Enantiospecific synthesis of pseudoacarviosin as a potential antidiabetic agent

A pseudo-1,4'- N-linked disaccharide, pseudoacarviosin 5, was constructed via a key palladium-catalyzed coupling reaction of pseudoglycosyl chloride 8 (prepared from d-glucose via a novel direct intramolecular aldol addition in 12 steps) and pseudo-4-amino-4,6-dideoxy-alpha- d-glucose 9 (prepared from l-arabinose via an unusual trans-fused isoxazolidine-selective intramolecular nitrone-alkene cycloaddition in 11 steps). Pseudoacarviosin 5 has been shown to be a potent inhibitor of alpha-glucosidases, particularly the intestinal mucosal enzymes sucrase and glucoamylase of relevance to blood glucose control.     

Enhanced selectivity for inhibition of analog-sensitive protein kinases through scaffold optimization

The ability to inhibit any protein kinase of interest with a small molecule is enabled by a combination of genetics and chemistry. Genetics is used to modify the active site of a single kinase to render it distinct from all naturally occurring kinases. Next, organic synthesis is used to develop a small molecule, which does not bind to wild-type kinases but is a potent inhibitor of the engineered kinase. This approach, termed chemical genetics, has been used to generate highly potent mutant kinase-specific inhibitors based on a pyrazolopyrimidine scaffold. Here, we asked if the selectivity of the resulting pyrazolopyrimidines could be improved, as they inhibit several wild-type kinases with low-micromolar IC₅₀ values. Our approach to improve the selectivity of allele-specific inhibitors was to explore a second kinase inhibitor scaffold. A series of 6,9-disubstituted purines was designed, synthesized, and evaluated for inhibitory activity against several kinases in vitro and in vivo. Several purines proved to be potent inhibitors against the analog-sensitive kinases and exhibited greater selectivity than the existing pyrazolopyrimidines.     

Evidence that monastrol is an allosteric inhibitor of the mitotic kinesin Eg5

Monastrol, a cell-permeable inhibitor of the kinesin Eg5, has been used to probe the dynamic organization of the mitotic spindle. The mechanism by which monastrol inhibits Eg5 function is unknown. We found that monastrol inhibits both the basal and the microtubule-stimulated ATPase activity of the Eg5 motor domain. Unlike many ATPase inhibitors, monastrol does not compete with ATP binding to Eg5. Monastrol appears to inhibit microtubule-stimulated ADP release from Eg5 but does not compete with microtubule binding, suggesting that monastrol binds a novel allosteric site in the motor domain. Finally, we established that (S)-monastrol, as compared to the (R)-enantiomer, is a more potent inhibitor of Eg5 activity in vitro and in vivo. Future structural studies should help in designing more potent Eg5 inhibitors for possible use as anticancer drugs and cell biological reagents.     

L-ascorbic acid alpha-glucoside formed by regioselective transglucosylation with rat intestinal and rice seed alpha-glucosidases: its improved stability and structure determination

The definite structure and chemical stability of a new glucoside of L-ascorbic acid (AA) which was enzymatically glucosylated with rat intestinal and rice seed alpha-glucosidases were reported. The stability of this AA derivative in water under aerobic conditions was proved by its remarkable resistance against enhanced oxidative degradation by heat, Cu2+ ion or ascorbate oxidase, and it was found to have no reducing activity toward radicals. These properties were obviously distinguishable from those of AA. This glucoside was effectively hydrolyzed by alpha-glucosidases which possessed the ability to synthesize itself, resulting in the liberation of AA activity. The conjugate was composed of equimoles of AA and glucose. Nuclear magnetic resonance spectra, mass spectra, pH profiles of ultraviolet spectra and pK(a) value of 3.10 supported the coupling of alpha-glucose to the 2-position of AA. From these results, its structure was assigned 2-O-alpha-D-glucopyranosyl-L-ascorbic acid, being distinct from 6-O-alpha-D-glucopyranosyl-L-ascorbic acid formed with Aspergillus niger alpha-glucosidase. These findings indicate that the 2-O-glucoside formed by regioselective transglucosylation withstands oxidative degradation even in aqueous solutions and it can be used as an available active AA source for multicomponent liquid products.     

Synthesis and structure-activity relationship of N-arylrolipram derivatives as inhibitors of PDE4 isozymes

Structure activity studies of N-phenylrolipram derivatives have led to the identification of highly potent PDE4 inhibitors. The potential of these inhibitors for cellular activity was routinely assessed in an assay of fMLP induced oxidative burst in human eosinophils. Since first generation PDE4 inhibitors have been plagued with a number of unwanted side effects, parallel structure activity studies for competition with the [3H]-rolipram binding site in rat brain were performed. In this fashion 5-[4-(3-cyclopentyloxy-4-methoxyphenyl)-2-oxo-pyrrolidin-1-yl]-3-(3-methoxybenzyloxy)benzoic acid N',N'-dimethylhydrazide (22) was identified as a potent inhibitor of PDE4 which exhibits >1000 fold selectivity versus PDE3, and is a nanomolar inhibitor in all the cellular assays tested. Studies on the stereoselectivity of PDE4 inhibition of this class of rolipram based compounds revealed, that for example (S)-11 is a more potent inhibitor than (R)-11. This effect can also be observed in primary human cells where the (S)-enantiomer is about 10 fold more potent than the corresponding (R)-enantiomer.     

How to Separate Kinase Inhibition from Undesired Monoamine Oxidase A Inhibition—The Development of the DYRK1A Inhibitor AnnH75 from the Alkaloid Harmine

The β-carboline alkaloid harmine is a potent DYRK1A inhibitor, but suffers from undesired potent inhibition of MAO-A, which strongly limits its application. We synthesized more than 60 analogues of harmine, either by direct modification of the alkaloid or by de novo synthesis of β-carboline and related scaffolds aimed at learning about structure–activity relationships for inhibition of both DYRK1A and MAO-A, with the ultimate goal of separating desired DYRK1A inhibition from undesired MAO-A inhibition. Based on evidence from published crystal structures of harmine bound to each of these enzymes, we performed systematic structure modifications of harmine yielding DYRK1A-selective inhibitors characterized by small polar substituents at N-9 (which preserve DYRK1A inhibition and eliminate MAO-A inhibition) and beneficial residues at C-1 (methyl or chlorine). The top compound AnnH75 remains a potent DYRK1A inhibitor, and it is devoid of MAO-A inhibition. Its binding mode to DYRK1A was elucidated by crystal structure analysis, and docking experiments provided additional insights for this attractive series of DYRK1A and MAO-A inhibitors.     

Identification of novel alpha-glucosidase inhibitors by screening libraries based on N- [4-(benzyloxy) benzoyl] alanine derivatives

A library of 72 compounds related to N- [4-(benzyloxy) benzoyl]alanine (I) was synthesized, prepared and screened for alpha-glucosidase inhibitory activity. Four compounds showed potent inhibition, six compounds moderate inhibition, and 16 were weak inhibitors. One compound, N- [4-(benzyloxy) benzoyl] serine, was found to be a potent inhibitor of alpha-glucosidase with 100% inhibition at 1 micro M. This inhibitor was at least five times more potent than the lead compound I.     

Differential effects of thiopeptide and orthosomycin antibiotics on translational GTPases

The ribosome is a major target in the bacterial cell for antibiotics. Here, we dissect the effects that the thiopeptide antibiotics thiostrepton (ThS) and micrococcin (MiC) as well as the orthosomycin antibiotic evernimicin (Evn) have on translational GTPases. We demonstrate that, like ThS, MiC is a translocation inhibitor, and that the activation by MiC of the ribosome-dependent GTPase activity of EF-G is dependent on the presence of the ribosomal proteins L7/L12 as well as the G' subdomain of EF-G. In contrast, Evn does not inhibit translocation but is a potent inhibitor of back-translocation as well as IF2-dependent 70S-initiation complex formation. Collectively, these results shed insight not only into fundamental aspects of translation but also into the unappreciated specificities of these classes of translational inhibitors.     

Discovery of kibdelomycin, a potent new class of bacterial type II topoisomerase inhibitor by chemical-genetic profiling in Staphylococcus aureus

Bacterial resistance to known therapeutics has led to an urgent need for new chemical classes of antibacterial agents. To address this we have applied?a Staphylococcus aureus fitness test strategy to natural products screening. Here we report the discovery of kibdelomycin, a novel class of antibiotics produced by a new member of the genus Kibdelosporangium. Kibdelomycin exhibits broad-spectrum, gram-positive antibacterial activity and is a potent inhibitor of DNA synthesis. We demonstrate through chemical genetic fitness test profiling and biochemical enzyme assays that kibdelomycin is a structurally new class of bacterial type II topoisomerase inhibitor preferentially inhibiting the ATPase activity of DNA gyrase and topoisomerase IV. Kibdelomycin is thus the first truly novel bacterial type II topoisomerase inhibitor with potent antibacterial activity discovered from natural product sources in more than six decades.     

Studies directed toward the elucidation of the pharmacophore of steroid-based Sonic Hedgehog signaling inhibitors

Previous work from our laboratory has established that the readily available steroid-based analog 2 of cyclopamine 1 is, like 1, a highly potent inhibitor of Hedgehog signaling. The first structure-activity relationship studies on 2, i.e., the synthesis and biological evaluation of both the C-17 epi analog 4 and the C-3 deoxy analog 11, both of which are more potent than cyclopamine 1, are described. The implications of these results for the emerging pharmacophore of these Sonic Hedgehog signaling inhibitors are discussed.     

A crystallographic investigation of phosphoantigen binding to isopentenyl pyrophosphate/dimethylallyl pyrophosphate isomerase

We report the crystallographic structures of the potent phosphoantigens Phosphostim (the bromohydrin of isopentenyl pyrophosphate) and E-4-hydroxy-3-methyl-but-2-enyl pyrophosphate bound to the mevalonate pathway enzyme isopentenyl pyrophosphate/dimethylallyl pyrophosphate isomerase (IPPI). Racemic Phosphostim forms covalent complexes with IPPI: a 4-thioether with C67 and a 4-ester with E116. Only the E116 ester forms with the chiral species, S-Phosphostim, with the w.t. enzyme, while the C67 thioether forms with a mutant Y104F IPPI. The potent phosphoantigen HMBPP also binds to IPPI, but is only a weak ( approximately 50 muM) inhibitor. These results strongly support an SN2 reaction for inhibition of IPPI by Phosphostim, in contrast to the SN1 or concerted type of reaction found with epoxide inhibitors, which react at C-3, and are of general interest in the context of the development of novel mevalonate pathway inhibitors. They also provide clues as to the nature of the binding site of synthetic phosphoantigens in gammadelta T cell activation. In particular, both bromohydrin and epoxy phosphoantigens are potent, irreversible inhibitors of IPPI while HMBPP is only a weak inhibitor, ruling out an IPPI or IPPI-like target for HMBPP in gammadelta T cell activation.     

Cytotoxic kurubasch aldehyde from Trichilia emetica

Kurubasch aldehyde, a sesquiterpenoid with an hydroxylated humulene skeleton, was isolated as free alcohol from Trichilia emetica Vahl. (Meliaceae), belonging to the order Sapindales. Related substances have been previously found in plants as esters of aromatic acids, and these plants were species belonging to the distant order Apiales. This is the first report of humulenes found in the genus Trichilia and only the second of humulenes in the order Sapindales. The aldehyde is a modest inhibitor of the growth of Plasmodium falciparum (IC50 76 microM) and slow-proliferating breast cancer cells MCF7 (78 microM), but a potent inhibitor of proliferation of S180 cancer cells (IC50 7.4 microM).     

A Strategy for Neuraminidase Inhibitors Using Mechanism‐Based Labeling Information

A potent inhibitor for Vibrio cholerae neuraminidase (VCNA) was developed by using a novel two‐step strategy, a target amino acid validation using mechanism‐based labeling information, and a potent inhibitor search using a focused library. The labeling information suggested the hidden dynamics of a loop structure of VCNA, which can be a potential target of the novel inhibitor. A focused library composed of 187 compounds was prepared from a 9‐azide derivative of 2,3‐dehydro‐N‐acetylneuraminic acid (DANA) to interrupt the function of the loop of the labeled residues. Inhibitor 3c showed potent inhibition properties and was the strongest inhibitor with FANA, a N‐trifluoroacetyl derivative of DANA. Validation studies of the inhibitor with a detergent and a Lineweaver–Burk plot suggested that the 9‐substitution group would interact hydrophobically with the target loop moiety, adding a noncompetitive inhibition property to the DANA skeleton. This information enabled us to design compound 4 having the combined structure of 3c and FANA. Compound 4 showed the most potent inhibition (K_i=73 nM , mixed inhibition) of VCNA with high selectivity among the tested viral, bacterial, and mammal neuraminidases.     

Stereoselective synthesis of F-ring saturated estrone-derived inhibitors of Hedgehog signaling based on cyclopamine

Previous work in this laboratory established that the readily available F-ring aromatic analog of cyclopamine is a highly potent inhibitor of Hedgehog signaling. The synthesis and biological evaluation of two F-ring saturated analogs that are more potent than the F-ring aromatic structure are reported.     

alpha-1,4-Glucan lyase performs a trans-elimination via a nucleophilic displacement followed by a syn-elimination

alpha-Glucan lyase (EC 4.2.2.13, GLase) cleaves alpha-1,4-glucosidic bonds via an elimination reaction to produce 1,5-d-anhydrofructose. GLase was inactivated by the mechanism based alpha-glucosidase inactivator, 5-fluoro-beta-l-idosyl fluoride. The trapped glycosyl-enzyme intermediate was isolated and the nucleophilic amino acid residue (Asp 553) identified is equivalent to the residue so identified in sequence-related alpha-glucosidases. This intermediate undergoes a syn-elimination reaction to release the product. Further evidence against a direct trans-elimination mechanism was provided by the absence of a primary kinetic isotope effect on the substrate substituted with deuterium at the C2 position.     

Inhibitory effects of galloylglucose on nicotinamide adenine dinucleotide dehydrogenases of the aerobic respiratory chain of Escherichia coli

The effects of pentagalloylglucose (1,2,3,4,6-penta-O-galloyl-beta-D-glucose) on the aerobic electron transport system of Escherichia coli were studied. The activity of nicotineamide adenine dinucleotide (NADH) reductase was inhibited by pentagalloylglucose, but the activities of succinate dehydrogenase, D-lactate dehydrogenase, and ubiquinol-1 (Q1H2) oxidase were not susceptible to the inhibitor. Because the presence of two kinds of NADH dehydrogenase in respiratory chain of Escherichia coli has been reported, we examined the effect of galloylglucose independently on both NADH dehydrogenases. Pentagalloylglucose is potent and specific inhibitor of both NADH dehydrogenases. One of the NADH dehydrogenases (NADH dh II) is more sensitive to the inhibitor than the other (NADH dh I).     

Bisubstrate inhibitors for the enzyme catechol-O-methyltransferase (COMT): influence of inhibitor preorganisation and linker length between the two substrate moieties on binding affinity

Inhibition of the enzyme catechol-O-methyltransferase (COMT) is an important approach in the treatment of Parkinson's disease. A series of new potent bisubstrate inhibitors for COMT, resulting from X-ray structure-based design and featuring adenosine and catechol moieties have been synthesised. Biological results show a large dependence of binding affinity on inhibitor preorganisation and the length of the linker between nucleoside and catechol moieties. The most potent bisubstrate inhibitor for COMT has an IC50 value of 9 nM. It exhibits competitive kinetics for the SAM and mixed inhibition kinetics for the catechol binding site. Its bisubstrate binding mode was confirmed by X-ray structure analysis of the ternary complex formed by the inhibitor, COMT and a Mg2+ ion.     

Synthesis and antifolate activity of 8,10-dideazaminopterin

A synthesis of 8,10-dideazaminopterin, using 2,4-diamino-6-bromomethyl-8-deazapteridine ( 2 ) as a key intermediate, is described. Condensation of the triphenylphosphinylide derived from 2 with p-formylbenzoyl-L-glutamate afforded a 9,10-dehydro-8,10-dideazaminopterin ester intermediate 5 . Hydrogenation of the olefinic linkage and subsequent hydrolysis of the glutamate ester gave the title compound. 8,10-Dideazaminopterin was a potent growth inhibitor of folate dependent bacteria. It was 16 times more potent then methotrexate as an inhibitor of dihydrofolate reductase derived from L1210 leukemia cells, and showed strong activity against L1210 in mice.     

Total synthesis of dehydroaltenusin

First total synthesis of dehydroaltenusin, a natural enzyme inhibitor, is described. The key step involves Suzuki-couplig reaction of aryl triflate prepared from 2,4,6-trihydroxy benzoic acid with a catechol-derived boronic acid. The synthetic sample was evaluated as a potent inhibitor against an eukaryotic DNA polymerase α.