Helical self-organization and hierarchical self-assembly of an oligoheterocyclic pyridine-pyridazine strand into extended supramolecular fibers

Molecular Sensing and Manipulation of Protein Oligomerization in Membrane Nanotubes with Bolaamphiphilic Foldamers

Adaptive and reversible self-assembly of supramolecular protein structures is a fundamental characteristic of dynamic living matter. However, the quantitative detection and assessment of the emergence of mesoscale protein complexes from small and dynamic oligomeric precursors remains highly challenging. Here, we present a novel approach utilizing a short membrane nanotube (sNT) pulled from a planar membrane reservoir as nanotemplates for molecular reconstruction, manipulation, and sensing of protein oligomerization and self-assembly at the mesoscale. The sNT reports changes in membrane shape and rigidity caused by membrane-bound proteins as variations of the ionic conductivity of the sNT lumen. To confine oligomerization to the sNT, we have designed and synthesized rigid oligoamide foldamer tapes (ROFTs). Charged ROFTs incorporate into the planar and sNT membranes, mediate protein binding to the membranes, and, driven by the luminal electric field, shuttle the bound proteins between the sNT and planar membranes. Using Annexin-V (AnV) as a prototype, we show that the sNT detects AnV oligomers shuttled into the nanotube by ROFTs. Accumulation of AnV on the sNT induces its self-assembly into a curved lattice, restricting the sNT geometry and inhibiting the material uptake from the reservoir during the sNT extension, leading to the sNT fission. By comparing the spontaneous and ROFT-mediated entry of AnV into the sNT, we reveal how intricate membrane curvature sensing by small AnV oligomers controls the lattice self-assembly. These results establish sNT-ROFT as a powerful tool for molecular reconstruction and functional analyses of protein oligomerization and self-assembly, with broad application to various membrane processes.

Polyheterocyclic peptidomimetics: Parallel solid phase synthesis of oligo cyclic guanidines and their inhibition activity against Mycobacterium tuberculosis DNA gyrase

Polyheterocycles are one of the most desired synthetic targets due to their numerous and valuable applications in various fields. We report the design and the parallel synthesis of novel linear oligocyclic guanidine peptidomimetics from predesigned reduced polyamides. A screening of these compounds identified active Mycobacterium tuberculosis DNA gyrase inhibitors which do not inhibit human DNA topoisomerase IIα and topoisomerase I.

The Diverse World of Foldamers: Endless Possibilities of Self-Assembly

Different classes of foldamers, which are synthetic oligomers that adopt well-defined conformations in solution, have been the subject of extensive studies devoted to the elucidation of the forces driving their secondary structures and their potential as bioactive molecules. Regardless of the backbone type (peptidic or abiotic), the most important features of foldamers are the high stability, easy predictability and tunability of their folding, as well as the possibility to endow them with enhanced biological functions, with respect to their natural counterparts, by the correct choice of monomers. Foldamers have also recently started playing a starring role in the self-assembly of higher-order structures. In this review, selected articles will be analyzed to show the striking number of self-assemblies obtained for foldamers with different backbones, which will be analyzed in order of increasing complexity. Starting from the simplest self-associations in solution (e.g., dimers of β-strands or helices, bundles, interpenetrating double and multiple helices), the formation of monolayers, vesicles, fibers, and eventually nanostructured solid tridimensional morphologies will be subsequently described. The experimental techniques used in the structural investigation, and in the determination of the driving forces and mechanisms underlying the self-assemblies, will be systematically reported. Where applicable, examples of biomimetic self-assembled foldamers and their interactions with biological components will be described.

Lewis acids in situ modulate pyridazine-imine Ni catalysed ethylene (co)polymerisation

The Lewis acid-base interaction between B(iii) Lewis acids and the pyridazine moiety reduced the electron density from the Ni center and in situ modulated the pyridazine-imine nickel catalyzed ethylene (co)polymerisation.

Conformationally Programmable Chiral Foldamers with Compact and Extended Domains Controlled by Monomer Structure

Foldamers are an important class of abiotic macromolecules, with potential therapeutic applications in the disruption of protein–protein interactions. The majority adopt a single conformational motif such as a helix. A class of foldamer is now introduced where the choice of heterocycle within each monomer, coupled with a strong conformation‐determining dipole repulsion effect, allows both helical and extended conformations to be selected. Combining these monomers into hetero‐oligomers enables highly controlled exploration of conformational space and projection of side‐chains along multiple vectors. The foldamers were rapidly constructed via an iterative deprotection‐cross‐coupling sequence, and their solid‐ and solution‐phase conformations were analysed by X‐ray crystallography and NMR and CD spectroscopy. These molecules may find applications in protein surface recognition where the interface does not involve canonical peptide secondary structures.

Supramolecular Helical Systems: Helical Assemblies of Small Molecules, Foldamers, and Polymers with Chiral Amplification and Their Functions

In this review, we describe the recent advances in supramolecular helical assemblies formed from chiral and achiral small molecules, oligomers (foldamers), and helical and nonhelical polymers from the viewpoints of their formations with unique chiral phenomena, such as amplification of chirality during the dynamic helically assembled processes, properties, and specific functionalities, some of which have not been observed in or achieved by biological systems. In addition, a brief historical overview of the helical assemblies of small molecules and remarkable progress in the synthesis of single-stranded and multistranded helical foldamers and polymers, their properties, structures, and functions, mainly since 2009, will also be described.

Hexagonal Lyotropic Liquid Crystal from Simple "Abiotic" Foldamers

The motivation of foldamer chemistry is to identify novel building blocks that have the potential to imitate natural species. Peptides and peptide mimetics can form stable helical conformations and further self-assemble into diverse aggregates in water, where it is difficult to isolate a single helix. In contrast, most "abiotic" foldamers may fold into helical structures in solution, but are difficult to assemble into tertiary ones. It remains a challenge to obtain "abiotic" species similar to peptides. In this paper, a novel foldamer scaffold, in which p-phenyleneethynylene units are linked by chiral carbon atoms, was designed and prepared. In very dilute solutions, these oligomers were random coils. The hexamer and octamers could form a hexagonal lyotropic liquid crystal (LC) in CH2Cl2 when the concentrations reached the critical values. The microscopic observations indicated that they could assemble into the nanofibers in the LC. Interestingly, after some LC phases were diluted at room temperature, the nanofibers could be preserved. The good stabilities of the assemblies are possibly attributed to a more compact backbone and more rigid side chains.

Controlled Folding, Motional, and Constitutional Dynamic Processes of Polyheterocyclic Molecular Strands

General design principles have been developed for the control of the structural features of polyheterocyclic strands and their effector-modulated shape changes. Induced defined molecular motions permit designed enforcement of helical as well as linear molecular shapes. The ability of such molecular strands to bind metal cations allows the generation of coiling/uncoiling processes between helically folded and extended linear states. Large molecular motions are produced on coordination of metal ions, which may be made reversible by competition with an ancillary complexing agent and fueled by sequential acid/base neutralization energy. The introduction of hydrazone units into the strands confers upon them constitutional dynamics, whereby interconversion between different strand compositions is achieved through component exchange. These features have relevance for nanomechanical devices. We present a morphological and functional analysis of such systems developed in our laboratories.

Synthesis of 1,8-diazaanthracenes as building blocks for internally functionalized aromatic oligoamide foldamers

The synthesis of a variety of 9-functionalized 1,8-diazaanthracene diesters and amino acids is described. Derivatization at the 9-position relies on facile reactions performed on the 9-chloro and 9-bromomethyl precursors. This has allowed the incorporation of nucleophilic or sensitive functional groups that otherwise cannot be incorporated under standard methods for synthesizing these compounds. Additionally, the synthesis of the protected amino acids via a high-yielding monosaponification and subsequent Curtius rearrangement has been accomplished on a multigram scale. These units, together with the functionalized derivatives, should prove to be useful monomers in the synthesis of aromatic oligoamide foldamers.

Dynamic as well as stable protein interactions contribute to genome function and maintenance

The cell nucleus is responsible for the storage, expression, propagation, and maintenance of the genetic material it contains. Highly organized macromolecular complexes are required for these processes to occur faithfully in an extremely crowded nuclear environment. In addition to chromosome territories, the nucleus is characterized by the presence of nuclear substructures, such as the nuclear envelope, the nucleolus, and other nuclear bodies. Other smaller structural entities assemble on chromatin in response to required functions including RNA transcription, DNA replication, and DNA repair. Experiments in living cells over the last decade have revealed that many DNA binding proteins have very short residence times on chromatin. These observations have led to a model in which the assembly of nuclear macromolecular complexes is based on the transient binding of their components. While indeed most nuclear proteins are highly dynamic, we found after an extensive survey of the FRAP literature that an important subset of nuclear proteins shows either very slow turnover or complete immobility. These examples provide compelling evidence for the establishment of stable protein complexes in the nucleus over significant fractions of the cell cycle. Stable interactions in the nucleus may, therefore, contribute to the maintenance of genome integrity. Based on our compilation of FRAP data, we propose an extension of the existing model for nuclear organization which now incorporates stable interactions. Our new “induced stability” model suggests that self-organization, self-assembly, and assisted assembly contribute to nuclear architecture and function.

Electrochemical synthesis and characterisation of alternating tripyridyl-dipyrrole molecular strands with multiple nitrogen-based donor-acceptor binding sites

Synthesis of alternating pyridine-pyrrole molecular strands composed of two electron-rich pyrrole units (donors) sandwiched between three pyridinic cores (acceptors) is described. The envisioned strategy was a smooth electrosynthesis process involving ring contraction of corresponding tripyridyl-dipyridazine precursors. 2,6-Bis[6-(pyridazin-3-yl)]pyridine ligands 2a-c bearing pyridine residues at the terminal positions were prepared in suitable quantities by a Negishi metal cross-coupling procedure. The yields of heterocyclic coupling between 2-pyridyl zinc bromide reagents 12a-c and 2,6-bis(6-trifluoromethanesulfonylpyridazin-3-yl)pyridine increased from 68 to 95% following introduction of electron-donating methyl groups on the metallated halogenopyridine units. Favorable conditions for preparative electrochemical reduction of tripyridyl-dipyridazines 2b,c were established in THF/acetate buffer (pH 4.6)/acetonitrile to give the targeted 2,6-bis[5-(pyridin-2-yl)pyrrol-2-yl]pyridines 1b and 1c in good yields. The absorption behavior of the donor-acceptor tripyridyl-dipyrrole ligands was evaluated and compared to theoretical calculations. Highly fluorescent properties of these chromophores were found (ν(em)≈2 × 10(4) cm(-1) in MeOH and CH(2)Cl(2)), and both pyrrolic ligands exhibit a remarkable quantum yield in CH(2)Cl(2) (φ(f)=0.10). Structural studies in the solid state established the preferred cis conformation of the dipyrrolic ligands, which adopting a planar arrangement with an embedded molecule of water having a complexation energy exceeding 10 kcal mol(-1). The ability of the tripyridyl-dipyrrole to complex two copper(II) ions in a pentacoordinate square was investigated.

Functionalized hydrophobic and hydrophilic self-assembled supramolecular rectangles

The synthesis of six new, functionalized 180 degrees pyridyl donor ligands and their coordination-driven self-assembly into supramolecular rectangles is reported. Three of the new donors have been functionalized with hydrophobic straight chain alkane units (C6, C12, and C18) while the remaining three have been functionalized with derivatized di-, tetra-, and hexaethylene glycol hydrophilic units (DEG, TEG, and HEG, respectively). The resulting self-assembled hydrophobic and hydrophilic supramolecular rectangles have been fully characterized by multinuclear NMR and electrospray ionization mass spectrometry. Molecular force field modeling suggests that the functionalized rectangles range in size from roughly 3.0 x 2.9 to 3.0 x 6.0 nm2 in size.

Driven Evolution of a Constitutional Dynamic Library of Molecular Helices Toward the Selective Generation of [2 × 2] Gridlike Arrays under the Pressure of Metal Ion Coordination

Constitutional dynamics, self-assembly, and helical-folding control are brought together in the efficient Sc(OTf)3/microwave-catalyzed transimination of helical oligohydrazone strands, yielding highly diverse dynamic libraries of interconverting constituents through assembly, dissociation, and exchange of components. The transimination-type mechanism of the ScIII-promoted exchange, as well as its regioselectivity, occurring only at the extremities of the helical strands, allow one to perform directional terminal polymerization/depolymerization processes when starting with dissymmetric strands. A particular library is subsequently brought to express quantitatively [2 x 2] gridlike metallosupramolecular arrays in the presence of ZnII ions by component recombination generating the correct ligand from the dynamic set of interconverting strands. This behavior represents a process of driven evolution of a constitutional dynamic chemical system under the pressure (coordination interaction) of an external effector (metal ions).

Phenanthroline Dicarboxamide-Based Helical Foldamers: Stable Helical Structures in Methanol

A series of new aromatic oligoamides 2-5 based on 1,10-phenanthroline diacid and o-phenylenediamine have been synthesized through a convergent segment coupling strategy. These oligomers can fold into well-defined helical structures in solution through intramolecular hydrogen bonds and aromatic stacking interactions, which has been established by 1H NMR, fluorescence, and UV/vis spectra. In particular, it was found that the oligomers were more favorable to fold into stable helical structures in methanol than in chloroform and dichloromethane. The helical foldamers formed in the solid state have been characterized by single-crystal X-ray diffraction analysis. The results showed that the high curvature of the strands led to one and a half turns for both 2 and 21, three turns for 4, and nearly four turns for 5.

Synthetic Approaches to Polypyridyl Bridging Ligands with Proximal Multidentate Binding Sites

[reactions: see text] A series of 12 bridging ligands was prepared. These ligands include a central linker appended to two 1,8-naphthyrid-2-yl or two 1,10-phenanthrolin-2-yl units. The linkers include pyridazin-3,6-diyl, 1,8-naphthyrid-2,7-diyl, 2,2'-bipyrid-6,6'-diyl, 1,10-phenanthrolin-2,9-diyl, 1,2-di(2'-pyrid-6'-yl)ethyne, and 3,6-di(2'-pyrid-6'-yl)pyridazine. The ligands were synthesized from the diacetyl derivative of the central linker by a Friedländer condensation with either 2-aminonicotinaldehyde or 8-amino-7-quinolinecarbaldehyde. The precursor diacetyl derivatives were, in turn, prepared by pathways involving Stille and Sonogashira couplings. Examination of the electronic absorption spectra of the bridging ligands shows the strongest correlation to be between pairs of ligands having the same central linker. Complexation studies will follow.

2,2‘;9‘,2‘ ‘-Ter[1,10]phenanthroline

The title molecule, 2,2';9',2''-ter[1,10]phenanthroline can be prepared from 2,9-dichloro-1,10-phenanthroline in three steps through the corresponding diacetyl intermediate. The ligand acts as a hexadentate with K+, while two molecules form a trinuclear, helical complex with Cu(I), which evidences pi-stacking interactions and Cu-Cu distances of 3.01-3.04 A. Electrochemical analysis shows a strong interaction between the Cu(I) centers.

Silver(I) Coordination Polymers Containing Heteroditopic Ureidopyridine Ligands: The Role of Ligand Isomerism, Hydrogen Bonding, and Stacking Interactions

New silver (I) coordination polymers has been successfully designed and synthesized using heteroditopic ureidopyridine ligands 1 and 2 via a combination of coordinations bonds, hydrogen bonding, and pi-pi stacking interactions. This study shows an example of the orientation of the pyridine nitrogen relative to the urea moiety (4-substituted, 1, or 3-substituted, 2), used to control the packing of resulting crystalline coordination polymers. The ureidopyridine ligands present some flexibility because of the conformational rotation around the central urea moiety. The co-complexation of the silver(I) cation by two pyridine moieties and of the PF(6)(-) counteranion by the urea moiety results in the formation of discrete [1(2)Ag](+)PF(6)(-), (3) and [2(2)Ag](+)PF(6)(-), (4) complexes presenting restricted rotation around the central urea functionality. The geometrical information contained in the structures of ligands 1 and 2 and the heteroditopic complexation of silver hexafluorophosphate are fully exploited in an independent manner resulting in the emergence of quasi-rigidly preorganized linear and angular building blocks of 3 and 4, respectively. Additional pi-pi stacking contacts involving interactions between the pi-donor benzene and the pi-acceptor pyridine systems reinforce and direct the self-assembly of the above-described combined structural motifs in the solid state. Accordingly, linear and tubular arrays of pi-pi stacked architectures are generated in the solid state by synergistic and sequential metal ion complexation, hydrogen bonding, and pi-pi stacking interactions.

Helical Nanofibers from Aqueous Self-Assembly of an Oligo(p-phenylene)-Based Molecular Dumbbell

We have synthesized an amphiphilic dumbbell-shaped molecule consisting of dodeca-p-phenylene and aliphatic polyether dendrons as flexible end groups. The molecular dumbbell in aqueous solution self-assembles into well-defined left-handed helical cylinders with a diameter (8 nm) of a molecular length scale and a pitch length of 5.6 nm, as confirmed by TEM. These elementary helical fibrils are further assembled to give left-handed superhelical fibers with lengths up to several micrometers. Such a well-defined helical arrangement of conjugated rod building blocks may provide a new strategy for the design of one-dimensional nanostructured materials with biomimetic, electronic, and photonic functions.