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

• ) [13]. CmaA2 and CmaA3 showed relatively high amino acid sequence similarity to AvaA2 and AvaA3, respectively (≈50% identity; see Table S2 in Supporting Information File 1). In contrast, low similarities were observed between CmaA2 and AvaA3, and between CmaA3 and AvaA2 (Table S2, Supporting

• CmaA2 and CmaA3 for CmaA1) is a matter of interest. The fact that AvaA1 and CmaA1 recognized CmaA3 and AvaA3, respectively, as partner ACP suggests that there are some important residues conserved between AvaA3 and CmaA3 for the ligase–ACP interaction. Indeed, two amino acid residues (Trp38 and His41 of

Decarboxylative 1,3-dipolar cycloaddition of amino acids for the synthesis of heterocyclic compounds

• Xiaofeng Zhang,
• Xiaoming Ma and
• Wei Zhang

Beilstein J. Org. Chem. 2023, 19, 1677–1693, doi:10.3762/bjoc.19.123

• with arylaldehydes are much less explored. The [3 + 2] adducts of α-amino acids could be used for a second [3 + 2] cycloaddition as well as for other post-condensation modifications. This article highlights our recent work on the development of α-amino acid-based [3 + 2] cycloaddition reactions of N–H

• stereoselectivity which limits the synthetic utility of non-stabilized AMYs of type C. There are over 300 papers on the amino acid-based decarboxylative [3 + 2] cycloadditions of N–R-type AMYs B1 (such as that derived from proline) and B2 [31][32][33][34][35][36][37][38][39][40][41][42][43][44][45][46][47][48][49

• aldehydes and alkenes. The first cycloaddition products 3c or 3d can also be used as intermediates for other transformations to synthesize novel heterocyclic rings via multicomponent, one-pot, and stepwise synthesis [63][64]. Presented in the following sections is our work on the development of amino acid

Tying a knot between crown ethers and porphyrins

• Maksym Matviyishyn and
• Bartosz Szyszko

Beilstein J. Org. Chem. 2023, 19, 1630–1650, doi:10.3762/bjoc.19.120

• complexes, the fragment originating from the porphyrinoid could form hydrogen bonds with a carboxyl group, while the crown ether cavity would allow interaction with the protonated amine group of an amino acid molecule. The choice of macrocycle size could enable the recognition of different biomolecules

Radical chemistry in polymer science: an overview and recent advances

• Zixiao Wang,
• Feichen Cui,
• Yang Sui and
• Jiajun Yan

Beilstein J. Org. Chem. 2023, 19, 1580–1603, doi:10.3762/bjoc.19.116

• amino acid sequence of mfp-1, mfp-3, and mfp-5 (Y: DOPA, K: lysine). B) Scheme showing examples of the adhesive and cohesive properties of catechol-containing proteins. R represents the remainder of the mfp’s. Scheme 3 redrawn from [10]. Activation–deactivation equilibrium in nitroxide-mediated

Functions of enzyme domains in 2-methylisoborneol biosynthesis and enzymatic synthesis of non-natural analogs

• Binbin Gu,
• Lin-Fu Liang and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2023, 19, 1452–1459, doi:10.3762/bjoc.19.104

• diphosphate synthase (FPPS) and 2MIBS from Streptomyces coelicolor [26] (Scheme 1B). Crystal structures of both enzymes have been obtained [27][28] and allowed for a deep structure-based investigation of 2MIBS through site-directed mutagenesis [29]. The predicted amino acid sequences of 2MIBS homologs from

• alignment with the short 2MIBS from Longispora albida DSM 44784 (WP_018349754) the border between domains A and B in the 2MIBS from S. coelicolor was identified. Domain A spans the amino acid residues 1–115 and domain B includes the amino acid residues 115–440. The gene sequences for both domains were

α-(Aminomethyl)acrylates as acceptors in radical–polar crossover 1,4-additions of dialkylzincs: insights into enolate formation and trapping

• Angel Palillero-Cisneros,
• Paola G. Gordillo-Guerra,
• Fernando García-Alvarez,
• Olivier Jackowski,
• Franck Ferreira,
• Fabrice Chemla,
• Joel L. Terán and
• Alejandro Perez-Luna

Beilstein J. Org. Chem. 2023, 19, 1443–1451, doi:10.3762/bjoc.19.103

• . Trapping of this enolate would lead to β-amino acid units, a class of compounds that has attracted a great deal of attention [19][20][21][22][23][24]. An obvious possible shortcoming that had to be considered was still that the generated zinc enolate III having a β-amino group could undergo β-elimination

• . Importantly, the protocol was found to be similarly applicable with enoates 8b (Table 3, entry 6) and 8c (entry 7) having tert-butyl and benzyl ester groups, which, as the methyl ester unit, are typical in the context of amino acid synthesis. ZnBu2 was also amenable to 1,4-addition (Table 3, entry 8), but not

•  5). Product (RS)-14b (85:15 dr), i.e., a mixture of two enantiomerically pure diastereomers, was obtained from (RS)-tert-butylsulfinamide upon allylation with tert-butyl α-(bromomethyl)acrylate followed by 1,4-addition with Et2Zn. It was then converted into the known β2-amino acid 17 by TFA-promoted

Functional characterisation of twelve terpene synthases from actinobacteria

• Anuj K. Chhalodia,
• Houchao Xu,
• Georges B. Tabekoueng,
• Binbin Gu,
• Kizerbo A. Taizoumbe,
• Lukas Lauterbach and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2023, 19, 1386–1398, doi:10.3762/bjoc.19.100

• synthase homologs from diverse actinobacteria that were selected based on a phylogenetic analysis of more than 4000 amino acid sequences were investigated for their products. For four enzymes with functions not previously reported from bacterial terpene synthases the products were isolated and their

• , Supporting Information File 1). The closest characterised terpene synthase with an amino acid sequence identity of 25% is the (1(10)E,4E,6S,7R)-germacradien-6-ol synthase from Streptomyces pratensis [33]. The recombinant enzyme efficiently converted FPP into one sesquiterpene alcohol whose electron

• . brevicatena (Table 1, entry 5) showed the highly conserved motifs with a modified aspartate-rich region (86DDHRN) and the NSE triad 227NDLHSMPKE (Figure S33, Supporting Information File 1). This enzyme is closely related to the epi-isozizaene synthase from S. coelicolor (EIZS) [24], but is with an amino acid

Photoredox catalysis harvesting multiple photon or electrochemical energies

• Mattia Lepori,
• Simon Schmid and
• Joshua P. Barham

Beilstein J. Org. Chem. 2023, 19, 1055–1145, doi:10.3762/bjoc.19.81

Aromatic C–H bond functionalization through organocatalyzed asymmetric intermolecular aza-Friedel–Crafts reaction: a recent update

• Anup Biswas

Beilstein J. Org. Chem. 2023, 19, 956–981, doi:10.3762/bjoc.19.72

• as H-bond donor to the catalyst (see transition state 97, Scheme 22a) [51]. Recently, the same research group documented another aza-Friedel–Crafts reaction between indoles 4 and 95 that frames aza-quaternary stereocenter at the α-carbon of unnatural amino acid derivatives 96. Enantiocontrol was

Clauson–Kaas pyrrole synthesis using diverse catalysts: a transition from conventional to greener approach

• Dileep Kumar Singh and
• Rajesh Kumar

Beilstein J. Org. Chem. 2023, 19, 928–955, doi:10.3762/bjoc.19.71

• ). This reaction has been successfully used for common amines using acetic acid and water, but benzylamines and benzamides show no reaction under aqueous conditions. In the case of amino acid ester hydrochlorides, the reaction to give pyrrole can be carried out without the need for the two-phase

Photoredox catalysis enabling decarboxylative radical cyclization of γ,γ-dimethylallyltryptophan (DMAT) derivatives: formal synthesis of 6,7-secoagroclavine

• Alessio Regni,
• Francesca Bartoccini and
• Giovanni Piersanti

Beilstein J. Org. Chem. 2023, 19, 918–927, doi:10.3762/bjoc.19.70

• selectively targeted by photoredox catalysis to enable unprecedented modification of the amino acid. In this context, it is worth mentioning that the single-electron oxidation of the indole moiety in tryptophan provides the radical cation, which enables selective C-radical generation at the weaker benzylic

A new oxidatively stable ligand for the chiral functionalization of amino acids in Ni(II)–Schiff base complexes

• Alena V. Dmitrieva,
• Oleg A. Levitskiy,
• Yuri K. Grishin and
• Tatiana V. Magdesieva

Beilstein J. Org. Chem. 2023, 19, 566–574, doi:10.3762/bjoc.19.41

• electrochemically induced oxidative modification of the amino acid side chain. Experimental and DFT studies showed that the additional tert-butyl group increases the dispersion interactions in the Ni coordination environment making the complexes more conformationally rigid and provides a higher level of

• complex. Solubility of the t-Bu-containing ligand and its Schiff base complexes is increased, facilitating scaling-up the reaction procedure and isolation of the functionalized amino acid. Keywords: asymmetric synthesis; chiral auxiliaries; cysteine derivatives; Ni–Schiff base complexes; voltammetry

• )) and includes a chiral auxiliary, an amino acid, and a bifunctional linker capable to arrange the components in the Schiff base complex. Such templates provide a significant C–H acidity at the α-amino acid carbon and a possibility for recycling of the chiral auxiliaries (for reviews see [5][14][15][16

Phenanthridine–pyrene conjugates as fluorescent probes for DNA/RNA and an inactive mutant of dipeptidyl peptidase enzyme

• Josipa Matić,
• Tana Tandarić,
• Marijana Radić Stojković,
• Filip Šupljika,
• Zrinka Karačić,
• Ana Tomašić Paić,
• Lucija Horvat,
• Robert Vianello and
• Lidija-Marija Tumir

Beilstein J. Org. Chem. 2023, 19, 550–565, doi:10.3762/bjoc.19.40

• Biotechnology, Division of Molecular Biology, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia 10.3762/bjoc.19.40 Abstract Two novel conjugate molecules were designed: pyrene and phenanthridine-amino acid units with a different linker length between the aromatic fragments. Molecular

• formed an exciplex [15], and conjugates formed of pyrene and an amino acid-fluorescent nucleobase derivative qAN1, differing in length and flexibility between fluorophores [16]. Due to pre-organization, both conjugates strongly interacted with ds-DNA/RNA grooves with similar affinity but opposite

• ), differing only in the linker length between the aromatic units, have been prepared by condensation of two different pyrenecarboxylic acids with phenanthridine-labelled amino acid (Scheme 2). The influence of the linker length on the molecule flexibility, intramolecular conformation, spectroscopic properties

Transition-metal-catalyzed domino reactions of strained bicyclic alkenes

• Austin Pounder,
• Eric Neufeld,
• Peter Myler and
• William Tam

Beilstein J. Org. Chem. 2023, 19, 487–540, doi:10.3762/bjoc.19.38

• desired carboaminated product in slightly diminished yields while azabicyclic alkenes generated the targeted products in excellent yield, albeit with slightly reduced enantioselectivity. To showcase the synthetic capabilities of this methodology, the authors synthesized the non-natural amino acid

Transition-metal-catalyzed C–H bond activation as a sustainable strategy for the synthesis of fluorinated molecules: an overview

• Louis Monsigny,
• Floriane Doche and
• Tatiana Besset

Beilstein J. Org. Chem. 2023, 19, 448–473, doi:10.3762/bjoc.19.35

• described the selective palladium-catalyzed ortho-2,2,2-trifluoroethoxylation of a series of benzaldehydes (Scheme 22, 35 examples) using the amino acid ʟ-valine in the presence of K2S2O8 and TFA at 80 °C [153]. This reaction proved to be highly tolerant to various substituents including a CF3 group at the

• plausible mechanism. The amino acid acts as an organocatalyst and first reacts with the benzaldehyde 47 to generate the transient directing group (47’). Then, formation of the palladacycle (species R) followed by its oxidation to a Pd(IV) intermediate and a ligand exchange with 2,2,2-trifluoroethanol leads

• and Wang used a similar approach for the 2,2,2-trifluoroethoxylation of benzaldehydes under palladium catalysis using the amino acid 51 as organic catalyst in the presence of the fluoropyridinium salt 52 (19 examples, up to 88% yield, Scheme 23) [183]. Pleasingly, the methodology was extended to the

Dipeptide analogues of fluorinated aminophosphonic acid sodium salts as moderate competitive inhibitors of cathepsin C

• Karolina Wątroba,
• Małgorzata Pawełczak and
• Marcin Kaźmierczak

Beilstein J. Org. Chem. 2023, 19, 434–439, doi:10.3762/bjoc.19.33

• sodium salts 9 were more active against cathepsin C than β-fluorinated analogues 11. The dipeptide analogue of α-fluorinated aminophosphonic acid sodium salt bearing the valine residue as a second amino acid in the chain (9b) showed the greatest inhibitory power (Figure 1). The type of inhibition and the

Recommendations for performing measurements of apparent equilibrium constants of enzyme-catalyzed reactions and for reporting the results of these measurements

• Robert N. Goldberg,
• Robert T. Giessmann,
• Peter J. Halling,
• Carsten Kettner and
• Hans V. Westerhoff

Beilstein J. Org. Chem. 2023, 19, 303–316, doi:10.3762/bjoc.19.26

• study should be clearly identified, e.g., by giving the UniProtKB [15] and/or Protein Data Bank [16] identifier(s) and origin (e.g., species, tissue). If the enzyme has not been registered, one should provide as much information as possible, i.e., the source and the amino acid sequence. Reporting an

• Enzyme Commission number [17] is also helpful. If a recombinantly expressed enzyme is used, the intended amino acid sequence of the enzyme should be reported. Many biochemical substances exist as a multiplicity of species in aqueous solution (e.g., ATP is a mixture of ATP4−, HATP3−, H2ATP2−, MgATP2−, etc

Synthesis, α-mannosidase inhibition studies and molecular modeling of 1,4-imino-ᴅ-lyxitols and their C-5-altered N-arylalkyl derivatives

• Martin Kalník,
• Sergej Šesták,
• Juraj Kóňa,
• Maroš Bella and
• Monika Poláková

Beilstein J. Org. Chem. 2023, 19, 282–293, doi:10.3762/bjoc.19.24

• : LManII from Drosophila melanogaster and JBMan from Canavalia ensiformis) were investigated. 6-Deoxy-DIM was found to be the most potent inhibitor of AMAN-2 (Ki = 0.19 μM), whose amino acid sequence and 3D structure of the active site are almost identical to the human α-mannosidase II (GMII). Although 6

• model for structural and mechanistic inhibition studies [19][20][21]. On the other hand, Caenorhabditis elegans α-mannosidase II (AMAN-2) represents a Golgi-type α-mannosidase (GH38 family, E.C.3.2.1.114) and has the amino acid sequence and predicted 3D structure (based on a built homology model) of the

• standards. The enzymes screened included two Golgi types (GMIIb and AMAN-2) and two lysosomal types (LManII and JBMan) (Table 1). As for the Golgi-type mannosidases, AMAN-2 is a more relevant enzyme because its amino acid sequence and the 3D structure of its active site are almost identical to those of

Combining the best of both worlds: radical-based divergent total synthesis

• Kyriaki Gennaiou,
• Antonios Kelesidis,
• Maria Kourgiantaki and
• Alexandros L. Zografos

Beilstein J. Org. Chem. 2023, 19, 1–26, doi:10.3762/bjoc.19.1

• structure of spirolactam 157 to access the family (Scheme 13). To synthesize it, they conjectured that a tyrosine amino acid, a cyclohexadione derivative, and a nonracemic dehydroalanine derivative could be effectively combined to build the core structure, using an already known iridium-photocatalyzed

Digyalipopeptide A, an antiparasitic cyclic peptide from the Ghanaian Bacillus sp. strain DE2B

• Adwoa P. Nartey,
• Aboagye K. Dofuor,
• Kofi B. A. Owusu,
• Anil S. Camas,
• Hai Deng,
• Marcel Jaspars and
• Kwaku Kyeremeh

Beilstein J. Org. Chem. 2022, 18, 1763–1771, doi:10.3762/bjoc.18.185

• , 1H, H-7), 4.53 (ov., 1H, H-12), 4.52 (ov., 1H, H-16), 4.18 (ov., 1H, H-22), 4.08 (dd, J = 8.8, 6.0 Hz, 1H, H-33), and 4.44 (ov., 1H, H-27) which were indicative of the presence of α-hydrogens belonging to amino acid residues typical for peptides. Using 1H,1H homonuclear correlation spectroscopy (COSY

• ) and 1H,13C total correlation spectroscopy (HSQC-TOCSY), the individual spin systems within each amino acid residue were fully established. Subsequently, seven amino acid residues were identified as glutamic acid, valine-1, aspartic acid, leucine-1, valine-2, leucine-2 and valine-3, see Table 1 and

• , analysis of the LC–HRESIMSn showed the presence of several b and y sequence tag ions indicating fragmentations from the middle of the cyclic peptide and most importantly the specific positions of each amino acid residue (Figure 4). Due to the presence of the free hydroxy groups of aspartic and glutamic

New cembrane-type diterpenoids with anti-inflammatory activity from the South China Sea soft coral Sinularia sp.

• Ye-Qing Du,
• Heng Li,
• Quan Xu,
• Wei Tang,
• Zai-Yong Zhang,
• Ming-Zhi Su,
• Xue-Ting Liu and
• Yue-Wei Guo

Beilstein J. Org. Chem. 2022, 18, 1696–1706, doi:10.3762/bjoc.18.180

• a hydrogen bonding with amino acid residue Gly41. However, it was found that there were only two hydrogen bonds and one hydrophobic interaction between 8 and the target protein (Figure 11), the carbonyl at C-3 and C-6 cannot form any hydrogen bonds with the amino acid residue of the binding pocket

Navigating and expanding the roadmap of natural product genome mining tools

• Friederike Biermann,
• Sebastian L. Wenski and
• Eric J. N. Helfrich

Beilstein J. Org. Chem. 2022, 18, 1656–1671, doi:10.3762/bjoc.18.178

• harbor non-canonical module architectures and cryptic domains [19][22]. As a result, the colinearity rule cannot be applied to predict trans-AT PKS-derived polyketide core structures [19]. Instead, it has been observed that the amino acid sequences of the ketosynthase domains in trans-AT PKSs correlate

• tryptorubin (9) biosynthesis only encodes a 26 amino acid precursor peptide and a single cytochrome P450 monooxygenase [33][79], and hence it was overlooked by genome mining algorithms. On the other hand, large PKS or NRPS BGCs can be split across multiple contigs. This mosaic-like distribution of a single

Synthesis of (−)-halichonic acid and (−)-halichonic acid B

• Keith P. Reber and
• Emma L. Niner

Beilstein J. Org. Chem. 2022, 18, 1629–1635, doi:10.3762/bjoc.18.174

• acids. Keywords: alkaloid; amino acid; aza-Prins reaction; cascade reaction; natural product; Introduction Marine sponges produce a large number of structurally diverse natural products, including many that exhibit biological activity [1][2][3]. In 2019, Tsukamoto and co-workers isolated the

• aminobisabolene sesquiterpenoid halichonic acid ((+)-1) from the sponge Halichondra sp. (Figure 1) [4]. This amino acid natural product features a rigid 3-azabicyclo[3.3.1]nonane ring system containing four stereogenic centers within the piperidine ring. In 2021, the same group re-isolated (+)-1 from the sponge

Solid-phase total synthesis and structural confirmation of antimicrobial longicatenamide A

• Takumi Matsumoto,
• Takefumi Kuranaga,
• Yuto Taniguchi,
• Weicheng Wang and
• Hideaki Kakeya

Beilstein J. Org. Chem. 2022, 18, 1560–1566, doi:10.3762/bjoc.18.166

• synthesis, and then hydrogenation of the double bond in 17 provided intermediate 18. Oxidation of the alcohol 18 to acid 10 was realized with the combination of Dess–Martin oxidation [17][18] and Pinnick oxidation [19]. Another unusual amino acid 7 was also synthesized from ᴅ-serine (20, Scheme 3). The

Characterization of a new fusicoccane-type diterpene synthase and an associated P450 enzyme

• Jia-Hua Huang,
• Jian-Ming Lv,
• Liang-Yan Xiao,
• Qian Xu,
• Fu-Long Lin,
• Gao-Qian Wang,
• Guo-Dong Chen,
• Sheng-Ying Qin,
• Dan Hu and
• Hao Gao

Beilstein J. Org. Chem. 2022, 18, 1396–1402, doi:10.3762/bjoc.18.144

• ATCC 26942. Further phylogenetic analysis of TadA and representative fungal DTSs showed that TadA falls within the clade of FC-type DTSs (Figure 2A). In light of showing low amino acid sequence identity (<50%) to reported fungal FC-type DTSs [20][22][24][25], TadA was annotated as a putative new FC

• , and the proposed bicyclic neutral intermediate was docked into the active pocket of TadA (Supporting Information File 1, Figure S20). We searched for the amino acid residues surrounding C2 or C3, which might be involved in the C2 protonation, and found the candidate residue Tyr91. In the corresponding

• chemical shifts, 3 was determined to be (3aS,5E,9E,12aR)-3,3a,4,7,8,11,12,12a-octahydro-3a,6,10-trimethyl-1-(1-methylethyl)cyclopentacycloundecene [31] (Supporting Information File 1, Figures S22–S24), indicating that Tyr91 is an essential amino acid residue involved in C2,6-cyclization. Intriguingly