A Chemical Biology Approach to Probing the Folding Pathways of the Inhibitory Cystine Knot (ICK) Peptide ProTx-II

Cysteine variants in PMM2 lead to protein instability and higher sensitivity to oxidative stress in PMM2-CDG

PMM2-congenital disorder of glycosylation (PMM2-CDG) is caused by genetic defects in PMM2, the gene encoding phosphomannomutase 2. Effective therapies for this disorder remain elusive. Recent studies emphasize cysteine's vulnerability to oxidative modifications that can instigate disease by facilitating inter-protein disulfide bonding, reducing protein mobility, highlighting its potential as a target for therapeutic intervention. Specifically, five cysteine-related pathogenic mutants have been identified in PMM2-CDG, namely Phe11Cys (F11C), Tyr64Cys (Y64C), Tyr76Cys (Y76C), Tyr106Cys (Y106C) and Gly228Cys (G228C), however the fundamental molecular mechanisms are still not fully understood. In this study, compared to wild-type (WT), Cys pathogenic mutants induced structural destruction, augmented hydrophobic exposure, reduced thermal stability, and a propensity to aggregate at physiological temperatures. Meanwhile, Cys mutants were sensitive to oxidative stress, which in the evident formation of aggregation. Molecular dynamics simulation revealed alterations in the core region and subunit binding free energy of homologous PMM2, instigated by the pathophysiogenic variants. Based on previous articles, we found cysteine pathogenic mutants can be partly rescued by celastrol. In summary, our findings provide critical insights into the molecular and functional impacts of specific cysteine variants in the PMM2 enzyme, offering a foundation for exploring novel therapeutic strategies for the prevention and treatment of PMM2-CDG.

Peptides originally derived from Chilobrachys jingzhao tarantula venom possess beneficial effects on pancreatic beta cell health and function

Clinical approval of the glucagon-like peptide-1 (GLP-1) mimetic exenatide for the treatment of type 2 diabetes highlights the therapeutic effectiveness of venom-derived peptides. In the present study, we examined and characterised the glucose-lowering potential of synthetic Jingzhaotoxin IX and Jingzhaotoxin XI peptides, which were originally isolated from the venom of the Chinese earth tarantula Chilobrachys jingzhao. Following confirmation of lack of beta-cell toxicity of synthetic peptides, assessment of enzymatic stability and effects on in vitro beta-cell function were studied, alongside putative mechanisms. Glucose homeostatic and appetite suppressive actions of Jingzhaotoxin IX and Jingzhaotoxin XI alone, or in combination with exenatide, were then assessed in normal overnight fasted C57BL/6 mice. Synthetic Jingzhaotoxin peptides were non-toxic and exhibited a decrease in mass of 6 Da in Krebs-Ringer bicarbonate buffer suggesting inhibitor cysteine knot (ICK)-like formation, but interestingly were liable to plasma enzyme degradation. The Jingzhaotoxin peptides evoked prominent insulin secretion from BRIN BD11 beta-cells, with activity somewhat characteristic of Kv2.1 channel binding. In addition, Jingzhaotoxin peptides enhanced beta-cell proliferation and provided significant protection against cytokine-induced apoptosis. When injected co-jointly with glucose, the Jingzhaotoxin peptides slightly decreased blood-glucose levels but had no effect on appetite in overnight fasted mice. Whilst the Jingzhaotoxin peptides did not enhance exenatide-induced benefits on glucose homeostasis, they augmented exenatide-mediated suppression of appetite. Taken together, these data highlight the therapeutic potential of tarantula venom-derived peptides, such as Jingzhaotoxin IX and Jingzhaotoxin XI either alone or in combination with exenatide, for diabetes and related obesity.

CysPresso: a classification model utilizing deep learning protein representations to predict recombinant expression of cysteine-dense peptides

BACKGROUND

Cysteine-dense peptides (CDPs) are an attractive pharmaceutical scaffold that display extreme biochemical properties, low immunogenicity, and the ability to bind targets with high affinity and selectivity. While many CDPs have potential and confirmed therapeutic uses, synthesis of CDPs is a challenge. Recent advances have made the recombinant expression of CDPs a viable alternative to chemical synthesis. Moreover, identifying CDPs that can be expressed in mammalian cells is crucial in predicting their compatibility with gene therapy and mRNA therapy. Currently, we lack the ability to identify CDPs that will express recombinantly in mammalian cells without labour intensive experimentation. To address this, we developed CysPresso, a novel machine learning model that predicts recombinant expression of CDPs based on primary sequence.

RESULTS

We tested various protein representations generated by deep learning algorithms (SeqVec, proteInfer, AlphaFold2) for their suitability in predicting CDP expression and found that AlphaFold2 representations possessed the best predictive features. We then optimized the model by concatenation of AlphaFold2 representations, time series transformation with random convolutional kernels, and dataset partitioning.

CONCLUSION

Our novel model, CysPresso, is the first to successfully predict recombinant CDP expression in mammalian cells and is particularly well suited for predicting recombinant expression of knottin peptides. When preprocessing the deep learning protein representation for supervised machine learning, we found that random convolutional kernel transformation preserves more pertinent information relevant for predicting expressibility than embedding averaging. Our study showcases the applicability of deep learning-based protein representations, such as those provided by AlphaFold2, in tasks beyond structure prediction.

Ring-Opening Polymerization of Amino Acid N-Carboxyanhydrides with Unprotected/Reactive Side Groups. I. d-Penicillamine N-Carboxyanhydride

The ring-opening (co)polymerization (ROP) of N-carboxyanhydride (NCA) monomers bearing unprotected/reactive side groups is rare and challenging. Here, we report the ROP of a d-penicillamine NCA (Pen-NCA) monomer for the synthesis of tertiary thiol-functionalized (co)polypeptides. Through judicious selection of reaction solvents and the use of benzoic acid as an additive in the ROP, the intramolecular isomerization side reactions of Pen-NCA are suppressed, generating homo- and copolypeptides with improved yield, high molecular weight, and narrow molecular weight distributions. Successful postpolymerization modifications of the d-Pen-containing copolypeptides on the tertiary thiols are achieved with high efficiency through thiol-Michael, S_N2, and nitrosylation reactions. This work provides an efficient protection-free approach to generating functional polypeptides and creates a fundamental understanding for Pen-NCA chemistry.

Development of ProTx-II Analogues as Highly Selective Peptide Blockers of Nav1.7 for the Treatment of Pain

Inhibitor cystine knot peptides, derived from venom, have evolved to block ion channel function but are often toxic when dosed at pharmacologically relevant levels in vivo. The article describes the design of analogues of ProTx-II that safely display systemic in vivo blocking of Na_v1.7, resulting in a latency of response to thermal stimuli in rodents. The new designs achieve a better in vivo profile by improving ion channel selectivity and limiting the ability of the peptides to cause mast cell degranulation. The design rationale, structural modeling, in vitro profiles, and rat tail flick outcomes are disclosed and discussed.

Scalable Biosynthetic Production of Knotted Peptides Enables ADME and Thermodynamic Folding Studies

Knotted peptides present a wealth of structurally diverse, biologically active molecules, with the inhibitor cystine knot/knottin class among the most ecologically common ones. Many of these natural products interact with extracellular targets such as voltage-gated ion channels with exquisite selectivity and potency, making them intriguing therapeutic modalities. Such compounds are often produced in low concentrations by intractable organisms, making structural and biological characterization challenging, which is frequently overcome by various expression strategies. Here, we sought to test a biosynthetic route for the expression and study of knotted peptides. We screened expression constructs for a biosynthesized knotted peptide to determine the most influential parameters for successful disulfide folding and used NMR spectroscopic fingerprinting to validate topological structures. We performed pharmacokinetic characterization, which indicated that the interlocking disulfide structure minimizes liabilities of linear peptide sequences, and propose a mechanism by which knotted peptides are cleared. We then developed an assay to monitor solution folding in real time, providing a strategy for studying the folding process during maturation, which provided direct evidence for the importance of backbone organization as the driving force for topology formation.