Conformational Selection Mechanism Provides Structural Insights into the Optimization of APC-Asef Inhibitors

Metastasis is the major cause of death in colorectal cancer and it has been proven that inhibiting an interaction between adenomatous polyposis coli (APC) and Rho guanine nucleotide exchange factor 4 (Asef) efficaciously restrain metastasis. However, current inhibitors cannot achieve a satisfying effect in vivo and need to be optimized. In the present study, we applied molecular dynamics (MD) simulations and extensive analyses to apo and holo APC systems in order to reveal the inhibitor mechanism in detail and provide insights into optimization. MD simulations suggested that apo APC takes on a broad array of conformations and inhibitors stabilize conformation selectively. Representative structures in trajectories show specific APC-ligand interactions, explaining the different binding process. The stability and dynamic properties of systems elucidate the inherent factors of the conformation selection mechanism. Binding free energy analysis quantitatively confirms key interface residues and guide optimization. This study elucidates the conformation selection mechanism in APC-Asef inhibition and provides insights into peptide-based drug design.     

Synthesis of Amphiphilic Supramolecular Miktoarm Star Copolymers by Molecular Recognition

Synthesis of novel amphiphilic supramolecular miktoarm star copolymers has been achieved through complementary molecular recognition and interactions between carboxy groups and amino groups. Polystyrenes carrying two and one carboxy groups at the middle of the polymer chain are used as precursors to react with poly(ethylene oxide) (PEO) end‐capped with a primary amine functionality (–NH₂) or a quaternary ammonium hydroxide functionality (–N⁺(CH₂CH₃)₃OH⁻). The result suggests that the basicity of the amine plays a key role in the molecular recognition procedure. The efficiency of ionic bond formation can be enhanced from 40% up to 97% by using PEO‐N⁺(CH₂CH₃)₃OH⁻ instead of PEO‐NH₂. The obtained supramolecular polymers can be dissociated in dilute acid solution at room temperature.

     

Structural Elucidation of the Mechanism of Molecular Recognition in Chiral Crystalline Sponges

To gain insight into chiral recognition in porous materials we have prepared a family of fourth generation chiral metal–organic frameworks (MOFs) that have rigid frameworks and adaptable (flexible) pores. The previously reported parent material, [Co₂(S‐mandelate)₂(4,4′‐bipyridine)₃](NO₃)₂, CMOM‐ 1S , is a modular MOF; five new variants in which counterions (BF₄^?, CMOM‐ 2S ) or mandelate ligands are substituted (2‐Cl, CMOM‐ 11R ; 3‐Cl, CMOM‐ 21R ; 4‐Cl, CMOM‐ 31R ; 4‐CH₃, CMOM‐ 41R ) and the existing CF₃SO₃^? variant CMOM‐ 3S are studied herein. Fine‐tuning of pore size, shape, and chemistry afforded a series of distinct host–guest binding sites with variable chiral separation properties with respect to three structural isomers of phenylpropanol. Structural analysis of the resulting crystalline sponge phases revealed that host–guest interactions, guest–guest interactions, and pore adaptability collectively determine chiral discrimination.     

分子印迹技术在生物大分子分离识别中的应用

分子印迹技术是近些年发展起来的模拟抗体-抗原相互作用原理的新技术。该文介绍了分子印迹技术的产生和发展,重点介绍了生物大分子印迹聚合物的制备条件、聚合方法及其识别机理,并对该技术的应用前景及目前存在的问题进行了探讨。     

A Uniqueness Theorem of Molecular Recognition

Phrased in terms of electron density deformations due to molecular interactions, an optimality condition, and the fundamental holographic properties of molecular electron densities, it is shown that molecular recognition is necessarily unique. A simple proof is given and the connections of this result with the Duality Principle of Molecular Recognition and related Selectivity Measures for molecular recognition are discussed.     

Synthesis,Application, and Molecular Recognition Mechanism Study of Phenylalanine Molecularly Imprinted Polymer

Abstract

Phenylalanine molecularly imprinted polymer was synthesized in the presence of triflouroacetic acid. HPLC‐MS evaluation showed it had good affinity toward its template among 16 amino acid mixtures. It was used for quantification of phenylalanine in protein hydrolysis solution and in serum without sample pre‐treatment. Further study revealed the molecular recognition mechanism involved size exclusion, hydrophobic interaction, and hydrogen bonding interaction. The molecularly imprinted polymer presented here can be used for actual sample analysis and the well characterized recognition mechanism can benefit the design, synthesis, and application of MIP.     

Specificity of Furanoside–Protein Recognition through Antibody Engineering and Molecular Modeling

Recognition of furanosides (five‐membered ring sugars) by proteins plays important roles in host–pathogen interactions. In comparison to their six‐membered ring counterparts (pyranosides), detailed studies of the molecular motifs involved in the recognition of furanosides by proteins are scarce. Here the first in‐depth molecular characterization of a furanoside–protein interaction system, between an antibody (CS‐35) and cell wall polysaccharides of mycobacteria, including the organism responsible for tuberculosis is reported. The approach was centered on the generation of the single chain variable fragment of CS‐35 and a rational library of its mutants. Investigating the interaction from various aspects revealed the structural motifs that govern the interaction, as well as the relative contribution of molecular forces involved in the recognition. The specificity of the recognition was shown to originate mainly from multiple CH–π interactions and, to a lesser degree, hydrogen bonds formed in critical distances and geometries.     

瓜环对氨基酸的分子识别研究

使用¹H NMR和UV-Vis光谱法研究了七、八元瓜环对九种天然氨基酸盐酸盐的分子识别作用. 结果表明, 瓜环对芳香侧基取代的L-酪氨酸、L-色氨酸、L-苯丙氨酸均能进行有效识别, 而侧链上不带芳香基团的氨基酸, 如L-组氨酸、L-谷氨酸、L-蛋氨酸、L-缬氨酸、L-白氨酸、L-丙氨酸, 与这些瓜环的作用相对较弱. 对于七元瓜环, 主客体间都以1∶1化学计量比形成包结物, 并得到它们相互作用的稳定常数; 八元瓜环与L-酪氨酸及L-色氨酸也以1∶1形成包结物, 而与L-苯丙氨酸以1∶2形成包结物. L-酪氨酸、L-色氨酸和L-苯丙氨酸荧光性质研究表明, 七、八元瓜环既可成为这些氨基酸荧光性质的增敏试剂, 也可成为它们荧光淬灭试剂, 这与氨基酸的结构有关.     

G-Quadruplex Recognition by DARPIns through Epitope/Paratope Analogy**

We investigated the mechanisms leading to the specific recognition of Guanine Guadruplex (G4) by DARPins peptides, which can lead to the design of G4 s specific sensors. To this end we carried out all-atom molecular dynamic simulations to unravel the interactions between specific nucleic acids, including human-telomeric (h-telo), Bcl-2, and c-Myc, with different peptides, forming a DARPin/G4 complex. By comparing the sequences of DARPin with that of a peptide known for its high affinity for c-Myc, we show that the recognition cannot be ascribed to sequence similarity but, instead, depends on the complementarity between the three-dimensional arrangement of the molecular fragments involved: the α-helix/loops domain of DARPin and the G4 backbone. Our results reveal that DARPins tertiary structure presents a charged hollow region in which G4 can be hosted, thus the more complementary the structural shapes, the more stable the interaction.     

Structural Analysis of Saccharomyces cerevisiae Dihydroorotase Reveals Molecular Insights into the Tetramerization Mechanism

Dihydroorotase (DHOase), a dimetalloenzyme containing a carbamylated lysine within the active site, is a member of the cyclic amidohydrolase family, which also includes allantoinase (ALLase), dihydropyrimidinase (DHPase), hydantoinase, and imidase. Unlike most known cyclic amidohydrolases, which are tetrameric, DHOase exists as a monomer or dimer. Here, we report and analyze two crystal structures of the eukaryotic Saccharomyces cerevisiae DHOase (ScDHOase) complexed with malate. The structures of different DHOases were also compared. An asymmetric unit of these crystals contained four crystallographically independent ScDHOase monomers. ScDHOase shares structural similarity with Escherichia coli DHOase (EcDHOase). Unlike EcDHOase, ScDHOase can form tetramers, both in the crystalline state and in solution. In addition, the subunit-interacting residues of ScDHOase for dimerization and tetramerization are significantly different from those of other DHOases. The tetramerization pattern of ScDHOase is also different from those of DHPase and ALLase. Based on sequence analysis and structural evidence, we identify two unique helices (α6 and α10) and a loop (loop 7) for tetramerization, and discuss why the residues for tetramerization in ScDHOase are not necessarily conserved among DHOases.     

Synthesis and Supramolecular Studies of Chiral Boronated Platinum(II) Complexes: Insights into the Molecular Recognition of Carboranes by β‐Cyclodextrin

The synthesis and characterisation of a novel isomeric family of closo‐carborane‐containing Pt^II complexes ((R/S)‐( 1 – 4 )?2 NO₃) are reported. Related complexes ( 5 ?NO₃ and 6 ?NO₃) that contain the 7,8‐nido‐carborane cluster were obtained from the selective deboronation of the 1,2‐closo‐carborane analogues. The corresponding water‐soluble supramolecular 1:1 host–guest β‐cyclodextrin (β‐CD) adducts ((R/S)‐( 1 – 4 ) ? β‐CD?2 NO₃) were also prepared and fully characterised. HR‐ESI‐MS experiments confirmed the presence of the host–guest adducts, and 2D‐¹H{¹¹B} ROESY NMR studies showed that the boron clusters enter the β‐CD from the side of the wider annulus. Isothermal titration calorimetry (ITC) experiments revealed enthalpically driven 1:1 and higher‐order supramolecular interactions between β‐CD and (R/S)‐( 1 – 4 )?2 NO₃ in aqueous solution. A comparison of the predominate 1:1 binding mode established that the affinity of β‐CD for the guest molecule is mainly influenced by the pyridyl ring substitution pattern and chirality of the host, whilst the nature of the closo‐carborane isomer also plays some role, with the most favourable structural features for β‐CD binding being the presence of the 4‐pyridyl ring, 1,12‐closo‐carborane, and an S configuration. The results reported here represent the first comprehensive calorimetric study of the supramolecular interactions between closo‐carborane compounds and β‐CD, and it provides fascinating insights into the structural features influencing the thermodynamics of this phenomenon.     

High Affinity Recognition of a Selected Amino Acid Epitope within a Protein by Cucurbit[8]uril Complexation

Supramolecular interactions between the host cucurbit[8]uril (CB[8]) and amino acids have been widely interrogated, but recognition of specific motifs within a protein domain have never been reported. A phage display approach was herein used to select motifs with the highest binding affinity for the heteroternary complex with methyl viologen and CB[8] (MV?CB[8]) within a vast pool of cyclic peptide sequences. From the selected motifs, an epitope consisting of three amino acid was extrapolated and incorporated into a solvent‐exposed loop of a protein domain; the protein exhibited micromolar binding affinity for the MV?CB[8] complex, matching that of the cyclic peptide. By achieving selective CB[8]‐mediated conjugation of a small molecule to a recombinant protein scaffold we pave the way to biomedical applications of this simple ternary system.     

Serine versus Threonine Glycosylation with α‐O‐GalNAc: Unexpected Selectivity in Their Molecular Recognition with Lectins

The molecular recognition of several glycopeptides bearing Tn antigen (α‐O‐GalNAc‐Ser or α‐O‐GalNAc‐Thr) in their structure by three lectins with affinity for this determinant has been analysed. The work yields remarkable results in terms of epitope recognition, showing that the underlying amino acid of Tn (serine or threonine) plays a key role in the molecular recognition. In fact, while Soybean agglutinin and Vicia villosa agglutinin lectins prefer Tn‐threonine, Helix pomatia agglutinin shows a higher affinity for the glycopeptides carrying Tn‐serine. The different conformational behaviour of the two Tn biological entities, the residues of the studied glycopeptides in the close proximity to the Tn antigen and the topology of the binding site of the lectins are at the origin of these differences.     

二茂铁甲酸分子印迹聚合物的制备和识别机理、结合特性

以二茂铁甲酸（FCA）为模板,选用不同的功能单体制备了一系列分子印迹聚合物,用平衡结合实验考察了它们对模板分子的结合性能。 结果表明,以甲基丙烯酸为功能单体制得的印迹聚合物P1对模板分子有很好的选择性,特异性吸附量ΔCP为23.18 μmol/g,印迹因子IF为2.33,竞争性结合实验结果表明,P1可以将模板分子从结构类似物中分离出来。 Scatchard方程研究表明,在研究的浓度范围内聚合物中形成了一类等价的结合位点,其对模板分子的平衡离解常数K=1.94 mmol/L,最大表观结合量Cpmax=92.33 μmol/g。 研究还表明,FCA的羧基是在聚合物的孔穴中产生识别位点的功能基,模板分子上的羧基与MAA的羧基形成双重氢键作用是分子识别的主要作用力。     

Molecular Recognition of the Fungicide Carbendazim by a Molecular Imprinted Polymer Obtained through a Mimic Template Approach

Abstract

A molecularly imprinted polymer recognizing the fungicide carbendazim was prepared using a mimicking template approach. Methyl-3-propylcarbamoyl-1H-benzimidazol-2-ylcarbamate was synthesized and used as a mimic template for polymer preparation. Selectivity of this polymer for carbendazim and structurally related substances (the template, fluberidazole, rabenzazole, thiabendazole, and benomyl and its two degradation products) was evaluated by liquid chromatography. Results demonstrate that imprinted polymer shows significant recognition properties for carbendazim, whereas the mimic and other carbendazim-related molecules are not recognized. This peculiar selectivity pattern can be explained as an imprinting effect due to the in situ formation of carbendazim from mimic degradation during the polymerization process.     

新型鹅去氧胆酸分子钳的设计合成和分子识别性质研究

以鹅去氧胆酸为隔离基, 芳香族化合物为手臂设计合成了一类新型的分子钳, 其结构经¹H NMR, IR, MS及元素分析确证. 利用紫外光谱滴定法考察了其与D/L氨基酸甲酯的对映选择性识别性能. 结果表明, 分子钳3a～3e对所考察的氨基酸甲酯均具有识别能力, 其对L-氨基酸甲酯的识别优于对D-氨基酸甲酯的识别. 从主客体的大小形状匹配及几何互补关系等方面对这些受体的识别能力及对映选择性进行了讨论.