Biomedical subjects

M J de Groot

Publications and source records attributed to M J de Groot.

39 records · Page 3Linked to original sources

PubMedDate not supplied

A predictive substrate model for rat glutathione S-transferase 4-4.

Molecular modeling techniques have been used to derive a substrate model for class mu rat glutathione S-transferase 4-4 (GST 4-4). Information on regio- and stereoselective product formation of 20 substrates covering three chemically and structurally different classes was used to construct a substrate model containing three interaction sites responsible for Lewis acid--Lewis base interactions (IS1, IS2, and IS3), as well as a region responsible for aromatic interactions (IS4). Experimental data suggest that the first protein interaction site (pIS1, interacting with IS1) corresponds with Tyr115, while the other protein interaction sites (pIS2 and pIS3) probably correspond with other Lewis acidic amino acids. All substrates exhibited positive molecular electrostatic potentials (MEPs) near the site of conjugation with glutathione (GSH), as well as negative MEP values near the position of groups with Lewis base properties (IS1, IS2, or IS3), which interact with pIS1, pIS2, or pIS3, respectively. Obviously, complementarity between the MEPs of substrates and protein in specific regions is important. The substrate specificity and stereoselectivity of GST 4-4 are most likely determined by pIS1 and the distance between the site of GSH attack and Lewis base atoms in the substrates which interact with either pIS2, pIS3, or a combination of these sites. Interaction between aromatic regions in the substrate with aromatic amino acids in the protein further stabilizes the substrate in the active site. The predictive value of the model has been evaluated by rationalizing the conjugation to GSH of 11 substrates of GST 4-4 (representing 3 classes of compounds) which were not used to construct the model. All known metabolites of these substrates are explained with the model. As the computer-aided predictions appear to correlate well with experimental results, the presented substrate model may be useful to identify new potential GST 4-4 substrates.

7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide↗

PubMedDate not supplied

A homology model for rat mu class glutathione S-transferase 4-4.

Glutathione S-transferases (GSTs) are an important class of phase II (de)toxifying enzymes, catalyzing the conjugation of glutathione (GSH) to electrophilic species. Recently, a number of cytosolic GSTs was crystallized. In the present study, molecular modeling techniques have been used to derive a three-dimensional homology model for rat GST 4-4 based upon the crystal structure of rat GST 3-3, both members of the mu class. GST 3-3 and GST 4-4 isoenzymes share a sequence homology of 88%. GST 4-4 distinguishes itself from GST 3-3 in being much more efficient and stereoselective in the nucleophilic addition of GSH to epoxides and alpha,beta-unsaturated ketones. GST 3-3, however, is much more efficient in catalyzing nucleophilic aromatic substitution reactions. In this study, several known substrates of GST 4-4 were selected and their GSH conjugates docked into the active site of GST 4-4. GSH conjugates of phenanthrene 9(S),10(R)-oxide and 4,5-diazaphenanthrene 9(S),10(R)-oxide were docked into the active site of both GST 3-3 and GST 4-4. From these homology modeling and docking data, the difference in stereoselectivity between GST 3-3 and GST 4-4 for the R- and S-configured carbons of the oxirane moiety could be rationalized. The data acquired from a recently derived small molecule model for GST 4-4 substrates were compared with the results of the present protein homology model of GST 4-4. The energy optimized positions of the conjugates in the protein model agreed very well with the original relative positions of the substrates within the substrate model, confirming the usefulness of small molecule models in the absence of structural protein data. The protein homology model, together with the substrate model, will be useful to further rationalize the substrate selectivity of GST 4-4, and to identify new potential GST 4-4 substrates.

Amino Acid Sequence↗

PubMedDate not supplied

A three-dimensional protein model for human cytochrome P450 2D6 based on the crystal structures of P450 101, P450 102, and P450 108.

Cytochromes P450 (P450s) constitute a superfamily of phase I enzymes capable of oxidizing and reducing various substrates. P450 2D6 is a polymorphic enzyme, which is absent in 5-9% of the Caucasian population as a result of a recessive inheritance of gene mutations. This deficiency leads to impaired metabolism of a variety of drugs. All drugs metabolized by P450 2D6 contain a basic nitrogen atom, and a flat hydrophobic region coplanar to the oxidation site which is either 5 or 7 A away from the basic nitrogen atom. The aim of this study was to build a three-dimensional structure for the protein and more specifically for the active site of P450 2D6 in order to determine the amino acid residues possibly responsible for binding and/ or catalytic activity. Furthermore, the structural features of the active site can be implemented into the existing small molecule substrate model, thus enhancing its predictive value with respect to possible metabolism by P450 2D6. As no crystal structures are yet available for membrane-bound P450s (such as P450 2D6), the crystal structures of bacterial (soluble) P450 101 (P450cam), P450 102 (P450BM3), and P450 108 (P450terp) have been used to build a three-dimensional model for P450 2D6 with molecular modeling techniques. Several important P450 2D6 substrates were consecutively docked into the active site of the protein model. The energy optimized positions of the substrates in the protein agreed well with the original relative positions of the substrates within the substrate model. This confirms the usefulness of small molecule models in the absence of structural protein data. Furthermore, the derived protein model indicates new leads for experimental validation and extension of the substrate model.

Amino Acid Sequence↗