4-(1-Methylamino)ethylidene-1,5-disubstituted pyrrolidine-2,3-diones: synthesis, anti-inflammatory effect and in silico approaches

• Nguyen Tran Nguyen,
• Vo Viet Dai,
• Luc Van Meervelt,
• Do Thi Thao and
• Nguyen Minh Thong

Beilstein J. Org. Chem. 2025, 21, 817–829, doi:10.3762/bjoc.21.65

• and protein which enhance the stability of the complex [37][38]. The molecular docking study evaluated the binding affinities of potential drug candidates (iNOS–5a, 5b, 5c, 5d, 5e) and the reference compound (iNOS–DEX) with the inducible nitric oxide synthase (iNOS) enzyme (Figure 4 and Figure 5). The

• , Trp194, Gly202, Pro350, Phe369, and Tyr489, further contributing to the stabilization of the ligand–protein complexes. More importantly, the occurrence of an electron-withdrawing group, nitro group (NO2), on the aromatic ring linked to the 1-position of the pyrrolidine-2,3-dione core may help compound 5e

• stabilized the ligand–protein complexes. Experimental evaluations have confirmed these findings in which compound 5e demonstrated the most potent inhibitory activity against iNOS, achieving an IC50 value of 43.69 ± 5.26 µM substantially lower than that of 5a (IC50 = 78.65 ± 6.88 µM) and 5b (IC50 = 95.66

Orthogonal photoswitching of heterobivalent azobenzene glycoclusters: the effect of glycoligand orientation in bacterial adhesion

• Leon M. Friedrich and
• Thisbe K. Lindhorst

Beilstein J. Org. Chem. 2025, 21, 736–748, doi:10.3762/bjoc.21.57

• the structural determinants of the recognition process is a prerequisite for understanding and manipulating carbohydrate–protein interactions, such as in the inhibition of carbohydrate-specific bacterial adhesion. For receptor binding, glycoligands have to be properly oriented in three-dimensional

• ; Introduction Carbohydrate–protein interactions are fundamental in cell biology, such as in cell–cell interactions, immune cell trafficking or bacterial adhesion, and therefore carbohydrate recognition is subject of intensive research. In particular, a plethora of synthetic glycoconjugates have been designed

• diverse interactions with primary and secondary carbohydrate binding sites of the protein [13]. For example, when an α-ᴅ-mannopyranosyl (Man) and a β-ᴅ-glucopyranosyl (Glc) unit were conjugated such that the relative orientation of the two sugar portions is varied – be it on enantiomeric or regioisomeric

Synthesis of HBC fluorophores with an electrophilic handle for covalent attachment to Pepper RNA

• Raphael Bereiter and
• Ronald Micura

Beilstein J. Org. Chem. 2025, 21, 727–735, doi:10.3762/bjoc.21.56

• fluorescent protein (GFP), has revolutionized genetics by providing highly accurate real-time detection of fusion proteins in vitro and in vivo [1]. Pioneering work on GFP-tagged proteins for real-time monitoring of gene expression was first reported by Chalfie and co-workers in 1994 [2]. For a long time

Origami with small molecules: exploiting the C–F bond as a conformational tool

• Patrick Ryan,
• Ramsha Iftikhar and
• Luke Hunter

Beilstein J. Org. Chem. 2025, 21, 680–716, doi:10.3762/bjoc.21.54

• *C1–O5 hyperconjugation. Therefore, if the anomeric oxygen is replaced with CH2 (e.g., 78, Figure 10), the anomeric bonds are able to rotate more freely, and this manifests in a reduced binding affinity for the protein target by 78 compared to 77. However, upon progressing to a CHF linkage (e.g., 79

• and 80, Figure 10), the molecule becomes more rigid again, this time due to dual σC–H → σ*C–F hyperconjugation. Notably, different conformations are preferred by the epimeric fluorinated analogues 79 and 80: analogue 79 is a good match for the parent disaccharide and retains its protein-binding

• which the conformation can be controlled by fluorine, is the natural product balanol (99, Figure 11) [112][167][168][169][170][171][172]. Balanol is an ATP mimic that inhibits protein kinase Cε (PKCε), an enzyme that is implicated in cancer. However, compound 99 also inhibits off-target kinases

Asymmetric synthesis of fluorinated derivatives of aromatic and γ-branched amino acids via a chiral Ni(II) complex

• Maurizio Iannuzzi,
• Thomas Hohmann,
• Michael Dyrks,
• Kilian Haoues,
• Katarzyna Salamon-Krokosz and
• Beate Koksch

Beilstein J. Org. Chem. 2025, 21, 659–669, doi:10.3762/bjoc.21.52

• spheres of protein engineering and medicinal chemistry. In the last decades, a large number of different synthetic strategies have been developed to produce a large variety of fluorinated amino acids. Still, obtaining fluorinated amino acids in great quantities can be challenging, or the corresponding

• amino acids. We synthesized two fluorinated analogs of phenylalanine, which are still unexplored in the context of peptide and protein chemistry. Furthermore, both diastereomers of trifluoroleucine were synthesized, demonstrating that the described strategy can also be applied to synthesize enantio‑ and

• -natural amino acids are pivotal in protein engineering and drug development. Over 30% of approved small‑molecule drugs today contain non‑canonical amino acid building blocks [1][2]. In peptide and protein engineering, non‑natural amino acids significantly increase the respective range of tools used to

Entry to 2-aminoprolines via electrochemical decarboxylative amidation of N‑acetylamino malonic acid monoesters

• Olesja Koleda,
• Janis Sadauskis,
• Darja Antonenko,
• Edvards Janis Treijs,
• Raivis Davis Steberis and
• Edgars Suna

Beilstein J. Org. Chem. 2025, 21, 630–638, doi:10.3762/bjoc.21.50

• -disubstituted piperidine-containing amino acid subunits. Likewise, a cyano-substituted cyclic aminal is a core structural unit of the fibroblast activation protein inhibitor 5 [3] (Figure 1). The widespread use of non-proteinogenic cyclic amino acids in drug discovery justifies both the design of new analogs

Photocatalyzed elaboration of antibody-based bioconjugates

• Marine Le Stum,
• Eugénie Romero and
• Gary A. Molander

Beilstein J. Org. Chem. 2025, 21, 616–629, doi:10.3762/bjoc.21.49

• decision-making [6][7]. Antibody–oligonucleotide conjugates, antibody–enzyme conjugates, antibody–polymer conjugates, antibody–nanomaterial conjugates, antibody–catalyst conjugates, and antibodies involved in protein degradation also play critical roles in biomedical research and therapies [2]. In whatever

• additionally generate an undesirable new stereocenter [26][27]. Few methods have been developed for the functionalization of tyrosine (Tyr) and tryptophan (Trp). With a low abundance (≈3%) in proteins, Tyr modifications are widely recognized for their ability to profoundly impact protein properties and

• different molecules, such as a drug and a targeting moiety. This technique has been shown to be useful in applications such as cell labeling, protein–protein interactions, and photoradiosynthesis of bioconjugates, but the most important challenge remains the lack of specificity to target one amino acid, and

Synthesis of N-acetyl diazocine derivatives via cross-coupling reaction

• Thomas Brandt,
• Pascal Lentes,
• Jeremy Rudtke,
• Michael Hösgen,
• Christian Näther and
• Rainer Herges

Beilstein J. Org. Chem. 2025, 21, 490–499, doi:10.3762/bjoc.21.36

• accumulation in the environment after excretion [1][6][7]. These superior properties of diazocines have been exploited in several applications such as the control of protein folding by implementation as cross-linkers between protein side chains [8] or in peptide backbones [9], as photoswitchable

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

• transcription or translation of the mRNA and results in altered transcript and/or protein levels [5]. In recent years, there has been a growing interest in the modification of preQ1. preQ1 derivatives, preQ1 analogs and mimics of preQ1 have greatly expanded our understanding of preQ1-binding biomolecules, such

• preQ1 congeners into oligonucleotide strands at specific recognition sites. In addition, the potential of modified preQ1 for protein enzyme-independent RNA labeling has also been demonstrated [12][17]. In a recent study [4], sequence-specific RNA–small molecule crosslinking (Scheme 1B) was achieved in

• our research program to tailor non-covalent RNA–small molecule ligands to their covalent counterparts. While “covalent drugs” have become a leading principle in medicinal chemistry in the “protein world” [35][36] – approximately 30% of all FDA-approved drugs form a covalent bond with their target

Identification and removal of a cryptic impurity in pomalidomide-PEG based PROTAC

• Bingnan Wang,
• Yong Lu and
• Chuo Chen

Beilstein J. Org. Chem. 2025, 21, 407–411, doi:10.3762/bjoc.21.28

• Bingnan Wang Yong Lu Chuo Chen Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Boulevard, Dallas, TX 75390-9038, USA 10.3762/bjoc.21.28 Abstract Chemically induced dimerization is a powerful tool for studying protein function, wherein the IMiD (the “immunomodulatory

• drug”) class of PROTAC molecules with a PEG linker is frequently used to promote targeted protein degradation. The standard protocol for their synthesis involves nucleophilic aromatic substitution of 4-fluorothalidomide with a PEG-amine. We report herein the identification of a commonly ignored

• contamination. Keywords: glutarimide; IMiD; impurity; nucleophilic acyl substitution; PROTAC; Introduction Targeted protein degradation capitalizing on the concept of chemically induced dimerization has emerged as a new therapeutic approach recently [1]. In particular, the modularity of proteolysis targeting

Synthesis, characterization, antimicrobial, cytotoxic and carbonic anhydrase inhibition activities of multifunctional pyrazolo-1,2-benzothiazine acetamides

• Ayesha Saeed,
• Shahana Ehsan,
• Muhammad Zia-ur-Rehman,
• Erin M. Marshall,
• Sandra Loesgen,
• Abdus Saleem,
• Simone Giovannuzzi and
• Claudiu T. Supuran

Beilstein J. Org. Chem. 2025, 21, 348–357, doi:10.3762/bjoc.21.25

• evolves [3]. Complex chemical scaffolds with more than one protein-engaging functionality in a single molecule are advantageous for selectivity. This concept of synergistic compounds and complex chemical interactions helps to boost biological activity and prolongs the emergence of resistance in pathogens

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

• Information File 1), it is likely that the activity of farinosones D (1) and A (2) does not interfere with the factors essential for fibronectin binding, particularly the fibronectin-binding proteins such as fibronectin binding protein (FnBPA and B) [18]. FnBPs are adhesions and are known to play a key role

Synthesis of disulfides and 3-sulfenylchromones from sodium sulfinates catalyzed by TBAI

• Zhenlei Zhang,
• Ying Wang,
• Xingxing Pan,
• Manqi Zhang,
• Wei Zhao,
• Meng Li and
• Hao Zhang

Beilstein J. Org. Chem. 2025, 21, 253–261, doi:10.3762/bjoc.21.17

• groups in organic synthesis [1][2][3][4]. In chemistry and biology, disulfide bonds play crucial roles in protein folding and stabilization [5][6][7][8] and in the rubber industry, they are used to link different polymer chains [9][10]. The disulfide bond backbone is commonly used as a linker for

Chemical glycobiology

• Elisa Fadda,
• Rachel Hevey,
• Benjamin Schumann and
• Ulrika Westerlind

Beilstein J. Org. Chem. 2025, 21, 8–9, doi:10.3762/bjoc.21.2

• certainly by choice, but also by necessity. It is difficult to convey to non-glycoscientists how we still struggle with challenges that have been solved years or decades ago for proteins and nucleic acids. When molecular cloning and recombinant protein production became routine, these technologies were not

• in the glycosciences. A key aspect is the modelling of protein–glycan interactions. Marcisz et al. study the power of umbrella sampling in distinguishing the interactions between different glycosaminoglycans and their receptors [14]. Nieto-Fabregat et al. provide a detailed overview on computational

Synthesis of extended fluorinated tripeptides based on the tetrahydropyridazine scaffold

• Thierry Milcent,
• Pascal Retailleau,
• Benoit Crousse and
• Sandrine Ongeri

Beilstein J. Org. Chem. 2024, 20, 3174–3181, doi:10.3762/bjoc.20.262

• ; Introduction The synthesis of molecules capable of mimicking the various secondary structures and key functions of proteins is a major challenge in medicinal chemistry, especially in the fields of protein–protein interactions [1][2]. Accordingly, the incorporation of heterocyclic amino acids into peptides

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

• antagonist of the N-methyl-ᴅ-aspartate (NMDA) receptor to regulate excessive glutamate stimulation [27]. The β-amyloid hypothesis for AD is based on the formation of senile plaques, which are formed after the accumulation of insoluble aggregates of β-amyloid protein, primarily Aβ-42, in the brain. The gene

• for amyloid precursor protein (APP), found on chromosome 21, undergoes a mutation that causes the production of Aβ-42 instead of Aβ-40. APP, a transmembrane protein, is typically cleaved by α-secretase and γ-secretase, which leads to the formation of soluble Aβ-40. However, when cleaved by β-secretase

• and γ-secretase, it produces Aβ-42. This form misfolds, leading to the formation of insoluble protein aggregates known as senile plaques, causing toxicity [28][29]. Oxidative stress occurs when there is an imbalance between prooxidants and antioxidants in the body, leading to damage in various

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

• protein sequencing by Edman degradation used to be standard practice in studying proteins but nowadays is rarely performed [39]. This is because the rules of transcription and translation are understood well enough for the sequence of a protein (its primary structure) to be predicted based on the

• recognizes and activates a specific substrate BB. Notably, the BBs are in most cases amino acids, wherein a much broader variety are used in NRP biosynthesis than the 20 canonical amino acids used in protein biosynthesis [52]. The modules are usually arranged co-linearly to the BGC sequence, which makes

• ]. It is unlikely that a Syn-BNP is able to target a specific protein or pathway, unless it in fact recapitulated key structural feature(s) of a NRP. These observations are a testament to the feasibility of this approach. This approach has also been applied to focus on NRPs with particular physical

Recent advances in transition-metal-free arylation reactions involving hypervalent iodine salts

• Ritu Mamgain,
• Kokila Sakthivel and
• Fateh V. Singh

Beilstein J. Org. Chem. 2024, 20, 2891–2920, doi:10.3762/bjoc.20.243

• ) [91]. This method manifests the synthesis of stable thioether-linked synthetic conjugates 93 and 96 displaying its efficacy via the alteration of the affibody zEGFR and the histone protein H2A. The procedure involved synthesizing the diaryliodonium salt and appraising the proficiency of oxime ligation

• chemistry on the histone H2A protein. The protein was demonstrated as the T120C mutant via site-directed mutagenesis in Escherichia coli and decontaminated by HPLC. A notable reconciliation was changing the aqueous buffer from HEPES to phosphate owing to side-product generation during the arylation in HEPES

• protein conjugate was effectively done with various hydroxylamines with the assistance of the nucleophilic catalyst 5-methoxyanthranilic acid. The resultant histone protein conjugates were functionalized with TAMRA, biotin and the cell-penetrating peptide 'penetratin' through oxime ligation, achieving

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

• controlled by such protein kinases. Therefore, the investigation of the influence of drugs on protein kinases plays an important role in current medicinal chemistry. Indigo naturalis is a traditional drug, derived from indigo plants, which has been used in China for centuries and also more recently against

• entirely cancelled by antioxidative pretreatment and cancer cell viability and proliferation were fully regenerated. Complete activation of cascades of caspases-3, -4, -6, -7, -8, and -9, loss of mitochondrial membrane potential, activation of proapoptotic PKCδ (protein kinase C delta), and inhibition of

Synthesis and antimycotic activity of new derivatives of imidazo[1,2-a]pyrimidines

• Dmitriy Yu. Vandyshev,
• Daria A. Mangusheva,
• Khidmet S. Shikhaliev,
• Kirill A. Scherbakov,
• Oleg N. Burov,
• Alexander D. Zagrebaev,
• Tatiana N. Khmelevskaya,
• Alexey S. Trenin and
• Fedor I. Zubkov

Beilstein J. Org. Chem. 2024, 20, 2806–2817, doi:10.3762/bjoc.20.236

• fingerprints (IFP) between the docking ligands and the protein shows that, similar to the reference ligand voriconazole, the compounds interact with the protein through hydrophobic interactions with hydrophobic residues of the protein and the formation of coordination bonds with the haem iron (Table 3). At the

• ) Superposition of docked compounds 4a–e and 5e in a CYP51 ACb. aThe amino acid residues of the protein are colored green, compound 4e is colored gold and the haem is colored grey. The heterocyclic nitrogen of compound 5e appears to be orientated towards iron and is located 2.8 Å away from it, which may indicate

• –protein interactions for voriconazole and compounds selected during docking.a Supporting Information Supporting Information File 14: General reaction procedures, compound characterization data, copies of NMR and mass spectra for all new products. Acknowledgements The research results were partially

Synthesis of fluoroalkenes and fluoroenynes via cross-coupling reactions using novel multihalogenated vinyl ethers

• Yukiko Karuo,
• Keita Hirata,
• Atsushi Tarui,
• Kazuyuki Sato,
• Kentaro Kawai and
• Masaaki Omote

Beilstein J. Org. Chem. 2024, 20, 2691–2703, doi:10.3762/bjoc.20.226

• fact, several inhibitors of the β-site amyloyd β A4 precursor protein cleaving enzyme (BACE1), which is involved in the production of β-amyloid, and fluoroalkene analogs of dipeptidyl peptidase-4 inhibitors have previously been reported [2][3]. These inhibitors possess higher drug efficacies than their

Applications of microscopy and small angle scattering techniques for the characterisation of supramolecular gels

• Connor R. M. MacDonald and
• Emily R. Draper

Beilstein J. Org. Chem. 2024, 20, 2608–2634, doi:10.3762/bjoc.20.220

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

• provide unprecedented depth of proteome coverage and the possibility to detect desired modified peptides with high sensitivity. The chemical ‘linker’ connecting an active compound–protein conjugate with a detection tag is the critical component of all chemical proteomic workflows. In this review, we

• disease [2][3]. In parallel, mass spectrometry (MS) has been crucial in many areas centered around the characterization of NPs [4]. First to annotate their often complex structures using diverse fragmentation techniques [4]. Nowadays, MS is applied for the identification of NPs’ cellular protein targets

• the desired protein coverage and robustness. Still, the critical part of the process starts with the careful design of a NP analogue and selection of the proper biological system, which may include animal models, 3D tissue-organoids, or 2D cell culture. Depending on the project aim, which typically

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

• nucleotides and amino acids, as well as energy molecules, salts, buffer, etc., are added. After successful protein synthesis, further substrates can be added for an enzyme activity assay. Although mimicking of cell-like conditions is an approach for optimization, the physical and chemical properties of CFPS

• 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

Natural resorcylic lactones derived from alternariol

• Joachim Podlech

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

• isolated. Nevertheless, alternariol sulfates were isolated from Alternaria sp. and alternariol-9-O-sulfate (14) turned out to be active against 23 protein kinases with IC50 values ranging from 0.22 to 8.4 µg/mL and to be cytotoxic against L5178Y cells (EC50: 4.5 µg/mL) [147]. The sulfated 9-O

• ] and Alternaria sp. [28][47][154] (Figure 8). It showed antioxidant activity with an IC50 value of 42.8 μM [153], inhibited about 90% of iNOS (inducible nitric oxide synthase) expression when applied at 20 μM, decreased the protein expression levels of pro-inflammatory cytokines (tumor necrosis factor

• -α, interleukin-6, and monocyte chemotactic protein 1), and reduced the production of NO as low as 10 μM in LPS-induced RAW264.7 cells [154]. Biosynthetic metabolization of alternariol and its 9-O-methyl ether is predominantly started with a hydroxylation in 4-position (c.f., chapter on biosynthesis