Mechanisms of molecular recognition in the pikromycin polyketide synthase

BACKGROUND: Modular polyketide synthases (PKSs) produce a wide range of medically significant compounds. In the case of the pikromycin PKS of Streptomyces venezuelae, four separate polypeptides (PikAI-PikAIV), comprising a total of one loading domain and six extension modules, generate the 14-membered ring macrolactone narbonolide. The polypeptide PikAIV contains a thioesterase (TE) domain and is responsible for catalyzing both the last elongation step with methylmalonyl CoA, and subsequent release of the final polyketide chain elongation intermediate from the PKS. Under certain growth conditions this polypeptide is synthesized from an alternative translational start site, giving rise to an N-terminal truncated form of PikAIV, containing only half of the ketosynthase (KS(6)) domain. The truncated form of PikAIV is unable to catalyze the final elongation step, but is able to cleave a polyketide chain from the preceding module on PikAIII (ACP(5)), giving rise to the 12-membered ring product 10-deoxymethynolide. RESULTS: S. venezuelae mutants expressing hybrid PikAIV polypeptides containing acyl carrier protein (ACP) and malonyl CoA specific acyltransferase (AT) domains from the rapamycin PKS were unable to catalyze production of 12- or 14-membered ring macrolactone products. Plasmid-based expression of a hybrid PikAIV containing the native KS(6) and TE domains, however, restored production of both narbonolide and 10-deoxymethynolide in the S. venezuelae AX912 mutant that generates a TE-deleted form of PikAIV. Use of alternative KS domains or deletion of the KS(6) domain within the hybrid PikAIV resulted in loss of both products. Plasmid-based expression of a TE domain of PikAIV as a separate polypeptide in the AX912 mutant resulted in greater than 50% restoration of 10-deoxymethynolide, but not in mutants expressing a hybrid PikAIV bearing an unnatural AT domain. Mutants expressing hybrid PikAIV polypeptides containing the natural AT(6) domains and different ACP domains efficiently produced polyketide products, but with a significantly higher 10-deoxymethynolide/narbonolide ratio than observed with native PikAIV. CONCLUSIONS: Dimerization of KS(6) modules allows in vivo formation of a PKS heterodimer using PikAIV polypeptides containing different AT and ACP domains. In such heterodimers, the TE domain and the AT(6) domain responsible for formation of the narbonolide product are located on different polypeptide chains. The AT(6) domain of PikAIV plays an important role in facilitating TE-catalyzed chain termination (10-deoxymethynolide formation) at the proceeding module in PikAIII. The pikromycin PKS can tolerate the presence of multiple forms (active and inactive) of PikAIV, and decreased efficiency of elongation by PikAIV can result in increased levels of 10-deoxymethynolide. These results provide new insight into functional molecular interactions and interdomain recognition in modular PKSs.     

Total synthesis of pikromycin

The total synthesis of pikromycin (6), the first isolated macrolide antibiotic, was achieved. The target macrolide was retrosynthetically divided into two parts, pikronolide (6a) (aglycon) and D-desosamine. The aglycon was synthesized using key reactions such as an asymmetric aldol reaction, Yamaguchi esterification, and ring-closing metathesis. The aglycon was coupled successfully with the trichloroacetimidate derivative of D-desosamine under Lewis acidic conditions to afford pikromycin. Narbomycin (5) was also synthesized from narbonolide (5a) under identical conditions.     

Biochemical investigation of pikromycin biosynthesis employing native penta- and hexaketide chain elongation intermediates

The unique ability of the pikromycin (Pik) polyketide synthase to generate 12- and 14-membered ring macrolactones presents an opportunity to explore the fundamental processes underlying polyketide synthesis, specifically the mechanistic details of chain extension, keto group processing, acyl chain release, and macrocyclization. We have synthesized the natural pentaketide and hexaketide chain elongation intermediates as N-acetyl cysteamine (NAC) thioesters and have used them as substrates for in vitro conversions with engineered PikAIII+TE and in combination with native PikAIII (module 5) and PikAIV (module 6) multifunctional proteins. This investigation demonstrates directly the remarkable ability of these monomodules to catalyze one or two chain extension reactions, keto group processing steps, acyl-ACP release, and cyclization to generate 10-deoxymethynolide and narbonolide. The results reveal the enormous preference of Pik monomodules for their natural polyketide substrates and provide an important comparative analysis with previous studies using unnatural diketide NAC thioester substrates.     

The hidden steps of domain skipping: macrolactone ring size determination in the pikromycin modular polyketide synthase

The pikromycin (Pik) polyketide synthase (PKS) from Streptomyces venezuelae comprises four multifunctional polypeptides (PikAI, PikAII, PikAIII, and PikAIV). This PKS can generate 12- and 14-membered ring macrolactones (10-deoxymethynolide and narbonolide, respectively) through the activity of its terminal modules (PikAIII and PikAIV). We performed a series of experiments involving the functional replacement of PikAIV in mutant strains with homodimeric and heterodimeric PikAIV modules to investigate the details of macrolactone ring size determination. The results suggest a new and surprising mechanism by which the penultimate hexaketide chain elongation intermediate is transferred from PikAIII ACP5 to PikAIV ACP6 before release by the terminal thioesterase domain. Elucidation of this chain transfer mechanism provides important new details about alternative macrolactone ring size formation in modular PKSs and contributes to the potential for rational design of structural diversity by combinatorial biosynthesis.     

Chemoenzymatic synthesis of the polyketide macrolactone 10-deoxymethynolide

The polyketide synthase-derived pikromycin thioesterase (Pik TE) is unique in its ability to catalyze the cyclization of 12- and 14-membered macrolactones. In this investigation, the total synthesis of the natural hexaketide chain elongation intermediate as its N-acetyl cysteamine (NAC) thioester has been achieved, and its reaction with Pik TE demonstrated the ability of Pik TE to catalyze its macrolactonization to the natural product 10-deoxymethynolide. A steady-state kinetic analysis of the hexaketide chain intermediate with Pik TE was done. A preliminary substrate specificity study with unnatural hexaketide analogues was accomplished, demonstrating the importance of total synthesis in obtaining access to advanced polyketide intermediates. The results show the sensitivity of Pik TE to minor substrate modifications, and illustrate the potential use of thioesterases as versatile macrolactonization catalysts.     

Catalyst economy. Part 2: Sequential metathesis—Kharasch sequences using the Grubbs metathesis catalysts

Sequential ring-closing metathesis (RCM)-Kharasch cyclizations are promoted by the Grubbs metathesis catalysts and provide rapid access to bicyclic lactones and lactams.     

Expression and kinetic analysis of the substrate specificity of modules 5 and 6 of the picromycin/methymycin polyketide synthase

Picromycin synthase (PICS) is a multifunctional, modular polyketide synthase (PKS) that catalyzes the conversion of methylmalonyl-CoA to narbonolide and 10-deoxymethynolide, the macrolide aglycone precursors of the antibiotics picromycin and methymycin, respectively. PICS modules 5 and 6 were each expressed in Escherichia coli with a thioesterase domain at the C-terminus to allow release of polyketide products. The substrate specificity of PICS modules 5+TE and 6+TE was investigated using N-acetylcysteamine thioesters of 2-methyl-3-hydroxy-pentanoic acid as diketide analogues of the natural polyketide chain elongation substrates. PICS module 5+TE could catalyze the chain elongation of only the syn diketide (2S,3R)-4, while PICS module 6+TE processed both syn diastereomers, (2S,3R)-4 and (2R,3S)-5, with a 2.5:1 preference in k(cat)/K(m) for 5 but did not turn over either of the two anti diketides. The observed substrate specificity patterns are in contrast to the 15-100:1 preference for 4 over 5 previously established for several modules of the closely related erythromycin PKS, 6-deoxyerythronolide B synthase (DEBS).     

Formal total synthesis of the polyketide macrolactone narbonolide

[reaction: see text] An improved synthesis of (3S)-3-dihydronarbonolide is reported that constitutes a formal total synthesis of the 14-membered macrolactone antibiotic narbonolide. The key step was an intramolecular Nozaki-Hiyama-Kishi coupling to accomplish macrocyclization in improved yield. The high level of convergence will also allow us to rapidly synthesize narbonolide analogues for the study of enzymes in the pikromycin biosynthetic pathway.     

Total synthesis of narbonolide and biotransformation to pikromycin

An improved total synthesis of narbonolide and its biotransformation to pikromycin is reported. This total synthesis utilized an intramolecular Nozaki-Hiyama-Kishi coupling that significantly improved macrocyclization yields (90-96%) and allowed for differentiation of the C3- and C5-oxidation states. A pikAI deletion mutant of Streptomyces venezuelae was used to biotransform synthetic narbonolide to pikromycin by glycosylation and oxidation in vivo. This integration of synthetic chemistry and engineered biotransformations holds great promise for the synthesis of novel macrolide analogues of biological interest.     

A domino ring-closing metathesis as a key-step in the synthesis of chiral lactones from d-mannitol

Chiral lactones were synthesized in six steps from d-mannitol. The key-step was a domino ring-closing metathesis reaction leading to the symmetric cleavage of a d-mannitol triene derivative and to the formation of two molecules of the desired lactone.     

A short olefin metathesis-based route to enantiomerically pure arylated dihydropyrans and alpha,beta-unsaturated delta-valero lactones

The synthesis of arylated dihydropyrans and unsaturated lactones starting from enantiomerically pure alpha-hydroxy ketones (prepared by an enzyme-catalyzed benzoin condensation) is described. The key steps are a highly diastereoselective addition of vinyl metal compounds under chelate control and a ruthenium-catalyzed ring-closing olefin metathesis reaction. Elucidation of the relative configuration of the final products was achieved by NOE experiments.     

Elucidating the mechanism of chain termination switching in the picromycin/methymycin polyketide synthase.

BACKGROUND: A single modular polyketide synthase (PKS) gene cluster is responsible for production of both the 14-membered macrolide antibiotic picromycin and the 12-membered macrolide antibiotic methymycin in Streptomyces venezuelae. Building on the success of the heterologous expression system engineered using the erythromycin PKS, we have constructed an analogous system for the picromycin/methymycin PKS. Through heterologous expression and construction of a hybrid PKS, we have examined the contributions that the PKS, its internal thioesterase domain (pikTE) and the Pik TEII thioesterase domain make in termination and cyclization of the two polyketide intermediates. RESULTS: The picromycin/methymycin PKS genes were functionally expressed in the heterologous host Streptomyces lividans, resulting in production of both narbonolide and 10-deoxymethynolide (the precursors of picromycin and methymycin, respectively). Co-expression with the Pik TEII thioesterase led to increased production levels, but did not change the ratio of the two compounds produced, leaving the function of this protein largely unknown. Fusion of the PKS thioesterase domain (pikTE) to 6-deoxyerythronolide B synthase (DEBS) resulted in formation of only 14-membered macrolactones. CONCLUSIONS: These experiments demonstrate that the PKS alone is capable of catalyzing the synthesis of both 14- and 12-membered macrolactones and favor a model by which different macrolactone rings result from a combination of the arrangement between the module 5 and module 6 subunits in the picromycin PKS complex and the selectivity of the pikTE domain.     

Interrogating the molecular basis for multiple macrolactone ring formation by the pikromycin polyketide synthase

The pikromycin polyketide synthase (PKS) is unique in its ability to generate both 12 and 14 membered ring macrolactones. As such, dissection of the molecular basis for controlling metabolic diversity in this system remains an important objective for understanding modular PKS function and expanding chemical diversity. Here, we describe a series of experiments designed to probe the importance of the protein-protein interaction that occurs between the final two monomodules, PikAIII (module 5) and PikAIV (module 6), for the production of the 12 membered ring macrolactone 10-deoxymethynolide. The results obtained from these in vitro studies demonstrate that PikAIII and PikAIV generate the 12 membered ring macrocycle most efficiently when engaged in their native protein-protein interaction. Accordingly, the data are consistent with PikAIV adopting an alternative conformation that enables the terminal thioesterase domain to directly off-load the PikAIII-bound hexaketide intermediate for macrocyclization.     

An Evans-Tishchenko-ring-closing metathesis approach to medium-ring lactones

A new approach to the synthesis of medium-ring lactones is reported based on sequential Evans-Tishchenko and ring-closing metathesis (RCM) reactions. High diastereoselectivity (>95:5) is demonstrated in the Evans-Tishchenko reaction of unsaturated aldehydes with unsaturated beta-hydroxy ketones, and conditions for the RCM cyclization of the resultant dienes have been optimized to give high yields of medium ring lactones. The synthetic utility of this sequence is demonstrated through generation of the fully functionalized core of octalactin A. [reaction: see text].     

Total synthesis of neomethymycin and novamethymycin

Total synthesis of neomethymycin and novamethymycin has been achieved. These two macrolides contains 12-membered macrolactones as aglycones and belong to the methymycin family of antibiotics, which appears in the pikromycin biosynthetic pathway. The segments in the 12-membered macrolactone that are responsible for causing structural difference in neomethymycin and novamethymycin were synthesized by starting with methyl d-(+)-lactate and d-glucose, for neomethynolide, and for novamethynolide, respectively. The key steps in synthesis of neomethynolide and novamethynolide, which are aglycones for neomethymycin and novamethymycin, respectively, were asymmetric aldol reactions, Yamaguchi esterification, and ring-closing metathesis using Grubbs’ second generation catalyst. Finally, the coupling of agylcones with the corresponding trichloroacetimidates, followed by deprotection, completed the total synthesis of these two macrolide antibiotics.     

Enantioselective synthesis of 10-epi-anamarine via an iterative dihydroxylation sequence

[reaction: see text] The enantioselective syntheses of 10-epi-anamarine and 5,10-epi,epi-anamarine have been achieved in 13 to 14 steps. The route relies upon an enantio- and regioselective Sharpless dihydroxylation of either dienoates or trienoates to establish the C-8 to C-11 stereochemistry. A diastereoselective Leighton allylation established the desired C-5 stereochemistry. The route also relies upon a ring-closing metathesis to establish the alpha,beta-unsaturated lactones.     

Polyketide double bond biosynthesis. Mechanistic analysis of the dehydratase-containing module 2 of the picromycin/methymycin polyketide synthase

Picromycin/methymycin synthase (PICS) is a modular polyketide synthase (PKS) that is responsible for the biosynthesis of both 10-deoxymethynolide (1) and narbonolide (2), the parent 12- and 14-membered aglycone precursors of the macrolide antibiotics methymycin and picromycin, respectively. PICS module 2 is a dehydratase (DH)-containing module that catalyzes the formation of the unsaturated triketide intermediate using malonyl-CoA as the chain extension substrate. Recombinant PICS module 2+TE, with the PICS thioesterase domain appended to the C-terminus to allow release of polyketide products, was expressed in Escherichia coli. Purified PICS module 2+TE converted malonyl-CoA and 4, the N-acetylcysteamine thioester of (2S,3R)-2-methyl-3-hydroxypentanoic acid, to a 1:2 mixture of the triketide acid (4S,5R)-4-methyl-5-hydroxy-2-heptenoic acid (5) and (3S,4S,5R)-3,5-dihydroxy-4-methyl-n-heptanoic acid-delta-lactone (10) with a combined kcat of 0.6 min(-1). The triketide lactone 10 is formed by thioesterase-catalyzed cyclization of the corresponding d-3-hydroxyacyl-SACP intermediate, a reaction which competes with dehydration catalyzed by the dehydratase domain. PICS module 2+TE showed a strong preference for the syn-diketide-SNAC 4, with a 20-fold greater kcat/K(m) than the anti-(2S,3S)-diketide-SNAC 14, and a 40-fold advantage over the syn-(2R,3S)-diketide-SNAC 13. PICS module 2(DH(0))+TE, with an inactivated DH domain, produced exclusively 10, while three PICS module 2(KR(0))+TE mutants, with inactivated KR domains, produced exclusively or predominantly the unreduced triketide ketolactone, (4S,5R)-3-oxo-4-methyl-5-hydroxy-n-heptanoic acid-delta-lactone (7). These studies establish for the first time the structure and stereochemistry of the intermediates of a polyketide chain elongation cycle catalyzed by a DH-containing module, while confirming the importance of key active site residues in both KR and DH domains.     

Ruthenium carbene complexes with N,N'-bis(mesityl)imidazol-2-ylidene ligands: RCM catalysts of extended scope

The ruthenium carbene complexes 3a,b bearing imidazol-2-ylidene ligands constitute excellent precatalysts for ring-closing metathesis (RCM) reactions allowing the formation of tri- and tetrasubstituted cycloalkenes. They also apply to annulations that are beyond the scope of the standard Grubbs carbene 1 as well as to ring-closing reactions of acrylic acid derivatives even if the resulting alpha,beta-unsaturated lactones (or lactams) are tri- or tetrasubstituted. The reactivity of 3a was found to be highly dependent on the reaction medium: particularly high reaction rates are observed in toluene, although this solvent also leads to an increased tendency of the catalyst to isomerize the double bonds of the substrates.     

Combining ring-closing metathesis and hydroformylation strategies: a novel approach to spirocyclic gamma-butyrolactones.

Di- or tetrahydropyrans with a vinyl side chain are obtained by diastereoselective ring-closing metathesis or by addition of vinylmagnesium chloride to an appropriately functionalized tetrahydropyranone. The resulting allylic alcohols are converted to spirocyclic hemiacetals under hydroformylation conditions. Oxidation yields the corresponding lactones.     

Highly efficient ruthenium catalysts for the formation of tetrasubstituted olefins via ring-closing metathesis

[reaction: see text] A series of ruthenium-based metathesis catalysts with N-heterocyclic carbene (NHC) ligands have been prepared in which the N-aryl groups have been changed from mesityl to mono-ortho-substituted phenyl (e.g., tolyl). These new catalysts offer an exceptional increase in activity for the formation of tetrasubstituted olefins via ring-closing metathesis (RCM), while maintaining high levels of activity in ring-closing metathesis (RCM) reactions that generate di- and trisubstituted olefins.