Substrate specificity of a ketosynthase domain involved in bacillaene biosynthesis

• Zhiyong Yin and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2024, 20, 734–740, doi:10.3762/bjoc.20.67

• = thioesterase. The black dot indicates a methyl branch introduced by the β-branching cassette. Synthesis of the BaeJ-KS2 substrate surrogates (S)-11 and (R)-11. Green dots represent 13C-labelled carbons. Supporting Information Supporting Information File 76: Experimental part and NMR spectra. Acknowledgements

Chemoenzymatic synthesis of macrocyclic peptides and polyketides via thioesterase-catalyzed macrocyclization

• Senze Qiao,
• Zhongyu Cheng and
• Fuzhuo Li

Beilstein J. Org. Chem. 2024, 20, 721–733, doi:10.3762/bjoc.20.66

• , and their hybrids, thioesterase (TE) domains play a significant role in late-stage macrocyclization. These domains can accept mimics of native substrates in vitro and exhibit potential for use in total synthesis. This review summarizes the recent advances of TE domains in the chemoenzymatic synthesis

• polyketides; thioesterase; Introduction Nonribosomal peptides, polyketides, and their hybrids exhibit significant diversity and a broad spectrum of bioactivities [1][2][3]. Particularly, macrocycles from these three categories of natural products are vital resources for developing pharmaceuticals and drug

• responsible for the structural diversity of natural products, both NRPS and PKS contain thioesterase (TE) domains in the final elongation module, which contribute to terminating biosynthesis [13][14]. Typically, TE domains cleave the thioester bond between the last PCP or ACP domain and the intermediate of

New variochelins from soil-isolated Variovorax sp. H002

• Jabal Rahmat Haedar,
• Aya Yoshimura and
• Toshiyuki Wakimoto

Beilstein J. Org. Chem. 2024, 20, 692–700, doi:10.3762/bjoc.20.63

• : epimerization domain, TE: thioesterase domain, KS: ketosynthase domain, AT: acyl transferase domain, KR: ketoreductase domain, TauD: taurine dioxygenase domain. Substrate specificity of A and KS domains is presented at the top of each module (FA: fatty acyl, Arg: arginine, MM: methyl malonyl, Asp: aspartic acid

A myo-inositol dehydrogenase involved in aminocyclitol biosynthesis of hygromycin A

• Michael O. Akintubosun and
• Melanie A. Higgins

Beilstein J. Org. Chem. 2024, 20, 589–596, doi:10.3762/bjoc.20.51

• 584 sequences were near an acyl synthase domain, 340 sequences by an acyl carrier protein domain, and 1,193 sequences by a thioesterase domain. In addition, Hyg17 works together with the aminotransferase Hyg8 to replace a hydroxy group with an amine generating an aminocyclitol from myo-inositol. We

Synthesis and biological profile of 2,3-dihydro[1,3]thiazolo[4,5-b]pyridines, a novel class of acyl-ACP thioesterase inhibitors

• Jens Frackenpohl,
• David M. Barber,
• Guido Bojack,
• Birgit Bollenbach-Wahl,
• Ralf Braun,
• Rahel Getachew,
• Sabine Hohmann,
• Kwang-Yoon Ko,
• Karoline Kurowski,
• Bernd Laber,
• Rebecca L. Mattison,
• Thomas Müller,
• Anna M. Reingruber,
• Dirk Schmutzler and
• Andrea Svejda

Beilstein J. Org. Chem. 2024, 20, 540–551, doi:10.3762/bjoc.20.46

• show good acyl-ACP thioesterase inhibition in line with strong herbicidal activity against commercially important weeds in broadacre crops, e.g., wheat and corn. The desired substituted 2,3-dihydro[1,3]thiazolo[4,5-b]pyridines were prepared via an optimized BH3-mediated reduction involving tris

• -dihydro[1,3]thiazolo[4,5-b]pyridine; acyl-ACP thioesterase; bioisostere; herbicide; heterocycle; Introduction The presence of weed infestations exerts a high strain on food production around the globe by depleting resources for the crops and facilitating the transmission of diseases [1]. Although

• with emphasis on the structural diversity of small-molecule ligands. In this context, acyl-acyl carrier protein (acyl-ACP) thioesterase inhibitors have shown a remarkable variability. Fatty acid thioesterase (FAT) enzymes represent a family of proteins exclusively found in higher plants. They mediate

Development of a chemical scaffold for inhibiting nonribosomal peptide synthetases in live bacterial cells

• Fumihiro Ishikawa,
• Sho Konno,
• Hideaki Kakeya and
• Genzoh Tanabe

Beilstein J. Org. Chem. 2024, 20, 445–451, doi:10.3762/bjoc.20.39

• arm in an adjacent peptidyl carrier protein (PCP). The amino acid loaded on the PCP then undergoes coupling with the amino acid loaded on the downstream PCP in the condensation (C) domain. Finally, the linear peptide on the PCP in the last module is either hydrolyzed or cyclized by a thioesterase (TE

• -specific A-domain; A2, ʟ-Pro-specific A-domain; A3, ʟ-Val-specific A-domain; A4, ʟ-Orn-specific A-domain; A5, ʟ-Leu-specific A-domain; E, epimerization domain; C, condensation domain; TE, thioesterase domain. (A) Adenylation reaction in a nonribosomal peptide synthetase. (B) Structures of aminoacyl-AMS

Identification of the p-coumaric acid biosynthetic gene cluster in Kutzneria albida: insights into the diazotization-dependent deamination pathway

• Seiji Kawai,
• Akito Yamada,
• Yohei Katsuyama and
• Yasuo Ohnishi

Beilstein J. Org. Chem. 2024, 20, 1–11, doi:10.3762/bjoc.20.1

• CmaA1. 3-ACA (3) is then synthesized from 3,4-AHBA-CmaA3 and malonyl-CmaA2 by the highly reducing type II PKS composed of four Cma proteins (CmaA4, CmaA5, CmaB, and CmaG), a dehydratase from fatty acid synthase, and an unknown thioesterase. CmaB should also stimulate the reaction in an unknown manner as

¹⁹F NMR as a tool in chemical biology

• Diana Gimenez,
• Aoife Phelan,
• Cormac D. Murphy and
• Steven L. Cobb

Beilstein J. Org. Chem. 2021, 17, 293–318, doi:10.3762/bjoc.17.28

Fabclavine diversity in Xenorhabdus bacteria

• Sebastian L. Wenski,
• Harun Cimen,
• Natalie Berghaus,
• Sebastian W. Fuchs,
• Selcuk Hazir and
• Helge B. Bode

Beilstein J. Org. Chem. 2020, 16, 956–965, doi:10.3762/bjoc.16.84

• , Supporting Information File 1). Nevertheless, X. innexi contains a tonB-homologue instead of the NUDIX-hydrolase fclA and an acyl-CoA-thioesterase instead of fclM and fclN, leading to the postulated compound Xenorhabdus lipoprotein toxin (Xlt, Figure S1, Supporting Information File 1) [27]. Furthermore

Genomics-inspired discovery of massiliachelin, an agrochelin epimer from Massilia sp. NR 4-1

• Jan Diettrich,
• Hirokazu Kage and
• Markus Nett

Beilstein J. Org. Chem. 2019, 15, 1298–1303, doi:10.3762/bjoc.15.128

• , fatty acyl-AMP ligase; ACP, acyl carrier protein; KS, β-ketoacyl synthase; AT, acyltransferase; KR, ketoreductase; C, condensation; A, adenylation; MT, methyltransferase; PCP, peptidyl carrier protein; TE, thioesterase. The asterisk indicates a methyltransferase-like epimerization domain. C) UV

Back to the future: Why we need enzymology to build a synthetic metabolism of the future

• Tobias J. Erb

Beilstein J. Org. Chem. 2019, 15, 551–557, doi:10.3762/bjoc.15.49

• cycle. To overcome the problem of unwanted malyl-CoA accumulation, a malyl-CoA thioesterase [59] had to be added to the synthetic network. This enzyme effectively recycles the dead-end metabolite back into two intermediates of the network, malate and free CoA, thus serving as a “proof-reading” enzyme at

Targeting the Pseudomonas quinolone signal quorum sensing system for the discovery of novel anti-infective pathoblockers

• Christian Schütz and
• Martin Empting

Beilstein J. Org. Chem. 2018, 14, 2627–2645, doi:10.3762/bjoc.14.241

• -aminobenzoylacetyl-CoA (2-ABA-CoA) under decarboxylation [28][29]. In a next step, the pathway-specific thioesterase PqsE generates 2-aminobenzoylacetate (2-ABA) [29]. It has been shown, that also the broad-specificity thioesterase TesB present in P. aeruginosa can catalyse this reaction [29]. The quinolone core is

• effects are mediated either through direct PqsR-dependent action or by PqsR-independent mechanisms, which are most likely due to the iron-chelating as well as antioxidant properties of PQS [33]. Furthermore, it has been unravelled that the thioesterase PqsE, whose biosynthetic function is dispensable due

• , their potency in attenuating biofilm formation was more pronounced than ciprofloxacin and linezolid itself. A docking study suggested PqsD to be the target of these compounds like 23 (Figure 10), although this remains speculative. PqsE inhibitors The pathway-specific thioesterase PqsE is not only

Volatiles from the tropical ascomycete Daldinia clavata (Hypoxylaceae, Xylariales)

• Tao Wang,
• Kathrin I. Mohr,
• Marc Stadler and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2018, 14, 135–147, doi:10.3762/bjoc.14.9

• are already defined. A third extension with malonyl-SCoA and methylation gives rise to intermediate C that can be released, e.g., by a thioesterase to the β-keto acid D, followed by spontaneous decarboxylation to 11a. Two structurally related molecules to 11a have been reported from endophytic

Strategies in megasynthase engineering – fatty acid synthases (FAS) as model proteins

• Manuel Fischer and
• Martin Grininger

Beilstein J. Org. Chem. 2017, 13, 1204–1211, doi:10.3762/bjoc.13.119

• SCFA yields, the approach turned out to be highly powerful compared to other strategies that were overwriting native synthesis with a short-chain acyl-ACP specific thioesterase that is inserted as extra domain into the polypeptide chain [60][61][62][63]. Further studies on FAS can be envisioned, i.e

• sets of catalytic domains highlighted. Abbreviations as introduced before; additionally, malonyl-/acetyl-transferase (MAT) and thioesterase (TE). Conformational flexibility of animal FAS, as indicated by arrows, is largely induced by a central waist. The reaction volume was calculated as cylinder as

Polyketide stereocontrol: a study in chemical biology

• Kira J. Weissman

Beilstein J. Org. Chem. 2017, 13, 348–371, doi:10.3762/bjoc.13.39

• positions in the polyketide chains. Building of the polyketide core is typically terminated by a thioesterase (TE) domain situated at the end of the final PKS multienzyme, which releases the product by hydrolysis or more usually macrolactonization, using an internal hydroxy nucleophile. This PKS-free

Biochemical and structural characterisation of the second oxidative crosslinking step during the biosynthesis of the glycopeptide antibiotic A47934

• Veronika Ulrich,
• Clara Brieke and
• Max J. Cryle

Beilstein J. Org. Chem. 2016, 12, 2849–2864, doi:10.3762/bjoc.12.284

• ), peptidyl carrier protein with phosphopantetheine linker (PCP; green), condensation (C; red), epimerisation (E; dark blue), P450-recruitment (X; blue) and thioesterase (TE; light grey) domain; the peptide is shown at its distinct stages of biosynthesis; the amino acid cyclisation steps are depicted with

Chemical probes for competitive profiling of the quorum sensing signal synthase PqsD of Pseudomonas aeruginosa

• Michaela Prothiwa,
• Dávid Szamosvári,
• Sandra Glasmacher and
• Thomas Böttcher

Beilstein J. Org. Chem. 2016, 12, 2784–2792, doi:10.3762/bjoc.12.277

• catalyzes the condensation with malonyl-CoA to form 2-aminobenzoylacetyl-CoA. The thioesterase PqsE hydrolyses the thioester to produce 2-aminobenzoylacetate (2-ABA) [13]. The PqsBC complex finally generates HHQ or other AQs in a decarboxylative condensation reaction of 2-ABA with fatty acids loaded on PqsC

A non-canonical peptide synthetase adenylates 3-methyl-2-oxovaleric acid for auriculamide biosynthesis

• Daniel Braga,
• Dirk Hoffmeister and
• Markus Nett

Beilstein J. Org. Chem. 2016, 12, 2766–2770, doi:10.3762/bjoc.12.274

• ]. Retrobiosynthetic analysis allowed the identification of a 14,130 bp-gene cluster, now referred to as aul-cluster (Figure 2), which putatively encodes two NRPSs (AulA and AulB) and one PKS (AulC) possessing domains that collectively allow and plausibly explains the assembly of 1. A gene for a type-II thioesterase

• carrier protein; AT, acyl transferase; C, condensation; KR, ketoreductase; KS, ketosynthase; PCP, peptidyl carrier protein; TE, thioesterase. The gene aulD encodes a type II thioesterase. Testing of AulA (A1-A2-KR-PCP) and a truncated variant (A2-KR-PCP) in the ATP-[32P]pyrophosphate exchange assay using

Biosynthesis of oxygen and nitrogen-containing heterocycles in polyketides

• Franziska Hemmerling and
• Frank Hahn

Beilstein J. Org. Chem. 2016, 12, 1512–1550, doi:10.3762/bjoc.12.148

• ) domains as well as ketoreductase (KR), dehydratase (DH), enoyl reductase (ER) and thioesterase (TE) domains [6][8]. The PKS intermediates remain tethered to the megaenzyme via a thioester linkage during the whole process. Among these domains, only TE domains participate in cyclisation reactions as part of

• 860 [162]. Similar to salinosporamide A (199), the respective biosynthetic gene cluster neither encodes a modular nor a lone-standing thioesterase domain. Instead, in vitro studies with the SNAC-thioester bound acyclic intermediate demonstrated the spontaneous heterocyclisation by nucleophilic attack

Cyclisation mechanisms in the biosynthesis of ribosomally synthesised and post-translationally modified peptides

• Andrew W. Truman

Beilstein J. Org. Chem. 2016, 12, 1250–1268, doi:10.3762/bjoc.12.120

• AYDG motif on the precursor peptide. This generates an acyl–enzyme intermediate, where the C-terminus of the peptide is bound to Ser783 as an ester. The N-terminal amino group then attacks this intermediate to generate a cyclic octapeptide. This is mechanistically similar to thioesterase-catalysed

Biosynthesis of α-pyrones

• Till F. Schäberle

Beilstein J. Org. Chem. 2016, 12, 571–588, doi:10.3762/bjoc.12.56

• terminal module, which results in a cis-configured double bond. Through the formation of the cis double bond the sterical arrangement of the nascent chain favors the lactone ring closure which results in the α-pyrone moiety. Hence, the polyketide is released from the assembly line, whereby the thioesterase

• by the thioesterase (TE) domain, resulting in 73. B) PKS type II: The precursor of the enterocin biosynthesis, comprising the uncommon benzoate starter unit, is shown attached to the ACP domain, which forms a complex with the KSα and the KSβ domain. Modification, rearrangement and lactonization of

Recent highlights in biosynthesis research using stable isotopes

• Jan Rinkel and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2015, 11, 2493–2508, doi:10.3762/bjoc.11.271

• : formyltransferase, A: adenylation, CP: peptidyl carrier protein, C: condensation, E/C: condensation + epimerization, TE: thioesterase). For the absolute configuration of incorporated amino acids relevant domains are highlighted with arrows. Modules not shown consist of alternating C and E/C. Asterisks indicate

Intermediates in monensin biosynthesis: A late step in biosynthesis of the polyether ionophore monensin is crucial for the integrity of cation binding

• Wolfgang Hüttel,
• Jonathan B. Spencer and
• Peter F. Leadlay

Beilstein J. Org. Chem. 2014, 10, 361–368, doi:10.3762/bjoc.10.34

• cyclisation is not initiated before the full-length chain is produced, and that the initial product of the PKS is a linear enzyme-bound (E,E,E)-triene, “premonensin” (2) [19]. The monensin PKS does not have a conventional C-terminal thioesterase domain that would catalyse polyketide chain release, and instead

• MonACPX, catalysed by the unusual thioesterase MonCII [20]. The evidently tight coupling between PKS-mediated chain assembly and oxidative cyclisation has hampered efforts to unravel the exact sequence and mechanism of events in the late stages of the biosynthesis. Indirect but suggestive evidence for the

• thioesterase MonCII. The results from the single mutants show that 3 is also a substrate for both MonD and MonE. In the ΔmonD strain substantial amounts of dehydroxydemethylmonensin (3) remain unconverted by MonE to dehydroxymonensin (5). In contrast, compound 3 was not detected in crude extracts of the ΔmonE

The regulation and biosynthesis of antimycins

• Ryan F. Seipke and
• Matthew I. Hutchings

Beilstein J. Org. Chem. 2013, 9, 2556–2563, doi:10.3762/bjoc.9.290

• , ketosynthase; AT, acyltransferase; ACP, acyl carrier protein; TE, thioesterase; *AntP is a pathway-specific kynureninase that is encoded by L- and I-form ant gene clusters. σAntA comprises a new subfamily of ECF RNA polymerase σ factors. σAntA amino acid sequences were aligned to amino acid sequences of random

Quantification of N-acetylcysteamine activated methylmalonate incorporation into polyketide biosynthesis

• Stephan Klopries,
• Uschi Sundermann and
• Frank Schulz

Beilstein J. Org. Chem. 2013, 9, 664–674, doi:10.3762/bjoc.9.75

• ][7][8]. Abbreviations: AT: acyltransferase, ACP: acyl carrier protein, KS: ketosynthase, KR: ketoreductase, DH: dehydratase, ER: enoylreductase, TE: thioesterase. Structures of erythromycin (left) and rapamycin (right). In this experiment both compounds were labeled in their methyl side chains with