Synthetic glycopeptides and glycoproteins with applications in biological research

• Ulrika Westerlind

Beilstein J. Org. Chem. 2012, 8, 804–818, doi:10.3762/bjoc.8.90

• tyrosine residues form the “tyrosine gate” [134]. By π–π stacking interactions with the aromatic tyrosine residues, monovalent α-mannose ligands containing hydrophobic aglycons, have shown increased binding affinities [128][135][136]. Employing multivalent ligands, the binding affinity to FimH could be

• ; in one of them the L-amino acids were replaced by D-amino acids (D-FD2, 51) to avoid proteolytic cleavage of the peptide construct [147]. Interestingly, it was found that the D-FD2 51 glycopeptide dendrimer showed a slightly weaker binding affinity to LecB, but the P. aeruginosa biofilm inhibitory

An easily accessible sulfated saccharide mimetic inhibits in vitro human tumor cell adhesion and angiogenesis of vascular endothelial cells

• Grazia Marano,
• Claas Gronewold,
• Martin Frank,
• Anette Merling,
• Christian Kliem,
• Sandra Sauer,
• Manfred Wiessler,
• Eva Frei and
• Reinhard Schwartz-Albiez

Beilstein J. Org. Chem. 2012, 8, 787–803, doi:10.3762/bjoc.8.89

• entire dataset, and to organize the results in such a way that areas on the protein surface exhibiting a strong binding affinity could be easily visualized by using standard display programs. In order to refine the docked structure of GSF a molecular dynamics (MD) simulation of the complex was performed

Chemo-enzymatic modification of poly-N-acetyllactosamine (LacNAc) oligomers and N,N-diacetyllactosamine (LacDiNAc) based on galactose oxidase treatment

• Christiane E. Kupper,
• Ruben R. Rosencrantz,
• Birgit Henßen,
• Helena Pelantová,
• Stephan Thönes,
• Anna Drozdová,
• Vladimir Křen and
• Lothar Elling

Beilstein J. Org. Chem. 2012, 8, 712–725, doi:10.3762/bjoc.8.80

• reaction mixture leads to the formation of α,β-unsaturated aldehydes. By branching, the avidity of glycans has been shown to increase, which is important for the binding affinity of lectins [56][57]. The chemically branched poly-LacNAc glycans may, moreover, serve as analogues to naturally occurring I

Investigation of the network of preferred interactions in an artificial coiled-coil association using the peptide array technique

• Raheleh Rezaei Araghi,
• Carsten C. Mahrenholz,
• Rudolf Volkmer and
• Beate Koksch

Beilstein J. Org. Chem. 2012, 8, 640–649, doi:10.3762/bjoc.8.71

• various degrees of binding affinity to the chimera. Based on the SI values, the α-mutants were classified into five interaction groups. As depicted in Figure 2 on the right-hand side, sequences with equal or slightly higher SI values compared to Acid-pp were classified as strong binders (only 22

• formation that are probably due to the destabilizing orientation of the polar hydroxyl group towards the hydrophobic core [21]. The clear decrease in binding affinity between chimera and Tyr-comprising mutants shows that the side chains at the artificial interface of the helix bundle experience an

• two Ile residues results in a medium binding affinity (Figure 4). This can be explained by the fact that, similarly to that of native coiled coils, the chimeric hydrophobic core is disrupted by excessively bulky side chains [22]. However, the preference for specific hydrophobic side chains in a and d

Azobenzene dye-coupled quadruply hydrogen-bonding modules as colorimetric indicators for supramolecular interactions

• Yagang Zhang and
• Steven C. Zimmerman

Beilstein J. Org. Chem. 2012, 8, 486–495, doi:10.3762/bjoc.8.55

• relationship has been developed for DAN·UG-based supramolecular-network polymer blends [40], and a redox-active eDAN unit was described wherein a >104-fold drop in binding affinity occurred upon reversible oxidation [41]. Herein, we extend the chemistry of the heterocyclic hydrogen bonding units (DAN and DeUG

Synthesis of fluorinated maltose derivatives for monitoring protein interaction by ¹⁹F NMR

• Michaela Braitsch,
• Hanspeter Kählig,
• Georg Kontaxis,
• Michael Fischer,
• Toshinari Kawada,
• Robert Konrat and
• Walther Schmid

Beilstein J. Org. Chem. 2012, 8, 448–455, doi:10.3762/bjoc.8.51

• -type 2-F-maltose isomers), which serve as internal standards, to rule out nonspecific binding and interactions, and thus increasing the reliability of this method. The 2-F-maltose reporter system was used to study the ligand binding affinity to MBP. “Fine tuning” by the regioselective fluorination of

Fifty years of oxacalix[3]arenes: A review

• Kevin Cottet,
• Paula M. Marcos and
• Peter J. Cragg

Beilstein J. Org. Chem. 2012, 8, 201–226, doi:10.3762/bjoc.8.22

• ) methylene groups had a binding affinity for linear primary alkyl ammonium ions from n-BuNH3+ to n-HexNH3+. 3.2 Upper-rim derivatives Although the lower rim has many advantages as a binding site for guests, not least in the relative ease with which substituents can be attached, the upper rim can also

(How) does 1,3,5-triethylbenzene scaffolding work? Analyzing the abilities of 1,3,5-triethylbenzene- and 1,3,5-trimethylbenzene-based scaffolds to preorganize the binding elements of supramolecular hosts and to improve binding of targets

• Xing Wang and
• Fraser Hof

Beilstein J. Org. Chem. 2012, 8, 1–10, doi:10.3762/bjoc.8.1

• 1,3,5-triethylbenzene template directs the binding elements toward the same face of the central ring, hence increasing the binding affinity. At the same time the 1,3,5-trimethylbenzene scaffold, without steric-gearing effects, has also been found to improve the binding affinities of hosts compared to

• methyl groups, but the size of this advantage can be small and is dependent on the groups involved. Keywords: binding affinity; entropy; molecular recognition; scaffolds; supramolecular hosts; triethylbenzene; trimethylbenzene; Introduction Supramolecular hosts use arrays of multiple weak interactions

• different 1,3,5-triethylbenzene-based and analogous 1,3,5-trimethylbenzene-based tripodal hosts for their respective guests. These results are reported in Table 3. From this limited amount of literature data we see a range of binding-affinity differences for ethyl- and methyl-substituted hosts, which range

Ratiometric fluorescent probe for enantioselective detection of D-cysteine in aqueous solution

• Xiao-bo Zhou,
• Wing-Hong Chan,
• Albert W. M. Lee and
• Chi-Chung Yeung

Beilstein J. Org. Chem. 2011, 7, 1508–1515, doi:10.3762/bjoc.7.176

• cadmium complex (Cd2+–ACAQ) can induce a distinctive ratiometric fluorescence change characterized by the formation of an obvious isoemissive point at 450 nm (Figure 3b). We envisioned that the strong binding affinity of cysteine to Cd2+ perturbs its interaction with ACAQ in such a way that the ICT

• decreased. It is noteworthy that irrespective of the exact solvent composition of the aqueous solutions the binding affinity of the probe to Cys is fairly strong, as evidenced by the binding constants. On the other hand, the Job’s plot confirms the 1:1 binding stoichiometry of the sensing ensemble and Cys

• synergistic binding affinity of its carboxyl group to Cd2+–ACAQ. Such a proposition was supported by the observation that by converting the carboxyl group of cysteine into its methyl ester, the quenching ability of the derivative toward the probe was greatly reduced. To evaluate the binding mode of the Cd2

Advances in synthetic approach to and antifungal activity of triazoles

• Kumari Shalini,
• Nitin Kumar,
• Sushma Drabu and
• Pramod Kumar Sharma

Beilstein J. Org. Chem. 2011, 7, 668–677, doi:10.3762/bjoc.7.79

• antimicrobial agents and the development of structurally new classes of antimicrobials with novel mechanisms of action as well as structural modifications to improve both their binding affinity and their spectrum of activity. One such strategy that has been pursued in recent years with increasing significance

Fluorometric recognition of both dihydrogen phosphate and iodide by a new flexible anthracene linked benzimidazolium-based receptor

• Kumaresh Ghosh and
• Debasis Kar

Beilstein J. Org. Chem. 2011, 7, 254–264, doi:10.3762/bjoc.7.34

• the key factors that regulate the PET to different extents. The binding affinity and selectivity of this simple fluororeceptor are associated with the combined effects of semi-rigid structures of receptor, charge-charge interactions, and the involvement of both N–H---O and C–H---O hydrogen bonds

pH-Responsive chromogenic-sensing molecule based on bis(indolyl)methene for the highly selective recognition of aspartate and glutamate

• Litao Wang,
• Xiaoming He,
• Yong Guo,
• Jian Xu and
• Shijun Shao

Beilstein J. Org. Chem. 2011, 7, 218–221, doi:10.3762/bjoc.7.29

• a basic H-bond acceptor moiety, could act not only as a color-reporting group but also as a binding affinity control group. The anion sensing properties of 1 based on acidic H-bond donor moiety have been studied previously in our laboratory [15]. The strong hydrogen bonding to, or protonation

An easy assembled fluorescent sensor for dicarboxylates and acidic amino acids

• Xiao-bo Zhou,
• Yuk-Wang Yip,
• Wing-Hong Chan and
• Albert W. M. Lee

Beilstein J. Org. Chem. 2011, 7, 75–81, doi:10.3762/bjoc.7.11

• . The receptor 1 was fully characterized by 1H, 13C NMR, and high resolution mass spectral analysis. To evaluate the binding affinity of the synthetic host to dicarboxylate guest molecules, fluorometric titration experiments were carried out with the concentration of 1 fixed at 5.0 × 10−6 M in

• present in aspartates weakened their interaction with sensor 1, presumably due to non-bonding repulsions. In contrast, in comparison with the association constant between sensor 1 and glutarate, sensor 1 exhibited a stronger binding affinity to D- and L-glutamate (Table 2). Interestingly, a marginal

• aspartate and glutamate. Experimental findings indeed corroborated well with such a supposition. Compared with the interaction of the control compounds (i.e., succinate and glutarate), sensor 2 demonstrated a 3–10 fold stronger binding affinity with aspartate and glutamate, respectively. For instance, the

The C–F bond as a conformational tool in organic and biological chemistry

• Luke Hunter

Beilstein J. Org. Chem. 2010, 6, No. 38, doi:10.3762/bjoc.6.38

• improved binding affinity. HIV reverse transcriptase inhibitor 22 and acid-stable fluorinated analogues 23–25. The F–C–C–O gauche effect influences the ring conformations of 23–25. Dihydroquinidine (26) and fluorinated analogues 27 and 28. Newman projections along the C9–C8 bonds of 27 and 28 show the

Molecular recognition of organic ammonium ions in solution using synthetic receptors

• Andreas Späth and
• Burkhard König

Beilstein J. Org. Chem. 2010, 6, No. 32, doi:10.3762/bjoc.6.32

• showed a considerable binding affinity and enantiomeric discrimination of aromatic amine salts [162]. The binding properties were evaluated by 1H NMR titration in acetonitrile. For the (R,R)- and (S,S)-configurated host with a phenyl residue, the highest differences in the Kass values were observed: (R

Efficient and improved synthesis of Telmisartan

• A. Sanjeev Kumar,
• Samir Ghosh and
• G. N. Mehta

Beilstein J. Org. Chem. 2010, 6, No. 25, doi:10.3762/bjoc.6.25

• , all of which contain a characteristic ortho functionalized biaryl moiety. Telmisartan (1, Boehringer Ingelheim, Micardis®) (Figure 1) is an important member of this class of top-selling drugs because it has the strongest binding affinity to the AT1 receptor, an excellent bioavailability, and a once

(Pseudo)amide-linked oligosaccharide mimetics: molecular recognition and supramolecular properties

• José L. Jiménez Blanco,
• Fernando Ortega-Caballero,
• Carmen Ortiz Mellet and
• José M. García Fernández

Beilstein J. Org. Chem. 2010, 6, No. 20, doi:10.3762/bjoc.6.20

• phosphate were obtained from NMR titration experiments for both series of glucooligomers. The binding affinity of the thiourea and guanidine oligomers was stronger than in the case of the urea analogues. Stimulated by the interesting supramolecular properties and applications of cyclodextrins (CDs), a range

• expression in living cells has required the development of modified oligonucleotides as potential therapeutic agents. A key goal in the design of such agents include increasing binding affinity while maintaining sequence specificity, resistance to degradation by nucleases and improved membrane permeability

Templated versus non-templated synthesis of benzo-21-crown-7 and the influence of substituents on its complexing properties

• Wei Jiang and
• Christoph A. Schalley

Beilstein J. Org. Chem. 2010, 6, No. 14, doi:10.3762/bjoc.6.14

• more efficient than the intramolecular macrocyclization without template. Pseudorotaxanes form with secondary ammonium ions bearing at least one alkyl chain narrow enough to slip into the crown ether. Substitution on benzo-21-crown-7 or on the secondary ammonium axle alters the binding affinity and

• of guest from secondary dibenzylammonium hexafluorophosphate (360 M−1, 1.0 mM, in acetone-d6) [31] to the anthracenyl methyl-substituted analogue 5-H•PF6 (496 M−1, 1.0 mM, in acetone-d6) [26] increases the binding affinity with DB24C8, which is mainly attributed to stronger π-π stacking interactions

• template during the synthesis of C7 from catechol and 3 results in a much more easily achievable separation of uncomplexed C7. We speculate that the lower solubility of this salt in organic solvent helps to separate the crown ether from the salt during the extraction. The effect of substituents on binding

Size selective recognition of small esters by a negative allosteric hemicarcerand

• Holger Staats and
• Arne Lützen

Beilstein J. Org. Chem. 2010, 6, No. 10, doi:10.3762/bjoc.6.10

• found to have a weak affinity for simple esters in a size selective manner in the absence of an effector whereas it does not show any binding affinity when it is coordinated to a tris(carbonyl)rhenium chloride fragment – thus showing negative cooperative allosteric behaviour. Results and Discussion

• rather observed an averaged signal very close to the one of the free guest due to the large excess of the free substrate. Despite the large excess of the free guest this also hints at a rather low binding affinity of 2 towards the esters as expected for the reasons given above. Addition of the larger

Recognition properties of receptors consisting of imidazole and indole recognition units towards carbohydrates

• Monika Mazik and
• André Hartmann

Beilstein J. Org. Chem. 2010, 6, No. 9, doi:10.3762/bjoc.6.9

• and interesting binding preferences of these acyclic compounds. Compared to the previously described acyclic receptors, compounds 4 and 5 showed significantly increased binding affinity towards β-galactoside. Both receptors display high β- vs. α-anomer binding preferences in the recognition of

• of DMSO-d6 a substantial fall in the binding affinity was observed. Studies that were performed with 4 and 11 in 5% DMSO-d6 in CDCl3 revealed K11 = 12000 M–1 and K21 = 3000 M–1, those performed with 5 and 11 indicated the formation of complexes with 1:1 receptor–sugar stoichiometry with K11 = 42000 M

• powerful monosaccharide receptor than the indole-based compound 5 and the previously described receptors 1–3. Compared to 1 and 2, incorporating only one imidazole or indole recognition unit, receptor 5 showed increased affinity to β-galactoside but decreased affinity to β-glucoside. The binding affinity

Synthesis and binding studies of two new macrocyclic receptors for the stereoselective recognition of dipeptides

• Ana Maria Castilla,
• M. Morgan Conn and
• Pablo Ballester

Beilstein J. Org. Chem. 2010, 6, No. 5, doi:10.3762/bjoc.6.5

• modulation of their binding affinity as a function of the hydrogen-bonding pattern exhibited by the target molecule. We also describe the levels of stereoselectivity displayed by these receptors in the recognition of the diastereoisomers and enantioisomers of Ala-Ala dipeptide. We explain the differences

• structures to examine the molecular recognition properties of receptors 1, 2, 15, and 17 (Figure 8). We selected a series of diamides to evaluate the effect that the hydrogen-bonding pattern produces in the binding affinity. We also investigated the molecular recognition properties of the receptor series

• clashes detected between the dipeptide side chains and the benzophenone linking units should significantly reduce the binding affinity of the cyclic receptors for this substrate or even favor the formation of an alternative complex with exo-geometry. Unexpectedly, the stability constant values that we

Quinoline based receptor in fluorometric discrimination of carboxylic acids

• Kumaresh Ghosh,
• Suman Adhikari,
• Asoke P. Chattopadhyay and
• Purnendu Roy Chowdhury

Beilstein J. Org. Chem. 2008, 4, No. 52, doi:10.3762/bjoc.4.52

• change in absorption of the receptor was noted after each addition. The binding constant values determined by this method are found to be less (Table 1) due to the presence of DMSO, a competitive hydrogen-bonding partner which reduces the binding affinity. Interestingly, as we move from receptor 1 to

8-epi-Salvinorin B: crystal structure and affinity at the κ opioid receptor

• Thomas A. Munro,
• Katharine K. Duncan,
• Richard J. Staples,
• Wei Xu,
• Lee-Yuan Liu-Chen,
• Cécile Béguin,
• William A. Carlezon Jr. and
• Bruce M. Cohen

Beilstein J. Org. Chem. 2007, 3, No. 1, doi:10.1186/1860-5397-3-1

• ) itself, whose binding affinity (Ki = 43 nM) was reportedly greater than that of the natural epimer 2a (111 nM).[8] To explore this anomaly, we submitted a new sample of 2b for in vitro testing at the KOR. Binding affinity, potency and efficacy were determined as previously described (Table 1).[26] The

• binding affinity of 2b (Ki = 304 nM) was lower than those previously reported for salvinorin B (2a) under the same conditions (66, 111 or 155 nM).[7][8][27] An early report that 2a was inactive employed a different radiolabeled ligand, [3H]bremazocine.[28] Subsequent testing with [3H]diprenorphine by the

• ), but the 8-epimer 4b showed high affinity at the KOR (49 nM).[23] In contrast, our current samples of both 4a and 4b showed no affinity at the KOR (Table 1). Given the very high binding affinity of 1a, contamination of an inactive or weakly active compound with even traces of 1a will cause large errors