Highly Stable Meldrum's Acid Derivatives for Irreversible Aqueous Covalent Modification of Amines

Covalent fragment approaches targeting non-cysteine residues

Covalent fragment approaches combine advantages of covalent binders and fragment-based drug discovery (FBDD) for target identification and validation. Although early applications focused mostly on cysteine labeling, the chemistries of available warheads that target other orthosteric and allosteric protein nucleophiles has recently been extended. The range of different warheads and labeling chemistries provide unique opportunities for screening and optimizing warheads necessary for targeting non-cysteine residues. In this review, we discuss these recently developed amino-acid-specific and promiscuous warheads, as well as emerging labeling chemistries, which includes novel transition metal catalyzed, photoactive, electroactive, and noncatalytic methodologies. We also highlight recent applications of covalent fragments for the development of molecular glues and proteolysis-targeting chimeras (PROTACs), and their utility in chemical proteomics-based target identification and validation.

Tailoring Dynamic Hydrogels by Controlling Associative Exchange Rates

Dithioalkylidenes are a newly-developed class of conjugate acceptors that undergo thiol exchange via an associative mechanism, enabling decoupling of key material properties for sustainability, biomedical, and sensing applications. Here, we show that the exchange rate is highly sensitive to the structure of the acceptor and tunable over four orders of magnitude in aqueous environments. Cyclic acceptors exchange rapidly, from 0.95 to 15.6 M-1s-1, while acyclic acceptors exchange between 3.77x10-3 and 2.17x10-2 M-1s-1. Computational, spectroscopic, and structural data suggest that cyclic acceptors are more reactive than their acyclic counterparts because of resonance stabilization of the tetrahedral exchange intermediate. We parametrize molecular reactivity with respect to computed descriptors of the electrophilic site and leverage this insight to design a compound with intermediate characteristics. Lastly, we incorporate this dynamic bond into hydrogels and demonstrate that the characteristic stress relaxation time (τ) is directly proportional to molecular kex.

Bioinspired one-pot furan-thiol-amine multicomponent reaction for making heterocycles and its applications

One-pot multicomponent coupling of different units in a chemoselective manner and their late-stage diversification has wide applicability in varying chemistry fields. Here, we report a simple multicomponent reaction inspired by enzymes that combines thiol and amine nucleophiles in one pot via a furan-based electrophile to generate stable pyrrole heterocycles independent of the diverse functionalities on furans, thiols and amines under physiological conditions. The resulting pyrrole provides a reactive handle to introduce diverse payloads. We demonstrate the application of Furan-Thiol-Amine (FuTine) reaction for the selective and irreversible labeling of peptides, synthesis of macrocyclic and stapled peptides, selective modification of twelve different proteins with varying payloads, homogeneous engineering of proteins, homogeneous stapling of proteins, dual modification of proteins with different fluorophores using the same chemistry and labeling of lysine and cysteine in a complex human proteome.

Dibenzocyclooctendiones (DBCDOs): Arginine-Selective Chemical Labeling Reagents Obtained through Benzilic Acid Rearrangement

We demonstrate that dibenzocyclooctendiones (DBCDOs) are efficient chemical reagents for the site-specific labeling of arginine-containing biomolecules. Unlike the commonly used probes, DBCDOs undergo an irreversible ring-contracted rearrangement with the guanidinium group on arginine residues under mild reaction conditions. The regioselective dual-labeled arginine residues were obtained in a one-pot reaction with our tested substrates. The efficiency of DBCDOs reactions and their ease of synthesis make DBCDOs an attractive choice for the site-selective bioconjugation of arginine.

"Indanonalkene" Photoluminescence Platform: Application in Real-Time Tracking the Synthesis, Remodeling, and Degradation of Soft Materials

In this Article, we present a strategy to visually track chemically triggered covalent bonding processes in gelation, remodeling, and degradation of soft materials, i.e., hydrogels, based on a new photoluminescence platform. Initially in the development of photoluminophors named "indanonalkenes", turn-on emission can be tracked and quantified in the optical reaction between a conjugate acceptor and amine derivatives. On this basis, fluorescence enhancement and mechanical changes were recorded during the gelation process through amine-thiol exchanges under organic and aqueous conditions. Next in macromolecular remodeling, we realized a stimulus-induced transformation of one architecture into another one, exploiting the orthogonality of chemical covalent bonding that could be visualized using luminescence. Furthermore, the hydrogel network can be degraded to release the coupling partner induced by ethylene diamine, and the process can be monitored using fluorescence changes and quantified through gel permeation chromatography, while the released components can be utilized again to regenerate a new hydrogel. In addition, the photographic images provide alternatives to fluorescence spectra and can be digitally processed to quantify the macroscopic changes, resulting in a photographic imaging approach. The real-time observation and quantification of chemically triggered polymeric formation, morphology, and degradation through luminescence in spatial and time scales herald a new generation of "smart" materials.

Chemically Triggered Click and Declick Reactions: Application in Synthesis and Degradation of Thermosetting Plastics

In this Letter, we report that two amines can be coupled together rapidly and quantitatively through amine-thiol scrambling using a bisvinylogous thioester conjugate acceptor under mild conditions. The resulting bisvinylogous amide conjugate acceptors can be decoupled via an ethylene diamine-induced cyclization. Four representative conjugate acceptors have been utilized in the couple-decouple reactions, which were monitored and characterized by nuclear magnetic resonance, high-resolution mass spectrometry, and UV-vis spectroscopy. Further, we applied these small-molecule-based "click-declick" reactions to polymer synthesis and degradation. Highly cross-linked polymers, i.e., plastics, were quantitatively synthesized by simple reactions between commercial tris(2-aminoethyl)amine and the conjugate acceptors without solvent and any initiator or catalyst through ball milling within 60 min. Significantly, these thermosetting plastics can be degraded within 3-24 h via addition of ethylene diamine. The multiple architectures, application to plastics synthesis, and chemically triggered clean degradation to the thermosets at mild conditions with little input of energy herald a new generation of "intelligent" materials.

Biomolecular labeling based on lysine-clickable 6π-azaelectrocyclization toward innovative cancer theranostics

An amino group at side chain of lysine residue can be targeted for protein modification because of the convenience for covalent bond formation. We have achieved an efficient protein modification by utilizing amine-clickable 6π-azaelectrocyclization, termed RIKEN click reaction recently, which enabled direct click labeling of protein without any introduction of specific functional groups such as alkynes and azides. On the basis of the RIKEN click reaction, we established the double click labeling method. The double click methods composed of copper-free strain-promoted [3 + 2] cyclization or tetrazine ligation and RIKEN click reaction were developed. The double click method realized highly effective proteins including radiolabeling of bioactive peptides and anti-tumor antibodies. In this personal review, the development of double click probes, practical radiolabeling of biological active molecules such as cyclic RGDyK peptides, proteins, and antibodies with α-emission or β-emission radionuclides, and their applications for PET imaging and α-emission cancer treatment are summarized.

Molecular Diversity via Tetrasubstituted Alkenes Containing a Barbiturate Motif: Synthesis and Biological Activity

The synthesis of a molecularly diverse library of tetrasubstituted alkenes containing a barbiturate motif is described. Base-induced condensation of N¹-substituted pyrimidine-2,4,6(1H,3H,5H)-triones with 5-(bis(methylthio)methylene)-2,2-dimethyl-1,3-dioxane-4,6-dione gave 3-substituted 5-(methylthio)-2H-pyrano[2,3-d]pyrimidine-2,4,7(1H,3H)-triones (‘pyranopyrimidinones’), regioselectively. A sequence of reactions involving ring-opening of the pyran moiety, displacement of the methylthio group with an amine, re-formation of the pyran ring, and after its final cleavage with an amine, gave tetrasubstituted alkenes (3-amino-3-(2,4,6-trioxotetrahydropyrimidin-5(2H)-ylidene)propanamides) with a diversity of substituents. Cleavage of the pyranopyrimidinones with an aniline was facilitated in 2,2,2-trifluoroethanol under microwave irradiation. Compounds were tested against Escherichia coli, Staphylococcus aureus, the yeast Schizosaccharomyces pombe, and the pathogenic fungus Candida albicans. No compounds exhibited activity against E. coli, whilst one compound was weakly active against S. aureus. Three compounds were strongly active against S. pombe, but none was active against C. albicans.