Effect of N-Butyl-N-Methyl-Morpholinium Bromide Ionic Liquid on the Conformation Stability of Human Serum Albumin

Factor defining the effects of tetraalkylammonium chloride on stability, folding, and dynamics of horse cytochrome c

This article describes the molecular mechanism by which tetraalkylammonium chloride ([R4N]Cl: R- = methyl (Me), ethyl (Et), propyl (Pr),butyl (Bu)) modulates the stability, folding, and dynamics of cytochrome c (Cyt c). Analysis of [R4N]Cl effects on thermal/chemical denaturations, millisecond refolding/unfolding kinetics, and slow CO-association kinetics of Cyt c without and with denaturant providing some significant results: (i) [R4N]Cl decreasing the unfolding free energy estimated by thermodynamic and kinetic analysis of thermal/chemical denaturation curves and kinetic chevrons (Log kobs-[GdmCl]) of Cyt c, respectively (ii) hydrophobicity of R-group of [R4N]Cl, preferential inclusion of [R4N]Cl at the protein surface, and destabilizing enthalpic attractive interactions of [Me4N]Cl and steric entropic interactions of [Et4N]Cl,[Pr4N]Cl and [Bu4N]Cl with protein contribute to [R4N]Cl-induced decrease thermodynamic stability of Cyt c (iii) [R4N]Cl exhibits an additive effect with denaturant to decrease thermodynamic stability and refolding rates of Cyt c (iv) low concentrations of [R4N]Cl (≤ 0.5 M) constrain the motional dynamics while the higher concentrations (>0.75 M [R4N]Cl) enhance the structural-fluctuations that denture protein (v) hydrophobicity of R-group of [R4N]Cl alters the [denaturant]-dependent conformational stability, refolding-unfolding kinetics, and CO-association kinetics of Cyt c. Furthermore, the MD simulations depicted that the addition of 1.0 M of [R4N]Cl increased the conformational fluctuations in Cyt c leading to decreased structural stability in the order [Me4N]Cl < [Et4N]Cl < [Pr4N]Cl < [Bu4N]Cl consistent with the experimental results.

Interactions of Turmeric- and Curcumin-Functionalized Gold Nanoparticles with Human Serum Albumin: Exploration of Protein Corona Formation, Binding, Thermodynamics, and Antifibrillation Studies

In order to better understand the bioavailability and biocompatibility of polyphenol-assisted surface-modified bioengineered nanoparticles in nanomedicine applications, here, we address a series of photophysical experiments to quantify the binding affinity of serum albumin toward polyphenol-capped gold nanoparticles. For this, two different gold nanoparticles (AuNPs) were synthesized via the green synthesis approach, where curcumin and turmeric extract act as reducing as well as capping agents. The size, surface charge, and surface plasmon bands of the AuNPs were highly affected by the adsorption of human serum albumin (HSA) during protein corona formation, which was investigated using dynamic light scattering (DLS), ξ-potential, ultraviolet-visible (UV-vis) spectroscopy, and transmission electron microscopy (TEM) measurements. Fluorescence-based methods, absorbance, and SERS experiments were carried out to evaluate the binding aspects of AuNPs with HSA. We found that the AuNPs show moderate binding affinity toward HSA (Kb ∼ 104 M-1), irrespective of the capping agents on the surface. Hydrophobic association, along with some contribution of electrostatic interaction, played a key role in the binding process. The binding interaction was more toward the subdomain IIA region of HSA, as indicated by the competitive displacement studies using site-specific binders (warfarin and flufenamic acid). Because of the large surface curvature of small-sized AuNPs, the secondary structural conformations of HSA were slightly altered, as revealed by circular dichroism (CD), Fourier transform infrared (FT-IR) spectroscopy, and surface-enhanced Raman scattering (SERS) measurements. Additionally, the findings of the binding interactions were re-evaluated using molecular dynamics (MD) simulation studies by determining the root-mean-square deviation (RMSD), root-mean-square fluctuation (RMSF), radius of gyration (Rg), and changes in the binding energy of HSA upon complexation with AuNPs. To determine the tentative evidence for pharmacokinetic administration, these biocompatible AuNPs were applied to inhibit the amyloid fibril formation of HSA and monitored by using the thioflavin T (ThT) assay, ANS fluorescence assay, fluorescence microscopic imaging, and FESEM. AuNPs were found to show better resistance toward fibrillation of the adsorbed protein.

Cationic Perylene Antivirals with Aqueous Solubility for Studies In Vivo

Perylene-based compounds are attracting significant attention due to their high broad-spectrum antiviral activity against enveloped viruses. Despite unambiguous results of in vitro studies and high selectivity index, the poor water solubility of these compounds prevented in vivo evaluation of their antiviral properties. In this work, we synthesized a series of compounds with a perylene pharmacophore bearing positively charged substituents to improve the aqueous solubility of this unique type of antivirals. Three types of charged groups were introduced: (1) quaternary morpholinium salts (3a-b); (2) a 2'-O-l-valinyl-uridine hydrochloride residue (8), and (3) a 3-methylbenzothiazolium cation (10). The synthesized compounds were evaluated based both on antiviral properties in vitro (CHIKV, SARS-CoV-2, and IAV) and on solubility in aqueous media. Compound 10 has the greatest aqueous solubility, making it preferable for pre-evaluation by intragastrical administration in a mouse model of lethal influenza pneumonia. The results indicate that the introduction of a positively charged group is a viable strategy for the design of drug candidates with a perylene scaffold for in vivo studies.

L-amino-acids as immunity booster against COVID-19: DFT, molecular docking and MD simulations

There is great interest to explore the importance of different amino-acids on immunity of human. Immunity helps to protect us from the pathogenic infections. The amino-acids are being use to give energy and is also used as an important basic molecule for the making of cells, protecting cell and others. Still, a little information is known for their importance in the inhibition of main protease of SARS-CoV-2. As known, tens of billions of humans are infected due to the SARS-CoV-2 and about a million of deaths are reported due to it or COVID. As of now, no promising drug is available in the market to cure the patients from this infection. Even, the medicines beings used for the partial cure may have some side effects. Therefore, the focus is to explore the natural amino-acids against the Mpro of SARS-CoV-2 as using of amino-acids is not toxic to humans. In the present work, authors have studied the amino-acids using DFT calculations and then they were explored for their promising role in the inhibition of main protease of SARS-CoV-2 using molecular docking and molecular dynamics simulations. Out of the 20 amino-acids, arginine found to best against the main protease of SARS-CoV-2 using the molecular docking and the binding energy was -0.94 kcal/ mol. Further, molecular dynamics simulations for the main protease of SARS-CoV-2 with and without arginine was performed using the Amber and different thermodynamic parameters like ΔH and TΔS to get ΔG, comes out to be 2.74 kcal/mol. It is expected that arginine can boost the immunity.

Interactions between main protease of SARS-CoV-2 and testosterone or progesterone using computational approach

SARS-CoV-2 is drastically spread across the globe in a short period of time and affects the lives of billions. There is a need to find the promising drugs like candidates against the inhibition of novel corona virus or SARS-CoV-2. Herein, the interaction on sex hormones (testosterone and progesterone) with Mpro of SARS-CoV-2 was investigated with the help of molecular docking. The binding energy for the formation complex between the progesterone and testosterone with main protease of SARS-CoV-2 are -86.05 and -91.84 kcal/mol, respectively. From this, it can be understood that testosterone showed better binding affinity with Mpro of nCoV and thus, more inhibition of the main protease. Then, the binding was further studied using molecular dynamics simulations at different temperatures (300, 310 and 325) K. It has been observed that the formations of complex between the Mpro of nCoV with testosterone/ progesterone is better at 300 K than 310 and 325 K. Further, it is found that the more effective binding of testosterone with Mpro of nCoV is observed than the progesterone based on the RMSD, RMSF and H-bond trajectories. Results indicate the promising nature of testosterone towards the inhibition of Mpro of nCoV.

Effect of imidazolium based ionic liquids on CO-association dynamics and thermodynamic stability of Ferrocytochrome c

Analysis of kinetic and thermodynamic parameters measured for CO-association reaction of Ferrocytochrome c (Ferrocyt c) under variable concentrations of 1-butyl-3-methylimidazolium with varying anion ([Bmim]X) (X = Cl^-, I^-, Br^-, HSO₄^-) at pH 7 revealed that the low concentration of [Bmim]X (≤0.5 M) constrains the CO-association dynamics of Ferrocyt c and typically follows the order: [Bmim]HSO₄ > [Bmim]Cl > [Bmim]Br > [Bmim]I. At relatively higher concentrations (>0.5), the chaotropic action of [Bmim]⁺ dominates which consequently increases the thermal-fluctuations responsible to denature the protein and thus accelerates the speed of CO-association reaction. Analysis of thermal denaturation curves of Ferrocyt c measured at different concentrations of [Bmim]X revealed that the [Bmim]X decreases the thermodynamic stability of protein and typically follows the order: [Bmim]I > [Bmim]Br > [Bmim]Cl > [Bmim]CH₃COO > [Bmim]HSO₄, demonstrating that the effect of [Bmim]X on thermodynamic stability of protein is not in accordance to Hofmeister series effect of anions because instead of increasing the kosmotropic anion carrying [Bmim]X ([Bmim]CH₃COO and [Bmim]HSO₄) also decreases the thermodynamic stability of protein.

Insight into interaction mechanism between theaflavin-3-gallate and α-glucosidase using spectroscopy and molecular docking analysis

To elucidate the α-glucosidase (α-GC) inhibitory mechanism of theaflavin-3-gallate (TF-3-G), their interaction mechanism was investigated using spectroscopy and molecular docking analysis. The inhibition ratio of TF-3-G against α-GC was determined to be 92.3%. Steady fluorescence spectroscopy showed that TF-3-G effectively quenched the intrinsic fluorescence of α-GC through static quenching, forming a stable complex through hydrophobic interactions. Formation of the TF-3-G/α-GC complex was also confirmed by resonance light scattering spectroscopy. Synchronous fluorescence spectroscopy and circular dichroism spectroscopy indicated that the secondary structure of α-GC was changed by TF-3-G. Molecular docking was used to simulate TF-3-G/α-GC complex formation, showing that TF-3-G might be inserted into the hydrophobic region around the active site of ɑ-GC, and bind with the catalytic Asp215 and Asp352 residues. The ɑ-GC inhibitory mechanism of TF-3-G was mainly attributed to the change in ɑ-GC secondary structure caused by the complex formation. PRACTICAL APPLICATIONS: α-Glucosidase (α-GC) can hydrolyze the glycosidic bonds of starch and oligosaccharides in food and release glucose. Therefore, the inhibition of α-GC activity has been used to treat postprandial hyperglycemia and type 2 diabetes mellitus. Theaflavin-3-gallate (TF-3-G), a flavonoid found in the fermentation products of black tea, exhibits strong inhibition of α-GC activity. However, the α-GC inhibitory mechanism of TF-3-G is unclear. This study aids understanding of this mechanism, and proposed a possibly basic theory for improving the medicinal value of TF-3-G in diabetes therapy.

Noncovalent Conjugates of Ionic Liquid with Antibacterial Peptide Melittin: An Efficient Combination against Bacterial Cells

Growing antibiotic resistance has become a major health problem and has encouraged many researchers to find an alternative class of antibiotics. Combination therapy (covalent/noncovalent) is supposed to increase antibacterial activity leading to a decrease in administration dosage, thus lowering the risk of adverse side effects. The covalent coupling sometimes leads to instability and loss in the structure of AMPs. Therefore, herein, we have reported innovative research involving the noncovalent coupling of melittin (MEL), an antimicrobial peptide with a series of synthesized less toxic pyrrolidinium-based ionic liquids (ILs) for which MTT assay was performed. The antibacterial results of conjugates showed remarkable improvement in the MIC value as compared to MEL and ILs alone against Escherichia coli and Staphylococcus aureus . In addition, hemocompatibility results suggested good selectivity of the noncovalent conjugate as a potential antibiotic agent. Further, the docking study was employed to acquire the most favorable conformation of MEL in the presence of ILs. The best possible complex was further studied using various spectroscopic techniques, which showed appreciable binding and stability of the complex.

Molecular Interaction of Amino Acid-Based Gemini Surfactant with Human Serum Albumin: Tensiometric, Spectroscopic, and Molecular Docking Study

Binding effect and interaction of N,N'-dialkyl cystine based gemini surfactant (GS); 2(C₁₂Cys) with human serum albumin (HSA) were systematically investigated by the techniques such as surface tension measurement, UV-visible spectroscopy, fluorescence spectroscopy, circular dichroism (CD) spectroscopy, and molecular docking studies. The surface tension measurement exhibited that HSA shifted the critical micelle concentration of the 2(C₁₂Cys) GS to the higher side that confirms the complex formation among 2(C₁₂Cys) GS and HSA which was also verified by UV-visible, fluorescence, and CD spectroscopy. Increase in the concentration of 2(C₁₂Cys) GS increases the absorption of the HSA protein but has a reverse effect on the fluorescence intensity. The analysis of UV-visible study with the help of a static quenching method showed that the value acquired for the bimolecular quenching constant (k _q) quenches the intrinsic fluorescence of the HSA protein. Synchronous fluorescence spectrometry declared that the induced-binding conformational changes in HSA and CD results explained the variations in the secondary arrangement of the protein in presence of 2(C₁₂Cys) GS. The present study revealed that the interaction between 2(C₁₂Cys) GS and HSA is important for the preparation and properties of medicines. Molecular docking study provides insight into the specific binding site of 2(C₁₂Cys) GS into the sites of HSA.

Interaction mechanism between α-glucosidase and A-type trimer procyanidin revealed by integrated spectroscopic analysis techniques

α-Glucosidase is an important enzyme in human intestine, and inhibition of its activity can lower blood sugar levels to effectively prevent hyperglycaemia induced tissue damage. Here, we investigated the inhibitory activities of procyanidins with different structures on α-glucosidase and the underlying mechanism. The results showed that the IC₅₀ of catechin and compounds 2-7 on α-glucosidase was lower than that of acarbose. A-type procyanidins might have better inhibitory activity than B-type procyanidins. In addition, there was no positive correlation between the polymerization degree of A-type procyanidin oligomer and its inhibitory effect on α-glucosidase. Compound 7 (A-type trimer) with the best inhibitory effect reversibly inhibited the activity of α-glucosidase in a mixed-type manner. Fluorescence data confirmed that the intrinsic fluorescence of α-glucosidase was quenched by compound 7 through static-dynamic quenching. The calculated thermodynamic parameters indicated that their binding was spontaneous and driven by hydrophobic interaction, which was also confirmed by the UV spectrum experiment. Besides, circular dichroism analysis displayed that their binding resulted in conformational changes of α-glucosidase characterized by a decrease in α-helix and an increase in β-sheet. The results demonstrate the ability of procyanidins to intervene in the progression of type 2 diabetes by inhibiting α-glucosidase.

Binding properties of sodium glucose co-transporter-2 inhibitor empagliflozin to human serum albumin: spectroscopic methods and computer simulations

Empagliflozin is an oral sodium glucose co-transporter-2 inhibitor for type 2 diabetes mellitus. The interaction between empagliflozin and human serum albumin (HSA) was investigated experimentally and theoretically. Fluorescence quenching and time-resolved fluorescence spectroscopy indicated that the quenching mechanism of empagliflozin and HSA was dynamic and that the effective binding constant at body temperature was 3.495 × 10³ M^-1. Thermodynamic parameters showed that hydrophobic forces were the major binding force in the interaction between empagliflozin and HSA. Circular dichroism, Fourier transform infrared, and 3 D fluorescence spectroscopy revealed that empagliflozin showed a slight change in secondary structure without changing the basic carbon framework of HSA. Site marker displacement experiments revealed that empagliflozin bound to site I of HSA, which was supported by molecular docking. Molecular dynamic simulations indicated that empagliflozin could bind to HSA stably. This study provided insights into the binding mechanism between empagliflozin and HSA.Communicated by Ramaswamy H. Sarma.

Dynamics of Ionic Liquid-Assisted Refolding of Denatured Cytochrome c: A Study of Preferential Interactions toward Renaturation

In vitro refolding of denatured protein and the influence of the alkyl chain on the refolding of a protein were tested using long chain imidazolium chloride salts, 1-methyl-3-octylimidazolium chloride [C₈mim][Cl], and 1-decyl-3-methylimidazolium chloride [C₁₀mim][Cl]. The horse heart cytochrome c (h-cyt c) was denatured by urea and guanidinium hydrochloride (GdnHCl), as well as by base-induced denaturation at pH 13, to provide a broad overview of the overall refolding behavior. The variation in the alkyl chain of the ionic liquids (ILs) showed a profound effect on the refolding of denatured h-cyt c. The ligand-induced refolding was correlated to understand the mechanism of the conformational stability of proteins in aqueous solutions of ILs. The results showed that the long chain ILs having the [C₈mim]⁺ and [C₁₀mim]⁺ cations promote the refolding of alkali-denatured h-cyt c. The IL having the [C₁₀mim]⁺ cation efficiently refolded the alkali-denatured h-cyt c with the formation of the MG state, whereas the IL having the [C₈mim]⁺ cation, which is known to be compatible for protein stability, shows slight refolding and forms a different transition state. The lifetime results show successful refolding of alkaline-denatured h-cyt c by both of the ILs, however, more refolding was observed in the case of [C₁₀mim][Cl], and this was correlated with the fast and medium lifetimes (τ₁ and τ₂) obtained, which show an increase accompanied by an increase in secondary structure. The hydrophobic interactions plays an important role in the refolding of chemically and alkali-denatured h-cyt c by long chain imidazolium ILs. The formation of the MG state by [C₁₀mim][Cl] was also confirmed, as some regular structure exists far below the CMC of IL. The overall results suggested that the [C₁₀mim]⁺ cation bound to the unfolded h-cyt c triggers its refolding by electrostatic and hydrophobic interactions that stabilize the MG state.

Heteroassembly Ability of Dicationic Ionic Liquids and Neutral Active Pharmaceutical Ingredients

Extensive investigation of interactions and aggregation properties of IL + API systems is necessary to apply ionic liquids (ILs) with different hydrophobic characteristics to drug delivery or in active pharmaceutical ingredient (API) formulations. Therefore, this study aims to investigate the heteroassembly between dicationic ILs ([BisOct(MIM)₂][2X], in which X is Br or BF₄, and [BisOct(BnIM)₂][2Br]), both in the absence and the presence of neutral APIs (salicylic acid, ibuprofen, and paracetamol) with different functional groups. Isothermal titration calorimetry results demonstrate that IL-API associations occur at very low concentrations of IL. These results were reinforced by electrospray ionization mass spectrometry with variable collision-induced dissociation, in which the IL dication interactions with APIs were detected. The strength of the dication-API interaction was determined from E _cm,1/2 data. The aggregation parameters (cac, ΔG _agg ^°, and K) between ILs and APIs were evaluated by conductivity. The ¹H NMR data showed that differences in chemical shifts provided relevant insights about interaction sites in both components.

Determining mushroom tyrosinase inhibition by imidazolium ionic liquids: A spectroscopic and molecular docking study

The inhibition effects of imidazolium ionic liquids (ILs) on the enzyme kinetics of mushroom tyrosinase is reported. A simple UV-VIS spectrophotometric assay was used to measure the reaction kinetics of the reaction between mushroom tyrosinase and L-dopa. Seven different imidazolium ILs, comprised of 1-alkyl-3-methylimidazolium ([Im_n1⁺], n=2, 4, 6) cations paired with several anions that included Cl^-, [NO₃^-], methanesulfonate ([MeSO₃^-]), trifluoromethanesulfonate (or triflate, [TFMS^-]), and bis(trifluoromethylsulfonyl)imide ([Tf₂N^-]). Lineweaver-Burk plots were generated from the recovered k_cat and K_m parameters using four to six substrate concentrations per measurement. The results show that mushroom tyrosinase activity was consistently inhibited by all of the ILs and that the type of inhibition was non-competitive in nearly all cases. Only the data for [Im₂₁⁺][Tf₂N^-] suggested that the inhibition mechanism was competitive with the substrate. Molecular docking simulations were performed using AutoDock4.2 and AutoDock Vina and revealed that all cations docked in the L-dopa active site. Anions showed varied results that included locations both within and outside of the active site.