Recent advances in the chemical synthesis and semi-synthesis of poly-ubiquitin-based proteins and probes

Deciphering the molecular interaction between Vitamin D3 and pepsin by in vitro and in silico perspectives

The current study explored the molecular interaction between Vitamin D3 (Vit D3) and pepsin using multi-spectroscopic, molecular dynamic simulation (MDS), and molecular docking. The fluorescence emission spectra discovered Vit D3 interacted with pepsin in a static quenching manner due to the formation of the steady-state complex. Thermodynamic data revealed the spontaneous binding of Vit D3 on pepsin. The formation of the Pepsin-Vit D3 complex was also validated by circular dichroism (CD) spectroscopy. The fluorescence and CD spectroscopy results revealed Vit D3 altered the tertiary and secondary structure of pepsin, respectively. Meanwhile, FTIR spectroscopy results revealed a hypochromic shift in the amide I and II peaks. Kinetic parameters showed Vit D3 inhibited the activity of pepsin by the uncompetitive process. Applied spectroscopic methods disclosed that Vit D3 binding to pepsin caused microenvironmental modifications around the aromatic residues of protein and changed its structure and function. Moreover, MD simulation and molecular docking were done to analyze the formation of Pepsin-Vit D3 complexes. Molecular docking findings demonstrated the interaction of Vit D3 with pepsin mainly involved van der Waals forces and hydrogen bonds that were in good agreement with the fluorescence results. Finally, MDS findings including RMSD, RMSF, and RG confirmed all the experimental data.

Exploring topological indices and entropy measures of phenylacetone monooxygenase by using Python coding

Topological indices are essential for evaluating a compound's physicochemical characteristics. Computing the various topological indices of any molecular structure helps to comprehend their physical characteristics and they are also extremely useful for predicting the properties of chemical and biological compounds in QSPR and QSAR studies.Similarly, Shanon entropy idea a bit different but provide the structural properties of a molecular graph. The atom in the molecular graph of PAMO are considered as a nodes and bonds are weighted edges. For computing the topological indices and edge weight based entropy for phenylacetone monooxygenase enzyme python has been utilized.

Efficient synthesis, stability-guided optimization and anticancer evaluation of bee venom peptide Melittin

Natural cytotoxic peptides (NCPs) are emerging sources of novel anticancer chemotherapeutics. Especially, Melittin, which is the major component of bee venom and the first-in-class NCP, has been considered as a promising anticancer scaffold. Nevertheless, as a classical linear, cationic, amphipathic, and membrane-lytic peptide, Melittin may be easily degraded by proteases, suffering from poor stability, moderate anticancer durability, and severe hemolysis. In this study, applying the terminal modification and hybridization strategies, ten Melittin-based derivatives were designed, synthesized, and investigated for their anticancer potential. The robust and economic synthetic method, in vitro anticancer efficiency, time-kill kinetics, serum stability, anti-migration activity, hemolysis effects, and anticancer mechanism were explored. As expected, the Melittin-based derivatives exhibited highly potent cytotoxicity against all six tested cancer cell lines. In particular, compared with natural Melittin, the derived peptides LJ-5 containing both N-terminal acetylation and C-terminal hydrazidation, and LJ-6, the methotrexate MTX-GFLG-Melittin conjugate exhibited significantly improved proteolytic stability, more durable anticancer efficiency, higher anti-migration activity, as well as reduced hemolysis effects. Besides, it was further verified that LJ-5 and LJ-6 could efficiently disrupt the integrity of cancer cell membrane, localize to the mitochondria and rapidly reduce the mitochondrial membrane potential of cancer cells. Collectively, the economic synthetic method and stability-guided optimization were conducted on Melittin, affording hydrolysis-resistant LJ-5 and LJ-6 that may serve as anticancer candidates and useful references for further optimizations of cytotoxic peptides.

Glyco-based building blocks for the chemical synthesis of glycoproteins

Glycoproteins, which are conjugates of glycans and proteins, are crucial in a wide variety of physiological and disease processes. Understanding the structures and functions of glycoproteins, as well as the regulation of glycosylation, is essential for studying the causes of diseases for intervention therapy. However, the detailed structure-function relationships and therapeutic applications of glycoproteins are hindered by their structural complexity and heterogeneity. Chemical protein synthesis is a powerful and effective strategy for producing homogeneous glycoforms of glycoproteins. The chemical synthesis of glycoproteins involves ligating different peptide and/or glycopeptide fragments, and the preparation of glycopeptide fragments requires the assembly of amino acid and glyco-based building blocks. This review provides a comprehensive and systematic survey of glyco-based building blocks for synthesizing homogeneous glycopeptides and glycoproteins, encompassing glyco-amino acids for direct SPPS and glyco-based donors for convergent sugar assembly. Additionally, an analysis of the applications of these building blocks in the chemical synthesis of representative glycoproteins with therapeutic potential is presented.

A Ligase-Based Two-Step Approach for the Generation of Bicyclic Peptides Containing a Benzylphenyl Thioether Framework

This study describes a ligase-based two-step strategy to prepare a unique type of bicyclic peptide molecules containing a benzyl phenyl thioether arm. Different from the conventional bicyclic peptide construction method, this study first utilizes peptide ligases (SrtA or OaAEP1) to introduce an arylthiol group into the parent peptides and then performs bicyclization of the peptides by using TBMB to generate the desired bicyclic peptides. Since the pKa of aryl thiols is lower than that of alkyl thiols, the bicyclization reaction of the peptides in our system can occur under low concentrations of TBMB or low pH conditions. The low concentrations of TBMB have little effect on the phage infectivity, which will help maintain the diversity of phage-displayed cyclic peptides. This study establishes a biocompatible ligase-mediated two-step strategy for the preparation of bicyclic peptides, which has potential applications in the discovery of bioactive cyclic peptide ligands.

Flexible Semi-synthesis of UFM11-82-Propargylamine by Aminolysis with Valine-Propargylamine

We report a novel semi-synthetic strategy of UFM11-82-propargylamine by N-S acyl transfer to give UFM11-80R thioester and subsequent aminolysis with valine-propargylamine. The use of the valine-propargylamine molecule overcomes the inability of the valine site to efficiently undergo the N-S acyl transfer. This strategy benefits from the availability of raw materials for bulk expression, and the resulting probe shows high selectivity toward UFM1-specific proteases in buffers and cell lysates.

N-tert-Butoxycarbonyl-N-(2-(tritylthio)ethoxy)glycine as a Building Block for Peptide Ubiquitination

N-Boc-N-(2-(tritylthio)ethoxy)glycine has been developed as a building block for peptide ubiquitination, which is fully compatible with solid-phase Fmoc chemistry and common peptide modifications including phosphorylation, methylation, acetylation, biotinylation, and fluorescence labeling. The optimal conditions for peptide cleavage and auxiliary removal were obtained. The utility of this building block in peptide ubiquitination was demonstrated by the synthesis of seven ubiquitinated histone and Tau peptides bearing various modifications. Cys residues were well tolerated and did not require orthogonal protection. The structural integrity and folding of the synthesized ubiquitinated peptides were confirmed by enzymatic deubiquitination of a fluorescently labeled ubiquitin conjugate. The synthetic strategy using this building block provides a practical approach for the preparation of ubiquitinated peptides with diverse modifications.

Chemical synthesis of a 28 kDa full-length PET degrading enzyme ICCG by the removable backbone modification strategy

Chemical protein synthesis offers a powerful way to access otherwise-difficult-to-obtain proteins such as mirror-image proteins. Although a large number of proteins have been chemically synthesized to date, the acquisition to proteins containing hydrophobic peptide fragments has proven challenging. Here, we describe an approach that combines the removable backbone modification strategy and the peptide hydrazide-based native chemical ligation for the chemical synthesis of a 28 kDa full-length PET degrading enzyme IGGC (a higher depolymerization efficiency of variant leaf-branch compost cutinase (LCC)) containing hydrophobic peptide segments. The synthetic ICCG exhibits the enzymatic activity and will be useful in establishing the corresponding mirror-image version of ICCG.

Simultaneous capture of ISG15 conjugating and deconjugating enzymes using a semi-synthetic ISG15-Dha probe

ISG15 is a ubiquitin-like (Ubl) protein attached to substrate proteins by ISG15 conjugating enzymes whose dysregulation is implicated in a multitude of disease processes, but the probing of these enzymes remains to be accomplished. Here, we describe the development of a new activity-based probe ISG15-Dha (dehydroalanine) through protein semi-synthesis. In vitro cross-linking and cell lysate proteomic profiling experiments showed that this probe can sequentially capture ISG15 conjugating enzymes including E1 enzyme UBA7, E2 enzyme UBE2L6, E3 enzyme HERC5, the previously known ISG15 deconjugating enzyme (USP18), as well as some other enzymes (USP5 and USP14) which we additionally confirmed to impart deISGylation activity. Collectively, ISG15-Dha provides a new tool that can simultaneously capture ISG15 conjugating and deconjugating enzymes for biochemical or pharmacological studies.

Electronic Supplementary Material

Supplementary material is available for this article at 10.1007/s11426-022-1455-x and is accessible for authorized users.

DIC/Oxyma-based accelerated synthesis and oxidative folding studies of centipede toxin RhTx

Coupling reagents play crucial roles in the iterative construction of amide bonds for the synthesis of peptides and peptide-based derivatives. The novel DIC/Oxyma condensation system featured with the low risk of explosion displayed remarkable abilities to inhibit racemization, along with efficient coupling efficiency in both manual and automated syntheses. Nevertheless, an ideal reaction molar ratio in DIC/Oxyma condensation system and the moderate reaction temperature by manual synthesis remain to be further investigated. Herein, the synthetic efficiencies of different reaction ratios between DIC and Oxyma under moderate reaction temperature were systematically evaluated. The robustness and efficiency of DIC/Oxyma condensation system are validated by the rapid synthesis of linear centipede toxin RhTx. Different folding strategies were applied for the construction of disulfide bridges in RhTx, which was further confirmed in assays of circular dichroism and patch-clamp electrophysiology evaluation. This work establishes the DIC/Oxyma-based accelerated synthesis of peptides under moderate condensation conditions, which is especially useful for the manual synthesis of peptides. Besides, the strategy presented here provides robust technical supports for the large-scale synthesis and oxidative folding of RhTx.

Synthetic Thiol and Selenol Derived Amino Acids for Expanding the Scope of Chemical Protein Synthesis

Cells employ post-translational modifications (PTMs) as key mechanisms to expand proteome diversity beyond the inherent limitations of a concise genome. The ability to incorporate post-translationally modified amino acids into protein targets via chemical ligation of peptide fragments has enabled the access to homogeneous proteins bearing discrete PTM patterns and empowered functional elucidation of individual modification sites. Native chemical ligation (NCL) represents a powerful and robust means for convergent assembly of two homogeneous, unprotected peptides bearing an N-terminal cysteine residue and a C-terminal thioester, respectively. The subsequent discovery that protein cysteine residues can be chemoselectively desulfurized to alanine has ignited tremendous interest in preparing unnatural thiol-derived variants of proteogenic amino acids for chemical protein synthesis following the ligation-desulfurization logic. Recently, the 21st amino acid selenocysteine, together with other selenyl derivatives of amino acids, have been shown to facilitate ultrafast ligation with peptidyl selenoesters, while the advancement in deselenization chemistry has provided reliable bio-orthogonality to PTMs and other amino acids. The combination of these ligation techniques and desulfurization/deselenization chemistries has led to streamlined synthesis of multiple structurally-complex, post-translationally modified proteins. In this review, we aim to summarize the latest chemical synthesis of thiolated and selenylated amino-acid building blocks and exemplify their important roles in conquering challenging protein targets with distinct PTM patterns.

Removable Backbone Modification (RBM) Strategy for the Chemical Synthesis of Hydrophobic Peptides/Proteins

Chemical synthesis can provide hydrophobic proteins with natural or man-made modifications (e.g. S-palmitoylation, site-specific isotope labeling and mirror-image proteins) that are difficult to obtain through the recombinant expression technology. The difficulty of chemical synthesis of hydrophobic proteins stems from the hydrophobic nature. Removable backbone modificaiton (RBM) strategy has been developed for solubilizing the hydrophobic peptides/proteins. Here we take the chemical synthesis of a S-palmitoylated peptide as an example to describe the detailed procedure of RBM strategy. Three critical steps of this protocol are: (1) installation of Lys6-tagged RBM groups into the peptides by Fmoc (9-fluorenylmethyloxycarbonyl) solid-phase peptide synthesis, (2) chemical ligation of the peptides, and (3) removal of the RBM tags by TFA (trifluoroacetic acid) cocktails to give the target peptide.

Chemical methods for studying the crosstalk between histone H2B ubiquitylation and H3 methylation

The reversible and dynamic post-translational modifications (PTMs) of histones in eukaryotic chromatin are intimately connected to cell development and gene function, and abnormal regulation of PTMs can result in cancer and neurodegenerative diseases. Specific combinations of these modifications are mediated by a series of chromatin proteins that write, erase, and read the "histone codes," but mechanistic studies of the precise biochemical and structural relationships between different sets of modifications and their effects on chromatin function constitute a unique challenge to canonical biochemical approaches. In the past decade, the development and application of chemical methods for investigating histone PTM crosstalks has received considerable attention in the field of chemical biology. In this review, taking the functional crosstalk between H2B ubiquitylation at Lys120 (H2BK120ub) and H3 methylation at Lys79 (H3K79me) as a typical example, we survey recent developments of different chemical methods, in particular, protein synthetic chemistry and protein-based chemical probes, for studying the mechanism of the functional crosstalks of histone PTMs.

Chemical approaches for the preparation of ubiquitinated proteins via natural linkages

Ubiquitination is an important posttranslation modification (PTM) that regulates a variety of cellular processes, including protein degradation, DNA repair, and viral infections. In this process, the C-terminal carboxyl group of ubiquitin (Ub) or poly-Ub is attached to the ε-amine of lysine (Lys) side chain of an acceptor protein through an isopeptide bond. Studying a molecular mechanism of ubiquitination and deubiquitination is fundamental for unraveling its precise role in health and disease and hence crucial for drug development. Enzymatic approaches for protein ubiquitination possess limited ability to selectivity install Ub or Ub chain on the desired position of an acceptor protein and often lead to heterogeneous mixtures. In the past decades, chemical protein (semi)synthesis has been proved to be an efficient tool to facilitate site-specific protein ubiquitination, which significantly contributes to decode the Ub signal at molecular and structural levels. In this review, we summarize the synthetic strategies developed for protein ubiquitination, and the achievements to generate monoubiquitinated, di-ubiquitinated, and tetraubiquitinated proteins with native isopeptide and ester bonds.

Total chemical synthesis of the phosphorylated p62 UBA domain reveals that Ser407Pi but not Ser403Pi enhances ubiquitin binding

As an autophagic adaptor, p62 specifically targets ubiquitinated proteins to an autophagosome for lysosomal degradation through a critical ubiquitin-associated (UBA) domain. Recent research studies reported that the Ser403 and Ser407 sites on the UBA domain were modified by phosphorylation, increasing the binding affinity between p62 and ubiquitin (Ub). However, the exact role of each phosphorylation site in the regulation of the UBA domain and Ub binding remains unclear. In this text, we applied total chemical synthesis to prepare four types of phosphorylated UBAs, among which the bisphosphorylated UBA was successfully synthesized via the pseudo-dipeptide unit and auxiliary-mediated hydrazide-based native chemical ligation (NCL). Isothermal titration calorimetry (ITC) assays showed that the phosphorylation at S407 enhanced the binding affinity between UBA and Ub, while that at S403 did not. It was suggested that phosphorylation at S407 might be important for promoting the interplay between the UBA domain and Ub, whereas phosphorylation at S403 was not directly involved in this interaction.

Development and application of ubiquitin-based chemical probes

Protein ubiquitination regulates almost every process in eukaryotic cells. The study of the many enzymes involved in the ubiquitination system and the development of ubiquitination-associated therapeutics are important areas of current research. Synthetic tools such as ubiquitin-based chemical probes have been making an increasing contribution to deciphering various biochemical components involved in ubiquitin conjugation, recruitment, signaling, and deconjugation. In the present minireview, we summarize the progress of ubiquitin-based chemical probes with an emphasis on their various structures and chemical synthesis. We discuss the utility of the ubiquitin-based chemical probes for discovering and profiling ubiquitin-dependent signaling systems, as well as the monitoring and visualization of ubiquitin-related enzymatic machinery. We also show how the probes can serve to elucidate the molecular mechanism of recognition and catalysis. Collectively, the development and application of ubiquitin-based chemical probes emphasizes the importance and utility of chemical protein synthesis in modern chemical biology.

This article reviews the design, synthesis, and application of different classes of Ub-based chemical probes.

An E1-Catalyzed Chemoenzymatic Strategy to Isopeptide-N-Ethylated Deubiquitylase-Resistant Ubiquitin Probes

Triazole-based deubiquitylase (DUB)-resistant ubiquitin (Ub) probes have recently emerged as effective tools for the discovery of Ub chain-specific interactors in proteomic studies, but their structural diversity is limited. A new family of DUB-resistant Ub probes is reported based on isopeptide-N-ethylated dimeric or polymeric Ub chains, which can be efficiently prepared by a one-pot, ubiquitin-activating enzyme (E1)-catalyzed condensation reaction of recombinant Ub precursors to give various homotypic and even branched Ub probes at multi-milligram scale. Proteomic studies using label-free quantitative (LFQ) MS indicated that the isopeptide-N-ethylated Ub probes may complement the triazole-based probes in the study of Ub interactome. Our study highlights the utility of modern protein synthetic chemistry to develop structurally and new families of tool molecules needed for proteomic studies.

Chemoenzymatic Semisynthesis of Proteins

Protein semisynthesis-defined herein as the assembly of a protein from a combination of synthetic and recombinant fragments-is a burgeoning field of chemical biology that has impacted many areas in the life sciences. In this review, we provide a comprehensive survey of this area. We begin by discussing the various chemical and enzymatic methods now available for the manufacture of custom proteins containing noncoded elements. This section begins with a discussion of methods that are more chemical in origin and ends with those that employ biocatalysts. We also illustrate the commonalities that exist between these seemingly disparate methods and show how this is allowing for the development of integrated chemoenzymatic methods. This methodology discussion provides the technical foundation for the second part of the review where we cover the great many biological problems that have now been addressed using these tools. Finally, we end the piece with a short discussion on the frontiers of the field and the opportunities available for the future.

Development of Ubiquitin Tools for Studies of Complex Ubiquitin Processing Protein Machines

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Ubiquitination is one of the most extensive post-translational modifications in eukaryotes and is involved in various physiological processes such as protein degradation, autophagy, protein interaction, and protein localization. The ubiquitin (Ub)-related protein machines include Ub-activating enzymes (E1s), Ub-conjugating enzymes (E2s), Ub ligases (E3s), deubiquitinating enzymes (DUBs), p97, and the proteasomes. In recent years, the role of DUBs has been extensively studied and relatively well understood. On the other hand, the functional mechanisms of the other more complex ubiquitin-processing protein machines (e.g., E3, p97, and proteasomes) are still to be sufficiently well explored due to their intricate nature. One of the hurdles facing the studies of these complex protein machines is the challenge of developing tailor-designed structurally defined model substrates, which unfortunately cannot be directly obtained using recombinant technology. Consequently, the acquisition and synthesis of the ubiquitin tool molecules are essential for the elucidation of the functions and structures of the complex ubiquitin-processing protein machines. This paper aims to highlight recent studies on these protein machines based on the synthetic ubiquitin tool molecules.