Total synthesis of amiclenomycin, an inhibitor of biotin biosynthesis

Sulfonium ion-promoted traceless Schmidt reaction of alkyl azides

Schmidt reaction by sulfonium ions is described. General primary, secondary, and tertiary alkyl azides were converted to the corresponding carbonyl or imine compounds without any trace of the activators. This bond scission reaction through 1,2-migration of C-H and C-C bonds was accessible to the one-pot substitution reaction.

Discovery of the Biosynthetic Machinery for Stravidins, Biotin Antimetabolites

Stravidins are peptide antibiotics produced by Streptomyces spp. Their antibacterial activity derives from an unusual amiclenomycin monomer, the warhead that inhibits biotin biosynthesis. Despite being discovered over five decades ago, stravidin biosynthesis has remained a mystery. Using our "metabologenomics" platform, we discover new stravidin analogues and identify the novel biosynthetic machinery responsible for their production. Analysis of the newly identified biosynthetic gene cluster (BGC) indicates the unusual amiclenomycin warhead is derived from chorismic acid, with initial steps similar to those involved in p-amino phenylalanine biosynthesis. However, a distinctive decarboxylation retains the nonaromatic character of a key ring and precedes a one-carbon extension to afford the warhead in its bioactive, untriggered state. Strikingly, we also identified two streptavidin genes flanking the new stravidin BGC reported here. This aligns with the known synergistic activity between the biotin-binding activity of streptavidin and the stravidins to antagonize both biotin biogenesis and bacterial growth.

Sulfones as Chemical Chameleons: Versatile Synthetic Equivalents of Small-Molecule Synthons

Sulfones are flexible functional groups that can act as nucleophiles, electrophiles, or even radicals. Changing the reaction conditions can completely alter the reactivity of a sulfonyl group, and as a result, molecules bearing multiple sulfones are versatile building blocks. This Review highlights the unique ability of 1,1- and 1,2-bis(sulfones) to masquerade as a vast array of reactive synthons including methane polyanions, vinyl cations, and all-carbon dipoles that would be difficult or impossible to access directly.

Designing Stability into Thermally Reactive Plumbylenes

Lead analogues of N-heterocyclic carbenes (NHPbs) are the least understood members of this increasingly important class of compounds. Here we report the design, preparation, isolation, structure, volatility, and decomposition pathways of a novel aliphatic NHPb: rac- N ², N ³-di- tert-butylbutane-2,3-diamido lead(II) (1Pb). The large steric bulk of the tert-butylamido moieties and rac-butane backbone successfully hinder redox decomposition pathways observed for diamidoethylene and -ethane backbone analogues, pushing the onset of thermal decomposition from below 0 °C to above 150 °C. With an exceptionally high vapor pressure of 1 Torr at 94 ± 2 °C and excellent thermal stability among Pb(II) complexes, 1Pb is a promising precursor for the chemical vapor deposition (CVD) and atomic layer deposition (ALD) of functional lead-containing materials.

Recent advances in the Overman rearrangement: synthesis of natural products and valuable compounds

This review documents the reports since 2005 on the Overman rearrangement, an important C–N bond forming reaction that has been profoundly used in the synthesis of natural products, synthetic intermediates, building blocks and valuable compounds.

The Role of Biotin in Bacterial Physiology and Virulence: a Novel Antibiotic Target for Mycobacterium tuberculosis

Biotin is an essential cofactor for enzymes present in key metabolic pathways such as fatty acid biosynthesis, replenishment of the tricarboxylic acid cycle, and amino acid metabolism. Biotin is synthesized de novo in microorganisms, plants, and fungi, but this metabolic activity is absent in mammals, making biotin biosynthesis an attractive target for antibiotic discovery. In particular, biotin biosynthesis plays important metabolic roles as the sole source of biotin in all stages of the Mycobacterium tuberculosis life cycle due to the lack of a transporter for scavenging exogenous biotin. Biotin is intimately associated with lipid synthesis where the products form key components of the mycobacterial cell membrane that are critical for bacterial survival and pathogenesis. In this review we discuss the central role of biotin in bacterial physiology and highlight studies that demonstrate the importance of its biosynthesis for virulence. The structural biology of the known biotin synthetic enzymes is described alongside studies using structure-guided design, phenotypic screening, and fragment-based approaches to drug discovery as routes to new antituberculosis agents.

Unexpected reactions of Grignard reagents with selected β-carboalkoxy substituted sulfinate esters

A series of six-membered rings bearing cis oriented vicinal carboxylate and sulfinate esters were treated with Grignard reagents with the intention of transforming them to β-carboalkoxy substituted sulfoxides. The expected outcome did not transpire and instead the substrates demonstrated the capacity to accept 3 equiv. of organometallic agent in an uncontrollable manner. As such, the substrates possessing eclipsing carboxylate and sulfinate esters accepted two organic ligands at the carboxylate functionality and one at the sulfinyl group. When isomer mixtures of sterically encumbered sulfinate esters were reacted, a single sulfoxide stereochemistry resulted. A mechanism involving the intermediacy of a sulfurane is proposed to account for the experimental observations.

Carbolithiation of Styrenes with N-tert-butyl aldimines

The addition of aldimine anions to styrene occurs upon the treatment of N-tert-butyl aldimine with LDA followed by the addition of styrene to give the corresponding aldehyde after hydrolysis. Cyclohexenyl amines are generated when the reactions are performed with unsaturated aldimines. This approach affords 4-phenyl substituted butanals and cyclohexenyl amines in a simple and inexpensive way.

Design and synthesis of potential mechanism-based inhibitors of the aminotransferase BioA involved in biotin biosynthesis

BioA, a pyridoxal 5'-phosphate (PLP) dependent aminotransferase, catalyzes the second step of biotin biosynthesis, converting 7-keto-8-aminopelargonic acid (KAPA) into 7,8-diaminopelargonic acid (DAPA). Amiclenomycin (ACM) isolated from cultures of different Streptomyces strains is a potent mechanism-based inhibitor of BioA that operates via an aromatization mechanism, irreversibly labeling the PLP cofactor. However, ACM is plagued by inherent chemical stability. Herein we describe the synthesis of four inhibitors, inspired by ACM but containing an allylic amine as the chemical warhead, designed to both improve stability and operate via a complementary Michael addition-pathway upon enzymatic oxidation of the allylic amine substrate to an enimine. Acyclic analogue M-1 contains a terminal olefin as the pro-Michael acceptor. The synthesis of M-1 features an alkyne-zipper reaction and the Overman rearrangement as key synthetic operations. The cyclic analogues M-2/3/4 contain either an endocyclic or exocyclic olefin as the pro-Michael acceptor. These were all prepared using a common strategy employing DIBAL reduction of a precursor bicyclic lactam, followed by in situ Horner-Wadsworth-Emmons (HWE) olefination as the key synthetic steps.

Mechanism-based inactivation by aromatization of the transaminase BioA involved in biotin biosynthesis in Mycobaterium tuberculosis

BioA catalyzes the second step of biotin biosynthesis, and this enzyme represents a potential target to develop new antitubercular agents. Herein we report the design, synthesis, and biochemical characterization of a mechanism-based inhibitor (1) featuring a 3,6-dihydropyrid-2-one heterocycle that covalently modifies the pyridoxal 5'-phosphate (PLP) cofactor of BioA through aromatization. The structure of the PLP adduct was confirmed by MS/MS and X-ray crystallography at 1.94 Å resolution. Inactivation of BioA by 1 was time- and concentration-dependent and protected by substrate. We used a conditional knock-down mutant of M. tuberculosis to demonstrate the antitubercular activity of 1 correlated with BioA expression, and these results provide support for the designed mechanism of action.

Pyridoxal-5'-phosphate-dependent enzymes involved in biotin biosynthesis: structure, reaction mechanism and inhibition

The four last steps of biotin biosynthesis, starting from pimeloyl-CoA, are conserved among all the biotin-producing microorganisms. Two enzymes of this pathway, the 8-amino-7-oxononanoate synthase (AONS) and the 7,8-diaminopelargonic acid aminotransferase (DAPA AT) are dependent on pyridoxal-5'-phosphate (PLP). This review summarizes our current understanding of the structure, reaction mechanism and inhibition on these two interesting enzymes. Mechanistic studies as well as the determination of the crystal structure of AONS have revealed a complex mechanism involving an acylation with inversion of configuration and a decarboxylation with retention of configuration. This reaction mechanism is shared by the homologous 5-aminolevulinate synthase and serine palmitoyltransferase. While the reaction catalyzed by DAPA AT is a classical PLP-dependent transamination, the inactivation of this enzyme by amiclenomycin, a natural antibiotic that is active against Mycobacterium tuberculosis, involves the irreversible formation of an adduct between PLP and amiclenomycin. Mechanistic and structural studies allowed the complete description of this unique inactivation mechanism. Several potent inhibitors of these two PLP-dependent enzymes have been prepared and might be useful as starting points for the design of herbicides or antibiotics. This article is part of a Special Issue entitled: Pyridoxal Phospate Enzymology.

Property tuning in charge-transfer chromophores by systematic modulation of the spacer between donor and acceptor

A series of donor-acceptor chromophores was prepared in which the spacer separating 4-dimethylanilino (DMA) donor and C(CN)(2) acceptor moieties is systematically varied. All of the new push-pull systems, except 4 b, are thermally stable molecules. In series a, the DMA rings are directly attached to the central spacer, whereas in series b additional acetylene moieties are inserted. X-ray crystal structures were obtained for seven of the new, intensely colored target compounds. In series a, the DMA rings are sterically forced out of the mean plane of the residual pi system, whereas the entire conjugated pi system in series b is nearly planar. Support for strong donor-acceptor interactions was obtained through evaluation of the quinoid character of the DMA ring and by NMR and IR spectroscopy. The UV/Vis spectra feature bathochromically shifted, intense charge-transfer bands, with the lowest energy transitions and the smallest optical gap being measured for the two-dimensionally extended chromophores 6 a and 6 b. The redox behavior of the push-pull molecules was investigated by cyclic voltammetry (CV) and differential pulse voltammetry (DPV). In the series 1 b, 2 b, 4 b, 5 b, in which the spacer between donor and acceptor moieties is systematically enlarged, the electrochemical gap decreases steadily from 1.94 V (1 b) to 1.53 V (5 b). This decrease is shown to be a consequence of a reduction in the D-A conjugation with increasing spacer length. Degenerate four-wave mixing experiments reveal high third-order optical nonlinearities, pointing to potentially interesting applications of some of the new chromophores in optoelectronic devices.

7,8-Diaminoperlargonic acid aminotransferase from Mycobacterium tuberculosis, a potential therapeutic target. Characterization and inhibition studies

Diaminopelargonic acid aminotransferase (DAPA AT), which is involved in biotin biosynthesis, catalyzes the transamination of 8-amino-7-oxononanoic acid (KAPA) using S-adenosyl-l-methionine (AdoMet) as amino donor. Mycobacterium tuberculosis DAPA AT, a potential therapeutic target, has been overproduced in Escherichia coli and purified to homogeneity using a single efficient step on a nickel-affinity column. The enzyme shows an electronic absorption spectrum typical of pyridoxal 5'-phosphate-dependent enzymes and behaves as a homotetramer in solution. The pH profile of the activity at saturation shows a single ionization group with a pK(a) of 8.0, which was attributed to the active-site lysine residue. The enzyme shows a Ping Pong Bi Bi kinetic mechanism with strong substrate inhibition with the following parameters: K(mAdoMet) = 0.78 +/- 0.20 mm, K(mKAPA) = 3.8 +/- 1.0 microm, k(cat) = 1.0 +/- 0.2 min(-1), K(iKAPA) = 14 +/- 2 microm. Amiclenomycin and a new analogue, 4-(4c-aminocyclohexa-2,5-dien-1r-yl)propanol (referred to as compound 1), were shown to be suicide substrates of this enzyme, with the following inactivation parameters: K(i) = 12 +/- 2 microm, k(inact) = 0.35 +/- 0.05 min(-1), and K(i) = 20 +/- 2 microm, k(inact) = 0.56 +/- 0.05 min(-1), for amiclenomycin and compound 1, respectively. The inactivation was irreversible, and the partition ratios were 1.0 and 1.1 for amiclenomycin and compound 1, respectively, which make these inactivators particularly efficient. compound 1 (100 microg.mL(-1)) completely inhibited the growth of an E. coli C268bioA mutant strain transformed with a plasmid expressing the M. tuberculosis bioA gene, coding for DAPA AT. Reversal of the antibiotic effect was observed on the addition of biotin or DAPA. Thus, compound 1 specifically targets DAPA AT in vivo.

N,N‘-Carbonyldiimidazole-Mediated Cyclization of Amino Alcohols to Substituted Azetidines and Other N-Heterocycles

Amino alcohols are important synthons for N-heterocycles. We have developed an efficient method to activate hydroxyl groups, which avoids the use of toxic reagents and tolerates a wide variety of functional groups. Our strategy has been applied to the synthesis of functionalized p-methoxyphenyl-protected azetidines, pyrrolidines, and piperidines. The required amino alcohols were synthesized according to an optimized proline-catalyzed Mannich protocol. An azetidine analogue of ezetimibe was synthesized to demonstrate the potential for the synthesis of drug-like molecules.

Inhibition of 7,8-diaminopelargonic acid aminotransferase by amiclenomycin and analogues

Cis and trans stereoisomers of amiclenomycin, a natural L-amino acid antibiotic, have been prepared using unequivocal routes. By using 1H NMR spectroscopy, the configuration of the six-membered ring of natural amiclenomycin was shown to be cis and not trans as originally proposed. Amiclenomycin and some synthetic analogues with the cis configuration irreversibly inactivate DAPA AT (7,8-diaminopelargonic acid aminotransferase), an enzyme involved in biotin biosynthesis, by forming an aromatic PLP (pyridoxal-5'-phosphate)-inhibitor adduct that is tightly bound to the active site. The following kinetic parameters for the inactivation of Escherichia coli DAPA AT by amiclenomycin were derived: K(I)=2 microM and k(inact)=0.4 min(-1). The structure of the aromatic adduct formed upon inactivation was confirmed by UV-visible spectroscopy, X-ray crystal structure determination and MS. Because Mycobacterium tuberculosis DAPA AT is a potential drug target, this enzyme was cloned, overexpressed and purified to homogeneity for biochemical characterization.

γ-p-Toluenesulfonyl-α,β-epoxysilane: A New and Practical Acrolein β-Anion Equivalent

[reaction: see text] Reaction of gamma-p-toluenesulfonyl-alpha,beta-epoxysilane with alkyl halides and aldehydes followed by treatment with n-Bu4NF affords alpha,beta-unsaturated aldehydes via a Brook rearrangement-mediated tandem process under extremely mild conditions.

Structural basis for the inhibition of the biosynthesis of biotin by the antibiotic amiclenomycin

The antibiotic amiclenomycin blocks the biosynthesis of biotin by inhibiting the pyridoxal-phosphate-dependent enzyme diaminopelargonic acid synthase. Inactivation of the enzyme is stereoselective, i.e. the cis isomer of amiclenomycin is a potent inhibitor, whereas the trans isomer is much less reactive. The crystal structure of the complex of the holoenzyme and amiclenomycin at 1.8 A resolution reveals that the internal aldimine linkage between the cofactor and the side chain of the catalytic residue Lys-274 is broken. Instead, a covalent bond is formed between the 4-amino nitrogen of amiclenomycin and the C4' carbon atom of pyridoxal-phosphate. The electron density for the bound inhibitor suggests that aromatization of the cyclohexadiene ring has occurred upon formation of the covalent adduct. This process could be initiated by proton abstraction at the C4 carbon atom of the cyclohexadiene ring, possibly by the proximal side chain of Lys-274, leading to the tautomer Schiff base followed by the removal of the second allylic hydrogen. The carboxyl tail of the amiclenomycin moiety forms a salt link to the conserved residue Arg-391 in the substrate-binding site. Modeling suggests steric hindrance at the active site as the determinant of the weak inhibiting potency of the trans isomer.