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

• , water network prediction, and 3D-QSAR. GRID 2021 introduced a new interface aimed at structure-based design. It enables users to explore binding sites using classic GRID MIFs, encompassing 74 different chemical types. Additionally, it offers a new molecular probe for generating MIFs specific to

A Diels–Alder probe for discovery of natural products containing furan moieties

• Alyssa S. Eggly,
• Namuunzul Otgontseren,
• Carson B. Roberts,
• Amir Y. Alwali,
• Haylie E. Hennigan and
• Elizabeth I. Parkinson

Beilstein J. Org. Chem. 2024, 20, 1001–1010, doi:10.3762/bjoc.20.88

• including fungal infections, and cancers. However, it is challenging to discover and isolate these small molecules from cell supernatant. The work described herein showcases the development of a molecular probe that can covalently modify furan moieties via a [4 + 2] Diels–Alder cycloaddition, making them

• easily identifiable on liquid chromatography–mass spectrometry (LC–MS). The molecular probe, which undergoes this reaction with a variety of furans, was designed with both a UV-tag and a mass tag to enable easy identification. The probe has been tested with a variety of purified furans, including natural

• products, methylenomycin furan (MMF) hormones, and MMF derivatives. Moreover, the molecular probe has been tested in crude supernatants of various Streptomyces strains and enables identification of MMFs. Keywords: Diels–Alder reaction; furans; methylenomycin furan hormones; natural products; reactivity

Nonenzymatic synthesis of anomerically pure, mannosyl-based molecular probes for scramblase identification studies

• Giovanni Picca,
• Markus Probst,
• Simon M. Langenegger,
• Oleg Khorev,
• Peter Bütikofer,
• Anant K. Menon and
• Robert Häner

Beilstein J. Org. Chem. 2020, 16, 1732–1739, doi:10.3762/bjoc.16.145

• membrane proteins [11][12]. The captured proteins would be subsequently identified by mass spectrometry, and their function in MPD scrambling validated by biochemical and genetic approaches. A suitable molecular probe and mimic of MPD (Figure 1) can be subdivided into three essential components: a β-ᴅ

• ][28][29]. The phosphoramidite approach was also applied to the synthesis of a second molecular probe, MPC-2, an anomerically pure, β-linked ᴅ-mannosephosphate derivative, which serves as a fluorescent MPD analog for scramblase activity screening assays. Although similar experiments have been described

• wherein the NBD can be detected with dithionite. The latter reduces the nitro group of the NBD rapidly into an amino group, rendering the fluorophore nonfluorescent [32][33][34]. While there are no noteworthy difficulties in the synthesis of the molecular probe MPC-1 to report, the same cannot be said for

Azologization and repurposing of a hetero-stilbene-based kinase inhibitor: towards the design of photoswitchable sirtuin inhibitors

• Christoph W. Grathwol,
• Nathalie Wössner,
• Sören Swyter,
• Adam C. Smith,
• Enrico Tapavicza,
• Robert K. Hofstetter,
• Anja Bodtke,
• Manfred Jung and
• Andreas Link

Beilstein J. Org. Chem. 2019, 15, 2170–2183, doi:10.3762/bjoc.15.214

• activity difference for the (E)- and (Z)-isomers needs dramatic improvement before a useful molecular probe can be obtained by this approach. Experimental General remarks All solvents and reagents were obtained from commercial suppliers and were used without purification. Anhydrous solvents were purchased

Design and synthesis of multivalent α-1,2-trimannose-linked bioerodible microparticles for applications in immune response studies of Leishmania major infection

• Chelsea L. Rintelmann,
• Tara Grinnage-Pulley,
• Kathleen Ross,
• Daniel E. K. Kabotso,
• Angela Toepp,
• Anne Cowell,
• Christine Petersen,
• Balaji Narasimhan and
• Nicola Pohl

Beilstein J. Org. Chem. 2019, 15, 623–632, doi:10.3762/bjoc.15.58

• study the mechanisms of immune modulation. In this study, a new bioerodible polyanhydride microparticle was designed and conjugated with a glycodendrimer molecular probe. This molecular probe incorporates a pathogen-like multivalent display of α-1,2-trimannose, for which a more efficient synthesis was

• -labile probe was found to increase T cell production, suggesting α-1,2-trimannose antigen presentation at the major histocompatibility complex II (MHC II) [41]. Based on our previous studies [11][40][41][42], we sought to design and synthesize a new Leishmania-associated molecular probe that could allow

• administration to L. major infected mice (Figure 4). Results and Discussion To further probe the biological mechanisms responsible for L. major immune regulation, a new adjuvant-like pathogen-associated molecular probe was designed to promote pathogen recognition receptor (PRR)-mediated internalization and slow

A small azide-modified thiazole-based reporter molecule for fluorescence and mass spectrometric detection

• Stefanie Wolfram,
• Hendryk Würfel,
• Stefanie H. Habenicht,
• Christine Lembke,
• Phillipp Richter,
• Eckhard Birckner,
• Rainer Beckert and
• Georg Pohnert

Beilstein J. Org. Chem. 2014, 10, 2470–2479, doi:10.3762/bjoc.10.258

• profiling (ABPP); bioorthogonal; click chemistry; mass defect; molecular probe; Introduction Fluorescent dyes are widely used for detection and monitoring in the fields of chemistry, biochemistry, molecular biology, medicine and material sciences. Due to sensitive and selective detection methods and

Synthesis and spectroscopic properties of 4-amino-1,8-naphthalimide derivatives involving the carboxylic group: a new molecular probe for ZnO nanoparticles with unusual fluorescence features

• Laura Bekere,
• David Gachet,
• Vladimir Lokshin,
• Wladimir Marine and
• Vladimir Khodorkovsky

Beilstein J. Org. Chem. 2013, 9, 1311–1318, doi:10.3762/bjoc.9.147

• (3H)-yl)benzoic acid (4) was found to be a sensitive molecular probe for ZnO nanoparticles. We investigated in detail one- and two-photon absorption properties of this fluorophore. In nonpolar solvents, the acid 4 absorbs at about 400 nm and fluoresces at 500 nm with a fluorescence lifetime of about 7

• electron-donating properties and weaker electron-accepting properties than ZnO [18]. Grafting to the surface of ZnO nanoparticles In order to investigate the behavior of acid 4 as a fluorescent molecular probe, preliminary experiments on grafting to the surface of ZnO nanoparticles (NPs) were carried out

• grafting. Conclusion Derivative 4 involving both the fluorophore moiety and the carboxylic group capable of binding the ZnO surface can serve as an efficient molecular probe owing to the high sensitivity to the polarity of the surroundings. Derivative 2 can also be used when fluorescence detection at

Synthesis of (−)-julocrotine and a diversity oriented Ugi-approach to analogues and probes

• Ricardo A. W. Neves Filho,
• Bernhard Westermann and
• Ludger A. Wessjohann

Beilstein J. Org. Chem. 2011, 7, 1504–1507, doi:10.3762/bjoc.7.175

• -4CR was utilized for the synthesis of a molecular probe prototype of 1, which can be used for intercalation studies (Scheme 3). For this propose, the natural product scaffold should be attached through a spacer to a reporter tag, which is normally a luminescent group or a dye. The advanced

• product in 51% overall yield. The versatility of the developed protocol was demonstrated in the synthesis of seven julocrotine analogues and a molecular probe utilizing Ugi-4CRs. The desired compounds 6a–g and 10 were obtained in good yields. Retrosynthetic scheme for (−)-julocrotine (1). Reactions and

Synthesis, reactivity and biological activity of 5-alkoxymethyluracil analogues

• Lucie Brulikova and
• Jan Hlavac

Beilstein J. Org. Chem. 2011, 7, 678–698, doi:10.3762/bjoc.7.80

• compound should serve as a molecular probe that facilitates selective detection of excess electron transfer or hole migration in DNA using gel electrophoresis. The synthesis of the desired phosphoramidite 150 (Scheme 25) started with the Pd-catalyzed cross-coupling of 5-iodo-2'-deoxyuridine (14) and a

Synthesis and crossover reaction of TEMPO containing block copolymer via ROMP

• Olubummo Adekunle,
• Susanne Tanner and
• Wolfgang H. Binder

Beilstein J. Org. Chem. 2010, 6, No. 59, doi:10.3762/bjoc.6.59

• reaction mixture, MALDI spectra were measured. As shown in Figure 8, homopolymer A25 can be desorbed well in MALDI, featuring the respective AnNa+-ions as a pure series. Thus the homopolymer An can serve as molecular probe for the subsequent desorption of the individual AnT1, 2, 5-species. The MALDI