Fumagalone,a reversible inhibitor of type 2 methionine aminopeptidase and angiogenesis

Fumagillin and ovalicin constitute a family of structurally related natural products that possess antiangiogenic activity. We report the synthesis of a new fumagillin analogue, fumagalone, in which the spiroepoxide group is replaced with an aldehyde. Fumagalone inhibits type 2 methionine aminopeptidase (MetAP2) with IC(50) = 8 microM and endothelial cell proliferation with IC(50) = 52 nM. With dialysis and competition assays, it was unambiguously demonstrated that binding of fumagalone to MetAP2 is reversible.     

Beta-phenyl cysteine: a leucine aminopeptidase inhibitor

Beta-phenyl cysteine: a leucine aminopeptidase inhibitor. The kinetic parameters of the inhibition of the leucine aminopeptidase by beta-phenyl cysteine are reported in this communication.     

Discovery and X-ray crystallographic analysis of a spiropiperidine iminohydantoin inhibitor of beta-secretase

A high-throughput screen at 100 microM inhibitor concentration for the BACE-1 enzyme revealed a novel spiropiperidine iminohydantoin aspartyl protease inhibitor template. An X-ray cocrystal structure with BACE-1 revealed a novel mode of binding whereby the inhibitor interacts with the catalytic aspartates via bridging water molecules. Using the crystal structure as a guide, potent compounds with good brain penetration were designed.     

Inhibition of enkephalin metabolism by, and antinociceptive activity of, bestatin, an aminopeptidase inhibitor

In the presence of thiorphan an 'enkephalinase' inhibitor, bestatin an aminopeptidase inhibitor of bacterial origin potently inhibited the hydrolysis of [3H][Leu5]enkephalin by slices from rat striatum with an IC50 value of about 0.2 microM whereas puromycin was approximately 1000 times less potent on this preparation. In vivo bestatin or thiorphan (but not puromycin) significantly protected [3H][Met5]enkephalin administered intracerebroventricularly to mice from hydrolysis and co-administration of these two peptidase inhibitors resulted in a strong reduction in the appearance of hydrolysis products in brain. In a parallel fashion the antinociceptive activity of [Met5]enkephalin in the mouse hot-plate test was additively potentiated by bestatin and thiorphan but not by puromycin. Finally both bestatin and thiorphan themselves displayed antinociceptive properties on either the hot-plate jump test or the phenyl-benzo-quinone writhing test. It is concluded that a bestatin-sensitive aminopeptidase activity together with the 'enkephalinase' activity plays a critical role in the inactivation of both exogenous and endogenous enkephalins.     

cis-fumagillin, a new methionine aminopeptidase (type 2) inhibitor produced by Penicillium sp. F2757

Selective inhibition against the yeast MetAP2 (methionine aminopeptidase type 2) was detected in the fermentation broth of a fungus F2757 that was later identified as Penicillium janczewskii. A new compound cis-fumagillin methyl ester (1) was isolated from the diazomethane treated fermentation extracts together with the known compound fumagillin methyl ester (2). The cis-fumagillin methyl ester, a stereoisomer of fumagillin methyl ester at the C2'-C3' position of the aliphatic side chain, selectively inhibited growth of the map1 mutant yeast strain (MetAP1 deletion strain) at a concentration as low as 1 ng. However, the wild type yeast w303 and the mutant map2 (MetAP2 deleted) strains were resistant up to 10 microg of the compound. In enzyme experiments, compound 1 inhibited the MetAP2 with an IC50 value of 6.3 nM, but it did not inhibit the MetAP1 (IC50 >200 microM). Compound 2 also inhibited the MetAP2 with an IC50 value of 9.2 nM and 105 microM against MetAP1.     

4-Aryl-1,2,3-triazole: a novel template for a reversible methionine aminopeptidase 2 inhibitor, optimized to inhibit angiogenesis in vivo

Inhibitors of human methionine aminopeptidase type 2 (hMetAP2) are of interest as potential treatments for cancer. A new class of small molecule reversible inhibitors of hMetAP2 was discovered and optimized, the 4-aryl-1,2,3-triazoles. Compound 24, a potent inhibitor of cobalt-activated hMetAP2, also inhibits human and mouse endothelial cell growth. Using a mouse matrigel model, this reversible hMetAP2 inhibitor was also shown to inhibit angiogenesis in vivo.     

Sulfotransferase structural biology and inhibitor discovery

Sulfotransferases catalyze the transfer of a sulfuryl group from 3'-phosphoadenosine 5'-phosphosulfate (PAPS) to proteins, carbohydrates and small molecules. The sulfotransferases comprise cytosolic and Golgi-resident enzymes; Golgi-resident enzymes represent fertile territory for identifying pharmaceutical targets. Structure-based sequence alignments indicate that the structural fold, and the PAPS-binding site, is conserved between the two classes. Initial efforts to identify sulfotransferase inhibitors by screening kinase inhibitor libraries yielded competitive inhibitors of PAPS with muM IC(50) values. Within particular classes of Golgi-resident sulfotransferases that show tight in vitro specificity, the substrate-binding site might be a suitable drug target, although sulfotransferases are generally assumed to be difficult to inhibit as a result of the expected size and chemical character of the substrate-binding site.     

Inhibition of geranylgeranyl diphosphate synthase by bisphosphonates: a crystallographic and computational investigation

We report the X-ray structures of several bisphosphonate inhibitors of geranylgeranyl diphosphate synthase, a target for anticancer drugs. Bisphosphonates containing unbranched side chains bind to either the farnesyl diphosphate (FPP) substrate site, the geranylgeranyl diphosphate (GGPP) product site, and in one case, both sites, with the bisphosphonate moiety interacting with 3 Mg (2+) that occupy the same position as found in FPP synthase. However, each of three "V-shaped" bisphosphonates bind to both the FPP and GGPP sites. Using the Glide program, we reproduced the binding modes of 10 bisphosphonates with an rms error of 1.3 A. Activities of the bisphosphonates in GGPPS inhibition were predicted with an overall error of 2x by using a comparative molecular similarity analysis based on a docked-structure alignment. These results show that some GGPPS inhibitors can occupy both substrate and product site and that binding modes as well as activity can be accurately predicted, facilitating the further development of GGPPS inhibitors as anticancer agents.     

The effect of different species aminopeptidase N structure on the activity screening of aminopeptidase N inhibitor

Aminopeptidase N (APN) is a transmembrane metallopeptidase, which participates in the tumor progress such as proliferation, attachment, angiogenesis and tumor invasion. All of this makes APN as a good chemical therapeutic anti-tumor target. In the present study, we got a novel compound 16l which markedly inhibited the enzyme activity of porcine APN, and the inhibition constant, K(i), of 16l are similar to the positive medicine Bestatin determined using porcine APN. However, when tested using human tumor cells, 16l couldn't effectively inhibit the enzyme activity, cell viability, cell migration and invasion. Computer aided drug design verified that because of the difference in structure, the binding pattern of 16l in the active site of homo sapien and porcine APN was different. The compound 16l could effectively inhibit the enzyme activity of porcine APN, but not homo sapien APN located on the surface of tumor cells. Therefore, the activity screening of APN inhibitor using aminopeptidase N from porcine should be only preliminary determination. The real activity screening should be determined using homo sapien aminopeptidase N.     

Conformation of peroxynitrite: determination by crystallographic analysis

Peroxynitrite is an inorganic toxin of biological importance. It is formed in vivo from the diffusion-limited reaction of nitrogen monoxide with superoxide. Due to the partial double bond between the nitrogen and the first peroxide oxygen, peroxynitrite can occur in two conformations, cis and trans. The synthesis of tetramethylammonium peroxynitrite in ammonia [Bohle, D. S., et al. (1994) J. Am. Chem. Soc. 116, 7423-7424] yields small crystals if the ammonia is left to evaporate slowly. X-ray structure analysis shows that peroxynitrite crystallizes in the cis form, relative to the N-O bond. Crystal twinning or disorder prevents the determination of accurate bond lengths and bond angles. However, a nearly flat (torsion angle of 22 degrees ) molecule with O=N, N-O, and O-O bond lengths of 1.16, 1.35, and 1.41 A, respectively, would fit the observed electron density best. The space group of tetramethylammonium peroxynitrite is Pmmn (59), and it has the following unit cell dimensions: a = 7.1778(11) A, b = 8.6893(13) A, and c = 5.7266(9) A.     

X-ray crystallographic analysis of picrates

Picric acid forms stable picrates with various organic molecules through pi- bonding or ionic bonding, and such picrates have been very useful for identification and qualitative analysis. As it seemed desirable to determine the crystal structures and the bonding mode of picrates of basic organic compounds, we have investigated the crystal structures of aromatic hydrocarbons, aromatic amino compounds, heterocyclic compounds and so on. A series of our studies on the crystal structure of basic organic compounds have shown that the complexes of picric acid and aromatic hydrocarbons are formed through pi-bonding, and those of aromatic heterocyclic compounds are formed through ionic and hydrogen bonding; in addition, some of them also have pi-bonding.     

Identification of promising methionine aminopeptidase enzyme inhibitors: A combine study of comprehensive virtual screening and dynamics simulation study

Methionine aminopeptidase (MetAP) enzymes play a critical role in bacterial cell survival by cleaving formyl-methionine initiators at N-terminal of nascent protein, a process which is vital in proper protein folding. This makes MetAP an attractive and novel antibacterial target to unveil promising antibiotics. In this study, the crystal structure of R. prowazekii MetAP was used in structure-based virtual screening of drug libraries such as Asinex antibacterial library and Comprehensive Marine Natural Products Database (CMNPD) to identify promising lead molecules against the enzyme. This shortlisted three drug molecules; BDE-25098678, BDE-30686468 and BDD_25351157 as most potent leads that showed strong binding to the MetAP enzyme. The static docked conformation of the compounds to the MetAP was reevaluated in molecular dynamics simulation studies. The analysis observed the docked complexes as stable structure with no major local or global deviations noticed. These findings suggest the formation of strong intermolecular docked complexes, which showed stable dynamics and atomic level interactions network. The binding free energy analysis predicted net MMGBSA energy of complexes as: BDE-25098678 (-73.41 kcal/mol), BDE-30686468 (-59.93 kcal/mol), and BDD_25351157 (-75.39 kcal/mol). In case of MMPBSA, the complexes net binding energy was as; BDE-25098678 (-77.47 kcal/mol), BDE-30686468 (-69.47 kcal/mol), and BDD_25351157 (-75.6 kcal/mol). Further, the compounds were predicted to follow the famous Lipinski rule of five and have non-toxic, non-carcinogenic and non-mutagenic profile. The screened compounds might be used in experimental test to highlight the real anti- R. prowazekii MetAP activity.     

Polymorphisms of methionine synthase and methionine synthase reductase and risk of lung cancer: a case-control analysis

Although tobacco is the major lung cancer risk factor, folate deficiency has also been implicated as a risk. Methionine synthase (MS; gene symbol, MTR) and methionine synthase reductase (MSR; gene symbol, MTRR) play important roles in the folate metabolism pathway. It was hypothesized that polymorphisms of MTR and MTRR are associated with lung cancer risk and interact with dietary intake of folate-related nutrients in lung cancer etiology. In a hospital-based, case-control study of 1,035 lung cancer cases and 1,148 controls of non-Hispanic whites, frequency matched by age, sex, ethnicity and smoking status, the MTR 2756A>G and MTRR 66A>G polymorphisms were genotyped. It was found that the MTRRG allele was associated with a significantly increased lung cancer risk [adjusted odd ratio (OR)=1.34, 95% confidence interval (CI)=1.06-1.70 for the AG genotype and OR=1.39, 95% CI=1.08-1.78 for the GG genotype compared to the AA genotype]. Further analysis suggested some evidence of gene-diet interactions between the MTRR 66A>G polymorphism and dietary intake of total folate and vitamin B12. When the two polymorphisms were evaluated together by the number of the variant alleles (i.e. the MTR2756G and MTRR66A), lung cancer risk was significantly increased in a dose-dependent manner (Ptrend=0.045). The risk of lung cancer was 1.29 (0.98-1.69) for one variant allele, and 1.36 (1.04-1.77) for two or more variant alleles compared to the wild-type (0 variant allele) genotype. In conclusion, our data provide evidence supporting the association between the MTR 2756A>G and MTRR 66A>G polymorphisms and lung cancer risk, which may be modulated by dietary nutrient intake.     

Metal-mediated inhibition of Escherichia coli methionine aminopeptidase: structure-activity relationships and development of a novel scoring function for metal-ligand interactions

We report the discovery of thiabendazole as a potent inhibitor (K(i) = 0.4 microM) of Escherichia coli methionine aminopeptidase (ecMetAP) and the synthesis and pharmacological evaluation of thiabendazole congeners with activity in the upper nanomolar range. Elucidation of the X-ray structure of ecMetAP in complex with thiabendazole and an unrelated inhibitor that was independently described by another group showed that that both compounds bind to an additional Co(II) ion at the entrance of the active site. This unexpected finding explains the inactivity of the compounds under in vivo conditions. It also allows us to discuss the structure-activity relationships of this series of compounds in a meaningful way, based upon docking runs with an auxiliary metal ion. We describe a new scoring function for the evaluation of metal-mediated inhibitor binding that, unlike the previously used scoring function implemented in the docking program, allows us to distinguish between active and inactive compounds. Finally, conclusions for the structure-based design of in vivo-active inhibitors of ecMetAP are drawn.