Flavonoids are a group of naturally occurring antioxidants, which over the past years have gained tremendous interest because of their possible therapeutic applicability. The mechanism of their antioxidant activity has been extensively studied over several decades. However, there is still much confusion about the molecular mechanism of radical scavenging and the relationship between structure and activity. Therefore, we have calculated the heat of formation and the geometry of both the parent compound and the corresponding radical using the ab initio program GAMESS. We have compared their differences in energy in order to gain insight into the stability of the radical and the ease with which it is formed. We have also investigated the spin density of the radical, to determine the delocalization possibilities. These calculated data were compared with experimental data from ESR (hyperfine coupling constants) and electrochemical oxidation (Ep/2) and were found to be in good agreement. By comparing the geometries of several flavonoids, we were able to explain the structural dependency of the antioxidant action of these compounds. The extremely good antioxidant activity of the flavonols could be explained by the formation of an intramolecular hydrogen bond.

Molecular modeling techniques were used to derive a predictive model for substrates of cytochrome P450 2D6, an isozyme known to metabolize only compounds with one or more basic nitrogen atoms. Sixteen substrates, accounting for 23 metabolic reactions, with a distance of either 5 A ("5-A substrates", e.g., debrisoquine) or 7 A ("7-A substrates", e.g., dextromethorphan) between oxidation site and basic nitrogen atom were fitted into one model by postulating an interaction of the basic nitrogen atom with a negatively charged carboxylate group on the protein. This acidic residue anchors and neutralizes the positively charged basic nitrogen atom of the substrates. In case of "5-A substrates" this interaction probably occurs with the carboxylic oxygen atom nearest to the oxidation site, whereas in the case of "7-A substrates" this interaction takes place at the other oxygen atom. Furthermore, all substrates exhibit a coplanar conformation near the oxidation site and have negative molecular electrostatic potentials (MEPs) in a part of this planar domain approximately 3 A away from the oxidation site. No common features were found in the neighbourhood of the basic nitrogen atom of the substrates studied so that this region of the active site can accommodate a variety of N-substituents. Therefore, the substrate specificity of P450 2D6 most likely is determined by the distance between oxidation site and basic nitrogen atom, by steric constraints near the oxidation site, and by the degree of complementarity between the MEPs of substrate and protein in the planar region adjacent to the oxidation site.(ABSTRACT TRUNCATED AT 250 WORDS)

A homology model building study of cytochrome P450 2D6 has been carried out based on the crystal structure of cytochrome P450 101. The primary sequences of P450 101 and P450 2D6 were aligned by making use of an automated alignment procedure. This alignment was adjusted manually by matching alpha-helices (C, D, G, I, J, K and L) and beta-sheets (beta 3/beta 4) of P450 101 that are proposed to be conserved in membrane-bound P450s (Ouzounis and Melvin [Eur. J. Biochem., 198 (1991) 307]) to the corresponding regions in the primary amino acid sequence of P450 2D6. Furthermore, alpha-helices B, B' and F were found to be conserved in P450 2D6. No significant homology between the remaining regions of P450 101 and P450 2D6 could be found and these regions were therefore deleted. A 3D model of P450 2D6 was constructed by copying the coordinates of the residues from the crystal structure of P450 101 to the corresponding residues in P450 2D6. The regions without a significant homology with P450 101 were not incorporated into the model. After energy-minimization of the resulting 3D model of P450 2D6, possible active site residues were identified by fitting the substrates debrisoquine and dextrometorphan into the proposed active site. Both substrates could be positioned into a planar pocket near the heme region formed by residues Val370, Pro371, Leu372, Trp316, and part of the oxygen binding site of P450 2D6. Furthermore, the carboxylate group of either Asp100 or Asp301 was identified as a possible candidate for the proposed interaction with basic nitrogen atom(s) of the substrates.(ABSTRACT TRUNCATED AT 250 WORDS)

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The cytochrome P-450 mediated activation of paracetamol (PAR) to the reactive electrophilic intermediate N-acetyl-p-benzoquinone imine (NAPQI) has been studied by use of SV 6-31G ab initio energy calculations and spin distributions. A simplified model for cytochrome P-450 has been used by substituting the proposed biologically active ferric-oxene state of cytochrome P-450 by a singlet oxygen atom. The results indicate that an initial hydrogen abstraction from the phenolic hydroxyl group is favored by 30.1 kcal/mol over an initial hydrogen abstraction from the acetylamino nitrogen atom. Metabolic activation of PAR via primary formation of a phenoxy radical seems the most likely mechanism. The calculated ab initio spin densities indicate that the radical formed by hydrogen abstraction from the phenolic hydroxyl group stays predominantly localized at the phenolic oxygen. A second hydrogen abstraction from the acetylamino nitrogen atom, giving rise to the reactive intermediate NAPQI, is then favored in terms of energy differences. The unpaired electron of the phenoxy radical was found to delocalize only to a small extent toward the carbon atoms at the ortho and para positions relative to the hydroxyl-containing ring carbon, but nevertheless a recombination reaction between a hydroxyl radical and these radicalized carbon atoms at the ortho or para positions could explain the formation of the minor metabolites 3-hydroxy-PAR and p-benzoquinone plus acetamide.