Studying specificity in protein–glycosaminoglycan recognition with umbrella sampling

• Mateusz Marcisz,
• Sebastian Anila,
• Margrethe Gaardløs,
• Martin Zacharias and
• Sergey A. Samsonov

Beilstein J. Org. Chem. 2023, 19, 1933–1946, doi:10.3762/bjoc.19.144

• ) with three different proteins (basic fibroblast growth factor, acidic fibroblast growth factor, and cathepsin K). The main focus of our study was to evaluate whether the US approach is able to reproduce experimentally obtained structures, and how useful it can be for getting a deeper understanding of

• basic fibroblast growth factor (PDB ID: 1BFC, https://doi.org/10.2210/pdb1BFC/pdb, [12]), acidic fibroblast growth factor (PDB ID: 2AXM, https://doi.org/10.2210/pdb2AXM/pdb, [13]), and cathepsin K (PDB ID: 3C9E, https://doi.org/10.2210/pdb3C9E/pdb, [36], and PDB ID: 4N8W, https://doi.org/10.2210/pdb4N8W

• growth factor, which when pulled back into the binding site led to low binding energies but a drastically different pose (partially perpendicular) of the ligand. Energy contributions of sulfated and unsulfated parts of the GAG were investigated from per residue decomposition of MM/GBSA analysis (Table 2

Facile and diastereoselective arylation of the privileged 1,4-dihydroisoquinolin-3(2H)-one scaffold

• Dmitry Dar’in,
• Grigory Kantin,
• Alexander Bunev and
• Mikhail Krasavin

Beilstein J. Org. Chem. 2022, 18, 1070–1078, doi:10.3762/bjoc.18.109

• receptors 1 [3], AChE and BACE-1 inhibitor 2 [4], inhibitor of oncogenic p53-MDM2 protein–protein interaction 3 [5], positive allosteric modulator of ionotropic glutamate receptor NMDA-1 4 [6], insulin-like growth factor 1 receptor inhibitor 5 [7], and metabotropic glutamate receptor 7 modulator 6 [8

Structural basis for endoperoxide-forming oxygenases

• Takahiro Mori and
• Ikuro Abe

Beilstein J. Org. Chem. 2022, 18, 707–721, doi:10.3762/bjoc.18.71

• , including the epidermal growth factor (EGF) domain, the membrane binding domain, and the catalytic domain (Figure 2A) [46][47][48][49][50][51]. The catalytic domain possesses two active sites, the cyclooxygenase- and heme-dependent peroxidase-sites, which are physically separated. The peroxidase-site

Terpenoids from Glechoma hederacea var. longituba and their biological activities

• Dong Hyun Kim,
• Song Lim Ham,
• Zahra Khan,
• Sun Yeou Kim,
• Sang Un Choi,
• Chung Sub Kim and
• Kang Ro Lee

Beilstein J. Org. Chem. 2022, 18, 555–566, doi:10.3762/bjoc.18.58

• , nerve growth factor (NGF) secretion stimulation activities in C6 glioma cells, and cytotoxic activities against four human cancer cell lines (A549, SK-OV-3, SK-MEL-2, and HCT15). Compounds 2 and 5–7 exhibited inhibitory effects on the NO production with IC50 values of 52.21, 47.90, 61.61, and 25.35 μM

Efficient N-arylation of 4-chloroquinazolines en route to novel 4-anilinoquinazolines as potential anticancer agents

• Rodolfo H. V. Nishimura,
• Thiago dos Santos,
• Valter E. Murie,
• Luciana C. Furtado,
• Leticia V. Costa-Lotufo and
• Giuliano C. Clososki

Beilstein J. Org. Chem. 2021, 17, 2968–2975, doi:10.3762/bjoc.17.206

• malignant tumors, including platelet-derived growth factor receptor beta (PDGFR-β), vessel epidermal growth factor receptor (VEGFR-2), and epidermal growth factor receptor (EGFR) [5][6]. In addition, these compounds may act as vascular disrupting agents and tubulin polymerization inhibitors, contributing to

Cryogels: recent applications in 3D-bioprinting, injectable cryogels, drug delivery, and wound healing

• Luke O. Jones,
• Leah Williams,
• Tasmin Boam,
• Martin Kalmet,
• Chidubem Oguike and
• Fiona L. Hatton

Beilstein J. Org. Chem. 2021, 17, 2553–2569, doi:10.3762/bjoc.17.171

• -containing cryogels with nerve growth factor to promote the growth of neurite cells [81]. Through the use of template-assisted photopolymerisation, cylindrical cryogels were formed as high aspect ratios are desired for bridging across regions when whole neural pathways or large brain areas are targeted

• cryogels include fertilizers for agrochemical applications [103], peptides [104], proteins [37], and growth factors [81][105][106]. For example, Lee et al. reported the use of a double cryogel structure for the delivery of growth factor for enhanced bone regeneration [105]. 5.4. Cryogels in wound healing

Phenolic constituents from twigs of Aleurites fordii and their biological activities

• Kyoung Jin Park,
• Won Se Suh,
• Da Hye Yoon,
• Chung Sub Kim,
• Sun Yeou Kim and
• Kang Ro Lee

Beilstein J. Org. Chem. 2021, 17, 2329–2339, doi:10.3762/bjoc.17.151

• the MTT assay. Measurement of NGF secretion and cell viability assays. C6 glioma cells (Korean Cell Line Bank, Seoul, Republic of Korea) were used to measure the release of nerve growth factor (NGF) into the culture medium. The C6 cells were seeded onto 24-well plates at a density of 1 × 105 cells

A systems-based framework to computationally describe putative transcription factors and signaling pathways regulating glycan biosynthesis

• Theodore Groth,
• Rudiyanto Gunawan and
• Sriram Neelamegham

Beilstein J. Org. Chem. 2021, 17, 1712–1724, doi:10.3762/bjoc.17.119

• -like; ii) and iii) luminal A and luminal B, respectively, which overexpress estrogen receptor ESR1; iv) Her2+ tumors, which overexpress the epidermal growth factor receptor (ERBB); and v) basal (triple negative), which express neither ESR1 nor ERBB. Each of these subtypes has unique signaling

Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications

• Nikita Brodyagin,
• Martins Katkevics,
• Venubabu Kotikam,
• Christopher A. Ryan and
• Eriks Rozners

Beilstein J. Org. Chem. 2021, 17, 1641–1688, doi:10.3762/bjoc.17.116

• conjugate approach involved the conjugation of PNA to (ᴅ)-insulin-like growth factor 1 peptide (IGF1) that enabled the delivery to cells expressing the IGF1 receptor [166]. Later developments adopted CPPs derived from natural proteins (Figure 12A), such as penetratin (16-amino acid peptide from the third

Application of the Meerwein reaction of 1,4-benzoquinone to a metal-free synthesis of benzofuropyridine analogues

• Rashmi Singh,
• Tomas Horsten,
• Rashmi Prakash,
• Swapan Dey and
• Wim Dehaen

Beilstein J. Org. Chem. 2021, 17, 977–982, doi:10.3762/bjoc.17.79

• ][21]. These compounds are presumably multitargeting drugs because of the diverse applications as insulin-like growth factor 1 receptor (IGF-1R) inhibitors [22], selective GSK-3β inhibitors important in Alzheimer's disease [23][24], and cyclin-dependent kinase (CDK) inhibitors [25][26][27]. Lastly, the

Enhanced target cell specificity and uptake of lipid nanoparticles using RNA aptamers and peptides

• Roslyn M. Ray,
• Anders Højgaard Hansen,
• Maria Taskova,
• Bernhard Jandl,
• Jonas Hansen,
• Citra Soemardy,
• Kevin V. Morris and
• Kira Astakhova

Beilstein J. Org. Chem. 2021, 17, 891–907, doi:10.3762/bjoc.17.75

• –maleimide–PEG into their LNPs to target epidermal growth factor receptor (EGFR)-positive cancer cells. The authors showed an increased delivery of siRNAs and fluorescent quantum dot nanocrystals both in vitro and in EGFR-positive tumor xenografts in mice [48]. In 2020, Chandra et al. used a maleimide–PEG in

• their LNP formulation to functionalize LNPs with an aptamer specific for the human epidermal growth factor 2 (HER2) receptor. Therein, functionalized LNPs increased siRNA delivery and subsequent sensitivity of the doxorubicin-resistant HER2-positive breast cancer cell lines by ≈2-fold over LNPs with no

Synthesis and physicochemical evaluation of fluorinated lipopeptide precursors of ligands for microbubble targeting

• Masayori Hagimori,
• Estefanía E. Mendoza-Ortega and
• Marie Pierre Krafft

Beilstein J. Org. Chem. 2021, 17, 511–518, doi:10.3762/bjoc.17.45

• step by washing. The human epidermal growth factor receptor-2 (HER2)-targeting KCCYSL peptide–(SG)n–lipids in which the (SG)n (n = 3, 5, 7) sequence was used as a spacer allowed the reduction of the steric hindrance when compared to the conventional PEG2000 spacer [28]. Liposomes containing these

¹⁹F NMR as a tool in chemical biology

• Diana Gimenez,
• Aoife Phelan,
• Cormac D. Murphy and
• Steven L. Cobb

Beilstein J. Org. Chem. 2021, 17, 293–318, doi:10.3762/bjoc.17.28

Chemical constituents of Chaenomeles sinensis twigs and their biological activity

• Joon Min Cha,
• Dong Hyun Kim,
• Lalita Subedi,
• Zahra Khan,
• Sang Un Choi,
• Sun Yeou Kim and
• Chung Sub Kim

Beilstein J. Org. Chem. 2020, 16, 3078–3085, doi:10.3762/bjoc.16.257

• viability (54.9 ± 2.8%). The other phytochemicals displayed mild or no NO inhibitory effects (IC50 > 50 μM). Also, the potential neurotrophic effect of the isolated compounds 1–12 was evaluated by assessing their induction levels of nerve growth factor (NGF) secretion in C6 cells (Table 4). Among the tested

• synthase (NOS) inhibitor ʟ-NMMA was employed. Graded sodium nitrite solutions were utilized to determine the nitrite concentrations. An MTT assay was used for the cell viability assay. Nerve growth factor and cell viability assays. Analogous as described in [13]. The C6 glioma cells (Korean Cell Line Bank

Bipolenins K–N: New sesquiterpenoids from the fungal plant pathogen Bipolaris sorokiniana

• Chin-Soon Phan,
• Hang Li,
• Simon Kessler,
• Peter S. Solomon,
• Andrew M. Piggott and
• Yit-Heng Chooi

Beilstein J. Org. Chem. 2019, 15, 2020–2028, doi:10.3762/bjoc.15.198

• effects on cells infected with respiratory syncytial virus [22][23], induction of aerial mycelium formation in Fusarium culmorum [24], and as an inhibitor of ubiquinol-cytochrome c reductase binding protein, blocking mitochondrial ROS-mediated vascular endothelial growth factor receptor type 2 signalling

A novel three-component reaction between isocyanides, alcohols or thiols and elemental sulfur: a mild, catalyst-free approach towards O-thiocarbamates and dithiocarbamates

• András György Németh,
• György Miklós Keserű and
• Péter Ábrányi-Balogh

Beilstein J. Org. Chem. 2019, 15, 1523–1533, doi:10.3762/bjoc.15.155

• ), a new quinazolinone derivative in 40% yield (Scheme 6). Notably, these heterocycles are known for their use as antitumor [101], anticonvulsant [102] or epidermal growth factor receptor tyrosine kinase inhibitory agents [103], JNK inhibitors [104] or 5-HT3 antagonists [105]. Earlier, a one-pot

Stereo- and regioselective hydroboration of 1-exo-methylene pyranoses: discovery of aryltriazolylmethyl C-galactopyranosides as selective galectin-1 inhibitors

• Alexander Dahlqvist,
• Axel Furevi,
• Niklas Warlin,
• Hakon Leffler and
• Ulf J. Nilsson

Beilstein J. Org. Chem. 2019, 15, 1046–1060, doi:10.3762/bjoc.15.102

• -linked glycans on the cell surface. Surface proteins such as integrins [6][7], vascular endothelial growth factor receptor [8], and lysosome-associated membrane proteins [9] are known to be crosslinked by galectins, giving galectins a modulating role in cell adhesion, blood vessel growth and cellular

Natural and redesigned wasp venom peptides with selective antitumoral activity

• Marcelo D. T. Torres,
• Gislaine P. Andrade,
• Roseli H. Sato,
• Cibele N. Pedron,
• Tania M. Manieri,
• Giselle Cerchiaro,
• Anderson O. Ribeiro,
• Cesar de la Fuente-Nunez and
• Vani X. Oliveira Jr.

Beilstein J. Org. Chem. 2018, 14, 1693–1703, doi:10.3762/bjoc.14.144

• (ATCC) were maintained in a mixture of Dulbecco’s Modified Eagle’s Medium and Ham’s F12 nutrient mixture supplemented with 5% inactivated horse serum, 10 μg mL−1 insulin, 0.02 μg mL−1 human epidermal growth factor, 0.5 μg mL−1 hydrocortisone, 0.10 μg mL−1 choleric toxin, 100 U mL−1 penicillin, and 100

An overview of recent advances in duplex DNA recognition by small molecules

• Sayantan Bhaduri,
• Nihar Ranjan and
• Dev P. Arya

Beilstein J. Org. Chem. 2018, 14, 1051–1086, doi:10.3762/bjoc.14.93

• conjugate in order to target -545 to -539 base pairs of human transforming growth factor-beta1 (hTGF-beta1) promoter and diminish the gene and protein expression [78]. The authors went on to confirm that conjugate 19 binds its corresponding target sequence whereas the mismatch conjugate fails to recognize

• and antiangiogenic properties and concluded that these conjugates drastically reduced the cell viability, body weight, ascites volume and downregulated the formation of neovasculature and production of Vascular Endothelial Growth Factor (VEGF). They further reported another novel benzimidazole

On the design principles of peptide–drug conjugates for targeted drug delivery to the malignant tumor site

• Eirinaios I. Vrettos,
• Gábor Mező and
• Andreas G. Tzakos

Beilstein J. Org. Chem. 2018, 14, 930–954, doi:10.3762/bjoc.14.80

• ., pentetreotide (DTPA-d-Phe-c[Cys-Phe-d-Trp-Lys-Thr-Cys]-Thr-ol) [71]. Epidermal growth factor (EGF): Epidermal growth factor receptor (EGFR) is a transmembrane protein belonging to the ErbB family of receptor tyrosine kinases which consists of 4 structurally-related members: EGFR/HER1 (ErbB-1), HER2/neu (ErbB-2

A novel synthetic approach to hydroimidazo[1,5-b]pyridazines by the recyclization of itaconimides and HPLC–HRMS monitoring of the reaction pathway

• Dmitry Yu. Vandyshev,
• Khidmet S. Shikhaliev,
• Andrey Yu. Potapov,
• Michael Yu. Krysin,
• Fedor I. Zubkov and
• Lyudmila V. Sapronova

Beilstein J. Org. Chem. 2017, 13, 2561–2568, doi:10.3762/bjoc.13.252

• imidazo[1,5-a]pyrazine structure show inhibitory activity against kinases BTK [1], MEK [2], ACK1 [3], mTORC1(2) [4], c-Src [5], growth factor IGF-1R [6] and act as the antagonists of Hedgehog pathway dependent malignancies [7]. Imidazo[1,5-a]pyrimidines are inhibitors of the bone morphogenic protein [8

Oxidative dehydrogenation of C–C and C–N bonds: A convenient approach to access diverse (dihydro)heteroaromatic compounds

• Santanu Hati,
• Ulrike Holzgrabe and
• Subhabrata Sen

Beilstein J. Org. Chem. 2017, 13, 1670–1692, doi:10.3762/bjoc.13.162

• alkaloids such as luotonin A, tryptanthrin and many more (Figure 1) [11][12]. Quinazoline derivatives work as potential inhibitors of epidermal growth factor (EGF) and tyrosine kinase receptors and also display antibacterial, antitubercular and antiviral properties [13][14][15][16]. Last but not the least

Synthesis of acylhydrazino-peptomers, a new class of peptidomimetics, by consecutive Ugi and hydrazino-Ugi reactions

• Angélica de Fátima S. Barreto,
• Veronica Alves dos Santos and
• Carlos Kleber Z. Andrade

Beilstein J. Org. Chem. 2016, 12, 2865–2872, doi:10.3762/bjoc.12.285

• cancer therapeutics for being an antagonist of the vascular endothelial growth factor receptor 2 [13]; peptoid 2 is a ligand of the protooncogene Crk [14]; and peptoids 3 and 4 showed a high affinity for the α1-adrenergic and μ-specific opiate receptors [15], respectively (Figure 2). Unlike peptides, in

Simple activation by acid of latent Ru-NHC-based metathesis initiators bearing 8-quinolinolate co-ligands

• Julia Wappel,
• Roland C. Fischer,
• Luigi Cavallo,
• Christian Slugovc and
• Albert Poater

Beilstein J. Org. Chem. 2016, 12, 154–165, doi:10.3762/bjoc.12.17

• transforming growth factor-beta (TGF-beta) are associated with a broad variety of diseases and that TGF-beta is biologically inert when takes part of the complex that bears its corresponding peptide [34]. From this latter latent complex, most available immunoassays require controlled activation by acid to

• release the TGF-beta. On the other hand, myostatin belongs to the transforming growth factor 13 superfamily, known because it decreases the skeletal muscle mass. Bearing the fact that experiments have shown that myostatin activity is detected only after activation by acid [35], myostatin demonstrates to

Synthesis of cyclic N¹-pentylinosine phosphate, a new structurally reduced cADPR analogue with calcium-mobilizing activity on PC12 cells

• Ahmed Mahal,
• Stefano D’Errico,
• Nicola Borbone,
• Brunella Pinto,
• Agnese Secondo,
• Valeria Costantino,
• Valentina Tedeschi,
• Giorgia Oliviero,
• Vincenzo Piccialli and
• Gennaro Piccialli

Beilstein J. Org. Chem. 2015, 11, 2689–2695, doi:10.3762/bjoc.11.289

• (3, Figure 1) [34] showed interesting activity on the PC12 cell line previously differentiated with the Nerve Growth Factor (NGF) (data not previously published). Starting from these data, we here report the synthesis and the preliminary biological activity of the new cyclic N1-pentylinosine