Biomedical subjects
Publications and source records attributed to Michael C Pirrung.
The metalation of oxazoles leads to ring opening to the isocyanoenolate that can be O-acylated to give the unsaturated isonitriles. These substances undergo conventional multicomponent reactions. The products of their reactions are readily converted to acyl substitution products by treatment with acid and a nucleophile. These unsaturated isonitriles are notable by their simple preparations and, unusually, their nonoffensive odors.
The parallels between organic reactions conducted with water as the solvent and reactions conducted under high pressure can be understood in light of theories of aqueous solvation and hydrophobic effects. Such parallels provide powerful tools for promoting reactions of nonpolar compounds.
LpxC [UDP-3-O-(R-3-hydroxymyristoyl)-GlcNAc deacetylase] is a metalloamidase that catalyzes the first committed step in the biosynthesis of the lipid A component of lipopolysaccharide. A previous study (H. R. Onishi, B. A. Pelak, L. S. Gerckens, L. L. Silver, F. M. Kahan, M. H. Chen, A. A. Patchett, S. M. Galloway, S. A. Hyland, M. S. Anderson, and C. R. H. Raetz, Science 274:980-982, 1996) identified a series of synthetic LpxC-inhibitory molecules that were bactericidal for Escherichia coli. These molecules did not inhibit the growth of Pseudomonas aeruginosa and were therefore not developed further as antibacterial drugs. The inactivity of the LpxC inhibitors for P. aeruginosa raised the possibility that LpxC activity might not be essential for all gram-negative bacteria. By placing the lpxC gene of P. aeruginosa under tight control of an arabinose-inducible promoter, we demonstrated the essentiality of LpxC activity for P. aeruginosa. It was found that compound L-161,240, the most potent inhibitor from the previous study, was active against a P. aeruginosa construct in which the endogenous lpxC gene was inactivated and in which LpxC activity was supplied by the lpxC gene from E. coli. Conversely, an E. coli construct in which growth was dependent on the P. aeruginosa lpxC gene was resistant to the compound. The differential activities of L-161,240 against the two bacterial species are thus the result primarily of greater potency toward the E. coli enzyme rather than of differences in the intrinsic resistance of the bacteria toward antibacterial compounds due to permeability or efflux. These data validate P. aeruginosa LpxC as a target for novel antibiotic drugs and should help direct the design of inhibitors against clinically important gram-negative bacteria.
Novel strategies are required to combat pox virus infections, whether caused by escape of viruses such as monkeypox from indigenous areas or intentional release of smallpox. Anti-smallpox drugs with a unique mode of antiviral action, inhibition of transcription termination, were known but not therapeutically useful. Using a combinatorial method, variants of the basic isatin-beta-thiosemicarbazone structure were prepared and examined for cytotoxicity and antiviral activity in vaccinia virus- and cowpox virus-infected human cells. Potent and much more selective N-aminomethyl-isatin-beta-thiosemicarbazones were discovered.
The principle of methyl scanning is proposed for determination of the sites of interaction between biologically active small molecules and their macromolecular target(s). It involves the systematic preparation of a family of methylated derivatives of a compound and their biological testing. As a functional assay, the method can identify the regions of a molecule that are important (and unimportant) for biological activity against even unknown targets, and thus provides an excellent complement to structural biology. Methyl scanning was applied to demethylasterriquinone B1, a small-molecule mimetic of insulin. A new, optimal total synthesis of this natural product was developed that enables the family of methyl scan derivatives to be concisely prepared for evaluation in a cellular assay. The results of this experiment were used to design a biotin-demethylasterriquinone conjugate for use as an affinity reagent. This compound was prepared in tens of milligram quantities in a four-step synthesis.
A method has been developed to sequentially add indole-3-mercurials to dichlorinated quinones using palladium catalysis. These reactions can be used in the modular assembly of bis(indol-3-yl)benzoquinones, a significant natural product family.
Two multicomponent reactions, the Ugi and Passerini reactions, are accelerated by the use of aqueous solutions. The rate enhancements compared to those by organic solvents can approach 300-fold. Reactions performed in water offer another advantage that products are often insoluble, permitting direct isolation by precipitation. The methods were applied to the preparation of three small combinatorial libraries.
A design principle for a two-photon photochemically removable protecting group based on sequential one-photon processes has been established. The expected performance of such groups in spatially directed photoactivation/photodeprotection has been shown by a kinetic analysis. One particular molecular class fitting into this design, the nitrobenzyl ethers of o-hydroxycinnamates, has been presented. An initial demonstration of two-photon deprotection of one such group prompted further optimization with respect to photochemical deprotection rate. This was accomplished by the preparation and screening of a 135-member indexed combinatorial library. Optimum performance for lambda >350 nm deprotection in organic solvent was found with 4,5-dialkoxy and -cyano substitution in the nitrobenzyl group and 4-methoxy substitution in the cinnamate.
Overexpression of the Cdc25A and Cdc25B dual-specificity phosphatases correlates with a wide variety of cancers, making the Cdc25s attractive drug targets for anticancer therapies. However, the search for good lead molecules has been hampered by the reactivity of the active site thiolate anion and the flat solvent-exposed active site region. We describe here the indolyldihydroxyquinones, a new class of inhibitors of Cdc25 that bind reversibly to the active site with submicromolar potency. Structure-activity relationships in the 50 derivatives of the lead molecule 2,5-dihydroxy-3-(1H-indol-3-yl)[1,4]benzoquinone show interesting and consistent trends identifying features required for inhibition of all three isoforms of Cdc25. The compounds do not show time-dependent inhibition, indicating that they form neither covalent adducts with nor oxidize the active site thiol. Our best compounds, 2,5-dihydroxy-3-(7-farnesyl-1H-indol-3-yl)[1,4]benzoquinone and 2,5-dihydroxy-3-(4,6-dichloro-7-farnesyl-1H-indol-3-yl)[1,4]benzoquinone, are competitive with substrate for the active site and yield K(i)s of 640 and 470 nM, respectively. Binding of the indolylhydroxyquinones is diminished by three, but not by six other, specific mutations in the active site region. Additionally, the flexible C-terminal tail required for binding of protein substrate is also required for binding derivatives with hydrophobic modifications at the 7-position. The indolyldihydroxyquinones compete effectively with the protein substrate for Cdc25 in vitro and lead to rapid cell death in vivo. Thus, the indolyldihydroxyquinones will serve as useful lead molecules for drug discovery and further cell-based studies on the role of Cdc25s in cell cycle control.
[structure: see text] A library of 49 illudinoids was prepared via a three-step synthesis using a parallel synthesizer and solid-phase extractive purification. Products could be rapidly prepared for initial biological testing against three cancer cell lines, which revealed library members that inhibit nonsmall cell lung cancer. The activities of the library members are not easily correlated with structure, meaning the empirical approach used here is essential for such nonintuitive discoveries.
A possible breakthrough in the treatment of diabetes was made with the discovery that a fungal natural product, demethylasterriquinone B1 (DAQ B1), is an orally active, small-molecule mimic of insulin. Subsequent work has shown that the glucose-lowering effects of DAQ B1 are not accompanied by enhanced vascular proliferation, which is a side effect of chronic insulin administration that can lead to arteriosclerosis. Our recent short and modular total synthesis of DAQ B1 could be readily modified to create congeners and afforded ample supplies of the natural product, which permitted intracellular signal transduction of DAQ B1 to be examined. The activities of DAQ B1 and over a dozen related structures were studied for insulin receptor (IR) and insulin receptor substrate-1 phosphorylation. Examination of the effect of DAQ B1 on kinases downstream of the IR in insulin signal transduction showed selective activation of Akt kinase (a metabolic effect) but not of extracellular-regulated kinase (a proliferative effect). The influence of DAQ B1 on gene expression (determined by a microarray study) was also divergent from that of insulin, which activates both proliferative and metabolic pathways. The action of DAQ B1 as a selective insulin receptor modulator can be accounted for by its ability to selectively activate one kinase among the many emanating from insulin receptor autophosphorylation and its reduced effects on gene expression.
LpxC is a zinc amidase that catalyses the second step of lipid A biosynthesis in Gram-negative bacteria. Oxazolines incorporating a hydroxamic acid, which is believed to coordinate to the single essential zinc ion, at the 4-position are known inhibitors of this enzyme. Some of these enzyme inhibitors exhibit antibacterial activity through their inhibition of LpxC. We recently developed a method for the synthesis of oxazolines using resin capture and ring-forming release that eliminates traditional purification steps and can be used in high-throughput synthesis. Using our method, oxazoline hydroxamates with diverse 2-substituents were prepared in library form as candidate inhibitors for LpxC. Two conventional methods for oxazoline synthesis were also applied to generate more than 70 compounds. The groups at the 2-position included a wide variety of substituted aromatic rings and a limited selection of alkyl groups. These compounds were screened against wild-type and LpxC inhibitor-sensitive strains of Escherichia coli, as well as wild-type Pseudomonas aeruginosa. Inhibition of the E. coli LpxC enzyme was also investigated. A broad correlation between enzyme inhibitory and antibacterial activity was observed, and novel compounds were discovered that exhibit antibacterial activity but fall outside earlier-known structural classes.
Three methods for the conjugate addition of indoles to 2,5-dichlorobenzoquinone have been developed. A wide variety of indoles substituted with halogen, alkyl, alkoxy, and aryl groups participate in anaerobic condensation reactions promoted by HCl, H2SO4, or CH3CO2H. The hydroquinone product is partially oxidized by excess dichlorobenzoquinone and fully converted to the 2,5-dichloro-3-(indol-3-yl)benzoquinone targets by DDQ or Ag2CO3 oxidation. 2,5-Dihydroxy-3-(indol-3-yl)benzoquinones can be obtained from the dichlorides by alkaline hydrolysis. The rotational characteristics of the biaryl bond created in these reactions have been examined by theoretical and spectroscopic methods.
Two total syntheses of the unsymmetrical bis-indolylquinone natural product demethylasterriquinone B1 (also known as L-783,281) have been accomplished. The first exploits a known base-promoted condensation of indoles with bromanil, which stops at monoaddition using the sterically hindered 2-isoprenylindole. This permits addition of the second indole, 7-prenylindole, which gives both meta- and para-substituted bis-indolylquinone products. This regiochemical control problem was solved by extension of a method we recently developed for acid-promoted addition of indoles to 2,5-dichlorobenzoquinone. Under our original mineral acid conditions, reaction of 2-isoprenylindole with dichlorobenzoquinone fails, but it succeeds with 3-bromo-2,5-dichlorobenzoquinone using acetic acid as the promoter. The regiochemistry established in such selectively bromine-substituted quinones can be exploited in Stille couplings. As a model system, the synthesis of demethylasterriquinone A1 was accomplished using as the key step a Stille coupling of a 2,5-dibromobenzoquinone with an (N-isoprenylindol-3-yl)tin, producing the para-substituted bis-indolylquinone exclusively. Use of a (7-prenylindole)tin in coupling with a bromo-2,5-dichloro-4-indolylbenzoquinone gives the demethylasterriquinone B1 precursor. The dihaloquinone products of these indole/quinone coupling processes can be hydrolyzed to the dihydroxyquinone natural products. Demethylasterriquinone B1 is of high recent interest as a small molecule insulin mimetic with oral anti-diabetic activity in mice.
UDP-3-O-[R-3-hydroxymyristoyl]-GlcNAc deacetylase (LpxC) is a zinc amidase that catalyzes the second step of lipid A biosynthesis in Gram negative bacteria. Known inhibitors of this enzyme are oxazolines incorporating a hydroxamic acid at the 4-position, which is believed to coordinate to the single essential zinc ion. A new structural class of inhibitors was designed to incorporate a more stable and more synthetically versatile isoxazoline core. The synthetic versatility of the isoxazoline allowed for a broad study of metal binding groups. Nine of 17 isoxazolines, each incorporating a different potential metal binding functional group, were found to exhibit enzyme inhibitory activity, including one that is more active than the corresponding hydroxamic acid. Additionally, a designed affinity label inhibits LpxC in a time-dependent manner.
The analysis of RNA splicing is important to understanding the diversity in protein sequences at specific disease loci, in the immune response, and across the proteome. The presence of each exon in a mature mRNA formed from a genomic sequence of n exons can be represented by a Boolean variable, enabling mRNA structure to be encoded by an n-bit binary number. The CD44 locus has been studied as an example of a variantly spliced RNA. Microarray methods can be used to address RNA splicing provided they exhibit high fidelity. Our previous work showed that the arrayed primer extension (APEX; single-nucleotide polymerase extension of microarrays of DNA primers) method gives high-fidelity, digital detection of nucleic acid sequences, and it has been used for the solution of Boolean computing problems. APEX was adapted to RNA analysis by the use of reverse transcriptase and arrays of primers specific to each exon in the CD44 locus. "Splicotypes" were readily assigned for a number of variant RNA templates. Because CD44 is known to be aberrantly spliced in a number of cancers, the RNA APEX method with a CD44 microarray was applied to samples from primary tumors of individual patients. Up to four different splicing forms of CD44 were detected, whereas there have been no previous reports of the presence of more than two CD44 isoforms within the same tissue.
Rhodium carboxylate-mediated reactions of diazoketones involving cyclopropanation, C-H insertion, and aromatic C-C double bond addition/electrocyclic ring opening obey saturation (Michaelis-Menten) kinetics. Axial ligands for rhodium, including aromatic hydrocarbons and Lewis bases such as nitriles, ethers, and ketones, inhibit these reactions by a mixed kinetic inhibition mechanism, meaning that they can bind both to the free catalyst and to the catalyst-substrate complex. Substrate inhibition can also be exhibited by diazocompounds bearing these groupings in addition to the diazo group. The analysis of inhibition shows that the active catalyst uses only one of its two coordination sites at a time for catalysis. Some ketones exhibit the interesting property that they selectively bind to the catalyst-substrate complex. The similarity of the kinetic constants from different types of reactions with similar diazoketones, regardless of the linking unit or the environment of the reacting alkene, suggests that the rate-determining step is the generation of the rhodium carbenoid. A very useful rhodium carboxylate catalyst for asymmetric synthesis, Rh(2)(DOSP)(4), shows slightly slower kinetic parameters than the achiral catalysts, implying that enantioselectivity of this catalyst is based on slowing reactions from one of the enantiotopic faces of the reactant, rather than any type of ligand-accelerated catalysis. A series of rhodium catalysts derived from acids with pK(a)s spanning 4 orders of magnitude give very similar kinetic constants.
A (19)F NMR method for encoding of combinatorial libraries has been developed. Aryl fluorides whose chemical shifts are modified by aromatic substituents were prepared and attached to resin support beads that were used in the split-pool synthesis of peptoids. The detection of the (19)F NMR signal of tags derived from a single "big bead" was demonstrated. The library diversity arises from peptoid amines and the cyclic anhydrides used in their acylation. The resulting 90-compound library was examined for metal ion binding, and novel ligands for iron and copper were discovered. Their binding constants were determined to be in the low micromolar range using conventional methods. The library was also examined for autocatalysis of acylation, and a molecule possessing the catalytic triad of serine proteases was deduced.