Improved deconvolution of natural products’ protein targets using diagnostic ions from chemical proteomics linkers

• Andreas Wiest and
• Pavel Kielkowski

Beilstein J. Org. Chem. 2024, 20, 2323–2341, doi:10.3762/bjoc.20.199

• complex formation between biotin and streptavidin (Kd ≈ 1 × 10−14 M) in aqueous solution. Another advantage is that after the enrichment and proteolytic digestion of each of the enriched proteins likely releases several suitable peptides for LC–MS/MS analysis resulting in a reliable identification of

• beads, the beads can be split into two portions from which one is analyzed by in-gel analysis first to determine the overall labeling and the other portion after on-beads trypsin digest is subjected to LC–MS/MS analysis. The AzKTB reagent can be synthetized by standard solid-phase peptide synthesis

Natural resorcylic lactones derived from alternariol

• Joachim Podlech

Beilstein J. Org. Chem. 2024, 20, 2171–2207, doi:10.3762/bjoc.20.187

• ) [162], and turned out to be a cholesterase inhibitor [258]. The oxidative metabolization of altenuene has been investigated [150][259] and it turned out that it is not metabolized by fecal microbiota [107]. Protocols for its standardized LC–MS/MS analysis have further been developed [121][122

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

• of the purified lanthipeptide were confirmed by MS–MS/MS analysis for cellulosin, while clostrisin was not post-translationally modified. Both peptides demonstrated antimicrobial activity against multidrug-resistant bacteria, such as a clinical strain of Staphylococcus epidermidis MIQ43 and

• purified samples of the C39 peptidase domain with purified CloA1 precursor peptide and CloA2 precursor peptide. The SDS-PAGE electrophoretic pattern confirmed the proteolytic reaction (Figure S7D, Supporting Information File 1). This was further confirmed through HPLC–MS–MS/MS analysis. Mass spectrometric

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

• formula of 5 was deduced as C49H85O17N11 (1098.6071 [M − H]−, calcd. 1098.6052), indicating the loss of two hydrogen atoms from variochelin B (2). Similar to 4, compound 5 also has a double bond in its fatty acyl moiety, as suggested by the MS/MS analysis (Figure 1 and Figure S34 in Supporting Information

A Streptomyces P450 enzyme dimerizes isoflavones from plants

• Run-Zhou Liu,
• Shanchong Chen and
• Lihan Zhang

Beilstein J. Org. Chem. 2022, 18, 1107–1115, doi:10.3762/bjoc.18.113

• range of m/z 50–1600. For MS–MS analysis, the collision-induced dissociation (CID) energy was set to 15–40 eV or 30–50 eV depending on the compounds. The HPLC–UV analysis of the chiral separation was conducted with a CHIRALCEL OX-3R column (150 mm × 4.6 mm, 3 μm, DAICEL) with isocratic 35% B at a flow

Tenacibactins K–M, cytotoxic siderophores from a coral-associated gliding bacterium of the genus Tenacibaculum

• Yasuhiro Igarashi,
• Yiwei Ge,
• Tao Zhou,
• Amit Raj Sharma,
• Enjuro Harunari,
• Naoya Oku and
• Agus Trianto

Beilstein J. Org. Chem. 2022, 18, 110–119, doi:10.3762/bjoc.18.12

• submicromolar to micromolar ranges. Their iron-chelating activity was comparable to deferoxamine mesylate. Keywords: desferrioxamine; marine obligate bacterium; MS/MS analysis; tenacibactin; Tenacibaculum; Introduction Marine organisms continue to be a prolific resource of new bioactive natural products that

• . The methylene carbon C35 adjacent to the hydroxamic acid group showed a smaller chemical shift (δC 28.0). The positional assignment of C34 and C35 was made by a ROESY correlation observed between H34 and 32-NH (Figure 2). To verify the structure deduced from the NMR analysis, an MS/MS analysis was

Semiautomated glycoproteomics data analysis workflow for maximized glycopeptide identification and reliable quantification

• Steffen Lippold,
• Arnoud H. de Ru,
• Jan Nouta,
• Peter A. van Veelen,
• Magnus Palmblad,
• Manfred Wuhrer and
• Noortje de Haan

Beilstein J. Org. Chem. 2020, 16, 3038–3051, doi:10.3762/bjoc.16.253

• on the following day. The precipitate was removed by centrifugation, and 40 µL of the supernatant was transferred to a V-bottom 96-well plate (Greiner). The sample was stored at −20 °C. LC–MS/MS analysis A 0.5 µL aliquot of the sample was analyzed five times with MS1 only (for MS1-based

• mode. The resolution was set to 120,000. The target for automatic gain control (AGC) was set to 400,000. The maximum injection time was 50 ms. An intensity threshold of 20,000 was applied. For MS/MS analysis, charge states 2–7 were included for stepped higher-energy C-trap dissociation (HCD) with a

• normalized collision energy (NCE) of 35% ± 5% (30%, 35%, and 40% combined in one spectrum), a maximum injection time of 60 ms, and a AGC target of 50,000. Additionally, MS/MS fragmentation was triggered for a HexNAc loss (204.087). For the triggered MS/MS analysis, a stepped HCD with an NCE of 35% ± 15% (20

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

• provide a proof-of-concept use of GlypNirO, we performed an exploratory reanalysis of a previously published dataset [20] obtained from the ProteomeXchange Consortium via the MassIVE repository (PXD003369, MSV000079426). This study performed glycoproteomic LC–MS/MS analysis of whole plasma or plasma

Synthesis of novel sulfide-based cyclic peptidomimetic analogues to solonamides

• José Brango-Vanegas,
• Luan A. Martinho,
• Lucinda J. Bessa,
• Andreanne G. Vasconcelos,
• Alexandra Plácido,
• Alex L. Pereira,
• José R. S. A. Leite and
• Angelo H. L. Machado

Beilstein J. Org. Chem. 2019, 15, 2544–2551, doi:10.3762/bjoc.15.247

• sulfhydryl group to the electrophilic MBH residue. Spectral characterization of the chemical structures of the solonamide analogues 9 The compounds were characterized by one- and two-dimensional NMR spectroscopy, infrared spectroscopy (IR) and mass spectrometry. The high-resolution MS/MS analysis allowed the

Diazirine-functionalized mannosides for photoaffinity labeling: trouble with FimH

• Femke Beiroth,
• Tomas Koudelka,
• Thorsten Overath,
• Stefan D. Knight,
• Andreas Tholey and
• Thisbe K. Lindhorst

Beilstein J. Org. Chem. 2018, 14, 1890–1900, doi:10.3762/bjoc.14.163

• attempts to identify the specific position of FimH labeling by peptic digestion of the labeled protein and following MS/MS analysis were unsuccessful. Conclusion In continuation of our earlier work, we have employed an advanced interdisciplinary approach to identify diazirine-labeled mannoside ligands for

Evidence for an iterative module in chain elongation on the azalomycin polyketide synthase

• Hui Hong,
• Yuhui Sun,
• Yongjun Zhou,
• Emily Stephens,
• Markiyan Samborskyy and
• Peter F. Leadlay

Beilstein J. Org. Chem. 2016, 12, 2164–2172, doi:10.3762/bjoc.12.206

• . lividans ML-A was grown on SFM agar containing added 4-guanidinobutyramide. After eight days, LC–MS/MS analysis of a methanol extract of the agar plate showed that azalomycin F3a, F4a and F5a were produced. No azalomycins were produced on control plates where 4-guanidinobutyramide was not present (Figure

Orthogonal dual-modification of proteins for the engineering of multivalent protein scaffolds

• Michaela Mühlberg,
• Michael G. Hoesl,
• Christian Kuehne,
• Jens Dernedde,
• Nediljko Budisa and
• Christian P. R. Hackenberger

Beilstein J. Org. Chem. 2015, 11, 784–791, doi:10.3762/bjoc.11.88

• successful glycan attachment was provided by tryptic digest and MS/MS-analysis of Gal-3, which showed functionalization of two specific Aha residues (see Table S5 in Supporting Information File 1). It should be noted that higher concentrations of Cu2+ also led to precipitation and loss of protein material

Clicked and long spaced galactosyl- and lactosylcalix[4]arenes: new multivalent galectin-3 ligands

• Silvia Bernardi,
• Paola Fezzardi,
• Gabriele Rispoli,
• Stefania E. Sestito,
• Francesco Peri,
• Francesco Sansone and
• Alessandro Casnati

Beilstein J. Org. Chem. 2014, 10, 1672–1680, doi:10.3762/bjoc.10.175

• -tagged full-length Gal-3 was expressed in E. coli BL21 and purified on IMAC (immobilized metal ion affinity chromatography) columns. Purified protein was characterized by SDS-PAGE electrophoresis, circular dichroism (CD), and MS/MS analysis upon digestion on trypsin gel (see Figure S15, Supporting

Synthesis of zearalenone-16-β,D-glucoside and zearalenone-16-sulfate: A tale of protecting resorcylic acid lactones for regiocontrolled conjugation

• Hannes Mikula,
• Julia Weber,
• Dennis Svatunek,
• Philipp Skrinjar,
• Gerhard Adam,
• Rudolf Krska,
• Christian Hametner and
• Johannes Fröhlich

Beilstein J. Org. Chem. 2014, 10, 1129–1134, doi:10.3762/bjoc.10.112

• cleavage using cerium ammonium nitrate (CAN) did not lead to the formation of the deprotected compound 20 (Scheme 5). Beside unreacted 19, LC–MS/MS analysis showed the formation of a product with an m/z value 16 amu higher than calculated for 19 indicating oxidation of this intermediate but no deprotection

New tridecapeptides of the theonellapeptolide family from the Indonesian sponge Theonella swinhoei

• Annamaria Sinisi,
• Barbara Calcinai,
• Carlo Cerrano,
• Henny A. Dien,
• Angela Zampella,
• Claudio D’Amore,
• Barbara Renga,
• Stefano Fiorucci and
• Orazio Taglialatela-Scafati

Beilstein J. Org. Chem. 2013, 9, 1643–1651, doi:10.3762/bjoc.9.188

• of 2, followed by ESI (positive ion mode) MS/MS analysis of the obtained acyclic methyl ester derivative provided key fragment peaks, shown in Figure 3, giving definitive confirmation of the sulfinyltheonellapeptolide gross structure. In addition to the pseudomolecular ion at m/z 1454 [M + H

Chemical–biological characterization of a cruzain inhibitor reveals a second target and a mammalian off-target

• Jonathan W. Choy,
• Clifford Bryant,
• Claudia M. Calvet,
• Patricia S. Doyle,
• Shamila S. Gunatilleke,
• Siegfried S. F. Leung,
• Kenny K. H. Ang,
• Steven Chen,
• Jiri Gut,
• Juan A. Oses-Prieto,
• Jonathan B. Johnston,
• Michelle R. Arkin,
• Alma L. Burlingame,
• Jack Taunton,
• Matthew P. Jacobson,
• James M. McKerrow,
• Larissa M. Podust and
• Adam R. Renslo

Beilstein J. Org. Chem. 2013, 9, 15–25, doi:10.3762/bjoc.9.3

• and MS/MS analysis using a hybrid linear ion-trap-Orbitrap mass spectrometer. Tandem mass spectra acquired were searched against the UniProtKb database employing ProteinProspector; four MS/MS spectra corresponding to the same peptide sequence were identified (Figure 7). This sequence was found to

En route to photoaffinity labeling of the bacterial lectin FimH

• Thisbe K. Lindhorst,
• Michaela Märten,
• Andreas Fuchs and
• Stefan D. Knight

Beilstein J. Org. Chem. 2010, 6, 810–822, doi:10.3762/bjoc.6.91

• shown both by MS/MS studies and by affino dot–blot analysis. Keywords: diazirines; FimH; lectins; MS/MS analysis; photoactive mannoside ligands; photoaffinity labeling; Introduction Photoaffinity labeling is a technique by which ligand binding sites of a receptor protein can be identified in solution