Bacterial β sliding clamp (β-clamp) is an emerging drug target currently lacking small-molecule inhibitors with good in vivo activity. Thus, there is a need for fast and simple screening methods for identifying inhibitor candidates. Here we demonstrate the use of nuclear magnetic resonance spectroscopy (NMR) for evaluating compound binding to the E. coli β-clamp. To identify suitable molecular probes, a series of tetrahydrocarbazoles were synthesized, some of which contain fluorine. Key challenges in the synthesis were formation of regioisomers during the Fischer indole reaction and reducing racemization at the stereogenic center. The tetrahydrocarbazoles were assayed against the E. coli β-clamp by saturation-transfer difference (STD) NMR, waterLOGSY and T1ρ. Analysis by isothermal titration calorimetry gave KD-values of 1.7-14 μM for three fluorinated probe candidates, and NMR chemical shift perturbation experiments confirmed these molecules to directly interact with the β-clamp binding pocket. Binding of the fluorinated molecules to β-clamp was easily observed with 19F-observed T2-based binding experiments, and proof of concept for a fluorine-based binding assay for E. coli β-clamp binders is provided.

• Klíčová slova
• (19)F NMR displacement assay, E. coli, Racemization, STD NMR, Tetrahydrocarbazole, β sliding clamp,
• MeSH
• Escherichia coli * účinky léků   MeSH
• halogenace MeSH
• karbazoly * chemie   chemická syntéza   farmakologie   metabolismus   MeSH
• magnetická rezonanční spektroskopie * MeSH
• molekulární sondy chemie   chemická syntéza   metabolismus   MeSH
• molekulární struktura MeSH
• proteiny z Escherichia coli metabolismus   antagonisté a inhibitory   chemie   MeSH
• vazba proteinů MeSH
• vazebná místa MeSH
• vztahy mezi strukturou a aktivitou MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• karbazoly * MeSH
• molekulární sondy MeSH
• proteiny z Escherichia coli MeSH

Albumin has consistently demonstrated its potential for enhancing the delivery of drugs and polymer-drug conjugates, binding via supramolecular forces within its multiple binding sites. Herein, we introduce saturation transfer difference (STD-NMR) as a method to identify the interactions between a polymer library and bovine serum albumin (BSA). With STD-NMR, the binding ability of polymers can be quickly screened by focusing on their individual structural features, making this technique more suitable for high throughput screening in comparison to traditional fluorescence studies.

• MeSH
• magnetická rezonanční spektroskopie metody   MeSH
• polymery * metabolismus   MeSH
• sérový albumin hovězí * chemie   MeSH
• vazba proteinů MeSH
• vazebná místa MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• polymery * MeSH
• sérový albumin hovězí * MeSH

Adenosine kinase (ADK) from Mycobacterium tuberculosis (Mtb) was selected as a target for design of antimycobacterial nucleosides. Screening of 7-(het)aryl-7-deazaadenine ribonucleosides with Mtb and human (h) ADKs and testing with wild-type and drug-resistant Mtb strains identified specific inhibitors of Mtb ADK with micromolar antimycobacterial activity and low cytotoxicity. X-ray structures of complexes of Mtb and hADKs with 7-ethynyl-7-deazaadenosine showed differences in inhibitor interactions in the adenosine binding sites. 1D (1)H STD NMR experiments revealed that these inhibitors are readily accommodated into the ATP and adenosine binding sites of Mtb ADK, whereas they bind preferentially into the adenosine site of hADK. Occupation of the Mtb ADK ATP site with inhibitors and formation of catalytically less competent semiopen conformation of MtbADK after inhibitor binding in the adenosine site explain the lack of phosphorylation of 7-substituted-7-deazaadenosines. Semiempirical quantum mechanical analysis confirmed different affinity of nucleosides for the Mtb ADK adenosine and ATP sites.

• MeSH
• adenin analogy a deriváty   chemie   MeSH
• adenosinkinasa antagonisté a inhibitory   chemie   metabolismus   MeSH
• adenosintrifosfát metabolismus   MeSH
• antituberkulotika chemie   farmakologie   MeSH
• konformace proteinů MeSH
• krystalografie rentgenová MeSH
• lidé MeSH
• mikrobiální testy citlivosti MeSH
• Mycobacterium tuberculosis účinky léků   enzymologie   MeSH
• nukleární magnetická rezonance biomolekulární MeSH
• preklinické hodnocení léčiv MeSH
• ribonukleosidy chemie   farmakologie   MeSH
• vazebná místa MeSH
• vztahy mezi strukturou a aktivitou MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• 7-deazaadenine MeSH Prohlížeč
• adenin MeSH
• adenosinkinasa MeSH
• adenosintrifosfát MeSH
• antituberkulotika MeSH
• ribonukleosidy MeSH

Fluorination of carbohydrate ligands of lectins is a useful approach to examine their binding profile, improve their metabolic stability and lipophilicity, and convert them into 19F NMR-active probes. However, monofluorination of monovalent carbohydrate ligands often leads to a decreased or completely lost affinity. By chemical glycosylation, we synthesized the full series of methyl β-glycosides of N,N'-diacetylchitobiose (GlcNAcβ(1-4)GlcNAcβ1-OMe) and LacdiNAc (GalNAcβ(1-4)GlcNAcβ1-OMe) systematically monofluorinated at all hydroxyl positions. A competitive enzyme-linked lectin assay revealed that the fluorination at the 6'-position of chitobioside resulted in an unprecedented increase in affinity to wheat germ agglutinin (WGA) by one order of magnitude. For the first time, we have characterized the binding profile of a previously underexplored WGA ligand LacdiNAc. Surprisingly, 4'-fluoro-LacdiNAc bound WGA even stronger than unmodified LacdiNAc. These observations were interpreted using molecular dynamic calculations along with STD and transferred NOESY NMR techniques, which gave evidence for the strengthening of CH/π interactions after deoxyfluorination of the side chain of the non-reducing GlcNAc. These results highlight the potential of fluorinated glycomimetics as high-affinity ligands of lectins and 19F NMR-active probes.

• Klíčová slova
• Alchemical free energy calculation, Chemical synthesis, Conformational analysis, ELLA, Fluorinated carbohydrates, Nuclear magnetic resonance, Wheat germ agglutinin,
• MeSH
• acetylglukosamin chemie   metabolismus   MeSH
• aglutininy z pšeničných klíčků * chemie   metabolismus   MeSH
• disacharidy * chemie   chemická syntéza   MeSH
• halogenace MeSH
• laktosa analogy a deriváty   MeSH
• molekulární struktura MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• N-acetylgalactosaminyl-1-4-N-acetylglucosamine MeSH Prohlížeč
• N,N-diacetylchitobiose MeSH Prohlížeč

DC-SIGN (dendritic cell-specific intercellular adhesion molecule-3-grabbing non-integrin) is a pattern recognition receptor expressed on immune cells and involved in the recognition of carbohydrate signatures present on various pathogens, including HIV, Ebola, and SARS-CoV-2. Therefore, developing inhibitors blocking the carbohydrate-binding site of DC-SIGN could generate a valuable tool to investigate the role of this receptor in several infectious diseases. Herein, we performed a fragment-based ligand design using 4-quinolone as a scaffold. We synthesized a library of 61 compounds, performed a screening against DC-SIGN using an STD reporter assay, and validated these data using protein-based 1H-15N HSQC NMR. Based on the structure-activity relationship data, we demonstrate that ethoxycarbonyl or dimethylaminocarbonyl in position 2 or 3 is favorable for the DC-SIGN binding activity, especially in combination with fluorine, ethoxycarbonyl, or dimethylaminocarbonyl in position 7 or 8. Furthermore, we demonstrate that these quinolones can allosterically modulate the carbohydrate binding site, which offers an alternative approach toward this challenging protein target.

• Publikační typ
• časopisecké články MeSH