New helical foldamers: heterogeneous backbones with 1:2 and 2:1 alpha:beta-amino acid residue patterns

Foldamers, oligomers with strong folding propensities, are subjects of growing interest because such compounds offer unique scaffolds for the development of molecular function. We report two new foldamer classes, oligopeptides with regular 1:2 or 2:1 patterns of alpha- and beta-amino acid residues. Two distinct helical conformations are detected via 2D NMR in methanol for each backbone. One of the helices for each backbone is characterized via X-ray crystallography.     

阴离子协同组装折叠体

折叠体研究的目的是设计、合成和表征具有折叠结构的人工合成寡聚物,这些折叠体的折叠结构和自然界中的生物大分子如蛋白质的结构相似但不雷同。折叠体的研究发展为分子识别特别是阴离子识别提供了一个简单而非常有效的工具。本综述将主要介绍近几年国内外关于阴离子协同组装的折叠体的研究进展,探讨了折叠体和阴离子的相互作用规律。     

Reactive sieving with foldamers: inspiration from nature and directions for the future

Over the past several decades, chemists have designed a myriad of supramolecular scaffolds for the purpose of mimicking enzyme behavior and creating more advanced catalysts. Foldamers, one class of supramolecular structures that feature rapid, modular synthesis and dynamic structural properties and have been widely investigated for their molecular recognition properties. Specifically, our group has designed a reactive m-phenyleneethynylene foldamer, which mimics the selective properties ("reactive sieving") of the isoleucine tRNA synthetase enzyme. In this concept we discuss examples that have inspired our research as well as potential directions for future advancement of this field.     

Supramolecular Self-Assembly of β3-Peptides Mediated by Janus-Type Recognition Units

To gain mechanistic insights, natural systems with biochemical relevance are inspiring for the creation of new biomimetics with unique properties and functions. Despite progress in rational design and protein engineering, folding and intramolecular organization of individual components into supramolecular structures remains challenging and requires controlled methods. Foldamers, such as β-peptides, are structurally well defined with rigid conformations and suitable for the specific arrangement of recognition units. Herein, we show the molecular arrangement and aggregation of β³-peptides into a hexameric helix bundle. For this purpose, β-amino acid side chains were modified with cyanuric acid and triamino-s-triazine as complementary recognition units. The pre-organization of the β³-peptides leads these Janus molecule pairs into a hexameric arrangement and a defined rosette nanotube by stacking. The helical conformation of the subunits was indicated by circular dichroism spectroscopy, while the supramolecular arrangement was detected by dynamic light scattering and confirmed by high-resolution electrospray ionization mass spectrometry (ESI-HRMS).     

Sulfono‐γ‐AApeptides as a New Class of Nonnatural Helical Foldamer

Foldamers offer an attractive opportunity for the design of novel molecules that mimic the structures and functions of proteins and enzymes including biocatalysis and biomolecular recognition. Herein we report a new class of nonnatural helical sulfono‐γ‐AApeptide foldamers of varying lengths. The crystal structure of the sulfono‐γ‐AApeptide monomer S6 illustrates the intrinsic folding propensity of sulfono‐γ‐AApeptides, which likely originates from the bulkiness of tertiary sulfonamide moiety. The two‐dimensional solution NMR spectroscopy data for the longest sequence S1 demonstrates a 10/16 right‐handed helical structure. Optical analysis using circular dichroism further supports well‐ defined helical conformation of sulfono‐γ‐AApeptides in solution containing as few as five building blocks. Future development of sulfono‐γ‐AApeptides may lead to new foldamers with discrete functions, enabling expanded application in chemical biology and biomedical sciences.     

Foldamer-tuned switching kinetics and metastability of [2]rotaxanes

Slip sliding away: Foldamers can function as modular stoppers to regulate the slippage and de-slippage of pseudorotaxanes and the switching kinetics and metastability of bistable rotaxanes. By simply changing the solvent or the length of the hydrogen-bonded foldamer, the lifetime of the metastable co-conformation state can be increased dramatically, from several minutes to as long as several days.     

Cyclic peptoids

Foldamers are an intriguing family of biomimetic oligomers that exhibit a propensity to adopt stable secondary structures. N-Substituted glycine oligomers, or "peptoids", are a prototypical example of these foldamer systems and are known to form a helix resembling that of polyproline type I. Ongoing studies seek to improve the stability of peptoid folding and to discover new secondary structure motifs. Here, we report that peptoids undergo highly efficient head-to-tail macrocyclization reactions. A diverse array of peptoid sequences from pentamers to 20mers were converted to macrocyclic products within 5 min at room temperature. The introduction of the covalent constraint enhances conformational ordering, allowing for the crystallization of a cyclic peptoid hexamer and octamer. We present the first X-ray crystallographic structures of peptoid hetero-oligomers, revealing that peptoid macrocycles can form a reverse-turn conformation.     

Building Proficient Enzymes with Foldamer Prostheses

Foldamers are non‐natural oligomers that adopt stable conformations reminiscent of those found in proteins. To evaluate the potential of foldameric subunits for catalysis, semisynthetic enzymes containing foldamer fragments constructed from α‐ and β‐amino acid residues were designed and characterized. Systematic variation of the α→β substitution pattern and types of β‐residue afforded highly proficient hybrid catalysts, thus demonstrating the feasibility of expanding the enzyme‐engineering toolkit with non‐natural backbones.     

Guiding bacteria with small molecules and RNA

Chemotactic bacteria navigate their chemical environment by coupling sophisticated information processing capabilities to molecular motors that propel the cells forward. The ability to reprogram bacteria to follow entirely new chemical signals would create powerful new opportunities in bioremediation, bionanotechnology, and synthetic biology. However, the complexities of bacterial signaling and limitations of current protein engineering methods combine to make reprogramming bacteria to follow novel molecules a difficult task. Here we show that by using a synthetic riboswitch rather than an engineered protein to recognize a ligand, E. coli can be guided toward and precisely localized to a completely new chemical signal.     

Frontiers of optofluidics in synthetic biology

The development of optofluidic-based technology has ushered in a new era of lab-on-a-chip functionality, including miniaturization of biomedical devices, enhanced sensitivity for molecular detection, and multiplexing of optical measurements. While having great potential, optofluidic devices have only begun to be exploited in many biotechnological applications. Here, we highlight the potential of integrating optofluidic devices with synthetic biological systems, which is a field focusing on creating novel cellular systems by engineering synthetic gene and protein networks. First, we review the development of synthetic biology at different length scales, ranging from single-molecule, single-cell, to cellular population. We emphasize light-sensitive synthetic biological systems that would be relevant for the integration with optofluidic devices. Next, we propose several areas for potential applications of optofluidics in synthetic biology. The integration of optofluidics and synthetic biology would have a broad impact on point-of-care diagnostics and biotechnology.     

New Advances in the Synthesis of Emerging Cyclic Amidrazones to Foster Bioisosterism of Azaheterocycles

The pace and the scope of new molecules design is often constrained by limitations in synthetic chemistry. The azaheterocyclic amidrazones are of particular interest for bioisosteric considerations in drug discovery. However, the lack of efficient synthetic access has undoubtedly hampered their occurrence in the drug chemical space. Our current results describe a robust synthetic access relying on cyclization of aminohydrazine in presence of various orthoesters by either metal free- or metal-catalyzed condensations. This optimized synthetic access to cyclic amidrazones as original scaffold should inspire the chemist community and further drive innovation in the design of molecular structure for many applications (for example, drugs, materials, dyes).     

DNA meets synthetic polymers--highly versatile hybrid materials

The combination of synthetic polymers and DNA has provided biologists, chemists and materials scientists with a fascinating new hybrid material. The challenges in preparing these molecular chimeras were overcome by different synthetic strategies that rely on coupling the nucleic acid moiety and the organic polymer in solution or on solid supports. The morphologies and functions of the bioorganic block copolymers can be controlled by the nature of the synthetic polymer segment as well as by the sequence composition and length of the DNA. Recent developments have expanded the scope and applications of these hybrid materials in a number of different areas including biology and medicine, as well as bio- and nanotechnology. Their usage ranges from gene delivery through to DNA detection to programmable nano-containers for DNA-templated organic reactions.     

CD1c presentation of synthetic glycolipid antigens with foreign alkyl branching motifs

Human CD1c is a protein that activates alphabeta T cells by presenting self antigens, synthetic mannosyl phosphodolichols, and mycobacterial mannosyl phosphopolyketides. To determine which molecular features of antigen structure confer a T cell response, we measured activation by structurally divergent Mycobacterium tuberculosis mannosyl-beta1-phosphomycoketides and synthetic analogs with either stereorandom or stereospecific methyl branching patterns. T cell responses required both a phosphate and a beta-linked mannose unit, and they showed preference for C(30-34) lipid units with methyl branches in the S-configuration. Thus, T cell responses were strongest for synthetic compounds that mimicked the natural branched lipids produced by mycobacterial polyketide synthase 12. Incorporation of methylmalonate to form branched lipids is a common bacterial lipid-synthesis pathway that is absent in vertebrates. Therefore, the preferential recognition of branched lipids may represent a new lipid-based pathogen-associated molecular pattern.     

固相同步多重肽合成

本文综述了近十年来在固相肽合成基础上发展的各种同步多重合成新技术。它们的应用可进一步提高肽合成的效率、降低成本,并将促进许多肽的结构-活性关系研究。因此,将对激素-受体间作用的机理研究、对分子免疫学的发展及研究新的肽类诊断试剂或疫苗均可创造较好的条件。     

Molybdenum-catalyzed reduction of molecular dinitrogen under mild reaction conditions

Quite recently we have found two nitrogen fixation systems catalyzed by molybdenum-dinitrogen complexes under mild reaction conditions; one is the transformation of molecular dinitrogen into its synthetic equivalent of ammonia and the other is that into ammonia. A molybdenum-dinitrogen complex bearing two ferrocenyl diphosphines works as a good catalyst in the transformation of molecular dinitrogen into silylamine, where up to 226 equiv are produced based on the catalyst. A dinitrogen-bridged dimolybdenum complex bearing a PNP-type pincer ligand works as a good catalyst in the direct transformation of molecular dinitrogen into ammonia, where up to 23 equiv are produced based on the catalyst. We believe that both systems provide a new aspect in the development of novel nitrogen fixation.     

Catalytic one-pot synthesis of cyclic amidines by virtue of tandem reactions involving intramolecular hydroamination under mild conditions

A new synthetic methodology for the generation of cyclic amidines has been developed by the reaction of 1,n-aminoalkynes with electron-deficient azides using a ruthenium catalyst at ambient temperature. The reaction proceeds most likely via a tandem sequence of intramolecular hydroamination of aminoalkynes, cycloaddition of azides with the resulting enamines, and rearrangement of triazoline intermediates. It demonstrates, as the proof-of-principle, that an equilibria cascade sequence can be favorably driven by an irreversible step, thus enabling a facile one-pot synthetic route to deliver molecular complexity under unprecedented mild conditions without relying on the traditional linear approaches.     

Influence of terminal substituents on the halide anion binding of foldamer-based receptors

Foldamers 1–4 incorporating different terminal substituents have been designed and synthesized for binding halide anions.~1H NMR titration experiments carried out in DMSO-d_6/CDCl_3(15/85, v/v)demonstrated that the short oligo (aryltriazole)s backbone 1 could not bind halide anions unless that amide H-bond donors were incorporated at the termini of the oligomer. Terminal substituents on oligo(aryltriazoleamide)s foldamers 2–4 display a considerable influence on the binding affinities of the foldamers for halide anions. Large steric hindrance of the terminal substituents was found to be unfavorable for binding halide anions, but aromatic π-π interactions between two terminal substituents are capable of stabilizing the conformation of foldamers thus giving rise to an enhancement in the binding strengths. However, the terminal substituents were found to hardly affect the binding selectivity in the studied cases.     

Synthetic mimics of mammalian cell surface receptors: prosthetic molecules that augment living cells

Specific receptors on the surface of mammalian cells actively internalize cell-impermeable ligands by receptor-mediated endocytosis. To mimic these internalizing receptors, my laboratory is studying artificial cell surface receptors that comprise N-alkyl derivatives of 3beta-cholesterylamine linked to motifs that bind cell-impermeable ligands. When added to living mammalian cells, these synthetic receptors insert into cellular plasma membranes, project ligand-binding small molecules or peptides from the cell surface, and enable living cells to internalize targeted proteins and other cell-impermeable compounds. These artificial receptors mimic their natural counterparts by rapidly cycling between plasma membranes and intracellular endosomes, associating with proposed cholesterol and sphingolipid-rich lipid raft membrane microdomains, and delivering ligands to late endosomes/lysosomes. This "synthetic receptor targeting" strategy is briefly reviewed here and contrasted with other related cellular delivery systems. Potential applications of artificial cell surface receptors as molecular probes, agents for cellular targeting, tools for drug delivery, and methods for ligand depletion are discussed. The construction of synthetic receptors as prosthetic molecules, designed to seamlessly augment the molecular machinery of living cells, represents an exciting new frontier in the fields of bioorganic chemistry and chemical biology.     

Template synthesized gold nanotube membranes for chemical separations and sensing

We have developed a new class of synthetic membranes that consist of a porous polymeric support that contains an ensemble of gold nanotubes that span the thickness of the support membrane. The support is a commercially-available microporous polycarbonate filter with cylindrical nanoscopic pores. The gold nanotubes are prepared via electroless deposition of Au onto the pore walls; i.e., the pores acts as templates for the nanotubes. We have shown that by controlling the Au deposition time, Au nanotubes that have effective inside diameters of molecular dimensions (< 1 nm) can be prepared. These membranes are a new class of molecular sieves and can be used to separate both small molecules and proteins on the basis of molecular size. In addition, the use of these membranes in new approaches to electrochemical sensing is reviewed here. In this case, a current is forced through the nanotubes, and analyte molecules present in a contacting solution phase modulate the value of this transmembrane current.     

分子识别指导下的有机分子设计、合成和组装——世纪交替时代的有机化学

在21世纪即将来临之际,有机化学将面临生命科学、环境科学和材料科学越来越多的挑战。本文回顾了在分子识别指导下的有机分子的设计、合成和组装这个新领域的诞生和发展,认为这个领域将成为新世纪有机化学发展的一个重要方向。它的发展和应用不仅使得有机化学可能较好地面对新挑战,同时能推动有机合成化学自身的发展。