Artificial transmembrane signal transduction mediated by dynamic covalent chemistry

Reversible formation of covalent adducts between a thiol and a membrane-anchored Michael acceptor has been used to control the activation of a caged enzyme encapsulated inside vesicles. A peptide substrate and papain, caged as the mixed disulfide with methane thiol, were encapsulated inside vesicles, which contained Michael acceptors embedded in the lipid bilayer. In the absence of the Michael acceptor, addition of thiols to the external aqueous solution did not activate the enzyme to any significant extent. In the presence of the Michael acceptor, addition of benzyl thiol led to uncaging of the enzyme and hydrolysis of the peptide substrate to generate a fluorescence output signal. A charged thiol used as the input signal did not activate the enzyme. A Michael acceptor with a polar head group that cannot cross the lipid bilayer was just as effective at delivering benzyl thiol to the inner compartment of the vesicles as a non-polar Michael acceptor that can diffuse across the bilayer. The concentration dependence of the output signal suggests that the mechanism of signal transduction is based on increasing the local concentration of thiol present in the vesicles by the formation of Michael adducts. An interesting feature of this system is that enzyme activation is transient, which means that sequential addition of aliquots of thiol can be used to repeatedly generate an output signal.

Reversible formation of covalent adducts between a thiol and a membrane-anchored Michael acceptor has been used to control the activation of a caged enzyme encapsulated inside vesicles.     

Visible-light-induced intramolecular charge transfer in the radical spirocyclisation of indole-tethered ynones

Indole-tethered ynones form an intramolecular electron donor–acceptor complex that can undergo visible-light-induced charge transfer to promote thiyl radical generation from thiols. This initiates a novel radical chain sequence, based on dearomatising spirocyclisation with concomitant C–S bond formation. Sulfur-containing spirocycles are formed in high yields using this simple and mild synthetic protocol, in which neither transition metal catalysts nor photocatalysts are required. The proposed mechanism is supported by various mechanistic studies, and the unusual radical initiation mode represents only the second report of the use of an intramolecular electron donor–acceptor complex in synthesis.

Indole-tethered ynones form an intramolecular electron donor–acceptor complex that can undergo visible-light-induced charge transfer to promote thiyl radical generation from thiols.     

Mechanism of inhibition of SARS-CoV-2 Mpro by N3 peptidyl Michael acceptor explained by QM/MM simulations and design of new derivatives with tunable chemical reactivity

The SARS-CoV-2 main protease (M^pro) is essential for replication of the virus responsible for the COVID-19 pandemic, and one of the main targets for drug design. Here, we simulate the inhibition process of SARS-CoV-2 M^pro with a known Michael acceptor (peptidyl) inhibitor, N3. The free energy landscape for the mechanism of the formation of the covalent enzyme-inhibitor product is computed with QM/MM molecular dynamics methods. The simulations show a two-step mechanism, and give structures and calculated barriers in good agreement with experiment. Using these results and information from our previous investigation on the proteolysis reaction of SARS-CoV-2 M^pro, we design two new, synthetically accessible N3-analogues as potential inhibitors, in which the recognition and warhead motifs are modified. QM/MM modelling of the mechanism of inhibition of M^pro by these novel compounds indicates that both may be promising candidates as drug leads against COVID-19, one as an irreversible inhibitor and one as a potential reversible inhibitor.

QM/MM simulations identify the mechanism of reaction of N3, a covalent peptidyl inhibitor of SARS-CoV-2 main protease. Modelling of two novel proposed compounds, B1 and B2, suggests that reversibility of covalent inhibition could be tailored.     

Dynamic reaction-induced phase separation in tunable,adaptive covalent networks

A series of catalyst-free, room temperature dynamic bonds derived from a reversible thia-Michael reaction are utilized to access mechanically robust dynamic covalent network films. The equilibrium of the thiol addition to benzalcyanoacetate-based Michael-acceptors can be directly tuned by controlling the electron-donating/withdrawing nature of the Michael-acceptor. By modulating the composition of different Michael-acceptors in a dynamic covalent network, a wide range of mechanical properties and thermal responses can be realized. Additionally, the reported systems phase-separate in a process, coined dynamic reaction-induced phase separation (DRIPS), that yields reconfigurable phase morphologies and reprogrammable shape-memory behaviour as highlighted by the heat-induced folding of a predetermined structure.

Dynamic covalent networks comprised of tunable thia-Michael bonds result in phase separated networks with tailorable mechanical and adaptive properties.     

Phase transfer of metal cations by induced dynamic carrier agents: biphasic extraction based on dynamic covalent chemistry

In contrast to the classical method where a single molecule is designed to extract metal cations under specific conditions, dynamic covalent chemistry provides an approach based on the implementation of an adaptive dynamic covalent library for inducing the generation of the extractant species. This approach has been applied to the liquid–liquid extraction of copper(ii) nitrate based on a dynamic library of acylhydrazones constituents that self-build and distribute through the interface of a biphasic system. The addition of copper(ii) cations to this library triggers a modification of its composition and the up-regulation of the ligand molecules driven by coordination to the metal cations. Among these, one species has proven to be sufficiently lipophilic to play the role of carrier agent and its formation by component exchange enables the partial extraction of the copper(ii). The study of different pathways to generate the dynamic covalent library demonstrates the complete reversibility and the adaptability of the system. The detailed analytical investigation of the system provides a means to assess the mechanism of the dynamic extraction process.

Phase transfer of Cu(ii) cations is achieved by component exchange in a dynamic covalent library of acylhydrazone ligands. B1/B2 component exchange leads to the generation of a lipophilic carrier agent that extracts Cu(ii) into chloroform.     

Catalytic asymmetric addition of thiols to silyl glyoxylates for synthesis of multi-hetero-atom substituted carbon stereocenters

A chiral Lewis acid-catalyzed enantioselective addition of thiols to silyl glyoxylates was developed. The reaction proceeds well with a broad range of thiols and acylsilanes, affording the target tertiary chiral α-silyl–α-sulfydryl alcohols with multi-hetero-atom carbon stereocenters in excellent yields (up to 99%) and enantioselectivities (up to 98% ee). A series of control experiments were conducted to elucidate the reaction mechanism.

Enantioselective addition of thiols to silyl glyoxylates for construction of a multi-hetero-atom substituted carbon stereocenter was described.     

3D-visualization of amyloid-β oligomer interactions with lipid membranes by cryo-electron tomography

Amyloid-β (Aβ) assemblies have been shown to bind to lipid bilayers. This can disrupt membrane integrity and cause a loss of cellular homeostasis, that triggers a cascade of events leading to Alzheimer''s disease. However, molecular mechanisms of Aβ cytotoxicity and how the different assembly forms interact with the membrane remain enigmatic. Here we use cryo-electron tomography (cryoET) to obtain three-dimensional nano-scale images of various Aβ assembly types and their interaction with liposomes. Aβ oligomers and curvilinear protofibrils bind extensively to the lipid vesicles, inserting and carpeting the upper-leaflet of the bilayer. Aβ oligomers concentrate at the interface of vesicles and form a network of Aβ-linked liposomes, while crucially, monomeric and fibrillar Aβ have relatively little impact on the membrane. Changes to lipid membrane composition highlight a significant role for GM1-ganglioside in promoting Aβ-membrane interactions. The different effects of Aβ assembly forms observed align with the highlighted cytotoxicity reported for Aβ oligomers. The wide-scale incorporation of Aβ oligomers and curvilinear protofibrils into the lipid bilayer suggests a mechanism by which membrane integrity is lost.

Cryo-electron tomography 3D imaging of amyloid-β oligomers carpeting the surface of lipid bilayers in near native conditions.     

The chronological evolution of small organic molecular fluorescent probes for thiols

Abnormal concentrations of biothiols such as cysteine, homocysteine and glutathione are associated with various major diseases. In biological systems, the structural similarity and functional distinction of these three small molecular thiols has not only required rigorous molecular design of the fluorescent probes used to detect each thiol specifically, but it has also inspired scientists to uncover the ambiguous biological relationships between these bio-thiols. In this minireview, we will discuss the evolution of small organic molecular fluorescent probes for the detection of thiols over the past 60 years, highlighting the potent methodologies used in the design of thiol probes and their particular applications in the semi-quantification of cellular thiols and real-time labelling. At the same time, the present challenges that limit their further application will be discussed. We hope that this minireview will promote future research to enable deeper insight into the crucial role of thiols in biological systems.

The chronological evolution of small organic molecular fluorescent probes for thiols: from separation dependency analysis to cellular specific analysis, what''s next?     

Directional molecular sliding movement in peptide hydrogels accelerates cell proliferation

Adjusting the mechanical cues generated in cellular microenvironments is important for manipulating cell behaviour. Here we report on mechanically dynamic hydrogels undergoing directional domain sliding motion and investigate the effect of the well-defined mechanical motion on accelerating cell proliferation. The mechanically dynamic hydrogels were prepared via self-assembly of an amphiphilic peptide consisting of two alternating polar and nonpolar domains cross-linked by disulfide bonds at a nonsymmetrical position. The cross-linked peptide assembled into entangled nanofibers driven by the hydrophobic collapse involving a partial-length sequence due to the covalent constraint. Reduction of the disulfide bonds led to formation of non-equilibrated peptide bilayers, which underwent directional domain sliding motion along each promoted by the thermodynamically favourable transition from the partial to full hydrophobic collapse. The mechanical cues resulting from the directional domain sliding motion within the mechanically dynamic hydrogels accelerated cell proliferation when incubating cells on the hydrogel, compared to the thermodynamically static counterparts, via a mechanotransduction mechanism as supported by the facilitated translocation of yes-associated proteins into the nucleus of the cells. Our finding demonstrates the great potential of mechanically dynamic hydrogels as new-generation biomimetic extracellular matrices in tissue engineering and regeneration.

Dynamic peptide hydrogels undergoing directional domain sliding movement upon release of covalent constraint accelerate cell proliferation through a mechanotransduction pathway.     

Streamlined construction of peptide macrocycles via palladium-catalyzed intramolecular S-arylation in solution and on DNA

A highly efficient and versatile method for construction of peptide macrocycles via palladium-catalyzed intramolecular S-arylation of alkyl and aryl thiols with aryl iodides under mild conditions is developed. The method exhibits a broad substrate scope for thiols, aryl iodides and amino acid units. Peptide macrocycles of a wide range of size and composition can be readily assembled in high yield from various easily accessible building blocks. This method has been successfully employed to prepare an 8-million-membered tetrameric cyclic peptide DNA-encoded library (DEL). Preliminary screening of the DEL library against protein p300 identified compounds with single digit micromolar inhibition activity.

A highly efficient and versatile method for construction of peptide macrocycles via palladium-catalyzed intramolecular S-arylation of alkyl and aryl thiols with aryl iodides under mild conditions is developed.     

Dissipative self-assembly,competition and inhibition in a self-reproducing protocell model

The bottom-up synthesis of artificial, life-like systems promises to enable the study of emergent properties distinctive to life. Here, we report protocell systems generated from phase-separated building blocks. Vesicle protocells self-reproduce through a phase-transfer mechanism, catalysing their own formation. Dissipative self-assembly by the protocells is achieved when a hydrolysis step to destroy the surfactant is introduced. Competition between micelle and vesicle based replicators for a common feedstock shows that environmental conditions can control what species predominates: under basic conditions vesicles predominate, but in a neutral medium micelles are selected for via a mechanism which inhibits vesicle formation. Finally, the protocells enable orthogonal reactivity by catalysing in situ formation of an amphiphilic organocatalyst, which after incorporation into the vesicle bilayer enantioselectively forms a secondary product.

The bottom-up synthesis of a self-reproducing protocell model enables the study of emergent properties distinctive to life.     

Pyrazolone ligation-mediated versatile sequential bioconjugations

Bioconjugation chemistries are critical tools in biotherapeutics discovery. The past efforts have been exclusively focused on two-segment conjugations. However, emerging research directions, such as polypharmacy biotherapeutics, desire multiple-component bioconjugations where more than two pharmacologically related biomolecules can be assembled into a single construct in high efficiency. We present here a set of sequential bioconjugation chemistries centered on a pyrazolone structural motif. It starts with a clickable “pyrazolone ligation” between a hydrazine group and a β-ketoester moiety followed by the conjugation between the newly formed pyrazolone core and an aldehyde-bearing biomolecule through a Knoevenagel reaction forming a Michael addition acceptor that can effectively capture a thiol-bearing biomolecule. When utilized intermolecularly, it quickly assembles four segments together forming a quadruple functional construct. When applied intramolecularly, it offers a set of highly diverse biomolecule scaffolds including stapled peptides and poly-macrocyclic peptides. We envision broad utilities of such sequential ligation chemistries.

A multiple component sequential bioconjugation chemistry establishes upon the joined force of hydrazine, β-keto ester, thiol and aldehyde.     

Pot and time economies in the total synthesis of Corey lactone

The Corey lactone is a highly versatile intermediate for the synthesis of a variety of prostaglandin hormones that natively control a multitude of important physiological processes. Starting from commercially available compounds, we herein disclose a time-economical, one-pot enantioselective preparation of the Corey lactone by virtue of a new diphenylprolinol silyl ether-mediated domino Michael/Michael reaction to afford the substituted cyclopentanone core in a formal (3 + 2) cycloadditive fashion. More broadly, this work advances the on-demand, gram-scale synthesis of high-value targets involving chemically orthogonal transformations, whereby distinct reactions of acids, bases, organometalics, reductants and oxidants can be carried out in a single reaction vessel in a sequential fashion.

The Corey lactone was synthesized by one-pot within 152 minutes from comercially available compounds using organocatalyst.     

Regiodivergent construction of medium-sized heterocycles from vinylethylene carbonates and allylidenemalononitriles

Medium-sized heterocycles exist in a broad spectrum of biologically active natural products and medicinally important synthetic compounds. The construction of medium-sized rings remains challenging, particularly the assembly of different ring sizes from the same type of substrate. Here we report palladium-catalyzed, regiodivergent [5 + 4] and [5 + 2] annulations of vinylethylene carbonates and allylidenemalononitriles. We describe the production of over 50 examples of nine- and seven-membered heterocycles in high isolated yields and excellent regioselectivities. We demonstrate the synthetic utility of this approach by converting a nine-membered ring product to an interesting polycyclic caged molecule via a [2 + 2] transannulation. Mechanistic studies suggest that the [5 + 2] annulation proceeds through palladium-catalyzed ring-opening/re-cyclization from the [5 + 4] adducts.

Here we report palladium-catalyzed, regiodivergent [5 + 4] and [5 + 2] annulations of vinylethylene carbonates and allylidenemalononitriles affording over 50 medium-sized heterocycles in high isolated yields with excellent regioselectivities.     

How the biomimetic assembly of membrane receptors into multivalent domains is regulated by a small ligand

In living cells, communication requires the action of membrane receptors that are activated following very small environmental changes. A binary all-or-nothing behavior follows, making the organism extremely efficient at responding to specific stimuli. Using a minimal system composed of lipid vesicles, chemical models of a membrane receptor and their ligands, we show that bio-mimetic ON/OFF assembly of high avidity, multivalent domains is triggered by small temperature changes. Moreover, the intensity of the ON signal at the onset of the switch is modulated by the presence of small, weakly binding divalent ligands, reminiscent of the action of primary messengers in biological systems. Based on the analysis of spectroscopic data, we develop a mathematical model that rigorously describes the temperature-dependent switching of the membrane receptor assembly and ligand binding. From this we derive an equation that predicts the intensity of the modulation of the ON signal by the ligand-messenger as a function of the pairwise binding parameters, the number of binding sites that it features and the concentration. The behavior of our system, and the model derived, highlight the usefulness of weakly binding ligands in the regulation of membrane receptors and the pitfalls inherent to their binding promiscuity, such as non-specific binding to the membrane. Our model, and the equations derived from it, offer a valuable tool for the study of membrane receptors in both biological and biomimetic settings. The latter can be exploited to program membrane receptor avidity on sensing vesicles, create hierarchical protocell tissues or develop highly specific drug delivery vehicles.

In lipid vesicles near their membrane phase-transition temperature, the presence of a small, weakly binding ligand tips the balance for the assembly of multivalent receptor domains. We recapitulate this behaviour using a global binding-clustering model.     

Engineering bio-mimicking functional vesicles with multiple compartments for quantifying molecular transport

Controlled design of giant unilamellar vesicles under defined conditions has vast applications in the field of membrane and synthetic biology. Here, we bio-engineer bacterial-membrane mimicking models of controlled size under defined salt conditions over a range of pH. A complex bacterial lipid extract is used for construction of physiologically relevant Gram-negative membrane mimicking vesicles whereas a ternary mixture of charged lipids (DOPG, cardiolipin and lysyl-PG) is used for building Gram-positive bacterial-membrane vesicles. Furthermore, we construct stable multi-compartment biomimicking vesicles using the gel-assisted swelling method. Importantly, we validate the bio-application of the bacterial vesicle models by quantifying diffusion of chemically synthetic amphoteric antibiotics. The transport rate is pH-responsive and depends on the lipid composition, based on which a permeation model is proposed. The permeability properties of antimicrobial peptides reveal pH dependent pore-forming activity in the model vesicles. Finally, we demonstrate the functionality of the vesicles by quantifying the uptake of membrane-impermeable molecules facilitated by embedded pore-forming proteins. We suggest that the bacterial vesicle models developed here can be used to understand fundamental biological processes like the peptide assembly mechanism or bacterial cell division and will have a multitude of applications in the bottom-up assembly of a protocell.

Giant vesicle functional models mimicking a bacterial membrane under physiological conditions are constructed.     

Activating mechanosensitive channels embedded in droplet interface bilayers using membrane asymmetry

Droplet microcompartments linked by lipid bilayers show great promise in the construction of synthetic minimal tissues. Central to controlling the flow of information in these systems are membrane proteins, which can gate in response to specific stimuli in order to control the molecular flux between membrane separated compartments. This has been demonstrated with droplet interface bilayers (DIBs) using several different membrane proteins combined with electrical, mechanical, and/or chemical activators. Here we report the activation of the bacterial mechanosensitive channel of large conductance (MscL) in a dioleoylphosphatidylcholine:dioleoylphosphatidylglycerol DIB by controlling membrane asymmetry. We show using electrical measurements that the incorporation of lysophosphatidylcholine (LPC) into one of the bilayer leaflets triggers MscL gating in a concentration-dependent manner, with partial and full activation observed at 10 and 15 mol% LPC respectively. Our findings could inspire the design of new minimal tissues where flux pathways are dynamically defined by lipid composition.

Electrophysiology shows asymmetric lysophosphatidylcholine-containing DIBs trigger mechanosensitive channel gating, enabling user-designed, autonomous flux pathways in droplet networks.     

Controlled dimerization of artificial membrane receptors for transmembrane signal transduction

In biology, membrane-spanning proteins are responsible for the transmission of chemical signals across membranes, including the signal recognition-mediated conformational change of transmembrane receptors at the cell surface, and a trigger of an intracellular phosphorylation cascade. The ability to reproduce such biological processes in artificial systems has potential applications in smart sensing, drug delivery, and synthetic biology. Here, an artificial transmembrane receptors signaling system was designed and constructed based on modular DNA scaffolds. The artificial transmembrane receptors in this system are composed of three functional modules: signal recognition, lipophilic transmembrane linker, and signal output modules. Adenosine triphosphate (ATP) served as an external signal input to trigger the dimerization of two artificial receptors on membranes through a proximity effect. This effect induced the formation of a G-quadruplex, which served as a peroxidase-like enzyme to facilitate a signal output measured by either fluorescence or absorbance in the lipid bilayer vesicles. The broader utility of this modular method was further demonstrated using a lysozyme-binding aptamer instead of an ATP-binding aptamer. Therefore, this work provides a modular and generalizable method for the design of artificial transmembrane receptors. The flexibility of this synthetic methodology will allow researchers to incorporate different functional modules while retaining the same molecular framework for signal transduction.

An artificial transmbrane signal transducer was developed through the chemical input-mediated dimerization of artificial DNA transmembrane receptors and the subsequent activation of a cascade of events inside the vesicles.     

Spontaneous S–Si bonding of alkanethiols to Si(111)–H: towards Si–molecule–Si circuits

We report the synthesis of covalently linked self-assembled monolayers (SAMs) on silicon surfaces, using mild conditions, in a way that is compatible with silicon-electronics fabrication technologies. In molecular electronics, SAMs of functional molecules tethered to gold via sulfur linkages dominate, but these devices are not robust in design and not amenable to scalable manufacture. Whereas covalent bonding to silicon has long been recognized as an attractive alternative, only formation processes involving high temperature and/or pressure, strong chemicals, or irradiation are known. To make molecular devices on silicon under mild conditions with properties reminiscent of Au–S ones, we exploit the susceptibility of thiols to oxidation by dissolved O₂, initiating free-radical polymerization mechanisms without causing oxidative damage to the surface. Without thiols present, dissolved O₂ would normally oxidize the silicon and hence reaction conditions such as these have been strenuously avoided in the past. The surface coverage on Si(111)–H is measured to be very high, 75% of a full monolayer, with density-functional theory calculations used to profile spontaneous reaction mechanisms. The impact of the Si–S chemistry in single-molecule electronics is demonstrated using STM-junction approaches by forming Si–hexanedithiol–Si junctions. Si–S contacts result in single-molecule wires that are mechanically stable, with an average lifetime at room temperature of 2.7 s, which is five folds higher than that reported for conventional molecular junctions formed between gold electrodes. The enhanced “ON” lifetime of this single-molecule circuit enables previously inaccessible electrical measurements on single molecules.

Spontaneously formed Si–S bonds enable monolayer and single-molecule Si–molecule–Si circuits.