Discovery of antimicrobial peptides clostrisin and cellulosin from Clostridium: insights into their structures, co-localized biosynthetic gene clusters, and antibiotic activity

• Moisés Alejandro Alejo Hernandez,
• Katia Pamela Villavicencio Sánchez,
• Rosendo Sánchez Morales,
• Karla Georgina Hernández-Magro Gil,
• David Silverio Moreno-Gutiérrez,
• Eddie Guillermo Sanchez-Rueda,
• Yanet Teresa-Cruz,
• Brian Choi,
• Armando Hernández Garcia,
• Alba Romero-Rodríguez,
• Oscar Juárez,
• Siseth Martínez-Caballero,
• Mario Figueroa and
• Corina-Diana Ceapă

Beilstein J. Org. Chem. 2024, 20, 1800–1816, doi:10.3762/bjoc.20.159

• was co-expressed with the corresponding precursor peptide in the same E. coli strain (expected size 150 kDa). The precursor peptides and the peptidase domain of CloPt1 were fused with a 6xHis tag at their N-terminal end for purification purposes (Figure S7 in Supporting Information File 1). After

• analysis of the CloA1 and CloA2 precursor peptides Clostrisin and cellulosin were purified through non-native means using a Ni2+ column due to a 6xHis tag at the N-terminal end, followed by elution via imidazole gradient (refer to Figures S7A and S7B in Supporting Information File 1 for SDS-PAGE analysis

• seconds off, for a total of 10 minutes at 4.0 potency). Finally, the sample was centrifuged for 30 min at 4 °C at 10,000 rpm. Supernatants were stored at −80 °C until purification. The C39 peptidase domain, and the clostrisin and cellulosin lanthipeptides were linked with a 6xHis N-terminal tag to perform

Chemo-enzymatic total synthesis: current approaches toward the integration of chemical and enzymatic transformations

• Ryo Tanifuji and
• Hiroki Oguri

Beilstein J. Org. Chem. 2024, 20, 1693–1712, doi:10.3762/bjoc.20.151

• prenyltransferase (PT) domain located at the C-terminus of BscA (Scheme 2A). Subsequently, the terpene cyclase (TC) domain at the N-terminal of BscA generates fusicocca-2,10(14)-diene (6), which bears the common 5/8/5 fused tricyclic scaffold common to this natural products family. Sequential oxidative conversions

Methyltransferases from RiPP pathways: shaping the landscape of natural product chemistry

• Maria-Paula Schröder,
• Isabel P.-M. Pfeiffer and
• Silja Mordhorst

Beilstein J. Org. Chem. 2024, 20, 1652–1670, doi:10.3762/bjoc.20.147

• [RMSD: 8.152 Å (109 to 109 atoms)], demonstrating the structural diversity among O-MTs (Figure 5). Streptomyces bottropensis produces various bottromycins, including bottromycin A2 (Figure 4) [79]. The precursor peptide consists of an N-terminal core and a rare C-terminal follower region. The

• occur at the N-terminal amide, the peptide backbone, as well as on amino acid side chain amides (Figure 1). While traditional synthesis of N-methylated peptides is challenging and time consuming, installation via RiPP maturases provides an easier, quicker, and greener approach to confer these attributes

• -terminal methyltransferases The α-amino group of N-terminal amino acid residues can either be mono-, di-, or trimethylated. This methylation step occurs after the core peptide is cleaved from the leader and can enhance the metabolic stability of the final peptide natural product [85]. Crocagin A is the

Mining raw plant transcriptomic data for new cyclopeptide alkaloids

• Draco Kriger,
• Michael A. Pasquale,
• Brigitte G. Ampolini and
• Jonathan R. Chekan

Beilstein J. Org. Chem. 2024, 20, 1548–1559, doi:10.3762/bjoc.20.138

• -translational modifications by specific tailoring enzymes [5][6]. This precursor peptide substrate can be subdivided into multiple segments including 1) an N-terminal leader or recognition sequence used for binding by the tailoring enzymes and 2) a core peptide that is targeted for modification by the

• . jasminoides that directly match this FFFY sequence (Figure 6A). Like other members of the Rubiaceae family [7][34], the tyrosine that forms the ether linkage remains intact, and not oxidatively decarboxylated as seen in members of the Rhamnaceae family. It is also predicted to contain a dimethylation at the N

• -terminal Phe residue. Additional 663.3192 and 581.3345 m/z features were also present in the GNPS network, but MS/MS fragmentation could not definitively support a specific structure. For a better understanding of the biosynthesis of burpitides in G. jasminoides, we explored the genomic context by using

Bioinformatic prediction of the stereoselectivity of modular polyketide synthase: an update of the sequence motifs in ketoreductase domain

• Changjun Xiang,
• Shunyu Yao,
• Ruoyu Wang and
• Lihan Zhang

Beilstein J. Org. Chem. 2024, 20, 1476–1485, doi:10.3762/bjoc.20.131

• KRC, the N-terminal helix αB and the lid region αFG located at the C-terminal of KRC (Figure 2d). Indeed, this lid region exhibits a direct interaction with the DH and DH-KR linker (Figure 2c). However, such interaction was not observed between the N-terminal helix αB and DH in the crystal structure

Cofactor-independent C–C bond cleavage reactions catalyzed by the AlpJ family of oxygenases in atypical angucycline biosynthesis

• Jinmin Gao,
• Liyuan Li,
• Shijie Shen,
• Guomin Ai,
• Bin Wang,
• Fang Guo,
• Tongjian Yang,
• Hui Han,
• Zhengren Xu,
• Guohui Pan and
• Keqiang Fan

Beilstein J. Org. Chem. 2024, 20, 1198–1206, doi:10.3762/bjoc.20.102

• analysis of the alp gene cluster from Streptomyces ambofaciens revealed AlpG as the homolog of JadH. The N-terminal His6-tagged construct of AlpG was expressed and purified to homogeneity in E. coli (Figure S2, Supporting Information File 1). The purified AlpG displayed a light yellow color, and the

• NdeI and HindIII, and cloned into pET28a to construct the expression plasmid of N-terminal His6-tagged AlpG. The codon-optimized flu17 gene was synthesized by Synbio Technologies, digested with NdeI and HindIII, and cloned into pET28a to afford the expression plasmid of N-terminal His6-tagged Flu17

• biosynthesis of fluostatins involves analogous B-ring cleavage and contraction steps as observed in kinamycin biosynthesis [2][13][19][26]. A sequence analysis of a reported fluostatin biosynthetic gene cluster in reassembled environmental DNA identified Flu17 as the putative ring opening oxygenase [8]. The N

Synthesis of 1,4-azaphosphinine nucleosides and evaluation as inhibitors of human cytidine deaminase and APOBEC3A

• Maksim V. Kvach,
• Stefan Harjes,
• Harikrishnan M. Kurup,
• Geoffrey B. Jameson,
• Elena Harjes and
• Vyacheslav V. Filichev

Beilstein J. Org. Chem. 2024, 20, 1088–1098, doi:10.3762/bjoc.20.96

• partially localised in the nucleus of cells and, in cancer cells, become genotoxic [24]. A3A and A3H are single-domain enzymes, whereas A3B is a double-domain enzyme, in which only the C-terminal domain (CTD) has catalytic activity, and the N-terminal domain (NTD) is responsible for binding of DNA and for

Enhancing structural diversity of terpenoids by multisubstrate terpene synthases

• Min Li and
• Hui Tao

Beilstein J. Org. Chem. 2024, 20, 959–972, doi:10.3762/bjoc.20.86

• TSs and three PTs to generate 4, 5 or geranylfarnesyl diphosphate (GFPP, 29, Figure 1), representative products 30–33 are shown in Figure 3a [28]. Notably, FgMS is a chimeric enzyme (PTTS) consisting of an N-terminal class I TS domain and a C-terminal GFPP synthase domain. Therefore, to block the

Synthesis and characterization of water-soluble C₆₀–peptide conjugates

• Yue Ma,
• Lorenzo Persi and
• Yoko Yamakoshi

Beilstein J. Org. Chem. 2024, 20, 777–786, doi:10.3762/bjoc.20.71

• of hydrophilic oligopeptide anchors (oligo-Lys, oligo-Glu, and oligo-Arg) were synthesized. A previously reported Prato reaction adduct of a biscarboxylic acid-substituted C60 derivative was subjected to a solid phase synthesis for amide formation with N-terminal amines of peptides on resin to

Genome mining of labdane-related diterpenoids: Discovery of the two-enzyme pathway leading to (−)-sandaracopimaradiene in the fungus Arthrinium sacchari

• Fumito Sato,
• Terutaka Sonohara,
• Shunta Fujiki,
• Akihiro Sugawara,
• Yohei Morishita,
• Taro Ozaki and
• Teigo Asai

Beilstein J. Org. Chem. 2024, 20, 714–720, doi:10.3762/bjoc.20.65

• determined to be (−)-sandaracopimaradiene (Figure 3B). We then turned our attention to the individual function of these enzymes. With this aim, AsPS and AsCPS were expressed in Escherichia coli as N-terminal hexa-histidine-tagged proteins and purified by Ni-affinity chromatography (see Supporting Information

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

• structure – a linear hexapeptide with β-hydroxyaspartate and hydroxamate functional groups, serving in iron-binding coordination. Three new variochelins C–E (3–5) were characterized by varied fatty acyl groups at their N-termini; notably, 4 and 5 represent the first variochelins with N-terminal unsaturated

• -guanidino-3-hydroxy-2-methylheptanoate, indicating that the N-terminal fatty acyl group is a tetradecanoic acid in 2 (Figure 1 and Figure S10 in Supporting Information File 1). Therefore, compound 2 is concluded to be the known lipohexapeptide variochelin B [5]. Compound 3 has the chemical formula of

• C45H79O17N11, as suggested by the HRESIMS data (m/z 1044.5603 for the [M − H]− ion), indicating the loss of two methylene groups (C2H4) from 1. In addition, the MS/MS fragmentation profile of 3 was consistent with those of 1 and 2, except for the loss of 28 mass units in the N-terminal Nγ-acyl-γ-amino acid

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

• (SORHA), Triticum aestivum (TRZAS), and Zea mays (ZEAMX). LpFAT A expression and purification: The fat a03 gene from Lemna paucicostata, in which the N-terminal amino acids representing the chloroplast transit peptide were replaced by an N-terminal 6xHis-tag, was cloned into a pET24 vector [3]. The LpFAT

Elucidating the glycan-binding specificity and structure of Cucumis melo agglutinin, a new R-type lectin

• Jon Lundstrøm,
• Emilie Gillon,
• Valérie Chazalet,
• Nicole Kerekes,
• Antonio Di Maio,
• Ten Feizi,
• Yan Liu,
• Annabelle Varrot and
• Daniel Bojar

Beilstein J. Org. Chem. 2024, 20, 306–320, doi:10.3762/bjoc.20.31

• confirmed and quantified this binding specificity in solution. Finally, we solved the high-resolution structure of the CMA1 N-terminal domain using X-ray crystallography, supporting our functional findings at the molecular level. Our study provides a comprehensive understanding of CMA1, laying the

• aligned the individual units of the tandem repeat CBM13 domains, indicated by the N-terminal (34-158) and C-terminal units (162-286) and compared those to the domains of ricin (Figure 1b). R-type lectins have a characteristic Q-x-W structural motif close to their binding site, which is highly conserved

• around W63 for the N-terminal domain and F273 for the C-terminal domain of CMA1. As binding specificities of melon lectins in general (beyond chitooligosaccharides), and CMA1 in particular, are still unknown, we set out to measure, quantify, and understand the glycan-binding properties of CMA1 in depth

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

• studied. Several 2-methylisoborneol synthases have a proline-rich N-terminal domain of unknown function. The results presented here demonstrate that this domain leads to a reduced enzyme activity, in addition to its ability to increase long-term solubility of the protein. Furthermore, the substrate scope

• versions of 2MIBSs exhibit a proline-rich N-terminal domain of unknown function that appears disordered in the crystal structure [28]. As a first aspect of this study, we have investigated the possible function of this N-terminal domain. 2MIBS is known to form several methylated monoterpenes as side

• changed alkylation pattern. Results and Discussion Function of the proline-rich N-terminal domain of 2MIBS S. coelicolor 2MIBS was selected to investigate the function of the proline-rich N-terminal domain (hereafter termed A domain, the C-terminal domain is named as domain B). Based on a sequence

Strategies to access the [5-8] bicyclic core encountered in the sesquiterpene, diterpene and sesterterpene series

• Cécile Alleman,
• Charlène Gadais,
• Laurent Legentil and
• François-Hugues Porée

Beilstein J. Org. Chem. 2023, 19, 245–281, doi:10.3762/bjoc.19.23

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

• minimally harbors three core domains, responsible for the activation and loading, tethering, and condensation of building blocks and intermediates. The biosynthesis is directional and starts at the N-terminal module with the activation and loading of the first building block onto the assembly line (Figure

On drug discovery against infectious diseases and academic medicinal chemistry contributions

• Yves L. Janin

Beilstein J. Org. Chem. 2022, 18, 1355–1378, doi:10.3762/bjoc.18.141

• -bearing substances, endowed with an antibacterial effect [58]. However, this compound was originally patented for a fungicide effect [59] and then found to also inhibit mammalian c-Jun N-terminal kinase [60]. Unsurprisingly, it was also reported in 2022 as a covalent inhibitor for the SARS-CoV-2 main

Make or break: the thermodynamic equilibrium of polyphosphate kinase-catalysed reactions

• Michael Keppler,
• Sandra Moser,
• Henning J. Jessen,
• Christoph Held and
• Jennifer N. Andexer

Beilstein J. Org. Chem. 2022, 18, 1278–1288, doi:10.3762/bjoc.18.134

• soluble enzymes and could be easily purified via Ni-NTA affinity chromatography using N-terminal His-tags, the PPK1 enzymes required an N-terminal maltose binding protein (MBP-tag) to improve solubility [46][47]. Trials to cleave the MBP-tag were unsuccessful and resulted in inactive protein aggregates

Identification of the new prenyltransferase Ubi-297 from marine bacteria and elucidation of its substrate specificity

• Jamshid Amiri Moghaddam,
• Huijuan Guo,
• Karsten Willing,
• Thomas Wichard and
• Christine Beemelmanns

Beilstein J. Org. Chem. 2022, 18, 722–731, doi:10.3762/bjoc.18.72

• and amplified sequences were then cloned into an expression pET28 plasmid containing an N-terminal 6-histidine tag sequence. Heterologous production of enzymes was achieved in E. coli BL21 and western blot analysis indicated the accumulation of His-tagged UbiA-297 (35 kD) within concentrated cell

Synthesis and bioactivity of pyrrole-conjugated phosphopeptides

• Qiuxin Zhang,
• Weiyi Tan and
• Bing Xu

Beilstein J. Org. Chem. 2022, 18, 159–166, doi:10.3762/bjoc.18.17

• cells by a naphthyl-capped phosphopeptide (Nap-ffpy, 1), we conjugated the heteroaromatic dipyrrole or tripyrrole motif at the N-terminal of short peptides containing phosphotyrosine or phosphoserine and examined the bioactivity of the resulting phosphopeptides (2–10). Although most of the

• of 1. These results suggest that a heteroaromatic motif at the N-terminal of peptides likely disfavors the formation of extensive nanofibers or morphological changes during enzymatic self-assembly, thus provide useful insights for the development of phosphopeptides as substrates of phosphatases for

• controlling cell fate. Keywords: cells; enzyme; N-terminal; peptides; pyrroles; self-assembly; Introduction Biomacromolecular assemblies have received considerable attention recently in the field of biomaterials [1][2][3][4][5][6][7], among which peptides are of particular interest because of their unique

Peptide stapling by late-stage Suzuki–Miyaura cross-coupling

• Hendrik Gruß,
• Rebecca C. Feiner,
• Ridhiwan Mseya,
• David C. Schröder,
• Michał Jewgiński,
• Kristian M. Müller,
• Rafał Latajka,
• Antoine Marion and
• Norbert Sewald

Beilstein J. Org. Chem. 2022, 18, 1–12, doi:10.3762/bjoc.18.1

• phthaloyl-protected N-terminal alanine was also used for macrocyclisation in peptide stapling [51][52]. Besides addressing the indole C2, the regioselective enzymatic halogenation at C5, C6, or C7 using FAD-dependent tryptophan halogenases opens a broad area of Pd-catalysed late-stage diversifications [53

• partner β-catenin. The N-terminal FITC-labelled RCM-stapled peptide fStAx-3 was synthesised as tracer for this study and its dissociation constant was determined to be 63 ± 6 nM in a direct fluorescence polarisation assay, which is in agreement with previously reported data [77]. Noteworthy, the isomer

First total synthesis of hoshinoamide A

• Haipin Zhou,
• Zihan Rui,
• Yiming Yang,
• Shengtao Xu,
• Yutian Shao and
• Long Liu

Beilstein J. Org. Chem. 2021, 17, 2924–2931, doi:10.3762/bjoc.17.201

• -Val5 and N-Me-ᴅ/ʟ-Phe2. Hoshinoamide C includes two N-methyl amino acids: N-Me-ᴅ-Phe2 and N-Me-ᴅ-IIe5. The C-terminal Pro is functionalized as methyl ester, while the N-terminal polypeptide is linked to the long alkyl chain amino acid Aha8/Ana8/Ama7 and p-hydroxybenzoic acid Hba9/Hba8. Hoshinoamides

Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications

• Nikita Brodyagin,
• Martins Katkevics,
• Venubabu Kotikam,
• Christopher A. Ryan and
• Eriks Rozners

Beilstein J. Org. Chem. 2021, 17, 1641–1688, doi:10.3762/bjoc.17.116

Antiviral therapy in shrimp through plant virus VLP containing VP28 dsRNA against WSSV

• Santiago Ramos-Carreño,
• Ivone Giffard-Mena,
• Jose N. Zamudio-Ocadiz,
• Alfredo Nuñez-Rivera,
• Ricardo Valencia-Yañez,
• Jaime Ruiz-Garcia,
• Maria Teresa Viana and
• Ruben D. Cadena-Nava

Beilstein J. Org. Chem. 2021, 17, 1360–1373, doi:10.3762/bjoc.17.95

• -dsRNA to form procapsids and CP-RNA complexes [42]. The dsRNA negative charges can be neutralized by the positive N-terminal protein in these procapsids [42]. However, procapsids are not suitable for any treatment because they do not efficiently protect their cargo. The dsRNA in the procapsids may be

Enhanced target cell specificity and uptake of lipid nanoparticles using RNA aptamers and peptides

• Roslyn M. Ray,
• Anders Højgaard Hansen,
• Maria Taskova,
• Bernhard Jandl,
• Jonas Hansen,
• Citra Soemardy,
• Kevin V. Morris and
• Kira Astakhova

Beilstein J. Org. Chem. 2021, 17, 891–907, doi:10.3762/bjoc.17.75

• peptides were included in this study and modified with an N-terminal lipid anchor for LNP postinsertion. The design of the lipid anchor includes two palmitoyl chains that are attached through a 1,2-diaminopropanoic acid moiety (Dap) on the N-terminus of each peptide, providing the lipidated peptides