Recent advances in enzyme-mediated peptide ligation

Design of a recombinant asparaginyl ligase for site-specific modification using efficient recognition and nucleophile motifs

Asparaginyl ligases have been extensively utilized as valuable tools for site-specific bioconjugation or surface-modification. However, the application is hindered by the laborious and poorly reproducible preparation processes, unstable activity and ambiguous substrate requirements. To address these limitations, this study employed a structure-based rational approach to obtain a high-yield and high-activity protein ligase called OaAEP1-C247A-aa55-351. It was observed that OaAEP1-C247A-aa55-351 exhibits appreciable catalytic activities across a wide pH range, and the addition of the Fe3+ metal ion effectively enhances the catalytic power. Importantly, this study provides insight into the recognition and nucleophile peptide profiles of OaAEP1-C247A-aa55-351. The ligase demonstrates a higher recognition ability for the "Asn-Ala-Leu" motif and an N-terminus "Arg-Leu" as nucleophiles, which significantly increases the reaction yield. Consequently, the catalytic activity of OaAEP1-C247A-aa55-351 with highly efficient recognition and nucleophile motif, "Asn-Ala-Leu" and "Arg-Leu" under the buffer containing Fe3+ is 70-fold and 2-fold higher than previously reported OaAEP1-C247A and the most efficient butelase-1, respectively. Thus, the designed OaAEP1-C247A-aa55-351, with its highly efficient recognition and alternative nucleophile options, holds promising potential for applications in protein engineering, chemo-enzymatic modification, and the development of drugs.

Research advances in peptide‒drug conjugates

Peptide‒drug conjugates (PDCs) are drug delivery systems consisting of a drug covalently coupled to a multifunctional peptide via a cleavable linker. As an emerging prodrug strategy, PDCs not only preserve the function and bioactivity of the peptides but also release the drugs responsively with the cleavable property of the linkers. Given the ability to significantly improve the circulation stability and targeting of drugs in vivo and reduce the toxic side effects of drugs, PDCs have already been extensively applied in drug delivery. Herein, we review the types and mechanisms of peptides, linkers and drugs used to construct PDCs, and summarize the clinical applications and challenges of PDC drugs.

Efficient Multiple Domain Ligation for Proteins Using Asparaginyl Endopeptidase by Selection of Appropriate Ligation Sites Based on Steric Hindrance

Three domain fragments of a multi-domain protein, ER-60, were ligated in two short linker regions using asparaginyl endopeptidase not involving denaturation. To identify appropriate ligation sites, by selecting several potential ligation sites with fewer mutations around two short linker regions, their ligation efficiencies and the functions of the ligated ER-60s were examined experimentally. To evaluate the dependence of ligation efficiencies on the ligation sites computationally, steric hinderances around the sites for the ligation were calculated through molecular dynamics simulations. Utilizing the steric hindrance, a site-dependent ligation potential index was introduced as reproducing the experimental ligation efficiency. Referring to this index, the reconstruction of ER-60 was succeeded by the ligation of the three domains for the first time. In addition, the new ligation potential index well-worked for application to other domain ligations. Therefore, the index may serve as a more time-effective tool for multi-site ligations.

Selective editing of a peptide skeleton via C-N bond formation at N-terminal aliphatic side chains

The applications of peptides and peptidomimetics have been demonstrated in the fields of therapeutics, diagnostics, and chemical biology. Strategies for the direct late-stage modification of peptides and peptidomimetics are highly desirable in modern drug discovery. Transition-metal-catalyzed C-H functionalization is emerging as a powerful strategy for late-stage peptide modification that is able to construct functional groups or increase skeletal diversity. However, the installation of directing groups is necessary to control the site selectivity. In this work, we describe a transition metal-free strategy for late-stage peptide modification. In this strategy, a linear aliphatic side chain at the peptide N-terminus is cyclized to deliver a proline skeleton via site-selective δ-C(sp3)-H functionalization under visible light. Natural and unnatural amino acids are demonstrated as suitable substrates with the transformations proceeding with excellent regio- and stereo-selectivity.

Application of Diversified Health Education Combined with Psychological Nursing in the Treatment of Patients with Infectious Bone Defects by Induction Membrane Surgery

Objective

To explore the application value of diversified health education combined with psychological nursing in the treatment of patients with infectious bone defects by induction membrane surgery.

Methods

A total of 52 patients with infectious bone defects treated by induction membrane surgery from May 2018 to January 2022 were selected as the research subjects and divided into an observation group (with diversified health education combined with psychological care) and a control group according to the random number table method (routine nursing care). There were 26 patients in each group, and the Hospital Anxiety and Depression Scale (HADS) and Self-Care Ability Scale (ESCA) were compared.

Results

At admission, there was no significant difference in anxiety dimension, depression dimension, and total score of anxiety and depression between the two groups (P > 0.05). At admission, there was no significant difference in self-care responsibility, self-concept, self-care skills, health knowledge level, and total score between the two groups (P > 0.05). Skills, health knowledge level, and total score were higher than those in the control group (P < 0.05). The total incidence of complications in the observation group was lower than that in the control group (P < 0.05).

Conclusion

Diversified health education combined with psychological nursing is beneficial to reduce negative emotions, improve self-care ability, and reduce the incidence of complications in the treatment of patients with infectious bone defects by induction membrane surgery.

Sortase A-mediated cyclization of novel polycyclic RGD peptides for ανβ3 integrin targeting

Cyclic arginine-glycine-aspartic (RGD) peptides that specifically bind to integrin α_νβ₃ have been developed for drug delivery, tracers, and imaging for tumor diagnosis and treatment. Herein, a series of polycyclic RGD peptides containing dual, tri, and tetra rings were designed and synthesized through sortase A-mediated ligation. An in vitro test on cell adhesion inhibition indicated that the RGD peptide containing tricylic structure exhibited outstanding potency and selectivity for α_νβ₃ integrin.

Asparaginyl Endopeptidase-Mediated Protein C-Terminal Hydrazinolysis for the Synthesis of Bioconjugates

Asparaginyl endopeptidases (AEPs) are cysteinyl enzymes naturally catalyzing the hydrolysis and transpeptidation reactions at Asx-Xaa bonds. These reactions go by a common acyl-enzyme thioester intermediate, which is either attacked by water (for a protease-AEP) or by a peptidic amine nucleophile (for a ligase-AEP) to form the respective hydrolysis or aminolysis product. Herein, we show that hydrazine and hydroxylamine, two α-effect nucleophiles, are capable of resolving the thioester intermediate to yield peptide and protein products containing a C-terminal hydrazide and hydroxamic acid functionality, respectively. The hydrazinolysis reaction exhibits very high efficiency and can be completed in minutes at a low enzyme-to-substrate ratio. We further show the utility of the so-formed asparaginyl hydrazide in native chemical ligation and hydrazone conjugation. Using an EGFR-targeting affibody as a model protein, we have showcased our methodology in the preparation of a number of protein ligation or conjugation products, which are decorated with various functional moieties. The Z_EGFR affibody-doxorubicin conjugate shows high selective binding and cytotoxicity toward the EGFR-positive A431 cells. Our results demonstrate the advantages of AEP-mediated protein hydrazinolysis as a simple and straightforward strategy for the precision manufacturing of protein bioconjugates.

Vypal2: A Versatile Peptide Ligase for Precision Tailoring of Proteins

The last two decades have seen an increasing demand for new protein-modification methods from the biotech industry and biomedical research communities. Owing to their mild aqueous reaction conditions, enzymatic methods based on the use of peptide ligases are particularly desirable. In this regard, the recently discovered peptidyl Asx-specific ligases (PALs) have emerged as powerful biotechnological tools in recent years. However, as a new class of peptide ligases, their scope and application remain underexplored. Herein, we report the use of a new PAL, VyPAL2, for a diverse range of protein modifications. We successfully showed that VyPAL2 was an efficient biocatalyst for protein labelling, inter-protein ligation, and protein cyclization. The labelled or cyclized protein ligands remained functionally active in binding to their target receptors. We also demonstrated on-cell labelling of protein ligands pre-bound to cellular receptors and cell-surface engineering via modifying a covalently anchored peptide substrate pre-installed on cell-surface glycans. Together, these examples firmly establish Asx-specific ligases, such as VyPAL2, as the biocatalysts of the future for site-specific protein modification, with a myriad of applications in basic research and drug discovery.

Therapeutic peptides for chemotherapy: Trends and challenges for advanced delivery systems

The past decades witnessed an increasing interest in peptides as clinical therapeutics. Rightfully considered as a potential alternative for small molecule therapy, these remarkable pharmaceuticals can be structurally fine-tuned to impact properties such as high target affinity, selectivity, low immunogenicity along with satisfactory tissue penetration. Although physicochemical and pharmacokinetic challenges have mitigated, to some extent, the clinical applications of therapeutic peptides, their potential impact on modern healthcare remains encouraging. According to recent reports, there are more than 400 peptides under clinical trials and 60 were already approved for clinical use. As the demand for efficient and safer therapy became high, especially for cancers, peptides have shown some exciting developments not only due to their potent antiproliferative action but also when used as adjuvant therapies, either to decrease side effects with tumor-targeted therapy or to enhance the activity of anticancer drugs via transbarrier delivery. The first part of the present review gives an insight into challenges related to peptide product development. Both molecular and formulation approaches intended to optimize peptide's pharmaceutical properties are covered, and some of their current issues are highlighted. The second part offers a comprehensive overview of the emerging applications of therapeutic peptides in chemotherapy from bioconjugates to nanovectorized therapeutics.

Approaches for peptide and protein cyclisation

The cyclisation of polypeptides can play a crucial role in exerting biological functions, maintaining stability under harsh conditions and conferring proteolytic resistance, as demonstrated both in nature and in the laboratory. To date, various approaches have been reported for polypeptide cyclisation. These approaches range from the direct linkage of N- and C- termini to the connection of amino acid side chains, which can be applied both in reaction vessels and in living systems. In this review, we categorise the cyclisation approaches into chemical methods (e.g. direct backbone cyclisation, native chemical ligation, aldehyde-based ligations, bioorthogonal reactions, disulphide formation), enzymatic methods (e.g. subtiligase variants, sortases, asparaginyl endopeptidases, transglutaminases, non-ribosomal peptide synthetases) and protein tags (e.g. inteins, engineered protein domains for isopeptide bond formation). The features of each approach and the considerations for selecting an appropriate method of cyclisation are discussed.

Amphiphilic mPEG-Modified Oligo-Phenylalanine Nanoparticles Chemoenzymatically Synthesized via Papain

Amphiphilic mPEG-modified peptide nanoparticles were developed from oligo-phenylalanine (OPhe) nanoparticles (NPs) synthesized via papain. Tyndall effects indicate that OPhe NPs are amphiphobic. Addition of protein perturbants, sodium dodecyl sulfate (SDS), and urea, in the dispersion solution of OPhe NPs can significantly reduce the R _h,m value of NPs, from approximately 749.2 nm to about 200 nm. Therefore, the hydrophobic interaction and hydrogen bonding play major roles in maintaining the aggregation of OPhe NPs. Using the "grafting to" method, the methoxypolyethylene-modified OPhe NPs (mPEG-g-OPhe NPs) were synthesized and characterized by Fourier transform infrared spectroscopy (FTIR), ¹H NMR, electrospray ionization mass spectrometry (ESI-MS), and dynamic light scattering (DLS). The attenuated total reflectance (ATR) spectrum of OPhe NPs and mPEG-g-OPhe NPs demonstrate that the secondary structures of these NPs are mainly β-type. mPEG-g-OPhe NPs can self-aggregate into spherical micelles both in water and cyclohexane. Increasing the chain length of the mPEG moiety, the critical micellar concentrations of mPEG-g-OPhe NPs increased in water but decreased in cyclohexane. The light stability, thermal stability, hydrolysis stability, and encapsulation stability of curcumin were significantly promoted by encapsulation in the micelles formed by mPEG-g-OPhe NPs. The protective effects regularly varied with the variations in the mPEG chain length of mPEG-g-OPhe NPs.

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.

Gene to diagnostic: Self immobilizing protein for silica microparticle biosensor, modelled with sarcosine oxidase

A rational design approach is proposed for a multifunctional enzyme reagent for point-of-care diagnostics. The biomaterial reduces downstream isolation steps and eliminates immobilization coupling chemicals for integration in a diagnostic platform. Fusion constructs combined the central functional assay protein (e.g. monomeric sarcosine oxidase, mSOx, horseradish peroxidase, HRP), a visualizing protein (e.g. mCherry) and an in-built immobilization peptide (e.g. R5). Monitoring protein expression in E.coli was facilitated by following the increase in mCherry fluorescence, which could be matched to a color card, indicating when good protein expression has occurred. The R5 peptide (SSKKSGSYSGSKGSKRRIL) provided inbuilt affinity for silica and an immobilization capability for a silica based diagnostic, without requiring additional chemical coupling reagents. Silica particles extracted from beach sand were used to collect protein from crude protein extract with 85-95% selective uptake. The silica immobilized R5 proteins were stable for more than 2 months at room temperature. The K_m for the silica-R5₂-mCh-mSOx-R5-6H was 16.5 ± 0.9 mM (compared with 16.5 ± 0.4 mM, 16.3 ± 0.3 mM, and 16.1 ± 0.4 mM for R5₂-mCh-mSOx-R5-6H, mSOx-R5-6H and mSOx-6H respectively in solution). The use of the "silica-enzymes" in sarcosine and peroxide assays was shown, and a design using particle sedimentation through the sample was examined. Using shadowgraphy and particle image velocimetry the particle trajectory through the sample was mapped and an hourglass design with a narrow waist shown to give good control of particle position. The hourglass biosensor was demonstrated for sarcosine assay in the clinically useful range of 2.5-10 μM in both a dynamic and end point measurement regime.

Enzymatic On-Resin Peptide Cleavage and in Situ Cyclization One-Pot Strategy for the Synthesis of Cyclopeptide and Cyclotide

A one-pot strategy combining sortase A mediated on-resin peptide cleavage and in situ cyclization was developed for the synthesis of cyclic peptides. This strategy was applied to synthesize head-to-tail cyclic antibacterial bovine lactoferricin peptide LFcinB_20-35 in a yield of 67%. The one-pot strategy was compatible with an oxidative folding reaction, and complex cyclotides containing one or two disulfide bonds, such as sunflower trypsin inhibitors-1 and α-conotoxin MII, were successfully synthesized in one pot in a yield of 77% and 61%, respectively.