Novel affinity ligands for chromatography using combinatorial chemistry

Spatially addressable combinatorial libraries were synthesized by solution phase chemistry and screened for binding to human serum albumin. Members of arylidene diamide libraries were among the best hits found, having submicromolar binding affinities. The results were analyzed by the frequency with which particular substituents appeared among the most potent compounds. After immobilization of the ligands either through the oxazolone or the amine substituent, characterization by surface plasmon resonance showed that ibuprofen affected the binding kinetics, but phenylbutazone did not. It is therefore likely that these compounds bind to Site 2 in sub domain IIIA of human serum albumin (HSA).     

Substituent cross-interaction effects on the electronic character of the C=N bridging group in substituted benzylidene anilines--models for molecular cores of mesogenic compounds. A 13C NMR study and comparison with theoretical results

13C NMR chemical shifts delta(C)(C=N) were measured in CDCl3 for a wide set of mesogenic molecule model compounds, viz. the substituted benzylidene anilines p-X-C6H4CH=NC6H4-p-Y (X = NO2, CN, CF3, F, Cl, H, Me, MeO, or NMe2; Y = NO2, CN, F, Cl, H, Me, MeO, or NMe2). The substituent dependence of delta(C)(C=N) was used as a tool to study electronic substituent effects on the azomethine unit. The benzylidene substituents X have a reverse effect on delta(C)(C=N): electron-withdrawing substituents cause shielding, while electron-donating ones behave oppositely, the inductive effects clearly predominating over the resonance effects. In contrast, the aniline substituents Y exert normal effects: electron-withdrawing substituents cause deshielding, while electron-donating ones cause shielding of the C=N carbon, the strengths of the inductive and resonance effects being closely similar. Additionally, the presence of a specific cross-interaction between X and Y could be verified. The electronic effects of the neighboring aromatic ring substituents systematically modify the sensitivity of the C=N group to the electronic effects of the benzylidene or aniline ring substituents. Electron-withdrawing substituents on the aniline ring decrease the sensitivity of delta(C)(C=N) to the substitution on the benzylidine ring, while electron-donating substituents have the opposite effect. In contrast, electron-withdrawing substituents on the benzylidene ring increase the sensitivity of delta(C)(C=N) to the substituent on the aniline ring, while electron-donating substituents act in the opposite way. These results can be rationalized in terms of the substituent-sensitive balance of the electron delocalization (mesomeric effects). The present NMR characteristics are discussed as regards the computational literature data. Valuable information has been obtained on the effects of the substituents on the molecular core of the mesogenic model compounds.     

Evidence of substituent-induced electronic interplay. Effect of the remote aromatic ring substituent of phenyl benzoates on the sensitivity of the carbonyl unit to electronic effects of phenyl or benzoyl ring substituents

Carbonyl carbon (13)C NMR chemical shifts delta(C)(C[double bond]O) measured in this work for a wide set of substituted phenyl benzoates p-Y-C(6)H(4)CO(2)C(6)H(4)-p-X (X = NO(2), CN, Cl, Br, H, Me, or MeO; Y = NO(2), Cl, H, Me, MeO, or NMe(2) ) have been used as a tool to study substituent effects on the carbonyl unit. The goal of the work was to study the cross-interaction between X and Y in that respect. Both the phenyl substituents X and the benzoyl substituents Y have a reverse effect on delta(C)(C[double bond]O). Electron-withdrawing substituents cause shielding while electron-donating ones have an opposite influence, with both inductive and resonance effects being significant. The presence of cross-interaction between X and Y could be clearly verified. Electronic effects of the remote aromatic ring substituents systematically modify the sensitivity of the C[double bond]O group to the electronic effects of the phenyl or benzoyl ring substituents. Electron-withdrawing substituents in one ring decrease the sensitivity of delta(C)(C[double bond]O) to the substitution of another ring, while electron-donating substituents inversely affect the sensitivity. It is suggested that the results can be explained by substituent-sensitive balance of the contributions of different resonance structures (electron delocalization, Scheme 1).     

Comparison of the electronic structures of imine and hydrazone side-chain functionalities with the aid of 13C and 15N NMR chemical shifts and PM3 calculations. The influence of C=N-substitution on the sensitivity to aromatic substitution

Benzaldehyde derivatives possessing a C=N double bond in the side-chain of the aromatic ring exhibit a reverse dependence of the (13)C NMR chemical shifts of the C=N carbon on the benzylidenic substituents X. Thus, electron-withdrawing substituents cause shielding (shift is reduced), while electron-donating ones cause deshielding. The origin of this phenomenon, which is in contrast with the idea of the generalized electronic effect, is extensively studied here by comparing the behavior of sets of benzaldehyde derivatives bearing various substitutents Y on the C=N nitrogen (Y-N=CH-C(6)H(4)-X). The effects of substituents X on the C=N unit change when Y is varied. Combination of the influences of the substituents X and Y gives a sensitive balance between the different resonance structures of the compounds. Our graphical treatment, where the rho(I) and rho(R) values observed for substituent X are plotted against the sigma(p)(+) value of substituent Y, is a novel use of Hammett-type substituent parameters. The justification of this method and our conclusions could be verified, for instance, by the fair correlation between the rho(I) or rho(R) values and the atomic charges of the imine carbon of the unsubstitued phenyl derivatives as well as by the correlations of the relevant bond orders and/or bond lengths both with the substituent parameters and with the atomic charges.     

Anion binding in aqueous solutions by N-(Isonicotinamido)-N'-phenylthiourea-based simple synthetic neutral receptors. role of the hydrophobic microenvironment of the receptor molecule

N-(Isonicotinamido)-N'-(substituted-phenyl)thioureas (1a-e, substituent X = p-OCH3, p-CH3, H, m-Br, and m-CF3) have been designed as neutral receptors, in order to prove the influence of conformational issues on the ability to bind anions in aqueous solutions. Compounds 1a-e were shown to create a hydrophobic microenvironment around the thiourea group, favoring hydrogen bonding interactions, by evidence from quantum mechanic calculations, thermodynamic analysis, NMR aromatic current shielding, and comparative anion binding. Referring to N-(substituted-benzamido)thioureas (2a-e, substituent Y = H, m-Cl, m-NO2, m,m-Cl,Cl, and p-NO2), we showed that, for the hydrophobic microenvironment to be operative in aqueous solutions, the amido -NH proton needs to be acidic enough.     

Subtype selectivity and flexibility of ionotropic glutamate receptors upon antagonist ligand binding

The binding modes of a set of known ionotropic glutamate receptor antagonist-ligands have been studied using homology modeling, molecular docking, molecular dynamics (MD) simulations and ab initio quantum mechanical calculations. The core structure of the studied ligands is the decahydroisoquinoline ring, which has a carboxylic acid group at position three and different negatively-charged substituents (R) at position six. The binding affinities of these molecules have been reported earlier. From the current study, the carboxylate group of the decahydroisoquinoline ring hydrogen bonds with Arg485, the amino group with Pro478 and Thr480, and the negatively charged substituent R interacts with the positively charged N-terminus of helix-F. The subtype selectivity of these ligands seems to be strongly dependent on the amino acid at position 650 (GluR2: leucine, GluR5: valine), which affects the conformation of the ligand and ligand-receptor interactions, but depends considerably on the size of the R-group of the ligand. In addition, the MD simulations also revealed that the relative positions of the S1 and S2 domains can alter significantly showing different "closure" and "rotational movements" depending on the antagonist-ligand that is bound. Accordingly, molecular docking of antagonist ligands into static crystal structures cannot sufficiently explain ligand binding and subtype selectivity.     

Structural Diversity of Copper(I)–N‐Heterocyclic Carbene Complexes; Ligand Tuning Facilitates Isolation of the First Structurally Characterised Copper(I)–NHC Containing a Copper(I)–Alkene Interaction

The preparation of a series of imidazolium salts bearing N‐allyl substituents, and a range of substituents on the second nitrogen atom that have varying electronic and steric properties, is reported. The ligands have been coordinated to a copper(I) centre and the resulting copper(I)–NHC (NHC=N‐heterocyclic carbene) complexes have been thoroughly examined, both in solution and in the solid‐state. The solid‐state structures are highly diverse and exhibit a range of unusual geometries and cuprophilic interactions. The first structurally characterised copper(I)–NHC complex containing a copper(I)–alkene interaction is reported. An N‐pyridyl substituent, which forms a dative bond with the copper(I) centre, stabilises an interaction between the metal centre and the allyl substituent of a neighbouring ligand, to form a 1D coordination polymer. The stabilisation is attributed to the pyridyl substituent increasing the electron density at the copper(I) centre, and thus enhancing the metal(d)‐to‐alkene(π*) back‐bonding. In addition, components other than charge transfer appear to have a role in copper(I)–alkene stabilisation because further increases in the Lewis basicity of the ligand disfavours copper(I)–alkene binding.     

Changes in Electron Structure of the Triple Bond in Substituted Acetylene and Diacetylene Derivatives

The substituent effect is usually considered by means of various Hammett-like substituent constants and is most often related to aromatic systems. Unlike this, we present results of our research on the influence of 27 substituents spanning a wide range of electronic properties, from strongly electron-withdrawing to strongly electron-donating, on the electron structure of X-substituted acetylenes and diacetylenes – thus the systems which until now have practically not been subject of any deeper studies. It is shown that the interaction through triple bond(s) is associated with a significant advantage of resonance effects and that the substituent effect transmitted by the C≡C−C≡C unit is about half of that transmitted by the C≡C unit alone. Substituent X mainly affects the closest carbon atom by means of proximity effect, hence changes of charge on this atom do not follow any substituent constants. The effect on further carbon atoms is much smaller. The presence of the C≡C−C≡C unit withdraws more charge from X than a triple bond alone, and hinders communication between X and the terminal H atom. Comparison of substituent effects to those present in X-substituted benzene derivatives shows that the electronic properties of the terminal hydrogen atom in acetylenes and diacetylenes are most similar to the electronic properties of ortho and para hydrogen atoms in X-substituted benzene derivatives.     

DFT prediction of ground-state spin multiplicity of cyclobutane-1,3-diyls: notable effects of two sets of through-bond interactions

DFT calculations (UB3LYP/6-31+G**) have been performed to predict the substituent effect on the ground-state spin-multiplicity and the singlet-triplet energy gap in cyclobutane-1,3-diyls, CB-DR. The ground state is calculated to be largely dependent on the substituents (X, Y) at the C2 and C4 positions. The substituent effects can be reasonably explained by the two sets of through-bond (TB) interactions which result from the coupling between the symmetric nonbonding molecular orbital (Psi(S)) and the C-X (Y) sigma and sigma* orbitals.     

CG base pair recognition by substituted phenylimidazole nucleosides

Four nonnatural imidazole nucleosides with different substituents were synthesized and studied for their binding to a CG Watson-Crick base pair by NMR spectroscopic techniques in an aprotic solvent. Concentration and temperature dependent measurements allowed the determination of association constants, association enthalpies and entropies. Strong binding was observed with analogues carrying an ureidophenyl substituent and corresponding enthalpies of association are compatible with the anticipated formation of three hydrogen bonds to the CG base pair. In contrast, only weak binding was observed for analogues with an aminophenyl or benzamidophenyl substituent. 2D NOE measurements at low temperatures confirm the proposed binding mode for the high-affinity ligands but indicate binding interactions for the weakly bound analogues different from the expected geometry.     

Z-selective synthesis of alpha,beta-unsaturated amides with triphenylsilylacetamides

With the purpose of developing a method of preparing Z-alpha,beta-unsaturated amides, the Peterson reaction of the (triphenylsilyl)acetamide Ph(3)SiCH(2)COX (1, X = NBn(2); 3, X = NMe(2)) with various aldehydes was examined. The reaction of aromatic aldehydes gave selectivities up to >97:3. It was found that the selectivity was a function of the electronic nature of the aromatic ring and higher Z selectivity was attained with electron-rich aldehydes. With aliphatic aldehydes selectivities up to 92:8 were achieved, and unlike with analogous phosphorus reagents, less sterically hindered aldehydes gave higher Z selectivity. Also, 3, which has a smaller amide group than 1, tended to give rise to higher selectivity. A comparison with the reaction of trimethylsilyl analogues revealed the significance of the phenyl substituents on the silyl group.     

Biarylpyrimidines: a new class of ligand for high-order DNA recognition

Biarylpyrimidines bearing omega-aminoalkyl substituents have been designed as ligands for high-order DNA structures: spectrophotometric, thermal and competition equilibrium dialysis assays showed that changing the functional group for substituent attachment from thioether to amide switches the structural binding preference from triplex to tetraplex DNA; the novel ligands are non-toxic and moderate inhibitors of human telomerase.     

(19)F-encoded combinatorial libraries: discovery of selective metal binding and catalytic peptoids

A (19)F NMR method for encoding of combinatorial libraries has been developed. Aryl fluorides whose chemical shifts are modified by aromatic substituents were prepared and attached to resin support beads that were used in the split-pool synthesis of peptoids. The detection of the (19)F NMR signal of tags derived from a single "big bead" was demonstrated. The library diversity arises from peptoid amines and the cyclic anhydrides used in their acylation. The resulting 90-compound library was examined for metal ion binding, and novel ligands for iron and copper were discovered. Their binding constants were determined to be in the low micromolar range using conventional methods. The library was also examined for autocatalysis of acylation, and a molecule possessing the catalytic triad of serine proteases was deduced.     

苯酰胺类D2受体显像剂的共平面效应

苯酰胺类化合物是多巴胺Ｄ2受体的拮抗剂,它不仅与Ｄ2受体的亲和力高,而且产生的锥体外副反应极轻,是一类很有应用潜力的抗精神病药物.放射性同位素(123Ｉ等)标记的苯酰胺类化合物可作为多巴胺Ｄ2受体显像剂用于临床诊断疾病.近年来,相继报导了一系列高亲和力的该类化合物,其中,123ＩＩＢＺＭ等已用于临床诊断疾病[1].本文在前文[2]苯酰胺类Ｄ2受体显像剂结构效应的研究基础上,利用ＳＹＢＹＬ6.4软件,研究了该类化合物分子的不同构象以及空间结构与结合活性之间的关系,证实了前文提出的由于分子内氢键形成六元共平面假想Ａ环、Ｂ环等是影响…     

15N NMR spectroscopy. 30—structure/shift relationships of oligopeptides and copolypeptides,including gramicidin S

The ¹⁵N NMR spectra of various oligopeptide derivatives of the Z? X? Y? Y? OMe structure, where X and Y are variable amino acids and Z is the benzyloxycarbonyl group, were measured in several protic and aprotic solvents. The shift difference of the ¹⁵N of the Y? Y and X? Y bond (neighbouring residue effect) is discussed with respect to the nature of X and Y with respect to the solvent. Oligopeptides of the Z? X? Y? Y? OH and n?H₃? X? Y? Y? OMe structures were compared with the Z-pëptide esters to investigate the spectroscopic influence of the protecting groups. The methyl ester hydrochlorides of the 25 most common amino acids were measured in water and DMSO to elucidate the solvent dependence of the substituent effects. Moreover, the methyl ester hydrochlorides were compared with Z-amino acids and N-acetyl-amino acid methyl esters in DMSO to establish whether the substituent effects depend on the nature of the amino acid derivatives. In this connection the assignments of the serine, threonine and glycine signals are discussed with respect to silk proteins. Furthermore, the assignments of the signals of copolypeptides by comparison with oligo- and homo-polypeptides are discussed. Finally, it was demonstrated that intramolecular H bonds cause downfied shifts of 7–10 ppm of the acceptor amide groups.     

Substituent effects on pyrid-2-yl ureas toward intramolecular hydrogen bonding and cytosine complexation

Equilibria between two conformational isomers of pyrid-2-yl ureas, the (E,Z) and (Z,Z) forms, have been studied in DMF-d(7) at -70 degrees C. Most of them show a small preference for the (E,Z) form with an equilibrium constant K(i) around 1-2. However, the K(i) value for 1-methyl-2-(3-(pyrid-2-yl)ureido)pyridinium iodide (12) was found to be 14.2 +/- 1.2. That is 1 order of magnitude larger than those of the others, which indicates that the positively charged 1-methylpyridinium-2-yl substituent would facilitate the (E,Z) form formation. Pyrid-2-yl ureas bind cytosine in DMF-d(7) with binding constants K(B) ranging from 30 to 1700 M(-1). Electron withdrawing substituents, such as the 4-O(2)NC(6)H(4)- or 1-methylpyridinium-4-yl substituent, preferentially facilitate the intermolecular cytosine complexation with large binding constants.     

Intramolecular thermal transformations of N-phthalimidoaziridines: 1,3-dipolar cyclo-addition and rearrangements*

The intramolecular thermal cycloaddition of N-phthalimidoaziridines at multiple bonds of substituents with the intermediate formation of azomethine ylides leads to condensed pyrrole derivatives, in which the five-membered ring is adjacent to a five-, six-, or seven-membered ring. Rearrangements, which sometimes become the predominant reactions, compete with cycloaddition. Thus, aziridines with aryl substituents readily isomerize to give imines with a 1,2-shift of the phthalimide group to one of the carbon atoms. Aziridines with one electron-withdrawing substituent probably do not open to give 1,3-dipoles but rather undergo a Cope-type rearrangement involving the three-membered ring and C = O bond of the second substituent. Even in intramolecular reactions, very low activity is found for the cyano group triple bond and aromatic ring bonds as dipolarophiles.     

Binding Interactions in Copper,Silver and Gold π-Complexes

The copper(I), silver(I), and gold(I) metals bind π-ligands by σ-bonding and π-back bonding interactions. These interactions were investigated using bidentate ancillary ligands with electron donating and withdrawing substituents. The π-ligands span from ethylene to larger terminal and internal alkenes and alkynes. Results of X-ray crystallography, NMR, and IR spectroscopy and gas phase experiments show that the binding energies increase in the order Ag<Cu<Au and the binding energies are slightly higher for alkynes than for alkenes. Modulation of the electron density at the metal using substituents on the ancillary ligands shows that the π-back bonding interaction plays a dominant role for the binding in the copper and gold complexes.     

Infrared spectra of heterocumulenes—VII: Correlations of infrared gruop wavenumbers and integrated absorption intensities in some heterocumulenes with substituent constants

A statistical evaluation of the empirical linear relations of the ν_as(X=Y=Z) integrated absorption intensities (A) in forty various heterocumulenes with substituent constants σ and σ⁺ has been carried out. The correlations of log A with substituent constants show that the positive sign of the slopes and ⁺ has been observed, suggesting that with all heterocumulenes studied the structure of the X=Y=Z group with cumulative bonds is dominant.     

Dramatic substituent effects on the mechanisms of nucleophilic attack on Se—S bridges

The reactions of XSeSX, XSeSY, and YSeSX (X, Y = CH₃, NH₂, OH, F) with F^? and CN^? nucleophiles have been investigated by means of B3PW91/6‐311+G(2df,p) and G4 calculations. In systems where the two substituents are not identical (XSeSY), the more stable of the two possible isomers corresponds to those in which the most electronegative substituent is attached to Se. Nucleophilic attack takes place at Se, independent of the nature of the nucleophile, with the only exception being XSeSF (X = CH₃, NH₂, OH), in which case the attack occurs at S. In agreement with recent results for disulfide and diselenide linkages, the mechanisms leading to Se—S bond cleavage are not always the more favorable ones because for highly electronegative substituents the most favorable process is fission of the chalcogen‐substituent bond. These dissimilarities in the observed reactivity pattern as a function of the electronegativity of the substituents are due to the fact that the σ‐type Se—S antibonding orbital, which for low‐electronegative substituents is the lowest unnoccupied molecular orbital (LUMO), becomes strongly destabilized when the electronegativity of the substituent increases, and is replaced by an antibonding π‐type Se‐X (or S‐X) orbital. In contrast, however, with what has been found for disulfide and diselenide derivatives, the observed reactivity does not change with the nature of the nucleophile. The activation strain model provides interesting insight into these processes, showing that in most cases the activation barriers are the consequence of subtle differences in the strain or in the interaction energies. © 2013 Wiley Periodicals, Inc.