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

Cage-like microstructures via sequential Ugi reactions in aqueous emulsions

• Rita S. Alqubelat,
• Yaroslava A. Menzorova and
• Maxim A. Mironov

Beilstein J. Org. Chem. 2024, 20, 2078–2083, doi:10.3762/bjoc.20.179

• substances [7]. A particularly interesting area is the use of colloidosomes to model processes in living cells and produce artificial protocells [8][9]. The enlargement of pores on the surface of colloidosomes leads to structures that resemble microscopic cages [10]. Obtaining such cage-like structures is

Allostreptopyrroles A–E, β-alkylpyrrole derivatives from an actinomycete Allostreptomyces sp. RD068384

• Marwa Elsbaey,
• Naoya Oku,
• Mohamed S. A. Abdel-Mottaleb and
• Yasuhiro Igarashi

Beilstein J. Org. Chem. 2024, 20, 1981–1987, doi:10.3762/bjoc.20.174

• by formyl and carboxyl functionalities. Compounds 1, 4, and 5 showed cytotoxicity against Kasumi-1 human acute myeloblastic leukemia cells with IC50 values of 103, 105, and 105 μM, respectively, which are less active than the anticancer agent cisplatin, with an IC50 value of 70 μM. Keywords

• cytotoxicity against Kasumi-1 human acute myeloblastic leukemia cells with IC50 values of 103, 105, and 105 while 2 and 3 were less active with IC50 values of 200 and 333 μM, respectively. Under the same experimental conditions, cisplatin, a positive control, inhibited the cell growth with an IC50 value of 70

A new platform for the synthesis of diketopyrrolopyrrole derivatives via nucleophilic aromatic substitution reactions

• Vitor A. S. Almodovar and
• Augusto C. Tomé

Beilstein J. Org. Chem. 2024, 20, 1933–1939, doi:10.3762/bjoc.20.169

• used in a wide range of applications, namely as organic semiconductors [8], acceptors for organic solar cells [9][10], as fluorescent probes [11][12][13], or as photosensitizers for photodynamic therapy and antimicrobial photodynamic therapy [14][15][16][17]. DPP derivatives with improved performance

Solvent-dependent chemoselective synthesis of different isoquinolinones mediated by the hypervalent iodine(III) reagent PISA

• Ze-Nan Hu,
• Yan-Hui Wang,
• Jia-Bing Wu,
• Ze Chen,
• Dou Hong and
• Chi Zhang

Beilstein J. Org. Chem. 2024, 20, 1914–1921, doi:10.3762/bjoc.20.167

• activity and thus block cancer formation [2]. Alangiumkaloids A, an isoquinolinone alkaloid isolated from Alangium salviiforlium, was reported to exhibit cytotoxic activity against cancer cells [3]. In 2018, duvelisib, a dual inhibitor of phosphoinositide-3 kinases, was firstly approved by the FDA for the

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

• , commercial compound 1 (Scheme 2) represents a rescaffolding exercise to pyridine retaining low inhibitory activity although it was found toxic in in vitro assays on a human T-cell line and PBMCs (periferal blood mononuclear cells). The derivatives (R)-2 and (S)-2 were elaborated by Berger et al. [7] in the

• acid (46). The major source of histamine are mast cells, although it is additionally biosynthesized in basophils, other immune cells, and tissues like intestinal mucosa, skin, or the heart [45][48]. Histamine plays many pivotal roles in the onset of allergies via Th2 cytokine secretion and inhibition

• of Th1 cytokine, leukotriene and chemokines release, or IL-6 induction. Histamine targets histamine receptors H1–4, triggering pro-inflammatory or anti-inflammatory events depending on the receptor type and cells involved [45][49]. Histamine also plays a critical role in both vertebrates and

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

• CloM1 and CloM2 with the CylM enzyme (PDB code: 5DZT). For the structural alignment of CloPt1 and CloPt2, the characterized protein PCAT1 (PDB code: 3QF4) was analyzed. Gene expression in E. coli and purification of CloA1 and CloA2 precursor peptides and C39 peptidase domain E. coli NiCO21 (DE3) cells

• 0.8. Cultures were incubated for 14 h, at 200 rpm, at 18 °C. Subsequently, cells were centrifuged at 10,000 rpm for 30 min at 4 °C. The resulting cell pellets were resuspended in 20 mL of LanA starting buffer (20 mM Tris pH 7.5, 500 mM KCl, 10% glycerol) and lysed by sonication (4.0 seconds on, 10

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

• 30 were obtained in moderate yields (ranging from 29% to 50%, Scheme 9) and were tested as anti-inflammatory drugs in RAW 264.7 cells and as inhibitors of rat ear edema. Unfortunately, the tested compounds exhibited weak activity in all assays. Khripach et al. reported a three-step sequence for the

• . Chromatographic purification was not required post-reaction. Some spiro products exhibited high binding affinity towards DNA, while others showed good cytotoxicity against different cancer cells (A545, MCF-7, HeLa, HL-60, SW480, HepG2, HT-29, and A549) with IC50 values within the micromolar range (2.18–18.54 µM

• synthesized compounds were evaluated for their DNA binding properties and screened for cytotoxicity against leukemia cancer cells (Jurkat), demonstrating IC50 values in the micromolar range (14.2 to 36.5 µM). Importantly, these derivatives exhibited minimal toxicity toward normal cells (PBMCs). Furthermore

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

• synthesized 44 and 47 with cultured M. alba cells. The formation of both diene 48 and DA adduct 3 were observed, indicating that M. alba cells harbor the key enzymes MaMO and MaDA. Based on these results, synthetic analogs of intermediate 44 were designed and exposed to the M. alba cells to explore the

• subsequently overexpressed in insect cells and purified as soluble proteins, culminating in the elucidation of the X-ray crystallographic structure of MaDA (Scheme 5B, PDB: 6JQH). With these key enzymes in hand, Lei and co-workers conducted a chemo-enzymatic total synthesis of 3 and related natural products

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

• 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

• member of the channel-forming, cytotoxic proteusins. It is biosynthesised by Microvirgula aerodenitrificans. Like polytheonamide B, aeronamide A shows cytotoxic activity against HeLa cells, with an IC50 of 1.48 nM. AerE, the PoyE homologue, installs five methylations on the amides of Asn25, Asn31, Asn37

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

• agarase was also reported from the same bacterium [27]. The recombinant enzyme (rAgaO) was expressed in B. subtilis cells to demonstrate that this enzyme was an endo-type β-agarase and degraded agarose to neoagarohexaose as the main product [27]. The enzyme rAgaO represents the first and only report on

• Gram-positive bacteria Kocuria rhizophila and S. aureus, Gram-negative bacterium Tenacibaculum maritimum, and a panel of fungi. These molecules also demonstrated moderate cytotoxicity against P388 murine leukemia cells. The bisindole alkaloid violacein (24, Figure 8) was isolated and characterized from

New triazinephosphonate dopants for Nafion proton exchange membranes (PEM)

• Fátima C. Teixeira,
• António P. S. Teixeira and
• C. M. Rangel

Beilstein J. Org. Chem. 2024, 20, 1623–1634, doi:10.3762/bjoc.20.145

• . Romão Ramalho, 59, 7000-671 Évora, Portugal 10.3762/bjoc.20.145 Abstract A new paradigm for energy is underway demanding decarbonized energy systems. Some of them rely on emerging electrochemical devices, crucial in hydrogen technologies, including fuel cells, CO2 and water electrolysers, whose

• N115, in the same experimental conditions. The Nafion-doped membrane with compound TP2 with a 1.0 wt % loading showed the highest proton conductivity with 84 mS·cm−1. Keywords: electrolyser; fuel cells; Nafion-modified membranes; phosphonates; proton exchange membranes; triazine; Introduction

• exchange membrane devices [5][6], such as proton exchange membrane fuel cells (PEMFCs) [3][7][8][9], due to their high-power density and high power-to-weight ratio, and CO2 electrolysers, which can reduce the polluting gas CO2 and produce syngas from the co-electrolysis of CO2 and water [10][11], or water

Supramolecular assemblies of amphiphilic donor–acceptor Stenhouse adducts as macroscopic soft scaffolds

• Ka-Lung Hung,
• Leong-Hung Cheung,
• Yikun Ren,
• Ming-Hin Chau,
• Yan-Yi Lam,
• Takashi Kajitani and
• Franco King-Chi Leung

Beilstein J. Org. Chem. 2024, 20, 1590–1603, doi:10.3762/bjoc.20.142

• functionalized with photoresponsive and photoabsorbing functional motifs, serving as the counterpart of natural photosystems. This allowed to construct smart materials that harvest light energy, e.g., solar cells, photosensitizers, and photochromic materials [1][2][3][4]. Supramolecular assemblies are commonly

• prepared by ejecting 5.0 wt % DAn solutions onto a bioinert glass-bottomed Petri dish by the shear-flow method, rinsing with PBS, and incubating with human-bone-marrow-derived mesenchymal stem cells (hBM-MSCs) at 37 °C and 5% CO2 for 3 days. hBM-MSCs have demonstrated importance in controlled

• differentiations and clinical translations. The DA11 scaffold remained intact after incubation at 37 °C, while the hBM-MSCs cells grew and attached onto the scaffold surface (Figure 6a and Figure 6b). However, the structural properties of the macroscopic soft DA11 scaffold could not be transferred to the attached

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

• ] or to mannosyl azobenzene-modified human cells [21] through photoswitching the orientation of the attached mannoside [22]. Photoswitchable glycooligomers [23] or glycodendrimers [24] have been investigated for the inhibition of PA lectin PA-IL or LecA and LecB. A variation of the IC50 value by a

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

• seven analogs for cytotoxicity against human colon carcinoma HCT-116 cells. Unfortunately, none of the compounds up to 10 μM showed any activity when tested in MTT-based cell viability assays. Conclusion Eunicellane diterpenoids have been known for over 50 years, but it was not until recently that their

Sustainable tandem acylation/Diels–Alder reaction toward versatile tricyclic epoxyisoindole-7-carboxylic acids in renewable green solvents

• Ayhan Yıldırım

Beilstein J. Org. Chem. 2024, 20, 1308–1319, doi:10.3762/bjoc.20.114

• oligopeptidase inhibitory activity in human cells [117]. The solvent mixture used to precipitate the product was removed from the filtrate using a rotary evaporator and it was found that the used bio-based solvents could be recovered in a near quantitative amount for reuse. The recovered SSO solvent was reused

Synthesis of indano[60]fullerene thioketone and its application in organic solar cells

• Yong-Chang Zhai,
• Shimon Oiwa,
• Shinobu Aoyagi,
• Shohei Ohno,
• Tsubasa Mikie,
• Jun-Zhuo Wang,
• Hirofumi Amada,
• Koki Yamanaka,
• Kazuhira Miwa,
• Naoyuki Imai,
• Takeshi Igarashi,
• Itaru Osaka and
• Yutaka Matsuo

Beilstein J. Org. Chem. 2024, 20, 1270–1277, doi:10.3762/bjoc.20.109

• -withdrawing substituents. Computational studies with density functional theory revealed the unique vibrations of the thioketone group in FIDS. The molecular structure of FIDS was confirmed by single-crystal X-ray analysis. Bulk heterojunction organic solar cells using three evaporable fullerene derivatives

• (FIDO, FIDS, C60) as electron-acceptors were compared, and the open-circuit voltage with FIDS was 0.16 V higher than that with C60. Keywords: C60; evaporable fullerene derivatives; organic photovoltaics; organic solar cells; thioketone; Introduction Fullerene is a carbon allotrope that has attracted

• improving their thermal stability, and more specifically, of designing evaporable fullerene derivatives [16][17][18]. Recently, we reported on perovskite solar cells fabricated with indano[60]fullerene ketone (FIDO), which was synthesized through fullerene cation chemistry. These cells demonstrated long

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

• . Both plasmids were confirmed by sequencing and transformed into E. coli BL21(DE3). Protein overproduction was induced with 0.1 mM isopropyl β-ᴅ-thiogalactopyranoside at 16 °C for 15 h. Cells were collected by centrifugation (8,000g, 15 min) at 4 °C. The pellets were resuspended in ice-cold 50 mM 3-(N

• -morpholino)propanesulfonic acid (MOPS) buffer (pH 7.5), and the cells were disrupted by ultrasonication to obtain the cell extract. Cell debris was removed by centrifugation (14,000g, 15 min). The proteins were purified by Ni-NTA agarose chromatography, desalted, and concentrated by centrifugation (8,000g

Two-fold addition reaction of silylene to C₆₀: structural and electronic properties of a bis-adduct

• Masahiro Kako,
• Masato Kai,
• Masanori Yasui,
• Michio Yamada,
• Yutaka Maeda and
• Takeshi Akasaka

Beilstein J. Org. Chem. 2024, 20, 1179–1188, doi:10.3762/bjoc.20.100

• with excellent properties as organic photovoltaic materials [9][10][11][12][13][14]. Furthermore, regioisomerically pure bis-functionalized fullerenes function better as electron acceptors in organic thin-film solar cells than mixtures of the corresponding regioisomers do [12][13][14]. Therefore

Bismuth(III) triflate: an economical and environmentally friendly catalyst for the Nazarov reaction

• Manoel T. Rodrigues Jr.,
• Aline S. B. de Oliveira,
• Ralph C. Gomes,
• Amanda Soares Hirata,
• Lucas A. Zeoly,
• Hugo Santos,
• João Arantes,
• Catarina Sofia Mateus Reis-Silva,
• João Agostinho Machado-Neto,
• Leticia Veras Costa-Lotufo and
• Fernando Coelho

Beilstein J. Org. Chem. 2024, 20, 1167–1178, doi:10.3762/bjoc.20.99

• 3-aryl-1-indanones) in good to excellent yield. The reaction did not require additives and was insensitive to both air and moisture. Preliminary biological evaluation of some indanones showed a promising profile against some human cancer line cells. Keywords: bismuth; catalysis; heterocycles

• ] and the broad spectrum of biological activities. Among the five-membered ring compounds, we find indanone (1, Figure 1). Within the class of indanones, we can highlight some interesting compounds. For example, nakiterpiosinone (2), which inhibits the growth of P388 mouse leukemia cells with an average

• tumor lines, HCT116 (colon adenocarcinoma), MCF7 (breast adenocarcinoma), SK-MEL-28 (melanoma), and NB4 (acute leukemia) by methylthiazol tetrazolium (MTT) assay, as previously described [85]. Among the tested cells, NB4 cells were the most sensitive ones, with 7 compounds (10aa,bk and 11aa,ad,ae,dc,bj

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

• (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

• nuclear and mitochondrial genomes [15]. This A3-induced mutational activity is used by viruses and cancer cells to increase the rates of mutagenesis, which allows them to escape adaptive immune responses and become drug resistant [16][17][18][19][20], leading to poor clinical outcomes. A range of genetic

Structure–property relationships in dicyanopyrazinoquinoxalines and their hydrogen-bonding-capable dihydropyrazinoquinoxalinedione derivatives

• Tural N. Akhmedov,
• Ajeet Kumar,
• Daken J. Starkenburg,
• Kyle J. Chesney,
• Khalil A. Abboud,
• Novruz G. Akhmedov,
• Jiangeng Xue and
• Ronald K. Castellano

Beilstein J. Org. Chem. 2024, 20, 1037–1052, doi:10.3762/bjoc.20.92

• 40 μM solutions of the DCPQs and DPQDs on a Cary 100 Bio spectrophotometer using 1 cm quartz cells. All solvents were HPLC grade (purchased from Fisher) and stored over 4 Å molecular sieves. The absorption intensity at λmax was then plotted against the concentration in all cases to confirm, by

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

• ; nevertheless, some promiscuous TSs accept multiple prenyl substrates and produce various products. In nature, the biosynthesis of prenyl substrates may have subcellular locations, and the available types of prenyl substrates are limited, especially for noncanonical substrates in living cells. Therefore, the

Monitoring carbohydrate 3D structure quality with the Privateer database

• Jordan S. Dialpuri,
• Haroldas Bagdonas,
• Lucy C. Schofield,
• Phuong Thao Pham,
• Lou Holland and
• Jon Agirre

Beilstein J. Org. Chem. 2024, 20, 931–939, doi:10.3762/bjoc.20.83

• modelling of glycoproteins and protein–carbohydrate complexes is pivotal in understanding the complex biochemical interactions that affect the physiological function of cells [1]. Any mechanistic analysis done with finely grained approaches such as QM/MM [2] relies heavily on the correctness of the starting