Effect of two imidazolium derivatives of ionic liquids on the structure and activity of adenosine deaminase

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.

Enhanced activity of Candida antarctica lipase B in cholinium aminoate ionic liquids: a combined experimental and computational analysis

As a class of ionic liquids with higher biocompatibility, cholinium aminoates ([Cho][AA]) hold potential as solvation media for enzymatic bioprocessing. Herein, solvation effect of [Cho][AA] on structural stability and enzymatic activity of Candida antarctica lipase B (CALB) was evaluated using experimental and computational approaches. Influence of [Cho][AA] on CALB stability was investigated using amino acid anions ([AA]-) with varying hydrophobicity levels. Choline phenylalaninate ([Cho][Phe]) resulted in 109.1% and 110.4% of relative CALB activity to buffer medium at 25 °C and 50 °C, respectively. Simulation results revealed the improvement of CALB's enzymatic activities by [AA]- with a strong hydrophobic character. Shielding of CALB from water molecules by [AA]- was observed. The level of CALB activity was governed by accumulation level of [AA]- at CALB's first hydration layer. The stronger interaction between His224 and Asp187 was postulated to be driven by [Cho][AA], resulting in the activity enhancement of CALB. The slight improvement of CALB activity in 0.05 M [Cho][Phe] at 50 °C could be due to the larger size of entrance to the catalytic site and the stronger interaction between the catalytic residues. The promising effect of [Cho][Phe] on CALB activation may stimulate research efforts in designing a 'fully green' bioreaction for various industrial applications.Communicated by Ramaswamy H. Sarma.

Efficient Antibacterial Dimeric Nitro Imidazolium Type of Ionic Liquids from a Simple Synthetic Approach

Synthesis of dimeric nitro-substituted imidazolium salts under the conventional/solvent-free method is reported. The solvent-free method is more important than the conventional one because of its shorter reaction time, higher yield from easily available starting material, environmental safety, and so forth. Counter anion exchange is carried out using inorganic salt, which is dissolved in deionized water at room temperature. In antibacterial studies, dimeric nitro-substituted imidazolium cations with bromide counter anions showed excellent inhibition against E. coli and P. aeruginosa bacteria. These experimental results were further supported by molecular docking studies. All the compounds (3-6) (a-d) showed excellent antibacterial activity than the standard drugs (gentamycin, nalidixic acid, oflaxacin, ciproflaxacin, and amikacin). Molecular docking studies showed strong hydrogen bonding, polar and hydrophobic interactions between the dimeric imidazolium salts, and Escherichia coli/Pseudomonas aeruginosa/Proteus vulgaris/Staphylococcus aureus receptors.

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.

Enhanced activity of hyperthermostable Pyrococcus horikoshii endoglucanase in superbase ionic liquids

Objectives

Ionic liquids (ILs) that dissolve biomass are harmful to the enzymes that degrade lignocellulose. Enzyme hyperthermostability promotes a tolerance to ILs. Therefore, the limits of hyperthemophilic Pyrococcus horikoschii endoglucanase (PhEG) to tolerate 11 superbase ILs were explored.

Results

PhEG was found to be most tolerant to 1-ethyl-3-methylimidazolium acetate ([EMIM]OAc) in soluble 1% carboxymethylcellulose (CMC) and insoluble 1% Avicel substrates. At 35% concentration, this IL caused an increase in enzyme activity (up to 1.5-fold) with CMC. Several ILs were more enzyme inhibiting with insoluble Avicel than with soluble CMC. K_m increased greatly in the presence ILs, indicating significant competitive inhibition. Increased hydrophobicity of the IL cation or anion was associated with the strongest enzyme inhibition and activation. Surprisingly, PhEG activity was increased 2.0–2.5-fold by several ILs in 4% substrate. Cations exerted the main role in competitive inhibition of the enzyme as revealed by their greater binding energy to the active site.

Conclusions

These results reveal new ways to design a beneficial combination of ILs and enzymes for the hydrolysis of lignocellulose, and the strong potential of PhEG in industrial, high substrate concentrations in aqueous IL solutions.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10529-022-03268-5.

Aqueous ionic liquids in comparison with standard co-solutes : Differences and common principles in their interaction with protein and DNA structures

Ionic liquids (ILs) are versatile solvents for a broad range of biotechnological applications. Recent experimental and simulation results highlight the potential benefits of dilute ILs in aqueous solution (aqueous ILs) in order to modify protein and DNA structures systematically. In contrast to a limited number of standard co-solutes like urea, ectoine, trimethylamine-N-oxide (TMAO), or guanidinium chloride, the large amount of possible cation and anion combinations in aqueous ILs can be used to develop tailor-made stabilizers or destabilizers for specific purposes. In this review article, we highlight common principles and differences between aqueous ILs and standard co-solutes with a specific focus on their underlying macromolecular stabilization or destabilization behavior. In combination with statistical thermodynamics theories, we present an efficient framework, which is used to classify structure modification effects consistently. The crucial importance of enthalpic and entropic contributions to the free energy change upon IL-assisted macromolecular unfolding in combination with a complex destabilization mechanism is described in detail. A special focus is also set on aqueous IL-DNA interactions, for which experimental and simulation outcomes are summarized and discussed in the context of previous findings.

Elucidating sequence and solvent specific design targets to protect and stabilize enzymes for biocatalysis in ionic liquids

For many different frameworks, the structure, function, and dynamics of an enzyme is largely determined by the nature of its interactions with the surrounding host environment, thus a molecular level understanding of enzyme/host interactions is essential to the design of new processes and applications. Ionic liquid (IL) solvents are a popular class of solvents in which to study enzyme behavior, yet it is still not possible to predict how a given enzyme will behave in a given IL solvent. Furthermore, a dearth of experimental data with which to evaluate simulation force fields has prevented the full integration of experimental and computational techniques to gain a complete picture of enzyme/IL interactions. Utilizing recently published crystallographic data of an enzyme in complex with an IL, this study aims to validate the use of current molecular force fields for studying enzyme/IL interactions, and to provide new mechanistic insight into enzyme stabilization in IL solvents. Classical molecular dynamics (MD) simulations have been performed on both the folded and unfolded state of Bacillus subtilis lipase A and a quadruple-mutant version of lipase A, in solutions of aqueous 1-butyl-3-methylimidazolium chloride. Results show classical MD simulations can predict the preferred surface binding locations of IL cations as well as reductions in IL anion binding to mutated surface residues with high accuracy. The results also point to a mechanistic difference between IL binding to the folded and unfolded state of an enzyme, which we call the "counter-ion effect". These findings could have important implications for future rational design efforts to stabilize enzymes in non-conventional media.

Aqueous ionic liquids and their influence on peptide conformations: denaturation and dehydration mechanisms

Low concentrated aqueous ionic liquids (ILs) and their influence on protein structures have attracted a lot of interest over the last few years. This can be mostly attributed to the fact that aqueous ILs, depending on the ion species involved, can be used as protein protectants or protein denaturants. Atomistic molecular dynamics (MD) simulations are performed in order to study the influence of different aprotic ILs on the properties of a short hairpin peptide. Our results reveal distinct binding and denaturation effects for 1-ethyl-3-methylimidazolium (EMIM) in combination with different anions, namely, chloride (CL), tetrafluoroborate (BF4) and acetate (ACE). The simulation outcomes demonstrate that the studied ILs with larger anions reveal a more pronounced accumulation behavior of the individual ion species around the peptide, which is accomplished by a stronger dehydration effect. We can relate these findings to the implications of the Kirkwood-Buff theory, which provides a thermodynamic explanation for the denaturation strength in terms of the IL accumulation behavior. The results for the spatial distribution functions, the binding energies and the local/bulk partition coefficients are in good agreement with metadynamics simulations in order to determine the energetically most stable peptide conformations. The free energy landscapes indicate a decrease of the denaturation strength in the order EMIM/ACE, EMIM/BF4 and EMIM/CL, which coincides with a decreasing size of the anion species. An analysis of the potential binding energies reveals that this effect is mainly of enthalpic nature.

Unraveling the effects of amino acid substitutions enhancing lipase resistance to an ionic liquid: a molecular dynamics study

The key properties affecting lipase resistance towards an ionic liquid are uncovered through a molecular dynamics study.

Highly functionalized piperidines: Free radical scavenging, anticancer activity, DNA interaction and correlation with biological activity

Twenty-five piperidines were studied as potential radical scavengers and antitumor agents. Quantitative interaction of compounds with ctDNA using spectroscopic techniques was also evaluated. Our results demonstrate that the evaluated piperidines possesses different abilities to scavenge the radical 2,2-diphenyl-1-picrylhydrazyl (DPPH) and the anion radical superoxide (^•O₂⁻). The piperidine 19 was the most potent radical DPPH scavenger, while the most effective to ^•O₂⁻ scavenger was piperidine 10. In general, U251, MCF7, NCI/ADR-RES, NCI-H460 and HT29 cells were least sensitive to the tested compounds and all compounds were considerably more toxic to the studied cancer cell lines than to the normal cell line HaCaT. The binding mode of the compounds and ctDNA was preferably via intercalation. In addition, these results were confirmed based on theoretical studies. Finally, a linear and exponential correlation between interaction constant (K_b) and GI₅₀ for several human cancer cell was observed.

Potential of ionic liquids for inhibiting the growth and β-lactamase production by Bacillus cereus EMB20

Present work reports the inhibition of Bacillus cereus EMB20 β-lactamase by a deep eutectic solvent, maline in an uncompetitive manner. Far-UV CD and intrinsic fluorescence spectroscopy revealed a disrupted secondary as well as tertiary structure as a function of maline concentration. The effect of individual components of maline on β-lactamase inhibition showed that malonic acid was mainly responsible for inhibiting the β-lactamase. Structural and docking studies found that malonic acid led to major perturbations in the secondary and tertiary structure of the enzyme while H-bonding with the active site residues. Further the antibacterial and cytotoxic studies also confirmed the potential of maline as a potent growth inhibitor of β-lactamase producing B. cereus EMB20.

Aqueous ionic liquids and their effects on protein structures: an overview on recent theoretical and experimental results

Ionic liquids (ILs) are used in a variety of technological and biological applications. Recent experimental and simulation results reveal the influence of aqueous ionic liquids on the stability of protein and enzyme structures. Depending on different parameters like the concentration and the ion composition, one can observe distinct stabilization or denaturation mechanisms for various ILs. In this review, we summarize the main findings and discuss the implications with regard to molecular theories of solutions and specific ion effects. A preferential binding model is introduced in order to discuss protein-IL effects from a statistical mechanics perspective. The value of the preferential binding coefficient determines the strength of the ion influence and indicates a shift of the chemical equilibrium either to the native or the denatured state of the protein. We highlight the role of water in order to explain the self-association behavior of the IL species and discuss recent experimental and simulation results in the light of the observed binding effects.

Enantioselectivity of d-amino acid oxidase in the presence of ionic liquids

In this paper, enantioselectivities of d-amino acid oxidase (DAAO) in ten ionic liquids were investigated in detail.

Hydrogen bonding-assisted interaction between amitriptyline hydrochloride and hemoglobin: spectroscopic and molecular dynamics studies

Herein, we have explored the interaction between amitriptyline hydrochloride (AMT) and hemoglobin (Hb), using steady-state and time-resolved fluorescence spectroscopy, UV-visible spectroscopy, and circular dichroism spectroscopy, in combination with molecular docking and molecular dynamic (MD) simulation methods. The steady-state fluorescence reveals the static quenching mechanism in the interaction system, which was further confirmed by UV-visible and time-resolved fluorescence spectroscopy. The binding constant, number of binding sites, and thermodynamic parameters viz. ΔG, ΔH, ΔS are also considered; result confirms that the binding of the AMT with Hb is a spontaneous process, involving hydrogen bonding and van der Waals interactions with a single binding site, as also confirmed by molecular docking study. Synchronous fluorescence, CD data, and MD simulation results contribute toward understanding the effect of AMT on Hb to interpret the conformational change in Hb upon binding in aqueous solution.

Evaluation of the toxicity of ionic liquids on trypsin: A mechanism study

The toxicity of ionic liquids (ILs) was evaluated by using trypsin as biomarker. Experimental results indicated that the trypsin activity was inhibited by ILs and the degree of inhibition highly depended on the chemical structures of ILs. Primary analysis illustrated that hydrophobicity of ILs was one of the driven forces ruling the ILs-trypsin interaction. Thermodynamic parameters, Gibbs free energy change (ΔG), enthalpy change (ΔH) and entropy change (ΔS) were obtained by analyzing the fluorescence behavior of trypsin in the presence of ILs. Both negative ΔH and ΔS suggested hydrogen bonding was the major driven force underlying the IL-trypsin interaction. To assess the toxicity of ILs, it should be considered the combination of the hydrogen bonding ability and hydrophobicity of ILs. A regression based model was established to correlate the relationship of the inhibitory ability, hydrophobicity and hydrogen bonding ability of ILs.

Interaction of three new tetradentates Schiff bases containing N2O2 donor atoms with calf thymus DNA

Interaction of 1,3-bis(2-hydroxy-benzylidene)-urea (H2L1), 1,3-bis(2-hydroxy-3-methoxy-benzylidene)-urea (H2L2) and 1,3-bis(2-hydroxy-3-methoxy-benzylidene)-urea nickel(II) (NiL2) with calf-thymus DNA were investigated by UV-vis absorption, fluorescence emission and circular dichroism (CD) spectroscopy as well as cyclic voltammetry, viscosity measurements, molecular docking and molecular dynamics simulation. Binding constants were determined using UV-vis absorption and fluorescence spectra. The results indicated that studied Schiff-bases bind to DNA in the intercalative mode in which the metal derivative is more effective than non metals. Their interaction trend is further determined by molecular dynamics (MD) simulation. MD results showed that Ni derivative reduces oligonucleotide intermolecular hydrogen bond and increases solvent accessible surface area more than other compounds.

Toxicity of ionic liquids: eco(cyto)activity as complicated, but unavoidable parameter for task-specific optimization

Rapid progress in the field of ionic liquids in recent decades led to the development of many outstanding energy-conversion processes, catalytic systems, synthetic procedures, and important practical applications. Task-specific optimization emerged as a sharpening stone for the fine-tuning of structure of ionic liquids, which resulted in unprecedented efficiency at the molecular level. Ionic-liquid systems showed promising opportunities in the development of green and sustainable technologies; however, the chemical nature of ionic liquids is not intrinsically green. Many ionic liquids were found to be toxic or even highly toxic towards cells and living organisms. In this Review, we show that biological activity and cytotoxicity of ionic liquids dramatically depend on the nature of a biological system. An ionic liquid may be not toxic for particular cells or organisms, but may demonstrate high toxicity towards another target present in the environment. Thus, a careful selection of biological activity data is a must for the correct assessment of chemical technologies involving ionic liquids. In addition to the direct biological activity (immediate response), several indirect effects and aftereffects are of primary importance. The following principal factors were revealed to modulate toxicity of ionic liquids: i) length of an alkyl chain in the cation; ii) degree of functionalization in the side chain of the cation; iii) anion nature; iv) cation nature; and v) mutual influence of anion and cation.