Reinforced molecular recognition as an alternative to rigid receptors

In theory, a perfectly rigid receptor will probably be an unbeatable binder. However, rigidity may not be easy to achieve in practice and it is certainly not Nature’s method to realise high affinity. In many proteins binding affinity is increased through non-covalent interactions within the protein. Thus there is a considerable incentive to follow Nature’s example and start exploring the use of secondary intra-receptor interactions to aid in the binding process. Secondary interactions within a receptor will reinforce host–guest binding when the same conformational rearrangement (or freezing of motion) is required for guest binding as for the formation of the intra-receptor interactions. Introducing secondary interactions will require rather elaborate synthetic receptors to be produced. With the recent developments in dynamic combinatorial chemistry, access to the desired structures should be facilitated. Whether or not this approach will develop into a practical method remains to be established, but even if it does not, efforts along these lines will lead to a better understanding of the complex interplay between molecular recognition, folding and dynamics.

An Approach to the de Novo Synthesis of Life

[Image: see text] As the remit of chemistry expands beyond molecules to systems, new synthetic targets appear on the horizon. Among these, life represents perhaps the ultimate synthetic challenge. Building on an increasingly detailed understanding of the inner workings of living systems and advances in organic synthesis and supramolecular chemistry, the de novo synthesis of life (i.e., the construction of a new form of life based on completely synthetic components) is coming within reach. This Account presents our first steps in the journey toward this long-term goal. The synthesis of life requires the functional integration of different subsystems that harbor the different characteristics that are deemed essential to life. The most important of these are self-replication, metabolism, and compartmentalization. Integrating these features into a single system, maintaining this system out of equilibrium, and allowing it to undergo Darwinian evolution should ideally result in the emergence of life. Our journey toward de novo life started with the serendipitous discovery of a new mechanism of self-replication. We found that self-assembly in a mixture of interconverting oligomers is a general way of achieving self-replication, where the assembly process drives the synthesis of the very molecules that assemble. Mechanically induced breakage of the growing replicating assemblies resulted in their exponential growth, which is an important enabler for achieving Darwinian evolution. Through this mechanism, the self-replication of compounds containing peptides, nucleobases, and fully synthetic molecules was achieved. Several examples of evolutionary dynamics have been observed in these systems, including the spontaneous diversification of replicators allowing them to specialize on different food sets, history dependence of replicator composition, and the spontaneous emergence of parasitic behavior. Peptide-based replicator assemblies were found to organize their peptide units in space in a manner that, inadvertently, gives rise to microenvironments that are capable of catalysis of chemical reactions or binding-induced activation of cofactors. Among the reactions that can be catalyzed by the replicators are ones that produce the precursors from which these replicators grow, amounting to the first examples of the assimilation of a proto-metabolism. Operating these replicators in a chemically fueled out-of-equilibrium replication-destruction regime was found to promote an increase in their molecular complexity. Fueling counteracts the inherent tendency of replicators to evolve toward lower complexity (caused by the fact that smaller replicators tend to replicate faster). Among the remaining steps on the road to de novo life are now to assimilate compartmentalization and achieve open-ended evolution of the resulting system. Success in the synthesis of de novo life, once obtained, will have far-reaching implications for our understanding of what life is, for the search for extraterrestrial life, for how life may have originated on earth, and for every-day life by opening up new vistas in the form living technology and materials

Efficient and Mild Microwave-Assisted Stepwise Functionalization of Naphthalenediimide with α-Amino Acids

Microwave dielectric heating proved to be an efficient method for the one-pot and stepwise syntheses of symmetrical and unsymmetrical naphthalenediimide derivatives of α-amino acids. Acid-labile side chain protecting groups are stable under the reaction conditions; protection of the α-carboxylic group is not required. The stepwise condensation of different amino acids resulted in high yields of unsymmetrical naphthalenediimides. The reaction proceeds without racemization and is essentially quantitative.

Tailor-made functionalized self-assembled peptide (nano)fibers and hydrogels, and methods, uses and kits related thereto

The invention relates to self-assembling peptide (nano)fibers, hydrogels, and methods, uses and intermediate products and kits relating thereto. Provided is a method for providing peptide-based functionally modified (nano)fibers, comprising (i) providing a fiber forming solution comprising pseudopeptide building blocks of the formula A-Peptide-B, wherein: Peptide is a moiety of 1 to 8 amino acid residues having a sequence that is predisposed to form a one-dimensional array, such as β-sheet fibrils; A is an aromatic moiety carrying two reactive thiol groups; and B is a reactive α-nucleophile; (ii) exposing the fiber forming solution to oxidizing conditions to induce supramolecular self-assembly of the pseudopeptide building blocks into peptide-based (nano)fibers; and (iii) contacting said (nano)fibers with at least one biologically relevant functional group of interest comprising reactivity C forming a reactive pair with B to obtain covalently functionally modified nanofibers

Automated device for continuous stirring while sampling in liquid chromatography systems

Ultra-performance liquid chromatography is a common analysis tool, and stirring is common in many laboratory setups. Here we show a device which enables continuous stirring of samples whilst inside an ultra-performance liquid chromatography system. Utilizing standard magnetic stirring bars that fit standard vials, the device allows for the automation of experimental setups that require stirring. The device is designed such that it can replace the standard sample holder and fits in its place, while being battery operated. The use of three-dimensional (3D) printing and commercially available parts enables low-effort and low-cost device production, as well as easy modifications. Testing the device was performed by video analysis and by following the kinetics of a dynamic combinatorial library that is known to be exquisitely sensitive to agitation, as a result of involving a fiber growth-breakage mechanism. Design files and schematics are provided

Controlling the Morphology of Aggregates of an Amphiphilic Synthetic Receptor through Host-Guest Interactions

A new amphiphilic receptor containing a macrocyclic anionic headgroup and a single alkyl chain was prepared through an efficient templated synthesis. The interdependence of the aggregation behavior and the host-guest chemistry was studied. In the absence of any guest the terminus of the alkyl chain of the receptor is included inside the hydrophobic cavity of the macrocycle (as evident from 1H NMR studies) leading to self-assembly into micrometer-long nanotubes (as evident from TEM studies). The alkyl chain can be displaced by an acridizinium bromide guest (as evident from 1H NMR and ITC), which leads to a dramatic change in aggregate size and morphology (as evident from DLS). Studies of the solubilization of Nile red suggest that the resulting aggregates are micelles with a cmc of around 35 µM. These results represent a new addition to the still small number of water-soluble amphiphilic receptors and one of the first examples in which specific host-guest chemistry controls the size and shape of nanoscale aggregates.