A room temperature ionic liquid as convenient solvent for the oxidative folding of conopeptides

Looking back: Developments in chemical protein synthesis in 2020

The world as we know it changed dramatically in the spring 2020 due to the Covid-19 pandemic. It was (and still is) a hard time for most of us. Luckily, the power of science enabled a good solution in form of a vaccine in less than 1 year. Of course, not only vaccine development boosted in 2020, but there were also several milestones in peptide chemistry. In this commentary, I would like to draw you away for a moment from the whole pandemic situation to discuss two exciting advances in chemical protein synthesis highlighted in 2020.

Native Chemical Ligation of Highly Hydrophobic Peptides in Ionic Liquid-Containing Media

The chemical synthesis of a highly hydrophobic membrane-associated peptide by native chemical ligation (NCL) in an ionic liquid (IL) [C₂mim][OAc]/buffer mixture was achieved by employing peptide concentrations up to 11 mM. NCL was studied at different pH and water content and compared to several “gold-standard” ligation protocols. The optimized reaction protocol for the NCL in IL required the addition of 40% water and pH adjustment to 7.0–7.5, resulting in ligation yields of up to 80–95% within 1 to 4 h. This new ligation protocol is generally applicable and outperforms current “gold-standard” NCL methods.

Challenges and Perspectives in Chemical Synthesis of Highly Hydrophobic Peptides

Solid phase peptide synthesis (SPPS) provides the possibility to chemically synthesize peptides and proteins. Applying the method on hydrophilic structures is usually without major drawbacks but faces extreme complications when it comes to "difficult sequences." These includes the vitally important, ubiquitously present and structurally demanding membrane proteins and their functional parts, such as ion channels, G-protein receptors, and other pore-forming structures. Standard synthetic and ligation protocols are not enough for a successful synthesis of these challenging sequences. In this review we highlight, summarize and evaluate the possibilities for synthetic production of "difficult sequences" by SPPS, native chemical ligation (NCL) and follow-up protocols.

Aqueous ionic liquids influence the disulfide bond isoform equilibrium in conotoxin AuIB: a consequence of the Hofmeister effect?

The appearance of several disulfide bond isoforms in multiple cysteine containing venom peptides poses a significant challenge in their synthesis and purification under laboratory conditions. Recent experiments suggest that careful tuning of solvent and temperature conditions can propel the disulfide bond isoform equilibrium in favor of the most potent, native form. Certain aqueous ionic liquids (ILs) have proven significantly useful as solvents for this purpose, while exceptions have also been noted. To elucidate the molecular level origin behind such a preference, we report a detailed explicit solvent replica exchange molecular dynamics study of a conotoxin, AuIB, in pure water and four different aqueous IL solutions (~45-60% v/v). The ILs studied here are comprised of cations like 1-ethyl-3-methyl-imidazolium (Im₂₁⁺) or 1-butyl-3-methyl-imidazolium (Im₄₁⁺) coupled with either acetate (OAc^-) or chloride (Cl^-) as the counter anion. Our simulations unfold interesting features of the conformational spaces sampled by the peptide and its solvation in pure water and aqueous IL solutions. Detailed investigation into populations of the globular disulfide bond isoform of AuIB in aqueous IL solutions reveal distinct trends which might be related to the Hofmeister effect of the cation and anion of the IL and of specific interactions of the aqueous IL solutions with the peptide. In accordance with experimental observations, the aqueous [Im₂₁][OAc] solution is found to promote the highest globular isoform population in AuIB.

Efficient Sustainable Tool for Monitoring Chemical Reactions and Structure Determination in Ionic Liquids by ESI-MS

An easy and convenient procedure is described for monitoring chemical reactions and characterization of compounds dissolved in ionic liquids using the well-known tandem mass spectrometry (MS/MS) technique. Generation of wastes was avoided by utilizing an easy procedure for analysis of ionic liquid systems without preliminary isolation and purification. The described procedure also decreased the risk of plausible contamination and damage of the ESI-MS hardware and increased sensitivity and accuracy of the measurements. ESI-MS detection in MS/MS mode was shown to be efficient in ionic liquids systems for structural and mechanistic studies, which are rather difficult otherwise. The developed ESI-MS/MS approach was applied to study samples corresponding to peptide systems in ionic liquids and to platform chemical directed biomass conversion in ionic liquids.

Oxidative folding of peptides with cystine-knot architectures: kinetic studies and optimization of folding conditions

Bioactive peptides often contain several disulfide bonds that provide the main contribution to conformational rigidity and structural, thermal, or biological stability. Among them, cystine-knot peptides-commonly named "knottins"-make up a subclass with several thousand natural members. Hence, they are considered promising frameworks for peptide-based pharmaceuticals. Although cystine-knot peptides are available through chemical and recombinant synthetic routes, oxidative folding to afford the bioactive isomers still remains a crucial step. We therefore investigated the oxidative folding of ten protease-inhibiting peptides from two knottin families, as well as that of an HIV entry inhibitor and of aprotinin, under two conventional sets of folding conditions and by a newly developed procedure. Kinetic studies identified folding conditions that resulted in correctly folded miniproteins with high rates of conversion even for highly hydrophobic and aggregation-prone peptides in concentrated solutions.

Ionic liquid applications in peptide chemistry: synthesis, purification and analytical characterization processes

This review aims to provide a comprehensive overview of the recent advances made in the field of ionic liquids in peptide chemistry and peptide analytics.

Synthesis and functional characterization of tridegin and its analogues: inhibitors and substrates of factor XIIIa

Tridegin, a 66-mer peptide isolated from the leech Haementeria ghilianii, is a potent inhibitor of the coagulation factor XIIIa. This paper describes the chemical synthesis of tridegin by two different strategies--solid-phase assembly and native chemical ligation--both followed by oxidation in solution phase. Tridegin and truncated analogues were examined for their activity and revealed a particular importance of the C-terminal region of the parent peptide. Based on these studies a minimal sequence required for factor XIIIa inhibition could be identified. Our data revealed that the glutamine residue at position 52 (Q52) of tridegin most likely binds to the active site of factor XIIIa and was therefore suggested to react with the enzyme. The function of the N-terminal region is also discussed, as the isolated C-terminal segment of tridegin lost its inhibitory activity rapidly in the presence of factor XIIIa, whereas this was not the case for the full-length inhibitor.

Optimization of oxidative folding methods for cysteine-rich peptides: a study of conotoxins containing three disulfide bridges

The oxidative folding of small, cysteine-rich peptides to selectively achieve the native disulfide bond connectivities is critical for discovery and structure-function studies of many bioactive peptides. As the propensity to acquire the native conformation greatly depends on the peptide sequence, numerous empirical oxidation methods are employed. The context-dependent optimization of these methods has thus far precluded a generalized oxidative folding protocol, in particular for peptides containing more than two disulfides. Herein, we compare the efficacy of optimized solution-phase and polymer-supported oxidation methods using three disulfide-bridged conotoxins, namely µ-SIIIA, µ-KIIIA and ω-GVIA. The use of diselenide bridges as proxies for disulfide bridges is also evaluated. We propose the ClearOx-assisted oxidation of selenopeptides as a fairly generalized oxidative folding protocol.

Molecular determinants for the subtype specificity of μ-conotoxin SIIIA targeting neuronal voltage-gated sodium channels

Voltage-gated sodium channels (Na(V) channels) play a pivotal role in neuronal excitability; they are specifically targeted by μ-conotoxins from the venom of marine cone snails. These peptide toxins bind to the outer vestibule of the channel pore thereby blocking ion conduction through Na(V) channels. μ-Conotoxin SIIIA from Conus striatus was shown to be a potent inhibitor of neuronal sodium channels and to display analgesic effects in mice, albeit the molecular targets are not unambiguously known. We therefore studied recombinant Na(V) channels expressed in mammalian cells using the whole-cell patch-clamp method. Synthetic μSIIIA slowly and partially blocked rat Na(V)1.4 channels with an apparent IC(50) of 0.56 ± 0.29 μM; the block was not complete, leaving at high concentration a residual current component of about 10% with a correspondingly reduced single-channel conductance. At 10 μM, μSIIIA potently blocked rat Na(V)1.2, rat and human Na(V)1.4, and mouse Na(V)1.6 channels; human Na(V)1.7 channels were only inhibited by 58.1 ± 4.9%, whereas human Na(V)1.5 as well as rat and human Na(V)1.8 were insensitive. Employing domain chimeras between rNa(V)1.4 and hNa(V)1.5, we located the determinants for μSIIIA specificity in the first half of the channel protein with a major contribution of domain-2 and a minor contribution of domain-1. The latter was largely accounted for by the alteration in the TTX-binding site (Tyr401 in rNa(V)1.4, Cys for Na(V)1.5, and Ser for Na(V)1.8). Introduction of domain-2 pore loops of all tested channel isoforms into rNa(V)1.4 conferred the μSIIIA phenotype of the respective donor channels highlighting the importance of the domain-2 pore loop as the major determinant for μSIIIA's subtype specificity. Single-site substitutions identified residue Ala728 in rNa(V)1.4 as crucial for its high sensitivity toward μSIIIA. Likewise, Asn889 at the homologous position in hNa(V)1.7 is responsible for the channel's reduced μSIIIA sensitivity. These results will pave the way for the rational design of selective Na(V)-channel antagonists for research and medical applications.

An unusual peptide from Conus villepinii: synthesis, solution structure, and cardioactivity

The venom of marine cone snails contains a variety of conformationally constrained peptides utilized by the animal to capture prey. Besides numerous conotoxins, which are characterized by complex disulfide patterns, other peptides with only a single disulfide bridge were isolated from different conus species. Here, we report the synthesis, structure elucidation and biological evaluation of the novel C-terminally amidated decapeptide CCAP-vil, PFc[CNSFGC]YN-NH(2), from Conus villepinii. The linear precursor peptide was generated by standard solid phase synthesis. Oxidation of the cysteine residues to yield the disulfide-bridged peptide was investigated under different conditions, including several ionic liquids (ILs) as new biocompatible reaction media. Among the examined ILs, 1-ethyl-3-methylimidazolium tosylate ([C(2)mim][OTs]) was most efficient for CCAP-vil oxidative folding, since oxidation occurred without any byproduct formation. The structure of CCAP-vil was determined by NMR methods in aqueous solution and revealed a loop structure adopting a type(I) beta-turn between residues 4-7 imposed by the flanking disulfide bridge. The amino acid side chains of Pro(1), Phe(2), Phe(6) and Tyr(9) point in three directions away from the cyclic core into the solvent creating a rather hydrophobic surface of the molecule. Based on sequence homology to cardioactive peptides (CAPs) from gastropods and arthropods, such as PFc[CNAFTGC]-NH(2) (CCAP), the influence of CCAP-vil on heart rate using zebrafish embryos was investigated. CCAP-vil reduced the heart rate immediately upon injection into the heart as well as upon indirect application indicating an opposite effect to the cardioaccelerating CCAP.

Determination of glucose and cellobiose dissolved in the ionic liquid 1-ethyl-3-methylimidazolium acetate using Fourier transform infrared spectroscopy

The conversion of biogenic carbohydrate feedstock to chemicals or energy equivalents is a promising approach to solve the problem of limited fossil fuel reserves. Some concepts to accomplish these transformations are based on ionic liquids (ILs) due to their ability to dissolve biopolymers, such as cellulose, and even complex biopolymer mixtures, such as wood. However, concerning control of such conversions, a reliable tool for process analytics is required. In this paper we demonstrate the applicability of Fourier transform infrared (FT-IR) spectroscopy to perform quantitative concentration measurements of glucose and cellobiose as two examples of carbohydrates dissolved in the room-temperature ionic liquid [EMIM][OAc] (1-ethyl-3-methylimidazolium acetate). For this purpose, binary mixtures in the range 0-20 wt% have been studied. A previously developed method for the data analysis, which was based on the Beer-Lambert relation, has been universalized by employing empirical correlations between the measured quantity (i.e., extinction) and the carbohydrate concentration. In the entire spectral range under investigation (500-4000 cm(-1)) numerous individual wave-numbers have been identified, allowing quantitative measurements with high accuracy and precision.