Peptide-based capsules with chirality-controlled functionalized interiors - rational design and amplification from dynamic combinatorial libraries

Molecular vessels from preorganised natural building blocks

Supramolecular vessels emerged as tools to mimic and better understand compartmentalisation, a central aspect of living matter. However, many more applications that go beyond those initial goals have been documented in recent years, including new sensory systems, artificial transmembrane transporters, catalysis, and targeted drug or gene delivery. Peptides, carbohydrates, nucleobases, and steroids bear great potential as building blocks for the construction of supramolecular vessels, possessing complexity that is still difficult to attain with synthetic methods - they are rich in functional groups and well-defined stereogenic centers, ready for noncovalent interactions and further functions. One of the options to tame the functional and dynamic complexity of natural building blocks is to place them at spatially designed positions using synthetic scaffolds. In this review, we summarise the historical and recent advances in the construction of molecular-sized vessels by the strategy that couples synthetic predictability and durability of various scaffolds (cyclodextrins, porphyrins, crown ethers, calix[n]arenes, resorcin[n]arenes, pillar[n]arenes, cyclotriveratrylenes, coordination frameworks and multivalent high-symmetry molecules) with functionality originating from natural building blocks to obtain nanocontainers, cages, capsules, cavitands, carcerands or coordination cages by covalent chemistry, self-assembly, or dynamic covalent chemistry with the ultimate goal to apply them in sensing, transport, or catalysis.

Convenient and efficient N-methylation of secondary amines under solvent-free ball milling conditions

In the present work, we report the development of a rapid, efficient, and solvent-free procedure for the N-methylation of secondary amines under mechanochemical conditions. After optimization of the milling parameters, a vibrational ball mill was used to synthesize 26 tertiary N-methylated amine derivatives in a short time of 20 min (30 Hz frequency) and high yields ranging from 78 to 95%. An exception was compounds having a hydroxyl group in their structure, for which a decrease in reaction efficiency was observed. During our research, we investigated alternate reaction selectivity occurring in compounds able to form ring closure products that are 3,4-dihydro-2H-1,3-benzoxazine derivatives instead of N-methylated products. The liquid-assisted grinding technique has been applied using formalin as a methylating agent and sodium triacetoxyborohydride as a reducing agent in a reductive amination reaction.

Rapid Access to Chiral and Tripodal Cavitands from β-Pinene

We report Pd-catalyzed cyclotrimerization of (+)-α-bromoenone, obtained from monoterpene β-pinene, into an enantiopure cyclotrimer. This C₃ symmetric compound has three bicyclo[3.1.1]heptane rings fused to its central benzene with each ring carrying a carbonyl group. The cyclotrimer undergoes diastereoselective threefold alkynylation with the lithium salts of five terminal alkynes (41-63 %, de=4-83 %). The addition enabled a rapid synthesis of a small library of novel chiral cavitands that, in shape, resemble a tripod stand. These molecular tripods include a tris-bicycloannelated benzene head attached to three alkyne legs twisted in one direction to form a nonpolar cavity with polar groups as feet. Tripods with methylpyridinium and methylisoquinolinium legs, respectively, form inclusion complexes with anti-inflammatory and chiral drugs (R)/(S)-ibuprofen and (R)/(S)-naproxen. The mode of binding shows drug molecules docked in the cavity of the host through ion-ion, cation-π, and C-H-π contacts that, in addition of desolvation, give rise to complexes having millimolar to micromolar stability in water. Our findings open the door to creating a myriad of enantiopure tripods with tunable functions that, in the future, might give novel chemosensors, catalysts or sequestering agents.

Purely Covalent Molecular Cages and Containers for Guest Encapsulation

Cage compounds offer unique binding pockets similar to enzyme-binding sites, which can be customized in terms of size, shape, and functional groups to point toward the cavity and many other parameters. Different synthetic strategies have been developed to create a toolkit of methods that allow preparing tailor-made organic cages for a number of distinct applications, such as gas separation, molecular recognition, molecular encapsulation, hosts for catalysis, etc. These examples show the versatility and high selectivity that can be achieved using cages, which is impossible by employing other molecular systems. This review explores the progress made in the field of fully organic molecular cages and containers by focusing on the properties of the cavity and their application to encapsulate guests.

Specific Noncovalent Association of Truncated exo-Functionalized Triangular Homochiral Isotrianglimines through Head-to-Head, Tail-to-Tail, and Honeycomb Supramolecular Motifs

Chiral isotrianglimines were synthesized by the [3 + 3] cyclocondensation of (R,R)-1,2-diaminocyclohexane with C5-substituted isophthalaldehyde derivatives. The substituent's steric and electronic demands and the guest molecules' nature have affected the conformation of individual macrocycles and their propensity to form supramolecular architectures. In the crystal, the formation of a honeycomb-like packing arrangement of the simplest isotrianglimine was promoted by the presence of toluene or para-xylene molecules. A less symmetrical solvent molecule might force this arrangement to change. Polar substituents present in the macrocycle skeleton have enforced the self-association of isotrianglimines in the form of tail-to-tail dimers. These dimers could be further arranged in higher-order structures of the head-to-head type, which were held together by the solvent molecules. Non-associating isotrianglimine formed a container that accommodated acetonitrile molecules in its cavity. The calculated dimerization energies have indicated a strong preference for the formation of tail-to-tail dimers over those of the capsule type.

Expanding structural diversity in a library of disulfide macrocycles through in-situ imide hydrolysis

We describe here an unorthodox approach to dynamic covalent chemistry in which the initially-unexpected in-situ hydrolysis of a bis-imide is employed to control the composition of a library of structurally diverse macrocycles. A single building block is used to generate a library of numerous disulfide-based architectures in a one-pot single-step process. The dual-stimuli method is based on simultaneous changes in pH and DMSO concentration to expand the structural diversity of the macrocyclic products. Mechanistic details of this complex process are investigated by the kinetics analysis. We delivered a facile strategy for the synthesis of water-soluble, multicomponent and dynamic macrocycles equipped with number of different functional groups, thus giving a prospect of their application in guest-driven phase transfer.

Enantioselective Construction of Modular and Asymmetric Baskets

The precise positioning of functional groups about the inner space of abiotic hosts is a challenging task and of interest for developing more effective receptors and catalysts akin to those found in nature. To address it, we herein report a synthetic methodology for preparing basket-like cavitands comprised of three different aromatics as side arms with orthogonal esters at the rim for further functionalization. First, enantioenriched A (borochloronorbornene), B (iodobromonorbornene), and C (boronorbornene) building blocks were obtained by stereoselective syntheses. Second, consecutive A-to-B and then AB-to-C Suzuki-Miyaura (SM) couplings were optimized to give enantioenriched ABC cavitand as the principal product. The robust synthetic protocol allowed us to prepare (a) an enantioenriched basket with three benzene sides and each holding either tBu, Et, or Me esters, (b) both enantiomers of a so-called "spiral staircase" basket with benzene, naphthalene, and anthracene groups surrounding the inner space, and (c) a photo-responsive basket bearing one anthracene and two benzene arms.

Solution NMR of synthetic cavity containing supramolecular systems: what have we learned on and from?

NMR has been instrumental in studies of both the structure and dynamics of molecular systems for decades, so it is not surprising that NMR has played a pivotal role in the study of host-guest complexes and supramolecular systems. In this mini-review, selected examples will be used to demonstrate the added value of using (multiparametric) NMR for studying macrocycle-based host-guest and supramolecular systems. We will restrict the discussion to synthetic host systems having a cavity that can engulf their guests thus restricting them into confined spaces. So discussion of selected examples of cavitands, cages, capsules and their complexes, aggregates and polymers as well as organic cages and porous liquids and other porous materials will be used to demonstrate the insights that have been gathered from the extracted NMR parameters when studying such systems emphasizing the information obtained from somewhat less routine NMR methods such as diffusion NMR, diffusion ordered spectroscopy (DOSY) and chemical exchange saturation transfer (CEST) and their variants. These selected examples demonstrate the impact that the results and findings from these NMR studies have had on our understanding of such systems and on the developments in various research fields.

Rational design of hyperstable antibacterial peptides for food preservation

We describe the design of peptides with properties like thermostability, pH stability, and antibacterial activity against a few bacterial food pathogens. Insights obtained from classical structure-function analysis of natural peptides and their mutants through antimicrobial and enzymatic assays are used to rationally develop a set of peptides. pH and thermostability assays were performed to demonstrate robust antimicrobial activity post-treatment with high temperatures and at wide pH ranges. We have also investigated the mode of action of these hyperstable peptides using membrane permeability assays, electron microscopy, and molecular dynamics simulations. Notably, through mutational studies, we show that these peptides elicit their antibacterial action via both membrane destabilization and inhibition of intracellular trypsin-the two functions attributable to separate peptide segments. Finally, toxicity studies and food preservation assays demonstrate the safety and efficacy of the designed peptides for food preservation. Overall, the study provides a general 'blueprint' for the development of stable antimicrobial peptides (AMPs). Insights obtained from this work may also be combined with combinatorial methods in high-throughput studies for future development of antimicrobials for various applications.

Concentration-Dependent Self-Assembly of an Unusually Large Hexameric Hydrogen-Bonded Molecular Cage

The sizes of available self-assembled hydrogen-bond-based supramolecular capsules and cages are rather limited. The largest systems have volumes of approximately 1400-2300 ų . Herein, we report a large, hexameric cage based on intermolecular amide-amide dimerization. The unusual structure with openings, reminiscent of covalently linked cages, is held together by 24 hydrogen bonds. With a diameter of 2.3 nm and a cavity volume of ∼2800 ų , the assembly is larger than any previously known capsule/cage structure relying exclusively on hydrogen bonds. The self-assembly process in chlorinated, organic solvents was found to be strongly concentration dependent, with the monomeric form prevailing at low concentrations. Additionally, the formation of host-guest complexes with fullerenes (C₆₀ and C₇₀ ) was observed.

Anion Binding of a Cyclopeptide-Derived Molecular Cage in Aqueous Solvent Mixtures

A molecular cage consisting of two cyclic hexapeptides with an alternating sequence of (2S,4S)-4-aminoproline and 6-aminopicolinic acid subunits, covalently linked via three diglycolic acid subunits, interacts with a variety of inorganic anions in acetonitrile/water. In the respective complexes, the anion resides in a cavity between the two cyclopeptide rings where it interacts with six converging NH groups. The cage binds sulfate anions in acetonitrile/water, 2 : 1 (v/v) with a log K_a of 6.7, ca. 2.5 orders of magnitude stronger than an analogous bis(cyclopeptide) with only one linker whose sulfate affinity log K_a amounts to 4.3. The preorganization induced by the three linking units is thus beneficial for sulfate binding. In addition, these linkers cause the dissociation of the sulfate complex to have a substantial Gibbs free energy of activation ΔG^≠ of 68.9 kJ mol^-1 and they also seem to affect anion selectivity as illustrated by the different effects some anions produce on the ¹ H NMR spectra of the triply and singly-linked bis(cyclopeptides). Such anion binding cages represent promising scaffolds to mimic natural anion receptors such as the sulfate-binding protein.

Tuning the Solubility of Self-Assembled Fluorescent Aromatic Cages Using Functionalized Amino Acid Building Blocks

We previously reported novel fluorescent aromatic cages that are self-produced using a set of orthogonal dynamic covalent reactions, operating simultaneously in one-pot, to assemble up to 10 components through 12 reactions into a single cage-type structure. We now introduce N-functionalized amino acids as new building blocks that enable tuning the solubility and analysis of the resulting cages. A convenient divergent synthetic approach was developed to tether different side chains on the N-terminal of a cysteine-derived building block. Our studies show that this chemical functionalization does not prevent the subsequent self-assembly and effective formation of desired cages. While the originally described cages required 94% DMSO, the new ones bearing hydrophobic side chains were found soluble in organic solvents (up to 75% CHCl3), and those grafted with hydrophilic side chains were soluble in water (up to 75% H2O). Fluorescence studies confirmed that despite cage functionalization the aggregation-induced emission properties of those architectures are retained. Thus, this work significantly expands the range of solvents in which these self-assembled cage compounds can be generated, which in turn should enable new applications, possibly as fluorescent sensors.