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Search for "antibodies" in Full Text gives 73 result(s) in Beilstein Journal of Organic Chemistry.
Beyond symmetric self-assembly and effective molarity: unlocking functional enzyme mimics with robust organic cages
Beilstein J. Org. Chem. 2025, 21, 421–443, doi:10.3762/bjoc.21.30
- enzyme dynamics. The wider history of supramolecular and cavity catalysis [3][13][15][16][17][18][19][21][48][49], and catalysis using confined transition-metal catalysts [50][51][52], dendrimers [53] or synzymes [54], micelles [55] or vesicles [56], catalytic antibodies [57][58][59] or molecularly
- fixed 2D orientations. Envious of the contemporary progress of catalytic antibodies, Rebek lamented the slow progress in these systems, concluding: if catalytically useful functionality can be introduced…[to the antibodies] …model systems such as ours may become the dinosaurs of the 1990s [108
Red light excitation: illuminating photocatalysis in a new spectrum
Beilstein J. Org. Chem. 2025, 21, 296–326, doi:10.3762/bjoc.21.22
Computational toolbox for the analysis of protein–glycan interactions
Beilstein J. Org. Chem. 2024, 20, 2084–2107, doi:10.3762/bjoc.20.180
- class of GBP is represented by anti-carbohydrate antibodies, that are generally produced by the host organism for example against bacterial, fungal, and viral carbohydrates [35]. Given the wide variety of biological processes influenced by the protein–glycan interplay, an increasing attention has been
- carbohydrates. It incorporates carbohydrate intrinsic (CHI) energy functions and explicit water to better handle glycosidic linkages and improve docking accuracy. When Vina-Carb was applied to antibodies, lectins, and carbohydrate binding modules (CBM), the success rates in predicting accurate binding modes
Methyltransferases from RiPP pathways: shaping the landscape of natural product chemistry
Beilstein J. Org. Chem. 2024, 20, 1652–1670, doi:10.3762/bjoc.20.147
- falls between small molecules and large biologicals such as antibodies. Small molecules typically weigh less than 900 Dalton (Da), while the molecular weight of large biologicals ranges from approximately 5,000 to 150,000 Da. Although some small RiPPs may be classified as small molecules, the majority
Introduction of a human- and keyboard-friendly N-glycan nomenclature
Beilstein J. Org. Chem. 2024, 20, 607–620, doi:10.3762/bjoc.20.53
- the following chapter. The “antibody glycan code” is a perfectly fine convention in the field of – surprise – antibodies, in particular recombinant IgGs, where G2F [62] stands for the therein relevant isomer A4A4F6 and not for any of the 40–50 possible other isobars [26]. The “Oxford code” and its
Elucidating the glycan-binding specificity and structure of Cucumis melo agglutinin, a new R-type lectin
Beilstein J. Org. Chem. 2024, 20, 306–320, doi:10.3762/bjoc.20.31
- lipid-linked glycans. Then the detecting solution composed of anti-polyHistidine (Sigma-Aldrich, Merck, SAB4200620) and biotin anti-mouse IgG (Sigma-Aldrich, Merck, B7264) antibodies (10 µg/mL, precomplexed in a ratio of 1:1) was overlaid onto the arrays for 1 h. The final detection was with a 30 min
Synthesis of ether lipids: natural compounds and analogues
Beilstein J. Org. Chem. 2023, 19, 1299–1369, doi:10.3762/bjoc.19.96
- noted that the design of new bioactive ELs is an alternative to others strategies (e.g., small molecules, antibodies) to modulate membrane proteins functions. Recent results from our group [41][42] and others renew the interest to develop new ether lipids with promising perspectives to address the
Non-peptide compounds from Kronopolites svenhedini (Verhoeff) and their antitumor and iNOS inhibitory activities
Beilstein J. Org. Chem. 2023, 19, 789–799, doi:10.3762/bjoc.19.59
- separated by 10% SDS-PAGE and transferred onto PVDF membranes. The membranes were blocked with 5% BSA and incubated with the indicated antibodies overnight at 4 °C. Following this, the membranes were incubated with horseradish peroxidase (HRP)-conjugated secondary antibody at room temperature. The ECL kit
Investigation of cationic ring-opening polymerization of 2-oxazolines in the “green” solvent dihydrolevoglucosenone
Beilstein J. Org. Chem. 2023, 19, 217–230, doi:10.3762/bjoc.19.21
- antibodies [10][11][12][13], anaphylaxis [14][15], and vacuolization [12], drives the search for alternatives [4][8]. POx have attracted the attention of scientists and companies in recent years as a promising material for pharmaceutical applications [16][17]. POx are obtained via cationic ring-opening
GlycoBioinformatics
Beilstein J. Org. Chem. 2021, 17, 2726–2728, doi:10.3762/bjoc.17.184
- article by Barnett et al. [2] uses molecular dynamics to show that O-linked glycosylation alters peptide conformation, which influences the binding of the peptides to antibodies, despite the fact that glycans are not directly involved in the binding. Another molecular modeling article by Fogarty et al. [3
Cryogels: recent applications in 3D-bioprinting, injectable cryogels, drug delivery, and wound healing
Beilstein J. Org. Chem. 2021, 17, 2553–2569, doi:10.3762/bjoc.17.171
- ., have shown similar effects as reported by Petrov et al. in 2007 [30] and 2009 [92]. More recently, cryogels have been used to tackle diseases such as cancer. Aliperta et al. have used cryogels in the sustained release of bispecific antibodies for cancer immunotherapy [93], combining stem cells with a
- biopolymeric cryogel DDS. Human mesenchymal stromal cells (MSCs) were gene-modified to secrete anti-CD33-anti-CD3 bispecific antibodies (bsAb) to be used for the treatment of acute myeloid leukaemia (AML). Macroporous star-shaped poly(ethylene glycol) (starPEG)-heparin cryogels were prepared by combining
Progress and challenges in the synthesis of sequence controlled polysaccharides
Beilstein J. Org. Chem. 2021, 17, 1981–2025, doi:10.3762/bjoc.17.129
- recognition by plant cell-wall antibodies. To avoid performing the challenging 1,2-cis glycosylation that would generate a mixture of anomers in AGA, the α(1–6) linkage between glucose and xylose was pre-installed in the disaccharide BB 16 (Scheme 3, highlighted in red) [104]. The orthogonal levulinoyl (Lev
- substitution. A collection of linear β(1–4)-ᴅ-xylan chains and with α(1–3)-ʟ-arabinofuranosyl branches was quickly assembled to identify the binding epitopes of monoclonal antibodies. These oligomers, together with other well-defined analogues obtained by chemoenzymatic synthesis, were converted to the
Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications
Beilstein J. Org. Chem. 2021, 17, 1641–1688, doi:10.3762/bjoc.17.116
Synthesis and physicochemical evaluation of fluorinated lipopeptide precursors of ligands for microbubble targeting
Beilstein J. Org. Chem. 2021, 17, 511–518, doi:10.3762/bjoc.17.45
- , which involves the use of targeting ligands, such as monoclonal antibodies, antibody fragments, proteins, peptides, and other small molecules, including vitamins and carbohydrates [7][8]. The targeting ligands are coupled to the surface of the carrier to selectively target tumor cells that overexpress a
- penetrating properties, such as the transactivator of the transcription (TAT) peptide. Moreover, peptides being smaller than the antibodies generally induce a lower immunogenicity [15][16][17]. Micro- and nanocarriers are often covered by poly(ethylene glycol) (PEG) stealth coatings that significantly enhance
Synthetic strategies of phosphonodepsipeptides
Beilstein J. Org. Chem. 2021, 17, 461–484, doi:10.3762/bjoc.17.41
- and phosphonate-linked analogues of naturally occurring peptides. They are more stable than phosphonopeptides and have been widely applied as enzyme inhibitors, haptens for the production of antibodies, biological agents, and prodrugs. The synthetic strategies towards phosphonodepsipeptides are
- than the corresponding phosphonopeptides because the phosphonate bond is more inert than a phopshonamidate bond. Phosphonodepsipeptides are widely used as enzyme inhibitors [6][7][8][9][10], haptens for inducing catalytic antibodies [11][12], and produgs [8][9][13]. They have potential applications as
- acids and hydroxy esters through phosphonochloridates as in situ-generated intermediates. To prepare an antigen to induce monoclonal catalytic antibodies capable of catalyzing peptide-bond formation reactions, the phosphonodepsidipeptide 39 was synthesized via the coupling of the hydroxy analog of
Semiautomated glycoproteomics data analysis workflow for maximized glycopeptide identification and reliable quantification
Beilstein J. Org. Chem. 2020, 16, 3038–3051, doi:10.3762/bjoc.16.253
- glycopeptide identification, curation, and quantification after RPLC separation and MS(/MS) detection. For this, a mix of the human plasma-enriched antibodies IgG and IgA was used as a representative glycoproteomics sample of moderate complexity. A similar approach can be applied to a more complex sample when
Comparative ligand structural analytics illustrated on variably glycosylated MUC1 antigen–antibody binding
Beilstein J. Org. Chem. 2020, 16, 2540–2550, doi:10.3762/bjoc.16.206
- between MUC1 and antibodies has received much attention, and the specificity of this interaction is of interest in improving the performance of these biomarker assays [12][13]. The extracellular domain of MUC1 contains a variable number of tandem repeats (VNTR). The VNTR region is comprised of a repeating
- . and others [14][16] provides a foundation for further investigation into the binding of glycopeptide antigens to antibodies using computational modeling. Molecular dynamics (MD) simulations and analysis thereof are a well-known ingredient of the in-silico process for mechanistic screening of
- glycopeptide fragment binding to antibodies. In this work, the peptide only antigen (Ala-Pro-Asp-Thr-Arg-Pro-Ala-Pro, APDTRPAP) and the Tn glycosylated antigen (APDT(Tn)RPAP) are considered in solution and complex with the AR20.5 antibody. The Tn-antigen is of interest as it is often found upregulated in
The B & B approach: Ball-milling conjugation of dextran with phenylboronic acid (PBA)-functionalized BODIPY
Beilstein J. Org. Chem. 2020, 16, 2272–2281, doi:10.3762/bjoc.16.188
- exploited in many applications including the selective sensing of saccharides, the separation and purification of glycoproteins, and the immobilization of antibodies in microarrays [17][18][19][20][21]. However, the synthesis of boronic esters is sometimes problematic, as it often requires a fine tuning of
- regard, we recently reported on the straightforward synthesis of probe 1 (Figure 1) where a phenylboronic acid (PBA) moiety was introduced at the meso position of a BODIPY core. We demonstrated the compound’s ability to bind the oligosaccharide chain of the Fc domain of monoclonal antibodies, through the
Tools for generating and analyzing glycan microarray data
Beilstein J. Org. Chem. 2020, 16, 2260–2271, doi:10.3762/bjoc.16.187
- , and could possibly promote cancer [4], and the O-glycan of PSGL-1 which is recognized by P- and L-selectin, which is critical for leukocyte recruitment [5][6]. Other roles of glycans (including glycosaminoglycans/proteoglycans) and glycan binding proteins (GBPs) (including lectins and antibodies) in
- biological systems have been discovered with respect to cancer, infectious diseases, and genetic disorders [7][8][9][10][11][12][13][14][15]. As a technology to study glycan recognition by GBPs, glycan microarrays offer an invaluable tool, and permit examination of all types of lectins, along with antibodies
- an earlier version containing fewer compounds. The database has samples consisting of animal GBPs (e.g., C-type lectins, siglecs, galectins), plant lectins, antibodies, serum samples, pathogens and microbial proteins, cells, and organisms. The website contains data available as downloadable .xlsx
Clustering and curation of electropherograms: an efficient method for analyzing large cohorts of capillary electrophoresis glycomic profiles for bioprocessing operations
Beilstein J. Org. Chem. 2020, 16, 2087–2099, doi:10.3762/bjoc.16.176
- ; electropherogram; glycosylation; monoclonal antibodies; peak picking; process development; Introduction Glycosylation is important for the efficacy and function of a majority of the most dominant biologic drugs currently on the global market. In the case of antibody-based biotherapeutics, the absence of
- set of glycosylation profiles derived from the bioprocessing and harvesting of Anti-HER-2 antibodies every day across 11 different culturing conditions. Specifically, Anti-HER-2 antibodies were harvested from 3 technical replicates for biological replicate across 12 days and 11 different culturing
- . Sample preparation of antibody N-glycans Protein A purification and buffer exchange: The collected cell supernatant was filtered through a 0.22 µM PVDF syringe filter (Sterile Millex Filter, Merck Millipore, Ireland). Antibodies were then purified using protein A spin trap columns (Protein A HP Spintrap
How and why plants and human N-glycans are different: Insight from molecular dynamics into the “glycoblocks” architecture of complex carbohydrates
Beilstein J. Org. Chem. 2020, 16, 2046–2056, doi:10.3762/bjoc.16.171
- the knowledge of their dynamic properties and flexibility. Also, consideration of these glycoblocks as spatial units can be useful to understand recognition by lectins and antibodies, which is often affected primarily by the targeted monosaccharide’s immediate vicinity and by its accessibility within
- of the N-glycan and its structural dynamics, therefore its selective recognition by lectin receptors and antibodies. The atomistic-level of detail information that the MD simulations provide us with, highlights that the effects of different functionalizations, in terms of monosaccharide types and
Synthesis of Streptococcus pneumoniae serotype 9V oligosaccharide antigens
Beilstein J. Org. Chem. 2020, 16, 1693–1699, doi:10.3762/bjoc.16.140
- degree of acetylation of the same pentasaccharide RU. The positions and degree of RU acetylation has been revised several times since the initial structure 1 was proposed in 1981 (2 and 3 in Figure 1) [20][21][22]. Antibodies raised against the natural 9V polysaccharide recognize the natural and the de-O
A smart deoxyribozyme-based fluorescent sensor for in vitro detection of androgen receptor mRNA
Beilstein J. Org. Chem. 2020, 16, 1135–1141, doi:10.3762/bjoc.16.100
- . Reproducibility and linearity are also very important as well as costs and ease of manufacturing each component of the biosensor. Unlike proteins or antibodies the nucleic acid-based biosensors (NAs) can be easily commercially synthesized, they are smaller, more stable, and can be repeatedly used without losing
Opening up connectivity between documents, structures and bioactivity
Beilstein J. Org. Chem. 2020, 16, 596–606, doi:10.3762/bjoc.16.54
- Google and indexed for chemistry searching [4][5]. Structures: A necessary focus of this article will be traditional small-molecule chemistry that is not too far outside the rule-of-five lead-like property space. In terms of connectivity antibodies, other protein biotherapeutics, as well as large
Automated glycan assembly of arabinomannan oligosaccharides from Mycobacterium tuberculosis
Beilstein J. Org. Chem. 2019, 15, 2936–2940, doi:10.3762/bjoc.15.288
- lipoarabinomannan (LAM) analogs in urine samples using the Alere lateral flow urine (LF)-LAM assay [13]. However, the low sensitivity of the Alere assay limits its scope. Glycan array screening of more than 100 monoclonal antibodies against more than 60 synthetic glycans related to the mycobacterial cell wall
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