When Supramolecular Chemistry Meets Chemical Biology: New Strategies to Target Proteins through Host-Guest Interactions

Small Molecule Drugs Triggered the Activation of Macrocycle Masked Proteins

On-demand activation of prodrugs represents an emerging and fast developing strategy to improve the therapeutic index of certain drugs. However, strategies to generate protein-based prodrugs with controllable activation are still limited. Here, we present a supramolecular masking strategy that enables on-demand activation of macrocycle-masked proteins with Food and Drug Administration (FDA)-approved oral drugs. Proteins of interest were engineered to incorporate two N-terminal peptide motifs, which were dimerized by cucurbit[8]uril (CB[8]) to form a supramolecular mask that sterically blocks functional protein interfaces, inhibiting interactions with targets or substrates. The inhibitory effect was selectively reversed by amantadine or memantine to restore the protein activity. This masking strategy was validated across various protein classes, including antibodies, cytokines, and enzymes. Activation of CB[8]-masked proteins was further demonstrated in living mice via FDA-approved small molecule treatments. Our method provided a supramolecular strategy for the selective activation of protein-based prodrugs and the development of next-generation protein therapeutics.

Theoretical investigation of tube-like supramolecular structures formed through bifurcated lithium bonds

The stability of three supramolecular naostructures, which are formed through the aggregation of identical belts of [12] arene containing p-nitrophenyllithium, 1,4-dilithiatedbenzene and 1,4-dinitrobenzene units, is investigated by density functional theory. The electrostatic potential calculations indicate the ability of these belts in forming bifurcated lithium bonds (BLBs) between the Li atoms of one belt and the oxygen atoms of the NO2 groups in the other belt, which is also confirmed by deformation density maps and quantum theory of atoms in molecules (QTAIM) analysis. Topological analysis and natural bond analysis (NBO) imply to ionic character for these BLBs with binding energies up to approximately - 60 kcal mol-1. The many-body interaction energy analysis shows the strong cooperativity belongs to the configuration with the highest symmetry (C4v) containing p-nitrophenyllithium fragments as the building unit. Therefore, it seems that this configuration could be a good candidate for designing a BLB-based supramolecular nanotube with infinite size in this study.

Molecular Approaches to Protein Dimerization: Opportunities for Supramolecular Chemistry

Protein dimerization plays a key role in many biological processes. Most cellular events such as enzyme activation, transcriptional cofactor recruitment, signal transduction, and even pathogenic pathways are significantly regulated via protein-protein interactions. Understanding and controlling the molecular mechanisms that regulate protein dimerization is crucial for biomedical applications. The limitations of engineered protein dimerization provide an opportunity for molecular chemistry to induce dimerization of protein in biological events. In this review, molecular control over dimerization of protein and activation in this respect are discussed. The well known molecule glue-based approaches to induced protein dimerization provide powerful tools to modulate the functionality of dimerized proteins and are shortly highlighted. Subsequently metal ion, nucleic acid and host-guest chemistry are brought forward as novel approaches for orthogonal control over dimerization of protein. The specific focus of the review will be on host-guest systems as novel, robust and versatile supramolecular approaches to modulate the dimerization of proteins, using functional proteins as model systems.