Use of Ionic Liquids in Protein and DNA Chemistry

Ionic liquids and their potential use in development and improvement of drug delivery systems: evidence of their tendency to promote drug accumulation in the brain

Ionic liquids (ILs) are considered salt in liquid state, which is composed of organic cations and anions with low melting points (<100 °C). ILs have become a major scientific area with an extensive range of applications including chemistry, electrochemistry, and pharmaceutics. ILs have received great research interest in the pharmaceutical field as solvents, anti-solvents, co-solvents, and reagents in synthesis and formulation. While therapeutic ILs have been investigated for oral and trans-dermal drug delivery systems showing promising compatibility with a wide range of therapeutics, enhanced drug permeation through the skin, and cell membrane solvation to open channels to facilitate molecular passage, their potential to cross the challenging blood-brain barrier (BBB) remains an unanswered question. IL-based therapies could potentially be a game changer for improving drug delivery to cellular targets both at and across the BBB. In this review, we discuss (1) the tunable physicochemical properties of ILs; (2) the vast and various applications of ILs in the development and improvement of drug delivery systems; and (3) ILs as a potential approach for increasing drug accumulation in the brain tissue.

Translation as a Biosignature

Life on Earth relies on mechanisms to store heritable information and translate this information into cellular machinery required for biological activity. In all known life, storage, regulation, and translation are provided by DNA, RNA, and ribosomes. Life beyond Earth, even if ancestrally or chemically distinct from life as we know it, may utilize similar structures: it has been proposed that charged linear polymers analogous to nucleic acids may be responsible for storage and regulation of genetic information in nonterran biochemical systems. We further propose that a ribosome-like structure may also exist in such a system, due to the evolutionary advantages of separating heritability from cellular machinery. In this study, we use a solid-state nanopore to detect DNA, RNA, and ribosomes, and we demonstrate that machine learning can distinguish between biomolecule samples and accurately classify new data. This work is intended to serve as a proof of principal that such biosignatures (i.e., informational polymers or translation apparatuses) could be detected, for example, as part of future missions targeting extant life on Ocean Worlds. A negative detection does not imply the absence of life; however, the detection of ribosome-like structures could provide a robust and sensitive method to seek extant life in combination with other methods. Key Words: RNA world-Darwinian evolution-Nucleic acids-Agnostic life detection. Astrobiology 24, 1257-1274.

Imidazolium-based ionic liquids support biosimilar flavin electron transfer

Understanding electron transport with electroactive microbes is key to engineering effective and scalable bio-electrochemical technologies. Much of this electron transfer occurs through small-molecule flavin mediators that perform one-electron transfers in abiotic systems but concerted two-electron transfer in biological systems, rendering abiotic systems less efficient. To boost efficiency, the principles guiding flavin electron transfer must be elucidated, necessitating a tunable system. Ionic liquids (ILs) offer such a platform due to their chemical diversity. In particular, imidazolium-containing ILs that resemble the amino acid histidine are bio-similar electrolytes that enable the study of flavin electron transfer. Using the model IL 1-ethyl-3-methylimidazolium ([Emim][BF4]), we observe concerted two-electron transfer between flavin mononucleotide and an unmodified glassy carbon electrode surface, while a one-electron transfer occurs in standard inorganic electrolytes. This work demonstrates the power of ILs to enable the mechanistic study of biological electron transfer, providing critical guidelines for improving electrochemical technologies based on these biological properties.

DNA nanotechnology in ionic liquids and deep eutectic solvents

Nucleic acids have the ability to generate advanced nanostructures in a controlled manner and can interact with target sequences or molecules with high affinity and selectivity. For this reason, they have applications in a variety of nanotechnology applications, from highly specific sensors to smart nanomachines and even in other applications such as enantioselective catalysis or drug delivery systems. However, a common disadvantage is the use of water as the ubiquitous solvent. The use of nucleic acids in non-aqueous solvents offers the opportunity to create a completely new toolbox with unprecedented degrees of freedom. Ionic liquids (ILs) and deep eutectic solvents (DESs) are the most promising alternative solvents due to their unique electrolyte and solvent roles, as well as their ability to maintain the stability and functionality of nucleic acids. This review aims to be a comprehensive, critical, and accessible evaluation of how much this goal has been achieved and what are the most critical parameters for accomplishing a breakthrough.

Impact of an Ionic Liquid Solution on Horseradish Peroxidase Activity

Horseradish peroxidase (HRP) is an enzyme that oxidizes pollutants from wastewater. A previous report indicated that peroxidases can have an enhancement in initial enzymatic activity in an aqueous solution of 0.26 M 1-ethyl-3-methylimidazolium ethyl sulfate ([EMIm][EtSO4]) at neutral pH. However, the atomistic details remain elusive. In the enzymatic landscape of HRP, compound II (Cpd II) plays a key role and involves a histidine (H42) residue. Cpd II exists as oxoferryl (2a) or hydroxoferryl (2b(FeIV)) forms, where 2a is the predominantly observed form in experimental studies. Intriguingly, the ferric 2b(FeIII) form seen in synthetic complexes has not been observed in HRP. Here, we have investigated the structure and dynamics of HRP in pure water and aqueous [EMIm][EtSO4] (0.26 M), as well as the reaction mechanism of 2a to 2b conversion using polarizable molecular dynamics (MD) simulations and quantum mechanics/molecular mechanics (QM/MM) calculations. When HRP is solvated in aq [EMIm][EtSO4], the catalytic water displaces, and H42 directly orients over the ferryl moiety, allowing a direct proton transfer (PT) with a significant energy barrier reduction. Conversely, in neat water, the reaction of 2a to 2b follows the previously reported mechanism. We further investigated the deprotonated form of H42. Analysis of the electric fields at the active site indicates that the aq [EMIm][EtSO4] medium facilitates the reaction by providing a more favorable environment compared with the system solvated in neat water. Overall, the atomic level supports the previous experimental observations and underscores the importance of favorable electric fields in the active site to promote catalysis.

Mechanisms of Biological Effects of Ionic Liquids: From Single Cells to Multicellular Organisms

The review presents a detailed discussion of the evolving field studying interactions between ionic liquids (ILs) and biological systems. Originating from molten salt electrolytes to present multiapplication substances, ILs have found usage across various fields due to their exceptional physicochemical properties, including excellent tunability. However, their interactions with biological systems and potential influence on living organisms remain largely unexplored. This review examines the cytotoxic effects of ILs on cell cultures, biomolecules, and vertebrate and invertebrate organisms. Our understanding of IL toxicity, while growing in recent years, is yet nascent. The established findings include correlations between harmful effects of ILs and their ability to disturb cellular membranes, their potential to trigger oxidative stress in cells, and their ability to cause cell death via apoptosis. Future research directions proposed in the review include studying the distribution of various ILs within cellular compartments and organelles, investigating metabolic transformations of ILs in cells and organisms, detailed analysis of IL effects on proteins involved in oxidative stress and apoptosis, correlation studies between IL doses, exposure times and resulting adverse effects, and examination of effects of subtoxic concentrations of ILs on various biological objects. This review aims to serve as a critical analysis of the current body of knowledge on IL-related toxicity mechanisms. Furthermore, it can guide researchers toward the design of less toxic ILs and the informed use of ILs in drug development and medicine.

Structural and mechanical behavior of type-I collagen fibrils in presence of induced electrostatic interactions through ionic liquids

Tuning the self-assembly of collagen has broad applications in the biomedical field owing to their desired biological performance as collagenous materials with tunable functionalities can further determine cellular responses. In this work, an attempt has been made to tune the self-assembly of collagen using ionic liquids, viz., imidazolium chloride (IC) and choline dihydrogen phosphate (CDHP) at its physiological pH, followed by probing assembled systems using various characterization methods. Turbidity measurements of fibrillar networks were performed to ascertain the rate of fibril formation in addition of imidazolium chloride and choline dihydrogen phosphate to collagen at physiological pH. Morphological changes were examined using Scanning Electron Microscope (SEM), binding affinities were measured by Microscale Thermophoresis (MST), in addition to, changes in the shear viscosity, mechanical strength of collagen fibrils when interacted with imidazolium and choline based ILs were carried out using rotational rheometer and Quartz Crystal Microbalance (QCM) measurements. Experimental result depicts that CDHP imparts better crosslinking as well as mechanical strength compare to IC, which is already known for destabilizing the triple helix structure is inhibiting the fibril formation. This self-assembled, ionic-liquid treated collagen-fibrillar system would accelerate various force modulated fibrillar network study, for mimicking the ECM and tissue engineering application.

Solvation of Model Biomolecules in Choline-Aminoate Ionic Liquids: A Computational Simulation Using Polarizable Force Fields

One can foresee a very near future where ionic liquids will be used in applications such as biomolecular chemistry or medicine. The molecular details of their interaction with biological matter, however, are difficult to investigate due to the vast number of combinations of both the biological systems and the variety of possible liquids. Here, we provide a computational study aimed at understanding the interaction of a special class of biocompatible ionic liquids (choline-aminoate) with two model biological systems: an oligopeptide and an oligonucleotide. We employed molecular dynamics with a polarizable force field. Our results are in line with previous experimental and computational evidence on analogous systems and show how these biocompatible ionic liquids, in their pure form, act as gentle solvents for protein structures while simultaneously destabilizing DNA structure.

Opposing roles of organic salts on mini-protein structure

We investigated the effects of 1-ethyl-3-methylimidazolium chloride ([EMIM][Cl]) and choline chloride ([Chol][Cl]) on the local environment and conformational landscapes of Trp-cage and Trpzip4 mini-proteins using experimental and computational approaches. Fluorescence experiments and computational simulations revealed distinct behaviors of the mini-proteins in the presence of these organic salts. [EMIM][Cl] showed a strong interaction with Trp-cage, leading to fluorescence quenching and destabilization of its native structural interactions. Conversely, [Chol][Cl] had a negligible impact on Trp-cage fluorescence at low concentrations but increased it at high concentrations, indicating a stabilizing role. Computational simulations elucidated that [EMIM][Cl] disrupted the hydrophobic core packing and decreased proline-aromatic residue contacts in Trp-cage, resulting in a more exposed environment for Trp residues. In contrast, [Chol][Cl] subtly influenced the hydrophobic core packing, creating a hydrophobic environment near the tryptophan residues. Circular dichroism experiments revealed that [Chol][Cl] stabilized the secondary structure of both mini-proteins, although computational simulations did not show significant changes in secondary content at the explored concentrations. The simulations also demonstrated a more rugged free energy landscape for Trp-cage and Trpzip4 in [EMIM][Cl], suggesting destabilization of the tertiary structure for Trp-cage and secondary structure for Trpzip4. Similar fluorescence trends were observed for Trpzip4, with [EMIM][Cl] quenching fluorescence and exhibiting stronger interaction, while [Chol][Cl] increased the fluorescence at high concentrations. These findings highlight the interplay between [EMIM][Cl] and [Chol][Cl] with the mini-proteins and provide a detailed molecular-level understanding of how these organic salts impact the nearby surroundings and structural variations. Understanding such interactions is valuable for diverse applications, from biochemistry to materials science.

Impact of Choline Hydroxide-Supported Magnetic Nanoparticles on Peroxidase Activity and Conformational Stability of Cytochrome c

Nanotechnology has advanced significantly; however, little is known about the potential implications on human health-related issues, particularly blood carrying enzymes. Ionic liquids are also well-recognized for maintaining the structure and activity of enzymes. In this regard, we delineate a facile synthetic approach of preparation of Fe3O4 nanoparticles (NPs) as well as choline hydroxide [CH][OH] ionic liquid (IL)-supported Fe3O4 NPs (Fe3O4-CHOH). This approach of combining magnetic nanoparticles (MNPs) with IL results in distinctive properties, which may offer enormous utility in the field of biomedical research due to the effortless separation of MNPs by an external magnetic field. Detailed characterization of MNPs including Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), Raman spectroscopy, transmission electron microscopy (TEM), and scanning electron microscopy (SEM) was carried out. The biomolecular interactions of Fe3O4 and Fe3O4-CHOH NPs with cytochrome c (Cyt c) were studied in detail using various spectroscopic and microscopic techniques. From spectroscopic studies, it can be concluded that the secondary structure of Cyt c is more stable in the presence of Fe3O4-CHOH NPs than Fe3O4 NPs. The binding constant of Cyt c in the presence of MNPs was also calculated using the Benesi-Hildebrand equation. Furthermore, dynamic light scattering (DLS), ζ-potential, and microscopic studies were performed to study the interaction of Cyt c with MNPs. These studies provided evidence favoring the formation of bionanoconjugates of Cyt c with MNPs. Moreover, the enzymatic activity of Cyt c increases in the presence of both MNPs. The peroxidase activity of Cyt c in MNPs explicitly elucidates that the enzyme is preserved for a long time in the presence of Fe3O4-CHOH NPs. Later on, TEM and field emission scanning electron microscopy (FESEM) were also performed to gather more information regarding the morphology of Cyt c in the presence of MNPs.

Ionic liquids in capillary electrophoresis analysis of proteins and carbohydrates

Ionic liquids (ILs), as non-molecular type solvents, possess excellent physical-chemical properties, which make them useful in important separation applications in gas chromatography, liquid chromatography, and capillary electrophoresis. Among a plethora of potential uses of ionic liquids in separation science, capillary electrophoresis can utilize its resolution-enhancing effect in the analysis of proteins and carbohydrates, via the formation of intermolecular interactions, e.g., hydrophobic, hydrogen bonding, or electrostatic. ILs and polymeric ionic liquids (PIL) also represent an excellent choice as background electrolyte (BGE) additives for capillary coatings in CE, which is especially important in protein analysis. Another interesting utilization of ILs is the fabrication of monoliths for capillary electrochromatography in which instance the mechanism of retention is based on ion exclusion interactions. Carbohydrates can also be readily analyzed by CE with the help of ionic liquids without the need for an extra derivatization step. One of the future perspectives on the use of ILs is their utilization in the recently emerging biopharmaceutical industry exploiting the increased resolution of proteins and carbohydrates, two of the important components of glycoprotein therapeutics. In this paper, we address the so-far not-reviewed ionic liquid-mediated analysis of proteins and carbohydrates by capillary electrophoresis-based techniques also addressing their impact on the separation mechanism.

Potentials of ionic liquids to overcome physical and biological barriers

Over the last decades, ionic liquids (IL) have shown great potential in non-invasive delivery starting from synthetic small molecules to biological large molecules. ILs are emerging as a particular class of drug delivery systems due to their unique physiochemical properties, simple surface modification, and functionalization. These features of IL help achieve specific design principles that are essential for a non-invasive drug delivery system. In this review, we have discussed IL and their applications in non-invasive drug delivery systems. We evaluated state-of-the-art development and advances of IL aiming to mitigate the biological and physical barriers to improve transdermal and oral delivery, summarized in this review. We also provided an overview of the various factors determining the systemic transportation of IL-based formulation. Additionally, we have emphasized how the ILs facilitate the transportation of therapeutic molecules by overcoming biological barriers.

How does ultrasound-assisted ionic liquid treatment affect protein? A comprehensive review of their potential mechanisms, safety evaluation, and physicochemical and functional properties

Proteins are essential to human health with enormous food applications. Despite their advantages, plant and animal proteins often exhibit limited molecular flexibility and poor solubility due to hydrogen bonds, hydrophobic interactions, and ionic interactions within their molecular structures. Thus, there is an urgent need to modify the rigid structure of proteins to enhance their stability and functional properties. Ultrasound-assisted ionic liquid (UA-IL) treatment for developing compound modification and producing proteins with excellent functional properties has received interest. However, no review specifically addresses the interactions between UA-ILs and proteins. Hence, this review focused on recent research advancements concerning the effects and potential reaction mechanisms of UA-ILs on the physicochemical properties (including particle size; primary, secondary, and tertiary structure; and surface morphology) as well as the functionality (such as solubility, emulsifying properties, and foaming ability) of proteins. Moreover, the safety evaluation of modified proteins was also discussed from various perspectives, such as acute and chronic toxicity, genotoxicity, cytotoxicity, and environmental and microbial toxicity. This review demonstrated that UA-IL treatment-induced protein structural changes significantly impact the functional characteristics of proteins. This treatment approach efficiently promotes protein structure stretching and spatial rearrangement through cavitation, thermal effects, and ionic interactions. As a result, the functional properties of modified proteins exhibited an obvious enhancement, thereby bringing more opportunities to utilize modified protein products in the food industry. Potential future directions for protein modification using UA-ILs were also proposed.

Concentrated ionic liquids for proteomics: Caveat emptor!

The use of concentrated ionic liquids (ILs) in the bioanalytical chemistry of proteins is sparse; typically, dilute aqueous IL solutions are used. Concentrated ILs have unique properties that may allow researchers to dissolve previously insoluble protein analytes, to increase the depth and robustness of sample preparation and the analysis of proteins. Previous research using concentrated ILs for this purpose is sparse and there is a need to systematically investigate the structure-activity relationship between the IL structure and its capacity to solubilise proteins. Here, bovine serum albumin was dissolved in various ionic liquids and monitored over time by light microscopy and SDS-PAGE. While qualitative, these measures provide a good estimate of, respectively, the dissolving power of an IL towards the given protein and the retained integrity of the protein. Hydrophilic ILs show the best solubilisation capacity and higher temperatures (in a restricted sense) improve the solubility of the protein. Higher temperatures and longer reaction times reduce the molecular weight of the protein, which could inhibit their applicability in proteomics, unless the conditions are judiciously controlled. Researchers should exercise caution when using concentrated ILs for protein analysis until the full scope and limitations are known, an aspect we are presently investigating.

Deciphering the Role of Anions of Ionic Liquids in Modulating the Structure and Stability of ct-DNA in Aqueous Solutions

Stabilizing biomolecules under ambient conditions can be extremely beneficial for various biological applications. In this context, the utilization of ionic liquids (ILs) in enhancing the stability and preservation of nucleic acids in aqueous solutions is found to be promising. While the role of the cationic moiety of ILs in the said event has been thoroughly explored, the importance of the anionic moiety in ILs, if any, is rather poorly understood. Herein, we examine the function of anions of ILs in nucleic acid stabilization by examining the stability and structure of calf thymus-DNA (ct-DNA) in the presence of various ILs composed of a common 1-ethyl-3-methylimidazolium cations (Emim+) and different anions, which includes Cl-, Br-, NO 3 - , Ac - , HS O 4 - and B F 4 - by employing various spectroscopic techniques as well as Molecular Dynamics (MD) simulation studies. Analysis of our data suggests that the chemical nature of anions including polarity, basicity, and hydrophilicity become an important factor in the overall DNA-IL interaction event. At lower concentrations, the interplay of intermolecular interaction between the IL anions with their respective cations and the solvent molecules becomes a very crucial factor in inducing their stabilizing effect on ct-DNA. However, at higher concentrations of ILs, the ct-DNA stabilization is additionally governed by specific-ion effect. MD simulation studies have also provided valuable insights into molecular-level understanding of the DNA-IL interaction event. Overall, the present study clearly demonstrated that along with the cationic moiety of ILs, the anions of ILs can play a significant role in deciding the stability of duplex DNA in aqueous solution. The findings of this study are expected to enhance our knowledge on understanding of IL-DNA interactions in a better manner and will be helpful in designing optimized IL systems for nucleic acid based applications.

Ionic Liquid-Induced Assembly of DNA at Air-Water Interface

DNA nanotechnology is the future of many products in the pharmaceutical and cosmetic industries. Self-assembly of this negatively charged biopolymer at surfaces and interfaces is an essential step to elaborate its field of applications. In this study, the ionic liquid (IL) monolayer-assisted self-assembly of DNA macromolecules at the air-water interface has been closely monitored by employing various quantitative techniques, namely, surface pressure-area (π-A) isotherms, surface potential, interfacial rheology, and X-ray reflectivity (XRR). The π-A isotherms reveal that the IL 1,3-didecyl 3-methyl imidazolium chloride induces DNA self-assembly at the interface, leading to a thick viscoelastic film. The interfacial rheology exhibits a notable rise in the viscoelastic modulus as the surface pressure increases. The values of storage and loss moduli measured as a function of strain frequency suggest a relaxation frequency that depends on the length of the macromolecule. The XRR measurements indicate a considerable increase in DNA layer thickness at the elevated surface pressures depending on the number of base pairs of the DNA. The results are considered in terms of the electrostatic and hydrophobic interactions, allowing a quantitative conclusion about the arrangement of DNA strands underneath the monolayer of the ILs at the air-water interface.

Confronting the Threat: Designing Highly Effective bis-Benzimidazolium Agents to Overcome Biofilm Persistence and Antimicrobial Resistance

The objective of this study is to take the initial steps toward developing novel antibiotics to counteract the escalating problem of antimicrobial and bacterial persistence, particularly in relation to biofilms. Our approach involves emulating the structural characteristics of cationic antimicrobial peptides. To circumvent resistance development, we have designed a library of bis-benzimidazolium salts that selectively target the microbial membranes in a nonspecific manner. To explore their structure-activity relationship, we conducted experiments using these compounds on various pathogens known for their resistance to conventional antibiotics, including Gram-positive methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococcus faecium (VRE), and Gram-negative Escherichia coli (E. coli). Notably, two bis-benzimidazolium salts exhibited robust antimicrobial activity while maintaining a high level of selectivity compared with mammalian cells. Our investigations revealed significant antibiofilm activity, as these compounds rapidly acted against established biofilms. In addition, bis-benzimidazolium compounds exhibited consistent results in resistance development and cross-resistance studies. Consequently, amphiphilic bis-benzimidazolium salts hold promise as potential candidates to combat resistance-associated infections.

Selective Near-Infrared Blood Detection Driven by Ionic Liquid-Dye-Albumin Nanointeractions

Due to its abundance in blood, a great deal of research has been undertaken to develop efficient biosensors for serum albumin and provide insight into the interactions that take place between these biosensing molecules and the protein. Near-infrared (NIR, >700 nm) organic dyes have been shown to be effective biosensors of serum albumin, but their effectiveness is diminished in whole blood. Herein, it is shown that an NIR sulfonate indolizine-donor-based squaraine dye, SO3SQ, can be strengthened as a biosensor of albumin through the addition of biocompatible ionic liquids (ILs). Specifically, the IL choline glycolate (1:1), at a concentration of 160 mM, results in the enhanced fluorescence emission ("switch-on") of the dye in the presence of blood. The origin of the fluorescence enhancement was investigated via methods, including DLS, ITC, and molecular dynamics. Further, fluorescence measurements were conducted to see the impact the dye-IL system had on the fluorescence of the tryptophan residue of human serum albumin (HSA), as well as to determine its apparent association constants in relation to albumin. Circular dichroism (CD) spectroscopy was used to provide evidence that the dye-IL system does not alter the secondary structures of albumin or DNA. Our results suggest that the enhanced fluorescence of the dye in the presence of IL and blood is due to diversification of binding sites in albumin, controlled by the interaction of the IL-dye-albumin complex.

N-Benzylethanolammonium Ionic Liquids and Molten Salts in the Synthesis of 68Ga- and Al18F-Labeled Radiopharmaceuticals

Ionic liquids (ILs), due to their structural features, have unique physical and chemical properties and are environmentally friendly. Every year, the number of studies devoted to the use of ILs in medicine and pharmaceutics is growing. In nuclear medicine, the use of ILs with self-buffering capacity in the synthesis of radiopharmaceuticals is extremely important. This research is devoted to obtaining new ionic buffer agents containing N-benzylethanolammonium (BEA) cations and anions of carboxylic acids. A series of new BEA salts was synthesized and identified by NMR (¹H, ¹³C), IR spectroscopy and elemental and thermal analysis. The crystal structures of BEA hydrogen succinate, hydrogen oxalate and oxalate were determined by x-ray diffraction. Newly synthesized compounds were tested as buffer solutions in ⁶⁸Ga- and Al¹⁸F-radiolabeling reactions with a series of bifunctional chelating agents and clinically relevant peptides used for visualization of malignancies by positron emission tomography. The results obtained confirm the promise of using new buffers in the synthesis of ⁶⁸Ga- and Al¹⁸F-labeled radiopharmaceuticals.

Design of ionic liquids containing glucose and choline as drug carriers, finding the link between QM and MD studies

Designing drug delivery systems for therapeutic compounds whose receptors are located in the cytosol of cells is challenging as a bilayer cell membrane is negatively charged. The newly designed drug delivery systems should assist the mentioned drugs in passing the membrane barriers and achieving their targets. This study concentrated on developing novel ionic liquids (ILs) that interact effectively with cell membranes. These ILs are based on glucose-containing choline and are expected to be non-toxic. The binding energies of the known pharmaceutically active ionic liquids were calculated at the B3LYP/6-311++G(d,p) level in the gas phase and compared with those of our newly designed carbohydrate-based ionic liquids. Subsequently, we employed MD simulations to obtain information about the interactions of these known and designed ILs with the cell membrane. In our approach, we adopted QM and MD studies and illustrated that there could be a link between the QM and MD results.

Assessing the Suitability of a Dicationic Ionic Liquid as a Stabilizing Material for the Storage of DNA in Aqueous Medium

The present study has been undertaken with an objective to find out a suitable medium for the long-term stability and storage of the ct-DNA structure in aqueous solution. For this purpose, the potential of a pyrrolidinium-based dicationic ionic liquid (DIL) in stabilizing ct-DNA structure has been investigated by following the DNA-DIL interaction. Additionally, in order to understand the fundamental aspects regarding the DNA-DIL interaction in a comprehensive manner, studies are also done by employing structurally similar monocationic ionic liquids (MILs). The investigations have been carried out both at ensemble-average and single molecular level by using various spectroscopic techniques. The molecular docking study has also been performed to throw more light into the experimental observations. The combined steady-state and time-resolved fluorescence, fluorescence correlation spectroscopy, and circular dichroism measurements have demonstrated that DILs can effectively be used as better storage media for ct-DNA as compared to MILs. Investigations have also shown that the extra electrostatic interaction between the cationic head group of DIL and the phosphate backbone of DNA is primarily responsible for providing better stabilization to ct-DNA, retaining its native structure in aqueous medium. The outcomes of the present study are also expected to provide valuable insights in designing new polycationic IL systems that can be used in nucleic acid-based applications.

Alternative Excipients for Protein Stabilization in Protein Therapeutics: Overcoming the Limitations of Polysorbates

Given their safety and efficiency in protecting protein integrity, polysorbates (PSs) have been the most widely used excipients for the stabilization of protein therapeutics for years. In recent decades, however, there have been numerous reports about visible or sub-visible particles in PS-containing biotherapeutic products, which is a major quality concern for parenteral drugs. Alternative excipients that are safe for parenteral administration, efficient in protecting different protein drugs against various stress conditions, effective in protein stabilization in high-concentrated liquid formulations, stable under the storage conditions for the duration of the product's shelf-life, and compatible with other formulation components and the primary packaging are highly sought after. The aim of this paper is to review potential alternative excipients from different families, including surfactants, carbohydrate- and amino acid-based excipients, synthetic amphiphilic polymers, and ionic liquids that enable protein stabilization. For each category, important characteristics such as the ability to stabilize proteins against thermal and mechanical stresses, current knowledge related to the safety profile for parenteral administration, potential interactions with other formulation components, and primary packaging are debated. Based on the provided information and the detailed discussion thereof, this paper may pave the way for the identification or development of efficient excipients for biotherapeutic protein stabilization.

Molecule(s) of Interest: I. Ionic Liquids-Gateway to Newer Nanotechnology Applications: Advanced Nanobiotechnical Uses', Current Status, Emerging Trends, Challenges, and Prospects

Ionic liquids are a potent class of organic compounds exhibiting unique physico-chemical properties and structural compositions that are different from the classical dipolar organic liquids. These molecules have found diverse applications in different chemical, biochemical, biophysical fields, and a number of industrial usages. The ionic liquids-based products and procedural applications are being developed for a number of newer industrial purposes, and academic uses in nanotechnology related procedures, processes, and products, especially in nanobiotechnology and nanomedicine. The current article overviews their uses in different fields, including applications, functions, and as parts of products and processes at primary and advanced levels. The application and product examples, and prospects in various fields of nanotechnology, domains of nanosystem syntheses, nano-scale product development, the process of membrane filtering, biofilm formation, and bio-separations are prominently discussed. The applications in carbon nanotubes; quantum dots; and drug, gene, and other payload delivery vehicle developments in the nanobiotechnology field are also covered. The broader scopes of applications of ionic liquids, future developmental possibilities in chemistry and different bio-aspects, promises in the newer genres of nanobiotechnology products, certain bioprocesses controls, and toxicity, together with emerging trends, challenges, and prospects are also elaborated.

Macrocyclic Ionic Liquids with Amino Acid Residues: Synthesis and Influence of Thiacalix[4]arene Conformation on Thermal Stability

Novel thiacalix[4]arene based ammonium ionic liquids (ILs) containing amino acid residues (glycine and L-phenylalanine) in cone, partial cone, and 1,3-alternate conformations were synthesized by alkylation of macrocyclic tertiary amines with N-bromoacetyl-amino acids ethyl ester followed by replacing bromide anions with bis(trifluoromethylsulfonyl)imide ions. The melting temperature of the obtained ILs was found in the range of 50−75 °C. The effect of macrocyclic core conformation on the synthesized ILs’ melting points was shown, i.e., the ILs in partial cone conformation have the lowest melting points. Thermal stability of the obtained macrocyclic ILs was determined via thermogravimetry and differential scanning calorimetry. The onset of decomposition of the synthesized compounds was established at 305−327 °C. The compounds with L-phenylalanine residues are less thermally stable by 3−19 °C than the same glycine-containing derivatives.

Applications of Ionic Liquids in Carboxylic Acids Separation

Ionic liquids (ILs) are considered a green viable organic solvent substitute for use in the extraction and purification of biosynthetic products (derived from biomass-solid/liquid extraction, or obtained through fermentation-liquid/liquid extraction). In this review, we analyzed the ionic liquids (greener alternative for volatile organic media in chemical separation processes) as solvents for extraction (physical and reactive) and pertraction (extraction and transport through liquid membranes) in the downstream part of organic acids production, focusing on current advances and future trends of ILs in the fields of promoting environmentally friendly products separation.

Enhanced structural stability of insulin aspart in cholinium aminoate ionic liquids

Cholinium aminoates [Ch][AA] have gained tremendous interest as a promising ionic liquid medium for the synthesis and storage of proteins. However, high alkalinity of [Ch][AA] limits its usage with pH-sensitive proteins. Here, we probed the structure, stability, and interactions of a highly unstable therapeutic protein, insulin aspart (IA), in a range of buffered [Ch][AA] (b-[Ch][AA]) using a combination of biophysical tools and in silico pipeline including ultraviolet-visible, fluorescence, and circular dichroism spectroscopies, dynamic light scattering measurements and molecular docking. b-[Ch][AA] used in the study differed in concentrations and their anionic counterparts. We reveal information on ion and residue specific solvent-protein interactions, demonstrating that the structural stability of IA was enhanced by a buffered cholinium prolinate. In comparison to the glycinate and alaninate anions, the hydrophilic prolinate anions established more hydrogen bonds with the residues of IA and provided a less polar environment that favours the preservation of IA in its active monomeric form, opening new opportunities for utilizing [Ch][AA] as storage medium.

Site-specific DNA functionalization through the tetrazene-forming reaction in ionic liquids

Site-specific chemical modification of unprotected DNAs through a phosphine-mediated amine–azide coupling reaction in ionic liquid.

Imidazolium-based ionic liquids with increasing alkyl chain length of cations decrease the stability and fibrillation propensity of lysozyme

Imidazolium ionic liquids with longer alkyl side chains show a larger destabilization effect on lysozyme. Increased hydrophobicity of the IL increases its binding affinity and inhibits the fibril formation of lysozyme.

TransfersomILs: From Ionic Liquids to a New Class of Nanovesicular Systems

Ionic liquids (ILs) have increasingly been studied as key materials to upgrade the performance of many pharmaceutical formulations. In controlled delivery systems, ILs have improved multiple physicochemical properties, showing the relevance of continuing to study their incorporation into these formulations. Transfersomes are biocompatible nanovesicular systems, quite useful in controlled delivery. They have promising characteristics, such as elasticity and deformability, making them suitable for cutaneous delivery. Nonetheless, their overall properties and performance may still be improved. Herein, new TransfersomILs systems to load rutin were developed and the physicochemical properties of the formulations were assessed. These systems were prepared based on an optimized formulation obtained from a Box-Behnken factorial design (BBD). The impact of imidazole-based ILs, cholinium-based ILs, and their combinations on the cell viability of HaCaT cells and on the solubility of rutin was initially assessed. The newly developed TransfersomILs containing rutin presented a smaller size and, in general, a higher association efficiency, loading capacity, and total amount of drug release compared to the formulation without IL. The ILs also promoted the colloidal stability of the vesicles, upgrading storage stability. Thus, ILs were a bridge to develop new TransfersomILs systems with an overall improved performance.

Influence of Environmental Parameters on the Stability of the DNA Molecule

Fluctuations in viscosity within the cell nucleus have wide limits. When a DNA molecule passes from the region of high viscosity values to the region of low values, open states, denaturation bubbles, and unweaving of DNA strands can occur. Stabilization of the molecule is provided by energy dissipation-dissipation due to interaction with the environment. Separate sections of a DNA molecule in a twisted state can experience supercoiling stress, which, among other things, is due to complex entropic effects caused by interaction with a solvent. In this work, based on the numerical solution of a mechanical mathematical model for the interferon alpha 17 gene and a fragment of the Drosophila gene, an analysis of the external environment viscosity influence on the dynamics of the DNA molecule and its stability was carried out. It has been shown that an increase in viscosity leads to a rapid stabilization of the angular vibrations of nitrogenous bases, while a decrease in viscosity changes the dynamics of DNA: the rate of change in the angular deviations of nitrogenous bases increases and the angular deformations of the DNA strands increase at each moment of time. These processes lead to DNA instability, which increases with time. Thus, the paper considers the influence of the external environment viscosity on the dissipation of the DNA nitrogenous bases' vibrational motion energy. Additionally, the study on the basis of the described model of the molecular dynamics of physiological processes at different indicators of the rheological behavior of nucleoplasm will allow a deeper understanding of the processes of nonequilibrium physics of an active substance in a living cell to be obtained.

Contrasting Effects of Ionic Liquids of Varying Degree of Hydrophilicity on the Conformational and Interfacial Properties of a Globular Protein

Ionic liquids (ILs), depending on their cation-anion combinations, are known to influence the conformational properties and activities of proteins in a nonuniform manner. To obtain microscopic understanding of such influence, it is important to characterize protein-IL interactions and explore the modified solvation environment around the protein. In this work, molecular dynamics (MD) simulations of the globular protein α-lactalbumin have been carried out in aqueous IL solutions containing 1-butyl-3-methylimidazolium cations (BMIM⁺) in combination with a series of anions with varying degree of hydrophilicity, namely, hexafluorophosphate (PF₆^-), ethyl sulfate (ETS^-), acetate (OAc^-), chloride (Cl^-), dicyanamide (DCA^-), and nitrate (NO₃^-) . The calculations revealed that ILs with hydrophobic and hydrophilic anions have contrasting influence on conformational flexibility of the protein. It is further observed that the BMIM⁺ cations exhibit site-specific orientations at the interface depending on the hydrophilicity of the anion component. Most importantly, the results demonstrated enhanced propensity of hydrophilic ILs to replace relatively weaker protein-water hydrogen bonds by stronger protein-IL hydrogen bonds at the protein surface as compared to the hydrophobic ILs. Such breaking of protein-water hydrogen bonds at a greater extent leads to greater loss of water hydrating the protein in the presence of hydrophilic ILs, thereby reducing the protein's stability.

An Ionic Liquid Medium Enables Development of a Phosphine-Mediated Amine-Azide Bioconjugation Method

While a diverse set of design strategies have produced various chemical tools for biomolecule labeling in aqueous media, the development of nonaqueous, biomolecule-compatible media for bioconjugation has significantly lagged behind. In this report, we demonstrate that an aprotic ionic liquid serves as a novel reaction solvent for protein bioconjugation without noticeable loss of the biomolecule functions. The ionic liquid bioconjugation approach led to discovery of a novel triphenylphosphine-mediated amine-azide coupling reaction that forges a stable tetrazene linkage on unprotected peptides and proteins. This strategy of using untraditional media would provide untapped opportunities for expanding the scope of chemical approaches for bioconjugation.

Insight into the thermal stability of DNA in hydrated ionic liquids from multi-wavelength UV resonance Raman experiments

The utility of ionic liquids (ILs) as alternative solvents for stabilizing and preserving the native structure of DNA over the long term may be envisaged for biotechnological and biomedical applications in the near future. The delicate balance between the stabilizing and destabilizing effects of IL-mediated interactions with the structure of DNA is complex and is still not well understood. This work reports a fundamental study dealing with the effect exerted by cations and anions in imidazolium-based ILs on the thermal structural stability of large nucleic acid molecules. Multi-wavelength UV resonance Raman spectroscopy is used for selectively detecting heat-induced structural transitions of DNA localized on specific base tracts. Our study reveals the establishment of preferential interactions between the imidazolium cations of ILs and the guanine bases in the DNA groove that lead to more effective stacking between the guanine bases even at high temperatures. Interestingly, we observe that this trend for ILs sharing the same chloride anion is further enhanced as the alkyl chain on the imidazolium cation gets shorter. The results from the present investigation lead to a more comprehensive view of the IL-mediated interactions with A-T and G-C base pairs during thermal unfolding.

Enhancement of the Catalytic Activity of Hammerhead Ribozymes by Organic Cations

Catalytic turnover is important for the application of ribozymes to biotechnology. However, the turnover is often impaired because of the intrinsic high stability of base pairs with cleaved RNA products. Here, organic cations were used as additives to improve the catalytic performance of hammerhead ribozyme constructs that exhibit different kinetic behaviors. Kinetic analysis of substrate cleavage demonstrated that bulky cations, specifically tetra-substituted ammonium ions containing pentyl groups or a benzyl group, have the ability to greatly increase the turnover rate of the ribozymes. Thermal stability analysis of RNA structures revealed that the bulky cations promote the dissociation of cleaved products and refolding of incorrectly folded structures with small disruption of the catalytic structure. The use of bulky cations is a convenient method for enhancing the catalytic activity of hammerhead ribozymes, and the approach may be useful for advancing ribozyme technologies.

An experimental approach probing the conformational transitions and energy landscape of antibodies: a glimmer of hope for reviving lost therapeutic candidates using ionic liquid

Understanding protein folding in different environmental conditions is fundamentally important for predicting protein structures and developing innovative antibody formulations. While the thermodynamics and kinetics of folding and unfolding have been extensively studied by computational methods, experimental methods for determining antibody conformational transition pathways are lacking. Motivated to fill this gap, we prepared a series of unique formulations containing a high concentration of a chimeric immunoglobin G4 (IgG4) antibody with different excipients in the presence and absence of the ionic liquid (IL) choline dihydrogen phosphate. We determined the effects of different excipients and IL on protein thermal and structural stability by performing variable temperature circular dichroism and bio-layer interferometry analyses. To further rationalise the observations of conformational changes with temperature, we carried out molecular dynamics simulations on a single antibody binding fragment from IgG4 in the different formulations, at low and high temperatures. We developed a methodology to study the conformational transitions and associated thermodynamics of biomolecules, and we showed IL-induced conformational transitions. We showed that the increased propensity for conformational change was driven by preferential binding of the dihydrogen phosphate anion to the antibody fragment. Finally, we found that a formulation containing IL with sugar, amino acids and surfactant is a promising candidate for stabilising proteins against conformational destabilisation and aggregation. We hope that ultimately, we can help in the quest to understand the molecular basis of the stability of antibodies and protein misfolding phenomena and offer new candidate formulations with the potential to revive lost therapeutic candidates.

From Water Solutions to Ionic Liquids with Solid State Nanopores as a Perspective to Study Transport and Translocation Phenomena

Solid state nanopores are single-molecular devices governed by nanoscale physics with a broad potential for technological applications. However, the control of translocation speed in these systems is still limited. Ionic liquids are molten salts which are commonly used as alternate solvents enabling the regulation of the chemical and physical interactions on solid-liquid interfaces. While their combination can be challenging to the understanding of nanoscopic processes, there has been limited attempts on bringing these two together. While summarizing the state of the art and open questions in these fields, several major advances are presented with a perspective on the next steps in the investigations of ionic-liquid filled nanopores, both from a theoretical and experimental standpoint. By analogy to aqueous solutions, it is argued that ionic liquids and nanopores can be combined to provide new nanofluidic functionalities, as well as to help resolve some of the pertinent problems in understanding transport phenomena in confined ionic liquids and providing better control of the speed of translocating analytes.

Influence of Alkyl Chain Length on Thermal Properties, Structure, and Self-Diffusion Coefficients of Alkyltriethylammonium-Based Ionic Liquids

The application of ionic liquids (ILs) has grown enormously, from their use as simple solvents, catalysts, media in separation science, or electrolytes to that as task-specific, tunable molecular machines with appropriate properties. A thorough understanding of these properties and structure-property relationships is needed to fully exploit their potential, open new directions in IL-based research and, finally, properly implement the appropriate applications. In this work, we investigated the structure-properties relationships of a series of alkyltriethylammonium bis(trifluoromethanesulfonyl)imide [TEA-R][TFSI] ionic liquids in relation to their thermal behavior, structure organization, and self-diffusion coefficients in the bulk state using DSC, FT-IR, SAXS, and NMR diffusometry techniques. The phase transition temperatures were determined, indicating alkyl chain dependency. Fourier-transformed infrared spectroscopy studies revealed the structuration of the ionic liquids along with alkyl chain elongation. SAXS experiments clearly demonstrated the existence of polar/non-polar domains. The alkyl chain length influenced the expansion of the non-polar domains, leading to the expansion between cation heads in polar regions of the structured IL. 1H NMR self-diffusion coefficients indicated that alkyl chain elongation generally caused the lowering of the self-diffusion coefficients. Moreover, we show that the diffusion of anions and cations of ILs is similar, even though they vary in their size.