Oxidative cyclization reagents reveal tryptophan cation-π interactions.

Methods for selective covalent modification of amino acids on proteins can enable a diverse array of applications, spanning probes and modulators of protein function to proteomics1-3. Owing to their high nucleophilicity, cysteine and lysine residues are the most common points of attachment for protein bioconjugation chemistry through acid-base reactivity3,4. Here we report a redox-based strategy for bioconjugation of tryptophan, the rarest amino acid, using oxaziridine reagents that mimic oxidative cyclization reactions in indole-based alkaloid biosynthetic pathways to achieve highly efficient and specific tryptophan labelling. We establish the broad use of this method, termed tryptophan chemical ligation by cyclization (Trp-CLiC), for selectively appending payloads to tryptophan residues on peptides and proteins with reaction rates that rival traditional click reactions and enabling global profiling of hyper-reactive tryptophan sites across whole proteomes. Notably, these reagents reveal a systematic map of tryptophan residues that participate in cation-π interactions, including functional sites that can regulate protein-mediated phase-separation processes.

Methionine oxidation activates pyruvate kinase M2 to promote pancreatic cancer metastasis.

Cancer mortality is primarily a consequence of its metastatic spread. Here, we report that methionine sulfoxide reductase A (MSRA), which can reduce oxidized methionine residues, acts as a suppressor of pancreatic ductal adenocarcinoma (PDA) metastasis. MSRA expression is decreased in the metastatic tumors of PDA patients, whereas MSRA loss in primary PDA cells promotes migration and invasion. Chemoproteomic profiling of pancreatic organoids revealed that MSRA loss results in the selective oxidation of a methionine residue (M239) in pyruvate kinase M2 (PKM2). Moreover, M239 oxidation sustains PKM2 in an active tetrameric state to promote respiration, migration, and metastasis, whereas pharmacological activation of PKM2 increases cell migration and metastasis in vivo. These results demonstrate that methionine residues can act as reversible redox switches governing distinct signaling outcomes and that the MSRA-PKM2 axis serves as a regulatory nexus between redox biology and cancer metabolism to control tumor metastasis.

Development of the Squaramide Scaffold for High Potential and Multielectron Catholytes for Use in Redox Flow Batteries.

Nonaqueous organic redox flow batteries (N-ORFBs) are a promising technology for grid-scale storage of energy generated from intermittent renewable sources. Their primary benefit over traditional aqueous RFBs is the wide electrochemical stability window of organic solvents, but the design of catholyte materials, which can exploit the upper range of this window, has proven challenging. We report herein a new class of N-ORFB catholytes in the form of squaric acid quinoxaline (SQX) and squaric acid amide (SQA) materials. Mechanistic investigation of decomposition in battery-relevant conditions via NMR, HRMS, and electrochemical methods enabled a rational design approach to optimizing these scaffolds. Three lead compounds were developed: a highly stable one-electron SQX material with an oxidation potential of 0.51 V vs Fc/Fc+ that maintained 99% of peak capacity after 102 cycles (51 h) when incorporated into a 1.58 V flow battery; a high-potential one-electron SQA material with an oxidation potential of 0.81 V vs Fc/Fc+ that demonstrated negligible loss of redox active material as measured by pre- and postcycling CV peak currents when incorporated in a 1.63 V flow battery for 110 cycles over 29 h; and a proof-of-concept two-electron SQA catholyte material with oxidation potentials of 0.48 and 0.85 V vs Fc/Fc+ that demonstrated a capacity fade of just 0.56% per hour during static H-cell cycling. These findings expand the previously reported space of high-potential catholyte materials and showcase the power of mechanistically informed synthetic design for N-ORFB materials development.

Supramolecular Catalyzed Cascade Reduction of Azaarenes Interrogated via Data Science.

Catalysis of multicomponent transformations requires controlled assembly of reactants within the active site. Supramolecular scaffolds possess synthetic microenvironments that enable precise modulation over noncovalent interactions (NCIs) engaged by reactive, encapsulated species. While molecular properties that describe the behavior of single guests in host cavities have been studied extensively, multicomponent transformations remain challenging to design and deploy. Here, simple univariate regression and threshold analyses are employed to model reactivity in a cascade reduction of azaarenes catalyzed by water-soluble metal organic cages. Yield and stereoselectivity models help deduce unknown mechanisms of reactivity by the multicomponent, host-guest complexes. Furthermore, a comprehensive model is established for NCIs driving stereoselectivity in the reported host-guest adducts.

Utopia Point Bayesian Optimization Finds Condition-Dependent Selectivity for N-Methyl Pyrazole Condensation.

Utopia Point Bayesian Optimization (UPBO) was used to identify reaction conditions that are highly selective for the formation of N1 and N2-methyl-3-aryl pyrazole constitutional isomers. UPBO was used to explore a wide chemical space and identify basic reaction conditions for a typically acid-catalyzed Knorr pyrazole condensation. These studies revealed that selectivity in the reaction stems from a condition-dependent equilibrium of intermediates prior to dehydration. For the N2-methyl isomer reaction pathway, a hemiaminal intermediate was found to form reversibly under the reaction conditions, enabling a highly selective synthesis of the N2 isomer upon dehydrative workup. UPBO was able to successfully optimize conversion and selectivity simultaneously with search spaces of >1 million potential variable combinations without the need for high-performance computational resources.

Heterogeneous Rhodium Single-Atom-Site Catalyst Enables Chemoselective Carbene N-H Bond Insertion.

Transition-metal-catalyzed carbene insertion reactions of a nitrogen-hydrogen bond have emerged as robust and versatile methods for the construction of C-N bonds. While significant progress of homogeneous catalytic metal carbene N-H insertions has been achieved, the control of chemoselectivity in the field remains challenging due to the high electrophilicity of the metal carbene intermediates. Herein, we present an efficient strategy for the synthesis of a rhodium single-atom-site catalyst (Rh-SA) that incorporates a Rh atom surrounded by three nitrogen atoms and one phosphorus atom doped in a carbon support. This Rh-SA catalyst, with a catalyst loading of only 0.15 mol %, exhibited exceptional catalytic performance for heterogeneous carbene insertion with various anilines and heteroaryl amines in combination with diazo esters. Importantly, the heterogeneous catalyst selectively transformed aniline derivatives bearing multiple nucleophilic moieties into single N-H insertion isomers, while the popular homogeneous Rh2(OAc)4 catalyst produced a mixture of overfunctionalized side products. Additionally, similar selectivities for N-H bond insertion with a set of stereoelectronically diverse diazo esters were obtained, highlighting the general applicability of this heterogeneous catalysis approach. On the basis of density functional theory calculations, the observed selectivity of the Rh-SA catalyst was attributed to the insertion barriers and the accelerated proton transfer assisted by the phosphorus atom in the support. Overall, this investigation of heterogeneous metal-catalyzed carbene insertion underscores the potential of single-atom-site catalysis as a powerful and complementary tool in organic synthesis.

Enantioselective Sulfonimidamide Acylation via a Cinchona Alkaloid-Catalyzed Desymmetrization: Scope, Data Science, and Mechanistic Investigation.

Methods to access chiral sulfur(VI) pharmacophores are of interest in medicinal and synthetic chemistry. We report the desymmetrization of unprotected sulfonimidamides via asymmetric acylation with a cinchona-phosphinate catalyst. The desired products are formed in excellent yield and enantioselectivity with no observed bis-acylation. A data-science-driven approach to substrate scope evaluation was coupled to high throughput experimentation (HTE) to facilitate statistical modeling in order to inform mechanistic studies. Reaction kinetics, catalyst structural studies, and density functional theory (DFT) transition state analysis elucidated the turnover-limiting step to be the collapse of the tetrahedral intermediate and provided key insights into the catalyst-substrate structure-activity relationships responsible for the origin of the enantioselectivity. This study offers a reliable method for accessing enantioenriched sulfonimidamides to propel their application as pharmacophores and serves as an example of the mechanistic insight that can be gleaned from integrating data science and traditional physical organic techniques.

Selective Deposition of N-Heterocyclic Carbene Monolayers on Designated Au Microelectrodes within an Electrode Array.

The incorporation of organic self-assembled monolayers (SAMs) in microelectronic devices requires precise spatial control over the self-assembly process. In this work, selective deposition of N-heterocyclic carbenes (NHCs) on specific electrodes within a two-microelectrode array is achieved by using pulsed electrodeposition. Spectroscopic analysis of the NHC-coated electrode arrays reveals that each electrode is selectively coated with a designated NHC. The impact of NHC monolayers on the electrodes' work function is quantified using Kelvin probe force microscopy. These measurements demonstrate that the work function values of each electrode can be independently tuned by the adsorption of a specific NHC. The presented deposition method enables to selectively coat designated microelectrodes in an electrode array with chosen NHC monolayers for tuning their chemical and electronic functionality.

CO2 reduction on pure Cu produces only H2 after subsurface O is depleted: Theory and experiment.

We elucidate the role of subsurface oxygen on the production of C2 products from CO2 reduction over Cu electrocatalysts using the newly developed grand canonical potential kinetics density functional theory method, which predicts that the rate of C2 production on pure Cu with no O is ∼500 times slower than H2 evolution. In contrast, starting with Cu2O, the rate of C2 production is >5,000 times faster than pure Cu(111) and comparable to H2 production. To validate these predictions experimentally, we combined time-dependent product detection with multiple characterization techniques to show that ethylene production decreases substantially with time and that a sufficiently prolonged reaction time (up to 20 h) leads only to H2 evolution with ethylene production ∼1,000 times slower, in agreement with theory. This result shows that maintaining substantial subsurface oxygen is essential for long-term C2 production with Cu catalysts.

Tunable Electrochemical Entropy through Solvent Ordering by a Supramolecular Host.

An aqueous electrochemically controlled host-guest encapsulation system demonstrates a large and synthetically tunable redox entropy change. Electrochemical entropy is the basis for thermally regenerative electrochemical cycles (TRECs), which utilize reversible electrochemical processes with large molar entropy changes for thermogalvanic waste-heat harvesting and electrochemical cooling, among other potential applications. A supramolecular host-guest system demonstrates a molar entropy change of 4 times that of the state-of-the-art aqueous TREC electrolyte potassium ferricyanide. Upon encapsulation of a guest, water molecules that structurally resemble amorphous ice are displaced from the host cavity, leveraging a change in the degrees of freedom and ordering of the solvent rather than the solvation of the redox-active species to increase entropy. The synthetic tunability of the host allows rational optimization of the system's ΔS, showing a range of -51 to -101 cal mol-1 K-1 (-2.2 to -4.4 mV K-1) depending on ligand and metal vertex modifications, demonstrating the potential for rational design of high-entropy electrolytes and a new strategy to overcome theoretical limits on ion solvation reorganization entropy.

Indolo[2,3-b]quinoxaline as a Low Reduction Potential and High Stability Anolyte Scaffold for Nonaqueous Redox Flow Batteries.

Redox flow batteries (RFBs) are a promising stationary energy storage technology for leveling power supply from intermittent renewable energy sources with demand. A central objective for the development of practical, scalable RFBs is to identify affordable and high-performance redox-active molecules as storage materials. Herein, we report the design, synthesis, and evaluation of a new organic scaffold, indolo[2,3-b]quinoxaline, for highly stable, low-reduction potential, and high-solubility anolytes for nonaqueous redox flow batteries (NARFBs). The mixture of 2- and 3-(tert-butyl)-6-(2-methoxyethyl)-6H-indolo[2,3-b]quinoxaline exhibits a low reduction potential (-2.01 V vs Fc/Fc+), high solubility (>2.7 M in acetonitrile), and remarkable stability (99.86% capacity retention over 49.5 h (202 cycles) of H-cell cycling). This anolyte was paired with N-(2-(2-methoxyethoxy)-ethyl)phenothiazine (MEEPT) to achieve a 2.3 V all-organic NARFB exhibiting 95.8% capacity retention over 75.1 h (120 cycles) of cycling.

Data Science-Enabled Palladium-Catalyzed Enantioselective Aryl-Carbonylation of Sulfonimidamides.

New methods for the general asymmetric synthesis of sulfonimidamides are of great interest due to their applications in medicinal chemistry, agrochemical discovery, and academic research. We report a palladium-catalyzed cross-coupling method for the enantioselective aryl-carbonylation of sulfonimidamides. Using data science techniques, a virtual library of calculated bisphosphine ligand descriptors was used to guide reaction optimization by effectively sampling the catalyst chemical space. The optimized conditions identified using this approach provided the desired product in excellent yield and enantioselectivity. As the next step, a data science-driven strategy was also used to explore a diverse set of aryl and heteroaryl iodides, providing key information about the scope and limitations of the method. Furthermore, we tested a range of racemic sulfonimidamides for compatibility of this coupling partner. The developed method offers a general and efficient strategy for accessing enantioenriched sulfonimidamides, which should facilitate their application in industrial and academic settings.

Discovery of Potent Pyrazoline-Based Covalent SARS-CoV-2 Main Protease Inhibitors.

While vaccines and antivirals are now being deployed for the current SARS-CoV-2 pandemic, we require additional antiviral therapeutics to not only effectively combat SARS-CoV-2 and its variants, but also future coronaviruses. All coronaviruses have relatively similar genomes that provide a potential exploitable opening to develop antiviral therapies that will be effective against all coronaviruses. Among the various genes and proteins encoded by all coronaviruses, one particularly "druggable" or relatively easy-to-drug target is the coronavirus Main Protease (3CLpro or Mpro), an enzyme that is involved in cleaving a long peptide translated by the viral genome into its individual protein components that are then assembled into the virus to enable viral replication in the cell. Inhibiting Mpro with a small-molecule antiviral would effectively stop the ability of the virus to replicate, providing therapeutic benefit. In this study, we have utilized activity-based protein profiling (ABPP)-based chemoproteomic approaches to discover and further optimize cysteine-reactive pyrazoline-based covalent inhibitors for the SARS-CoV-2 Mpro. Structure-guided medicinal chemistry and modular synthesis of di- and tri-substituted pyrazolines bearing either chloroacetamide or vinyl sulfonamide cysteine-reactive warheads enabled the expedient exploration of structure-activity relationships (SAR), yielding nanomolar potency inhibitors against Mpro from not only SARS-CoV-2, but across many other coronaviruses. Our studies highlight promising chemical scaffolds that may contribute to future pan-coronavirus inhibitors.

Modification of Cysteine-Substituted Antibodies Using Enzymatic Oxidative Coupling Reactions.

Cysteines are routinely used as site-specific handles to synthesize antibody-drug conjugates for targeted immunotherapy applications. Michael additions between thiols and maleimides are some of the most common methods for modifying cysteines, but these functional groups can be difficult to prepare on scale, and the resulting linkages have been shown to be reversible under some physiological conditions. Here, we show that the enzyme tyrosinase, which oxidizes conveniently accessed phenols to afford reactive ortho-quinone intermediates, can be used to attach phenolic cargo to cysteines engineered on antibody surfaces. The resulting linkages between the thiols and ortho-quinones are shown to be more resistant than maleimides to reversion under physiological conditions. Using this approach, we construct antibody conjugates bearing cytotoxic payloads, which exhibit targeted cell killing, and further demonstrate this method for the attachment of a variety of cargo to antibodies, including fluorophores and oligonucleotides.

Hybrid Catalysts for Enantioselective Photo-Phosphoric Acid Catalysis.

The syntheses of two novel, organic, and chiral photocatalysts are presented. By combining donor-acceptor cyanoarene-based photocatalysts with a chiral phosphoric acid, bifunctional catalysts have been designed. In preliminary proof-of-concept reactions, their use in both enantioselective energy transfer and photoredox catalysis is demonstrated.

Exploiting non-covalent π interactions for catalyst design.

Molecular recognition, binding and catalysis are often mediated by non-covalent interactions involving aromatic functional groups. Although the relative complexity of these so-called π interactions has made them challenging to study, theory and modelling have now reached the stage at which we can explain their physical origins and obtain reliable insight into their effects on molecular binding and chemical transformations. This offers opportunities for the rational manipulation of these complex non-covalent interactions and their direct incorporation into the design of small-molecule catalysts and enzymes.

High-spatial-resolution mapping of catalytic reactions on single particles.

The critical role in surface reactions and heterogeneous catalysis of metal atoms with low coordination numbers, such as found at atomic steps and surface defects, is firmly established. But despite the growing availability of tools that enable detailed in situ characterization, so far it has not been possible to document this role directly. Surface properties can be mapped with high spatial resolution, and catalytic conversion can be tracked with a clear chemical signature; however, the combination of the two, which would enable high-spatial-resolution detection of reactions on catalytic surfaces, has rarely been achieved. Single-molecule fluorescence spectroscopy has been used to image and characterize single turnover sites at catalytic surfaces, but is restricted to reactions that generate highly fluorescing product molecules. Herein the chemical conversion of N-heterocyclic carbene molecules attached to catalytic particles is mapped using synchrotron-radiation-based infrared nanospectroscopy with a spatial resolution of 25 nanometres, which enabled particle regions that differ in reactivity to be distinguished. These observations demonstrate that, compared to the flat regions on top of the particles, the peripheries of the particles-which contain metal atoms with low coordination numbers-are more active in catalysing oxidation and reduction of chemically active groups in surface-anchored N-heterocyclic carbene molecules.

Systematic identification of engineered methionines and oxaziridines for efficient, stable, and site-specific antibody bioconjugation.

The field of chemical modification of proteins has been dominated by random modification of lysines or more site-specific labeling of cysteines, each with attendant challenges. Recently, we have developed oxaziridine chemistry for highly selective modification of methionine called redox-activated chemical tagging (ReACT) but have not broadly tested the molecular parameters for efficient and stable protein modification. Here we systematically scanned methionines throughout one of the most popular antibody scaffolds, trastuzumab, used for antibody engineering and drug conjugation. We tested the expression, reactivities, and stabilities of 123 single engineered methionines distributed over the surface of the antibody when reacted with oxaziridine. We found uniformly high expression for these mutants and excellent reaction efficiencies with a panel of oxaziridines. Remarkably, the stability to hydrolysis of the sulfimide varied more than 10-fold depending on temperature and the site of the engineered methionine. Interestingly, the most stable and reactive sites were those that were partially buried, presumably because of their reduced access to water. There was also a 10-fold variation in stability depending on the nature of the oxaziridine, which was determined to be inversely correlated with the electrophilic nature of the sulfimide. Importantly, the stabilities of the best analogs were sufficient to support their use as antibody drug conjugates and potent in a breast cancer mouse xenograft model over a month. These studies provide key parameters for broad application of ReACT for efficient, stable, and site-specific antibody and protein bioconjugation to native or engineered methionines.

An isolated water droplet in the aqueous solution of a supramolecular tetrahedral cage.

Water under nanoconfinement at ambient conditions has exhibited low-dimensional ice formation and liquid-solid phase transitions, but with structural and dynamical signatures that map onto known regions of water's phase diagram. Using terahertz (THz) absorption spectroscopy and ab initio molecular dynamics, we have investigated the ambient water confined in a supramolecular tetrahedral assembly, and determined that a dynamically distinct network of 9 ± 1 water molecules is present within the nanocavity of the host. The low-frequency absorption spectrum and theoretical analysis of the water in the Ga4L612- host demonstrate that the structure and dynamics of the encapsulated droplet is distinct from any known phase of water. A further inference is that the release of the highly unusual encapsulated water droplet creates a strong thermodynamic driver for the high-affinity binding of guests in aqueous solution for the Ga4L612- supramolecular construct.

A Porous Crystalline Nitrone-Linked Covalent Organic Framework.

Herein, we report the synthesis of a nitrone-linked covalent organic framework, COF-115, by combining N, N', N', N'''-(ethene-1, 1, 2, 2-tetrayltetrakis(benzene-4, 1-diyl))tetrakis(hydroxylamine) and terephthaladehyde via a polycondensation reaction. The formation of the nitrone functionality was confirmed by solid-state 13 C multi cross-polarization magic angle spinning NMR spectroscopy of the 13 C-isotope-labeled COF-115 and Fourier-transform infrared spectroscopy. The permanent porosity of COF-115 was evaluated through low-pressure N2 , CO2 , and H2 sorption experiments. Water vapor and carbon dioxide sorption analysis of COF-115 and the isoreticular imine-linked COF indicated a superior potential of N-oxide-based porous materials for atmospheric water harvesting and CO2 capture applications. Density functional theory calculations provided valuable insights into the difference between the adsorption properties of these COFs. Lastly, photoinduced rearrangement of COF-115 to the associated amide-linked material was successfully demonstrated.