Overview of the Regulation of Disulfide Bond Formation in Peptide and Protein Folding

FDA's stamp of approval: Unveiling peptide breakthroughs in cardiovascular diseases, ACE, HIV, CNS, and beyond

Peptides exhibit significant specificity and effective interaction with therapeutic targets, positioning themselves as key players in the global pharmaceutical market. They offer potential treatments for a wide range of diseases, including those that pose significant challenges. Notably, the peptide trofinetide (Daybue) marked a groundbreaking achievement by providing the first-ever cure for Rett syndrome, and several peptides have secured FDA approval as first-in-class medications. Furthermore, peptides are expanding their presence in areas traditionally dominated by either small or large molecules. A noteworthy example is the FDA approval of motixafortide (Aphexda) as the first peptide-based chemokine antagonist. Here, the focus will be on the analysis of FDA-approved peptides, particularly those targeting cardiovascular diseases, human immunodeficiency, central nervous system diseases, and various other intriguing classes addressing conditions such as osteoporosis, thrombocytopenia, Cushing's disease, and hypoglycemia, among others. The review will explore the chemical structures of the peptides, their indications and modes of action, the developmental trajectory, and potential adverse effects.

Confirmation of the Disulfide Connectivity and Strategies for Chemical Synthesis of the Four-Disulfide-Bond-Stabilized Aspergillus giganteus Antifungal Protein, AFP

Emerging fungal infections require new, more efficient antifungal agents and therapies. AFP, a protein from Aspergillus giganteus with four disulfide bonds, is a promising candidate because it selectively inhibits the growth of filamentous fungi. In this work, the reduced form of AFP was prepared using native chemical ligation. The native protein was synthesized via oxidative folding with uniform protection for cysteine thiols. AFP's biological activity depends heavily on the pattern of natural disulfide bonds. Enzymatic digestion and MS analysis provide proof for interlocking disulfide topology (abcdabcd) that was previously assumed. With this knowledge, a semi-orthogonal thiol protection method was designed. By following this strategy, out of a possible 105, only 6 disulfide isomers formed and 1 of them proved to be identical with the native protein. This approach allows the synthesis of analogs for examining structure-activity relationships and, thus, preparing AFP variants with higher antifungal activity.

Tauroursodeoxycholic acid attenuates cisplatin-induced ototoxicity by inhibiting the accumulation and aggregation of unfolded or misfolded proteins in the endoplasmic reticulum

Cisplatin-induced ototoxicity is one of the important reasons that limit the drug's clinical application, and its mechanism has not been fully elucidated so far. The aim of this study was to explore the attenuate effect of tauroursodeoxycholic acid (TUDCA), a proteostasis promoter, on cisplatin-induced ototoxicity in vivo and in vitro, and to explore its possible mechanism. Auditory brainstem response (ABR) was measured to identify the attenuate effects of TUDCA administered subcutaneously [500 mg/kg/d × 3d, cisplatin: 4.6 mg/kg/d × 3d, intraperitoneal injection (i.p.)] or trans-tympanically (0.5 mg/mL, cisplatin: 12 mg/kg, i.p. with a pump) in Sprague-Dawley (SD) rats subjected to cisplatin-induced hearing loss. The cochlear explants of neonatal rats and OC1 auditory hair cell-like cell lines cultured in vitro were used to observe the number of apoptotic cells and the endoplasmic reticulum (ER) stress in the control, cisplatin (5 μM for 48 h for cochlear explants, 10 μM for 24 h for OC1 cells), and cisplatin + TUDCA (1 mM for 24 h for cochlear explants, 1.6 mM for 24 h for OC1 cells) groups. Differences in the expression of key proteins in the ER protein quality control (ERQC) system were detected. The changes in the attenuate effect of TUDCA on cisplatin-induced ototoxicity after down-regulating calreticulin (CRT), UDP-glucose ceramide glucosyltransferase-like 1 (UGGT1), and OS9 ER lectin (OS9) were also measured. The effect of TUDCA (10 mM) on stabilizing unfolded or misfolded proteins (UFP/MFP) was analyzed in a cell-free 0.2 % bovine serum albumin (BSA) aggregation system in vitro. Both the subcutaneous and trans-tympanic TUDCA administration alleviated cisplatin-induced increase in ABR thresholds in rats. TUDCA was able to reduce cisplatin-induced apoptosis and alleviate ER stress in cochlear explants and OC1 cells. Under the cisplatin treatment, the expression levels of CRT, UGGT1, and OS9 in the auditory hair cell increased, and the expression of total ubiquitinated proteins decreased. TUDCA attenuated the effect of cisplatin on UGGT1 and OS9, and recovered the protein ubiquitination levels. After down-regulating CRT, UGGT1, or OS9, the protective effect of TUDCA decreased. In the cell-free experimental system, TUDCA inhibited the aggregation of denatured BSA molecules. In summary, TUDCA can attenuate cisplatin-induced ototoxicity, possibly by inhibiting the accumulation and aggregation of UFP/MFP and the associated ER stress.

Revisiting the Formation of a Native Disulfide Bond: Consequences for Protein Regeneration and Beyond

Oxidative protein folding involves the formation of disulfide bonds and the regeneration of native structure (N) from the fully reduced and unfolded protein (R). Oxidative protein folding studies have provided a wealth of information on underlying physico-chemical reactions by which disulfide-bond-containing proteins acquire their catalytically active form. Initially, we review key events underlying oxidative protein folding using bovine pancreatic ribonuclease A (RNase A), bovine pancreatic trypsin inhibitor (BPTI) and hen-egg white lysozyme (HEWL) as model disulfide bond-containing folders and discuss consequential outcomes with regard to their folding trajectories. We re-examine the findings from the same studies to underscore the importance of forming native disulfide bonds and generating a “native-like” structure early on in the oxidative folding pathway. The impact of both these features on the regeneration landscape are highlighted by comparing ideal, albeit hypothetical, regeneration scenarios with those wherein a native-like structure is formed relatively “late” in the R→N trajectory. A special case where the desired characteristics of oxidative folding trajectories can, nevertheless, stall folding is also discussed. The importance of these data from oxidative protein folding studies is projected onto outcomes, including their impact on the regeneration rate, yield, misfolding, misfolded-flux trafficking from the endoplasmic reticulum (ER) to the cytoplasm, and the onset of neurodegenerative disorders.

Distinct 3-disulfide-bonded isomers of tridegin differentially inhibit coagulation factor XIIIa: The influence of structural stability on bioactivity

Tridegin is a 66mer cysteine-rich coagulation factor XIIIa (FXI-IIa) inhibitor from the giant amazon leech Haementeria ghilianii of yet unknown disulfide connectivity. This study covers the structural and functional characterization of five different 3-disulfide-bonded tridegin isomers. In addition to three previously identified isomers, one isomer containing the inhibitory cystine knot (ICK, knottin) motif, and one isomer with the leech antihemostatic protein (LAP) motif were synthesized in a regioselective manner. A fluorogenic enzyme activity assay revealed a positive correlation between the constriction of conformational flexibility in the N-terminal part of the peptide and the inhibitory potential towards FXI-IIa with clear differences between the isomers. This observation was supported by molecular dynamics (MD) simulations and subsequent molecular docking studies. The presented results provide detailed structure-activity relationship studies of different tridegin disulfide isomers towards FXI-IIa and reveal insights into the possibly existing native linkage compared to non-native disulfide tridegin species.

Stepwise Construction of Disulfides in Peptides

The disulfide bond plays an important role in biological systems. It defines global conformation, and ultimately the biological activity and stability of the peptide or protein. It is frequently present, singly or multiply, in biologically important peptide hormones and toxins. Numerous disulfide-containing peptides have been approved by the regulatory agencies as marketed drugs. Chemical synthesis is one of the prerequisite tools needed to gain deep insights into the structure-function relationships of these biomolecules. Along with the development of solid-phase peptide synthesis, a number of methods of disulfide construction have been established. This minireview will focus on the regiospecific, stepwise construction of multiple disulfides used in the chemical synthesis of peptides. We intend for this article to serve a reference for peptide chemists conducting complex peptide syntheses and also hope to stimulate the future development of disulfide methodologies.

Use of Protein Folding Reagents

The reagents and methods for purification and use of the most commonly used denaturants, guanidine hydrochloride (guanidine-HCl) and urea, are described. Other protein denaturants and reagents used to fold proteins are briefly mentioned. Sulfhydryl reagents (reducing agents) and "oxido-shuffling" (or oxidative regeneration) systems are also described.

Cellular disulfide bond formation in bioactive peptides and proteins

Bioactive peptides play important roles in metabolic regulation and modulation and many are used as therapeutics. These peptides often possess disulfide bonds, which are important for their structure, function and stability. A systematic network of enzymes--a disulfide bond generating enzyme, a disulfide bond donor enzyme and a redox cofactor--that function inside the cell dictates the formation and maintenance of disulfide bonds. The main pathways that catalyze disulfide bond formation in peptides and proteins in prokaryotes and eukaryotes are remarkably similar and share several mechanistic features. This review summarizes the formation of disulfide bonds in peptides and proteins by cellular and recombinant machinery.