Identification of cellular targets of a series of boron heterocycles using TIPA II-A sensitive target identification platform

One of the hurdles in the discovery of antibiotics is the difficulty of linking antibacterial compounds to their cellular targets. Our laboratory has employed a genome-wide approach of over-expressing essential genes in order to identify cellular targets of antibacterial inhibitors. Our objective in this project was to develop and validate a more sensitive disk diffusion based platform of target identification (Target Identification Platform for Antibacterials version 2; TIPA II) using a collection of cell clones in an Escherichia coli mutant (AS19) host with increased outer membrane permeability. Five known antibiotics/inhibitors and 28 boron heterocycles were tested by TIPA II assay, in conjunction with the original assay TIPA. The TIPA II was more sensitive than TIPA because eight boron heterocycles previously found to be inactive to AG1 cells in TIPA assays exhibited activity to AS19 cells. For 15 boron heterocycles, resistant colonies were observed within the zones of inhibition only on the inducing plates in TIPA II assays. DNA sequencing confirmed that resistant clones harbor plasmids with fabI gene as insert, indicating that these boron heterocycles all target enoyl ACP reductase. Additionally, cell-based assays and dose response curved obtained indicated that for two boron heterocycle inhibitors, the fabI cell clone in AG1 (wild-type) host cells exhibited at least 11 fold more resistance under induced conditions than under non-induced conditions. Moreover, TIPA II also identified cellular targets of known antibacterial inhibitors triclosan, phosphomycin, trimethoprim, diazaborine and thiolactomycin, further validating the utility of the new system.

Crystallographic insights into the structure-activity relationships of diazaborine enoyl-ACP reductase inhibitors

Enoyl-ACP reductase, the last enzyme of the fatty-acid biosynthetic pathway, is the molecular target for several successful antibiotics such as the tuberculosis therapeutic isoniazid. It is currently under investigation as a narrow-spectrum antibiotic target for the treatment of several types of bacterial infections. The diazaborine family is a group of boron heterocycle-based synthetic antibacterial inhibitors known to target enoyl-ACP reductase. Development of this class of molecules has thus far focused solely on the sulfonyl-containing versions. Here, the requirement for the sulfonyl group in the diazaborine scaffold was investigated by examining several recently characterized enoyl-ACP reductase inhibitors that lack the sulfonyl group and exhibit additional variability in substitutions, size and flexibility. Biochemical studies are reported showing the inhibition of Escherichia coli enoyl-ACP reductase by four diazaborines, and the crystal structures of two of the inhibitors bound to E. coli enoyl-ACP reductase solved to 2.07 and 2.11 Å resolution are reported. The results show that the sulfonyl group can be replaced with an amide or thioamide without disruption of the mode of inhibition of the molecule.

A zwitterion produced by a strong intramolecular N→B interaction in 1-hydroxy-2-(pyridin-2-ylcarbonyl)benzo[d][1,2,3]diazaborinine

2-Acylated 2,3,1-benzodiazaborines can display unusual structures and reactivities. The crystal structure analysis of the boron heterocycle obtained by condensing 2-formylphenylboronic acid and picolinohydrazide reveals it to be an N→B-chelated zwitterionic tetracycle (systematic name: 1-hydroxy-11-oxo-9,10,17λ5-triaza-1λ4-boratetracyclo[8.7.0.02,7.012,17]heptadeca-3,5,7,12,14,16-hexaen-17-ylium-1-uide), C13H10BN3O2, produced by the intramolecular addition of the Lewis basic picolinoyl N atom of 1-hydroxy-2-(pyridin-2-ylcarbonyl)benzo[d][1,2,3]diazaborinine to the boron heterocycle B atom acting as a Lewis acid. Neither of the other two pyridinylcarbonyl isomers (viz. nicotinoyl and isonicotinoyl) are able to adopt such a structure for geometric reasons. A favored yet reversible chelation equilibrium provides an explanation for the slow D2O exchange observed for the OH resonance in the1H NMR spectrum, as well as for its unusual upfield chemical shift. Deuterium exchange may take place solely in the minor open (unchelated) species present in solution.

Synthesis, characterization, and antibacterial activity of structurally complex 2-acylated 2,3,1-benzodiazaborines and related compounds

A set of 2-acylated 2,3,1-benzodiazaborines and some related boron heterocycles were synthesized, characterized, and tested for antibacterial activity against Escherichia coli and Mycobacterium smegmatis. By high-field solution NMR, the heretofore unknown class of 2-acyl-1-hydroxy-2,3,1-diazaborines has been found to be able to exist in several interconvertable structural forms along a continuum comprised of an open hydrazone a, a monomeric B-hydroxy diazaborine b, and an anhydro dimer c. X-Ray crystallography of one of the anhydro dimers, 17c, revealed it to have an unprecedented structure featuring a double intramolecular O→B chelation. The crystal structure of another compound, 37, showed it to be based on a new pentacyclic B heterocycle framework. Nine compounds were found to possess activities against E. coli, and two others were active against M. smegmatis. The finding that these two contain isoniazid covalently embedded in their structures suggests that they might possibly be acting as prodrugs of this well-known antituberculosis agent in vivo.

1-Hydroxy-1H-benzo[d][1,2,6]oxazaborinin-4(3H)-one

The structure of the title compound, C(7)H(6)BNO(3), a new boron heterocycle, prepared by the condensation of (2-ethoxycarbonylphenyl)boronic acid and hydroxylamine, reveals the specific mode of intramolecular condensation between a phenylboronic acid and an ortho hydroxamic acid substituent. The crystal structure shows that dehydration occurs to form a planar oxazaborinine ring possessing both phenol-like B-O-H and lactam functional groups. In the extended structure, intermolecular hydrogen bonding generates a 14-membered ring. To our knowledge, this is the first crystal structure determination involving a six-membered ring that exhibits consecutive B-OH, O, NH, and C=O functional groups.

Synthesis of new transglycosidically tethered 5'-nucleotides constrained to a highly biologically relevant profile

A new motif for restricting 5'-nucleotides to highly biologically relevant conformations has been developed. The 5',6-oxomethylene transglycosidically tethered versions of uridine 5'-monophosphate and 2'-deoxyuridine 5'-monophosphate (1 and 2, respectively) were synthesized in 10-11 steps from their respective natural nucleoside precursors along routes general to the preparation of tethered versions of a wide variety of 5'-nucleotide-based compounds. In both routes, a shelf-stable 6-hydroxymethyl pyrimidine nucleoside 5'-carboxaldehyde is the key intermediate. It exists in a carbohydrate-like fashion in a cyclic hemiacetal form under aprotic conditions. The phosphorylated cyclic hemiacetals 1 and 2 were isolated as binary mixtures of 5'-diastereomers differing principally in the trajectory of the phosphate group with respect to the carbohydrate. By (1)H NMR, both 1 and 2 were demonstrated to be stable to hydrolysis at ambient temperature in D(2)O solution for at least 2 months. The oxomethylene transglycosidic tether as deployed in 1 and 2 leaves all of the native 5'-nucleotide molecular recognition sites intact while it restricts the framework to a low-energy anti glycosyl conformation and an extended phosphate disposition. This provides a spatial presence that approximates nearly three-quarters of the protein-bound 5'-nucleotide ligands described in the Protein Data Bank. The tether has a low structural and electronic impact, occupies a region of space (over the beta-face of the furan ring) seldom penetrated by proteins, and should be accommodated as readily on purine-based 5'-nucleotide frameworks as on pyrimidine-based ones. Because of its unique and attractive features, this new motif for the conformational restriction of 5'-nucleotides is expected to be useful for producing probes of structure/function relationships and in assessing the conformational binding requirements that enzymes and receptor sites have for their natural 5'-nucleotide-based ligands.

The Structural Basis for Hydrolysis Resistance in the Esters of (2-Formylphenyl)boronic Acid 2,4-Dinitrophenylhydrazones

Under conditions that typically afford bicyclic boron heterocycles directly, (2-formylphenyl)boronic acids react with 2,4-dinitrophenylhydrazine in ethanol to give highly waterresistant diethyl boronate esters. Two such 2,4-dinitrophenylhydrazones were prepared and their X-ray crystal structures determined. Contrary to a previous suggestion that their unusual stability is due to an intramolecular N→B coordination giving a six-membered BN2C3 ring system based on a (Z)-hydrazone, these compounds instead were found to be (E)-hydrazones internally stabilized by a weak intramolecular interaction between nitrogen and boron from within a five-membered ring. Further study revealed that the electron deficiency of the starting hydrazine reagent plays a key role in determining the structure of the hydrazone isolated, and that the water-resistant boronate esters can be hydrolyzed under forcing conditions to the boronic acids.

Boron therapeutics on the horizon

No pharmaceutical based on boron has yet made it to market, but this may soon change. The new millennium has brought with it some unique classes of bioactive boron compounds that are sufficiently mature in development to be considered significant and timely advances in their respective chemotherapeutic areas. Because boron is seldom seen as a constituent of a bioactive agent, this review relates some of the pertinent biologic and physiologic properties of boron and then describes in detail those boron-based agents clearly visible on the therapeutic horizon. Highlighted agents include boronic acids and boron heterocycles as potent proteasome inhibitors, beta-lactamase inhibitors, dipeptidyl peptidase inhibitors, inositol trisphosphate receptor modulators, antibacterials, and antiestrogens. As these new agents are welcomed into the therapeutic armamentarium, others will surely follow and the prescribing clinician will already have an awareness and appreciation of the unique benefits that these compounds have to offer.

Synthesis of 6-formyluridine 5'-monophosphate: 6-formyl-UMP

A synthesis of 6-formyluridine 5'-monophosphate (6-formylUMP) in 6 steps starting from uridine is described. This approach should be applicable to the preparation of other O5'-phosphorylated 6-formylUrds such as 6-formylUDP and 6-formylUTP.

Enzyme-catalyzed therapeutic agent (ECTA) design: activation of the antitumor ECTA compound NB1011 by thymidylate synthase

The in vivo administration of enzyme-inhibiting drugs for cancer and infectious disease often results in overexpression of the targeted enzyme. We have developed an enzyme-catalyzed therapeutic agent (ECTA) approach in which an enzyme overexpressed within the resistant cells is recruited as an intracellular catalyst for converting a relatively non-toxic substrate to a toxic product. We have investigated the potential of the ECTA approach to circumvent the thymidylate synthase (TS) overexpression-based resistance of tumor cells to conventional fluoropyrimidine [i.e. 5-fluorouracil (5-FU)] cancer chemotherapy. (E)-5-(2-Bromovinyl)-2'-deoxy-5'-uridyl phenyl L-methoxyalaninylphosphoramidate (NB1011) is a pronucleotide analogue of (E)-5-(2-bromovinyl)-2'-deoxyuridine (BVdU), an antiviral agent known to be a substrate for TS when in the 5'-monophosphorylated form. NB1011 was synthesized and found to be at least 10-fold more cytotoxic to 5-FU-resistant, TS-overexpressing colorectal tumor cells than to normal cells. This finding demonstrates that the ECTA approach to the design of novel chemotherapeutics results in compounds that are selectively cytotoxic to tumor cell lines that overexpress the target enzyme, TS, and therefore may be useful in the treatment of fluoropyrimidine-resistant cancer.

A boron-containing estrogen mimic

A prototype of a new class of 2,3,1-benzodiazaborine-based estrogen mimics is described. 1,2-Dihydro-1,6-dihydroxy-2-(2-methoxy-6-pyridyl)-2,3,1-benzodiazabor ine, (6), was obtained as a crystalline monohydrate (C13H12BN3O3.H2O) after regioselective BBr3-mediated O-demethylation of the condensation product formed from 2-formyl-4-methoxybenzeneboronic acid and 2-hydrazino-6-methoxypyridine. As intended by design, the solid-state structure of (6) features an intramolecular hydrogen-bond association between the donor B--OH group and the acceptor pyridine ring N, a connection which constitutes an additional 'virtual' six-membered ring, thereby providing for an overall topography closely matching that of a tetracyclic steroid. Specifically, prototype (6) can be viewed as a boron-containing mimic of the O17-methyl ether derivatives of dihydroequilenin or estradiol.

A 2-alkyl substituted 2,3,1-benzodiazaborine

The structure of the fourth member of a family of structurally related 2,3,1-benzodiheteroborines has been solved by crystallographic means, providing data for proper direct comparison with the others. The title compound, 1,2-dihydro-1-hydroxy-2-methyl-2,3,1-benzodiazaborine (C8H9BN2O) is obtained via condensation of 2-formylbenzeneboronic acid and methylhydrazine, and is similar in most respects to its 2-unsubstituted parent, in internal geometry and intramolecular association topography, but has some subtle oxazaborine-like characteristics.

Effect of a chemical modification on the hydrated adenosine intermediate produced by adenosine deaminase and a model reaction for a potential mechanism of action of 5-aminoimidazole ribonucleotide carboxylase

Using the hydrated adenosine intermediate (6R)-6-amino-1, 6-dihydro-6-hydroxy-9-(beta-D-ribofuranosyl)purine (2) produced by adenosine deaminase (ADA, EC 3.5.4.4) as a starting point, the active site probe and inhibitor platform 5-(formylamino)imidazole riboside (FAIRs, 4) was designed by removal of the-C6(OH)(NH2)-molecular fragment of 2 generated by the early events of the enzyme-catalyzed hydrolysis. FAIRs was synthesized directly from the sodium salt of 5-amino-1-(beta-D-ribofuranosyl)imidazole-4-carboxylic acid (CAIR) along a reaction sequence involving a tandem N-formylation/decarboxylation that may have a mechanistic connection to the Escherichia coli purE-catalyzed constitutional isomerization of N5-CAIR to CAIR. The physical and spectral properties of FAIRs were elucidated, its X-ray crystal and NMR solution structures were determined, and its interaction with ADA was investigated. Crystalline FAIRs exists solely as the Z-formamide rotamer and exhibits many of the same intramolecular hydrogen bonding events known to contribute to the association of Ado to ADA. In water and various organic solvents, however, FAIRs exists as NMR-distinct, slowly interconverting Z and E rotamers. This truncated enzymatic tetrahedral intermediate analog was determined to be a competitive inhibitor of ADA with an apparent Ki binding constant of 40 microM, a value quite close to that (33 microM) of the natural substrate's K(m). The actual species selected for binding by ADA, though, is likely the minor hydroxyimino prototropic form of Z-FAIRs possessing a far lower true Ki value. As the structural features of FAIRs appear well-suited to support its use as a template for constructing active site probes of both ADA and AIR carboxylases, a variety of carbohydrate-protected versions of FAIRs suitable for facile aglycon elaborations were synthesized. The N3-alkylation, N3-borane complexation, and C4-iodination of some of these were investigated in order to assess physicochemical properties that may assist in the elucidation of mechanisms for the AIR carboxylases. The survey of these properties taken together with a reasonable mechanism for the model CAIRs-->FAIRs synthetic transformation is interpreted to support a mechanism for the purE-catalyzed N5-CAIR-->CAIR biosynthetic one that involves a carboxylative sp3-rehybridization of the imidazole C4 atom rather than one possessing a dipole-stabilized C4 sp2 carbanionic intermediate.

A triphenylboroxin derivative possessing two intramolecular chelates

Condensation of 2-formylbenzeneboronic acid and 1,1-dimethylhydrazine afforded the title compound, bis(8-B-4)-1,3,5-tris[2-[(N,N-dimethylhydrazono)methyl]-phenyl)]b oroxin, C27H33B3N6O3, a tridehydro cyclic trimer of the expected simple benzaldehyde hydrazone and the first triphenylboroxin derivative found to possess two B chelating interactions. The double chelation induces molecular asymmetry but effects only a slight puckering in the central boroxin ring.

Synthetic approaches to the guanosine and xanthosine analogues 5-amino-3-beta-D-ribofuranosylpyrazolo[3,4-e][1,3]oxazin-7-one and 3-beta-D-ribofuranosylpyrazolo[3,4-e][1,3]oxazine-5,7-dione and studies of their antitumor potential

5-Amino-3-beta-D-ribofuranosylpyrazolo[3,4-e][1,3]oxazin-7-o ne has been synthesized via cyclization of the appropriately protected pyrazofurin derivatives and subsequent transformations of the heterocyclic moiety. This guanosine analogue was marginally cytotoxic to L1210 cells in vitro. The xanthosine analogue 3-beta-D-ribofuranosylpyrazolo[3,4-e][1,3]oxazine-5,7-dione was also synthesized, and was found to be highly cytotoxic. It appeared to act as a prodrug of pyrazofurin.

Nonenzymatic synthesis of 5-aminoimidazole ribonucleoside and recognition of its facile rearrangement

5-Amino-1-beta-D-ribofuranosylimidazole 5'-monophosphate (AIR, 1) is the ubiquitous precursor to the purine ribonucleotides in vivo, and it serves as the biochemical precursor to the pyrimidine portion of thiamin (vitamin B1) in certain prokaryotic organisms. The corresponding ribonucleoside (AIRs, 5b) was prepared via chemical (nonenzymatic) synthesis from 5-amino-1-beta-D-ribofuranosylimidazole-4-carboxamide. The tri-O-acetylated derivative of AIRs (5a) was also prepared, and it was shown to undergo a facile ring transformation in aqueous pH 7 buffer to afford N-(imidazol-4-yl)-2,3,5-tri-O-acetyl-D-ribofuranosylamine as a 1:2 mixture of alpha and beta anomers (6a). Under similar conditions, compound 5b affords the corresponding unprotected beta-ribonucleosides 6b. This Dimroth-type ring transformation reaction of 5 to 6, which occurs primarily in neutral aqueous solution, may be responsible for the previously reported lability of AIRs and its derivatives. It may also have relevance to the postulated early biotic pathway to the 9- and 3-substituted purine nucleotide components of an all-purine biopolymer.

Potential tumor- or organ-imaging agents. 27. Polyiodinated 1,3-disubstituted and 1,2,3-trisubstituted triacylglycerols

A series of glyceryl 1,3-bis- and 1,2,3-tris[omega-(3-amino-2,4,6-triiodophenyl)alkanoates] were synthesized, radioiodinated with iodine-125, and evaluated for their ability to selectively localize in the liver for potential use as hepatographic imaging agents. Of the nine target compounds synthesized and evaluated in rats, glyceryl 1,2,3-tris[3-(3-amino-2,4,6-triiodophenyl)propionate] (5b) displayed rapid and sustained liver specificity. This agent was found to accumulate in the liver in concentrations of 60, 75, and 86% of the administered dose at 5 min, 30 min, and 24 h, respectively. Moreover, the 24-h liver-to-blood ratio of 235 justifies further studies in higher animal species.

7 alpha-substituted derivatives of androstenedione as inhibitors of estrogen biosynthesis

In an effort to obtain more information on the structure-activity relationship among the 7 alpha-(phenylthio)androstenedione inhibitors of the enzyme aromatase, a series of compounds containing both electron-donating and electron-withdrawing ring substituents was synthesized and tested for aromatase inhibitory activity. No linear correlation between substituent electronic effects and inhibitory activity was observed. The halogen-containing compounds, particularly 8, appeared to be quite potent inhibitors. The 125I analogue of 8 was synthesized in order to evaluate the possibility of side-chain elimination under the assay conditions. Approximately 90% of [125I]-8 remained intact for up to 1 h under assay conditions.

Esters of iopanoic acid as liver-specific CT contrast agents: biodistribution and CT evaluation

The synthesis and preliminary biodistribution data for a series of sterol-like esters of iopanoic acid having potential value as liver-specific CT contrast agents are described. Structural modification of the sterol portion of the iopanoate ester afforded a group of compounds that displayed tissue specificity similar to cholesteryl iopanoate, the prototype ester of this series, but were rapidly cleared from the target tissues after hydrolysis. From the biodistribution data, the most promising of these agents, pregnenolone iopanoate (PI), was evaluated by CT in rabbits receiving a radiologic dose equivalent to 30 mg I/kg. The hepatic parenchyma was enhanced within 2 h of infusion to a maximal level of 31 HU above precontrast values. Hepatic CT attenuation returned to normal within 24 h. However, CT performed after PI infusion into Vx2 tumor-bearing rabbits failed to provide superior images compared with those acquired following bolus administration of urographic contrast.

Potential tumor- or organ-imaging agents. 23. Sterol esters of iopanoic acid

A series of sterol esters of iopanoic acid was synthesized and evaluated for their potential to selectively localize in liver and steroid-secreting tissues for possible application in either computed tomography or nuclear medicine imaging. Unlike free iopanoic acid (1), which was rapidly cleared following intravenous administration to rats, cholesteryl iopanoate (2) was found to accumulate in liver, adrenal cortex, and ovary. At 24 h, the ovary was found to contain the highest concentration of 2. The ability of 2 to accumulate in the above tissues was attributed to its resistance to hydrolysis. Pregnenolone iopanoate (3) and dehydroepiandrosterone iopanoate (4), on the other hand, were shown to reach unusually high concentrations in the adrenal cortex within 0.5 h of administration but declined to much lower levels by 24 h. Lipid extraction of tissues showed 3 and 4 to be susceptible to in vivo hydrolysis, which undoubtedly was a major factor in their clearance from adrenal tissue.