Črtomir Podlipnik

Interactions of different polyphenols with bovine serum albumin using fluorescence quenching and molecular docking

Polyphenols are responsible for the major organoleptic characteristics of plant-derived foods and beverages. Here, we investigated the binding of several polyphenols to bovine serum albumin (BSA) at pH 7.5 and 25°C: catechins [(-)-epigallocatechin-3-gallate, (-)-epigallocatechin, (-)-epicatechin-3-gallate], flavones (kaempferol, kaempferol-3-glucoside, quercetin, naringenin) and hydroxycinnamic acids (rosmarinic acid, caffeic acid, p-coumaric acid). Fluorescence emission spectrometry and molecular docking were applied to compare experimentally determined binding parameters with molecular modelling. Among these polyphenols, (-)-epicatechin-3-gallate showed the highest Stern-Volmer modified quenching constant, followed by (-)-epigallocatechin-3-gallate. Similarly, (-)-epicatechin-3-gallate had the highest effect on the Circular Dichroic spectrum of BSA, while the changes induced by other polyphenols were negligible. Molecular docking predicted high binding energies for (-)-epicatechin-3-gallate and (-)-epigallocatechin-3-gallate for the binding site on BSA near Trp213. Our data reveal that the polyphenol structures significantly affect the binding process: the binding affinity generally decreases with glycosylation and reduced numbers of hydroxyl groups on the second aromatic ring.

Thermodynamic fingerprints of ligand binding to human telomeric G-quadruplexes.

Thermodynamic studies of ligand binding to human telomere (ht) DNA quadruplexes, as a rule, neglect the involvement of various ht-DNA conformations in the binding process. Therefore, the thermodynamic driving forces and the mechanisms of ht-DNA G-quadruplex-ligand recognition remain poorly understood. In this work we characterize thermodynamically and structurally binding of netropsin (Net), dibenzotetraaza[14]annulene derivatives (DP77, DP78), cationic porphyrin (TMPyP4) and two bisquinolinium ligands (Phen-DC3, 360A-Br) to the ht-DNA fragment (Tel22) AGGG(TTAGGG)3 using isothermal titration calorimetry, CD and fluorescence spectroscopy, gel electrophoresis and molecular modeling. By global thermodynamic analysis of experimental data we show that the driving forces characterized by contributions of specific interactions, changes in solvation and conformation differ significantly for binding of ligands with low quadruplex selectivity over duplexes (Net, DP77, DP78, TMPyP4; KTel22 ≈ KdsDNA). These contributions are in accordance with the observed structural features (changes) and suggest that upon binding Net, DP77, DP78 and TMPyP4 select hybrid-1 and/or hybrid-2 conformation while Phen-DC3 and 360A-Br induce the transition of hybrid-1 and hybrid-2 to the structure with characteristics of antiparallel or hybrid-3 type conformation.

Synthesis and affinity evaluation of a small library of bidentate cholera toxin ligands: towards nonhydrolyzable ganglioside mimics

A small library of nonhydrolyzable mimics of GM1 ganglioside, featuring galactose and sialic acid as pharmacophoric carbohydrate residues, was synthesized and tested. All compounds were synthesized from readily available precursors using high-performance reactions, including click chemistry protocols, and avoiding O-glycosidic bonds. Some of the most active molecules also feature a point of further derivatization that can be used for conjugation with polyvalent aglycons. Their affinity towards cholera toxin was assessed by weak affinity chromatography, which allowed a systematic evaluation and selection of the best candidates. Affinity could be enhanced up to one or two orders of magnitude over the affinity of the individual pharmacophoric sugar residues.

Recognition of Human Tumor Necrosis Factor α (TNF-α) by Therapeutic Antibody Fragment ENERGETICS AND STRUCTURAL FEATURES

Background: Human TNF-α is a cytokine involved in many disease-related cellular processes. Results: High affinity binding of therapeutic antibody (inhibitor) to native and molten globule-like TNF-α conformation is driven by specific noncovalent interactions. Conclusion: Binding-coupled conformational changes are crucial for antibody-TNF-α recognition. Significance: This work helps learn which forces drive unfolding of TNF-α and its recognition by monoclonal antibodies and how they affect TNF-α activity regulation. Human tumor necrosis factor α (TNF-α) exists in its functional state as a homotrimeric protein and is involved in inflammation processes and immune response of a human organism. Overproduction of TNF-α results in the development of chronic autoimmune diseases that can be successfully treated by inhibitors such as monoclonal antibodies. However, the nature of antibody-TNF-α recognition remains elusive due to insufficient understanding of its molecular driving forces. Therefore, we studied the energetics of binding of a therapeutic antibody fragment (Fab) to the native and non-native forms of TNF-α by employing calorimetric and spectroscopic methods. Global thermodynamic analysis of data obtained from the corresponding binding and urea-induced denaturation experiments has been supported by structural modeling. We demonstrate that the observed high affinity binding of Fab to TNF-α is an enthalpy-driven process due mainly to specific noncovalent interactions taking place at the TNF-α-Fab binding interface. It is coupled to entropically unfavorable conformational changes and accompanied by entropically favorable solvation contributions. Moreover, the three-state model analysis of TNF-α unfolding shows that at physiological concentrations, TNF-α may exist not only as a biologically active trimer but also as an inactive monomer. It further suggests that even small changes of TNF-α concentration could have a considerable effect on the TNF-α activity. We believe that this study sets the energetic basis for understanding of TNF-α inhibition by antibodies and its unfolding linked with the concentration-dependent activity regulation.

Binding of flavonoids to staphylococcal enterotoxin B

Staphylococcal enterotoxins are metabolic products of Staphylococcus aureus that are responsible for the second-most-commonly reported type of food poisoning. Polyphenols are known to interact with proteins to form complexes, the properties of which depend on the structures of both the polyphenols and the protein. In the present study, we investigated the binding of four flavonoid polyphenols to Staphylococcal enterotoxin B (SEB) at pH 7.5 and 25 °C: (-)-epigallocatechin-3-gallate (EGCG), (-)-epigallocatechin (EGC), kaempferol-3-glucoside (KAM-G) and kaempferol (KAM). Fluorescence emission spectrometry and molecular docking were applied to compare experimentally determined binding parameters with molecular modeling. EGCG showed an order of magnitude higher binding constant (1.4 × 10(5) M(-1)) than the other studied polyphenols. Our blind-docking results showed that EGCG and similar polyphenolic ligands is likely to bind to the channel at the surface of SEB that is responsible for the recognition of the T-cell beta chain fragment and influence the adhesion of SEB to T cells.

Synthesis and Rotational Isomerism of 1-Substituted Methyl (S)-[5-(2-Nitrophenyl)-1H-pyrazole-4-carbonyl]alaninates

Seven title compounds 12a-g and the (S)-prolinate analogue 13 were prepared in five steps from 2-nitrobenzoic acid (7). Reduction of the nitro group followed by derivatization of the so formed anilines 14 gave the N-alkyl-(15a-c), N-acyl-(16a,b and 19), and N-vinyl derivative 20. NMR spectra of (S)-alanine and (S)-proline derived compounds 12, 13, 14-16, 19, and 20 exhibited two sets of signals corresponding to pairs of conformational diastereomers. The free energy barriers of rotation, ΔG(‡)298 = 82-86 kJ mol(-1), were determined by (1)H NMR for 12a, 12d, 12f, and 12g and evaluated by DFT calculations.

DNA–Polyelectrolyte Complexation Study: The Effect of Polyion Charge Density and Chemical Nature of the Counterions

Complexes of polycations and DNA, also known as polyplexes, have been extensively studied in the past decade, as potential gene delivery systems. Their stability depends strongly on the characteristics of the polycations, as well as the nature of the added salt. We present here a study of the DNA ionene complexation in which we used fluorescence, UV, and CD spectroscopy, combined with molecular dynamics computer simuations, to systematically examine the influence of the polycation charge density, as well as the influence of the nature of the counterion, on the stability of these systems. Ionenes as polycations, depending on their structural characteristics, have previously been found to possess low cytotoxicity, and are therefore particularly interesting as potential gene delivery agents. The results show that the DNA solutions in the presence of the polycation are more stable in the case of very large or very small ionene charge density, suggesting different mechanism of complexation. The computer simulations show that the ionenes with high charge density bind to the minor groove of the DNA molecules, while the ionenes with lower charge density bind to the major groove of the DNA. The nature of the counterions play only a minor role: precipitation of the DNA molecules occurs at slightly lower ionene concentration when fluoride counterion are present, compared to the bromide counterions.

Strategies for the Development of Small Molecule Inhibitors of Ebola Viral Infection

The recent outbreak of Ebola viral disease (EVD) in West Africa reminded us that an effective anti-viral treatment still does not exist, despite the significant progress that has recently been made in understanding biology and pathology of this lethal disease. Currently, there are no approved vaccine and/or prophylactic medication for the treatment of EVD in the market. However, the serious pandemic potential of EVD mobilized research teams in the academy and the pharmaceutical industry in the effort to find an Ebola cure as fast as possible. In this chapter, we are giving the condensed review of different approaches and strategies in search of a drug against Ebola. We have been focusing on the review of the targets that could be used for in silico, in vitro, and/or in vivo drug design of compounds that interact with the targets in different phases of the Ebola virus life cycle.