3D-QSAR using 'multiconformer' alignment: the use of HASL in the analysis of 5-HT1A thienopyrimidinone ligands.

The observed 5-HT1A and alpha1-adrenergic receptor (alpha1-AR) receptor binding properties of a series of 23 thienopyrimidinones were used to develop HASL 3D-QSAR models. A single, low energy conformer of the most active analogue in the series, which was consistent with NMR structural studies, was chosen as a template molecule. Alignments of all the molecules to the template were provided by an Amber/MM2 superposition force field. In this manner, each molecule was represented by five separate low energy conformers which were subsequently used in the generation of HASL 3D-QSAR models. Models derived from multiple conformers were found to exhibit enhanced predictivity compared to models based on single, low energy conformers. In addition, the use of contour imaging of HASL multi-conformer model interactions was found to lead to a more consistent interpretation of those molecular features most significant for 5-HT1A receptor binding.

Comparison of 3D quantitative structure-activity relationship methods: analysis of the in vitro antimalarial activity of 154 artemisinin analogues by hypothetical active-site lattice and comparative molecular field analysis.

Two three-dimensional quantitative structure-activity relationship (3D-QSAR) methods, comparative molecular field analysis (CoMFA) and hypothetical active site lattice (HASL), were compared with respect to the analysis of a training set of 154 artemisinin analogues. Five models were created, including a complete HASL and two trimmed versions, as well as two CoMFA models (leave-one-out standard CoMFA and the guided-region selection protocol). Similar r2 and q2 values were obtained by each method, although some striking differences existed between CoMFA contour maps and the HASL output. Each of the four predictive models exhibited a similar ability to predict the activity of a test set of 23 artemisinin analogues, although some differences were noted as to which compounds were described well by either model.

Antiulcer agents. 6. Analysis of the in vitro biochemical and in vivo gastric antisecretory activity of substituted imidazo[1,2-a]pyridines and related analogues using comparative molecular field analysis and hypothetical active site lattice methodologies.

A number of substituted imidazo[1,2-a]pyridines and related analogues were selected for analysis of their in vitro biochemical and in vivo gastric antisecretory activity using comparative molecular field analysis (CoMFA) and hypothetical active site lattice (HASL) methodologies. The training set of compounds selected included those that were also chosen for an extensive molecular modeling study initiated, using the active analog approach, to define the pharmacophore by means of which 1 and its analogues interact with the gastric proton pump enzyme, H+/K(+)-ATPase. Using either CoMFA or HASL, it was possible to identify an optimal alignment paradigm of the proposed bioactive conformation for this series to reasonably predict the in vitro H+/K(+)-ATPase inhibitory potency in the purified enzyme model and the in vivo intravenous gastric antisecretory activity for compounds outside of the training set. Furthermore, the steric and electrostatic effects suggested by these two independent methods and their influence on determining biological activity were consistent and complementary to each other.

Three-dimensional pharmacophores from binding data.

The application of HASL (hypothetical active site lattice) methodology has been successfully extended to generate putative pharmacophoric patterns in three dimensions capable of quantitatively predicting binding activity. The transformation of a HASL model to a pharmacophore is illustrated using pKi values published for 84 HIV-1 protease inhibitors. Starting with a HASL model generated at 2.00 A and containing 899 lattice points, a selective trimming process was used to identify significant lattice points. In this manner, a set of 11 points was found which represents a potential pharmacophoric pattern and predicts the pKi activity of the 84-inhibitor set with a correlation (r2) of 0.827. Furthermore, the locations of these points were found to coincide with a number of strategic binding areas within the known active site structure HIV-1 protease, thus providing a physical confirmation of their relevancy.

An application of 3D-QSAR to the analysis of the sequence specificity of DNA alkylation by uracil mustard.

The sequence specificity of DNA alkylation by uracil mustard was examined using a novel three-dimensional QSAR method known as HASL, or the hypothetical active site lattice. The structures of a variety of 4-mer sequences obtained from pBR322 and SV40 were related to their degree of guanine-N7 alkylation by uracil mustard. The resulting correlations were found to point to a significant contribution from bases on the 3' side of the target guanine nucleotide. The HASL models derived from the analysis of 52 guanine-containing 4-mer sequences were used to highlight those atomic features in the favored TGCC sequence that were found most important in determining specificity. It was found that the NH2-O systems present in the two GC base pairs on the 3' side of the target guanine were significantly correlated to the degree of alkylation by uracil mustard. This finding is consistent with a prealkylation binding event occurring between these sites along the major groove and the uracil mustard O2/O4 system.

The hypothetical active site lattice. An approach to modelling active sites from data on inhibitor molecules.

Microcomputer-assisted methods are described that allow the mathematical construction of a hypothetical active site lattice (HASL) which can model enzyme-inhibitor interactions and provides predictive structure-activity relationships for a set of competitive inhibitors. The inhibitor set can be structurally dissimilar, including acyclic and cyclic moieties normally refractory to classical parameter-based quantitative structure-activity relationship strategies. With use of three-dimensional Cartesian coordinates representing energy-minimized inhibitor conformations, a four-dimensional space-filling description is generated, wherein the fourth dimension can be a user-selected physiochemical property such as hydrophobicity or electron density. The multidimensional lattices thus generated are used to quantitatively compare molecules to one another. Composite lattices of more than one molecule are merged with binding data to form a HASL capable of predicting inhibitor binding and relative orientation. Details of the algorithms and assumptions utilized are illustrated for competitive inhibitors of yeast glyoxalase-I and E. coli dihydrofolate reductase.

Quantitative structure-activity relationships for 2-[(phenylmethyl)sulfonyl]pyridine 1-oxide herbicides.

Phenyl-substituted analogues of 2-[(phenylmethyl)sulfonyl]pyridine 1-oxide preemergent herbicides were examined in order to determine quantitative relationships between structure and activity against the following three weed species: switch grass (Panicum virgatum L.), barnyard grass (Echinochloa crusgalli L. Beauv.), and green foxtail (Setaria viridis L. Beauv.). Analogues were chosen to provide maximum parameter orthogonality. Regression analysis yielded structure-activity relationships wherein the most significant substituent parameters associated with herbicidal activity were found to be the partition coefficient (pi), the molar refractivity (MR), and two indicator variables, Z (denoting the presence of an alpha-methyl group) and H (denoting an ortho substituent capable of hydrogen bonding). For green foxtail, the structure-activity relationship was found to be: -log ED50 = 0.43 pi -0.052MR + 0.50H + 0.24Z + 0.61, where ED50 is expressed in moles per acre. The regression equations were found to explain 79-93% of the bioactivity for the three weed species studied. It was further shown that these equations represent the best possible correlations within the limitations of the biological data.

Synthesis and evaluation of alpha-hydroxythiol esters as antitumor agents and glyoxalase I inhibitors.

Synthesis of a series of alpha-hydroxythiol esters made available, for the first time, product-like molecules that were evaluated as inhibitors of the enzyme glyoxalase I and as potential antitumor agents. All the alpha-hydroxythiol esters tested were competitive inhibitors of the enzyme, albeit weak; however, the relative [I]50 values suggested information about the active site. Antileukemic activity in L1210 lymphoid leukemia indicated no significant activity by these alpha-hydroxythiol esters.