Shape‐Persistent and Adaptive Multivalency: Rigid Transgeden (TGD) and Flexible PAMAM Dendrimers for Heparin Binding

This study investigates transgeden (TGD) dendrimers (polyamidoamine (PAMAM)‐type dendrimers modified with rigid polyphenylenevinylene (PPV) cores) and compares their heparin‐binding ability with commercially available PAMAM dendrimers. Although the peripheral ligands are near‐identical between the two dendrimer families, their heparin binding is very different. At low generation (G1), TGD outperforms PAMAM, but at higher generation (G2 and G3), the PAMAMs are better. Heparin binding also depends strongly on the dendrimer/heparin ratio. We explain these effects using multiscale modelling. TGD dendrimers exhibit “shape‐persistent multivalency”; the rigidity means that small clusters of surface amines are locally well optimised for target binding, but it prevents the overall nanoscale structure from rearranging to maximise its contacts with a single heparin chain. Conversely, PAMAM dendrimers exhibit “adaptive multivalency”; the flexibility means individual surface ligands are not so well optimised locally to bind heparin chains, but the nanostructure can adapt more easily and maximise its binding contacts. As such, this study exemplifies important new paradigms in multivalent biomolecular recognition.     

"Pocket dendrimers" as nanoscale receptors for bimolecular guest accommodation

A new series of dendrimer receptors was prepared by combining a (tetraphenylporphinato)zinc(II) core and benzyl ether type dendritic substituents. Since one direction of the (tetraphenylporphinato)zinc(II) was not substituted by a dendritic residue, the resulting unsymmetrical dendrimers have "pockets" available for access of external substrates. Molecular modeling, NMR measurements, and zinc-coordination experiments revealed that the third-generation dendrimer of this type exhibited characteristic inclusion of coordinative pyridine guests. When diamidopyridine moiety was introduced into the dendrimer pocket, a thymine derivative was bound through complementary hydrogen bonding. Two different kinds of substrates, pyridine and thymine derivatives, were simultaneously accommodated in the nanoscale pocket and bimolecular guest accommodation was realized with the designed dendrimer receptor.     

Self-Assembly in Natural and Unnatural Systems

Although there are no fundamental factors hindering the development of nanoscale structures, there is a growing realization that “engineering down” approaches, in other words a reduction in the size of structures generated by lithographic techniques below the present lower limit of roughly 1 μm, may become impractical. It has, therefore, become increasingly clear that only by the development of a fundamental understanding of the self-assembly of large-scale biological structures, which exist and function at and beyond the nanoscale, downwards, and the extension of our knowledge regarding the chemical syntheses of small-scale structures upwards, can the gap between the promise and the reality of nanosystems be closed. This kind of construction of nanoscale structures and nanosystems represents the so-called “bottom up” or “engineering up” approach to device fabrication. Significant progress can be made in the development of nanoscience by transferring concepts found in the biological world into the chemical arena. Central to this mission is the development of simple chemical systems capable of instructing their own organization into large aggregates of molecules through their mutual recognition properties. The precise programming of these recognition events, and hence the correct assembly of the growing superstructure, relies on a fundamental understanding and the practical exploitation of non-covalent bonding interactions between and within molecules. The science of supramolecular chemistry—chemistry beyond the molecule in its very broadest sense—has started to bridge the yawning gap between molecular and macro-molecular structures. By utilizing inter-actions as diverse as aromatic π–π stacking and metal–ligand coordination for the information source for assembly processes, chemists have, in the last decade, begun to use biological concepts such as self-assembly to construct nanoscale structures and superstructures with a variety of forms and functions. Here, we provide a flavor of how self-assembly operates in natural systems and can be harnessed in unnatural ones.     

Dendrimeric Bisphosphonates for Multivalent Protein Surface Binding

A single weak‐binding event is multiplied into an efficient receptor site for protein surfaces (<10^?1 to >10⁶ M ^?1 in buffered aqueous solution) in a biomimetic fashion. This has hitherto been done with natural host/guest pairs, but not with artificial receptors. The organic reaction presented is one of very few that enable chemists to fuse multiple ionic building blocks covalently in highly polar solution; this one‐pot reaction proceeds with virtually quantitative yield. According to this concept, other building blocks with aldehyde groups can likewise be multiplied into monodisperse functional dendrimers. Small basic proteins are bound by octameric dendrimers in 1:1 or 1:2 complexes with millimolar to submicromolar affinities. The complexation event is studied independently in buffered aqueous solution by three different spectroscopic methods (PFG‐LED, UV/Vis, and fluorescence). Potential new applications include recombinant protein purification through Arg tags on immobilized dendrimers and on/off switching of protein function by reversible active‐site capping of enzymes.     

Molecular Recognition by a Short Partial Peptide of the Adrenergic Receptor: A Bottom‐Up Approach

Receptor–neurotransmitter molecular recognition is key for neurotransmission. Although crystal structures of the receptors are known, the mechanism for recognition is not clear. Reported here is the ultraviolet (UV) and infrared (IR) spectra of complexes between a partial peptide (SIVSF), mimicking the binding motif of a catechol ring in the adrenergic receptor, and various ligands. The UV spectra show that two isomers coexist in the complex of SIVSF with properly recognized ligands, such as protonated adrenaline (adrenalineH⁺). From IR spectra, they are assigned to catechol‐ and amino‐bound structures. The catechol‐bound structure is not observed when the ligand is replaced by nonproper molecules, such as noradrenalineH⁺. The results suggest that SIVSF not only recognizes the catechol ring but can distinguish differences in the amine side chain. The method provides a new possibility for screening molecules as potential therapeutics for activating the receptor.     

One-armed artificial receptors for the binding of polar tetrapeptides in water: probing the substrate selectivity of a combinatorial receptor library

We have recently developed a new class of one-armed artificial receptors 1 for the binding of the polar tetrapeptide N-Ac-D-Glu-L-Lys-D-Ala-D-Ala-OH (EKAA) 2 in water using a combined combinatorial and statistical approach. We have now further probed the substrate selectivity of this receptor library 1 by screening a second tetrapeptide substrate (3) with the inverse sequence N-Ac-D-Ala-D-Ala-L-Lys-D-Glu-OH (AAKE). This "inverse" substrate is also efficiently bound by our receptors, with K(ass) approximately 6000 M(-1) for the best receptors, as determined both by a quantitative on-bead binding assay and by UV and fluorescence titration studies in free solution. Hence, the inverse tetrapeptide 3 is in general bound two to three times less efficiently than the "normal" peptide 2 (K(ass) approximately 17,000 M(-1)), even though the complexation mainly involves long-range electrostatic interactions and both the receptor and substrate are rather flexible. Molecular modeling and ab initio calculations have been used to rationalize the observed substrate selectivity and to analyze the various binding interactions within the complex.     

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。     

Supramolecular Chemistry—Scope and Perspectives Molecules,Supermolecules, and Molecular Devices (Nobel Lecture)

Supramolecular chemistry is the chemistry of the intermolecular bond, covering the structures and functions of the entities formed by association of two or more chemical species. Molecular recognition in the supermolecules formed by receptor-substrate binding rests on the principles of molecular complementarity, as found in spherical and tetrahedral recognition, linear recognition by coreceptors, metalloreceptors, amphiphilic receptors, and anion coordination. Supramolecular catalysis by receptors bearing reactive groups effects bond cleavage reactions as well as synthetic bond formation via cocatalysis. Lipophilic receptor molecules act as selective carriers for various substrates and make it possible to set up coupled transport processes linked to electron and proton gradients or to light. Whereas endoreceptors bind substrates in molecular cavities by convergent interactions, exoreceptors rely on interactions between the surfaces of the receptor and the substrate; thus new types of receptors, such as the metallonucleates, may be designed. In combination with polymolecular assemblies, receptors, carriers, and catalysts may lead to molecular and supramolecular devices, defined as structurally organized and functionally integrated chemical systems built on supramolecular architectures. Their recognition, transfer, and transformation features are analyzed specifically from the point of view of molecular devices that would operate via photons, electrons, or ions, thus defining fields of molecular photonics, electronics, and ionics. Introduction of photosensitive groups yields photoactive receptors for the design of light-conversion and charge-separation centers. Redox-active polyolefinic chains represent molecular wires for electron transfer through membranes. Tubular mesophases formed by stacking of suitable macrocyclic receptors may lead to ion channels. Molecular self-assembling occurs with acyclic ligands that form complexes of double-helical structure. Such developments in molecular and supramolecular design and engineering open perspectives towards the realization of molecular photonic, electronic, and ionic devices that would perform highly selective recognition, reaction, and transfer operations for signal and information processing at the molecular level.     

Pyrrolic Tripodal Receptors for the Molecular Recognition of Carbohydrates: Ditopic Receptors for Dimannosides

Synthetic ditopic receptors, designed for the molecular recognition of dimannosides, have been prepared by bridging two monotopic units effectively recognizing mannosides with linkers of the appropriate size and flexibility, endowed with hydrogen‐bonding groups. Affinities toward the α and β glycosides of the biologically relevant Manα(1–2)Man disaccharide were measured by NMR spectroscopy and isothermal titration calorimetry (ITC) in polar organic media (30–40 % DMF in chloroform). Significant selectivities and affinities in the micromolar range were observed in most cases, with two newly designed receptors being the most effective receptors of the set, together with a distinct preference of the dimannosides for the (S) enantiomer of the receptor in all cases. A 3D view of the recognition mode was elucidated by a combined NMR spectroscopic/molecular modeling approach, showing the dimannoside included in the cleft of the receptor. Compared to the monotopic precursors, the ditopic receptors showed markedly improved recognition properties, proving the efficacy of the modular receptor design for the recognition of disaccharides.     

Optical sensing based on analyte recognition by enzymes,carriers and molecular interactions

Despite the tremendous variety of methods suitable for sensing applications, we face the fact that chemical sensors displaying sensitivity, selectivity and reversibility are still scarce and are mostly confined to low-molecular-weight species. Obviously, it is not the lack of optical (or other) transduction methods that limit the performance of present day sensor desingns, but rather the insufficient selectivity of the recognition process, particularly in the field of sensors for organic and bioorganic species. The use of enzymes, ion carriers and natural or synthetic receptor/carriers which can under go specific interactions with the species to be recognized (such as through hydrogen bonding or charge-transfer interaction) can result in specific recognition and, consequently, sensing. Examples for optical sensing schemes for clinically or biologically important species including enzyme substrates, metabolites, drugs, alkali and ammonium ions and other will be given. In enzyme-based sensors various options exist: depending on which species is immobilized, assays for substrates (such as glucose, ethanol, lactate or creatine), enzymes (such as esterases) or inhibitors (such as organophosphates) can be designed. In addition, the intrinsic optical properties of certain enzymes, coenzymes or metabolites can be utilized for sensing purposes, a fact that presents an interesting alternative to enzyme sensors with chemical transducers.Notwithstanding the selectivity of biocatalytic sensors, their stability and sensitivity is moderate. Bioorganic synthetic molecules which can recognize and reversibly bind other species offer an attractive alternative, particularly in terms of stability. However, quite a different situation is found in such cases because receptors, in contrast to enzymes, do not “digest” their substrates. Hence, while the steady-state response in enzyme-based sensors is a result of kinetic equilibration, substrate binding in non-metabolizing receptors results in thermodynamic equilibration. However, most existing receptors (except antibodies) lack the unique specificity of enzymes. On the other side, new bioorganic molecules and stable receptor/carriers along with polymer materials of proper permeation selectivity can help to overcome current limitations of protein-based systems. Neutral ion carriers, which may be considered as ion receptors, are a useful example of sometimes highly specific recognition/carrier molecules with excellent stability. Unfortunately, no receptor /carrier molecules of similar specificity do exist yet for most other organic and clinical parameters of interest. There is an obvious need for new and stable molecules suitable for specific recognition of low-molecular weight organic species.We will report on the use of such new receptor/carrier molecules, the respective sensor materials, and how the process of recognition can be coupled to optical transduction. Such receptors/carriers also allow other kinds of discriminations: if, for instance, it is enantio-selective (i.e. preferably binds one species out of a pair of optical isomers), a fairly specific recognition of enantiomers of biogenic amines (such as some drugs and biogenic amines) will become possible. Specific examples will also be given of new types of sensors based on recognition by charge-transfer interaction, through-space interaction and hydrogen bonding, with fair specificity for thiamine, penicilline, nitrate, salicylate and cholic acids. Finally, current problems and the significant challenges for sensors research in the 1990s will be discussed.     

Nanoparticles: scaffolds for molecular recognition

Monolayer and mixed-monolayer protected clusters (MPCs and MMPCs) have great potential to combine molecular functionality with the intrinsic properties of nanometer-sized scaffolds. This synergy can be used to create complex functional devices, including redox-active, electronic, or magnetic storage devices, solution-based sensors, and highly efficient catalysts. This review outlines some of the recent developments in nanoscale receptors based on synthetic and nonbiological recognition elements. In these nanoparticle systems, molecular recognition is achieved by covalent attachment of receptors on the nanoparticles coupled with noncovalent interactions to target substrates. Synthetic host-guest systems, hydrogen bonding, change in redox states, pi-pi stacking, rotaxane formation, and ion recognition are the main topics covered in this review.     

Synthesis and Antimicrobial Activity of Unsymmetrical Dendrimers With Indazole,Salicylates and Anthranilates as Surface Units

Unsymmetrical dendrimers with indazole and methyl/ ethyl/ isopropyl salicylates as surface units and 4‐(bromomethyl)phenol as core unit were synthesized in good yields by O‐alkylation. Similarly unsymmetrical dendrimers with indazole and methyl/ ethyl/ isopropyl anthranilates as surface units and 4‐hydroxybenzoic acid as core unit were synthesized in good yields by amide coupling reaction. The antimicrobial activities of the newly synthesized dendrimers were evaluated against four human pathogenic bacteria viz., E. coli, S. aureus, P. aeruginosa and B. subtilis under in vitro conditions by “cup plate method”.     

Coordination‐Driven Switching of a Preorganized and Cooperative Calix[4]pyrrole Receptor

The study of preorganization in receptors, particularly in cooperative receptors, and their reversible control by external stimuli is important for elucidating design strategies that can lead to increased sensitivity and external control of molecular recognition. In this work we present the design, synthesis, and operation of an asymmetric tetrathiafulvalene (TTF)–calix[4]pyrrole receptor appended with a pyridine moiety. ¹H NMR spectroscopy was employed to demonstrate that intramolecular complexation between the receptor and the pyridine moiety leads to a preorganized receptor. Absorption and ¹H NMR spectroscopy along with a computational investigation were used to demonstrate the ability of the receptor to complex the substrate 1,3,5‐trinitrobenzene (TNB) and that the receptor can be reversibly modulated between negative and positive cooperativity by employing external stimuli in the form of Zn^II. Fitting procedures incorporating multiple datasets and fitting to multiple equilibria simultaneously have been employed to quantitatively determine the preorganization effects.     

Artificial ditopic Arg-Gly-Asp (RGD) receptors

Covalent fusion of two artificial recognition motifs for arginine and aspartate resulted in a new class of ditopic RGD receptor molecules, 1-4. The two binding sites for the oppositely charged amino acid residues are linked by either flexible linkers of different length (in 1-3) or a rigid aromatic spacer (in 4). These spacers are shown to be critical for the complexation efficiency of the artificial hosts. If the linkers are too flexible, as in 1-3, an undesired intramolecular self-association occurs within the host and competes with, and thereby weakens, substrate binding. The rigid aromatic linker in 4 prevents any intramolecular self-association and hence efficient RGD binding is observed, even in buffered water (association constant of K(a) approximately 3000 m(-1)). A further increase in hydrophobic contacts, as in host 16, can complement the specific Coulomb attractions, thereby leading to an even more stable complex (Ka=5000 m(-1)). The recognition events have been studied with NMR spectroscopy, UV/Vis spectroscopy, and fluorescence titrations.     

Synthesis of Glycopeptides,Partial Structures of Biological Recognition Components [New Synthetic Methods (67)]

Glycopeptides are partial structures of the connecting regions of glycoproteins and, like these, always contain glycosidic bonds between the carbohydrate and peptide parts. Glycoproteins are not only widely distributed but are also decisive factors in post-translational biological selectivity, especially in biological recognition. Targeted syntheses of glycopeptides require stereoselective formation of the glycosidic bonds between the carbohydrate and the peptide parts and protective group methods that enable selective deblocking of only one functional group in these polyfunctional molecules. These heavy demands have been met by the well-established use of benzylic protective groups, which can be removed by hydrogenolysis, combined with the use of base-labile 2-phosphonioethoxycarbonyl (Peoc) or 9-fluorenylmethoxycarbonyl (Fmoc) protective groups or of bromoethyl esters, which can be removed under neutral conditions. The acidolysis of tert-butyloxycarbonyl (Boc) groups and of tert-butyl esters has also been successfully used, although, under acidic conditions, anomerization or rupture of the glycosidic bonds may occur, especially when nucleophiles are present. The stable, two-stage 2-(pyridyl)ethoxycarbonyl (Pyoc) protective groups allow a more reliable synthesis of complex glycopeptides since they can be removed, after modifications, under mild conditions. Particularly suitable for the synthesis of sensitive glycopeptides are the stable allyl protective groups. They can be removed from the complex glycopeptides in a highly selective and effective manner by means of noble-metal catalysts under practically neutral conditions. These methods have been employed to synthesize glycopeptides corresponding to partial structures of interesting glycoproteins. Deprotected glyopeptides representing tumor-associated antigen structures can be coupled to bovine serum albumin, which serves as a biological carrier molecule, without the necessity of using an artificial coupling component (spacer).     

Comparison of facially amphiphilic biaryl dendrimers with classical amphiphilic ones using protein surface recognition as the tool

Facially amphiphilic biaryl dendrimers are compared with the more classical benzyl ether amphiphilic dendrimers for molecular recognition, using protein binding as the probe. The protein used for the proposed study is chymotrypsin (ChT). A generation-dependent binding affinity was observed with the benzyl ether dendrimers, while the affinities were independent of generation in the case of the biaryl dendrimers. Similarly, although the ligands incorporated in both dendrons are the same, the biaryl dendrimers are able to bind more proteins compared to the benzyl ether dendrimers. For example, G3-dendron of biaryl dendrimer can bind six molecules of chymotrypsin, whereas G3-analogue of benzyl ether dendrimers can bind only three molecules of chymotrypsin. This result is consistent with our hypothesis that the internal layers of the facially amphiphilic biaryl dendrons are solvent-exposed and accessible for recognition. In addition, the systematic size differences in dendrons were also used to gain insights into the substrate selectivity that the enzyme gains upon binding to a ligand scaffold.     

Computational Design and Study of Artificial Selenoenzyme with Controllable Activity Based on an Allosteric Protein Scaffold

The establishment of new enzymatic function in an existing scaffold is a great challenge for protein engineers. In previous work, a highly efficient artificial selenoenzyme with controllable activity was constructed, based on a Ca²⁺-responsive recoverin (Rn) protein. In this study, a design strategy combining docking, molecular dynamics, and MM-PBSA is presented, to predict the catalytically active site of glutathione peroxidase (GPx) on the allosteric domain of Rn. The energy contributions of the binding hot spot residues are evaluated further by energy decomposition analysis to determine the detailed substrate recognition mechanism of Rn, which provides clear guidance for artificial enzyme design for improved substrate binding (Michaelis–Menten constant, K_m).     

Synthesis and Enantioselective Discrimination of Chiral Fluorescence Receptors Bearing Amino Acid Units

Two chiral fluorescence receptors （1, 2） were synthesized, and their structures were characterized by IR, ^1H NMR, ^13C NMR, mass spectra and elemental analysis. The chiral recognition of receptors was studied by ^1H NMR and fluorescence spectra. The results demonstrate that receptors and dibenzoyl tartrate anion formed a 1 ： 1 complex. The receptor 1 exhibited a good enantioselective recognition ability toward the enantiomers of dibenzoyl tartrate anion.     

Synthesis of new unsymmetrical optically active (s)-(+)-naproxen dendrimers

Preparation of new unsymmetrical optically active (s)-(+)-naproxen dendrimers containing 2-hydroxymethyl-1,4-butanediol and 2,2-bis(hydroxymethyl)-1,4-butanediol cores is described. These polyarylester dendrimers are unsymmetrical with respect to chain lengths and aid in studying controlled drug delivery based on differential enzymatic cleavage. Synthesis of a new acid dendritic wedge containing (s)-(+)-naproxen is also reported.     

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.