Broad substrate stereospecificity of the Mycobacterium tuberculosis 7-keto-8-aminopelargonic acid synthase: Spectroscopic and kinetic studies

Biotin is an essential enzyme cofactor required for carboxylation and transcarboxylation reactions. The absence of the biotin biosynthesis pathway in humans suggests that it can be an attractive target for the development of novel drugs against a number of pathogens. 7-Keto-8-aminopelargonic acid (KAPA) synthase (EC 2.3.1.47), the enzyme catalyzing the first committed step in the biotin biosynthesis pathway, is believed to exhibit high substrate stereospecificity. A comparative kinetic characterization of the interaction of the mycobacterium tuberculosis KAPA synthase with both L- AND D-alanine was carried out to investigate the basis of the substrate stereospecificity exhibited by the enzyme. The formation of the external aldimine with D-alanine (k = 82.63 m(-1) s(-1)) is approximately 5 times slower than that with L-alanine (k = 399.4 m(-1) s(-1)). In addition to formation of the external aldimine, formation of substrate quinonoid was also observed upon addition of pimeloyl-CoA to the preformed d-alanine external aldimine complex. However, the formation of this intermediate was extremely slow compared with the substrate quinonoid with L-alanine and pimeloyl-CoA (k = 16.9 x 10(4) m(-1) s(-1)). Contrary to earlier reports, these results clearly show that D-alanine is not a competitive inhibitor but a substrate for the enzyme and thereby demonstrate the broad substrate stereospecificity of the M. tuberculosis KAPA synthase. Further, d-KAPA, the product of the reaction utilizing D-alanine inhibits both KAPA synthase (Ki = 114.83 microm) as well as 7,8-diaminopelargonic acid synthase (IC50 = 43.9 microm), the next enzyme of the pathway.     

Synthesis and antibacterial activity of mechanism-based inhibitors of KDO8P synthase and DAH7P synthase

KDO8PS (3-deoxy-D-manno-2-octulosonate-8-phosphate synthase) and DAH7PS (3-deoxy-D-arabino-2-heptulosonate-7-phosphate synthase) are attractive targets for the development of new anti-infectious agents. Both enzymes appear to proceed via a common mechanism involving the reaction of phosphoenolpyruvate (PEP) with arabinose 5-phosphate or erythrose-4-phosphate, to produce the corresponding ulosonic acids, KDO8P and DAH7P, respectively. The synthesis of new inhibitors closely related to the supposed tetrahedral intermediate substrates for the enzymes is described. The examination of the antibacterial activity of these derivatives is reported.     

Structure of a Peptidal Antibiotic P168 Produced by Paecilomyces lilacinus (Thom) Samson

( + )-α-Kainic acid (1) was synthesized by starting from a building block, N-Boc-3-acetoxyallylglycine ethyl ester (2). The key intermediate, a methyl 4-[(tert-butoxycarbonyl)prenylamino]-5-hydroxy-2-pentenoate derivative (9), was prepared from 2 in eight synthetic steps. After converting 10 into a methyl ester (11), intramolecular ene-carbocyclization of 11 gave a pyrrolidine derivative (12), which was converted to 1 in a moderate yield.     

Discovery of novel fatty acid synthase (FAS) inhibitors based on the structure of ketoaceyl synthase (KS) domain

Development of fatty acid synthase (FAS) inhibitors has increasingly attracted much attention in recent years due to their potential therapeutic use in obesity and cancers. In this investigation, pharmacophore modeling based on the first crystal structure of human KS domain of FAS was carried out. The established pharmacophore model was taken as a 3D query for retrieving potent FAS inhibitors from the chemical database Specs. Docking study was further carried out to refine the obtained hit compounds. Finally, a total of 28 compounds were selected based on the ranking order and visual examination, which were first evaluated by a cell line-based assay. Seven compounds that have good inhibition activity against two FAS overexpressing cancer cell lines were further evaluated by an enzyme-based assay. One compound with a new chemical scaffold was found to have low micromolar inhibition potency against FAS, which has been subjected to further chemical structural modification.     

7-Dehydroagapanthagenin and 8(14)-dehydroagapanthagenin,two new spirostan sapogenins from Agapanthus africanus

Besides sitosterol, yuccagenin (1a) and agapanthagenin (2a), the two new spirostan sapogenins 7-dehydroagapanthagenin (3a) and 8(14)-dehydroagapanthagenin (4a) have been isolated from the rhizomes of Agapanthus africanus and their structures determined.     

The structure of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis reveals a common catalytic scaffold and ancestry for type I and type II enzymes

The shikimate pathway, responsible for the biosynthesis of aromatic compounds, is essential for the growth of Mycobacterium tuberculosis and is a potential target for the design of new anti-tuberculosis drugs. The first step of this pathway is catalyzed by 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (DAH7PS). The DAH7PSs have been classified into two apparently unrelated types and, whereas structural data have been obtained for the type I DAH7PSs, no structural information is available for their type II counterparts. The type II DAH7PS from M.tuberculosis has been expressed in Escherichia coli, purified, functionally characterized and crystallized. It is found to be metal ion-dependent and subject to feedback inhibition by phenylalanine, tryptophan, tyrosine and chorismate, with a significant synergistic effect when tryptophan is used in combination with phenylalanine. The crystal structure of M.tuberculosis DAH7PS has been determined by single-wavelength anomalous diffraction and refined at 2.3A in complex with substrate phosphoenolpyruvate and Mn(2+). The structure reveals a tightly associated dimer of (beta/alpha)(8) TIM barrels. The monomer fold, the arrangement of key residues in the active site, and the binding modes of PEP and Mn(2+), all match those of the type I enzymes, and indicate a common ancestry for the type I and type II DAH7PSs, despite their minimal sequence identity. In contrast, the structural elements that decorate the core (beta/alpha)(8) fold differ from those in the type I enzymes, consistent with their different regulatory and oligomeric properties.     

Pyrazinamide, but not pyrazinoic acid, is a competitive inhibitor of NADPH binding to Mycobacterium tuberculosis fatty acid synthase I

Pyrazinamide (PZA), an essential component of short-course anti-tuberculosis chemotherapy, was shown by Saturation Transfer Difference (STD) NMR methods to act as a competitive inhibitor of NADPH binding to purified Mycobacterium tuberculosis fatty acid synthase I (FAS I). Both PZA and pyrazinoic acid (POA) reversibly bind to FAS I but at different binding sites. The competitive binding of PZA and NADPH suggests potential FAS I binding sites. POA was not previously known to have any specific binding interactions. The STD NMR of NADPH bound to the mycobacterial FAS I was consistent with the orientation reported in published single crystal X-ray diffraction studies of fungal FAS I. Overall the differences in binding between PZA and POA are consistent with previous recognition of the importance of intracellular accumulation of POA for anti-mycobacterial activity.     

Structure of the complex of heptakis(2,6-di-O-methyl)-beta-cyclodextrin with (2,4-dichlorophenoxy)acetic acid

The structure of the complex formed by heptakis(2,6-di-O-methyl)-beta-cyclodextrin and (2,4-dichlorophenoxy)acetic acid was studied by X-ray diffraction. The dichlorophenyl moiety of the guest molecule was found outside the host hydrophobic cavity in the primary methoxy groups region whereas the oxyacetic acid chain penetrates the cavity from the primary face. The host molecules stacks along the a crystal axis forming a column. In the space between three successive hosts of the column, a guest molecule is accommodated.     

Synthesis, characterization and crystal structure of manganese (IV) complex derived from salicylic acid

The binuclear manganese (IV) [Mn₂(Hsal)₄(OH)₄] (H₂sal = salicylic acid) complex has been obtained from a complex reaction mixture in methanol consisting of Mn(II)(OAc)₂ · 4H₂O, GS ( a reagent obtained by refluxing glycine and salicylaldehyde in 1:1 molar ratio in methanol), monosodium salicylate and pyridine. The compound contains a distorted octahedral MnO₆ coordination unit of potential importance to high oxidation state manganese bimolecules.     

Sonochemical synthesis of a new nano-plate lead(II) coordination polymer constructed of maleic acid

A new nano-sized lead(II) coordination polymer of maleic acid (H₂Mal), [Pb(μ₇-Mal)]_n (1), has been synthesized by sonochemical method and characterized by scanning electron microscopy, X-ray powder diffraction, elemental analyses and IR spectroscopy. The compound 1 was structurally characterized by single-crystal X-ray diffraction. Thermal stability of nano and bulk samples of compound 1 were studied and compared with each other. After calcination of nano-sized compound 1 at 600 °C, pure phase micro-sized lead(II) oxide has been produced.     

Investigation on the coordination modes: Syntheses, characterization and crystal structures of diorganotin (IV) dichloride with 4(5)-imidazoledithiocarboxylic acid

A series of diorganotin (IV) complexes of the types of R₂SnCl(SSCC₃H₃N₂) (R = CH₃1, ⁿBu 2, C₆H₅3 and C₆H₅CH₂4), R₂Sn(SSCC₃H₃N₂)₂ (R = CH₃5, ⁿBu 6, C₆H₅7 and C₆H₅CH₂8) and R₂Sn(SSCC₃H₂N₂) (R = CH₃9, ⁿBu 10, C₆H₅11 and C₆H₅CH₂12) have been obtained by reactions of 4(5)-imidazoledithiocarboxylic acid with diorganotin (IV) dichlorides in the presence of sodium ethoxide. All complexes are characterized by elemental, IR, ¹H, ¹³C and ¹¹⁹Sn NMR spectra analyses. Also, the complexes 1, 7 and 9 are characterized by X-ray crystallography diffraction analyses, which reveal that the complex 1 is monomeric structure with five-coordinate tin (IV) atom, the complex 7 is monomeric structure with six-coordinate tin (IV) atom and the complex 9 is one-dimensional chain with five-coordinate tin (IV) atom.     

13C NMR spectra of 1, 3, 6 -trihydroxy-7-methoxy-8-(3, 7 -dimethyl-2,6-octadienyl) xanthone and its dimethyl derivative

The ¹³C NMR spectra of 1, 3, 6-trihydroxy-7-methoxy-8-(3, 7-dimethyl-2, 6-octadienyl)xanthone and its dimethyl derivative are discussed. The data obtained confirmed the assigned structures. The geometrical configuration of the C₁₀ dienyl side-chain has been deduced as trans.     

Guaiacylglycerol-7'-O-methyl 8'-vanillic acid ether and related compounds from Boreava orientalis

The threo and erythro forms of guaiacylglycerol-7'-O-methyl 8'-vanillic acid ethers, threo and erythro guaiacylglycerol 8'-vanillin ethers, and threo guaiacylglycerol 8'-(4-hydroxymethyl-2-methoxyphenyl) ether have been isolated from fruits of Boreava orientalis. Structural determinations were made on the basis of UV, MS, 1H- and 13C-NMR spectral data, including two-dimensional shift correlation. The relative configurations were assigned on the basis of 1H-NMR chemical shifts.     

1,3,6-Trihydroxy-7-methoxy-8-(3,7-dimethyl-2,6-octadienyl)xanthone from Garcinia cowa

1,3,6-Trihydroxy-7-methoxy-8-(3,7-dimethyl-2,6-octadienylxanthone has been isolated from the stems of Garcinia cowa.     

Syntheses and crystal structures of dimethyltin (IV) derivatives with 2,6-pyridinedicarboxylic acid

A novel cyclic dimethyltin complex [Me₂Sn(2,6-pdc)]₃ (1) (2,6-pdc = 2,6-pyridinedicarboxylate) was synthesized by the reaction of dimethyltin (IV) dichloride and 2,6-pyridinedicarboxylate acid in methanol under solvothermal conditions (150 °C). However, under room temperature (25 °C), we obtained a ladder complex [Me₂Sn(2,6-pdc)]₂(MeOH)₂ (2). Characterization of complexes 1 and 2 was achieved using elemental analysis, IR, ¹H, ¹³C and ¹¹⁹Sn NMR spectra and X-ray diffraction. X-ray data of 1 revealed that it was an unusual cyclic complex with a discrete cyclotrinuclear unit, in which the 12-membered cyclic cavity is almost completely planar. X-ray data of 2 showed that it was a ladder complex, in which a crystallizing methanol molecule is found in each formula unit.     

Polycytidylate and poly(7-deazaguanylate): A pair of complementary templates

We have studied the template-directed oligomerization on polycytidylic acid of the 5-phosphoro(2-methyl)imidazolides of a number of analogues of guanosine. None of the analogues reacted as efficiently as the original guanosine compound, and only the 7-deazaguanosine analogue gives a detectable yield of oligomers. Similar results are described for a reaction involving the intramolecular template-directed elongation of a short oligocytidylate primer.Oligocytidylates containing five or more cytidylate residues are extended on the single-stranded regions of poly(G). In the present study we show that these oligocytidylates are extended efficiently by reaction with cytidine-5-phosphoro(2-methyl) imidazolide on a poly(7-deazaguanylic acid) template. The products are considerably longer than those obtained using a polyguanylic acid template. We believe that the formation of a tetrahelix inhibits the latter reaction, while poly(7-deazaguanylate) does not aggregate and, therefore, acts as a more efficient template. This work identifies for the first time a pair of homopolymers each of which facilitates the template-directed elongation of the other.Deceased Correspondence to: L.E. Orgel