Multicomponent reactions driving the discovery and optimization of agents targeting central nervous system pathologies

• Lucía Campos-Prieto,
• Aitor García-Rey,
• Eddy Sotelo and
• Ana Mallo-Abreu

Beilstein J. Org. Chem. 2024, 20, 3151–3173, doi:10.3762/bjoc.20.261

• biomolecules like DNA and lipids. Lipid peroxidation and membrane disruption can cause random cross-linking, resulting in cell death and the fragmentation of proteins and enzymes. Elevated concentrations of reactive oxygen species (ROS) from various molecular processes contribute to the oxidation of proteins

• leading proposal to explain AD etiology. Based on this hypothesis, compounds that inhibit γ-secretase, one of the enzymes responsible for forming Aβ, are potential therapeutics for AD. In 2024, Fragkiadakis et al. [47] developed a rapid synthesis of benzodioxepinones. The attention was focused on the

• benzodioxepinones 12 in all cases (Scheme 11). The synthesized compounds demonstrated excellent drug-like features. Parkinson disease (PD) Knoevenagel–Michael addition/cyclization (MCR 3 + 2): Sirtuins, a group of enzymes that rely on NAD+ to function as protein deacetylases, have garnered attention across multiple

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

• corresponding nucleic acid sequence. Proteinaceous enzymes then go on to catalyze biosynthetic reactions that put together small molecule building blocks (BB) to generate natural products with extremely diverse chemical structures. Because the intricacy of this process is not fully understood, scientists still

• need to wait for enzymes to complete the entire course of biosynthesis, and then characterize chemical structure of the final natural product. While a generalized algorithm is not yet available, scientists in recent years have made some headways toward predicting the chemical structure of a natural

• the discovery of a new NRP. Conversely, every “unpredictable” A domain, if its substrate specificity were to be experimentally determined, is guaranteed to be a new datapoint. In fact, various in vitro substrate characterization assays that studied A domains as stand-alone enzymes have been reported

N-Glycosides of indigo, indirubin, and isoindigo: blue, red, and yellow sugars and their cancerostatic activity

• Peter Langer

Beilstein J. Org. Chem. 2024, 20, 2840–2869, doi:10.3762/bjoc.20.240

• , and Parkinson's disease, cardiovascular diseases, inflammation, AIDS and others have their origin in context with the activities of protein kinases, such as glycogen synthase kinase-3 (GSK-3β) and cyclin-dependent kinases (CDK’s). The phosphorylation of the amino acid moieties of several enzymes is

Young investigators in natural products chemistry, biosynthesis, and enzymology

• Jeffrey D. Rudolf,
• Lena Barra and
• Takayoshi Awakawa

Beilstein J. Org. Chem. 2024, 20, 2720–2721, doi:10.3762/bjoc.20.229

• . Their privileged structures have led organic and bioorganic chemists to develop methods to construct them. Our fundamental knowledge in enzymology is continually expanded by enzymes involved in natural products biosynthesis, as their production requires evolved enzymes to perform chemical reactions

• clusters, and enzymes, development of chemical probes, biocatalysis and chemoenzymatic total synthesis, enzymatic mechanisms, and computational investigations of chemical structures and reactions. All of the major classes of natural products are represented here: nonribosomal peptides, ribosomally

Tandem diazotization/cyclization approach for the synthesis of a fused 1,2,3-triazinone-furazan/furoxan heterocyclic system

• Yuri A. Sidunets,
• Valeriya G. Melekhina and
• Leonid L. Fershtat

Beilstein J. Org. Chem. 2024, 20, 2342–2348, doi:10.3762/bjoc.20.200

• products and pharmacologically active molecules. For example, nucleic acids, proteins and enzymes, hormones and vitamins, essential for the functioning of a living organism, also contain nitrogen frameworks [1][2]. Besides that, nitrogen-containing compounds are widely used in medicine as antibiotics

Catalysing (organo-)catalysis: Trends in the application of machine learning to enantioselective organocatalysis

• Stefan P. Schmid,
• Leon Schlosser,
• Frank Glorius and
• Kjell Jorner

Beilstein J. Org. Chem. 2024, 20, 2280–2304, doi:10.3762/bjoc.20.196

• . Keywords: catalyst design; machine learning; modelling; organocatalysis; selectivity prediction; Introduction Since the beginning of the 21st century, organocatalysts [1] have established themselves as a third group of homogeneous catalysts, next to biocatalysts [2] (enzymes) and transition metal-based

Cell-free protein synthesis with technical additives – expanding the parameter space of in vitro gene expression

• Tabea Bartsch,
• Stephan Lütz and
• Katrin Rosenthal

Beilstein J. Org. Chem. 2024, 20, 2242–2253, doi:10.3762/bjoc.20.192

• established itself as a successful tool in organic synthesis. A particularly fast technique for screening enzymes is the in vitro expression or cell-free protein synthesis (CFPS). The system is based on the transcription and translation machinery of an extract-donating organism to which substrates such as

• tested additives. Keywords: cell-free protein synthesis; cGAS; Escherichia coli cell-free extract; sfGFP; TX-TL; Introduction In addition to other applications such as biomanufacturing or biosensing, cell-free protein synthesis (CFPS) of enzymes has established itself as a tool for rapid screening of

• water, is better accepted than DMSO. In vitro thscGAS-sfGFP production with additives The CPFS system used, or CFPS in general, is not further optimized for the production of thscGAS-sfGFP or other specific enzymes. By default, GFP is generally used as a model protein to optimize the composition of CFPS

O,S,Se-containing Biginelli products based on cyclic β-ketosulfone and their postfunctionalization

• Kateryna V. Dil and
• Vitalii A. Palchykov

Beilstein J. Org. Chem. 2024, 20, 2143–2151, doi:10.3762/bjoc.20.184

• chemistry highlights derivatives capable of interacting with multiple receptors or enzymes, making them ideal candidates for drug discovery. Dihydropyrimidinones (DHPMs) and their derivatives are particularly noteworthy within this category. Accordingly, their synthesis is of significant interest for

Factors influencing the performance of organocatalysts immobilised on solid supports: A review

• Zsuzsanna Fehér,
• Dóra Richter,
• Gyula Dargó and
• József Kupai

Beilstein J. Org. Chem. 2024, 20, 2129–2142, doi:10.3762/bjoc.20.183

• restrictions in mobility, limiting their ability to undergo conformational changes necessary for catalysis, especially in the case of enzymes [72][78]. Overall, covalent tethering techniques are the preferred approach to designing stable heterogeneous organocatalysts, provided that the covalent modification

• showed that the activity of a difunctional organocatalyst in lactose hydrolysis was improved 5.2-fold by immobilisation on different solid supports that mimic the active site channels of enzymes [113]. In a solid-supported system, the solvent can exert a different influence on the catalytic activity

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

• decarboxylase (Scheme 8) [45][46][47]. Histamine is commonly degradated by two enzymes: diamine oxidase (DAO) to produce (imidazol-4-yl)acetic acid (44), or histamine N-methyltransferase (HMT) to N-methylhistamine 45. Monoamine oxidase B (MAO-B) transforms N-methylhistamine into (N-methylimidazol-4-yl)acetic

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

• -free conditions. Although some new metal or Brønsted acid catalysts have been reported in the last few years, the main innovations can be found in the use of organic catalysts, enzymes, and compartmentations. A few reports on the in situ generation of reactants and on the reaction conducted under flow

• et al. reported the first biocatalytic GBB reaction using lipase [21]. The model reaction depicted in Scheme 2 (R = t-Bu) was tested in ethanol at room temperature with various enzymes, where Candida antarctica lipase B (CALB) and Aspergillus niger gave best results, affording 3 in 63% and 64% yields

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

• is recognized by post-translational enzymes and a core peptide where these enzymes produce the formation of Dha-Cys or Dhb-Cys residues. The post-translational modification enzymes involved span different functional domains (a cyclase and a dehydratase), and their activity is tightly controlled at

• leads to its production during mid-exponential and log-phase [19]. To date, five classes of lanthipeptide synthetases have been identified [20] and are the basis for classifying lanthipeptide gene clusters. For the class II lanthipeptide synthetases discussed in this work, multidomain LanM enzymes

• chemical structures of these lantibiotics make them promising candidates for treating drug-resistant pathogens, and the characterization of these compounds from Clostridium provides an opportunity to develop new antibiotics. Results and Discussion Genome mining of LanM enzymes’ sequence diversity to

Synthesis of polycyclic aromatic quinones by continuous flow electrochemical oxidation: anodic methoxylation of polycyclic aromatic phenols (PAPs)

• Hiwot M. Tiruye,
• Solon Economopoulos and
• Kåre B. Jørgensen

Beilstein J. Org. Chem. 2024, 20, 1746–1757, doi:10.3762/bjoc.20.153

• (PAHs) by cytochrome P450 (CYP) and other metabolic enzymes [7][8]. Main metabolic pathways form quinone isomers of benzo[a]pyrene [8], naphthalene [9][10], and benzene [11]. Numerous methods for the oxidation of phenols or their derivatives to quinones have been described [12]. Oxidation with Fremy’s

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

• -enzymatic synthesis, featuring the late-stage enzymatic oxidation of chemically synthesized intricate scaffolds are attracting increasing attention. A collaboration between Stoltz and Arnold led to the pioneering accomplishment in the total synthesis of nigelladine A by exploiting P450 enzymes engineered

• hybrid syntheses of cotylenol (1) and brassicicenes [19]. The key oxidative allylic rearrangement was conducted enzymatically, while the skeletal rearrangement originally mediated by P450 enzymes in the biosynthetic pathway was achieved through chemical transformation. Hence, this strategy can be

• of scaffold 6 yield a series of intermediates and natural products, including cotylenol (1) and brassicicenes I and B (9 and 10), as well as brassicicene O (12), which possesses a distinct scaffold resulting from a skeletal rearrangement. To the core scaffold 6, the P450 enzymes, BscB and BscC

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

• -translational modifications; ribosomal peptides; SAM-dependent enzymes; Introduction In the complex landscape of natural product biosynthesis, ribosomally synthesised and post-translationally modified peptides (RiPPs) stand out as a fascinating class of compounds with both structural diversity and unique

• ; this reaction is catalysed by S-adenosylmethionine (SAM or AdoMet)-dependent methyltransferases (MTs). These enzymes are known for their excellent chemo-, regio-, and stereoselectivity [3][4][5][6]. Their ability to introduce methyl groups at specific positions within ribosomal peptides equips the

• atom, describing O-, N-, C-, and S-MTs; halide MTs have not (yet) been identified in RiPP pathways. The enzymes described below are either conventional SAM-dependent MTs or radical SAM (rSAM) MTs; rSAM MTs are one subfamily of the large rSAM enzyme superfamily, which encompasses enzymes catalysing a

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

• 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

• . Together with the emerging field of natural product discovery from Microbulbifer bacteria, this genus of obligate marine bacteria is well validated to be a valuable source of biopolymer degrading enzymes. In this review, we outline the discovery of Microbulbifer enzymes that have substantial biocatalytic

• distributions and origins of Microbulbifer bacteria strains, degradation enzymes, and secondary metabolite discoveries. A focus is placed on the novel chemical structures reported with reference to their biological activities and the biosynthetic studies they have inspired. Review Biopolymer degrading enzymes

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

• biosynthetic enzymes. Ultimately proteolysis releases the modified core peptide as the mature RiPP natural product [5][6]. In the case of the newly described burpitide family of RiPPs, the defining feature is the presence of amino acid side-chain crosslinks installed by a copper-dependent burpitide cyclase [4

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

• natural products containing a foundational 6/10-bicyclic framework and can be divided into two main classes, cis and trans, based on the configurations of their ring fusion at C1 and C10. Previous studies on two bacterial diterpene synthases, Bnd4 and AlbS, revealed that these enzymes form cis- and trans

• 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

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

• a previously unrecognized facet of these enzymes as cofactor-independent oxygenases when employing the hydroquinone intermediate CR1 as a substrate. The enzymes autonomously drive oxidative ring cleavage and rearrangement reactions of CR1, yielding products identical to those observed in cofactor

• •−. Our findings illuminate a substrate-controlled catalytic mechanism of AlpJ-family oxygenases, expanding the realm of cofactor-independent oxygenases. Notably, AlpJ-family oxygenases stand as a pioneering example of enzymes capable of catalyzing oxidative reactions in either an FADH2/FMNH2-dependent or

• and 3 through a rare Mannich reaction. This results in the formation of prekinamycin harboring a diazo group [14]. Given the presence of AlpJ-like oxygenases and ʟ-glutamylhydrazine biosynthetic enzymes in the gene clusters of lomaiviticin, nenestatin, and fluostatins [16][17][18][19][20], it is

Stability trends in carbocation intermediates stemming from germacrene A and hedycaryol

• Naziha Tarannam,
• Prashant Kumar Gupta,
• Shani Zev and
• Dan Thomas Major

Beilstein J. Org. Chem. 2024, 20, 1189–1197, doi:10.3762/bjoc.20.101

• monoterpenes (C10), sesquiterpenes (C15), and diterpenes (C20). Enzymes such as monoterpene, sesquiterpene, and diterpene synthases act on geranyl diphosphate (GPP), farnesyl diphosphate (FPP), and geranylgeranyl diphosphate (GGPP) to yield mono-, sesqui-, and diterpenes, respectively. These linear precursors

• formation of (6,6) vs (5,7) is rooted in very slight changes in mechanism (protonation at C1 vs C10), it is of interest to understand whether there is a systematic difference in energy. In cases where enzymes use pathways with high-energy intermediates, the enzyme active site must in some way direct the

• . Interestingly, enzymes which catalyze reactions proceeding via these intermediates must contend with these intrinsic stability tendencies [24][25][27][28][46][47][48][49][50][51]. We further found that the M06-2X functional in conjunction with a modest split valence basis set provides rather accurate energies

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

• accelerated by enzymes. These enzymes share a similar mechanism of cytosine deamination and a similar tertiary structure. Despite this similarity, individual enzymes are selective for the corresponding cytosine-containing substrates with little or no cross-reactivity. Cytosine deaminase, which is present in

• (MDS) and chronic myelomonocytic leukaemia (CMML) [8]. In normal human cells, the enzyme family A3 [9][10][11][12] disables pathogens by scrambling ssDNA by cytosine to uracil mutation (Figure 1A) [9][10][13][14]. However, several enzymes, particularly A3A, A3B, A3H and A3G, deaminate cytosine in human

• , biochemical and structural studies support a model in which this A3-mediated mutagenesis promotes tumour evolution and strongly influences disease trajectories, including the development of drug resistance and metastasis [18][19][20][21][22][23]. Of the seven A3 enzymes, three (A3A, A3B and A3H) are at least

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

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

• TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan, Hubei 430071, China 10.3762/bjoc.20.86 Abstract Terpenoids are one of the largest class of natural products with diverse structures and activities. This enormous diversity is embedded in enzymes called terpene synthases (TSs), which

• converted into (poly)cyclic skeletons, including hemiterpenes, monoterpenes, sesquiterpenes, diterpenes, sesterterpenes, and triterpenes, by a large class of enzymes called terpene synthases (TSs) (Figure 1). The reactions of TSs are one of the most important factors contributing to terpene diversity, as

• . Notably, MSTSs can also convert noncanonical prenyl substrates, including chemically synthesized analogs and bio-originated 6-, 7-, 8-, 11-, and 16-carbon substrates generated by methyltransferases or engineered lepidopteran mevalonate pathways. The multisubstrate features of these enzymes have often been

(Bio)isosteres of ortho- and meta-substituted benzenes

• H. Erik Diepers and
• Johannes C. L. Walker

Beilstein J. Org. Chem. 2024, 20, 859–890, doi:10.3762/bjoc.20.78

• 50% inhibition concentration of selected CYP450 enzymes (IC50). Cis-2,6-disubstituted [2]-ladderanes Brown and co-workers recently proposed cis-2,6-disubstituted bicyclo[2.2.0]hexanes ([2]-ladderanes) as isosteric replacements for meta-benzenes. An exit vector analysis indicated that the substituent

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

• 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

• metabolic enzymes. In addition, it has been shown to irreversibly inhibit isocitrate lyase 1 (ICL1) from Mycobacterium tuberculosis [40], and key metabolic protein for these pathogens [41]. Isocitrate lyases convert isocitrate to glyoxylate and succinate. Deprotonation of 3NP (pKa = 9.0) results in the

• noursei, an NNG-producing bacterium, did not reveal any NnlA homologs. Interestingly, four NMOs are annotated in the S. noursei genome. These enzymes could protect S. noursei from NNG toxicity during its biosynthesis. Meanwhile, we posit that NnlA protects non-NNG producing bacteria from exposure. In vivo