Putative active site template model for cytochrome P4502C9 (tolbutamide hydroxylase).

Binding of substrates to the active site of cytochrome P450 enzymes largely relies on hydrophobic interactions. However, other binding interactions can take place giving the enzyme high regioselectivity and even stereoselectivity. For instance, within the major human cytochrome P450s involved in drug metabolism, cytochrome P4502D6 (CYP2D6) relies on an ion-pair interaction as a major binding factor. There are now a number of substrates reported that have routes of metabolism ascribed specifically to cytochrome P4502C9 (CYP2C9), the isoform mainly responsible for tolbutamide hydroxylation. Although chemically diverse, these substrates have the capability to be hydrogen bond donors (or acceptors). The substrate specificity has been rationalized in terms of a hydrogen bond donor/acceptor model and, by use of molecular modeling, an active site template model for CYP2C9 has been generated. The substrates modeled were phenytoin, warfarin, ibuprofen, naproxen, diclofenac, delta 1-tetrahydrocannabinol, 58C80, and tolbutamide. In addition to the substrates, the potent, selective inhibitor sulfaphenazole was also included in the modeling. An initial hydrogen bond donor site (N2) was identified on phenytoin, the most rigid of the substrates. Corresponding hydrogen bond donation sites were then identified on all of the molecules studied. Using molecular modeling, the site of metabolism and the hydrogen bond donation sites of the molecules were then overlaid on phenytoin to produce the putative active site model. The resultant model is described by a, the distance between the site of metabolism (Y), and the hydrogen bond donor heteroatom (X) and C, the angle between this and the hydrogen bond. The mean dimensions (+/- SD) for the nine substrates and one inhibitor (a = 6.7 +/- 1.0 A, C = 133 +/- 21 degrees) illustrate the degree of overlap achieved.

Determination of receptor-bound drug conformations by QSAR using flexible fitting to derive a molecular similarity index.

Results are presented for a QSAR analysis of bisamidines, using a similarity index as descriptor. The method allows for differences in conformation of bisamidines at the receptor site to be taken into consideration. In particular, it has been suggested by others that pentamidine binds in the minor groove of DNA in a so-called isohelical conformation, and our QSAR supports this suggestion. The molecular similarity index for comparison of molecules can be used as a parameter for correlating and hence rationalising the activity as well as suggesting the design of bioactive molecules. The studied compounds had been evaluated for potency against Leishmania mexicana amazonensis, and this potency was used as a dependent variable in a series of QSAR analyses. For the calculation of similarity indexes, each analogue was in turn superimposed on a chosen lead compound in a reference conformation, either extended or isohelical, maximising overlap and hence similarity by flexible fitting.

A molecular modelling study of the interaction of noradrenaline with the beta 2-adrenergic receptor.

A model of the beta 2-adrenergic receptor binding site is built from the primary structure of the receptor, experimental evidence for key binding residues and analogy with a homologous protein of partially determined structure. It is suggested that residues Trp-109, Thr-110 and Asp-113 are involved in ligand binding. Noradrenaline is successfully docked into this model, and the results of an INDO molecular orbital calculation on the complex indicate that a charge transfer interaction between Trp-109 and noradrenaline is possible.

1,3-Diamino-6,7-dimethoxyisoquinoline derivatives as potential alpha 1-adrenoceptor antagonists.

Treatment of 2-methyl-4,5-dimethoxybenzonitrile (3) with LDA followed by reaction with an N,N-disubstituted cyanamide provided a series of 1,3-diamino-6,7-dimethoxyisoquinolines (2), which were evaluated for alpha-adrenoceptor binding affinity and antihypertensive activity. 1-Amino-3-(dimethylamino)-6,7-dimethoxyisoquinoline (4) showed no significant affinity (Ki much greater than 10(-6) M) for alpha 1-adrenoceptors, while the corresponding 3-(2-furoylpiperazin-1-yl) analogue (8; Ki = 1.6 X 10(-7) M) was some 1000-fold less potent than prazosin. pKa data showed that N-2 protonation (34%) of 4 (pKa = 7.1) would occur at physiological pH, in agreement with X-ray crystallographic analysis of 8.HCl. Comparison of positive charge distribution following protonation of 4 with the corresponding quinoline and quinazoline cations confirmed N-1 protonation is required for these heterocyclic nuclei to bind efficiently to the alpha 1-adrenoceptor. Computer-assisted comparison of the X-ray structures of 8 and prazosin suggested that the 4.0 kcal/mol difference in alpha 1-adrenoceptor binding energies was largely due to salt-bridge formation (ca. 3.0 kcal/mol) between the protonated quinazoline and the receptor protein. None of the isoquinolines (2) proved to be effective antihypertensive agents in rats even when administered at relatively high doses (10 mg/kg). These results support the hypothesis that the antihypertensive activity of prazosin, doxazosin, and related derivatives derives solely from alpha 1-adrenoceptor blockade.

A theoretical study of angiotensin-converting enzyme inhibitors.

INDO molecular orbital calculations are reported for 35 selected angiotensin-converting enzyme inhibitors. QSARs are developed between pI50 data and molecular electronic indices. The QSARs obtained reflect the importance of both charge-charge interactions between inhibitor and receptor and of specific interactions between groups on the inhibitor with points around the molecule which are postulated to correspond to binding sites at the receptor.

Rationalization of drug complexation in aqueous solution by use of Hückel frontier molecular orbitals.

The complexation of certain drug molecules with niacinamide in aqueous solution was explained by the application of Hückel frontier molecular orbital calculations. A linear relationship was observed between the association constants derived from phase solubility studies and the interaction energy predicted by frontier molecular orbital calculations.