral silica materials fabricated by using amphiphilic peptides as building blocks. Three particular biomineralization approaches are described based on different kinds of geometry of amphiphilic peptides: the influence of the specific amino acid proline in the peptide sequence, the hydrophilicity of amphiphilic peptides, and different kinds of hydrophobic tails in amphiphilic peptides. These strategies are useful for designing peptides toward the bottom‐up synthesis of nanomaterials as well as improving the understanding of the mechanism of peptide self‐assembly.     

Chemical Synthesis of Proteins Containing 300 Amino Acids

Chemical synthesis of proteins containing up to 300 amino acids may cover 30%-50% of all the proteins encountered in biomedical studies and may provide an alternate approach to the usually used recombinant expression technology, vastly expanding the chemical space of the latter. In the present review article, we tried to survey the recent progresses made for more rapid synthesis of increasingly long peptides and more efficient ligation of multiple peptide segments. The developments of seminal methods by many research groups have greatly contributed to the recent breakthroughs in the successful total synthesis of a number of functionally important proteins, such as oligoubiquitins, bacterial GroEL/ES chaperones, and mirror-image DNA polymerases. Through these studies, a potential bottleneck has also been recognized for the chemical synthesis of large proteins, namely, how to ensure that each peptide segment from a large protein avoids unfavorable aggregation when dissolved in aqueous solution. Many new methods, such as removable backbone modification(RBM) strategy have been developed to overcome this bottleneck, while more studies need to be carried out to develop more effective and less costly methods that ultimately, may lead to fully automatable chemical synthesis of customized proteins of 300 amino acids bearing any artificial designs.     

蛋白质的化学全合成

含有非天然氨基酸的蛋白质（如翻译后修饰蛋白质、修饰有探针分子的蛋白质等）是化学生物学中重要的生理活性分子。这些分子难以通过生物表达来获取，而必须使用化学方法来合成。半胱氨酸肽片段连接方法是目前应用于蛋白质化学全合成中的一种重要方法，该方法能够在温和的水溶液中高效地实现肽片段的连接，从而生成天然或者非天然的蛋白质。本文系统地综述了半胱氨酸肽片段连接方法的基本原理，详细讨论了近年来人们对该方法的一些重要改进。最后又介绍了该方法在几类重要的蛋白质分子合成中的代表性应用。     

Recent advances in enzyme-mediated peptide ligation

Artificial synthesis and site-specific modification of peptides and proteins have evolved into an indispensable tool for protein engineers and chemical biologists. Chemical and enzymatic approaches to peptide ligation are important alternatives of recombinant DNA technology for protein synthesis and modification. In the past decades, several natural peptide ligases have been discovered. Additionally, protein engineering for improving the ligation efficiencies of the natural peptide ligase and reversing the functionality of protease have provided more powerful peptide ligases. Herein, we briefly summarized the advances of enzyme-mediated peptide ligation and their application in protein synthesis and modification.     

Synthesis of Phosphonopeptides Using Pivaloyl Chloride

Abstract

Aminopnospnonic acids can be used as components in the synthesis of peptides resulting in the phosphonopeptides, which are interesting not only from the chemical point of view but also for their promising biological properties. An aminophosphonic acid unit can be attached to the C-terminus of amino acids or peptides by the usual methods of peptide chemistry. However, the specific properties of aminophos-phonates can sometimes lead to complications, for example formation of by products (1). de have tested the method of phospnonopeptide synthesis using pivaloyl chloride. It was found that dialkyl esters of 1-aminoalkylphosphonic acids readily react with mixed anhydrides of N-protected amino acid and pivalic acid to give the fully protected phosphonopeptides with good yields.     

Chemoselective Ligation and Modification Strategies for Peptides and Proteins

The investigation of biological processes by chemical methods, commonly referred to as chemical biology, often requires chemical access to biologically relevant macromolecules such as peptides and proteins. Building upon solid‐phase peptide synthesis, investigations have focused on the development of chemoselective ligation and modification strategies to link synthetic peptides or other functional units to larger synthetic and biologically relevant macromolecules. This Review summarizes recent developments in the field of chemoselective ligation and modification strategies and illustrates their application, with examples ranging from the total synthesis of proteins to the semisynthesis of naturally modified proteins.     

Selective N-terminal modification of peptides and proteins: Recent progresses and applications

Numerous strategies for linking desired chemical probes with target peptides and proteins have been developed and applied in the field of biological chemistry. Approaches for site-specific modification of native amino acid residues in test tubes and biological contexts represent novel biological tools for understanding the role of peptides and proteins. Selective N-terminal modification strategies have been broadly studied especially in the last 10 years, as N-terminal positions are typically so...     

Recent developments in capillary and microchip electroseparations of peptides (2017–mid 2019)

The review presents a comprehensive survey of recent developments and applications of high performance capillary and microchip electroseparation methods (zone electrophoresis, isotachophoresis, isoelectric focusing, affinity electrophoresis, electrokinetic chromatography, and electrochromatography) for analysis, micropreparation, and physicochemical and biochemical characterization of peptides since 2017 up to about the middle of 2019. Progress in the study of electromigration properties of peptides and in the methodology of their analysis (sample preseparation, preconcentration and derivatization, adsorption suppression, EOF control, and detection) are described. Advances in CE and CEC methods are demonstrated and their applications in the following areas are presented: qualitative and quantitative analysis, determination in complex (bio)matrices, monitoring of chemical and enzymatical reactions and physical changes, amino acid, sequence and chiral analysis, and peptide mapping of proteins. In addition, micropreparative separations and determinations of important physicochemical characteristics of peptides by CE and CEC methods are reported.     

Easy Production of “Difficult Peptides” Using Cell-Free Protein Synthesis and a New Methionine Analogue as a Latent Peptide Cleavage Site

Aliphatic γ-chloro-α-amino acids incorporated in place of their canonical analogues through cell-free protein synthesis act as heat-labile linkers, offering a useful strategy for the straightforward production of target peptides as fusion proteins, from which the targets are readily released. Until now, the natural abundance of aliphatic amino acids in peptides has limited the scope of the method, as it leads to undesired cleavage sites in synthesized products, but here the authors report the development of a new cleavable chloro amino acid that incorporates in place of the relatively rare amino acid methionine, thus greatly expanding the scope of producible targets. This new strategy is employed for simplified peptide synthesis with a methionine-free fusion partner, allowing single-site incorporation of the cleavable linker for clean release and easy purification of the target peptide. Its utility is demonstrated through the straightforward preparation of two peptides reported to be challenging targets and not accessible through standard solid-phase chemical methodologies, as well as analogues.     

Sustainable Peptide Synthesis Enabled by a Transient Protecting Group

The growing interest in synthetic peptides has prompted the development of viable methods for their sustainable production. Currently, large amounts of toxic solvents are required for peptide assembly from protected building blocks, and switching to water as a reaction medium remains a major hurdle in peptide chemistry. We report an aqueous solid‐phase peptide synthesis strategy that is based on a water‐compatible 2,7‐disulfo‐9‐fluorenylmethoxycarbonyl (Smoc) protecting group. This approach enables peptide assembly under aqueous conditions, real‐time monitoring of building block coupling, and efficient postsynthetic purification. The procedure for the synthesis of all natural and several non‐natural Smoc‐protected amino acids is described, as well as the assembly of 22 peptide sequences and the fundamental issues of SPPS, including the protecting group strategy, coupling and cleavage efficiency, stability under aqueous conditions, and crucial side reactions.     

The design, synthesis and application of stereochemical and directional peptide isomers: a critical review

Physiological processes are regulated to a large extent by physical and chemical interactions between polypeptides. Although many small molecules have been discovered that can modulate such interactions and may be useful as drugs, the design of these agents purely from the knowledge of the details of a given protein-protein interaction, or through screening, remains difficult. Therefore, the peptidomimetic process, which aims at using peptides derived from either polypeptide binding partner directly, or after modification to improve affinity and physicochemical properties, continues to be attractive. The vast majority of naturally occurring polypeptides are composed of L-amino acids. Because natural proteins need to be metabolised, L-amino acid polypeptides are very prone to proteolytic degradation, a property that severely limits their therapeutic application. The proteolytic machinery is not well equipped to deal with D-amino acid polypeptides, however, and it is this finding above all else that has spurned research into stereochemical and directional manipulation of peptide chains. The expectation has been that systematic inversion of the stereochemistry at the peptide backbone alpha-carbon atoms, if accompanied by chain reversal, should yield proteolytically stable retro-inverso peptide isomers, whose side chain topology, in the extended conformation, corresponds closely to that of a native sequence, and whose biological activity emulates that of a parent polypeptide. The actual structural implications of modifying amino acid stereochemistry and peptide bond direction are reviewed critically here and the reasons for the lack of general success with this strategy are discussed. The application of polypeptides is particularly pertinent to synthetic vaccine design. Interestingly, the retro-inverso strategy has been more successful for immunological applications than elsewhere; recent finding are collated in this review. Partial rather than global retro-inversion holds much promise since the loss of crucial backbone hydrogen-bonding through peptide bond reversal can be avoided, while still permitting stabilisation of selected hydrolysis-prone peptide bonds. Generically applicable synthetic methods for such partially modified retro-inverso peptides are not as yet available; progress towards this goal is also summarised.     

Synthesis of Peptide Cysteine Dimedone Using Fmoc-Cys(Dmd)-OH: Glutathione Cysteine Dimedone as a Probe in Investigating the Sulfenic Acid Mediated Oxidation of Glutathione

Dimedone is the most widely used chemical probe for detection of cysteine sulfenic acid in peptides and proteins. The reaction of dimedone with cysteine sulfenic acid results in the formation of unique cysteine dimedone motif containing thioether bridge. Based on the structure of cysteine dimedone residue in polypeptide, a new building block of Fmoc-Cys(Dmd)-OH was developed for solid phase synthesis of peptide cysteine dimedone. Mass spectrometric sequencing of synthetic peptides have confirmed successful incorporation of cysteine dimedone in peptide chain using HBTU/HOBt as a coupling agent. The new method permits synthesis of peptides containing both cysteine thiol and cysteine dimedone in the same sequence which was difficult to achieve by conventional methods. The synthetic peptide of glutathione cysteine dimedone was used as a standard in probing the air-mediated oxidation of thiol to disulfide form of glutathione. The co-elution of standard peptide and reaction mixture of oxidation of glutathione in presence of dimedone using RP-HPLC have confirmed the formation of glutathione cysteine sulfenic as an intermediate in the air-mediated oxidation of glutathione. The synthetic peptides of cysteine dimedone may find application in the field of redox proteomics and generation of antibodies against modified cysteine residue.     

Front Cover: Katritzky Salts for the Synthesis of Unnatural Amino Acids and Late-Stage Functionalization of Peptides (Eur. J. Org. Chem. 12/2023)

Peptide drug discovery often benefits from the large structural diversity permitted by unnatural amino acids (UAAs). Indeed, numerous approved peptide drugs include UAAs in their sequences. Therefore, innovative chemical approaches either to synthesize UAAs or to allow late-stage functionalization of peptides are emerging themes in peptide drug discovery. Thanks to the recent advances in deaminative strategies using alkylpyridiniums salts, often referred to as Katritzky salts, a variety of radical alkylation methods have been developed. In recent years the use of Katritzky salts have become popular in peptide chemistry due to their ease of preparation from a primary amine, which is a predominant functional group in amino acids. This review highlights the progress that has been made by using Katritzky salts in the synthesis of UAAs, late-stage peptide functionalization, and peptide macrocyclization.     

Solid-phase synthesis of peptide and glycopeptide thioesters through side-chain-anchoring strategies

An efficient new strategy for the synthesis of peptide and glycopeptide thioesters is described. The method relies on the side-chain immobilization of a variety of Fmoc-amino acids, protected at their C-termini, on solid supports. Once anchored, peptides were constructed using solid-phase peptide synthesis according to the Fmoc protocol. After unmasking the C-terminal carboxylate, either thiols or amino acid thioesters were coupled to afford, after cleavage, peptide and glycopeptide thioesters in high yields. Using this method a significant proportion of the proteinogenic amino acids could be incorporated as C-terminal amino acid residues, therefore providing access to a large number of potential targets that can serve as acyl donors in subsequent ligation reactions. The utility of this methodology was exemplified in the synthesis of a 28 amino acid glycopeptide thioester, which was further elaborated to an N-terminal fragment of the glycoprotein erythropoietin (EPO) by native chemical ligation.     

Towards the Chemical Synthesis of Proteins

The chemical total synthesis of proteins using solid supports has made great progress. It is therefore becoming a reality what E. Fischer already predicted in 1902 1 1 Cited from Nobel Lectures—Chemistry 1901-1921, Elsevier, Amsterdam 1966, p. 34.
: “I foresee the time when physiological chemistry… is able to prepare synthetic enzymes.” The synthesis of peptides of up to 20 amino acids by the well-established solid-phase procedure on polymeric supports (SPPS) has made great progress through the development of newer supports. At the same time, methods have emerged which facilitate the separation and characterization of peptides, thus allowing optimization of the synthesis of pure materials. The new supports which enable one to synthesize peptides by a rapid continuous flow procedure are characterized by hydrophilicity, beads of approximately equal size, similar swelling properties in the solvents used for peptide synthesis, and stability at high pressure. With graft copolymers of weakly cross-linked polystyrene and linear polyethylene glycol (PEG), the synthetic cycle for coupling of one amino acid can routinely be reduced to 10–20 min with a concomitant higher yield. With beads of monodispersed graft copolymer of 10 μm diameter, a synthetic cycle can, in principle, be shortened to 1–5 min. By utilizing this high-speed solid-phase procedure, larger peptides up to the size of proteins could also be prepared in a few hours. With newer mass spectroscopic methods such as ion-spray mass spectrometry, peptides of up to a molecular mass of 100 kDa can be characterized, and with the advent of capillary electrophoresis, another very efficient separation tool, besides HPLC, is at our disposal.