Synthetic Platform Research Articles

Programming Surface Motility and Modulating Physiological Behaviors of Bacteria via Biosurfactant-Mimetic Polyurethanes.

Modulating microbial motility and physiology can enhance the production of bacterial macromolecules and small molecules. Herein, a platform of water-soluble and amphiphilic peptidomimetic polyurethanes is reported as a means of regulating bacterial surface behavior and the concomitant production of extracellular polymeric substances (EPS). It is demonstrated that carboxyl (-COOH)-containing polyurethanes exhibited 17-fold and 80-fold enhancements in Pseudomonas aeruginosa (P. aeruginosa) swarming and twitching areas, respectively. Conversely, an amine (-NH2)-functionalized polyurethane reduces the P. aeruginosa swarming area by 58%. Similar influences on the surface motility of Escherichia coli (E. coli) and a nonswarming P. aeruginosa mutant strain are also observed. Notably, -COOH polyurethanes completely wet the agar hydrogel surface and promote bacterial surface proliferation, resulting in enhanced EPS and rhamnolipid production. The programming of bacterial spatial migration into designed patterns is achieved by leveraging the opposing influences of -NH2 and -COOH polyurethanes. The results highlight the potential of this synthetic polyurethane platform and potentially other polymer systems as an exciting approach to control bacterial surface behaviors and influence the production of engineered living materials.

Utilizing Alkyne-Nitrone Cycloaddition for the Convenient Multi-Component Assembly of Protein Degraders and Biological Probes.

Proteolysis-targeting chimeras (PROTACs) have become a popular therapeutic strategy, and the development of multi-functional PROTACs has added complexity to their synthetic process. Although click reactions have been widely applied to prepare highly functionalized biomolecules, most of them are limited to two-component reactions, restricting the creation of more complex structures. Here, we developed a convenient multi-component assembly strategy via strain-promoted alkyne-nitrone cycloaddition (SPANC), which can be extended to a 3-component reaction when combined with nitrone formation. Using the 2-component assembly, we demonstrated the targeted protein degradation with both preassembled and in-cell assembled PROTACs. This strategy was also applied to facilitate the screening of E3 ligases in PROTACs and the preparation of various biological probes. Moreover, the 3-component assembly, via sequential nitrone formation and SPANC, enabled the synthesis of trifunctional 3-component PROTACs. The N-substituent, serving as an additional functional moiety, was designed as a photocage for sterically controlling PROTAC activity. The 3-component assembly can be further modified to provide additional control or enhance the cell-targeting ability of PROTACs. In short, our multi-component SPANC assembly strategy offers a modular and versatile synthetic platform for creating multi-functional PROTACs and biological probes.

Enhancer cooperativity can compensate for loss of activity over large genomic distances.

Enhancers are short DNA sequences that activate their target promoter from a distance; however, increasing the genomic distance between the enhancer and the promoter decreases expression levels. Many genes are controlled by combinations of multiple enhancers, yet the interaction and cooperation of individual enhancer elements are not well understood. Here, we developed a synthetic platform in mouse embryonic stem cells that allows building complex regulatory landscapes from the bottom up. We tested the system by integrating individual enhancers at different distances and confirmed that the strength of an enhancer contributes to how strongly it is affected by increased genomic distance. Furthermore, synergy between two enhancer elements depends on the distance at which the two elements are integrated: introducing a weak enhancer between a strong enhancer and the promoter strongly increases reporter gene expression, allowing enhancers to activate from increased genomic distances.

Synthesis of P(V)-Stereogenic Phosphorus Compounds via Organocatalytic Asymmetric Condensation.

Enantioenriched phosphorus(V)-stereogenic compounds, featuring a pentavalent phosphorus atom as the stereogenic center, are crucial in various natural products, drugs, bioactive molecules, and catalysts/ligands. While a handful of stereoselective synthetic approaches have been developed, achieving direct stereocontrol at the phosphorus atom through catalytic generation of phosphorus(V)-heteroatom bonds continues to be a formidable challenge. Here, we disclose an organocatalytic asymmetric condensation strategy that employs a novel activation mode of stable feedstock phosphinic acids by the formation of mixed phosphinic anhydride as the reactive species to facilitate further catalyst-controlled asymmetric P-O bond formations, involving a dynamic kinetic asymmetric transformation (DYKAT) process with alcohol nucleophiles via a cinchonidine-derived bifunctional catalyst. The resulting H-phosphinate intermediates allow further stereospecific derivatizations, affording modular access to a diverse library of chiral phosphonates and phosphonamidates with notable antibacterial activity. Furthermore, this synthetic platform facilitates P-O/N coupling with various natural products and drugs, presenting a valuable tool for medicine and agrochemical discovery.

Modular Synthetic Platform to Tailor Therapeutic-Specific Delivery in Injectable Hydrogels.

Injectable thermoresponsive hydrogels (thermogels), valued for their conformability and minimal invasiveness, are increasingly used as in situ forming implants for drug delivery and as regenerative scaffolds. These gels exhibit sol-to-gel phase transitions at body temperature. As localized depots and scaffolds, these gels determine the chemical and mechanical environments and could dramatically influence the release kinetics of drugs or the fate of cells. Current synthetic approaches for thermogels, however, often limit the ability to fully exploit interactions between the thermogel matrix and the encapsulated agent. In this study, we introduce a modular synthetic platform for creating a library of functionalized polyurethane thermogels that enables customization of gelation properties and intermolecular interactions. These thermogels can exhibit a wide range of stiffness, offer complementary ionic interactions, and enhance hydrophobic interactions and hydrogen bonding. By leveraging these tunable interactions between the thermogelling scaffold, functional groups, and encapsulated agents, we achieved sustained and controlled release, from days to over 6 months, for both low and high molecular weight drug analogs. Release profiles varied from monophasic to biphasic and triphasic depending on the compatibility between the thermogel properties and the encapsulated agents. The design rules identified here support the development of drug-specific formulations, facilitating precise, sustained, and modulated release tailored to therapeutic needs. Beyond providing an adaptable strategy for customizable injectable drug depots, this synthetic strategy lays the groundwork for future iterations of multi stimuli-responsive thermogels with enhanced bioactivity, advancing the potential for customizable, biointeractive therapeutic systems.

Catalytic Enantioselective Functionalization of Maleimides: An Update

Comprehensive SummaryMaleimide derivatives are well‐established reactive intermediates also found in natural products, synthetic pharmaceuticals and functional polymers. Their specific reactivity found widespread applications in the field of bioconjugation and allowed for the development of highly selective functionalizations based on simple additions and cycloadditions with the possible control of central and C–N axial chirality. These multisite‐reactive scaffolds have aroused a long‐standing interest throughout the scientific community more particularly as powerful electrophilic partners and more recently as nucleophilic partners in some specific transformations. The persistent interest in these easily accessible synthetic platforms over the last decade has enabled the development of new enantioselective transformations and the major advancements in this field are presented in this review. Key Scientists

5]Helicene Based π-Conjugated Macrocycles with Persistent Figure-Eight and Möbius Shapes: Efficient Synthesis, Chiral Resolution and Bright Circularly Polarized Luminescence.

π-Conjugated chiral shape-persistent molecular nanocarbons hold great potential as chiroptical materials, though their synthesis remains a considerable challenge. Here, we present a simple approach using Suzuki coupling of a [5]helicene building block with various aromatic units, enabling the one-pot synthesis of a series of chiral macrocycles with persistent figure-eight and Möbius shapes. Single-crystal structures of 7 compounds were solved, and 22 enantiomers were separated by preparative chiral HPLC. A notable pyrene-bridged figure-eight macrocycle, with its rigid, fully π-conjugated and overcrowded structure, exhibited pure excimer emission and outstanding circularly polarized luminescence (CPL) properties, including a large dissymmetric factor (|glum|=3.8×10-2) and significant CPL brightness (BCPL=710.5 M-1cm-1). This method provides a versatile synthetic platform for producing various chiral D2-symmetric figure-eight macrocycles and singly or triply twisted Möbius macrocycles with C2 and D3 symmetry, offering tunable chiroptical properties for CPL applications.

5]Helicene Based π‐Conjugated Macrocycles with Persistent Figure‐Eight and Möbius Shapes: Efficient Synthesis, Chiral Resolution and Bright Circularly Polarized Luminescence

Abstractπ‐Conjugated chiral shape‐persistent molecular nanocarbons hold great potential as chiroptical materials, though their synthesis remains a considerable challenge. Here, we present a simple approach using Suzuki coupling of a [5]helicene building block with various aromatic units, enabling the one‐pot synthesis of a series of chiral macrocycles with persistent figure‐eight and Möbius shapes. Single‐crystal structures of 7 compounds were solved, and 22 enantiomers were separated by preparative chiral HPLC. A notable pyrene‐bridged figure‐eight macrocycle, with its rigid, fully π‐conjugated and overcrowded structure, exhibited pure excimer emission and outstanding circularly polarized luminescence (CPL) properties, including a large dissymmetric factor (|glum|=3.8×10−2) and significant CPL brightness (BCPL=710.5 M−1cm−1). This method provides a versatile synthetic platform for producing various chiral D2‐symmetric figure‐eight macrocycles and singly or triply twisted Möbius macrocycles with C2 and D3 symmetry, offering tunable chiroptical properties for CPL applications.

C-H Trifluoromethylthiolation of aldehyde hydrazones.

The selective C-H trifluoromethylthiolation of aldehyde hydrazones afforded interesting fluorinated building blocks, which could be used as a synthetic platform. Starting from readily available (hetero)aromatic and aliphatic hydrazones, the formation of a C-SCF3 bond was achieved under oxidative and mild reaction conditions in the presence of the readily available AgSCF3 salt via a one-pot sequential process (28 examples, up to 91% yield). Mechanistic investigations revealed that AgSCF3 was the active species in the transformation.

Organocatalytic Electrophilic Arene Amination: Rapid Synthesis of 2-Quinolones.

For decades, the synthesis of 2-quinolones, a crucial structural motif in pharmaceuticals and agrochemicals, has relied heavily on costly noble metal complexes and structurally complex ligands. Despite considerable efforts from synthetic chemists, a mild, metal-free, environmentally friendly, and cost-effective approach has remained elusive. This study introduces a robust, metal-free synthetic platform that leverages an innovative organoiodine-catalyzed electrophilic arene C(sp2)-H amination strategy to efficiently produce a wide range of new and modifiable 2-quinolones. Moreover, this study allows ready synthetic access to novel 8-aryl-substituted 2-quinolones, uncovering new chemical spaces with significant potential for medicinal applications.

Synthesis of Aza‐S(VI) Fluorides and Primary Sulfonimidamides from Sulfinylamines

AbstractAza‐S(VI) fluorides are crucial compounds in the synthesis of various S(VI) derivatives, which find broad applications in drug discovery. However, the synthesis of sulfonimidoyl and sulfondiimidoyl fluorides have been relatively underexplored, often requiring lengthy reaction sequences and/or the use of hazardous gaseous reagents. In this study, we present a rapid one‐pot method for producing sulfonimidoyl fluorides from sulfinylamines via a nucleophilic addition/electrophilic fluorination sequence. Similarly, sulfondiimidoyl fluorides can be synthesized using the same sequence, preceded by the formation of unsymmetrical sulfurdiimides readily generated in situ from sulfinylamines. Whereas isolation of sulfondiimidoyl fluorides was not feasible, they could be efficiently converted into primary sulfonimidamides by base hydrolysis in a one‐pot process. Furthermore, we explored the reactivity of aza‐S(VI) fluorides with various nucleophiles, demonstrating a versatile synthetic platform for the synthesis of aza‐S(VI) compounds.

Structure and sequence engineering approaches to improve invivo expression of nucleic acid-delivered antibodies.

Monoclonal antibodies are an important class of biologics with over 160 Food and Drug Administration/European Union-approved drugs. A significant bottleneck to global accessibility of recombinant monoclonal antibodies stems from complexities related to their production, storage, and distribution. Recently, gene-encoded approaches such as mRNA, DNA, or viral delivery have gained popularity, but ensuring biologically relevant levels of antibody expression in the host remains a critical issue. Using a synthetic DNA platform, we investigated the role of antibody structure and sequence toward invivo expression. SARS-CoV-2 antibody 2196 was recently engineered as a DNA-encoded monoclonal antibody (DMAb-2196). Utilizing an immunoglobulin heavy and light chain "chain-swap" methodology, we interrogated features of DMAb-2196 that can modulate invivo expression through rational design and structural modeling. Comparing these results to natural variation of antibody sequences resulted in development of an antibody frequency score that aids in the prediction of expression-improving mutations by leveraging antibody repertoire datasets. We demonstrate that a single amino acid mutation identified through this score increases invivo expression up to 2-fold and that combinations of mutations can also enhance expression. This analysis has led to a generalized pipeline that can unlock the potential for invivo delivery of therapeutic antibodies across many indications.

Universal and scalable synthesis of photochromic single-atom catalysts for plastic recycling

Metal oxide nanostructures with single-atomic heteroatom incorporation are of interest for many applications. However, a universal and scalable synthesis approach with high heteroatom concentrations represents a formidable challenge, primarily due to the pronounced structural disparities between Mhetero–O and Msub–O units. Here, focusing on TiO2 as the exemplified substrate, we present a diethylene glycol-assisted synthetic platform tailored for the controlled preparation of a library of M1-TiO2 nanostructures, encompassing 15 distinct unary M1-TiO2 nanostructures, along with two types of binary and ternary composites. Our approach capitalizes on the unique properties of diethylene glycol, affording precise kinetic control by passivating the hydrolytic activity of heteroatom and simultaneously achieving thermodynamic control by introducing short-range order structures to dissipate the free energy associated with heteroatom incorporation. The M1-TiO2 nanostructures, characterized by distinctive and abundant M–O–Ti units on the surface, exhibit high efficiency in photochromic photothermal catalysis toward recycling waste polyesters. This universal synthetic platform contributes to the preparation of materials with broad applicability and significance across catalysis, energy conversion, and biomedicine.

Transcriptional response of Methanosarcina acetivorans to repression of the energy-conserving methanophenazine: CoM-CoB heterodisulfide reductase enzyme HdrED.

Methane-producing archaea are key organisms in the anaerobic carbon cycle. These organisms, also called methanogens, grow by converting substrate to methane gas in a process called methanogenesis. Previous research showed that the reduction of the terminal electron acceptor is the rate-limiting step in methanogenesis by Methanosarcina acetivorans. In order to gain insight into how the cells sense and respond to the availability of the terminal electron acceptor, we designed an experiment to deplete cells of the essential terminal oxidase enzyme, HdrED. We found that the depletion of HdrED in vivo results in a higher abundance of transcripts for methyltransferases (mtaC2, mtaB3, mtaC3), coenzyme B biosynthesis, C1 metabolism, and pyrimidine compounds. In most cases, these changes were distinct from transcript abundance changes observed during the transition from exponential growth to stationary phase cultures. These data implicate the methylotrophic methanogenesis regulator MsrC (MA4383) in CoM-S-S-CoB heterodisulfide sensing and indicate cells have a specific mechanism to sense intracellular ratio of CoM-S-S-CoB, coenzyme M, and coenzyme B thiols and further suggest transcripts encoding translation and methanogenesis functions are controlled by feed-forward regulation depending on substrate availability.IMPORTANCEMethanosarcina is an emerging model archaeon and synthetic biology platform for the production of renewable energy and sustainable chemicals to reduce dependence on petroleum. Research into metabolic networks and gene regulation in this organism and other methanogens will inform genome-scale metabolic modeling and microbial function prediction in uncultured or non-model anaerobes and archaea. This study suggests methanogens use unknown mechanisms to efficiently couple methanogenesis to gene regulation via CoM-S-S-CoB and ATP availability.

Zinc‐Catalyzed Enantioselective Formal (3+2) Cycloadditions of Bicyclobutanes with Imines: Catalytic Asymmetric Synthesis of Azabicyclo[2.1.1]hexanes

AbstractThe cycloaddition reaction involving bicyclo[1.1.0]butanes (BCBs) offers a versatile and efficient synthetic platform for producing C(sp3)‐rich rigid bridged ring scaffolds, which act as phenyl bioisosteres. However, there is a scarcity of catalytic asymmetric cycloadditions of BCBs to fulfill the need for enantioenriched saturated bicycles in drug design and development. In this study, an efficient synthesis of valuable azabicyclo[2.1.1]hexanes (aza‐BCHs) by an enantioselective zinc‐catalyzed (3+2) cycloadditions of BCBs with imines is reported. The reaction proceeds effectively with a novel type of BCB that incorporates a 2‐acyl imidazole group and a diverse array of alkynyl‐ and aryl‐substituted imines. The target aza‐BCHs, which consist of α‐chiral amine fragments and two quaternary carbon centers, are efficiently synthesized with up to 94 % and 96.5:3.5 er under mild conditions. Experimental and computational studies reveal that the reaction follows a concerted nucleophilic ring‐opening mechanism of BCBs with imines. This mechanism is distinct from previous studies on Lewis acid‐catalyzed cycloadditions of BCBs.

Zinc-Catalyzed Enantioselective Formal (3+2) Cycloadditions of Bicyclobutanes with Imines: Catalytic Asymmetric Synthesis of Azabicyclo[2.1.1]hexanes.

The cycloaddition reaction involving bicyclo[1.1.0]butanes (BCBs) offers a versatile and efficient synthetic platform for producing C(sp3)-rich rigid bridged ring scaffolds, which act as phenyl bioisosteres. However, there is a scarcity of catalytic asymmetric cycloadditions of BCBs to fulfill the need for enantioenriched saturated bicycles in drug design and development. In this study, an efficient synthesis of valuable azabicyclo[2.1.1]hexanes (aza-BCHs) by an enantioselective zinc-catalyzed (3+2) cycloadditions of BCBs with imines is reported. The reaction proceeds effectively with a novel type of BCB that incorporates a 2-acyl imidazole group and a diverse array of alkynyl- and aryl-substituted imines. The target aza-BCHs, which consist of α-chiral amine fragments and two quaternary carbon centers, are efficiently synthesized with up to 94 % and 96.5:3.5 er under mild conditions. Experimental and computational studies reveal that the reaction follows a concerted nucleophilic ring-opening mechanism of BCBs with imines. This mechanism is distinct from previous studies on Lewis acid-catalyzed cycloadditions of BCBs.

Leveraging Synthetic Virology for the Rapid Engineering of Vesicular Stomatitis Virus (VSV)

Vesicular stomatitis virus (VSV) is a prototype RNA virus that has been instrumental in advancing our understanding of viral molecular biology and has applications in vaccine development, cancer therapy, antiviral screening, and more. Current VSV genome plasmids for purchase or contract virus services provide limited options for modification, restricted to predefined cloning sites and insert locations. Improved methods and tools to engineer VSV will unlock further insights into long-standing virology questions and new opportunities for innovative therapies. Here, we report the design and construction of a full-length VSV genome. The 11,161 base pair synthetic VSV (synVSV) was assembled from four modularized DNA fragments. Following rescue and titration, phenotypic analysis showed no significant differences between natural and synthetic viruses. To demonstrate the utility of a synthetic virology platform, we then engineered VSV with a foreign glycoprotein, a common use case for studying viral entry and developing anti-virals. To show the freedom of design afforded by this platform, we then modified the genome of VSV by rearranging the gene order, switching the positions of VSV-P and VSV-M genes. This work represents a significant technical advance, providing a flexible, cost-efficient platform for the rapid construction of VSV genomes, facilitating the development of innovative therapies.

Intelligent guide RNA: dual toehold switches for modulating luciferase in the presence of trigger RNA

The CRISPR system finds extensive application in molecular biology, but its continuous activity can yield adverse effects. Leveraging programmable CRISPR/Cas9 function via nano-device mediation effectively mitigates these drawbacks. The integration of RNA-sensing platforms into CRISPR thus empowers it as a potent tool for processing internal cell data and modulating gene activity. Here, an intelligent guide RNA—a cis-repressed gRNA synthetic circuit enabling efficient recognition of specific trigger RNAs—is developed. This platform carries two toehold switches and includes an inhibited CrRNA sequence. In this system, the presence of cognate trigger RNA promotes precise binding to the first toehold site, initiating a cascade that releases CrRNA to target a reporter gene (luciferase) in this study. Decoupling the CrRNA segment from the trigger RNA enhances the potential of this genetic logic circuit to respond to specific cellular circumstances, offering promise as a synthetic biology platform.

Energy transfer-mediated multiphoton synergistic excitation for selective C(sp3)–H functionalization with coordination polymer

Activation and selective oxidation of inert C(sp3)–H bonds remain one of the most challenging tasks in current synthetic chemistry due to the inherent inertness of C(sp3)–H bonds. In this study, inspired by natural monooxygenases, we developed a coordination polymer with naphthalenediimide (NDI)-based ligands and binuclear iron nodes. The mixed-valence FeIIIFeII species and chlorine radicals (Cl•) are generated via ligand-to-metal charge transfer (LMCT) between FeIII and chlorine ions. These Cl• radicals abstract a hydrogen atom from the inert C(sp3)–H bond of alkanes via hydrogen atom transfer (HAT). In addition, NDI converts oxygen to 1O2 via energy transfer (EnT), which then coordinates to FeII, forming an FeIV = O intermediate for the selective oxidation of C(sp3)–H bonds. This synthetic platform, which combines photoinduced EnT, LMCT and HAT, provides a EnT-mediated parallel multiphoton excitation strategy with kinetic synergy effect for selective C(sp3)–H oxidation under mild conditions and a blueprint for designing coordination polymer-based photocatalysts for C(sp3)–H bond oxidation.

A molecular-chemistry-manipulation strategy toward functional lignin-based porous carbon nanospheres with tunable-pore structure

Porous carbon nanospheres derived from biomass materials have inspired numerous interests in various areas. Nevertheless, their fabrications mainly depend on template-assisted or chemical activation routes. Here, a molecular-chemistry-manipulation strategy was proposed innovatively by taking advantage of the heterogeneous self-condensation characters of lignin molecules under thermal stimulation, opening a practical and versatile synthetic platform for the construction of lignin-based hierarchical porous carbon nanospheres (LHPCS). We can manipulate the condensed kinetics by tuning the environmental variables and forming designated nanospheres with inhomogeneous molecular chemistry. This intraparticle difference could provide a possibility to tune its refined structure for synthesizing hierarchical porous carbon nanospheres. Such LHPCS behaved the specific surface area of 962 m2 g−1 and pore volume of 0.76 cm3 g−1, as well as regulable pore ratios (15.5–22.9 % of macropore, 12.7–37 % for mesopore and 45–68.9 % for micropore). Besides, the monodisperse spherical morphology with hierarchical interleaved channels affords them excellent performance in optical management and energy storage, including pore-determined photothermal properties, extremely low reflectance of ca. 1.9 %, stable multi-angles specular reflectance, and anti-self-discharge induced by charge rearrangement. Our proposed molecular chemistry strategy provides an alternative pathway for constructing gradient and adjustable pore structures.