Importance of specific hydrogen-bond donor-acceptor interactions for the key carbocycle-forming reaction catalyzed by 2-deoxy-scyllo-inosose synthase in the biosynthesis of 2-deoxystreptamine-containing aminocyclitol antibiotics

Diastereoselective synthesis of new O-alkylated and C-branched inositols and their corresponding fluoro analogues

Efficient routes were developed for the diastereoselective synthesis of new O-alkylated and C-branched inositols and their corresponding fluoro analogues. The key steps of the synthesis were the easy accessibility of different types of arms in term of configuration (myo and scyllo), the linking method and length, which could modulate the biological properties. These inositol derivatives, bearing an arm terminated either with a hydroxy group or a fluorine atom, could be interesting candidates for diastereoisomeric intermediates and biological evaluations, especially for PET imaging experiments.

Aminoglycoside Antibiotics: New Insights into the Biosynthetic Machinery of Old Drugs

2-Deoxystreptamine (2DOS) is the unique chemically stable aminocyclitol scaffold of clinically important aminoglycoside antibiotics such as neomycin, kanamycin, and gentamicin, which are produced by Actinomycetes. The 2DOS core can be decorated with various deoxyaminosugars to make structurally diverse pseudo-oligosaccharides. After the discovery of biosynthetic gene clusters for 2DOS-containing aminoglycoside antibiotics, the function of each biosynthetic enzyme has been extensively elucidated. The common biosynthetic intermediates 2DOS, paromamine and ribostamycin are constructed by conserved enzymes encoded in the gene clusters. The biosynthetic intermediates are then converted to characteristic architectures by unique enzymes encoded in each biosynthetic gene cluster. In this Personal Account, we summarize both common biosynthetic pathways and the pathways used for structural diversification.

Simple one-pot regioselective 6-O-phosphorylation of carbohydrates and trehalose desymmetrization

Biologically essential carbohydrate 6-phosphates, especially trehalose 6-phosphate, can be synthesized easily in excellent overall yields in 2 steps involving minimum protecting group manipulations. We can cleave the diphenylphosphate group for further synthetic objectives.

Biosynthetic enzymes for the aminoglycosides butirosin and neomycin

Butirosin and neomycin belong to a family of clinically valuable 2-deoxystreptamine (2DOS)-containing aminoglycoside antibiotics. The biosynthetic gene clusters for butirosin and neomycin were identified in 2000 and in 2005, respectively. In recent years, most of the enzymes encoded in the gene clusters have been characterized, and thus almost all the biosynthetic steps leading to the final antibiotics have been understood. This knowledge could shed light on the complex biosynthetic pathways for other related structurally diverse aminoglycoside antibiotics. In this chapter, the enzymatic reactions in the biosynthesis of butirosin and neomycin are reviewed step by step.

Structure of 2-deoxy-scyllo-inosose synthase, a key enzyme in the biosynthesis of 2-deoxystreptamine-containing aminoglycoside antibiotics, in complex with a mechanism-based inhibitor and NAD+

A key enzyme in the biosynthesis of clinically important aminoglycoside antibiotics is 2-deoxy-scyllo-inosose synthase (DOIS), which catalyzes carbocycle formation from D-glucose-6-phosphate to 2-deoxy-scyllo-inosose through a multistep reaction. This reaction mechanism is similar to the catalysis by dehydroquinate synthase (DHQS) of the cyclization of 3-deoxy-D-arabino-heputulosonate-7-phosphate to dehydroquinate in the shikimate pathway, but significant dissimilarity between these enzymes is also known, particularly in the stereochemistry of the phosphate elimination reaction and the cyclization. Here, the crystal structures of DOIS from Bacillus circulans and its complex with the substrate analog inhibitor carbaglucose-6-phosphate, NAD+, and Co2+ have been determined to provide structural insights into the reaction mechanism. The complex structure shows that an active site exists between the N-terminal and C-terminal domains and that the inhibitor coordinates a cobalt ion in this site. Two subunits exist as a dimer in the asymmetric unit. The two active sites of the dimer were observed to be different. One contains a dephosphorylated compound derived from the inhibitor and the other includes the inhibitor without change. The present study suggested that phosphate elimination proceeds through syn-elimination assisted by Glu 243 and the aldol condensation proceeds via a boat conformation. Also discussed are significant similarities and dissimilarities between DOIS and DHQS, particularly in terms of the structure at the active site and the reaction mechanism.

Role of glutamate 243 in the active site of 2-deoxy-scyllo-inosose synthase from Bacillus circulans

2-Deoxy-scyllo-inosose (DOI) synthase is involved in the biosynthesis of 2-deoxystreptamine-containing aminoglycoside antibiotics and catalyzes the carbocyclic formation from d-glucose-6-phosphate (G-6-P) into DOI. The reaction mechanism is proposed to be similar to that of dehydroquinate (DHQ) synthase in the shikimate pathway, and includes oxidation of C-4, beta-elimination of phosphate, reduction of C-4, ring opening, and intramolecular aldol cyclization. To investigate the reaction mechanism of DOI synthase, site-directed mutational analysis of three presumable catalytically important amino acids of DOI synthase derived from the butirosin producer Bacillus circulans (BtrC) was carried out. Steady state and pre-steady state kinetic analysis suggested that E243 of BtrC is catalytically involved in the phosphate elimination step. Further analysis of the mutant E243Q of BtrC using substrate analogue, glucose-6-phosphonate, clearly confirmed that E243 was responsible to abstract a proton at C-5 in G-6-P and set off phosphate elimination. This glutamate residue is completely conserved in all DOI synthases identified so far and the corresponding amino acid of DHQ synthase is completely conserved as asparagine. Therefore, this characteristic glutamate residue of DOI synthase is a key determinant to distinguish the reaction mechanism between DOI synthase and DHQ synthase as well as primary sequence.

Biosynthesis of 2-Deoxystreptamine-containing Antibiotics in Streptoalloteichus hindustanus JCM 3268: Characterization of 2-Deoxy-scyllo-inosose Synthase

A part of the new biosynthetic gene cluster for 2-deoxystreptamine-containing antibiotics was identified from Streptoalloteichus hindustanus. The alloH gene in the gene cluster was deduced to encode 2-deoxy-scyllo-inosose synthase and the expressed protein AlloH was confirmed to have this enzyme activity. Furthermore, biochemical properties of AlloH were studied.

Regio- and Stereoselective Synthesis of Aminoinositols and 1,2-Diaminoinositols from Conduritol B Epoxide

[Chemical reaction: See text] A systematic approach to the regio- and stereoselective synthesis of aminoinositols and 1,2-diaminoinositols arising from tetra-O-benzylconduritol B epoxide (9) and its aziridine analogue 22, respectively, is described. In all cases, the synthetic methodologies rely on the regio- and stereocontrolled azidolysis of the starting precursors to give the corresponding trans regioadducts. Subsequent functional group manipulation under strict configurational control affords the isomeric cis adducts. Chemoselective functionalization of the diamine moiety in 1,2-diaminoinositol derivatives can be achieved by the proper design of the reaction sequence and choice of reagents. The described protocols allow efficient access to each of the eight possible configurations of the 1,2-diamino and 1,2-amino alcohol moieties from chemical modifications of the epoxide moiety on the common precursor 9.

Highly-functionalised difluorinated cyclohexane polyols via the Diels–Alder reaction: regiochemical control via the phenylsulfonyl group

A difluorinated dienophile underwent cycloaddition reactions with a range of furans to afford cycloadducts which could be processed regio- and stereoselectively via episulfonium ions, generated by the reaction between their alkenyl groups and phenylsulfenyl chloride. The oxabicyclic products were oxidised to the phenylsulfonyl level and ring opened via E1(C)B or reductive desulfonative pathways to afford, ultimately, difluorinated cyclohexene or cyclohexane polyols.

Stereospecificity of hydride transfer in NAD+-catalyzed 2-deoxy-scyllo-inosose synthase, the key enzyme in the biosynthesis of 2-deoxystreptamine-containing aminocyclitol antibiotics

The key enzyme in the biosynthesis of clinically important aminocyclitol antibiotics is 2-deoxy-scyllo-inosose synthase (DOIS), which converts ubiquitous d-glucose 6-phosphate (G-6-P) into the specific carbocycle, 2-deoxy-scyllo-inosose with an aid of NAD(+)-NADH recycling. The NAD(+)-dependent first step of the DOIS reaction was examined in detail by the use of 6-phosphonate and 6-homophosphonate analogs of G-6-P. Both analogs showed competitive inhibition against the DOIS reaction with K(i) values of 1.3 and 2.8 mM, respectively, due to their inability for the subsequent phosphate elimination. Based on the direct spectrophotometric observation of NADH formed by the hydride transfer from 6-phosphonate to NAD(+), the stereospecificity of the hydride transfer in the DOIS reaction was analyzed with 6-[4-(2)H]phosphonate and was found to be pro-R specific.

A Potentially Divergent and Rapid Route to Analogues of Deoxycyclitols, Pentopyranoses, 6-Deoxyhexoses, and Hexoses

Direct precursors to analogues of pentopyranoses, 6-deoxyhexoses, and hexoses, in which a CF(2) center replaces the pyranose oxygen, have been synthesized rapidly from trifluoroethanol. A simple scaleable allylation reaction delivers ethers which undergo dehydrofluorination/metalation, followed by addition to either acrolein or cinnamaldehyde, to afford allylic alcohols. Fluorine-assisted [3,3]-rearrangement followed by reduction with sodium borohydride delivers diols, which undergo RCM smoothly to afford cyclohexene diols.

Isolation and characterization of the tobramycin biosynthetic gene cluster from Streptomyces tenebrarius

The biosynthetic gene cluster for tobramycin, a 2-deoxystreptamine-containing aminoglycoside antibiotic, was isolated from Streptomyces tenebrarius ATCC 17920. A genomic library of S. tenebrarius was constructed, and a cosmid, pST51, was isolated by the probes based on the core regions of 2-deoxy-scyllo-inosose (DOI) synthase, and L-glutamine:DOI aminotransferase and L-glutamine:scyllo-inosose aminotransferase. Sequencing of 33.9 kb revealed 24 open reading frames (ORFs) including putative tobramycin biosynthetic genes. We demonstrated that one of these ORFs, tbmA, encodes DOI synthase by in vitro enzyme assay of the purified protein. The catalytic residues of TbmA and dehydroquinate synthase were studied by homology modeling. The gene cluster found is likely to be involved in the biosynthesis of tobramycin.

Highly-functionalised difluorinated (hydroxymethyl)conduritol analogues via the Diels-Alder reactions of a difluorinated dienophile

A difluorodienophile, synthesised using a Stille coupling reaction underwent tin(iv)-catalysed cycloaddition with three furans to afford oxa[2.2.1]bicycloheptenes in good yield. Reduction of ester and carbamate carbonyl groups and diol protection as the acetonide set the stage for palladium-catalysed hydrostannylation in two cases. Treatment of the stannanes with methyllithium triggered ring-opening to afford highly-functionalised difluorinated cyclohexenols which could be deprotected to afford (hydroxymethyl)conduritol analogues.

Active Site Mapping of 2-Deoxy-scyllo-inosose Synthase, the Key Starter Enzyme for the Biosynthesis of 2-Deoxystreptamine. Mechanism-Based Inhibition and Identification of Lysine-141 as the Entrapped Nucleophile

A key enzyme in the biosynthesis of clinically important aminoglycoside antibiotics including neomycin, kanamycin, gentamicin, etc. is 2-deoxy-scyllo-inosose synthase (DOIS), which catalyzes the carbocycle formation from d-glucose-6-phosphate to 2-deoxy-scyllo-inosose (DOI). To clarify its precise reaction mechanism and crucial amino acid residues in the active site, we took advantage of a mechanism-based inhibitor carbaglucose-6-phosphate (pseudo-dl-glucose, C-6-P) with anticipation of its conversion to a reactive alpha,beta-unsaturated carbonyl intermediate. It turned out that C-6-P clearly showed time- and concentration-dependent inhibition against DOIS, and the molecular mass of the resulting modified-DOIS with C-6-P was 160 mass units larger than that of native DOIS. Thus, the expected alpha,beta-unsaturated intermediate appeared to trap a specific nucleophilic group in the active site through the Michael-type 1,4-addition. The covalently modified amino acid residue was determined to be Lys-141 by means of enzymatic digestion and subsequent LC/MS and LC/MS/MS of the digest. Also discussed are the role of Lys-141 in the substrate recognition and the reaction pathway and comparison with evolutionary related dehydroquinate synthase.

Inhibition of mandelate racemase by alpha-fluorobenzylphosphonates

Mandelate racemase catalyzes the interconversion of the enantiomers of mandelic acid. The enzyme binds the intermediate analogues (R)- and (S)-alpha-fluorobenzylphosphonate, and alpha,alpha-difluorobenzylphosphonate with 100-2500 times less affinity than it exhibits for (R,S)-alpha-hydroxybenzylphosphonate at pH 7.5. This apparent low affinity, relative to that of alpha-hydroxybenzylphosphonate, arises from the altered pKa values of the alpha-fluorobenzylphosphonates. For example, (S)-alpha-fluorobenzylphosphonate is bound with the same affinity as the substrate at pH 7.5, but this affinity is increased approximately 6-fold at pH 6.3.

Catalytic asymmetric synthesis of a 1-deoxy-1,1-difluoro-D-xylulose

[reaction: see text] A new route, of potential strategic importance, to a difluorosugar analogue has been developed. Key steps included a Stille coupling and a highly regio- and enantioselective dihydroxylation of a highly substituted diene. Protecting groups were chosen to enhance the reactivity of the disubstituted allylic fragment in the AD reaction and allow deprotection under orthogonal conditions.

Basic and reductive sulfone-directed ring-opening reactions of difluorinated oxa[2.2.1]bicycloheptanes

Phenylsulfenyl chloride reacts with racemic endo Diels-Alder adduct 4 (DEC = CONEt(2)) to afford lactone 8, which can be reduced and protected in a series of high-yielding steps. Key sulfone 10 can be ring opened under strong base conditions to afford vinyl sulfone 11. Attempted desulfonation resulted in the formation of a monofluoroalkene, but a direct desulfonation/eliminative ring opening with strain relief delivered highly functionalized monocyclic species 16. [reaction: see text]