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

• proteins allows peptides to disturb protein–protein interactions, which is a challenging task for small molecules. The principles of RiPP biosynthesis make the RiPP technology an ideal platform for the generation of designed peptides and allow tailored derivatisation of these peptides. The RiPP technology

• analogues [48][49][50][51][52]. The PURE system is a well-established method for rapidly expressing functional proteins. However, synthesising peptides with unnatural amino acids remains a labour-intensive process. tRNAs charged with unnatural or modified amino acids cannot be easily replenished within the

• system and must be prepared beforehand. The incorporation of unnatural amino acids by the ribosome is less efficient and leads to incomplete translation, resulting in shunt products. Additionally, ribosome recycling efficiency and synthesis of full length proteins declines with length of the primary

Polymer degrading marine Microbulbifer bacteria: an un(der)utilized source of chemical and biocatalytic novelty

• Weimao Zhong and
• Vinayak Agarwal

Beilstein J. Org. Chem. 2024, 20, 1635–1651, doi:10.3762/bjoc.20.146

• [48]. The three-dimensional structure of CEST revealed that it belongs to the α/β-class of proteins consisting of a central six-stranded β-sheet flanked by eight α-helices. Site-directed mutagenesis indicated that a Ser-His-Glu catalytic triad was essential for the enzyme activity [48]. Another cold

Regio- and stereochemical stability induced by anomeric and gauche effects in difluorinated pyrrolidines

• Ana Flávia Candida Silva,
• Francisco A. Martins and
• Matheus P. Freitas

Beilstein J. Org. Chem. 2024, 20, 1572–1579, doi:10.3762/bjoc.20.140

• of the pyrrolidine ring in proline motifs has been found to induce significant conformational changes that impact the structure and biological roles of modified peptides and proteins. Vicinal difluorination of fluoroproline, for example, in (3S,4R)-3,4-difluoroproline, serves to mitigate the inherent

• pervade biochemistry in peptides and proteins. The chemical and biological properties of substituted pyrrolidine derivatives, along with many other compounds, hinge on the relative stereochemistry. It is well established that the presence of fluorine in an organic molecule can significantly influence the

• conformational stability of proline-rich proteins such as collagen [2]. Therefore, pyrrolidine derivatives are particularly susceptible to conformational control induced by a fluorine substituent. The 5-membered pyrrolidine ring is a cyclic alkylamine that adopts a conformation that resembles the familiar

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

• (Figure 1). Recent enzymatic reconstitution has demonstrated that the burpitide cyclases can function either autocatalytically (fused) or as traditional stand-alone proteins with separate free peptide substrates (split) [4][7][8][9][10][11]. When fully matured, burpitides possess a wide range of

• base pairs (Figure 6B). While the proposed gene cluster is missing a potential peptidase, it contains all the other proteins necessary for the biosynthesis of GJA649 and the other putative G. jasminoides cyclopeptide alkaloids. New cyclopeptide alkaloids in Alternanthera bettzickiana Based on the

Photoswitchable glycoligands targeting Pseudomonas aeruginosa LecA

• Yu Fan,
• Ahmed El Rhaz,
• Stéphane Maisonneuve,
• Emilie Gillon,
• Maha Fatthalla,
• Franck Le Bideau,
• Guillaume Laurent,
• Samir Messaoudi,
• Anne Imberty and
• Juan Xie

Beilstein J. Org. Chem. 2024, 20, 1486–1496, doi:10.3762/bjoc.20.132

• bacterial infections occur by adhesion to host tissues through receptor–ligand interaction between bacterial carbohydrate-binding proteins (lectins) and oligosaccharides at the host cell surface. Pseudomonas aeruginosa (PA), a Gram-negative, opportunistic and ubiquitous environmental bacterium, is known as

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

• . Cofactor-independent oxidative ring cleavage and rearrangement reactions of CR1 (8) catalyzed by homologous proteins of AlpJ To extend the generality of our findings, we assessed the cofactor-independent catalytic capabilities of other homologous proteins of AlpJ. Previous investigations indicated that the

• -morpholino)propanesulfonic acid (MOPS) buffer (pH 7.5), and the cells were disrupted by ultrasonication to obtain the cell extract. Cell debris was removed by centrifugation (14,000g, 15 min). The proteins were purified by Ni-NTA agarose chromatography, desalted, and concentrated by centrifugation (8,000g

• -independent AlpJ-family oxygenases. Supporting Information Supporting Information File 44: Sequence comparison results and phylogenetic tree of AlpJ-family enzymes and anthrone oxygenases, crystal structures of AlpJ and ActVA-Orf6, SDS-PAGE of purified proteins, HPLC traces of prosthetic group identification

Novel analogues of a nonnucleoside SARS-CoV-2 RdRp inhibitor as potential antivirotics

• Luca Julianna Tóth,
• Kateřina Krejčová,
• Milan Dejmek,
• Eva Žilecká,
• Blanka Klepetářová,
• Lenka Poštová Slavětínská,
• Evžen Bouřa and
• Radim Nencka

Beilstein J. Org. Chem. 2024, 20, 1029–1036, doi:10.3762/bjoc.20.91

• directly act as a viral messenger RNA and encodes essential enzymes for replication [3]. Inhibiting these nonstructural proteins that are part of the replication complex has already shown great success in antiviral therapy [4][5][6][7]. The viral RNA-dependent RNA polymerase (RdRp) is encoded in all RNA

Activity assays of NnlA homologs suggest the natural product N-nitroglycine is degraded by diverse bacteria

• Kara A. Strickland,
• Brenda Martinez Rodriguez,
• Ashley A. Holland,
• Shelby Wagner,
• Michelle Luna-Alva,
• David E. Graham and
• Jonathan D. Caranto

Beilstein J. Org. Chem. 2024, 20, 830–840, doi:10.3762/bjoc.20.75

• contaminants but are either undissociated higher oligomer states or are oligomers whose formation is induced by SDS treatment, which has been observed for other proteins [29][30]. To characterize these oligomer states of native protein, analytical size exclusion chromatography data were collected (Figure 2B

• nm/A280 nm ratio for each homolog was greater than 1.0, consistent with high occupancy of heme incorporation in the proteins. Iron analyses of each of the homologs were consistent with this conclusion; the heme iron concentrations per protein were consistent with stoichiometric or nearly

• structure of oligomeric proteins [31]. The highest ranked model is shown in Figure 5. AlphaFold predicted a canonical α/β fold with high confidence, between residues Arg16 and Gly146 (Figure 5A). Structural clustering using Foldseek Cluster identified substantial similarities to other PAS domain proteins

Methodology for awakening the potential secondary metabolic capacity in actinomycetes

• Shun Saito and
• Midori A. Arai

Beilstein J. Org. Chem. 2024, 20, 753–766, doi:10.3762/bjoc.20.69

• chaxalactins A–C (16–18), and polycyclic polyether natural products designated terrosamycins A and B (19, 20), respectively [55][56]. Thus, the OSMAC strategy has been successfully applied over the last 10 years to generate new secondary metabolites from a single microbial strain. Sensor proteins for medium

• structure. Saito et al. are now interested in determining how and why these HSMs are produced. First, when actinomycetes sense heat stress, repression mediated by heat shock sensor proteins such as HrcA, HspR, and RheA is released. The expression of various genes, such as those encoding heat shock proteins

• is regulated by such heat shock sensors. Although long-term high-temperature culture experiments are employed in this study, reactive oxygen species (ROS) may exert a stronger effect than high temperature. In actinomycetes, several sensor proteins for ROS have been reported (e.g., SoxR and OxyR

Research progress on the pharmacological activity, biosynthetic pathways, and biosynthesis of crocins

• Zhongwei Hua,
• Nan Liu and
• Xiaohui Yan

Beilstein J. Org. Chem. 2024, 20, 741–752, doi:10.3762/bjoc.20.68

• , and UGTs are the key players in crocin biosynthesis. Empowered by the genomic, transcriptomic, and metabolomic analysis and biochemical characterization, many such enzymes have been identified. Some proteins, exemplified by GjCCD4a and GjUGT94E13, exhibit broad substrate promiscuity and high catalytic

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

• : the acyl transferases (AT) for loading of the starter or extender units, the acyl carrier proteins (ACP) for anchoring the growing polyketide chain, and the ketosynthases (KS) for merging of the next extender unit with the existing chain by a decarboxylative Claisen condensation [2][4]. Today a high

• is still important. Previous approaches to determine KS domain specificities have involved mass spectrometry (MS)-based methods [22][23], MS analysis of trypsin-digested proteins [24], and radiochemical assays [25]. Here, we report on a new method using 13C-labelled substrate surrogates in

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

• peptides and even small proteins. In the chemoenzymatic synthesis of macrocyclic peptides, SPPS strategies provide highly efficient routes to access linear precursors, accelerating the development of enzymatic macrocyclization. The tyrocidines Tyrocidine A (1), a cyclic decapeptide isolated from Bacillus

• domains along with their associated peptidyl carrier proteins (PCPs): daptomycin and A54145 PCP-TE [55]. A series of thiophenol-activated precursors were tolerated by these enzymes to produce daptomycin derivatives, A54145 as well as hybrid molecules of the two compounds, which pushed forward the better

• exhibit a potent ability to induce tubulin depolymerization [77], originally isolated from the cyanobacteria Nostoc sp. ATCC 53789 [78]. Notably, the cryptophycins cannot serve as substrates for P-glycoprotein and multiple drug resistance-associated proteins, making them attractive as chemotherapeutic

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

• TCs, AsPS and AsCPS, in the fungus Arthrinium sacchari. AsPS consists of catalytically active α and inactive β domains, whereas AsCPS contains βγ domains and a truncated α domain. Heterologous expression in Aspergillus oryzae and biochemical characterization of recombinant proteins demonstrated that

• 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

• File 1, Figure S3). The purified proteins were incubated in the presence of GGPP and Mg2+. GC–MS analysis of the hexane extract revealed the enzyme-dependent formation of compound 1 (Figure 4A and Figure S2 in Supporting Information File 1). The formation of 1 was not observed when either AsPS or AsCPS

Recent developments in the engineered biosynthesis of fungal meroterpenoids

• Zhiyang Quan and
• Takayoshi Awakawa

Beilstein J. Org. Chem. 2024, 20, 578–588, doi:10.3762/bjoc.20.50

• chair–chair stereocontrol, the structure basis of InsA7 should be unique. A structural comparison of InsB2 and InsA7 will help to clarify the differences in their structural bases. Recent advances in artifical intelligence (AI) have even made the structural modeling of membrane-bound proteins possible

Possible bi-stable structures of pyrenebutanoic acid-linked protein molecules adsorbed on graphene: theoretical study

• Yasuhiro Oishi,
• Motoharu Kitatani and
• Koichi Kusakabe

Beilstein J. Org. Chem. 2024, 20, 570–577, doi:10.3762/bjoc.20.49

• of molecules based on nanoscience can lead to a better understanding of the behavior of target biomaterials and improve the sensitivity of specific dynamical systems, such as biosensors. In this study, we investigate the behavior of proteins immobilized with linker molecules on graphene substrates

• . It is known that graphene may not easily adsorb proteins [1]. On the other hand, proteins can be immobilized on graphene by using appropriate linker molecules, such as 1-pyrenebutanoic acid succinimidyl ester (PASE). Actually, pyrene and its derivatives have been demonstrated to form stable bindings

• can be expected for proteins immobilized on graphene. As a result, we propose a strategy for improving the accuracy of the sensing process in elastic wave measurement sensors through antigen/antibody reactions. Results and Discussion PASE and PASE-derivatives on graphene Among pyrene derivatives, PASE

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

• 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

Switchable molecular tweezers: design and applications

• Pablo Msellem,
• Maksym Dekthiarenko,
• Nihal Hadj Seyd and
• Guillaume Vives

Beilstein J. Org. Chem. 2024, 20, 504–539, doi:10.3762/bjoc.20.45

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

• biosynthesis by using small molecules can help to elucidate their natural functions and their potential as therapeutic targets. NRPs are synthesized by large, versatile, and multifunctional proteins called nonribosomal peptide synthetases (NRPSs), which are composed of multiple modules and subdivided domains

• differences in the composition of cell membranes and presence of efflux pumps [9]. Specific protein labeling using a chemical probe can help to identify, characterize, and visualize target proteins [10][11]. The first chemical probe used for A-domains in NRPSs was reported by Marahiel et al. [8]. They

• derivatives can penetrate cells and interact with A-domains in live bacterial cells, resulting in the competitive inhibition of the labeling by ʟ-Phe-AMS-BPyne. The substituent group (R; gray) of ʟ-Phe-AMS derivatives could facilitate their cell penetration. After UV irradiation (365 nm), the labeled proteins

Green and sustainable approaches for the Friedel–Crafts reaction between aldehydes and indoles

• Periklis X. Kolagkis,
• Eirini M. Galathri and
• Christoforos G. Kokotos

Beilstein J. Org. Chem. 2024, 20, 379–426, doi:10.3762/bjoc.20.36

• reduction in the concentration of these cytokines, as well as, increased intestinal permeability and improved expression of tight junction proteins that control the polarity of cells when using DIM in Caco-2 human cells [3]. BIMs have also been linked with the therapy of various cancers with one of their

• ]. DIM has also been found to initiate the expression of tumor suppressing proteins (ATM, p21, p27kip), which control cell growth and protect cells against ionizing radiation, which can cause DNA mutations, decreasing the overall risk of breast cancer [1][5][6]. The cytotoxicity of DIM and BIMs in

• antiviral properties. BIMs function as selective antibacterial agents against several virulent Escherichia coli (E. coli) strains, which can cause many gut and urinary tract infections. They act by damaging DNA molecules and inhibiting their replication in bacteria, while also targeting the proteins that

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

• biology, and biomedicine. These carbohydrate-binding proteins boast a range of functions, acting as recognition modules in cell–molecule and cell–cell interactions, thereby playing vital roles in immune defense, regulation of growth, and apoptosis [1]. In plants, they serve as essential components in

• hexa-His tag, cleavable by TEV (Tobacco etch virus) protease. Despite the presence of the DsbC signal peptide, we did not observe periplasmic localization, and all proteins were instead purified from the cytoplasm. Ni-NTA affinity chromatography followed by TEV protease cleavage of the fusion construct

• , Merck, #56749) to remove all contaminants and unbound proteins. CMA1 was eluted by a 20 mL linear gradient from 50 mM to 500 mM imidazole in buffer A. The fractions were analyzed by SDS-PAGE with 15% gel and those containing CMA1 were collected and deprived of imidazole by buffer exchange in buffer A

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

• biosynthesis by heterologous expression of the cma cluster and in vitro enzyme assays using recombinant Cma proteins. The ATP-dependent diazotase CmaA6 catalyzed the diazotization of both 3-aminocoumaric acid and 3-aminoavenalumic acid using nitrous acid in vitro. In addition, the high efficiency of the CmaA6

• on an ava cluster-related BGC in Kutzneria albida JCM 3240. We showed that this BGC is involved in p-coumaric acid biosynthesis by heterologous expression in Streptomyces albus J1074 and several in vitro biochemical experiments using recombinant proteins. CmaA6 was shown to catalyze the diazotization

• confirmed that the cma cluster is responsible for p-coumaric acid (5) biosynthesis, in which the number of condensations of the malonyl units was one time less than that in the biosynthesis of avenalumic acid. In vitro analysis of recombinant Cma proteins To further understand the biosynthetic machinery

Studying specificity in protein–glycosaminoglycan recognition with umbrella sampling

• Mateusz Marcisz,
• Sebastian Anila,
• Margrethe Gaardløs,
• Martin Zacharias and
• Sergey A. Samsonov

Beilstein J. Org. Chem. 2023, 19, 1933–1946, doi:10.3762/bjoc.19.144

• proteins. The structural and functional heterogeneities of GAGs as well as their ability to bind specific proteins are determined by the sugar composition of the GAG, the size of the GAG chains, and the degree and pattern of sulfation. A deep understanding of the interactions in protein–GAG complexes is

• ) with three different proteins (basic fibroblast growth factor, acidic fibroblast growth factor, and cathepsin K). The main focus of our study was to evaluate whether the US approach is able to reproduce experimentally obtained structures, and how useful it can be for getting a deeper understanding of

• be a potential mechanism of GAG particular sequence recognition by proteins. Keywords: glycosaminoglycan; molecular docking; protein–glycosaminoglycan interaction specificity; RS-REMD; umbrella sampling; Introduction Glycosaminoglycans (GAGs) are long linear periodic anionic polydisperse

N-Boc-α-diazo glutarimide as efficient reagent for assembling N-heterocycle-glutarimide diads via Rh(II)-catalyzed N–H insertion reaction

• Grigory Kantin,
• Pavel Golubev,
• Alexander Sapegin,
• Alexander Bunev and
• Dmitry Dar’in

Beilstein J. Org. Chem. 2023, 19, 1841–1848, doi:10.3762/bjoc.19.136

• ubiquitin-proteasome degradation system, it has been achieved to approach previously considered undruggable targets and conceive remedies for drug-resistant targets [4]. The given TPD's benefit over traditional inhibition; numerous proteins have been set for proteasomal degradation by transmuting accessible

• small molecule inhibitors into PROTACs. The RAS proteins, once seen as drug-resistant, became susceptible and a series of covalent inhibitors [5][6][7] were synthesized to bind to KRASG12C. The application of the PROTAC principle has demonstrated the feasibility of endogenous degradation of KRAS [8][9

GlAIcomics: a deep neural network classifier for spectroscopy-augmented mass spectrometric glycans data

• Thomas Barillot,
• Baptiste Schindler,
• Baptiste Moge,
• Elisa Fadda,
• Franck Lépine and
• Isabelle Compagnon

Beilstein J. Org. Chem. 2023, 19, 1825–1831, doi:10.3762/bjoc.19.134

• impact for the society in regard to the United Nations sustainable development goal [1]. The major roadblock to carbohydrate sequencing is intrinsically due to their unique molecular properties, among biopolymers. In contrast with proteins and DNA, which are linear polymers made of a limited number of

Sulfur-containing spiroketals from Breynia disticha and evaluations of their anti-inflammatory effect

• Ken-ichi Nakashima,
• Naohito Abe,
• Masayoshi Oyama,
• Hiroko Murata and
• Makoto Inoue

Beilstein J. Org. Chem. 2023, 19, 1604–1614, doi:10.3762/bjoc.19.117

• potent compound 7 was found to significantly inhibit the production of IL-1β and IL-6 proteins, as revealed by the analysis of culture supernatants. Keywords: anti-inflammatory; Breynia disticha; RAW 264.7 cells; sesquiterpenoids; sulfur-containing compounds; Introduction Breynia disticha J.R.Forst