Pattern-based peptide recognition

Nature's use of sensor arrays in the mammalian olfactory and gustatory systems has encouraged supramolecular chemists to take a new approach to molecular recognition. Pattern-based recognition involves the use of sensor arrays to create fingerprints for analytes. The use of sensing arrays has paved the way for systems capable of identifying biological analytes that would have been difficult targets using the traditional "lock-and-key" approach to sensor design.     

Biquinolino-modified beta-cyclodextrin dimers and their metal complexes as efficient fluorescent sensors for the molecular recognition of steroids

A series of bridged beta-cyclodextrin (beta-CyD) dimers possessing functional tethers of various lengths was synthesized in moderate yield by the treatment of 2,2'-biquinoline- 4,4'-dicarboxylic dichloride with beta-CyD or mono[6-oligo(ethylenediamino)-6-deoxy]-beta-CyDs. The products were 2,2'-biquinoline-4,4'-dicarboxy-bridged bis(6-O-beta-CyD) (8), N,N'-bis(2-aminoethyl)-2,2'-biquinoline-4,4'-dicarboxamide-bridged bis(6-amino-6-deoxy-beta-CyD) (9), and N,N'-bis(5-amino-3-azapentyl)-2,2'-biquinoline-4,4'-dicarboxamide-bridged bis(6-amino-6-deoxy-beta-CyD) (10). The reaction of 8-10 with copper perchlorate give their copper(II) complexes 11-13 in satisfactory yields of over 77 %. All the bis(beta-CyD)s 8-13 act as efficient fluorescent sensors and display remarkable fluorescence enhancement upon addition of optically inert steroids. The inclusion complexation behaviors of 8-13 when treated with the representative steroids cholate (14), deoxycholate (15), and glycocholate (16) in aqueous solution at 25 degrees C were investigated by means of UV/Vis spectroscopy, conductivity and fluorescence measurements, circular dichroism spectroscopy, and 2D NMR spectroscopy. The tether length of bis(beta-CyD) 9 allows it to adopt a cooperative host-tether-guest binding mode in which the spacer and guest are co-included in the two CyD cavities. As a result of this cooperation, 9 has a stability constant (K(s)) about 2x10(2) times higher than that of monomodified beta-CyD 4 for inclusion complexation with cholate. Metallooligo(beta-CyD)s with four beta-CyD units have enhanced binding abilities compared with monomodified beta-CyDs. These metallo compounds have binding affinities for guest steroids that are up to 50-4.1x10(3) times higher than those of CyDs 2-4. The guest-induced fluorescence enhancement of bis(CyD)s opens a new channel for the design of sensor materials. The complex stability constants of these compounds are discussed from the viewpoint of induced-fit interaction and cooperative multiple binding between host and guest.     

Acid/base controllable molecular recognition

The study of controllable molecular recognition in supramolecular receptors is important for elucidating design strategies that can lead to external control of molecular recognition applications. In this work, we present the design and synthesis of an asymmetric (TTF) tetrathiafulvalene-calix[4]pyrrole receptor and show that its recognition of 1,3,5-trinitrobenzene (TNB) can be controlled by an acid/base input. The new receptor is composed of three identical TTF units and a fourth TTF unit appended with a phenol moiety. Investigation of the host-guest complexation taking place between the TTF-calix[4]pyrrole receptor and the TNB guests was studied by means of absorption and (1)H NMR spectroscopy; this revealed that the conformation of the molecular receptor can be switched between locked and unlocked states by using base and acid as the input. In the unlocked state, the receptor is able to accommodate two TNB guest molecules, whereas the guests are not able to bind to the receptor in the locked state. This work serves to illustrate how external control (acid/base) of a receptor may be used to direct the molecular recognition of guests (TNBs). It has led to a new controllable molecular recognition system that functions as an acid/base switch.     

Chiral diaminopyrrolic receptors for selective recognition of mannosides, part 2: a 3D view of the recognition modes by X-ray, NMR spectroscopy, and molecular modeling

The structural features of a representative set of five complexes of octyl α- and β-mannosides with some members of a new generation of chiral tripodal diaminopyrrolic receptors, namely, (R)-5 and (S)- and (R)-7, have been investigated in solution and in the solid state by a combined X-ray, NMR spectroscopy, and molecular modeling approach. In the solid state, the binding arms of the free receptors 7 delimit a cleft in which two solvent molecules are hydrogen bonded to the pyrrolic groups and to the benzenic scaffold. In a polar solvent (CD(3)CN), chemical shift and intermolecular NOE data, assisted by molecular modeling calculations, ascertained the binding modes of the interaction between the receptor and the glycoside for these complexes. Although a single binding mode was found to adequately describe the complex of the acyclic receptor 5 with the α-mannoside, for the complexes of the cyclic receptors 7 two different binding modes were required to simultaneously fit all the experimental data. In all cases, extensive binding through hydrogen bonding and CH-π interactions is responsible for the affinities measured in the same solvent. Furthermore, the binding modes closely account for the recognition preferences observed toward the anomeric glycosides and for the peculiar enantiodiscrimination properties exhibited by the chiral receptors.     

具有分子识别功能的树状大分子

简单介绍了近年来高分子领域中十分活跃的树状大分子的应用进展，着重介绍了具有分子识别功能的树状大分子在萃取分离、增溶、识别肿瘤细胞……等方面的应用。引用文献34篇。     

Directed molecular recognition: furfurylamine appended ditopic receptor for succinic acid

A furfurylamine appended ditopic receptor (R1) for dicarboxylic acids has been designed and synthesised. The association constants (K_a) between receptors and dicarboxylic acids have been determined using UV–vis and NMR titration techniques. The binding constant (K_a) of succinic acid with R1 was observed maximum, which implies the optimum chain length selectivity for succinic acid. Theoretical calculation and molecular modelling using Gaussian 03 program also support the optimised receptor's cavity for succinic acid.     

Morphological similarity: A 3D molecular similarity method correlated with protein-ligand recognition

Recognition of small molecules by proteins depends on three-dimensional molecular surface complementarity. However, the dominant techniques for analyzing the similarity of small molecules are based on two-dimensional chemical structure, with such techniques often outperforming three-dimensional techniques in side-by-side comparisons of correlation to biological activity. This paper introduces a new molecular similarity method, termed morphological similarity (MS), that addresses the apparent paradox. Two sets of molecule pairs are identified from a set of ligands whose protein-bound states are known crystallographically. Pairs that bind the same protein sites form the first set, and pairs that bind different sites form the second. MS is shown to separate the two sets significantly better than a benchmark 2D similarity technique. Further, MS agrees with crystallographic observation of bound ligand states, independent of information about bound states. MS is efficient to compute and can be practically applied to large libraries of compounds.     

Azulene‐Based Macrocyclic Receptors for Recognition and Sensing of Phosphate Anions

Herein we report the synthesis and detailed studies of the anion‐binding properties of two 20‐membered macrocyclic tetramide receptors: one symmetrical, containing two identical azulene‐based bisamide units, the other a hybrid, containing a dipicolinic bisamide unit and an azulene‐based bisamide unit. Analysis of the crystal structures of the macrocyclic receptors revealed their preference for adopting similar well‐preorganized bent‐sheet conformations, both as free receptors and in their complexes with anions. Studies of the optical properties of both receptors revealed abilities to selectively sense phosphate anions (H₂PO₄^?, HP₂O₇^3?), allowing for naked‐eye detection of the presence of these guests in DMSO. Binding studies in solution confirmed that the receptors bind strongly to a series of anions even in highly demanding media, such as mixtures of DMSO with water or with methanol. Comparison of the anion affinity of linear analogues with that of the macrocyclic receptors evidenced the importance of macrocyclic topology. Quantitative analysis revealed that the macrocyclic receptors are selective for H₂PO₄^? over other anions. The affinity to H₂PO₄^? seen for the symmetrical receptor, containing two azulene‐based subunits, is much higher than for the hybrid macrocycle containing both the azulene‐based and pyridine‐derived subunits. This highlights that the azulene‐based building block serves efficiently as both a binding site and a structure‐preorganizing motif.     

Tripodal pyrrolotetrathiafulvalene receptors for recognition of electron-deficient molecular guests

We report the synthesis of tripodal receptors with monopyrrolo-tetrathiafulvalene arms 1a,b, based on 1,3,5-substituted 2,4,6-triethylbenzene scaffold. The three converging pyrrolotetrathiafulvalene groups form an electron rich cone-shaped binding site. Molecular hosts 1a,b are capable of binding neutral electron deficient guests in solution, as well as positively charged pyridinium species in the gas phase.     

Quantifying intermolecular interactions: guidelines for the molecular recognition toolbox

Molecular recognition events in solution are affected by many different factors that have hampered the development of an understanding of intermolecular interactions at a quantitative level. Our tendency is to partition these effects into discrete phenomenological fields that are classified, named, and divorced: aromatic interactions, cation-pi interactions, CH-O hydrogen bonds, short strong hydrogen bonds, and hydrophobic interactions to name a few.1 To progress in the field, we need to develop an integrated quantitative appreciation of the relative magnitudes of all of the different effects that might influence the molecular recognition behavior of a given system. In an effort to navigate undergraduates through the vast and sometimes contradictory literature on the subject, I have developed an approach that treats theoretical ideas and experimental observations about intermolecular interactions in the gas phase, the solid state, and solution from a single simplistic viewpoint. The key features are outlined here, and although many of the ideas will be familiar, the aim is to provide a semiquantitative thermodynamic ranking of these effects in solution at room temperature.     

Pattern recognition strategies for molecular surfaces: III. Binding site prediction with a neural network

An algorithm for the identification of possible binding sites of biomolecules, which are represented as regions of the molecular surface, is introduced. The algorithm is based on the segmentation of the molecular surface into overlapping patches as described in the first article of this series.1 The properties of these patches (calculated on the basis of physical and chemical properties) are used for the analysis of the molecular surfaces of 7821 proteins and protein complexes. Special attention is drawn to known protein binding sites. A binding site identification algorithm is realized on the basis of the calculated data using a neural network strategy. The neural network is able to classify surface patches as protein-protein, protein-DNA, protein-ligand, or nonbinding sites. To show the capability of the algorithm, results of the surface analysis and the predictions are presented and discussed with representative examples.     

Squaramides: bridging from molecular recognition to bifunctional organocatalysis

In this minireview, squaramides are presented from their roots as artificial anion receptors in molecular recognition studies to their recent advances as powerful bifunctional hydrogen-bonding catalysts in asymmetric organocatalysis. The main features of the squaramido functionality and the direct comparison with the analogous ureas and thioureas are also discussed.     

A novel strapped porphyrin receptor for molecular recognition

A novel strapped porphyrin receptor Zn1, in which two electron-rich bis(p-phenylene)-34-crown ether-10 units are incorporated, has been designed and synthesized from the newly developed intermediate 7 for investigating new chemistry of molecular recognition. ¹H NMR and UV-Vis studies revealed that Zn1 displays relatively weak binding abilities to neutral electron deficient naphthalene-1,8,4,5-tetracarboxydiimide (NDI) derivatives 13 (no simple complexing stoichiometry was observed), 19 (K_a=48(±5) M⁻¹) and 30 (K_a=46(±5) M⁻¹) in chloroform-d, strong binding ability to pyridine derivative 25, (K_a=1.5(±0.12)×10³ M⁻¹) in chloroform, moderately strong binding ability to tetracationic compound 35·4PF₆ (K_a=475(±50) M⁻¹) in acetone-d₆, and very strong binding affinity to compound 22 (K_a=6.5(±0.7)×10⁵ M⁻¹), which consists of one pyridine and two NDI units, in chloroform. Remarkable cooperative effect of the intermolecular metal-ligand coordination and donor-acceptor interactions in complex Zn1·22 was observed by comparing the complexing behaviors between Zn1 and the appropriately designed guests. Complex Zn1·22 possesses an unique three-dimensional tri-site binding feature. For comparison, the complexing affinity of 1 toward compounds 13, 19, and 30 in chloroform-d and 35·4PF₆ in acetone-d₆ has also been investigated and the binding patterns in different complexes were explored. The results demonstrate that strapped porphyrin derivatives are ideal precursors for constructing new generation of three-dimensional multi-site artificial receptors for molecular recognition and host-guest chemistry.     

Dipyrrolyl-functionalized bipyridine-based anion receptors for emission-based selective detection of dihydrogen phosphate

New cationic anion receptors, based on the use of pyrrole-substituted bipyridine and coordinated to transition metals, are described. Specifically, polypyridine-ruthenium and -rhodium cores have been functionalized to generate an anion binding site. The design was chosen to probe the influence of the pyrrole-to-pyrrole separation on anion-binding affinities and selectivities; this distance is greater in the new systems of this report (receptors 1 and 2) relative to that present in related dipyrrolyl quinoxaline based receptors 3 and 4. Solution-phase anion-binding studies, carried out by means of (1)H NMR spectroscopic titrations in [D(6)]DMSO and isothermal titration calorimetry (ITC) in DMSO, reveal that 1 and 2 bind most simple anions with substantially higher affinity than either 3 or 4. In the case of chloride anion, structural studies, carried out by means of single-crystal X-ray diffraction analyses, are consistent with the solution-phase results and reveal that receptors 1 and 2 are both able to stabilize complexes with this halide anion in the solid state.