Potent antimicrobial small molecules screened as inhibitors of tyrosine recombinases and Holliday junction-resolving enzymes.

Holliday junctions (HJs) are critical intermediates in many recombination-dependent DNA repair pathways. Our lab has previously identified several hexameric peptides that target HJ intermediates formed in DNA recombination reactions. One of the most potent peptides, WRWYCR, is active as a homodimer and has shown bactericidal activity partly because of its ability to interfere with DNA repair proteins that act upon HJs. To increase the possibility of developing a therapeutic targeting DNA repair, we searched for small molecule inhibitors that were functional surrogates of the peptides. Initial screens of heterocyclic small molecule libraries resulted in the identification of several N-methyl aminocyclic thiourea inhibitors. Like the peptides, these inhibitors trapped HJs formed during recombination reactions in vitro, but were less potent than the peptides in biochemical assays and had little antibacterial activity. In this study, we describe the screening of a second set of libraries containing somewhat larger and more symmetrical scaffolds in an effort to mimic the symmetry of a WRWYCR homodimer and its target. From this screen, we identified several pyrrolidine bis-cyclic guanidine inhibitors that also interfere with processing of HJs in vitro and are potent inhibitors of Gram-negative and especially Gram-positive bacterial growth. These molecules are proof-of-principle of a class of compounds with novel activities, which may in the future be developed into a new class of antibiotics that will expand the available choices for therapy against drug-resistant bacteria.

Small molecule functional analogs of peptides that inhibit lambda site-specific recombination and bind Holliday junctions.

Our lab has isolated hexameric peptides that are structure-selective ligands of Holliday junctions (HJ), central intermediates of several DNA recombination reactions. One of the most potent of these inhibitors, WRWYCR, has shown antibacterial activity in part due to its inhibition of DNA repair proteins. To increase the therapeutic potential of these inhibitors, we searched for small molecule inhibitors with similar activities. We screened 11 small molecule libraries comprising over nine million individual compounds and identified a potent N-methyl aminocyclic thiourea inhibitor that also traps HJs formed during site-specific recombination reactions in vitro. This inhibitor binds specifically to protein-free HJs and can inhibit HJ resolution by RecG helicase, but only showed modest growth inhibition of bacterial with a hyperpermeable outer membrane; nonetheless, this is an important step in developing a functional analog of the peptide inhibitors.

Identification of potent and highly selective chiral tri-amine and tetra-amine mu opioid receptors ligands: an example of lead optimization using mixture-based libraries.

The generation of chiral polyamine libraries has been successfully accomplished in our laboratory following exhaustive reduction of resin-bound peptides. Herein, we report the synthesis and screening results of a positional scanning mixture-based library of chiral hepta-amines in a radioreceptor assay for the opioid receptor. The positional scanning hepta-amine library was generated by the exhaustive reduction of a library of 34,012,070 hexapeptides. Following screening of the entire library, combinations of the most active functionalities found at each position were used to synthesize and screen 40 individual hepta-amines and served as starting 'hits' for further SAR studies. The individual compounds showed IC(50) values ranging from 14 to 345 nM. As might be anticipated by the known studies of mu opiate antagonists, the identified active hepta-amines possessed aromatic rings derived from phenylalanine and tyrosine amino acid side chains. Following SAR studies, a truncation analog, reduced and permethylated YYF-NH(2), was found to be highly active (0.5 nM) as a selective mu antagonist in the guinea pig ileum bioassay.

Solid phase synthesis of 3,4,7-trisubstituted 4,5,8,9-tetrahydro-3H-imidazo[1,2-a][1,3,5]triazepin-2(7H)-thiones and N-alkyl-4,5,7,8-tetrahydro-3H-imidazo[1,2-a][1,3,5]triazepin-2-amines.

The solid-phase parallel synthesis of 3,4,7-trisubstituted 4,5,8,9-tetrahydro-3H-imidazo[1,2-a][1,3,5]triazepin-2(7H)-thiones and N-alkyl-4,5,7,8-tetrahydro-3H-imidazo[1,2-a][1,3,5]triazepin-2-amines starting from resin-bound dipeptides is described. The key synthetic steps involve the cylization of an amino and a guanidino functionality using thiocarbonyldiimidazole and the subsequent transformation of the resulting thiourea moiety to a substituted guanidine group using HgCl(2) and various amines. Following cleavage from the resin, the desired products were obtained in good yields and good to moderate purities, depending on the building blocks employed.

Combinatorial chemistry: libraries from libraries, the art of the diversity-oriented transformation of resin-bound peptides and chiral polyamides to low molecular weight acyclic and heterocyclic compounds.

Combinatorial chemistry has deeply impacted the drug discovery process by accelerating the synthesis and screening of large numbers of compounds having therapeutic and/or diagnostic potential. These techniques offer unique enhancement in the potential identification of new and/or therapeutic candidates. Our efforts over the past 10 years in the design and diversity-oriented synthesis of low molecular weight acyclic and heterocyclic combinatorial libraries derived from amino acids, peptides, and/or peptidomimetics are described. Employing a "toolbox" of various chemical transformations, including alkylation, oxidation, reduction, acylation, and the use of a variety of multifunctional reagents, the "libraries from libraries" concept has enabled the continued development of an ever-expanding, structurally varied series of organic chemical libraries.

A traceless approach for the solid-phase synthesis of 6-amino-1,3,5-triazine-2,4-diones.

A traceless approach for the solid-phase synthesis of 6-amino-1,3,5-triazine-2,4-diones is described. Reaction of resin-bound S-methylisothiourea with isocyanates yielded resin-bound iminoureas 3, which reacted with amines to afford the corresponding guanidines 4. Following intramolecular cyclizative cleavage of the resin-bound guanidines using potassium ethoxide as a base, the desired products 5 were obtained in good yields and high purities.

Small-molecule antagonists of apoptosis suppressor XIAP exhibit broad antitumor activity.

Apoptosis resistance commonly occurs in cancers, preventing activation of Caspase family cell death proteases. XIAP is an endogenous inhibitor of Caspases overexpressed in many cancers. We developed an enzyme derepression assay, based on overcoming XIAP-mediated suppression of Caspase-3, and screened mixture-based combinatorial chemical libraries for compounds that reversed XIAP-mediated inhibition of Caspase-3, identifying a class of polyphenylureas with XIAP-inhibitory activity. These compounds, but not inactive structural analogs, stimulated increases in Caspase activity, directly induced apoptosis of many types of tumor cell lines in culture, and sensitized cancer cells to chemotherapeutic drugs. Active compounds also suppressed growth of established tumors in xenograft models in mice, while displaying little toxicity to normal tissues. These findings validate IAPs as targets for cancer drug discovery.

The combined solid/solution-phase synthesis of nitrosamines: the evolution of the "libraries from libraries" concept.

The generation of diverse chemical libraries using the "libraries from libraries" concept by combining solid-phase and solution-phase methods is described. The central features of the approaches presented are the use of solid-phase synthesis methods for the generation of a combinatorial polyamine library. Following cleavage from the resin with HF, the polyamine library was reacted with ethyl nitrite in the solution phase to yield the desired nitrosamine library in good yield and purity. The approaches described enable the efficient syntheses of individual nitrosamines as well as mixture-based nitrosamine libraries.

Use of Vilsmeier reagent for the solid-phase synthesis of 1,5-disubstituted 4,5-dihydro-1H-imidazoles and disubstituted 4,5-dihydro-1H-imidazolylbenzimidazoles.

The solid-phase synthesis of novel imidazolines and dihydroimidazolylbenzimidazoles is described. Resin-bound diamines, derived from resin-bound N-acylated amino acid amides, were cyclized using Vilsmeier reagent to yield imidazolines following cleavage. Similarly, cyclization of resin-bound tetraamines having two secondary amines and an o-dianiline yielded dihydroimidazolylbenzimidazoles following cleavage.

Efficient solid-phase synthesis of 1,3,5-trisubstituted 1,3,5-triazine-2,4,6-triones.

The solid-phase synthesis of 1,3-disubstituted and 1,3,5-trisubstituted 1,3,5-triazine-2,4,6-triones from MBHA and Wang resin is described. Reaction of resin-bound amino acids with isocyanates yield resin-bound ureas, which further react with chlorocarbonyl isocyanate in toluene at 65 degrees C to selectively afford the resin-bound 1,3-disubstituted 1,3,5-triazine-2,4,6-triones. Selective alkylation at the N-5 position of the resin-bound 1,3-disubstituted 1,3,5-triazine-2,4,6-triones was accomplished by treatment with alkyl halides in the presence of 1,8-diazabicyclo[5.4.0]undec-7-ene (DBU). The desired products were cleaved from their solid support and obtained in good yield and purity. The method can be employed in production of toltrazuril analogue libraries for identification of new anticoccidial agents.

Determination of isokinetic ratios necessary for equimolar incorporation of carboxylic acids in the solid-phase synthesis of mixture-based combinatorial libraries.

The methods used to study the relative reaction rates of 45 different aliphatic and aromatic carboxylic acids when coupled to resin-bound amino acid amides is described. Competition experiments involving the coupling of incoming carboxylic acids to resin-bound amino acid amides were performed. The relative composition of each N-acylated amino acid amide in the resulting mixtures was compared to controls prepared by physically mixing equal aliquots of individual compounds in order to study the relative reaction rates of the incoming carboxylic acids. The ratios of the incoming carboxylic acids were then iteratively adjusted to yield as close to equimolar products as possible. As expected, the steric and electronic nature of the incoming carboxylic acids was found to influence their relative reaction rates. The steric hindrance of the resin-bound amino acid appears to have a proportional effect on the reaction rates of the incoming carboxylic acids. N-acylated amino acid amides in the final mixtures, prepared using the final isokinetic ratios, were found to be approximately equimolar.

A traceless approach for the parallel solid-phase synthesis of 2-(arylamino)quinazolinones.

A traceless approach for the parallel solid-phase synthesis of 2-arylamino-substituted quinazolinones is described. Acylation of MBHA resin with o-nitrobenzoic acid derivatives, followed by reduction of the nitro group with tin chloride, generated a resin-bound o-anilino derivative. Reaction of resin-bound o-anilino derivative with arylisothiocyanates yielded resin-bound thioureas, which reacted with amines in the present of Mukaiyama's reagent (2-chloro-1-methylpyridinium iodide) to afford resin-bound guanidines. Following intramolecular cyclization of the resin-bound guanidines during cleavage from the resin by HF/anisole (95/5) for 1.5 h at 0 degrees C, the desired products were obtained in good yield and purity.

Parallel solid-phase synthesis of trisubstituted triazinobenzimidazolediones.

An efficient method for the solid-phase synthesis of trisubstituted [1,3,5]triazino[1,2-a]benzimidazole-2,4(3H,10H)-diones from resin-bound amino acids is described. N-acylation of the primary amine of a resin-bound amino acid with 4-fluoro-3-nitrobenzoic acid, followed by displacement of the fluoro group and reduction of the nitro group, generated a resin-bound o-dianilino derivative. The dianilino compound was treated with cyanogen bromide to generate the corresponding iminobenzimidazole, which, following treatment with N-(chlorocarbonyl)isocyanate, afforded the resin-bound triazinodione derivative. Alkylation of the triazinodione compound with an alkyl halide yielded, following cleavage of the solid-support, the trisubstituted [1,3,5]triazino[1,2-a]benzimidazole-2,4(3H,10H)-dione.

Novel approaches for the solid-phase synthesis of biheterocyclic dihydroimidazole analogues.

The solid-phase syntheses of dihydroimidazolyl 2-alkylthiobenzimidazoles, dihydroimidazolyl 2-alkylsulfonylbenzimidazoles, dihydroimidazolyl dihydroquinoxalin-2,3-diones, and dihydroimidazolyl dihydrobenzimidazol-2-imines are described. Following reduction of a resin-bound amino acid amide, the primary amine of the resulting resin-bound diamine was N-acylated with 4-fluoro-3-nitrobenzoic acid. Treatment with POCl3 led to formation of a dihydroimidazole derivative via dehydrative cyclization. The resin-bound dihydroimidazole derivative was then used as the key starting material for the synthesis of the aforementioned biheterocycles. Following cleavage, the resulting compounds, obtained in moderate yield and good purity, were characterized by LC-MS and 1H NMR and 13C NMR spectroscopy.

Solid-phase synthesis of 1,5-disubstituted 2-aryliminoimidazolidines.

The solid-phase synthesis of 1,5-disubstituted 2-aryliminoimidazolidines, starting from resin-bound N-acylated amino acid amides, is described. Exhaustive reduction of resin-bound acylated amino acid amides with borane-THF afforded the corresponding disecondary amines. Further reaction with arylisothiocyanates in the presence of mercuric chloride (HgCl(2)) yielded the corresponding resin-bound 1,5-disubstituted 2-aryliminoimidazolidines. Cleavage of the product from the resin using HF/anisole (95/5) for 1.5 h at 0 degrees C gave the desired products in good yield and purity. The preparation of a large combinatorial library of such compounds is also discussed.

Solid-phase synthesis of linear ureas tethered to hydantoins and thiohydantoins.

An efficient method for the solid-phase synthesis of hydantoins and thiohydantoins tethered to ureas, starting from a resin-bound amino acid, is presented. Following reduction of the amide with borane-THF, a second amino acid was selectively coupled to the primary amine followed by treatment of the secondary amine by an isocyanate to generate the corresponding urea. Hydantoin and thiohydantoin formation was achieved through the use of carbonyldiimidazole and thiocarbonyldiimidazole, respectively. Cleavage from the solid support using hydrogen fluoride, followed by extraction and lyophilization, provided the desired urea-linked heterocyclic compounds in good yield and high purity.