Affinity capillary electrophoresis for the assessment of binding affinity of carbohydrate‐based cholera toxin inhibitors

Developing tools for the study of protein carbohydrate interactions is an important goal in glycobiology. Cholera toxin inhibition is an interesting target in this context, as its inhibition may help to fight against cholera. For the study of novel ligands an affinity capillary electrophoresis (ACE) method was optimized and applied. The method uses unlabeled cholera toxin B‐subunit (CTB) and unlabeled carbohydrate ligands based on ganglioside GM1‐oligosaccharides (GM1os). In an optimized method at pH 4, adsorption of the protein to the capillary walls was prevented by a polybrene‐dextran sulfate‐polybrene coating. Different concentrations of the ligands were added to the BGE. CTB binding was observed by a mobility shift that could be used for dissociation constant (K_d) determination. The K_d values of two GM1 derivatives differed by close to an order of magnitude (600 ± 20 nM and 90 ± 50 nM) which was in good agreement with the differences in their reported nanomolar IC₅₀ values of an ELISA‐type assay. Moreover, the selectivity of GM1os towards CTB was demonstrated using Influenza hemagglutinin (H5) as a binding competitor. The developed method can be an important platform for preclinical development of drugs targeting pathogen‐induced secretory diarrhea.     

Computation of the binding affinities of catechol‐O‐methyltransferase inhibitors: Multisubstate relative free energy calculations

Alchemical free energy simulations are amongst the most accurate techniques for the computation of the free energy changes associated with noncovalent protein–ligand interactions. A procedure is presented to estimate the relative binding free energies of several ligands to the same protein target where multiple, low‐energy configurational substates might coexist, as opposed to one unique structure. The contributions of all individual substates were estimated, explicitly, with the free energy perturbation method, and combined in a rigorous fashion to compute the overall relative binding free energies and dissociation constants. It is shown that, unless the most stable bound forms are known a priori, inaccurate results may be obtained if the contributions of multiple substates are ignored. The method was applied to study the complex formed between human catechol‐O‐methyltransferase and BIA 9‐1067, a newly developed tight‐binding inhibitor that is currently under clinical evaluation for the therapy of Parkinson's disease. Our results reveal an exceptionally high‐binding affinity (K_d in subpicomolar range) and provide insightful clues on the interactions and mechanism of inhibition. The inhibitor is, itself, a slowly reacting substrate of the target enzyme and is released from the complex in the form of O‐methylated product. By comparing the experimental catalytic rate (k_cat) and the estimated dissociation rate (k_off) constants of the enzyme‐inhibitor complex, one can conclude that the observed inhibition potency (K_i) is primarily dependent on the catalytic rate constant of the inhibitor's O‐methylation, rather than the rate constant of dissociation of the complex. © 2012 Wiley Periodicals, Inc.     

Template‐Assembled Synthetic G‐Quadruplex (TASQ): A Useful System for Investigating the Interactions of Ligands with Constrained Quadruplex Topologies

A new biomolecular device for investigating the interactions of ligands with constrained DNA quadruplex topologies, using surface plasmon resonance (SPR), is reported. Biomolecular systems containing an intermolecular‐like G‐quadruplex motif 1 (parallel G‐quadruplex conformation), an intramolecular G‐quadruplex 2 , and a duplex DNA 3 have been designed and developed. The method is based on the concept of template‐assembled synthetic G‐quadruplex (TASQ), whereby quadruplex DNA structures are assembled on a template that allows precise control of the parallel G‐quadruplex conformation. Various known G‐quadruplex ligands have been used to investigate the affinities of ligands for intermolecular 1 and intramolecular 2 DNA quadruplexes. As anticipated, ligands displaying a π‐stacking binding mode showed a higher binding affinity for intermolecular‐like G‐quadruplexes 1 , whereas ligands with other binding modes (groove and/or loop binding) showed no significant difference in their binding affinities for the two quadruplexes 1 or 2 . In addition, the present method has also provided information about the selectivity of ligands for G‐quadruplex DNA over the duplex DNA. A numerical parameter, termed the G‐quadruplex binding mode index (G4‐BMI), has been introduced to express the difference in the affinities of ligands for intermolecular G‐quadruplex 1 against intramolecular G‐quadruplex 2 . The G‐quadruplex binding mode index (G4‐BMI) of a ligand is defined as follows: G4‐BMI=K_D^intra/K_D^inter, where K_D^intra is the dissociation constant for intramolecular G‐quadruplex 2 and K_D^inter is the dissociation constant for intermolecular G‐quadruplex 1 . In summary, the present work has demonstrated that the use of parallel‐constrained quadruplex topology provides more precise information about the binding modes of ligands.     

Multivalent Gold Glycoclusters: High Affinity Molecular Recognition by Bacterial Lectin PA‐IL

Multivalent protein‐carbohydrate interactions are involved in the initial stages of many fundamental biological and pathological processes through lectin–carbohydrate binding. The design of high affinity ligands is therefore necessary to study, inhibit and control the processes governed through carbohydrate recognition by their lectin receptors. Carbohydrate‐functionalised gold nanoclusters (glyconanoparticles, GNPs) show promising potential as multivalent tools for studies in fundamental glycobiology research as well as biomedical applications. Here we present the synthesis and characterisation of galactose functionalised GNPs and their effectiveness as binding partners for PA‐IL lectin from Pseudomonas aeruginosa. Interactions were evaluated by hemagglutination inhibition (HIA), surface plasmon resonance (SPR) and isothermal titration calorimetry (ITC) assays. Results show that the gold nanoparticle platform displays a significant cluster glycoside effect for presenting carbohydrate ligands with almost a 3000‐fold increase in binding compared with a monovalent reference probe in free solution. The most effective GNP exhibited a dissociation constant (K_d) of 50 nM per monosaccharide, the most effective ligand of PA‐IL measured to date; another demonstration of the potential of glyco‐nanotechnology towards multivalent tools and potent anti‐adhesives for the prevention of pathogen invasion. The influence of ligand presentation density on their recognition by protein receptors is also demonstrated.     

A Highly K+‐Selective Two‐Photon Fluorescent Probe

A highly K⁺‐selective two‐photon fluorescent probe for the in vitro monitoring of physiological K⁺ levels in the range of 1–100 mM is reported. The two‐photon excited fluorescence (TPEF) probe shows a fluorescence enhancement (FE) by a factor of about three in the presence of 160 mM K⁺, independently of one‐photon (OP, 430 nm) or two‐photon (TP, 860 nm) excitation and comparable K⁺‐induced FEs in the presence of competitive Na⁺ ions. The estimated dissociation constant (K_d) values in Na⁺‐free solutions (K_d^OP=(28±5) mM and K_d^TP=(36±6) mM ) and in combined K⁺/Na⁺ solutions (K_d^OP=(38±8) mM and K_d^TP=(46±25) mM ) reflecting the high K⁺/Na⁺ selectivity of the fluorescent probe. The TP absorption cross‐section (σ_2PA) of the TPEF probe+160 mM K⁺ is 26 GM at 860 nm. Therefore, the TPEF probe is a suitable tool for the in vitro determination of K⁺.     

Evaluation of the performance of four molecular docking programs on a diverse set of protein‐ligand complexes

Many molecular docking programs are available nowadays, and thus it is of great practical value to evaluate and compare their performance. We have conducted an extensive evaluation of four popular commercial molecular docking programs, including Glide, GOLD, LigandFit, and Surflex. Our test set consists of 195 protein‐ligand complexes with high‐resolution crystal structures (resolution ≤2.5 Å) and reliable binding data [dissociation constant (K_d) or inhibition constant (K_i)], which are selected from the PDBbind database with an emphasis on diversity. The top‐ranked solutions produced by these programs are compared to the native ligand binding poses observed in crystal structures. Glide and GOLD demonstrate better accuracy than the other two on the entire test set. Their results are also less sensitive to the starting structures for docking. Comparison of the results produced by these programs at three different computation levels reveal that their accuracy are not always proportional to CPU cost as one may expect. The binding scores of the top‐ranked solutions produced by these programs are in low to moderate correlations with experimentally measured binding data. Further analyses on the outcomes of these programs on three suites of subsets of protein‐ligand complexes indicate that these programs are less capable to handle really flexible ligands and relatively flat binding sites, and they have different preferences to hydrophilic/hydrophobic binding sites. Our evaluation can help other researchers to make reasonable choices among available molecular docking programs. It is also valuable for program developers to improve their methods further. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

De Novo Design and Synthesis of a γ‐Turn Peptidomimetic Scaffold and Its Application as JNK3 Allosteric Ligand

As a way to develop a neuroprotective agent for the JNK3‐JIP1‐binding site, peptidomimetics of JIP‐1 as JNK3 allosteric regulators have been examined. The study consisted of in silico scaffold hopping, molecular docking, solution and solid‐phase peptide syntheses, and K_d measurements using surface plasmon resonance. As a peptidomimetic of JIP1, heptamer mimetic 16 (K_d=2.72 μm ) displayed a higher affinity than decamer JIP1 (K_d=23.6 μm ). The high affinity of 16 implies that the characteristic γ‐turn mimetic structure, “”Φ‐X‐Φ“ hydrophobic motif in 16 , increased its affinity toward the JIP‐site of JNK3.     

Darstellung,Kristallstrukturen, Schwingungsspektren und Normalkoordinatenanalysen der mer‐Trihalogeno‐tris‐Pyridin‐Osmium(III)Komplexe mer‐[OsX3Py3], X = Cl,Br, I

Synthesis, Crystal Structures, Vibrational Spectra, and Normal Coordinate Analyses of the mer ‐Trihalogeno‐tris‐Pyridine‐Osmium(III) Complexes mer‐[OsX₃Py₃], X = Cl, Br, I By reaction of the hexahalogenoosmates(IV) with pyridine and iso‐amylalcohol mer‐trihalogeno‐tris‐pyridine‐osmium(III) complexes are formed and purified by chromatography. X‐ray structure determinations on single crystals have been performed of mer‐[OsBr₃Py₃] (monoclinic, space group P2₁/n, a = 9.098(5), b = 12.864(5), c = 15.632(5) Å, β = 90.216(5)°, Z = 4) and mer‐[OsI₃Py₃] (monoclinic, space group P2₁/n, a = 9.0952(17), b = 13.461(4), c = 15.891(10), β = 91.569(5)°, Z = 4). The pyridine rings are twisted propeller‐like against the N₃ meridional plane with mean angles of 49° (Cl), 46° (Br), 44° (I). Based on the molecular parameters of the X‐ray structure determinations and assuming C₂ point symmetry, the IR and Raman spectra are assigned by normal coordinate analysis. Due to the stronger trans influence of pyridine as compared with the halide ligands for N'–Os–X ^· axes significantly different valence force constants are observed in comparison with symmetrically coordinated octahedron axes: f_d(OsCl) = 1.74, f_d(OsCl^·) = 1.49, f_d(OsBr) = 1.43, f_d(OsBr ^· ) = 1.18, f_d(OsI) = 0.99, f_d(OsI ^· ) = 0.96, f_d(OsN) between 1.96 and 2.07 and f_d(OsN') between 2.13 and 2.32 mdyn/Å.     

Steric and Electronic Effects on an Antibody‐Catalyzed Diels–Alder Reaction

A series of substituted thiophene dioxides was tested as diene substrates for the antibody 1E9, which was elicited with a hexachloronorbornene derivative and normally catalyzes the inverse electron‐demand Diels–Alder reaction between 2,3,4,5‐tetrachlorothiophene dioxide (TCTD) and N‐ethylmaleimide (NEM). Previous structural and computational studies had suggested that the catalytic efficiency of this system derives in part from a very snug fit between the apolar active site and the transition state of this reaction. Nevertheless, replacing all the Cl‐atoms in the hapten with Br‐atoms leads to no loss in affinity (K_d=0.1 nM ), indicating substantial conformational flexibility in the residues that line the binding pocket. Consistent with this observation, the 2,3,4,5‐tetrabromothiophene dioxide is a good substrate for the antibody (k_cat=1.8 min^?1, K_NEM=14 μM ), despite being considerably larger than TCTD. In contrast, normal electron‐demand Diels–Alder reactions between NEM and unsubstituted thiophene dioxide or 2,3,4,5‐tetramethylthiophene dioxide, which are much smaller or nearly isosteric with TCTD, respectively, are not detectably accelerated. These results show that the electronic properties of the 1E9 active site are optimized to a remarkable degree for the inverse electron‐demand Diels–Alder reaction for which it was designed. Indeed, they appear to play a more important role in catalysis than simple proximity effects.     

Kinetics of Iterative Carbohydrate Transfer to Polysaccharide Catalyzed by Chondroitin Polymerase on a Highly Sensitive Flow‐Type 27 MHz Quartz‐Crystal Microbalance

Using a highly sensitive flow‐type 27 MHz quartz crystal microbalance, we could detect a small mass change during stepwise and alternating one‐sugar transfer of glucuronic acid (GlcA) and N‐acetylgalactosamine (GalNAc) to an acceptor, catalyzed by chondroitin polymerase from Escherichia coli strain K4 (K4CP), and analyze the elongation mechanism of K4CP. K4CP was found to bind strongly to a chondroitin acceptor (K_d=0.97 μM ). Although the binding affinity and the catalytic rate constant for each monomer were considerably different, the apparent catalytic efficiency (k_cat/K_m) was similar (6.3×10⁴ M ^?1 s^?1 for GlcA transfer and 3.4×10⁴ M ^?1 s^?1 for the GalNAc transfer). This is reasonable for the smooth alternating elongation of GlcA and GalNAc on the acceptor. This is the first study to report the determination of kinetic parameters for enzymatic, alternated, sugar elongation.     

In situ green synthesis of Cu‐Ni bimetallic nanoparticles supported on reduced graphene oxide as an effective and recyclable catalyst for the synthesis of N‐benzyl‐N‐aryl‐5‐amino‐1H‐tetrazoles

In the present work, for the first time we have designed a novel approach for the synthesis of N‐benzyl‐N‐aryl‐5‐amino‐1H‐tetrazoles using reduced graphene oxide (rGO) decorated with Cu‐Ni bimetallic nanoparticles (NPs). In situ synthesis of Cu/Ni/rGO nanocomposite was performed by a cost efficient, surfactant‐free and environmentally benign method using Crataegus azarolus var. aronia L. leaf extract as a stabilizing and reducing agent. Phytochemicals present in the extract can be used to reduce Cu²⁺ and Ni²⁺ ions and GO to Cu NPs, Ni NPs and rGO, respectively. Analyses by means of FT‐IR, UV–Vis, EDS, TEM, FESEM, XRD and elemental mapping confirmed the Cu/Ni/rGO formation and also FT‐IR, NMR, and mass spectroscopy as well as elemental analysis were used to characterize the tetrazoles. The Cu/Ni/rGO nanocomposite showed the superior catalytic activity for the synthesis of N‐benzyl‐N‐aryl‐5‐amino‐1H‐tetrazoles within a short reaction time and high yields. Furthermore, this protocol eliminates the need to handle HN₃.     

Application of plug–plug technique to ACE experiments for discovery of peptides binding to a larger target protein: A model study of calmodulin‐binding fragments selected from a digested mixture of reduced BSA

To discover peptide ligands that bind to a target protein with a higher molecular mass, a concise screening methodology has been established, by applying a “plug–plug” technique to ACE experiments. Exploratory experiments using three mixed peptides, mastoparan‐X, β‐endorphin, and oxytocin, as candidates for calmodulin‐binding ligands, revealed that the technique not only reduces the consumption of the protein sample, but also increases the flexibility of the experimental conditions, by allowing the use of MS detection in the ACE experiments. With the plug–plug technique, the ACE–MS screening methodology successfully selected calmodulin‐binding peptides from a random library with diverse constituents, such as protease digests of BSA. Three peptides with K_d values between 8–147 μM for calmodulin were obtained from a Glu‐C endoprotease digest of reduced BSA, although the digest showed more than 70 peaks in its ACE–MS electropherogram. The method established here will be quite useful for the screening of peptide ligands, which have only low affinities due to their flexible chain structures but could potentially provide primary information for designing inhibitors against the target protein.     

Effect of sampling on BACE‐1 ligands binding free energy predictions via MM‐PBSA calculations

The BACE‐1 enzyme is a prime target to find a cure to Alzheimer's disease. In this article, we used the MM‐PBSA approach to compute the binding free energies of 46 reported ligands to this enzyme. After showing that the most probable protonation state of the catalytic dyad is mono‐protonated (on ASP32), we performed a thorough analysis of the parameters influencing the sampling of the conformational space (in total, more than 35 μs of simulations were performed). We show that ten simulations of 2 ns gives better results than one of 50 ns. We also investigated the influence of the protein force field, the water model, the periodic boundary conditions artifacts (box size), as well as the ionic strength. Amber03 with TIP3P, a minimal distance of 1.0 nm between the protein and the box edges and a ionic strength of I = 0.2 M provides the optimal correlation with experiments. Overall, when using these parameters, a Pearson correlation coefficient of R = 0.84 (R ² = 0.71) is obtained for the 46 ligands, spanning eight orders of magnitude of K _d (from 0.017 nm to 2000 μM, i.e., from −14.7 to −3.7 kcal/mol), with a ligand size from 22 to 136 atoms (from 138 to 937 g/mol). After a two‐parameter fit of the binding affinities for 12 of the ligands, an error of RMSD = 1.7 kcal/mol was obtained for the remaining ligands. © 2017 Wiley Periodicals, Inc.     

A Highly K+‐Selective Fluorescent Probe – Tuning the K+‐Complex Stability and the K+/Na+ Selectivity by Varying the Lariat‐Alkoxy Unit of a Phenylaza[18]crown‐6 Ionophore

A desirable goal is to synthesize easily accessible and highly K⁺/Na⁺‐selective fluoroionophores to monitor physiological K⁺ levels in vitro and in vivo. Therefore, highly K⁺/Na⁺‐selective ionophores have to be developed. Herein, we obtained in a sequence of only four synthetic steps a set of K⁺‐responsive fluorescent probes 4 , 5 and 6 . In a systematic study, we investigated the influence of the alkoxy substitution in ortho position of the aniline moiety in π‐conjugated aniline‐1,2,3‐triazole‐coumarin‐fluoroionophores 4 , 5 and 6 [R=MeO ( 4 ), EtO ( 5 ) and iPrO ( 6 )] towards the K⁺‐complex stability and K⁺/Na⁺ selectivity. The highest K⁺‐complex stability showed fluoroionophore 4 with a dissociation constant K_d of 19 mm , but the K_d value increases to 31 mm in combined K⁺/Na⁺ solutions, indicating a poor K⁺/Na⁺ selectivity. By contrast, 6 showed even in the presence of competitive Na⁺ ions equal K_d values (K_d^K+=45 mm and K_d^K+/Na+=45 mm ) and equal K⁺‐induced fluorescence enhancement factors (FEFs=2.3). Thus, the fluorescent probe 6 showed an outstanding K⁺/Na⁺ selectivity and is a suitable fluorescent tool to measure physiological K⁺ levels in the range of 10–80 mm in vitro. Further, the isopropoxy‐substituted N‐phenylaza[18]crown‐6 ionophore in 6 is a highly K⁺‐selective building block with a feasible synthetic route.     

Organic Ligand Binding by a Hydrophobic Cavity in a Designed Tetrameric Coiled‐Coil Protein

The design and characterization of a hydrophobic cavity in de novo designed proteins provides a wide range of information about the functions of de novo proteins. We designed a de novo tetrameric coiled‐coil protein with a hydrophobic pocketlike cavity. Tetrameric coiled coils with hydrophobic cavities have previously been reported. By replacing one Leu residue at the a position with Ala, hydrophobic cavities that did not flatten out due to loose peptide chains were reliably created. To perform a detailed examination of the ligand‐binding characteristics of the cavities, we originally designed two other coiled‐coil proteins: AM2, with eight Ala substitutions at the adjacent a and d positions at the center of a bundled structure, and AM2W, with one Trp and seven Ala substitutions at the same positions. To increase the association of the helical peptides, each helical peptide was connected with flexible linkers, which resulted in a single peptide chain. These proteins exhibited CD spectra corresponding to superhelical structures, despite weakened hydrophobic packing. AM2W exhibited binding affinity for size‐complementary organic compounds. The dissociation constants, K_d, of AM2W were 220 nM for adamantane, 81 μM for 1‐adamantanol, and 294 μM for 1‐adamantaneacetic acid, as measured by fluorescence titration analyses. Although it was contrary to expectations, AM2 did not exhibit any binding affinity, probably due to structural defects around the designed hydrophobic cavity. Interestingly, AM2W exhibited incremental structure stability through ligand binding. Plugging of structural defects with organic ligands would be expected to facilitate protein folding.     

Exploring Weak Ligand–Protein Interactions by Long‐Lived NMR States: Improved Contrast in Fragment‐Based Drug Screening

Ligands that have an affinity for protein targets can be screened very effectively by exploiting favorable properties of long‐lived states (LLS) in NMR spectroscopy. In this work, we describe the use of LLS for competitive binding experiments to measure accurate dissociation constants of fragments that bind weakly to the ATP binding site of the N‐terminal ATPase domain of heat shock protein 90 (Hsp90), a therapeutic target for cancer treatment. The LLS approach allows one to characterize ligands with an exceptionally wide range of affinities, since it can be used for ligand concentrations [L] that are several orders of magnitude smaller than the dissociation constants K_D. This property makes the LLS method particularly attractive for the initial steps of fragment‐based drug screening, where small molecular fragments that bind weakly to a target protein must be identified, which is a difficult task for many other biophysical methods.     

New dsDNA‐Binding Hybrid Molecules Combining an Unnatural Peptide and an Intercalating Moiety

In our search for new dsDNA‐binding ligands, combinatorial chemistry was first applied to select unnatural oligopeptides with moderate affinity for dsDNA. To enhance the binding affinity of a heptapeptide lead structure, Ac‐Arg‐Ual‐Sar‐Chi‐Chi‐Tal‐Arg‐NH₂ (K_d=4.9?10^?4 M ), the compound was conjugated to different heteropolyaromatic moieties by means of a variety of linker arms. Glycine, β‐alanine, glycyl‐glycine, glycyl‐β‐alanine, γ‐aminobutyric acid, and 6‐aminocaproic acid were used as spacers, representing different lengths and/or flexibilities. The intercalators coupled to the oligopeptide were acridine, fluorenone, anthracene, anthraquinone, and 3,8‐diamino‐5‐methyl‐6‐phenylphenantridinium (methidium). The binding capacities of these new hybrid molecules to dsDNA have been investigated by gel retardation and footprinting assays. The results show that, by conjugating the unnatural oligopeptide to intercalators, the affinity for dsDNA could be enhanced more than 100‐fold. For methidium‐β‐alanyl‐glycyl‐Arg‐Ual‐Sar‐Chi‐Chi‐Tal‐Arg‐NH₂ (K_d of 2.1?10^?6 M ), the interaction with dsDNA was dominated by the intercalator in such a way that the sequence specificity of the heptapeptide was changed. The interaction with dsDNA of hybrid molecules of other intercalators was mainly governed by the oligopeptide, since the sequence selectivity of the heptapeptide was conserved. In general, the linker arm glycine (shortest spacer) and glycine‐β‐alanine were preferred over β‐alanine, glycyl‐glycine and the more‐flexible spacers γ‐aminobutyric acid and 6‐aminocaproic acid. This way new hybrid molecules endowed with dsDNA affinities of ca. 10^?6 M and displaying different sequence selectivities have been developed. Therefore, combinations of such unnatural peptides with intercalators can be used to broaden the knowledge about the sequence‐selective recognition of dsDNA.     

Synthesis of new proton‐ionizable crown ether compounds containing substituted lh‐pyridin‐4‐one subcyclic units

Five novel pyridono‐18‐crown‐6 ( 10‐14 ) and two new benzyloxy‐substituted pyridino‐18‐crown‐6 ( 15 and 16 ) ligands have been prepared. By the catalytic hydrogenative removal of the benzyl group from the benzyloxy moiety at position 4 of the pyridine ring of 15 and 16 , pyridono‐18‐crown‐6 ethers 5 and 12 were obtained. These ligands were transformed to their 3,5‐dibromo ( 10 and 13 ) and 3,5‐dinitro derivatives ( 11 and 14 ) by treatment with bromine in methylene chloride and nitric acid in acetic anhydride, respectively. The latter proton‐ionizable crown ethers have pK_avalues of about 7.5 for 10 and 13 and 4.5 for 11 and 14 . Thus, they are good candidates for complexation and proton‐coupled transport of selected cations.     

Studies on the non‐covalent interactions between cyclodextrins and aryl alkanol piperazine derivatives by mass spectrometry and fluorescence spectroscopy

The non‐covalent complexes of α‐ and β‐cyclodextrins (α‐, β‐CDs) with two aryl alkanol piperazine derivatives (Pipe I and Pipe II) have been studied by electrospray ionization mass spectrometry (ESI‐MS) and fluorescence spectroscopy. The ESI‐MS experimental results demonstrated that Pipe I can conjugate to β‐CD and form 1:1 or 1:2 stoichiometric non‐covalent complexes, and Pipe II can only form 1:1 complexes with α‐ or β‐CD. Fluorescence spectra indicated that the fluorescence intensities of Pipe I and Pipe II can be enhanced by increasing the content of β‐CD. The mass spectrometric titration experiments showed that the dissociation constants K_d1 were 5.77 and 9.52 × 10^?4 mol L^?1 for the complexes of α‐CD with Pipe I and Pipe II, respectively, revealing that the binding of α‐CD‐Pipe I was stronger than α‐CD‐Pipe II. The K_d1 and K_d2 values were 9.81 × 10^?4 mol L^?1 and 1.11 × 10^?7 (mol L^?1)² for 1:1 and 1:2 complexes of Pipe I with β‐CD, respectively. The K_d values obtained from fluorescence spectroscopy were in agreement with those from ESI‐MS titration. Copyright © 2010 John Wiley & Sons, Ltd.