Konstantinos D. Papavasileiou

A Comprehensive Computational Study of the Interaction between Human Serum Albumin and Fullerenes

Human serum albumin (HSA) is the most abundant blood plasma protein, which transports fatty acids, hormones, and drugs. We consider nanoparticle-HSA interactions by investigating the binding of HSA with three fullerene analogs. Long MD simulations, quantum mechanical (fragment molecular orbital, energy decomposition analysis, atoms-in-molecules), and free energy methods elucidated the binding mechanism in these complexes. Such a systematic study is valuable due to the lack of comprehensive theoretical approaches to date. The main elements of the mechanism include the following: binding to IIA site results in allosteric modulation of the IIIA and heme binding sites with an increase in α-helical structure of IIIA. Fullerenes displayed high binding affinities for HSA; therefore, HSA can be used as a fullerene carrier, facilitating any toxic function the fullerene may exert. Complex formation is driven by hydrogen bonding, van der Waals, nonpolar, charge transfer, and dispersion energy contributions. Proper functionalization of C60 has enhanced its binding to HSA by more than an order of magnitude. This feature may be important for biological applications (e.g., photodynamic therapy of cancer). Satisfactory agreement with relevant experimental and theoretical data has been obtained.

A two-dimensional magnetic hybrid material based on intercalation of a cationic Prussian blue analog in montmorillonite nanoclay

A highly ordered two-dimensional hybrid magnetic nanocomposite has been prepared by synthesizing and intercalating a new cationic aluminum-hydroxy ferric ferrocyanide compound into a cation-adsorbing nanoclay (montmorillonite). Chemical and structural properties were investigated by X-ray diffraction, transmission electron microscopy, thermogravimetric and differential thermal analyses, Fourier transform infrared, X-ray photoemission, and Mössbauer spectroscopies. Elemental analysis was based on proton-induced gamma ray emission and X-ray fluorescence spectroscopy data, N/C elemental ratios, and cation-exchange capacity measurements. Magnetic properties were studied by SQUID magnetometry. The results suggest: (i) that the cationic Prussian blue analog comprises Al-hydroxy cations embedded into a monolayer thick two-dimensional ferric ferrocyanide array; and (ii) that the clay-Prussian blue nanohybrid consists of such arrays stacked between the clay layers. The latter material orders ferromagnetically at approximately 5K showing a hundred times higher remanence than that of the starting material, soluble Prussian blue (ammonium ferric ferrocyanide).

Computational investigation of fullerene-DNA interactions: Implications of fullerene’s size and functionalization on DNA structure and binding energetics

DNA is the building block of life, as it carries the biological information controlling development, function and reproduction of all organisms. However, its central role in storing and transferring genetic information can be severely hindered by molecules with structure altering abilities. Fullerenes are nanoparticles that find a broad spectrum of uses, but their toxicological effects on living organisms upon exposure remain unclear. The present study examines the interactions of a diverse array of fullerenes with DNA, by means of Molecular Dynamics and MM-PBSA methodologies, with special focus on structural deformations that may hint toxicity implications. Our results show that pristine and hydroxylated fullerenes have no unwinding effects upon DNA structure, with the latter displaying binding preference to the DNA major groove, achieved by both direct formation of hydrogen bonds and water molecule mediation. Fluorinated derivatives are capable of penetrating DNA structure, forming intercalative complexes with high binding affinities.

Elucidation of the binding mechanism of renin using a wide array of computational techniques and biological assays.

We investigate the binding mechanism in renin complexes, involving three drugs (remikiren, zankiren and enalkiren) and one lead compound, which was selected after screening the ZINC database. For this purpose, we used ab initio methods (the effective fragment potential, the variational perturbation theory, the energy decomposition analysis, the atoms-in-molecules), docking, molecular dynamics, and the MM-PBSA method. A biological assay for the lead compound has been performed to validate the theoretical findings. Importantly, binding free energy calculations for the three drug complexes are within 3 kcal/mol of the experimental values, thus further justifying our computational protocol, which has been validated through previous studies on 11 drug-protein systems. The main elements of the discovered mechanism are: (i) minor changes are induced to renin upon drug binding, (ii) the three drugs form an extensive network of hydrogen bonds with renin, whilst the lead compound presented diminished interactions, (iii) ligand binding in all complexes is driven by favorable van der Waals interactions and the nonpolar contribution to solvation, while the lead compound is associated with diminished van der Waals interactions compared to the drug-bound forms of renin, and (iv) the environment (H2O/Na(+)) has a small effect on the renin-remikiren interaction.

An integrated bacterial system for the discovery of chemical rescuers of disease-associated protein misfolding

Protein misfolding and aggregation are common pathological features of several human diseases, including Alzheimer’s disease and type 2 diabetes. Here, we report an integrated and generalizable bacterial system for the facile discovery of chemical rescuers of disease-associated protein misfolding. In this system, large combinatorial libraries of macrocyclic molecules are biosynthesized in Escherichia coli cells and simultaneously screened for their ability to rescue pathogenic protein misfolding and aggregation using a flow cytometric assay. We demonstrate the effectiveness of this approach by identifying drug-like, head-to-tail cyclic peptides that modulate the aggregation of the Alzheimer’s disease-associated amyloid β peptide. Biochemical, biophysical and biological assays using isolated amyloid β peptide, primary neurons and various established Alzheimer’s disease nematode models showed that the selected macrocycles potently inhibit the formation of neurotoxic amyloid β peptide aggregates. We also applied the system to the identification of misfolding rescuers of mutant Cu/Zn superoxide dismutase—an enzyme linked with inherited forms of amyotrophic lateral sclerosis. Overall, the system enables the identification of molecules with therapeutic potential for rescuing the misfolding of disease-associated polypeptides.A fluorescence-based assay is used to screen cyclic peptides for their activity in preventing protein misfolding, an event that can generate pathogenic aggregates that lead to diseases such as Alzheimer’s disease or amyotrophic lateral sclerosis..

CHAPTER 4:The Chemistry of Betaine

In this short overview, a summary and brief explanation of the most important biological functions of betaine is attempted, under the prism of its chemistry and physical properties behavior. Simply put, betaine is an organic molecule and its structure is that of the amino acid glycine, with the difference being that the amino group is trimethylated. Several plants have natural abundance of betaine, while humans either obtain betaine by food intake or synthesize it through choline oxidation. This molecule belongs to the general family of osmolytes, since it is found to play an osmoprotective role during osmotic stress environmental conditions in bacterial, plant and human cells. Moreover, betaine acts as a methyl donor during DNA methylation, resulting to a crucial organic molecule for biological processes of major importance for cells function. Betaine contributes to the stabilization of proteins as well as DNA structure, indirectly, namely through its direct interactions with water molecules close to the hydration shell of proteins and DNA. All the above-mentioned physicochemistry-related biological functions of betaine are briefly exhibited in this chapter.

Characterization of Water Solubility in n-Octacosane Using Raman Spectroscopy

In this study, we demonstrate the ability of polarization-difference Raman spectroscopy (PDRS) to detect dissolved free water molecules in a n-octacosane (n-C28H58) liquid-rich phase, and thus to determine its solubility, at temperatures and pressures relevant to the Fischer-Tropsch synthesis. Our results for the pure alkane reveal thermal decomposition above a temperature of 500 K as well as an increase of gauche conformers of the alkane chains with an increase in temperature. For binary homogeneous mixtures, raw spectra obtained from two different polarization scattering geometries did not show a relevant signal in the OH stretching frequency range. In contrast, isotropic spectra obtained from the PDRS technique reveal a narrow and tiny peak associated with the dangling OH bonds. Over the complete range of temperatures and pressures, no signature of hydrogen-bonded water molecules was observed in the isotropic Raman scattering intensities. A thorough investigation covering a large range of temperatures and pressures using PDRS signals showed that the higher the fraction of gauche conformers of hydrocarbon, the higher the solubility of water. The proportion of gauche and trans conformers was found to be water-concentration-independent, and the intensity of the OH-dangling peak increased linearly with increasing the vapor partial pressure of water. Therefore, we established a relation between a relevant intensity ratio and the concentration of water obtained from SAFT calculations. Contrary to the results from relevant literature, the calibration factor was found to be temperature-independent between 424 and 572 K. The isotropic Raman scattering intensities are corrected in order to provide a better representation of the vibrational density of states. The influence of correction of the isotropic scattering intensities on the solubility measurements as well as on the analysis of the molecular arrangement is discussed.

CHAPTER 8:Assays of Betaines using 1H NMR Spectroscopy

In this short review, an attempt is made to highlight the biological importance as well as the impact of glycine betaine and other N-methylated compounds, structurally similar to glycine betaine, revealed by 1H-NMR spectroscopy. Namely, glycine betaines, trimethylamines, trimethylamine-N-oxides, proline betaines, carnitines, cholines and trigonellines identification and quantification solely via 1H-NMR spectroscopy in complex biomixtures are pointed out through selected longitudinal research studies. Moreover, these indicative examples certify that these metabolites are not only essential for proper biological function of all kinds of living organisms but also their concentration-level variations establish them as nutritional and medicinal biomarkers. Simultaneously, 1H-NMR spectroscopy is proved to be a trustful, accurate, noninvasive analytical tool in modern biomedicine and pharmaceutical research fields.