Synthesis of electrophile-tethered preQ₁ analogs for covalent attachment to preQ₁ RNA

• Laurin Flemmich and
• Ronald Micura

Beilstein J. Org. Chem. 2025, 21, 483–489, doi:10.3762/bjoc.21.35

• antibiotic properties, others expand the chemical diversity and thus the functional sophistication of ribonucleic acids, as in the case of Q [3]. In most bacteria, Q biosynthesis is tightly regulated by riboswitches, which are highly structured RNA elements located mostly in the 5’-leader of messenger RNA

• naturally in mRNA riboswitches in bacteria and is involved in ligand-dependent gene regulation. Therefore, this riboswitch (like others) has become an attractive target for drug design. To date, most known RNA–small molecule binders interact in a non-covalent manner. The compounds presented here are part of

Antibiofilm and cytotoxic metabolites from the entomopathogenic fungus Samsoniella aurantia

• Rita Toshe,
• Syeda J. Khalid,
• Blondelle Matio Kemkuignou,
• Esteban Charria-Girón,
• Paul Eckhardt,
• Birthe Sandargo,
• Kunlapat Nuchthien,
• J. Jennifer Luangsa-ard,
• Till Opatz,
• Hedda Schrey,
• Sherif S. Ebada and
• Marc Stadler

Beilstein J. Org. Chem. 2025, 21, 327–339, doi:10.3762/bjoc.21.23

• 2656), Schizosaccharomyces pombe (DSM 70572), Rhodotorula glutinis (DSM 10134), and Wickerhamomyces anomalus (DSM 6766). Additionally, various Gram-positive bacteria such as Staphylococcus aureus (DSM 346), Bacillus subtilis (DSM 10), Mycobacterium smegmatis (ATCC 700084), and Gram-negative bacteria

• including Acinetobacter baumannii (DSM 30008), Escherichia coli (DSM 1116), Chromobacterium violaceum (DSM 30191), and Pseudomonas aeruginosa (PA14) were included in the assessment. Gentamicin and nystatin served as positive controls against most bacteria and all fungi, respectively. For specific

Discovery of ianthelliformisamines D–G from the sponge Suberea ianthelliformis and the total synthesis of ianthelliformisamine D

• Sasha Hayes,
• Yaoying Lu,
• Bernd H. A. Rehm and
• Rohan A. Davis

Beilstein J. Org. Chem. 2024, 20, 3205–3214, doi:10.3762/bjoc.20.266

• antibacterial agents [20][21]. The absence of polyamine chains in ianthelliformisamines D–G (4–7) could explain the loss of activity seen in our assessment against P. aeruginosa. The synthetic molecule of 7 has been tested by other researchers against Gram-negative bacteria including P. aeruginosa with reported

• /461/463 [M + H]+. Bacterial strains and media Wild-type Pseudomonas aeruginosa strain PAO1 (prototrophic wild-type) [25] was used in this study. Bacteria were grown in Luria–Bertani (LB) medium (10 g/L tryptone, 10 g/L sodium chloride and 5 g/L yeast extract). Biofilm inhibition assay The overnight

• ) and diluted to an OD600 of 0.01. Test compounds (15 µL) were loaded prior to the addition of bacteria (135 µL) into 96-well plates. The plates were incubated for 24 h at 37 °C in static conditions. The effects of compounds on bacterial growth and the viability of biofilm bacteria was determined by the

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

• based on a dataset of known pairs of nonribosomal code/substrate BB. c) An analysis that compared the known vs predicted NRP BBs grouped based on their chemical structures found both oversampled (green)/underexplored (blue) niches in the NRP chemical space; the analysis was performed across all bacteria

Natural resorcylic lactones derived from alternariol

• Joachim Podlech

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

• contamination with the strongly mutagenic altertoxins [82][83]. When administered to rats, AME induced gene mutations, chromosome breakage, and DNA damage [114]. AME turned out to be active against bacteria (Bacillus subtilis, Staphylococcus haemolyticus, Agrobacterium tumefaciens, Pseudomonas lachrymans

• , and 1.7 μM, respectively) [160], and further bacteria [164] and showed antimicrobial activity against Trypanosoma brucei rhodesiense, Leishmania donovani, and Plasmodium falciparum (IC50: 13.6, 7.5, 28.3 µM) [159]. It was cytotoxic against soybean cell cultures with an EC50 value of 0.63 µM [158] and

• ), Bacillus cereus (MIC values of 8–32 μg/mL [187][193], and further bacteria [163]. It turned out to be active against Trypanosoma brucei rhodesiense and Leishmania donovani (IC50 values of 1.5, 7.1 μM, respectively) and further protozoa [159]. It furthermore showed some radical scavenging activities [163

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

• in bacteria, which are able to use most of the mammalian sugar units to construct their glycoconjugates but, in addition, can also use a wide variety of particular, and potentially endless, monosaccharides that are instead not present in eukaryotes (Figure 2). This huge diversity and complexity

2-Heteroarylethylamines in medicinal chemistry: a review of 2-phenethylamine satellite chemical space

• Carlos Nieto,
• Alejandro Manchado,
• Ángel García-González,
• David Díez and
• Narciso M. Garrido

Beilstein J. Org. Chem. 2024, 20, 1880–1893, doi:10.3762/bjoc.20.163

• thiohistidine (89) were evaluated for skincare anti-inflammatory properties by Brancaccio et al. (Scheme 12) [64]. These compounds, biosynthesized by microalgae, bacteria and marine invertebrates feature skin protection via Nrf2 activation (nuclear factor erythroid 2-related factor 2). Antimalarial properties

The Groebke–Blackburn–Bienaymé reaction in its maturity: innovation and improvements since its 21st birthday (2019–2023)

• Cristina Martini,
• Muhammad Idham Darussalam Mardjan and
• Andrea Basso

Beilstein J. Org. Chem. 2024, 20, 1839–1879, doi:10.3762/bjoc.20.162

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

• associated bioactive peptides. Keywords: antimicrobials; genome mining; lantibiotics; lanthipeptides; multi-drug resistant bacteria; natural products; Introduction Antimicrobial resistance (AMR) is a significant public health challenge. Only in 2019, there were 4.95 million deaths associated with AMR [1

• . Furthermore, the increasing availability of genomic data has led to the development of bioinformatics tools, such as AntiSMASH [3], Bagel4 [4], and RiPPMiner [5], that have emerged to streamline the process of exploring and discovering BGCs in bacteria, known as genome mining. Genome mining has emerged as a

Syntheses and medicinal chemistry of spiro heterocyclic steroids

• Laura L. Romero-Hernández,
• Ana Isabel Ahuja-Casarín,
• Penélope Merino-Montiel,
• Sara Montiel-Smith,
• José Luis Vega-Báez and
• Jesús Sandoval-Ramírez

Beilstein J. Org. Chem. 2024, 20, 1713–1745, doi:10.3762/bjoc.20.152

• , while antibacterial activity was tested against Gram-positive and Gram-negative bacteria. Unfortunately, all compounds exhibited very low activity in these assays. However, the oxathiaphospholanes were evaluated for their antifungal properties against Candida albicans and Saccharomyces cerevisiae, where

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

• the specialised metabolism of bacteria and fungi. Each NRPS module is minimally composed of a condensation (C) domain, an adenylation (A) domain, and a peptidyl carrier protein (PCP or thiolation/T domain), and one module typically incorporates one amino acid into the final natural product. In

• of core peptide sequences [100][101]. Type IV borosins are more distantly related homologues found in bacteria; although it was originally believed that borosins occur mainly in fungi, Cho et al. and Imani et al. both demonstrated that type IV borosin BGCs are widespread in bacteria and have

• proteusin family of RiPPs. They are produced by the tunicate symbiont Candidatus Entotheonella factor and exhibit membrane activity against Gram-positive bacteria and are highly cytotoxic. Cytotoxicity was tested with murine leukaemia cells; polytheonamide A, B, and C showed IC50 values between 68 and 78 pg

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

• Weimao Zhong Vinayak Agarwal School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA 10.3762/bjoc.20.146 Abstract Microbulbifer is a genus of halophilic bacteria that are

• commonly detected in the commensal marine microbiomes. These bacteria have been recognized for their ability to degrade polysaccharides and other polymeric materials. Increasingly, Microbulbifer genomes indicate these bacteria to be an untapped reservoir for novel natural product discovery and biosynthetic

• novelty. In this review, we summarize the distribution of Microbulbifer bacteria, activities of the various polymer degrading enzymes that these bacteria produce, and an up-to-date summary of the natural products that have been isolated from Microbulbifer strains. We argue that these bacteria have been

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

• discovering diverse natural products from bacteria and fungi. In plants, this approach is often more limited due to the lack of available annotated genomes and transcriptomes combined with a less consistent clustering of biosynthetic genes. The recently identified burpitide class of ribosomally synthesized

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

• the bacteria. Bacterial lectins are therefore attractive targets for the development of new antibiotic-sparing anti-infective drugs. For example, some Escherichia coli fimbrial lectin FimH inhibitors are currently in clinical development to treat and prevent urinary tract infections [9][10]. A large

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

• from different strains of bacteria only retain the sequences from one of the sources. For example, only the erythromycin PKS from Saccharopolyspora erythraea were retained. (b) To associate sequence information with reliable absolute configuration of the product, the stereochemical configurations of

Synthesis of substituted triazole–pyrazole hybrids using triazenylpyrazole precursors

• Simone Gräßle,
• Laura Holzhauer,
• Nicolai Wippert,
• Olaf Fuhr,
• Martin Nieger,
• Nicole Jung and
• Stefan Bräse

Beilstein J. Org. Chem. 2024, 20, 1396–1404, doi:10.3762/bjoc.20.121

• immobilized building blocks. Biologically active pyrazole–triazole hybrids 1–4: inhibitory effect on cholera bacteria [13], antimicrobial properties [14], P2X7 antagonists (depression) [15] and ERK3 inhibition [12]. Synthesized triazole–pyrazole hybrids 21aa–vg. Literature-reported synthetic routes to

Computation-guided scaffold exploration of 2E,6E-1,10-trans/cis-eunicellanes

• Zining Li,
• Sana Jindani,
• Volga Kojasoy,
• Teresa Ortega,
• Erin M. Marshall,
• Khalil A. Abboud,
• Sandra Loesgen,
• Dean J. Tantillo and
• Jeffrey D. Rudolf

Beilstein J. Org. Chem. 2024, 20, 1320–1326, doi:10.3762/bjoc.20.115

• family members in bacteria and plants [4], these diterpenoids have four main structural differences: the number and location of oxidized carbons, the absence or presence of transannular ether bridges, the configuration (cis or trans) of the bicyclic ring fusion, and the presence and configuration (E or Z

• from bacteria and forms albireticulene (2), a C1 diastereomer of 1 that also features the 2E alkene [7]. Two coral enzymes, BaTC-2 and EcTPS1, were found to form klysimplexin R (3), a 2Z-cis-eunicellane [8][9]. Recently, a third bacterial version, MicA, was identified as producing the 2Z-trans

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

• bacteria and fungi but not in mammalian cells, acts only on cytosine. Cytidine deaminase (CDA) as a key enzyme in the pyrimidine salvage pathway in mammals deaminates both cytidine and 2'-deoxycytidine. Members of the apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like (APOBEC) family, such as

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

• the supply of prenyl substrates can significantly change the product profile of promiscuous TSs, thereby generating terpenes with novel structures. MSTSs from bacteria According to previous studies, plants and fungi are the major producers of terpenoids [30][31][32][33]. Recently, an increasing number

• of TSs have been discovered in bacteria [32][33]. VenA from Streptomyces venezuelae ATCC 15439 was characterized as a promiscuous class I TS that converts 3 to geraniol (24.2% yield), 4 to seven sesquiterpenes (24.6% yield), and 5 to four diterpenes (31.2% yield), with venezuelaene A (35, Figure 3b

• distinct primary structures with class I TSs, its crystal structure reveals a similar overall structure of BalTS to the α-domain of class I TSs and therefore was proposed as class IB, a new subclass of TSs [37]. The discovery of TSs from bacteria not only expands the diversity of terpene skeletons but also

Confirmation of the stereochemistry of spiroviolene

• Yao Kong,
• Yuanning Liu,
• Kaibiao Wang,
• Tao Wang,
• Chen Wang,
• Ben Ai,
• Hongli Jia,
• Guohui Pan,
• Min Yin and
• Zhengren Xu

Beilstein J. Org. Chem. 2024, 20, 852–858, doi:10.3762/bjoc.20.77

• cyclization process of fungi-derived deoxyconidiogenol and bacteria-derived spiroviolene by sharing the common C6-cation intermediate IM-3 with cyclopiane skeleton (Scheme 1A). Conclusion We have unambiguously confirmed the structural revision of spiroviolene with cis-oriented 19- and 20-methyl groups by

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

• antibiotic activity towards Gram-negative bacteria. An NNG degrading heme enzyme, called NnlA, has recently been discovered in the genome of Variovorax sp. strain JS1663 (Vs NnlA). Evidence is presented that NnlA and therefore, NNG degradation activity is widespread. To achieve this objective, we

• characterized and tested the NNG degradation activity of five Vs NnlA homologs originating from bacteria spanning several classes and isolated from geographically distinct locations. E. coli transformants containing all five homologs converted NNG to nitrite. Four of these five homologs were isolated and

• NnlA cannot degrade the NNG analog 2-nitroaminoethanol. The combined data strongly suggest that NnlA enzymes specifically degrade NNG and are found in diverse bacteria and environments. These results imply that NNG is also produced in diverse environments and NnlA may act as a detoxification enzyme to

Discovery and biosynthesis of bacterial drimane-type sesquiterpenoids from Streptomyces clavuligerus

• Dongxu Zhang,
• Wenyu Du,
• Xingming Pan,
• Xiaoxu Lin,
• Fang-Ru Li,
• Qingling Wang,
• Qian Yang,
• Hui-Min Xu and
• Liao-Bin Dong

Beilstein J. Org. Chem. 2024, 20, 815–822, doi:10.3762/bjoc.20.73

• University, Nanjing 211198, China 10.3762/bjoc.20.73 Abstract Drimane-type sesquiterpenoids (DMTs) are characterized by a distinctive 6/6 bicyclic skeleton comprising the A and B rings. While DMTs are commonly found in fungi and plants, their presence in bacteria has not been reported. Moreover, the

• analogs. This discovery not only broadens the known chemical diversity of DMTs from bacteria, but also provides new insights into DMT biosynthesis in bacteria. Keywords: bacterial terpenoid; cytochrome P450s; drimane-type sesquiterpenoid; Streptomyces clavuligerus; terpenoid biosynthesis; Introduction

• associated with DMT biosynthesis have been identified in bacteria, the corresponding natural DMTs have not been discovered [17]. In this study, we isolated and characterized three drimenol congeners (2–4) from Streptomyces clavuligerus (Figure 2a). In the genome of S. clavuligerus, we identified a cav

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

• Zeeck and co-workers in the early 2000s, is a method in which the target bacteria are cultured under various conditions (medium composition, temperature, pH, oxygen supply, light quality and quantity, addition of precursors and enzyme inhibitors, etc.) and all metabolites obtained from them are analyzed

• in the genetically programmed death of the producing organism. In addition, Nishiyama et al. suggested that actinorhodin (8) produced by Streptomyces coelicolor A3(2) functions as an organocatalyst to kill bacteria by catalyzing the production of toxic levels of H2O2 [99]. They also suggested that

• Streptomyces and mycolic acid-containing bacteria (MACB) activates secondary metabolism [111]. In their method, direct attachment by live MACB cells is thought to alter secondary metabolism in the Streptomyces cells [112]. Using this method, Onaka et al. identified a variety of new compounds, such as

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

• efficacious in preventing macular degeneration, cataracts, and cardiovascular diseases [83]. Many microorganisms, such as bacteria, cyanobacteria, and microalgae, can also produce 7 [84]. The biosynthesis of 7 in bacteria is analogous to that in plants. The difference is that in bacteria, 7 is formed through

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

• organism shares the same habitat with the predator Myxococcus xanthus that feeds on other bacteria including B. subtilis, and bacillaene is the primary factor conferring B. subtilis cells resistance to predation by M. xanthus [8]. The identification of its biosynthetic gene cluster (bae) revealed that the