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

• glycoprotein as pointed out by Crispin and collaborators [8], and more recently the realisation that high-energy ring conformations, a rare event in six-membered pyranosides, were present in ca. 15% of the N-glycan components of glycoproteins in the PDB [3]. Many of these findings originated the development of

• new resources, including services and databases [9][10][11][12][13], and standalone software [14][15][16][17][18]. Among these, the Privateer software package has been a key tool for glycoprotein and protein–carbohydrate complex validation: Privateer analyses the conformational plausibility of each

Chemoenzymatic synthesis of macrocyclic peptides and polyketides via thioesterase-catalyzed macrocyclization

• Senze Qiao,
• Zhongyu Cheng and
• Fuzhuo Li

Beilstein J. Org. Chem. 2024, 20, 721–733, doi:10.3762/bjoc.20.66

• exhibit a potent ability to induce tubulin depolymerization [77], originally isolated from the cyanobacteria Nostoc sp. ATCC 53789 [78]. Notably, the cryptophycins cannot serve as substrates for P-glycoprotein and multiple drug resistance-associated proteins, making them attractive as chemotherapeutic

Radical chemistry in polymer science: an overview and recent advances

• Zixiao Wang,
• Feichen Cui,
• Yang Sui and
• Jiajun Yan

Beilstein J. Org. Chem. 2023, 19, 1580–1603, doi:10.3762/bjoc.19.116

• glycoprotein (≈1–2%), laccase (≈0.2%), and stellacyanin (≈0.02%) [6][7]. Urushiol is the main active coating-forming ingredient of the resin. A typical urushiol is shown in Scheme 2. In a humid and warm environment, urushiol absorbs oxygen from air and is oxidized to a phenolic oxygen free radical under the

Anomeric 1,2,3-triazole-linked sialic acid derivatives show selective inhibition towards a bacterial neuraminidase over a trypanosome trans-sialidase

• Peterson de Andrade,
• Sanaz Ahmadipour and
• Robert A. Field

Beilstein J. Org. Chem. 2022, 18, 208–216, doi:10.3762/bjoc.18.24

• ) has also been introduced at C-2 of α-triazole-linked sialic acid derivatives modified at C-9 as ligands for the transmembrane glycoprotein CD22 [21]. In this sense, we have synthesised a small series of 1,2,3-triazole-linked sialic acid derivatives via copper-catalysed azide–alkyne cycloaddition

GlycoBioinformatics

• Kiyoko F. Aoki-Kinoshita,
• Frédérique Lisacek,
• Niclas Karlsson,
• Daniel Kolarich and
• Nicolle H. Packer

Beilstein J. Org. Chem. 2021, 17, 2726–2728, doi:10.3762/bjoc.17.184

• , type and linkage of glycoconjugate (e.g., N-linked, O-linked glycoprotein, glycolipid, proteoglycan), association with, and regulation of, expression in particular tissues or cell types, and interaction with biological surroundings. With this definition, it is obvious that glycobioinformatics is

The ethoxycarbonyl group as both activating and protective group in N-acyl-Pictet–Spengler reactions using methoxystyrenes. A short approach to racemic 1-benzyltetrahydroisoquinoline alkaloids

• Marco Keller,
• Karl Sauvageot-Witzku,
• Franz Geisslinger,
• Nicole Urban,
• Michael Schaefer,
• Karin Bartel and
• Franz Bracher

Beilstein J. Org. Chem. 2021, 17, 2716–2725, doi:10.3762/bjoc.17.183

• TPC2 cation channels and the tumor cell line VCR-R CEM, and did not exhibit P-glycoprotein blocking activity. But due to their free phenolic groups they can serve as valuable intermediates for novel derivatives addressing all of these targets, based on previous evidence for structure–activity

• . Interestingly, macrocyclic bisbenzylisoquinolines such as tetrandrine [48][49] and related alkaloids [50], have been reported to inhibit P‐glycoprotein (P-gp), a crucial factor of multidrug resistance in cancer. This is noteworthy as multidrug resistance is still a major problem in cancer therapy and no

• compounds 2a–f, 3a–c and 4 regarding their P-glycoprotein blocking potential. For that, we used the P-glycoprotein substrate calcein as reporter dye and analyzed intracellular calcein fluorescence of P-glycoprotein overexpressing VCR-R CEM cells by flow cytometry. An increase of the calcein-positive

Antiviral therapy in shrimp through plant virus VLP containing VP28 dsRNA against WSSV

• Santiago Ramos-Carreño,
• Ivone Giffard-Mena,
• Jose N. Zamudio-Ocadiz,
• Alfredo Nuñez-Rivera,
• Ricardo Valencia-Yañez,
• Jaime Ruiz-Garcia,
• Maria Teresa Viana and
• Ruben D. Cadena-Nava

Beilstein J. Org. Chem. 2021, 17, 1360–1373, doi:10.3762/bjoc.17.95

• ) encapsidates the dsRNA of 563 bp, are shown to silence the WSSV glycoprotein VP28 (dsRNAvp28). In experimental challenges in vivo, the VLPs- dsRNAvp28 protect shrimp against WSSV up to 40% by oral administration and 100% by IM. The novel research demonstrates that plant VLPs, which avoid zoonosis, can be

• entry, binding and assembly of the virion. Previous studies have shown that silencing these structural proteins in WSSV challenge assays, increases shrimp survival [10][11][17][18][19][20][21]. The VP28 glycoprotein plays an important role in systemic infection by interacting with cell membrane proteins

• , and it is one of the most abundant proteins along with VP26 (≈60%) in the external WSSV surface [21][22]. The RNAi trials using an intramuscular injection (IM) have shown that VP28 glycoprotein is the target of choice to block WSSV infection in shrimp [14][23][24]. However, RNAi intramuscular (IM

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

• LNPs that can cross the BBB, we developed and assessed two approaches. The first was centered on the BBB-penetrating trans-activator of transcription (Tat) peptide or the peptide T7, and the other on RNA aptamers targeted to glycoprotein gp160 from human immunodeficiency virus (HIV) or C-C chemokine

The preparation and properties of 1,1-difluorocyclopropane derivatives

• Kymbat S. Adekenova,
• Peter B. Wyatt and
• Sergazy M. Adekenov

Beilstein J. Org. Chem. 2021, 17, 245–272, doi:10.3762/bjoc.17.25

Supramolecular polymerization of sulfated dendritic peptide amphiphiles into multivalent L-selectin binders

• David Straßburger,
• Svenja Herziger,
• Katharina Huth,
• Moritz Urschbach,
• Rainer Haag and
• Pol Besenius

Beilstein J. Org. Chem. 2021, 17, 97–104, doi:10.3762/bjoc.17.10

• ] promotes the binding of ligands exhibiting a high local negative charge density, such as sulfotyrosinated P-selectin glycoprotein ligand-1 (PSGL-1) [23] or heparin [24]. A versatile synthetic ligand that takes advantage of binding to cationic target sites, is dendritic polyglycerol sulfate [25] (dPGS), due

One-pot multicomponent green Hantzsch synthesis of 1,2-dihydropyridine derivatives with antiproliferative activity

• Giovanna Bosica,
• Kaylie Demanuele,
• José M. Padrón and
• Adrián Puerta

Beilstein J. Org. Chem. 2020, 16, 2862–2869, doi:10.3762/bjoc.16.235

• the general procedure. Biological screening The 1,4-DHP scaffold displays an extensive range of biological activities, including reversing multidrug resistance (through the inhibition of the P-glycoprotein) [26] and antiproliferative effects on human cancer cell lines [27]. We wondered whether the

A consensus-based and readable extension of Linear Code for Reaction Rules (LiCoRR)

• Benjamin P. Kellman,
• Yujie Zhang,
• Emma Logomasini,
• Eric Meinhardt,
• Karla P. Godinez-Macias,
• Austin W. T. Chiang,
• James T. Sorrentino,
• Chenguang Liang,
• Bokan Bao,
• Yusen Zhou,
• Sachiko Akase,
• Isami Sogabe,
• Thukaa Kouka,
• Elizabeth A. Winzeler,
• Iain B. H. Wilson,
• Matthew P. Campbell,
• Sriram Neelamegham,
• Frederick J. Krambeck,
• Kiyoko F. Aoki-Kinoshita and
• Nathan E. Lewis

Beilstein J. Org. Chem. 2020, 16, 2645–2662, doi:10.3762/bjoc.16.215

• , cytoplasm (bacteria and archaea), or lysosome (degradation, Man-6-P dephosphorylation and lysosomal glycoprotein biosynthesis [33][34] or paucimannose recycling [35]), are important constraints on glycosylation [36], therefore, the addition of this information to the Linear Code reaction rules provides

• rule can be extended to glycopeptides providing a means of representing glycans directly embedded in a glycopeptide. “PEP(Gal[3S]b3(GNb6)AN)TIDE” would describe a trisaccharide O-glycan bound to the threonine of an eponymously named glycoprotein. Overall, the consensus in these representations centers

Comparative ligand structural analytics illustrated on variably glycosylated MUC1 antigen–antibody binding

• Christopher B. Barnett,
• Tharindu Senapathi and
• Kevin J. Naidoo

Beilstein J. Org. Chem. 2020, 16, 2540–2550, doi:10.3762/bjoc.16.206

• approach by investigating the in-silico binding of a peptide and glycopeptide epitope of the glycoprotein Mucin 1 (MUC1) binding with the antibody AR20.5. To study the binding, we performed molecular dynamics simulations using OpenMM and then used the Galaxy platform for data analysis. The same analysis

• under observation, could be readily applied to other binding problems as part of a general strategy in drug design or mechanistic analysis. Keywords: binding; conformation; Galaxy; glycoprotein; in silico; Introduction A typical sequence of events in research and discovery is noticing a critical

Leveraging glycomics data in glycoprotein 3D structure validation with Privateer

• Haroldas Bagdonas,
• Daniel Ungar and
• Jon Agirre

Beilstein J. Org. Chem. 2020, 16, 2523–2533, doi:10.3762/bjoc.16.204

• the validation of 3D glycoprotein structures. Keywords: electron cryomicroscopy; glycoinformatics; glycomics; Privateer; X-ray crystallography; Introduction Glycosylation-related processes are prevalent in life. The attachment of carbohydrates to macromolecules extends the capabilities of cells to

• virus uses the haemagglutinin glycoprotein to recognise and bind sialic acid decorations of human cells in the respiratory tract [7]. Glycosylation is also used by pathogens to evade the host’s immune system via glycan shields [8][9][10], and thereby to delay an immune response [11]. The structural

• and protein interactions [12]. Unfortunately, significant challenges have affected the determination of glycoprotein structures for decades and have had a detrimental impact on the quality and reliability of the produced models. Anomalies have been reported regarding carbohydrate nomenclature [13

Computational tools for drawing, building and displaying carbohydrates: a visual guide

• Kanhaya Lal,
• Rafael Bermeo and
• Serge Perez

Beilstein J. Org. Chem. 2020, 16, 2448–2468, doi:10.3762/bjoc.16.199

• GIF format. GLYCAM-web- Carbohydrate Builder can be used to prepare the system for MD simulation as it solvates the glycans and also generates the topology and coordinate files. In addition to its carbohydrate builder, Glycam-web consists of additional tools like glycoprotein builder and

GlypNirO: An automated workflow for quantitative N- and O-linked glycoproteomic data analysis

• Toan K. Phung,
• Cassandra L. Pegg and
• Benjamin L. Schulz

Beilstein J. Org. Chem. 2020, 16, 2127–2135, doi:10.3762/bjoc.16.180

• , and 93 increased and 67 decreased in HCC in non-depleted plasma (P < 0.05, Figure 2a and 2b). This analysis with GlypNirO of site-specific relative glycoform abundance confirmed that HCC was associated not only with changes in glycoprotein abundance in plasma, but with changes in the proportions of

• N271 and haptoglobin N184 (Figure 3a and 3b), with increased abundance of non-sialylated N-glycans at fibrinogen N78 (Figure 3c), and decreased abundance of trisialylated N-glycans at alpha-2-HS-glycoprotein N176 (Figure 3d). Together, this suggests an overall decrease in sialylation of N-glycans

• O-glycan on fibrinogen alpha chain G272GSTSYGTGSETESPR (Figure 5a). HCC patients showed a relative decrease in disialylated and an increase in monosialylated O-glycan abundance on both plasma protease C1 inhibitor V45AATVISK and histidine-rich glycoprotein S271STTKPPFKPHGSR (Figure 5b and 5c

Clustering and curation of electropherograms: an efficient method for analyzing large cohorts of capillary electrophoresis glycomic profiles for bioprocessing operations

• Ian Walsh,
• Matthew S. F. Choo,
• Sim Lyn Chiin,
• Amelia Mak,
• Shi Jie Tay,
• Pauline M. Rudd,
• Yang Yuansheng,
• Andre Choo,
• Ho Ying Swan and
• Terry Nguyen-Khuong

Beilstein J. Org. Chem. 2020, 16, 2087–2099, doi:10.3762/bjoc.16.176

• optimize bioprocessing and biologic quality. Conclusion Fluctuations of glycomic profiles are a result of environmental and biochemical pathways of the glycoprotein. Understanding these effects requires a high-throughput analytical technique whereby diverse glycomic profiles of the glycoprotein/s can be

• were made according to the manufacturer’s instructions. This protocol was adapted to a 96-well PCR plate. Two hundred (200 µL) of magnetic beads were used per 100 µg of glycoprotein. The magnetic bead storage solution was removed using a plate magnet. Antibodies of 100 µg in 10 µL (10 µg/µL) aliquots

• using UPLC-MS The supernatant was purified using Protein A HP SpinTrap (GE Healthcare). The purified glycoprotein obtained was buffer exchanged into water using a 10 kDa molecular weight cut-off filter (Merck Millipore) to eliminate any salts and nucleophiles that could interfere with the subsequent

Synthesis and conformational preferences of short analogues of antifreeze glycopeptides (AFGP)

• Małgorzata Urbańczyk,
• Michał Jewgiński,
• Joanna Krzciuk-Gula,
• Jerzy Góra,
• Rafał Latajka and
• Norbert Sewald

Beilstein J. Org. Chem. 2019, 15, 1581–1591, doi:10.3762/bjoc.15.162

• microscopic mechanism of ice–glycoprotein interaction is still unknown. Therefore, it is an interesting area for further research [3][10][11]. Some studies have highlighted the role of irreversible adsorption of AFGPs onto growing ice surface and incorporation of hydroxy groups of the disaccharide subunit

Lectins of Mycobacterium tuberculosis – rarely studied proteins

• Katharina Kolbe,
• Sri Kumar Veleti,
• Norbert Reiling and
• Thisbe K. Lindhorst

Beilstein J. Org. Chem. 2019, 15, 1–15, doi:10.3762/bjoc.15.1

• , using purified proteins, Alteri et al. detected laminin as a ligand for MTP [108]. While the exact structure recognized by MTP has yet to be determined, laminin is a glycoprotein and so it is conceivable that MTP binds to mono- or oligosaccharide constituents of this protein. Type IV pili Type IV pili

Protein–protein interactions in bacteria: a promising and challenging avenue towards the discovery of new antibiotics

• Laura Carro

Beilstein J. Org. Chem. 2018, 14, 2881–2896, doi:10.3762/bjoc.14.267

• disrupts the LFA-1/ICAM-1 interaction used for the treatment of dry eye disease [31][32], and tirofiban (6, Figure 2), a platelet glycoprotein IIb/IIIa inhibitor indicated in acute coronary syndrome [33]. In addition to small molecules, natural products have been shown to be able to modulate protein

Novel solid-phase strategy for the synthesis of ligand-targeted fluorescent-labelled chelating peptide conjugates as a theranostic tool for cancer

• Sagnik Sengupta,
• Mena Asha Krishnan,
• Premansh Dudhe,
• Ramesh B. Reddy,
• Bishnubasu Giri,
• Sudeshna Chattopadhyay and
• Venkatesh Chelvam

Beilstein J. Org. Chem. 2018, 14, 2665–2679, doi:10.3762/bjoc.14.244

• membrane antigen (PSMA) [7][8][9] and the folate receptor [10][11][12][13] are well characterized and most attractive cancer biomarkers present in primary and metastatic stages of prostate and ovarian cancers, respectively. PSMA belongs to a family of type II membrane bound glycoprotein over-expressed on

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

• utilization of paclitaxel are its high hydrophobicity, requiring suitable vehicles to effectively deliver it to tumor tissues, and the development of multidrug resistance due to the P-glycoprotein-mediated efflux [85][92]. Paclitaxel stabilizes microtubules by binding specifically to the beta-tubulin subunit

Synthesis and in vitro biochemical evaluation of oxime bond-linked daunorubicin–GnRH-III conjugates developed for targeted drug delivery

• Sabine Schuster,
• Beáta Biri-Kovács,
• Bálint Szeder,
• Viktor Farkas,
• László Buday,
• Zsuzsanna Szabó,
• Gábor Halmos and
• Gábor Mező

Beilstein J. Org. Chem. 2018, 14, 756–771, doi:10.3762/bjoc.14.64

• regulatory pituitary glycoprotein luteinizing hormone (LH) and follicle stimulating hormone (FSH) which act on the gonads and regulate the production of the sex steroids androgen and estrogen [2]. In the last decades a large number of synthetic GnRH-I-analogues has been designed with the purpose to interact

Carbohydrate inhibitors of cholera toxin

• Vajinder Kumar and
• W. Bruce Turnbull

Beilstein J. Org. Chem. 2018, 14, 484–498, doi:10.3762/bjoc.14.34

• spacing’s to maximize interactions with the target protein. Dynamic light scattering and analytical ultracentrifugation demonstrated that the glycoprotein formed a 1:1 complex with the target CTB protein and was highly effective as an inhibitor with an IC50 value of 104 pM. Multivalent inhibitors with more

Synthetic and semi-synthetic approaches to unprotected N-glycan oxazolines

• Antony J. Fairbanks

Beilstein J. Org. Chem. 2018, 14, 416–429, doi:10.3762/bjoc.14.30

• interconversions, and peracetylation were followed by conversion to the oxazoline, using TMSBr, BF3·Et2O and collidine, and finally deacetylation. It was found that the incorporated azide was tolerated by the ENGase enzyme (Endo A), and so a modified glycoprotein (RNase) was made by enzymatic attachment of this

• respect to total synthesis. Neither Kajihara nor others have yet to employ these routes to the production of N-glycan oxazolines. The soy bean approach Soy bean agglutinin is a glycoprotein decorated with high mannose glycans [96]. Isolation of soy bean agglutinin from unroasted soy bean flour is achieved