Investigation of a Catenane with a Responsive Noncovalent Network: Mimicking Long-Range Responses in Proteins

Heterochiral coupling to bilateral β-turn structured azapeptides bearing two remote chiral centers

Enantioselective synthesis governed by chiral catalysts has been extensively developed, but that without any chiral auxiliaries or chiral catalysts is rare, particularly when remote stereogenic centers are involved. Here we report an enantioselectivity of heterochiral coupling in the one-pot reaction of racemic hydrazides with achiral 1,4-bis(isothiocyanine)benzene, yielding preferentially the heterochiral bilateral azapeptides over the homochiral ones. Despite bearing two hydrogen-bonded β-turn structures that allow intramolecular chiral transfer, the bilateral azapeptide products have two chiral centers separated by 14 atoms or 15 bonds, which prevent the direct intramolecular asymmetric communication between the two chiral centers. Interestingly, the heterochiral azapeptides feature intermolecular hydrogen bonding stacking between homochiral β-turns to form a superstructure of alternative M- and P-helices in the crystals. In contrast, the homochiral azapeptide counterparts adopt a β-sheet-like structure, which is less favorable compared to the helical-like superstructure from heterochiral azapeptides, accounting for the favored heterochiral coupling of the one-pot reaction. This work demonstrates enantioselective synthesis involving distant chiral centers through the formation of biomimetic superstructures, opening up new possibilities for the regulation of enantioselectivity.

Stimulus-Induced Relief of Intentionally Incorporated Frustration Drives Refolding of a Water-Soluble Biomimetic Foldamer

Frustrated, or nonoptimal, interactions have been proposed to be essential to a protein's ability to display responsive behavior such as allostery, conformational signaling, and signal transduction. However, the intentional incorporation of frustrated noncovalent interactions has not been explored as a design element in the field of dynamic foldamers. Here, we report the design, synthesis, characterization, and molecular dynamics simulations of the first dynamic water-soluble foldamer that, in response to a stimulus, exploits relief of frustration in its noncovalent network to structurally rearrange from a pleated to an intercalated columnar structure. Thus, relief of frustration provides the energetic driving force for structural rearrangement. This work represents a previously unexplored design element for the development of stimulus-responsive systems that has potential application to materials chemistry, synthetic biology, and molecular machines.

Mismatched covalent and noncovalent templating leads to large coiled coil-templated macrocycles

Herein we describe the use of dynamic combinatorial chemistry to self-assemble complex coiled coil motifs. We amide-coupled a series of peptides designed to form homodimeric coiled coils with 3,5-dithiobenzoic acid (B) at the N-terminus and then allowed each B-peptide to undergo disulfide exchange. In the absence of peptide, monomer B forms cyclic trimers and tetramers, and thus we expected that addition of the peptide to monomer B would shift the equilibrium towards the tetramer to maximize coiled coil formation. Unexpectedly, we found that internal templation of the B-peptide through coiled coil formation shifts the equilibrium towards larger macrocycles up to 13 B-peptide subunits, with a preference for 4, 7, and 10-membered macrocycles. These macrocyclic assemblies display greater helicity and thermal stability relative to intermolecular coiled coil homodimer controls. The preference for large macrocycles is driven by the strength of the coiled coil, as increasing the coiled coil affinity increases the fraction of larger macrocycles. This system represents a new approach towards the development of complex peptide and protein assemblies.

Identification of β-strand mediated protein-protein interaction inhibitors using ligand-directed fragment ligation

β-Strand mediated protein-protein interactions (PPIs) represent underexploited targets for chemical probe development despite representing a significant proportion of known and therapeutically relevant PPI targets. β-Strand mimicry is challenging given that both amino acid side-chains and backbone hydrogen-bonds are typically required for molecular recognition, yet these are oriented along perpendicular vectors. This paper describes an alternative approach, using GKAP/SHANK1 PDZ as a model and dynamic ligation screening to identify small-molecule replacements for tranches of peptide sequence. A peptide truncation of GKAP functionalized at the N- and C-termini with acylhydrazone groups was used as an anchor. Reversible acylhydrazone bond exchange with a library of aldehyde fragments in the presence of the protein as template and in situ screening using a fluorescence anisotropy (FA) assay identified peptide hybrid hits with comparable affinity to the GKAP peptide binding sequence. Identified hits were validated using FA, ITC, NMR and X-ray crystallography to confirm selective inhibition of the target PDZ-mediated PPI and mode of binding. These analyses together with molecular dynamics simulations demonstrated the ligands make transient interactions with an unoccupied basic patch through electrostatic interactions, establishing proof-of-concept that this unbiased approach to ligand discovery represents a powerful addition to the armory of tools that can be used to identify PPI modulators.

Balancing interactions in proline-based receptors for chiral recognition of l-/d-DOPA

Proline based receptors (1-14) attached with phenylboronic acid and benzaldehyde binding groups at the N-/C- or C-/N-termini of the proline residue were created for chiral recognition of l-/d-DOPA, in an attempt to examine if balancing the two binding events would influence the recognition. By changing the positions of boronic acid and aldehyde groups substituted on the phenyl rings (1-4, 5-8) and the site at which phenylboronic acid and benzaldehyde moieties attached respectively to the N- and C-termini or C- and N-termini of the proline residue (1-4vs.5-8), and by introducing an electron-withdrawing fluorine atom in the phenyl ring of the weaker binder the benzaldehyde moiety (11vs.1, 14vs.5), we were able to show that a better balance of the two binding events does improve the chiral recognition. This finding can only be made with the current version of receptors that were equipped with two different binding groups. Together with the finding that the chiral recognition performance in mixed organic-aqueous solutions is tunable by varying the solvent composition, we have now arrived at a protocol for designing proline based receptors for extended applications in chiral recognition.

Remote electrochemical modulation of pKa in a rotaxane by co-conformational allostery

Allosteric control, one of Nature's most effective ways to regulate functions in biomolecular machinery, involves the transfer of information between distant sites. The mechanistic details of such a transfer are still an object of intensive investigation and debate, and the idea that intramolecular communication could be enabled by dynamic processes is gaining attention as a complement to traditional explanations. Mechanically interlocked molecules, owing to the particular kind of connection between their components and the resulting dynamic behavior, are attractive systems to investigate allosteric mechanisms and exploit them to develop functionalities with artificial species. We show that the pK_a of an ammonium site located on the axle component of a [2]rotaxane can be reversibly modulated by changing the affinity of a remote recognition site for the interlocked crown ether ring through electrochemical stimulation. The use of a reversible ternary redox switch enables us to set the pK_a to three different values, encompassing more than seven units. Our results demonstrate that in the axle the two sites do not communicate, and that in the rotaxane the transfer of information between them is made possible by the shuttling of the ring, that is, by a dynamic intramolecular process. The investigated coupling of electron- and proton-transfer reactions is reminiscent of the operation of the protein complex I of the respiratory chain.

The role of CH/π interactions in the high affinity binding of streptavidin and biotin

The streptavidin-biotin complex has an extraordinarily high affinity (Ka: 10¹⁵mol^-1) and contains one of the strongest non-covalent interactions known. This strong interaction is widely used in biological tools, including for affinity tags, detection, and immobilization of proteins. Although hydrogen bond networks and hydrophobic interactions have been proposed to explain this high affinity, the reasons for it remain poorly understood. Inspired by the deceased affinity of biotin observed for point mutations of streptavidin at tryptophan residues, we hypothesized that a CH/π interaction may also contribute to the strong interaction between streptavidin and biotin. CH/π interactions were explored and analyzed at the biotin-binding site and at the interface of the subunits by the fragment molecular orbital method (FMO) and extended applications: PIEDA and FMO4. The results show that CH/π interactions are involved in the high affinity for biotin at the binding site of streptavidin. We further suggest that the involvement of CH/π interactions at the subunit interfaces and an extended CH/π network play more critical roles in determining the high affinity, rather than involvement at the binding site.