Comparative molecular field analysis (CoMFA), a three-dimensional, quantitative structure-activity relationship (QSAR) paradigm, was used to examine the correlations between the calculated physicochemical properties and the in vitro activities of a series of human immunodeficiency virus (HIV-1) protease inhibitors. The training set consisted of 59 molecules from five structurally-diverse transition-state isostere classes: hydroxyethylamine, statine, norstatine, keto amide, and dihydroxyethylene. The availability of X-ray crystallographic data for at least one representative from each class bound to the protease provided information regarding not only the active conformation of each ligand but also, via superimposition of protease backbones, the relative positions of each ligand with respect to one another in the active site of the enzyme. Once aligned, these molecules served as templates on which additional congeners were field-fit minimized. Additional alignment rules were derived from minimizations of the ligands in the active site of the semirigid protease. The predictive ability of each resultant model was evaluated using a test set comprised of molecules containing a novel transition-state isostere: hydroxyethylurea. Crystallographic studies (Getman, D. P.; et al. J. Med. Chem. 1993, 36, 288-291) indicated an unexpected binding mode for this series of compounds which precluded the use of the field-fit minimization alignment technique. The test set molecules were, therefore, subjected to a limited systematic search in conjunction with active-site minimization. The conformer of each molecule expressing the lowest interaction energy with the active site was included in the test set. Field-fit minimization of neutral molecules to crystal ligands and active-site minimizations of protonated ligands yielded predictive correlations for HIV-1 protease inhibitors. The use of crystallographic data in the determination of alignment rules and field-fit minimization as a molecular alignment tool in the absence of direct experimental data regarding binding modes is strongly supported by these results.

Empirical force fields for minimum searching in the tryptophan-histidine intermolecular energy surface were used. Fourteen principal minima were identified. For each of these structures the intermolecular energies were computed by using single point correlated ab initio calculation with a split valence and a correlation consistent valence double-ζ basis set. The force field determined complexes have much larger correlated ab initio stabilization energy than those reported in previous studies where a purely ab initio search method was used. The largest stabilization energy was found for a T-shaped complex stabilized by a NH‚‚‚N hydrogen bond. Stacked structures with superimposed and parallel-displaced imidazole rings were also found to be very stable.

Histone deacetylases are promising molecular targets for the development of antitumor agents. A novel series of histone deacetylase inhibitors of the hydroxamic acid type were synthesized for structure-activity studies. Thirteen tricyclic dibenzodiazepine, -oxazepine, and -thiazepine analogues were studied and shown to induce variable degrees of histone H3/H4 and tubulin acetylation in a cellular model of myeloid leukemia sensitive to all-trans retinoic acid (ATRA). Multiparametric correlations between acetylation of the three substrates, tumor cell growth inhibition, and ATRAdependent cytodifferentiation were performed, providing information on the chemical functionalities governing these activities. For two analogues, antitumor activity in the animal was demonstrated.KEYWORDS HDAC inhibitors, hydroxamic acid, retinoic acid, antiproliferative effect, differentiation H istone deacetylase (HDAC) proteins are classified in four groups (class I-IV) based on function and sequence similarity. A common observation in neoplastic cells is high level expression of class I and II HDACs with corresponding hypoacetylation of histones.1 Increased HDAC activity may play a critical role in the pathogenesis of leukemia.2 HDACs of significance for cancer cell biology reside not only in the nucleus but also in the cytoplasm, where they act on substrates other than histones. Within class I, HDACs 1, 2, and 8 are primarily found in the nucleus. Class II HDACs (HDAC 4, 5, 6, 7, 9, and 10) are able to shuttle in and out of the nucleus depending on different signals.3 HDAC 6 is primarily a cytoplasmic enzyme, deacetylating proteins like tubulin, Hsp90, and cortactin. 4 Transformed cells are generally more sensitive to HDAC inhibitor-induced growth inhibition and apoptosis than their normal counterparts.5 Hence, anticancer therapeutic strategies based on HDAC inhibitors have raised significant interest. Some of the most powerful natural and synthetic HDAC inhibitors 6 are derivatives of hydroxamic acid. Here, we describe the chemical synthesis and the pharmacologic characterization of a novel series of hydroxamic acid derivatives characterized by tricyclic dibenzo-diazepine, -oxazepine, and -thiazepine rings. As the catalytic domain of all HDAC isoforms is highly conserved, 7 our approach was to design novel molecules targeting the variable external part of the channel leading to the catalytic center. We studied the effects of a limited number of systematic modifications to the tricyclic core, keeping the hydroxamic group and the linker chain of our molecules constant. The tricyclic core was selected, as structural modifications affecting hydrogen bonding, electronic features, and angles between the two aromatic rings can be easily obtained by accessible chemical modifications. Test compounds (0.01, 0.1, 1.0, 10, and 50 μM) were initially screened using an enzymatic assay measuring the total HDAC activity in HeLa cell extracts, which resulted in the selection of 13 molecules. Scheme 1 illustrates the synthesis and structures o...

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