Chemical zymogens for the protein cysteinome

Artificial Receptor in Synthetic Cells Performs Transmembrane Activation of Proteolysis

The design of artificial, synthetic cells is a fundamentally important and fast-developing field of science. Of the diverse attributes of cellular life, artificial transmembrane signaling across the biomolecular barriers remains a high challenge with only a few documented successes. Herein, the study achieves signaling across lipid bilayers and connects an exofacial enzymatic receptor activation to an intracellular biochemical catalytic response using an artificial receptor. The mechanism of signal transduction for the artificial receptor relies on the triggered decomposition of a self-immolative linker. Receptor activation ensues its head-to-tail decomposition and the release of a secondary messenger molecule into the internal volume of the synthetic cell. Transmembrane signaling is demonstrated in synthetic cells based on liposomes and mammalian cell-sized giant unilamellar vesicles and illustrates receptor performance in cell mimics with a diverse size and composition of the lipid bilayer. In giant unilamellar vesicles, transmembrane signaling connects exofacial receptor activation with intracellular activation of proteolysis. Taken together, the results of this study take a step toward engineering receptor-mediated, responsive behavior in synthetic cells.

Receptor-Mediated Transmembrane Activation of Protein Folding in Synthetic Cells

Synthetic cells are a rapidly maturing platform with emerging applications in biomedicine and biotechnology. The specific novelty of this work is that we develop synthetic cells that respond to an extracellular stimulus by performing the folding of an encapsulated polypeptide into a functional enzyme. To this end, we developed artificial transmembrane signaling receptors. These contain an extracellular enzyme-responsive group, a self-immolative linker as the mechanism of signal transduction, and a secondary messenger molecule with intracellular activity. The secondary messenger is chosen such that it initiates protein refolding from the denatured polypeptide. Results of this study expand the molecular toolbox for the design of synthetic cells with life-like, responsive behavior.

Self-Immolative Polymers Derived from Renewable Resources via Thiol-Ene Chemistry

The development of polymers from renewable resources is a promising approach to reduce reliance on petrochemicals. In addition, depolymerization is attracting significant attention for the breakdown of polymers at their end-of-life or to achieve specific stimuli-responsive functions. However, the design of polymers incorporating both of these features remains a challenge. Herein, we report a new class of self-immolative polymers based on lignin-derived aldehydes via a simple thiol-ene polymerization. These self-immolative polymers undergo cascade degradation in response to specific stimuli through alternating 1,6-elimination and cyclization reactions. The two methoxy substituents on the syringaldehyde monomer accelerated the desired depolymerization reaction, while enhancing stability against undesired backbone hydrolysis. Moreover, diverse responsive end-caps could be introduced through post-polymerization functionalization from a single polymer precursor.

Artificial Internalizing Receptors: Intracellular Delivery of Cargo Through Bio-Orthogonal Recognition

Drug targeting is a methodology that helps to overcome the side effects of therapeutic molecules. However, insufficient targeting specificity and the on-target/off-site delivery leave much room for improvement in the targeting endeavors. One approach to enhance the specificity of drug targeting is to engineer artificial receptors with recognition ligands not observed in nature. To this end, artificial internalizing receptors that feature cholesterylamine as the artificial pull-in mechanism, and an anti-fluorescein antibody as the exofacial recognition and capture tool are developed. Fluorescein labeling is among the most routine techniques in biochemistry and can readily provide a way to make cognate derivatives for receptor-mediated endocytosis using these artificial receptors. Herein, the synthesis and the structure-activity relationship for these artificial receptors are detailed, their potency and efficacy in mediating drug delivery for the antibody-drug conjugates are illustrated, and the scope and limitations of targeting the chemically engineered cells via artificial receptors are investigated. Taken together, the presented data explore an innovative approach to drug targeting and contribute to the development of techniques in cell engineering using the tools of chemistry.

Steps Toward Recapitulating Endothelium: A Perspective on the Next Generation of Hemocompatible Coatings

Endothelium, the lining in this blood vessel, orchestrates three main critical functions such as protecting blood components, modulating of hemostasis by secreting various inhibitors, and directing clot digestion (fibrinolysis) by activating tissue plasminogen activator. No other surface can perform these tasks; thus, the contact of blood and blood-contacting medical devices inevitably leads to the activation of coagulation, often causing device failure, and thromboembolic complications. This perspective, first, discusses the biological mechanisms of activation of coagulation and highlights the efforts of advanced coatings to recapitulate one characteristic of endothelium, hereafter single functions of endothelium and noting necessity of the synergistic integration of its three main functions. Subsequently, it is emphasized that to overcome the challenges of blood compatibility an endothelium-mimicking system is needed, proposing a synergy of bottom-up synthetic biology, particularly synthetic cells, with passive- and bioactive surface coatings. Such integration holds promise for developing advanced biomaterials capable of recapitulating endothelial functions, thereby enhancing the hemocompatibility and performance of blood-contacting medical devices.

Unnatural enzyme activation by a metal-responsive regulatory protein

As a result of calcium ion binding, the calcium-dependent regulatory protein calmodulin (CaM) undergoes a conformational change, enabling it to bind to and activate a variety of enzymes. However, the detoxification enzyme glutathione S-transferase (GST) is notably not among the enzymes activated by CaM. In this study, we demonstrate the feasibility of establishing, in vitro, an artificial regulatory link between CaM and GST using bifunctional chemical transducer (CT) molecules possessing binders for CaM and GST. We show that the CTs convert the constitutively active GST into a triggerable enzyme whose activity is unnaturally regulated by the CaM conformational state and consequently, by the level of calcium ions. The ability to reconfigure the regulatory function of CaM demonstrates a novel mode by which CTs could be employed to mediate artificial protein crosstalk, as well as a new means to achieve artificial control of enzyme activity by modulating the coordination of metal ions. Within this study, we also investigated the impact of covalent interaction between the CTs and the enzyme target. This investigation offers further insights into the mechanisms governing the function of CTs and the possibility of rendering them isoform specific.

Biological applications of lipoic acid-based polymers: an old material with new promise

Lipoic acid (LA) is a versatile antioxidant that has been used in the treatment of various oxidation-reduction diseases over the past 70 years. Owing to its large five-membered ring tension, the dynamic disulfide bond of LA is highly active, enabling the formation of poly(lipoic acid) (PLA) via ring-opening polymerization (ROP). Herein, we first summarize disulfide-mediated ROP polymerization strategies, providing basic routes for designing and preparing PLA-based materials. PLA, as a biologically derived, low toxic, and easily modified material, possesses dynamic disulfide bonds and universal non-covalent carboxyl groups. We also shed light on the biomedical applications of PLA-based materials based on their biological and structural features and further divide recent works into six categories: antibacterial, anti-inflammation, anticancer, adhesive, flexible electronics, and 3D-printed tissue scaffolds. Finally, the challenges and future prospects associated with the biomedical applications of PLA are discussed.

Engineering Anti-CRISPR Proteins to Create CRISPR-Cas Protein Switches for Activatable Genome Editing and Viral Protease Detection

Proteins capable of switching between distinct active states in response to biochemical cues are ideal for sensing and controlling biological processes. Activatable CRISPR-Cas systems are significant in precise genetic manipulation and sensitive molecular diagnostics, yet directly controlling Cas protein function remains challenging. Herein, we explore anti-CRISPR (Acr) proteins as modules to create synthetic Cas protein switches (CasPSs) based on computational chemistry-directed rational protein interface engineering. Guided by molecular fingerprint analysis, electrostatic potential mapping, and binding free energy calculations, we rationally engineer the molecular interaction interface between Cas12a and its cognate Acr proteins (AcrVA4 and AcrVA5) to generate a series of orthogonal protease-responsive CasPSs. These CasPSs enable the conversion of specific proteolytic events into activation of Cas12a function with high switching ratios (up to 34.3-fold). These advancements enable specific proteolysis-inducible genome editing in mammalian cells and sensitive detection of viral protease activities during virus infection. This work provides a promising strategy for developing CRISPR-Cas tools for controllable gene manipulation and regulation and clinical diagnostics.

Integrative chemoproteomics reveals anticancer mechanisms of silver(i) targeting the proteasome regulatory complex

Silver compounds have favorable properties as promising anticancer drug candidates, such as low side effects, anti-inflammatory properties, and high potential to overcome drug resistance. However, the exact mechanism by which Ag(i) confers anticancer activity remains unclear, which hinders further development of anticancer applications of silver compounds. Here, we combine thermal proteome profiling, cysteine profiling, and ubiquitome profiling to study the molecular mechanisms of silver(i) complexes supported by non-toxic thiourea (TU) ligands. Through the formation of AgTU complexes, TU ligands deliver Ag+ ions to cancer cells and tumour xenografts to elicit inhibitory potency. Our chemical proteomics studies show that AgTU acts on the ubiquitin-proteasome system (UPS) and disrupts protein homeostasis, which has been identified as a main anticancer mechanism. Specifically, Ag+ ions are released from AgTU in the cellular environment, directly target the 19S proteasome regulatory complex, and may oxidize its cysteine residues, thereby inhibiting proteasomal activity and accumulating ubiquitinated proteins. After AgTU treatment, proteasome subunits are massively ubiquitinated and aberrantly aggregated, leading to impaired protein homeostasis and paraptotic death of cancer cells. This work reveals the unique anticancer mechanism of Ag(i) targeting the 19S proteasome regulatory complex and opens up new avenues for optimizing silver-based anticancer efficacy.

Artificial Protein Crosstalk with a Molecule that Exchanges Binding Partners

Drawing inspiration from allosteric signaling enzymes, whose catalytic and regulatory units are non-covalently linked, we have devised a method to establish unnatural, effector-mediated enzyme activation within native cells. The feasibility of this approach is demonstrated by introducing a synthetic regulatory unit (sRU) onto glycogen synthase kinase 3 (GSK-3) through non-covalent means. Our study reveals that this synthetic regulator mediates an unnatural crosstalk between GSK-3 and lactate dehydrogenase A (LDHA), whose expression is regulated by cellular oxygen levels. Specifically, with this approach, the constitutively active GSK-3 is transformed into an activable enzyme, whereas LDHA is repurposed as an unnatural effector protein that controls the activity of the kinase, making it unnaturally dependent on the cell's hypoxic response. These findings demonstrate a step toward imitating the function of effector-regulated cell-signaling enzymes, which play a key biological role in mediating the response of cells to changes in their environment. In addition, at the proof-of-principle level, our results indicate the potential to develop a new class of protein inhibitors whose inhibitory effect in cells is dictated by the cell's environment and consequent protein expression profile.

Chemical Zymogens and Transmembrane Activation of Transcription in Synthetic Cells

In this work, synthetic cells equipped with an artificial signaling pathway that connects an extracellular trigger event to the activation of intracellular transcription are engineered. Learning from nature, this is done via an engineering of responsive enzymes, such that activation of enzymatic activity can be triggered by an external biochemical stimulus. Reversibly deactivated creatine kinase to achieve triggered production of adenosine triphosphate, and a reversibly deactivated nucleic acid polymerase for on-demand synthesis of RNA are engineered. An extracellular, enzyme-activated production of a diffusible zymogen activator is also designed. The key achievement of this work is that the importance of cellularity is illustrated whereby the separation of biochemical partners is essential to resolve their incompatibility, to enable transcription within the confines of a synthetic cell. The herein designed biochemical pathway and the engineered synthetic cells are arguably primitive compared to their natural counterpart. Nevertheless, the results present a significant step toward the design of synthetic cells with responsive behavior, en route from abiotic to life-like cell mimics.

Click to Self-immolation: A "Click" Functionalization Strategy towards Triggerable Self-Immolative Homopolymers and Block Copolymers

Self-immolative polymers (SIPs) are a class of degradable macromolecules that undergo stimuli-triggered head-to-tail depolymerization. However, a general approach to readily end-functionalize SIP precursors for programmed degradation remains elusive, restricting access to complex, functional SIP-based materials. Here we present a "click to self-immolation" strategy based on aroyl azide-capped SIP precursors, enabling the facile construction of diverse SIPs with different trigger units through a Curtius rearrangement and alcohol/thiol-isocyanate "click" reaction. This strategy is also applied to polymer-polymer coupling to access fully depolymerizable block copolymer amphiphiles, even combining different SIP backbones. Our results demonstrate that the depolymerization can be actuated efficiently under physiologically-relevant conditions by the removal of the trigger units and ensuing self-immolation of the p-aminobenzyl carbonate linkage, indicating promise for controlled release applications involving nanoparticles and hydrogels.

Directional Shunting of Photogenerated Carriers in POM@MOF for Promoting Nitrogen Adsorption and Oxidation

The efficient catalysis of nitrogen (N2 ) into high-value N-containing products plays a crucial role in the N economic cycle. However, weak N2 adsorption and invalid N2 activation remain two major bottlenecks in rate-determining steps, leading to low N2 fixation performance. Herein, an effective dual active sites photocatalyst of polyoxometalates (POMs)-based metal-organic frameworks (MOFs) is highlighted via altering coordination microenvironment and inducing directional shunting of photogenerated carriers to facilitate N2 /catalyst interaction and enhance oxidation performance. MOFs create more open unsaturated metal cluster sites with unoccupied d orbital possessing Lewis acidity to accept electrons from the 3σg bonding orbital of N2 for storage by combining with POMs to replace bidentate linkers. POMs act as electron sponges donating electrons to MOFs, while the holes directional flow to POMs. The hole-rich POMs with strong oxidation capacity are easily involved in oxidizing adsorbed N2 . Taking UiO-66 (C48 H28 O32 Zr6 ) and Mo72 Fe30 ([Mo72 Fe30 O252 (CH3 COO)12 {Mo2 O7 (H2 O)}2 {H2 Mo2 O8 (H2 O)}(H2 O)91 ]·150H2 O) as an example, Mo72 Fe30 @UiO-66 shows twofold enhanced adsorption of N2 (250.5 cm3  g-1 ) than UiO-66 (122.9 cm3 g-1 ) at P/P0  = 1. And, the HNO3 yield of Mo72 Fe30 @UiO-66 is 702.4 µg g-1  h-1 , ≈7 times and 24 times higher than UiO-66 and Mo72 Fe30 . This work provides reliable value for the storage and relaying artificial N2 fixation.

Emerging Trends in the Chemistry of End-to-End Depolymerization

Over the past couple of decades, polymers that depolymerize end-to-end upon cleavage of their backbone or activation of a terminal functional group, sometimes referred to as "self-immolative" polymers, have been attracting increasing attention. They are of growing interest in the context of enhancing polymer degradability but also in polymer recycling as they allow monomers to be regenerated in a controlled manner under mild conditions. Furthermore, they are highly promising for applications as smart materials due to their ability to provide an amplified response to a specific signal, as a single sensing event is translated into the generation of many small molecules through a cascade of reactions. From a chemistry perspective, end-to-end depolymerization relies on the principles of self-immolative linkers and polymer ceiling temperature (Tc). In this article, we will introduce the key chemical concepts and foundations of the field and then provide our perspective on recent exciting developments. For example, over the past few years, new depolymerizable backbones, including polyacetals, polydisulfides, polyesters, polythioesters, and polyalkenamers, have been developed, while modern approaches to depolymerize conventional backbones such as polymethacrylates have also been introduced. Progress has also been made on the topological evolution of depolymerizable systems, including the introduction of fully depolymerizable block copolymers, hyperbranched polymers, and polymer networks. Furthermore, precision sequence-defined oligomers have been synthesized and studied for data storage and encryption. Finally, our perspectives on future opportunities and challenges in the field will be discussed.

Transmembrane signaling by a synthetic receptor in artificial cells

Signal transduction across biological membranes is among the most important evolutionary achievements. Herein, for the design of artificial cells, we engineer fully synthetic receptors with the capacity of transmembrane signaling, using tools of chemistry. Our receptors exhibit similarity with their natural counterparts in having an exofacial ligand for signal capture, being membrane anchored, and featuring a releasable messenger molecule that performs enzyme activation as a downstream signaling event. The main difference from natural receptors is the mechanism of signal transduction, which is achieved using a self-immolative linker. The receptor scaffold is modular and can readily be re-designed to respond to diverse activation signals including biological or chemical stimuli. We demonstrate an artificial signaling cascade that achieves transmembrane enzyme activation, a hallmark of natural signaling receptors. Results of this work are relevant for engineering responsive artificial cells and interfacing them and/or biological counterparts in co-cultures.

Electrocatalytic Depolymerization of Self-Immolative Poly(Dithiothreitol) Derivatives

We report the use of electrogenerated anthraquinone radical anion (AQ•-) to trigger fast catalytic depolymerization of polymers derived from poly(dithiothreitol) (pDTT)-a self-immolative polymer (SIP) with a backbone of dithiothreitols connected with disulfide bonds and end-capped via disulfide bonds to pyridyl groups. The pDTT derivatives studied include polymers with simple thiohexyl end-caps or modified with AQ or methyl groups by Steglich esterification. All polymers were shown to be depolymerized using catalytic amounts of electrons delivered by AQ•-. For pDTT, as little as 0.2 electrons per polymer chain was needed to achieve complete depolymerization. We hypothesize that the reaction proceeds with AQ•- as an electron carrier (either molecularly or as a pendant group), which transfers an electron to a disulfide bond in the polymer in a dissociative manner, generating a thiyl radical and a thiolate. The rapid and catalytic depolymerization is driven by thiyl radicals attacking other disulfide bonds internally or between pDTT chains in a chain reaction. Electrochemical triggering works as a general method for initiating depolymerization of pDTT derivatives and may likely also be used for depolymerization of other disulfide polymers.