Chemical structure metagenomics of microbial natural products: surveying nonribosomal peptides and beyond

• Thomas Ma and
• John Chu

Beilstein J. Org. Chem. 2024, 20, 3050–3060, doi:10.3762/bjoc.20.253

• biased towards (or against) certain amino acids; while these trends are statistically valid, whether there is an underlying chemical principle that governs the observed selectivity remains unclear [52]. For example, tailoring enzymes for β-hydroxylation most often act on aspartate and asparagine. In

Computational toolbox for the analysis of protein–glycan interactions

• Ferran Nieto-Fabregat,
• Maria Pia Lenza,
• Angela Marseglia,
• Cristina Di Carluccio,
• Antonio Molinaro,
• Alba Silipo and
• Roberta Marchetti

Beilstein J. Org. Chem. 2024, 20, 2084–2107, doi:10.3762/bjoc.20.180

• glycosylation: i) N-glycosylation, where a N-acetylglucosamine (GlcNAc) is linked to the nitrogen atom of an asparagine side chain [28]; ii) O-glycosylation, where a GlcNAc or N-acetylgalactosamine (GalNAc) is linked to the hydroxy group of a serine or threonine residue [29]; iii) C-glycosylation, where a

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

• /mL [107][108][109]. While originally thought to be of NRPS origin due to their extensive modifications, Freeman et al. discovered in 2012 that polytheonamides are actually of ribosomal origin [108]. Polytheonamides A and B contain eight methylated asparagine residues (Figure 4), all of which are

• installed by the MT PoyE. Interestingly, two of these methylated asparagine residues also carry a hydroxy group at the β-carbon, which does not appear to affect the methylations. Renevey and Riniker demonstrated that the N-methylated asparagine residues of polytheonamide B are essential for the stability of

• its β-helical structure; reversion of the N-methylation led to complete conformation loss. The methylated asparagine residues at positions 16, 22, and 28 form an intramolecular chain of hydrogen bonds along the outside of the β-helix. Hydrogen atoms from the amide methyl group form hydrogen bonds with

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

• specificity. Our binding data and structural information lead us to the conclusion that crucially positioned asparagine residues facilitate this unusual binding specificity that delineates CMA1 from typical R-type lectins such as RCA1. Together, these results advance our knowledge of R-type lectins in general

A one-pot electrochemical synthesis of 2-aminothiazoles from active methylene ketones and thioureas mediated by NH₄I

• Shang-Feng Yang,
• Pei Li,
• Zi-Lin Fang,
• Sen Liang,
• Hong-Yu Tian,
• Bao-Guo Sun,
• Kun Xu and
• Cheng-Chu Zeng

Beilstein J. Org. Chem. 2022, 18, 1249–1255, doi:10.3762/bjoc.18.130

• working electrode rather than exploring other options. As shown in Table 1, when the electrolysis of 1a with 2a was performed in aqueous DMSO at a constant current of 5 mA/cm2 using NH4I as the mediator, LiClO4 as electrolyte and asparagine as additive in an undivided cell, the desired product 3a was

• changed from 2:1 to 1:14 (Table 1, entry 7). When the reaction was performed in H2O, 3a was obtained in 51% yield (Table 1, entry 8). It was observed that the additive plays an important role, among which ᴅʟ-alanine was proved to be the best, although asparagine, ʟ-phenylalanine, ʟ-aspartic acid and ʟ

A systems-based framework to computationally describe putative transcription factors and signaling pathways regulating glycan biosynthesis

• Theodore Groth,
• Rudiyanto Gunawan and
• Sriram Neelamegham

Beilstein J. Org. Chem. 2021, 17, 1712–1724, doi:10.3762/bjoc.17.119

• reticulum. The enzymes involved is such synthesis include the ALG (asparagine-linked N-glycosylation) enzymes and additional proteins (part of OSTA and OSTB) involved in the transfer of the glycan to the nascent protein. 5) Complex N-glycans: This pathway includes glycogenes responsible for processing the N

Molecular basis for protein–protein interactions

• Brandon Charles Seychell and
• Tobias Beck

Beilstein J. Org. Chem. 2021, 17, 1–10, doi:10.3762/bjoc.17.1

• interactions but have a high propensity to form interprotein interactions. In contrast, serine, threonine, asparagine (polar uncharged), alanine, valine, isoleucine (hydrophobic), cysteine, proline, and glycine are less likely to form interprotein interactions and bifurcated interactions. The binding mode in

NMR Spectroscopy of supramolecular chemistry on protein surfaces

• Peter Bayer,
• Anja Matena and
• Christine Beuck

Beilstein J. Org. Chem. 2020, 16, 2505–2522, doi:10.3762/bjoc.16.203

• achieved by expression in minimal media in the presence of 15N ammonium salts. A 1H,15N-HSQC spectrum shows all N–H correlations that are moderately stable and do not exchange with the solvent water too quickly, which includes the amide NHs and some side chain NHs, e.g., the side chain amides of asparagine

GlypNirO: An automated workflow for quantitative N- and O-linked glycoproteomic data analysis

• Toan K. Phung,
• Cassandra L. Pegg and
• Benjamin L. Schulz

Beilstein J. Org. Chem. 2020, 16, 2127–2135, doi:10.3762/bjoc.16.180

• cysteines was set as a fixed modification, and dynamic modifications included deamidation of asparagine, monooxidised methionine, and the formation of pyroglutamate at N-terminal glutamic acid and glutamine. All variable modifications were set as “Common 1” allowing each modification to be present once on a

Synthesis of new asparagine-based glycopeptides for future scanning tunneling microscopy investigations

• Laura Sršan and
• Thomas Ziegler

Beilstein J. Org. Chem. 2020, 16, 888–894, doi:10.3762/bjoc.16.80

• Laura Srsan Thomas Ziegler Institute of Organic Chemistry, University of Tübingen, Auf der Morgenstelle 18, 72076 Tübingen, Germany 10.3762/bjoc.16.80 Abstract For investigations on the biological functions of oligosaccharides and peptidomimetics, new asparagine-based mono- and disaccharides

• cell surfaces for future investigations by combined preparative mass spectroscopy and scanning tunneling microscopy (STM) using soft-landing electrospray beam deposition (ES-IBD), on metal surfaces. Keywords: amino acids; asparagine; carbohydrates; glycopeptides; peptidomimetics; Introduction

• mechanisms of the interaction of glycopeptides with the cell surface [16]. Our focus lay on the preparation of glycopeptide libraries containing ʟ-asparagine since many saccharides on the cell surface are N-glycosidically linked to this amino acid [8]. The most abundant sugars found in these asparagine

Lectins of Mycobacterium tuberculosis – rarely studied proteins

• Katharina Kolbe,
• Sri Kumar Veleti,
• Norbert Reiling and
• Thisbe K. Lindhorst

Beilstein J. Org. Chem. 2019, 15, 1–15, doi:10.3762/bjoc.15.1

• modifications of glycocalyx proteins are N-glycans (asparagine-linked) and O-glycans (serine- or threonine-linked), while glycosphingolipids are the major subclass of glycosylated lipids in the cell membrane of human cells (Figure 2). While many core elements of glycocalyx oligosaccharides are conserved between

Asymmetric synthesis of propargylamines as amino acid surrogates in peptidomimetics

• Matthias Wünsch,
• David Schröder,
• Tanja Fröhr,
• Lisa Teichmann,
• Sebastian Hedwig,
• Nils Janson,
• Clara Belu,
• Jasmin Simon,
• Shari Heidemeyer,
• Philipp Holtkamp,
• Jens Rudlof,
• Lennard Klemme,
• Alessa Hinzmann,
• Beate Neumann,
• Hans-Georg Stammler and
• Norbert Sewald

Beilstein J. Org. Chem. 2017, 13, 2428–2441, doi:10.3762/bjoc.13.240

• % [21]. Synthesis of propargylamines containing electron-withdrawing substituents Aromatic and carbonyl substituents in the Cβ-position of propargylamines (occurring in analogoues of the amino acids phenylalanine, tyrosine, histidine, tryptophan, aspartic acid and asparagine) increase the acidity of the

Intramolecular glycosylation

• Xiao G. Jia and
• Alexei V. Demchenko

Beilstein J. Org. Chem. 2017, 13, 2028–2048, doi:10.3762/bjoc.13.201

• asparagine was attached both to a mannose donor and a trihydroxymannose acceptor, and the central amino acid unit(s) was varied. Intramolecular glycosylation was carried out with NIS/TfOH, resulting in a mixture of disaccharide products showing slight regioselectivity bias towards the formation of (1→3

A new member of the fusaricidin family – structure elucidation and synthesis of fusaricidin E

• Marcel Reimann,
• Louis P. Sandjo,
• Luis Antelo,
• Eckhard Thines,
• Isabella Siepe and
• Till Opatz

Beilstein J. Org. Chem. 2017, 13, 1430–1438, doi:10.3762/bjoc.13.140

• most likely shows similarity to the fatty acid synthesis pathway [2]. All fusaricidins have three amino acids (L-Thr, D-allo-Thr, and D-Ala) in common and are mostly isolated in pairs which differ in a single amino acid (asparagine vs glutamine). There are several known members of the fusaricidin

• ][7]. Two new compounds were obtained from fermentation of Paenibacillus sp. strain Lu16774 as an inseparable mixture of two homologous cyclic depsipeptides containing either glutamine (in 1) or asparagine (in 2). Initially, the absolute and relative configuration of the isoleucine residue was unknown

• H–C interactions, these resonances were assigned to the β-CH2 group of asparagine (Asn) in the lower homologue 2. Thus, the conclusion was supported by reported data for Asn in other fusaricidins [9] in conjunction to fragments obtained from the tandem mass of the parent peak at m/z 961.6 (Figure 3

From chemical metabolism to life: the origin of the genetic coding process

• Antoine Danchin

Beilstein J. Org. Chem. 2017, 13, 1119–1135, doi:10.3762/bjoc.13.111

Posttranslational isoprenylation of tryptophan in bacteria

• Masahiro Okada,
• Tomotoshi Sugita and
• Ikuro Abe

Beilstein J. Org. Chem. 2017, 13, 338–346, doi:10.3762/bjoc.13.37

• also critical for the isoprenylation activity, similar to the second aspartate residue in SARM in the FPP and GGPP synthases [45][46]. In addition, the first amino acid residue of the pseudo-SARM in ComQ, asparagine (or glycine), is crucial for the ComQ function. Particularly, the mutation from

• asparagine to aspartate drastically decreased the geranylation activity. In contrast, the last three amino acid residues of the pseudo-SARM in ComQ are replaceable, without the loss of ComQ function. Thus, for tryptophan isoprenylation the ComQ must have the sequence NDxxx (or GDxxx) in the pseudo-SARM

Mechanistic investigations on six bacterial terpene cyclases

• Patrick Rabe,
• Thomas Schmitz and
• Jeroen S. Dickschat

Beilstein J. Org. Chem. 2016, 12, 1839–1850, doi:10.3762/bjoc.12.173

• usual asparagine, obviously without effect on the enzyme function, the pyrophosphate sensor R-196 and the 327RY dimer. Terpene cyclases with close homology are encoded in more than 40 genome sequenced streptomycetes that all show an altered NSE triad starting with either proline or alanine. The closest

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

• to a histidine or an asparagine residue in their active site. This exchange avoids the dehydration reaction and might facilitate the activation of the hydroxy group for nucleophilic attack on the Michael system by proton abstraction. PS domains also form a distinct phylogenetic clade compared to DH

• contains pieC and pieD whose gene products were annotated as a hypothetical protein and an asparagine synthase, respectively. While inactivation of pieD led to complete abolishment of piericidin A1 (221) production, inactivation of pieC only led to a decrease in titre to about 35–50% of the wild-type

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

• [92][93][94]. McjC was identified as the macrolactam synthetase using both genetic inactivation in E. coli and in vitro analysis of purified protein [95]. McjC has homology to asparagine synthetases and the reaction they catalyse is mechanistically similar [96], although McjC lacks the N-terminal

Antibiotics from predatory bacteria

• Juliane Korp,
• María S. Vela Gurovic and
• Markus Nett

Beilstein J. Org. Chem. 2016, 12, 594–607, doi:10.3762/bjoc.12.58

• possess antioxidative properties and might thus confer resistance towards oxidative stress [63]. Structurally, the DKxanthenes harbor a hydrophilic asparagine moiety attached to a hydrophobic polyene chain bearing an additional oxazoline and pyrrol ring system. Their production seems to be universal among

Active site diversification of P450cam with indole generates catalysts for benzylic oxidation reactions

• Paul P. Kelly,
• Anja Eichler,
• Susanne Herter,
• David C. Kranz,
• Nicholas J. Turner and
• Sabine L. Flitsch

Beilstein J. Org. Chem. 2015, 11, 1713–1720, doi:10.3762/bjoc.11.186

• were identified in seven sub-libraries (Figure 1, bottom). Among this new population, structural and functional diversity was evident as can be seen from the grid structure (Figure 1, bottom) representing all active variant combinations identified across libraries I–VII. Cysteine, asparagine and

Pyridinoacridine alkaloids of marine origin: NMR and MS spectral data, synthesis, biosynthesis and biological activity

• Louis P. Sandjo,
• Victor Kuete and
• Maique W. Biavatti

Beilstein J. Org. Chem. 2015, 11, 1667–1699, doi:10.3762/bjoc.11.183

• studies performed on this topic. Riddick showed the oxidation product of tryptophan (61) (kynurenine (62)) as the precursor for the biosynthesis of pyridoacridines (Figure 6) [74]. Kynurenine (62) with acetic acid forms the quinolinone 63, which in presence of amino acids such as cysteine, asparagine

Design and synthesis of multivalent neoglycoconjugates by click conjugations

• Feiqing Ding,
• Li Ji,
• Ronny William,
• Hua Chai and
• Xue-Wei Liu

Beilstein J. Org. Chem. 2014, 10, 1325–1332, doi:10.3762/bjoc.10.134

• ][27][28][29][30][31]. The α-GalNAc-linked glycopeptides, α-N-glycosidically linked to the polypeptide chain through the amido nitrogen of an asparagine residue at the N-terminal [32], were found to be the most important semi-synthetic glycoconjugates, usually modified from their naturally occurring

Isocyanide-based multicomponent reactions towards cyclic constrained peptidomimetics

• Gijs Koopmanschap,
• Eelco Ruijter and
• Romano V.A. Orru

Beilstein J. Org. Chem. 2014, 10, 544–598, doi:10.3762/bjoc.10.50

C–C Bond formation catalyzed by natural gelatin and collagen proteins

• Dennis Kühbeck,
• Basab Bijayi Dhar,
• Eva-Maria Schön,
• Carlos Cativiela,
• Vicente Gotor-Fernández and
• David Díaz Díaz

Beilstein J. Org. Chem. 2013, 9, 1111–1118, doi:10.3762/bjoc.9.123

• degree of deamidation of glutamine and asparagine. Besides traditional applications in the food industry, gelatin has also gained attention in the scientific community as a reducing ligand and supporting media for the preparation of uniform metal nanoparticle catalysts [2][3][4]. In addition, the average