In order to investigate features essential for the modes of action of MAO, we have calculated pKa values of three relevant tyrosine residues in the MAO B active site, with and without dopamine bound as the substrate (as well as the pKa of the dopamine itself in the active site). In conjunction with additional experimental and computational work, the data presented here should lead toward a deeper understanding of mechanisms of the catalytic activity and irreversible inhibition of MAO B, which can allow for the design of novel and improved MAO B inhibitors.
COBISS.SI-ID: 4948506
Hydration of histamine was examined by infrared spectroscopy and Car Parrinello molecular dynamics simulation. Histamine is a neurotransmitter and inflammation mediator, which at physiological pH conditions is present mainly in monocationic form. Our focus was on the part of vibrational spectra that corresponds to histamine NH stretching, since these degrees of freedom are essential for its interactions with either water molecules or transporters and receptors. Assignment of the experimental spectra revealed a broad feature between 3350 and 2300 cm(1), being centered at 2950 cm(1), which includes a mixed contribution from the ring NH and the aminoethyl NH stretching vibrations. Computational analysis was performed in two ways: first, by making Fourier transformation on the autocorrelation function of all four NH bond distances recorded during CPMD run, and second, and most importantly, by incorporating quantum effects through applying an a posteriori quantization of all NH stretching motions utilizing our snapshot analysis of the fluctuating proton potential. The one dimensional vibrational Schroedinger equation was solved numerically for each snapshot, and the NH stretching envelopes were calculated as a superposition of the 0)1 transitions. The agreement with the experiment was much better in the case of the second approach. Our calculations clearly demonstrated that the ring amino group absorbs at higher frequencies than the remaining three amino NH protons of the protonated aminoethyl group, implying that the chemical bonding in the former group is stronger than in the three amino NH bonds, thus forming weaker hydrogen bonding with the surrounding solvent molecules. In this way the results of the simulation complemented the experimental spectrum that cannot distinguish between the two sets of protons. The effects of deuteration were also considered. The resulting ND absorption is narrower and redshifted. The presented methodology is of general applicability to strongly correlated systems, and it is particularly tuned to provide computational support to vibrational spectroscopy. Perspectives are given for its future applications in computational studies of tunneling in enzyme reactive centers and for receptor activation.
COBISS.SI-ID: 4658202
Monoamine oxidases (MAOs) are flavoenzymes important in regulating amine neurotransmitter levels and are the central pharmacological targets in treating depression and Parkinson disease. On the basis of quantum chemical calculations, we have proposed a new twostep hydride mechanism for the MAO-catalysed oxidative deamination of amines. In the ratelimiting first step, through its N5 atom, the flavin abstracts a hydride anion from the substrate alpha carbon atom and forms a strong covalent adduct with the thus created cation. This is followed by flavin N1 deprotonation of the substrate amino group, facilitated with two active-site water molecules, to produce fully reduced flavin, FADH2, and neutral imine. We have demonstrated that our mechanism is in agreement with available experimental data and provided evidence against both traditional polar nucleophilic and single electron radical pathways. These results provide valuable information for mechanistic studies on other flavoenzymes and for the design of new antidepressants and antiparkinsonian drugs.
COBISS.SI-ID: 5142810
Starting from the available structural information about the binding of the natural product inhibitor, clorobiocin, we identified a novel series of 4,5`bithiazoles inhibitors of the DNA gyrase B with a low micromolar inhibitory activity, by implementing a two-step structure-based design procedure. This novel class of DNA gyrase inhibitors was extensively investigated by various techniques: Differential Scanning Fluorimetry (DSF), Surface Plasmon Resonance (SPR) and microscale thermophoresis (MST). The binding mode of the most potent inhibitor was revealed by X-ray crystallography, confirming our initial in silico binding model.
COBISS.SI-ID: 4999450
DNA topoisomerases comprise an important family of enzymes that catalyse the induction of topological changes in the DNA molecule. Due to their ability to modulate the topology of the DNA molecule, represent an important collection of design targets for novel anticancer drugs. The published review provides an overview of the development of catalytic inhibitors of the human topoisomerase II enzyme as potential novel anticancer agents. The group of catalytic topoII inhibitors is classified into four types according to their molecular mechanism of action: inhibitors that bind to the ATP binding site, inhibitors that prevent the ATP hydrolysis step and trap the enzyme in a closed clamp, inhibitors that block the DNA cleavage and inhibitors that prevent the enzyme binding to the DNA.
COBISS.SI-ID: 5190682