Elucidation of Biosynthetic Pathways of Natural Products

During the last decade, we have revealed biosynthetic pathways responsible for the formation of important and chemically complex natural products isolated from various organisms through genetic manipulation. Detailed in vivo and in vitro characterizations enabled elucidation of unexpected mechanisms of secondary metabolite biosynthesis. This personal account focuses on our recent efforts in identifying the genes responsible for the biosynthesis of spirotryprostatin, aspoquinolone, Sch 210972, pyranonigrin, fumagillin and pseurotin. We exploit heterologous reconstitution of biosynthetic pathways of interest in our study. In particular, extensive involvement of oxidation reactions is discussed. Heterologous hosts employed here are Saccharomyces cerevisiae, Aspergillus nidulans and A. niger that can also be used to prepare biosynthetic intermediates and product analogs by engineering the biosynthetic pathways using the knowledge obtained by detailed characterizations of the enzymes. (998 char.)     

Oxidative trans to cis Isomerization of Olefins in Polyketide Biosynthesis

Geometric isomerization can expand the scope of biological activities of natural products. The observed chemical diversity among the pseurotin‐type fungal secondary metabolites is in part generated by a trans to cis isomerization of an olefin. In vitro characterizations of pseurotin biosynthetic enzymes revealed that the glutathione S‐transferase PsoE requires participation of the bifunctional C‐methyltransferase/epoxidase PsoF to complete the trans to cis isomerization of the pathway intermediate presynerazol. The crystal structure of the PsoE/glutathione/presynerazol complex indicated stereospecific glutathione–presynerazol conjugate formation is the principal function of PsoE. Moreover, PsoF was identified to have an additional, unexpected oxidative isomerase activity, thus making it a trifunctional enzyme which is key to the complexity generation in pseurotin biosynthesis. Through the study, we identified a novel mechanism of accomplishing a seemingly simple trans to cis isomerization reaction.     

Unprecedented 1,14‐seco‐Crotofolanes from Croton insularis: Oxidative Cleavage of Crotofolin C by a Putative Homo‐Baeyer–Villiger Rearrangement

EBC‐162 isolated from Croton insularis, obtained from the northern rainforest of Australia, was structurally affirmed as crotofolin C ( 4 ). Novel oxidative degradation products, EBC‐233 and EBC‐300, which are the first crotofolane endoperoxides, were also isolated. Both endoperoxides were found to be stable intermediates, which are proposed to undergo an unprecedented homo‐Baeyer–Villiger biosynthetic rearrangement to give a new class of 1,14‐seco‐crotofolane diterpenes. Prolonged storage of all isolates assisted in authenticating their natural product status. Anticancer activities of reported compounds are presented.     

Biosynthesis of the N–N‐Bond‐Containing Compound l‐Alanosine

The formation of a N?N bond is a unique biochemical transformation, and nature employs diverse biosynthetic strategies to activate nitrogen for bond formation. Among molecules that contain a N?N bond, biosynthetic routes to diazeniumdiolates remain enigmatic. We here report the biosynthetic pathway for the diazeniumdiolate‐containing amino acid l ‐alanosine. Our work reveals that the two nitrogen atoms in the diazeniumdiolate of l ‐alanosine arise from glutamic acid and aspartic acid, and we clarify the early steps of the biosynthetic pathway by using both in vitro and in vivo approaches. Our work demonstrates a peptidyl‐carrier‐protein‐based mechanism for activation of the precursor l ‐diaminopropionate, and we also show that nitric oxide can participate in non‐enzymatic diazeniumdiolate formation. Furthermore, we demonstrate that the gene alnA, which encodes a fusion protein with an N‐terminal cupin domain and a C‐terminal AraC‐like DNA‐binding domain, is required for alanosine biosynthesis.     

Control of the Stereochemical Course of [4+2] Cycloaddition during trans‐Decalin Formation by Fsa2‐Family Enzymes

Enzyme‐catalyzed [4+2] cycloaddition has been proposed to be a key transformation process in various natural product biosynthetic pathways. Recently Fsa2 was found to be involved in stereospecific trans‐decalin formation during the biosynthesis of equisetin, a potent HIV‐1 integrase inhibitor. To understand the mechanisms by which fsa2 determines the stereochemistry of reaction products, we sought an fsa2 homologue that is involved in trans‐decalin formation in the biosynthetic pathway of an enantiomerically opposite analogue, and we found phm7, which is involved in the biosynthesis of phomasetin. A decalin skeleton with an unnatural configuration was successfully constructed by gene replacement of phm7 with fsa2, thus demonstrating enzymatic control of all stereochemistry in the [4+2] cycloaddition. Our findings highlight enzyme‐catalyzed [4+2] cycloaddition as a stereochemically divergent step in natural product biosynthetic pathways and open new avenues for generating derivatives with different stereochemistry.     

Copper‐Catalyzed Aerobic Oxidations of 3‐N‐Hydoxyaminoprop‐1‐ynes to Form 3‐Substituted 3‐Amino‐2‐en‐1‐ones: Oxidative Mannich Reactions with a Skeletal Rearrangement

Cu‐catalyzed aerobic oxidations of readily available 3‐N‐hydroxyaminopro‐1‐ynes with water, alcohols, or thiols to form diverse 3‐substituted 3‐amino‐2‐en‐1‐ones are described. The utility of this catalysis is manifested by a wide scope of applicable N‐hydroxyl propargylamines and nucleophiles, thus enabling the design of one‐pot cascade or two‐step sequential reactions. Besides synthetic significances, such oxidative Mannich reactions are mechanistically interesting because structurally reorganized products were obtained. Our mechanistic studies reveal that the aerobic oxidations involve initial formation of nitrone intermediates, followed by the attack of nucleophiles. Herein, water and MeOH implement the conversion of nitrone intermediates to reaction products in two distinct pathways.     

In situ detection of the intermediates in the biosynthesis of surfactin,a lipoheptapeptide from Bacillus subtilis OKB 105, by whole‐cell cell matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry in combination with mutant analysis

An innovative technique to investigate the intermediates involved in the biosynthesis of the lipoheptapeptide surfactin from Bacillus subtilis OKB105 combining whole‐cell matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry (MALDI‐TOFMS) with targeted generation of knock‐out mutants was demonstrated. This method allows efficient, sensitive detection of biosynthetic intermediates in a minimum of time directly at the outer surface of microbial cells picked from agar plates or in surface extracts prepared thereof. Biosynthesis of surfactin is encoded by the srf‐operon which is organized into four open reading frames which have been attributed to three multifunctional NRPS enzymes (SrfA‐C) and a thioesterase/acyltransferase enzyme SrfD. For the wild‐type strain OKB 105 only the end product surfactin was found mass spectrometrically. For the detection of lipopeptide intermediates three plasmid‐ and transposon‐insertion mutants were generated interrupting the surfactin assembly line at defined positions. Strain LAB 327 was mutated in the spacer region between enzymes SrfA and B. Here only SrfA was active with the lipotripeptide β‐OH‐acyl‐L‐Glu‐L‐Leu‐D‐Leu as the end product. Mutant OKB 120 bears a transposon mutation in SrfB between the first and second amino acid activating modules SrfB1 and SrfB2. It showed all intermediates from the lipodi‐ until to the lipotetrapeptide β‐OH‐acyl‐L‐Glu‐L‐Leu‐D‐Leu‐L‐Val. In LAB 223 SrfC was knocked out by a transposon mutation. It produced the lipohexapeptide β‐OH‐acyl‐L‐Glu‐L‐Leu‐D‐Leu‐L‐Val‐L‐Asp‐D‐Leu. Our work highlights the applicability and the potential of whole‐cell MALDI‐TOFMS as an innovative efficient tool for the analysis of intermediate steps of biosynthetic pathways. Copyright © 2009 John Wiley & Sons, Ltd.     

Water‐Promoted Ring‐Opening Reactions of N‐Substituted Saccharins and Phthalimides by Amines

The reactions of N‐substituted saccharins and phthalimides with amines were promoted by water. Various o‐sulfamoyl benzamides and N,N′‐disubstituted phthalamides were prepared in moderate to good yields. These reactions have prominent advantages, such as short reaction time, less by‐products and simple isolation of the products. Water can probably stabilize the reaction intermediates and facilitate precipitation of the ring‐opening products. When steric hindrance arose, hydrolytic compounds, either free acid or salts of the acids, were obtained. Possible reason for the formation of amine salts of o‐sulfamoyl benzoic acids was proposed.     

Heavy Heparin: A Stable Isotope‐Enriched,Chemoenzymatically‐Synthesized,Poly‐Component Drug

Heparin is a highly sulfated, complex polysaccharide and widely used anticoagulant pharmaceutical. In this work, we chemoenzymatically synthesized perdeuteroheparin from biosynthetically enriched heparosan precursor obtained from microbial culture in deuterated medium. Chemical de‐N‐acetylation, chemical N‐sulfation, enzymatic epimerization, and enzymatic sulfation with recombinant heparin biosynthetic enzymes afforded perdeuteroheparin comparable to pharmaceutical heparin. A series of applications for heavy heparin and its heavy biosynthetic intermediates are demonstrated, including generation of stable isotope labeled disaccharide standards, development of a non‐radioactive NMR assay for glucuronosyl‐C5‐epimerase, and background‐free quantification of in vivo half‐life following administration to rabbits. We anticipate that this approach can be extended to produce other isotope‐enriched glycosaminoglycans.     

Heavy Heparin: A Stable Isotope‐Enriched,Chemoenzymatically‐Synthesized,Poly‐Component Drug

Heparin is a highly sulfated, complex polysaccharide and widely used anticoagulant pharmaceutical. In this work, we chemoenzymatically synthesized perdeuteroheparin from biosynthetically enriched heparosan precursor obtained from microbial culture in deuterated medium. Chemical de‐N‐acetylation, chemical N‐sulfation, enzymatic epimerization, and enzymatic sulfation with recombinant heparin biosynthetic enzymes afforded perdeuteroheparin comparable to pharmaceutical heparin. A series of applications for heavy heparin and its heavy biosynthetic intermediates are demonstrated, including generation of stable isotope labeled disaccharide standards, development of a non‐radioactive NMR assay for glucuronosyl‐C5‐epimerase, and background‐free quantification of in vivo half‐life following administration to rabbits. We anticipate that this approach can be extended to produce other isotope‐enriched glycosaminoglycans.     

Novel Synthesis of 1,3‐Thiazine and Pyrimidinethione Derivatives from (1‐Aryl ethylidene)hydrazinecarbothioamides and Tetracyanoethylene

1,3‐Thiazine‐5,6,6‐tricarbonitrile and 2‐thioxo‐2,3‐dihydropyrimidine‐4,5‐dicarbonitriles derivatives were synthesized via interactions between (1‐aryl ethylidene)hydrazinecarbothioamides and tetracyanoethylene to give the derivatives of tetracyanoethane and tricyanovinylation intermediates, followed by heterocyclization. The structures of the products have been confirmed by different spectroscopic analyses. A rational for the formation of the products is presented.     

Biomimetic Total Synthesis of Hyperjapones A–E and Hyperjaponols A and C

Hyperjapones A–E and hyperjaponols A–C are complex natural products of mixed aromatic polyketide and terpene biosynthetic origin that have recently been isolated from Hypericum japonicum. We have synthesized hyperjapones A–E using a biomimetic, oxidative hetero‐Diels–Alder reaction to couple together dearomatized acylphloroglucinol and cyclic terpene natural products. Hyperjapone A is proposed to be the biosynthetic precursor of hyperjaponol C through a sequence of: 1) epoxidation; 2) acid‐catalyzed epoxide ring‐opening; and 3) a concerted, asynchronous alkene cyclization and 1,2‐alkyl shift of a tertiary carbocation. Chemical mimicry of this proposed biosynthetic sequence allowed a concise total synthesis of hyperjaponol C to be completed in which six carbon–carbon bonds, six stereocenters, and three rings were constructed in just four steps.     

Unexpected Imidazoquinoxalinone Annulation Products in the Photoinitiated Reaction of Substituted‐3‐Methyl‐Quinoxalin‐2‐Ones with N‐Phenylglycine

Photoinduced electron transfer between N ‐phenylglycine (NPG) and electronically excited triplets of 7‐substituted‐3‐methyl‐quinoxalin‐2‐ones in acetonitrile generate the respective ion radical pair, where by decarboxylation the phenyl‐amino‐alkyl radical, PhNHCH₂?, is generated. This radical reacts with the 3‐methyl‐quinoxalin‐2‐ones ground states, leading to the product 2. Other, unexpected, 7‐substituted‐1,2,3,3a‐tetrahydro‐3a‐methyl‐2‐phenylimidazo[1,5‐a]quinoxalin‐4(5H)‐ones, annulation products, 3a–f, were generated; likely by the addition of two PhNHCH₂? radicals, to positions 3 and 4 of the quinoxalin‐2‐ones. The reaction mechanism includes a photoinduced one electron transfer initiation step, propagation steps involving radical intermediates and NPG with radical chain termination steps that lead to the respective products 2a–f and 3a–f and NPG by‐products. The proposed mechanism accounts for the strong dependency found for the initial photoconsumption quantum yields on the electron‐withdrawing power of the substituent. Therefore, photolysis of common reactants widely used such as NPG and substituted quinoxalin‐2‐ones may provide a simple synthetic way to the unusual, unreported tetrahydro‐imidazoquinoxalinones 3a–f.     

10‐Step Asymmetric Total Synthesis and Stereochemical Elucidation of (+)‐Dragmacidin D

The asymmetric synthesis of dragmacidin D ( 1 ) was completed in 10 steps. Its sole stereocenter was set by using direct asymmetric alkylation enabled by a C₂‐symmetric tetramine and lithium N‐(trimethylsilyl)‐tert‐butylamide as the enolization reagent. A central Larock indole synthesis was employed in a convergent assembly of the heterocyclic subunits. The stereochemical evidence from this work strongly supports the predicted S configuration at the 6′′′ position, which is consistent with other members of the dragmacidin family of natural products.     

An Efficient Synthesis of Isomeric 1‐(1‐Alkyl‐1H‐pyrazolyl) Ethanones

A simple and versatile general method for the preparation of N‐substituted 3‐, 4‐, or 5‐acetylpyrazoles from corresponding acids via hydrolysis and decarboxylation of substituted diethyl [(1‐alkyl‐1H‐pyrazolyl)carbonyl]malonates was developed. Title compounds were prepared in three steps without isolation of intermediates in 48–82% overall yield.     

Synthetic Studies towards Pseurotin A. Part 3. Synthesis of a related highly functionalized γ-lactone

A new general concept for the total synthesis of pseurotin A ( 1 ), a secondary metabolite of Pseudeurotium ovalis STOLK , which possesses a highly substituted 1-oxa-7-azaspiro[4.4]nonane skeleton, is presented. A key intermediate of the planned reaction sequence is the functionalized γ-lactone 8 . The corresponding protected compound 52 was prepared using (S)-O,O-isopropylideneglyceraldehyde ( 13 ) and the bromoacetal 14 as starting material. γ-Lactone 52 was obtained in enantiomerically pure state in ten steps. It possesses the desired configuration.     

Enantioselective Synthesis of Ethyl 4,5,7,8,9‐Penta‐O‐acetyl‐2,6‐anhydro‐ 3‐deoxy‐D‐erythro‐L‐gluca‐nononate: a 2‐Monodeoxygenated Derivative of `2‐Keto‐3‐deoxy‐D‐glycero‐D‐galacto‐nononic Acid'

A study aimed at developing an enantioselective synthesis of the title compound 23 , a 2‐monodeoxy analogue of the naturally occurring (+)‐2‐keto‐3‐deoxy‐D ‐glycero‐D ‐galacto‐2‐nononic acid (KDN), is reported. From D ‐mannose as starting material, the chiral 1,3‐diene 10 , activated by a silyloxy substituent at C(2), was prepared in six steps (Scheme 1). However, the intermediates were often contaminated with varying amounts of by‐products arising from overoxidation during cleavage with periodic acid. An alternative route starting from the inexpensive and readily available D ‐isoascorbic acid ( 12 ), though a little longer than the first, satisfactorily circumvented the purification problem and led to the desired dienes 17 in good yields (scheme 2). The [Co^II(S,S)‐(+)‐salen]‐catalyzed hetero‐Diels‐Alder reactions of the aforementioned dienes with ethyl glyoxylate proceeded smoothly at room temperature, giving the dihydropyrano adducts 18 in moderate yields (Scheme 3). Dihydroxylation of 18a followed by reduction of the keto function gave the desired 4,5‐trans dihydroxy moiety of the KDN framework (Scheme 4, see 21 ). The spectroscopic data of the penta‐O‐acetylated 2‐deoxy‐KDN ethyl ester 23 were consistent with those reported for the corresponding methyl ester derived from natural KDN.     

Biosynthesis and Ether‐Bridge Formation in Nargenicin Macrolides

The nargenicin family of antibiotics are macrolides containing a rare ether‐bridged cis‐decalin motif. Several of these compounds are highly active against multi‐drug resistant organisms. Despite the identification of the first members of this family almost 40 years ago, the genetic basis for the production of these molecules and the enzyme responsible for formation of the oxa bridge, remain unknown. Here, the 85 kb nargenicin biosynthetic gene cluster was identified from a human pathogenic Nocardia arthritidis isolate and this locus is solely responsible for nargenicin production. Further investigation of this locus revealed a putative iron‐α‐ketoglutarate‐dependent dioxygenase, which was found to be responsible for the formation of the ether bridge from the newly identified deoxygenated precursor, 8,13‐deoxynargenicin. Uncovering the nargenicin biosynthetic locus provides a molecular basis for the rational bioengineering of these interesting antibiotic macrolides.     

Biosynthesis‐Assisted Structural Elucidation of the Bartolosides,Chlorinated Aromatic Glycolipids from Cyanobacteria

The isolation of the bartolosides, unprecedented cyanobacterial glycolipids featuring aliphatic chains with chlorine substituents and C‐glycosyl moieties, is reported. Their chlorinated dialkylresorcinol (DAR) core presented a major structural‐elucidation challenge. To overcome this, we discovered the bartoloside (brt) biosynthetic gene cluster and linked it to the natural products through in vitro characterization of the DAR‐forming ketosynthase and aromatase. Bioinformatic analysis also revealed a novel potential halogenase. Knowledge of the bartoloside biosynthesis constrained the DAR core structure by defining key pathway intermediates, ultimately allowing us to determine the full structures of the bartolosides. This work illustrates the power of genomics to enable the use of biosynthetic information for structure elucidation.