Drug–protein recognition processes investigated by NMR relaxation data

Chiral distinction between hydroxychloroquine enantiomers in binding to angiotensin-converting enzyme 2, the forward receptor of SARS-CoV-2

Soon after the outset of the Coronavirus Disease 2019 (COVID-19) pandemic (March-April 2020), formulations of the old antimalarial racemic drug hydroxychloroquine (HCQ) sulfate were authorized by the U.S. Food and Drug Administration (FDA) for emergency treatment of hospitalized patients with COVID-19. A call for the chiral switch of HCQ to the single enantiomer (S)-(+)-HCQ for treating the disease followed. The above authorizations were later withdrawn. Angiotensin-converting enzyme 2 (ACE2) has been recognized to be the forward receptor of SARS-CoV-2, the virus responsible for COVID-19. The objective of the present study was to evaluate the chiral distinction in the potential preferential binding of the HCQ enantiomers to ACE2, as a basis for its future drug repurposing, using high-field solution Nuclear Magnetic Resonance (NMR) spectroscopy. Proton selective spin-lattice relaxation rates were measured for selected diagnostic nuclei; in particular, protons belonging to the quinoline ring proved to be the most affected by the presence of the protein, for both (S)-(+)-HCQ and (R)-(-)-HCQ enantiomers. An increase in mono-selective relaxation rates was observed for both enantiomers. A significant difference in the magnitude of the increase was detected for all protons investigated, up to a 5-fold and an 8-fold increase in the case of (R)-(-)-HCQ and (S)-(+)-HCQ, respectively. Furthermore, comparison between the normalized mono-selective relaxation rates of the two HCQ enantiomers in their binary mixtures with ACE2 pointed out a certain preference for the (S)-(+)-HCQ enantiomer over (R)-(-)-HCQ in the interaction with ACE2. The findings form the basis for a future application of the drug repurposing/chiral-switch combination strategy to racemic HCQ in previously reported indications for hydroxychloroquine treatment and in the search for new indications in which ACE2 receptors are involved.

NMR Investigation of the Interaction of Three Non-Steroidal Anti-Inflammatory Drugs with Human Serum Albumin

The understanding of the interaction between non-steroidal anti-inflammatory drugs and human serum albumin plays a fundamental role in the development of new drugs and new therapeutic strategies. Several studies have been performed, nevertheless, the interaction phenomena are still not fully understood. In this work, high-field solution Nuclear Magnetic Resonance (NMR) spectroscopy was applied to compare the strength of the interaction of diclofenac sodium salt, ketorolac tris salt and flurbiprofen sodium salt toward albumin. To this aim, mono- and bi-selective relaxation rate measurements were performed by applying selective π-pulses at the selected frequencies and by following magnetization recovery. On the basis of the dependence of relaxation parameters on albumin concentration, normalized affinity indexes were calculated for several protons of the drugs. Affinity indexes for diclofenac were about five-fold higher in comparison with ketorolac and flurbiprofen. Aromatic moieties of the three drugs and methine protons at the chiral centers of ketorolac and flurbiprofen were more involved in the interaction with albumin. In conclusion, NMR spectroscopy allows not only for the comparison of drug-to-protein affinities but also points out the nature of the drug sites that are more extensively involved in the interaction.

In vitro interaction of organophosphate metabolites with bovine serum albumin: A comparative 1H NMR, fluorescence and molecular docking analysis

Since the exposure of organophosphate pesticides are known to cause severe health consequences, it is important to understand the molecular interaction of these pesticides metabolites with vital biomolecules, especially with the proteins. Here, considering bovine serum albumin (BSA) as a model protein, we have examined its interaction with two selected organophosphate metabolites, 3,5,6-trichloro-2-pyridinol (TCPy) and paraoxon methyl (PM). TCPy and PM are resultant metabolites of two most widely used organophosphate pesticides chlorpyrifos and parathion respectively. ¹H NMR line broadening, selective spin-lattice relaxation rate measurements, saturation transfer difference (STD) NMR of both TCPy and PM were carried out in the presence and absence of BSA. The obtained values of the affinity index (A), binding constants (K_a) and thermodynamic parameters indicated strong organophosphates-BSA interaction. Further, fluorescence quenching data on TCPy-BSA and PM-BSA interactions strongly supported the NMR results, besides providing the stoichiometry of these complexes. Molecular docking analysis unraveled viable, strong hydrogen bonds and electrostatic interactions in TCPy-BSA and PM-BSA complexes. This study also revealed substantial time-dependent changes in the ¹H NMR intensity of PM in the presence of BSA, which suggests faster degradation of PM with increasing protein concentration during protein-metabolite interactions. The hydrolysis is attributed to the esterase-like action of BSA. The result provides key insights into the direct interaction of the organophosphate metabolites with a biologically important carrier protein, serum albumin.

Investigation of relaxation times in 5-fluorouracil and human serum albumin mixtures

Background

Human serum albumin (HSA) is often selected as a subject of any study because albumin is the most abundant protein in human blood plasma. NMR is recognized as a valuable method to determine the structure of proteins-ligand and protein-drug complexes.

Objective – Aim of the study

In this study, protein drug interactions were investigated using 5-Fluorouracil anti-cancer drug and human serum albumin protein.

Materials and methods

In this context 400 MHz NMR spectrometry was used and NMR relaxation rates in drug-albumin complex were investigated with respect to increase albumin concentration and increase in 5-Fluorouracil (5-FU)-albumin solution temperature.

Results

The results of this study indicated that 5-FU had a weak association with albumin, and it easily dissociated from the protein to which it was attached.

Conclusion

The obtained results also gave us useful information about molecular dynamics of drug-albumin interactions.

Effect of resveratrol on platelet aggregation by fibrinogen protection

The effect of resveratrol (RSV) in inhibiting platelet adhesion and aggregation, as well as fibrinogen (FBG) conformational changes promoted by epinephrine (EP), were studied, by using complementary experimental techniques. NMR and IR spectroscopies were used to investigate possible protective effects by RSV towards FBG, in presence of EP. The protective effect of RSV towards FBG was highlighted by spin nuclear relaxation experiments that were interpreted for determining the thermodynamic equilibrium constants of FBG-EP interaction, and by infrared measurements, that showed EP-induced conformational changes of FBG. The ability of RSV in inhibiting platelet adhesion and aggregation promoted by EP was evaluated by scanning electron microscopy (SEM), measuring the platelet adhesion and aggregation degree, in comparison to data obtained for platelet aggregation in platelet rich plasma (PRP). The experimental combined approach pointed out that RSV is able to protect both FBG and platelets from the denaturant and aggregating action of EP at stress level concentration.

Hydrolytic inhibition of α-chymotrypsin by 2,8,14,20-tetrakis(D-leucyl-D-valinamido)resorc[4]arenecarboxylic acid: a spectroscopic NMR and computational combined approach

The stereochemical features of 2,8,14,20-tetrakis(D-leucyl-D-valinamido)resorc[4]arenecarboxylic acid and the N-succinyl-L-alanyl-L-alanyl-L-prolyl-L-phenylalanine-4-nitroanilide polypeptide substrate were investigated by nuclear magnetic resonance spectroscopy. Proton selective relaxation parameters gave the basis for the inhibitory activity of resorcin[4]arene in the hydrolysis of the polypeptide substrate by α-chymotrypsin. Results showed that an interaction between the resorcin[4]arene and α-chymotrypsin does occur, and involves the hydrophobic moiety of the macrocycle. This interaction is further reinforced by polar groups located on the side chains of the resorcin[4]arene, whereas the macrocycle-polypeptide substrate interaction is negligible. Conformational analysis and interaction studies carried out by molecular modeling are in good agreement with the NMR data, thus providing an additional support to the rationalization of the inhibitory potential of resorcin[4]arenes on the α-chymotrypsin activity.

Binding mechanism of tauroursodeoxycholic acid to human serum albumin: insights from NMR relaxation and docking simulations

Binding patterns and structure–affinity relationship of tauroursodeoxycholic acid with human serum albumin were established by NMR methodology and docking simulations.

Inhibition of human neutrophil elastase by pentacyclic triterpenes

SCOPE

Inhibiting human neutrophil elastase (HNE) is a promising strategy for treating inflammatory lung diseases, such as H1N1 and SARS virus infections. The use of sivelestat, the only clinically registered synthesized HNE inhibitor, is largely limited by its risk of organ toxicity because it irreversibly inhibits HNE. Therefore, potent reversible HNE inhibitors are promising alternatives to sivelestat.

METHODS AND RESULTS

An in vitro HNE inhibition assay was employed to screen a series of triterpenes. Six pentacyclic triterpenes, but not tetracyclic triterpenes, significantly inhibited HNE. Of these pentacyclic triterpenes, ursolic acid exhibited the highest inhibitory potency (IC50 = 5.51 µM). The HNE inhibitory activity of ursolic acid was further verified using a mouse model of acute smoke-induced lung inflammation. The results of nuclear magnetic resonance and HNE inhibition kinetic analysis showed that the pentacyclic triterpenes competitively and reversibly inhibited HNE. Molecular docking experiments indicated that the molecular scaffold, 28-COOH, and a double bond at an appropriate location in the pentacyclic triterpenes are important for their inhibitory activity.

CONCLUSION

Our results provide insights into the effects of pentacyclic triterpenes on lung inflammatory actions through reversible inhibition of HNE activity.

Water-protein interactions: the secret of protein dynamics

Water-protein interactions help to maintain flexible conformation conditions which are required for multifunctional protein recognition processes. The intimate relationship between the protein surface and hydration water can be analyzed by studying experimental water properties measured in protein systems in solution. In particular, proteins in solution modify the structure and the dynamics of the bulk water at the solute-solvent interface. The ordering effects of proteins on hydration water are extended for several angstroms. In this paper we propose a method for analyzing the dynamical properties of the water molecules present in the hydration shells of proteins. The approach is based on the analysis of the effects of protein-solvent interactions on water protons NMR relaxation parameters. NMR relaxation parameters, especially the nonselective (R₁^NS ) and selective (R₁^SE ) spin-lattice relaxation rates of water protons, are useful for investigating the solvent dynamics at the macromolecule-solvent interfaces as well as the perturbation effects caused by the water-macromolecule interactions on the solvent dynamical properties. In this paper we demonstrate that Nuclear Magnetic Resonance Spectroscopy can be used to determine the dynamical contributions of proteins to the water molecules belonging to their hydration shells.

Direct interaction of ONO-5046 with human neutrophil elastase through ¹H NMR and molecular docking

Human neutrophil elastase (HNE) has been implicated as a major contributor in the pathogenesis of diseases, such as pulmonary emphysema, acute lung injury (ALI), acute respiratory distress syndrome (ARDS), and other inflammatory diseases. Therefore, searching for appropriate and potential human neutrophil elastase inhibitors (HNEI) that would restore the balance between the free enzyme and the endogenous inhibitors would be of therapeutic interest. ONO-5046 is the first specific HNEI to improve respiratory function and protect lung tissues against various lung injuries. However, the mechanism of ONO-5046 to HNE is still unclear. In this study, the binding properties of ONO-5046 were investigated through (1)H NMR, molecular docking, and bioassay methods to understand the effect of ONO-5046 to HNE. The proton spin-lattice relaxation rate and molecular rotational correlation time results indicated that ONO-5046 has higher affinity with HNE. The molecular docking study showed that ONO-5046 is perfectly matched for the primary enzyme specificity pocket (S1 pocket), and is tightly bound to this pocket of HNE through hydrophobic and hydrogen bonding interactions. The results of both methods were validated through analysis of the HNE inhibitory activity bioassay of ONO-5046 with an IC(50) value of 87.05 nM. Our data suggested that ONO-5046 could bind to HNE through direct interaction, and that molecular docking and NMR methods are valid approaches to survey new HNEI.

Interaction between vine pesticides and bovine serum albumin studied by nuclear spin relaxation data

Pesticides are chemicals usually used in agriculture to prevent possible diseases to crops, such as grapes, caused by parasites. Even if most of the pesticides are degraded during the wine process, residual levels remain in the final product. The most commonly used pesticides in vine belong to several classes of chemical compounds; among them, triazoles and anilinopyrimidines have been commercially used since the 1970s and 1990s, respectively. In this work, we investigated the interaction between three of the most used fungicides belonging to the chemical classes mentioned above (myclobutanil, triadimenol, and pyrimethanil) and bovine serum albumin (BSA) by nuclear spin relaxation analysis. We found that all of the pesticides were able to form a complex with BSA; nevertheless, there were strong differences in their affinity toward the plasma protein. The nuclear magnetic resonance approach used on the basis of the analysis of selective relaxation rate enhancements of pesticide protons in the presence of BSA allowed for the calculation of the affinity indexes and the equilibrium constants of the three systems. Myclobutanil showed the highest affinity toward BSA, whereas triadimenol gave the weakest interaction with the protein. The differences in the capacity of the three pesticides to bind to albumin highlighted the existence of different binding strengths on the protein. These results indicate that myclobutanil and triadimenol, despite their structure similarity, may have very different residence times in the plasma and rates of clearance.

Interaction of quercetin and its conjugate quercetin 3-O-beta-D-glucopyranoside with albumin as determined by NMR relaxation data

NMR methodology has been developed in order to study phytochemical-macromolecular receptor interactions. This approach is based on the analysis of proton selective spin-lattice relaxation rate enhancements of the ligand in the presence of the macromolecule, to calculate an affinity index, [ A] L (T) , related to the strength of the interaction process. This index has been modified by normalization to the relaxation rate of the free ligand, in order to take into account the effects of motional anisotropies and different proton densities. The normalized affinity index, [ A N ] L (T) , isolates the contribution due to a decrease in the ligand dynamics caused by the binding with the protein. This methodology has been applied to the interaction between two flavonoids (quercetin, 1, and quercetin 3-O-beta-D-glucopyranoside, 2) and bovine serum albumin (BSA). The calculated values of the affinity indexes and thermodynamic equilibrium constants suggested a much stronger capacity of 1 to interact with BSA when compared with its glucosylated derivative, 2.

Fibrinogen−Catecholamine Interaction as Observed by NMR and Fourier Transform Infrared Spectroscopy

In this work, the interactions between the main catecholamines-epinephrine and norepinephrine-and fibrinogen were investigated by NMR and Fourier transform infrared spectroscopies. The two hormones were found to interact with fibrinogen and to affect the protein secondary structure to a different extent. In particular, the protein selectively binds epinephrine at both the basal and stress concentrations, while it shows a weak nonspecific interaction with norepinephrine. The interaction with the stress level of epinephrine leads to drastic protein conformational changes, whereas norepinephrine does not affect fibrinogen secondary structure, even at stress concentration.

1H and 19F NMR relaxation studies of fleroxacin with Micrococcus luteus

In order to investigate and characterize interaction processes between the fluoroquinolone fleroxacin and bacterial cells we used non-selective (all resonances are excited), selective (observed resonance is excited) spin-lattice relaxation rates and spin-spin relaxation measurements. The signals of three hydrogens at different moieties of the fleroxacin molecule were considered to get an insight in the complexation behavior. The enhancement of selective relaxation rates was observed with increasing fleroxacin concentrations and keeping the bacterial mass constant. The obtained relaxation rates of the affected hydrogens were analyzed via a Lineweaver-Burk-plot to determine the KD values. Furthermore, 19F NMR spectra were recorded and spin-spin relaxation rates (R2) were determined by a Carr-Purcell-Meiboom-Gill (CPMG) pulse sequence. Because of the dependency of the line width of NMR peaks on transversal relaxation time T2, we compared the line width at half-height at different fleroxacin concentrations in order to investigate the involvement of fluorine atoms in different positions in the complexation. All findings point to core quinolone moiety to be involved in the interaction with bacterial cells.