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

Use of ionic liquids in amidation reactions for proteolysis targeting chimera synthesis

Selective degradation of disease-causing proteins using proteolysis targeting chimeras (PROTACs) has gained great attention, thanks to its several advantages over traditional therapeutic modalities. Despite the advances made so far, the structural chemical complexity of PROTACs poses challenges in their synthetic approaches. PROTACs are typically prepared through a convergent approach, first synthesizing two fragments separately (target protein and E3 ligase ligands) and then coupling them to produce a fully assembled PROTAC. The amidation reaction represents the most common coupling exploited in PROTACs synthesis. Unfortunately, the overall isolated yields of such synthetic procedures are usually low due to one or more purification steps to obtain the final PROTAC with acceptable purity. In this work, we focused our attention on the optimization of the final amidation step for the synthesis of an anti-SARS-CoV-2 PROTAC by investigating different amidation coupling reagents and a range of alternative solvents, including ionic liquids (ILs). Among the ILs screened, [OMIM][ClO4] emerged as a successful replacement for the commonly used DMF within the HATU-mediated amidation reaction, thus allowing the synthesis of the target PROTAC under mild and sustainable conditions in very high isolated yields. With the optimised conditions in hand, we explored the scalability of the synthetic approach and the substrate scope of the reaction by employing different E3 ligase ligand (VHL and CRBN)-based intermediates containing linkers of different lengths and compositions or by using different target protein ligands. Interestingly, in all cases, we obtained high isolated yields and complete conversion in short reaction times.

Chronic and intergenerational toxic effects of 1-decyl-3-methylimidazolium hexafluorophosphate on the water flea, Moina macrocopa

With the increasing use and production of "green solvents" ionic liquids (ILs) and their known stability in the environment, the potential adverse effects of ILs have become a focus of research. In the present study, acute, chronic, and intergenerational toxic effects of an imidazolium-based ionic liquid, 1-decyl-3-methylimidazolium hexafluorophosphate ([Demim]PF6), on Moina macrocopa were investigated following the parental exposure. The results showed that [Demim]PF6 exhibited high toxicity to M. macrocopa, and the long-term exposure significantly inhibited the survivorship, development, and reproduction of the water flea. Furthermore, it is also observed that [Demim]PF6 induced toxic effects in the following generation of M. macrocopa, resulting in the complete cessation of reproduction in the first offspring generation, and the growth of the organisms was also significantly affected. These findings provided a novel insight into the intergenerational toxicity induced by ILs to crustaceans and suggested that these compounds pose potential risks to the aquatic ecosystem.

Evaluation of new L-amino acids triethanolammonium salts usability for controlling protease activity

Twenty new triethanolammonium amino acid salts (TEA AA) have been prepared from triethanolammonium hydroxide and L-amino acids. The physicochemical properties of TEA AA depended on the applied amino acid. Five of the synthesised salts, i.e. mono- and bis-salts of L-glutamic acid, L-aspartic acid, and TEA salt of l-glutamine were solids with melting points between 127.32 °C to 171.51 °C. The other TEA AA exhibited glass transition temperatures from -68.45 °C for TEA Ser to -6.27 °C for TEA Trp and were assigned as amino acid ionic liquids (AAILs). The TEA His was characterised by the highest thermal stability, with an average temperature of 5 % weight loss at 186.4 °C, whereas the lowest stability was determined for TEA Asp (107.5 °C). The developed salts were tested as reaction medium additives for proteolytic enzymes (papain, subtilisin, bromelain). Most AAILs showed an inhibitory effect on tested proteases but with different mechanisms related to the enzyme substrate specificity and structural diversity. The TEA Ser was the most effective competitive inhibitor (K_i = 0.24 10^-4 mol/L) for bromelain, while TEA Val uncompetitive inhibitor for papain (K_i = 0.25 10^-4 mol/L). The developed TEA AA salts exhibit potential as enzyme-controlling agents for use in industrial processes.

Hydrogen bonds-triggered differential extraction efficiencies for bifenthrin by three polymeric ionic liquids with varying anions based on FT-IR spectroscopy

Herein, we fabricated three imidazolium-based polymeric ionic liquids (PILs) with different anions (P[VEIM]BF4, P[VEIM]PF6 and P[VEIM]Br), and analyzed their differential extraction efficiencies for bifenthrin through H-bonding induced effects. Three PILs all presented an irregular block structure with rough surface and lower specific-surface area (SSA, 11.2-18.7 m2 g-1) than carbon-based nanomaterials. They formed hydrogen bonds with free-water molecules in the lattice of PILs, including C2,4,5-H⋯O-H, Br⋯H-O-H⋯Br, O-H⋯Br, C2,4,5-H⋯F-P, P-F⋯H-O-H⋯F-P, C2,4,5-H⋯F-B and B-F⋯H-O-H⋯F-B. After extraction, the O-H stretching-vibration peak was prominently intensified, whereas the C-H bond varied slightly concomitant with reduced B-F and P-F vibration. Theoretically, the C-H vibration should become more intense in the C4,5-H⋯H2O and C2-H⋯H2O bonds after extraction in contrast to before extraction. These contrary spectral changes demonstrated that the hydrogen bonds between cations in the PILs and free-water molecules were broken after extraction, yielding the H-bonding occurrence between bifenthrin and H-O-H in the lattice. As a time indicator for the free-water binding and releasing process, the highest slope for the plot of I t /I 0 against time implied that the shortest time was required for P[VEIM]PF6 to reach an adsorption equilibrium. Overall, the strong hydrophobicity, small SSA and electrostatic-repulsion force for P[VEIM]PF6 are all not conducive to its efficient adsorption. Beyond our anticipation, P[VEIM]PF6 provided the highest extraction recovery for bifenthrin up to 92.4% among three PILs. Therefore, these data lead us to posit that the above high efficiency results from the strongest H-bonding effect between P[VEIM]PF6 and bifenthrin. These findings promote our deep understanding of PILs-triggered differential efficiency through a H-bonding induced effect.

Green solvents for the formation of amide linkages

The formation of the amide bond is among the most commonly performed transformations in the pharmaceutical industry and the wider chemical industry. The current methods for its installation in organic compounds frequently rely on the use of large amounts of organic solvents, mainly N,N-dimethylformamide (DMF), N-methylpyrrolidone (NMP), and dichloromethane (DCM), which have been associated with adverse environmental and health concerns over the last decades. This fact led academia and industry to make significant efforts toward the development of synthetic routes with the aim to avoid, reduce or replace the use of hazardous solvents. The present review fits into this framework and discusses the literature existing over the past ten years on strategies for reducing and replacing hazardous solvents, focusing on the use of biobased and neoteric solvents, such as ionic liquids and deep eutectic solvents (ILs and DESs, respectively), and on the reaction media that proved to be greener alternatives for amide bond formation.

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.

Advances in Processing Chitin as a Promising Biomaterial from Ionic Liquids

Chitin isolated through microwave-assisted dissolution using ionic liquids is a high molecular weight (MW) polymer that can be manufactured into materials of different architectures (e.g., fibers, films, microspheres, nanostructured materials) to be used as wound care dressings, drug delivery devices, scaffolds, etc. However, because of differences from traditional isolation methods and, thus, differences in polymer length and degree of deacetylation, it could exhibit bio-related properties that differ from those of traditionally 'pulped' chitin. Here we present the initial assessments of bio-related chitin properties in order to provide a useful scientific basis for clinical applications: biocompatibility, cytotoxicity (intracutaneous reactivity), wound healing efficacy, histological evaluation of the wounds treated with chitin dressing, and antibacterial activity. We also provide the studies that outline potential applications of chitin as a raw polymer for preparation of biomaterials. Graphical Abstract.

Hierarchical Assembly of Tough Bioelastomeric Egg Capsules is Mediated by a Bundling Protein

Marine snail egg capsules are shock-absorbing bioelastomers made from precursor "egg case proteins" (ECPs) that initially lack long-range order. During capsule formation, these proteins self-assemble into coiled-coil filaments that subsequently align into microscopic layers, a multiscale process which is crucial to the capsules' shock-absorbing properties. In this study, we show that the self-assembly of ECPs into their functional capsule material is mediated by a bundling protein that facilitates the aggregation of coiled-coil building blocks and their gelation into a prefinal capsule prior to final stabilization. This low molecular weight bundling protein, termed Pugilina cochlidium Bundling Protein (PcBP), led to gelation of native extracts from gravid snails, whereas crude extracts lacking PcBP did not gelate and remained as a protein solution. Refolding and reconcentration of recombinant PcBP induced bundling and aggregation of ECPs, as evidenced by ECPs oligomerization. We propose that the secretion of PcBP in vivo is a time-specific event during the embryo encapsulation process prior to cross-linking in the ventral pedal gland (VPG). Using molecular dynamics (MD) simulations, we further propose plausible disulfide binding sites stabilizing two PcBP monomers, as well as a polarized surface charge distribution, which we suggest plays an important role in the bundling mechanism. Overall, this study shows that controlled bundling is a key step during the extra-cellular self-assembly of egg capsules, which has previously been overlooked.

Biological Activity of Ionic Liquids and Their Application in Pharmaceutics and Medicine

Ionic liquids are remarkable chemical compounds, which find applications in many areas of modern science. Because of their highly tunable nature and exceptional properties, ionic liquids have become essential players in the fields of synthesis and catalysis, extraction, electrochemistry, analytics, biotechnology, etc. Apart from physical and chemical features of ionic liquids, their high biological activity has been attracting significant attention from biochemists, ecologists, and medical scientists. This Review is dedicated to biological activities of ionic liquids, with a special emphasis on their potential employment in pharmaceutics and medicine. The accumulated data on the biological activity of ionic liquids, including their antimicrobial and cytotoxic properties, are discussed in view of possible applications in drug synthesis and drug delivery systems. Dedicated attention is given to a novel active pharmaceutical ingredient-ionic liquid (API-IL) concept, which suggests using traditional drugs in the form of ionic liquid species. The main aim of this Review is to attract a broad audience of chemical, biological, and medical scientists to study advantages of ionic liquid pharmaceutics. Overall, the discussed data highlight the importance of the research direction defined as "Ioliomics", studies of ions in liquids in modern chemistry, biology, and medicine.

The Anticancer Potential of Ionic Liquids

Among the many challenges that the pharmaceutical industry currently faces is the need to develop innovative and effective therapies. The investigation of alternative and effective therapies against cancer is a current goal of the pharmaceutical industry. Ionic liquids (ILs) have emerged recently as a topic of study by researchers in the pharmaceutical industry in their search for new therapeutic agents. By definition, ILs are organic salts with melting points below 100 °C that are composed only by ions. Their main advantage lies in the numerous possible combinations of cations and anions, which allow adjustments in their physicochemical properties. The combination between ILs and active pharmaceutical ingredients (APIs) may improve the properties of APIs. In addition, the antitumor properties of these compounds have been described. Several studies have reported the use of ILs in biomedical applications as therapeutic agents, namely as antitumor agents. This review describes the recent proposed applications of ILs as antitumor agents.

Nonclassical Routes for Amide Bond Formation

The present review offers an overview of nonclassical (e.g., with no pre- or in situ activation of a carboxylic acid partner) approaches for the construction of amide bonds. The review aims to comprehensively discuss relevant work, which was mainly done in the field in the last 20 years. Organization of the data follows a subdivision according to substrate classes: catalytic direct formation of amides from carboxylic and amines ( section 2 ); the use of carboxylic acid surrogates ( section 3 ); and the use of amine surrogates ( section 4 ). The ligation strategies (NCL, Staudinger, KAHA, KATs, etc.) that could involve both carboxylic acid and amine surrogates are treated separately in section 5 .

Meta-analysis of ionic liquid literature and toxicology

A meta-analysis was conducted to compare the total amount of ionic liquid (IL) literature (n = 39,036) to the body of publications dealing with IL toxicity (n = 213) with the goal of establishing the state of knowledge and existing information gaps. Additionally, patent literature pertaining to issued patents utilizing ILs (n = 3358) or dealing with IL toxicity (n = 112) were analyzed. Total publishing activity and patent count served to gauge research activity, industrial usage and toxicology knowledge of ILs. Five of the most commonly studied IL cations were identified and used to establish a relationship between toxicity data and potential of commercial use: imidazolium, ammonium, phosphonium, pyridinium, and pyrrolidinium. Toxicology publications for all IL cations represented 0.55% ± 0.27% of the total publishing activity; compared with other industrial chemicals, these numbers indicate that there is still a paucity of studies on the adverse effects of this class of chemical. Toxicity studies on ILs were dominated by the use of in vitro models (18%) and marine bacteria (15%) as studied biological systems. Whole animal studies (n = 87) comprised 31% of IL toxicity studies, with a subset of in vivo mammalian models consisting of 8%. Human toxicology data were found to be limited to in vitro analyses, indicating substantial knowledge gaps. Risks from long-term and chronic low-level exposure to ILs have not been established yet for any model organisms, reemphasizing the need to fill crucial knowledge gaps concerning human health effects and the environmental safety of ILs. Adding to the existing knowledge of the molecular toxicity characteristics of ILs can help inform the design of greener, less toxic and more benign IL technologies.

Exploring the structure and stability of amino acids and glycine peptides in biocompatible ionic liquids

Amino acids (AAs) are vital components for a variety of biological systems and can be linked through covalent bonds (or peptide bonds) to form a protein structure.

Peptide Synthesis in Ionic Liquids (PEPSIL): All You Need is in the Toolbox!

This personal account describes our studies regarding peptide synthesis in ionic liquids (PEPSIL). In addition, we summarize our experiments in which the use of ionic liquids gives simple and promising access to unnatural amino acids in an enantiomerically enriched form. Extension of PEPSIL method to complex structures such as cyclopeptides is also discussed. Some of these cyclopeptides are the direct precursors of bioactive and pharmaceutical compounds.

Ionic Liquids in Capillary Electrophoresis

Recently, a great interest was drawn toward ionic liquids (ILs) in analytical separation techniques. ILs possess many properties making them excellent additives in capillary electrophoresis (CE) background electrolytes (BGE). The most important property is the charge of the dissolved ions in BGE enabling the cations to interact with deprotonated silanol groups on the capillary surface and thereby modifying the electroosmotic flow (EOF). Ionic and/or proton donor-acceptor interactions between analyte and IL are possible interactions facilitating new kinds of separation mechanisms in CE. Further advantages of ILs are the high conductivity, the environmentally friendliness, and the good solubility for organic and inorganic compounds. The most commonly used ILs in capillary electrophoresis are dialkylimidazolium-based ILs, whereas for enantioseparation a lot of innovative chiral cations and anions were investigated.ILs are reported to be additives to a normal CE background electrolyte or the sole electrolyte in CE, nonaqueous CE (NACE), micellar electrokinetic chromatography (MEKC), and in enantioseparation. An overview of applications and separation mechanisms reported in the literature is given here, in addition to the enantioseparation of pseudoephedrine using tetrabutylammonium chloride (TBAC) as IL additive to an ammonium formate buffer containing β-cyclodextrin (β-CD).

Ionic Liquids Beyond Simple Solvents: Glimpses at the State of the Art in Organic Chemistry

Within the last 25 years ionic liquids have written a tremendous success story, which is documented in a nearly uncountable amount of original research papers, reviews, and numerous applications in research and industry. These days, ionic liquids can be considered as a mature class of compounds for many different applications. Frequently, they are used as neoteric solvents for chemical tansformations, and the number of reviews on this field of research is huge. In this focused review, though, we are trying to evaluate the state of the art of ionic liquid chemistry beyond using them simply as solvents for chemical transformations. It is not meant to be a comprehensive overview on the topic; the choice of emphasis and examples rather refects the authors' personal view on the field. We are especially highlighting fields in which we believe the most fundamental developments within the next five years will take place: biomass processing, (chiral) ionic liquids from natural sources, biotransformations, and organic synthesis.