A traceless linker for aliphatic amines that rapidly and quantitatively fragments after reduction

Reduction sensitive linkers (RSLs) have the potential to transform the field of drug delivery due to their ease of use and selective cleavage in intracellular environments. However, despite their compelling attributes, developing reduction sensitive self-immolative linkers for aliphatic amines has been challenging due to their poor leaving group ability and high pK_a values. Here a traceless self-immolative linker composed of a dithiol-ethyl carbonate connected to a benzyl carbamate (DEC) is presented, which can modify aliphatic amines and release them rapidly and quantitatively after disulfide reduction. DEC was able to reversibly modify the lysine residues on CRISPR–Cas9 with either PEG, the cell penetrating peptide Arg₁₀, or donor DNA, and generated Cas9 conjugates with significantly improved biological properties. In particular, Cas9–DEC–PEG was able to diffuse through brain tissue significantly better than unmodified Cas9, making it a more suitable candidate for genome editing in animals. Furthermore, conjugation of Arg₁₀ to Cas9 with DEC was able to generate a self-delivering Cas9 RNP that could edit cells without transfection reagents. Finally, conjugation of donor DNA to Cas9 with DEC increased the homology directed DNA repair (HDR) rate of the Cas9 RNP by 50% in HEK 293T cell line. We anticipate that DEC will have numerous applications in biotechnology, given the ubiquitous presence of aliphatic amines on small molecule and protein therapeutics.

Reduction sensitive linkers (RSLs) have the potential to transform the field of drug delivery due to their ease of use and selective cleavage in intracellular environments.     

Coordination-based self-assembled capsules (SACs) for protein,CRISPR–Cas9, DNA and RNA delivery

Biologics, such as functional proteins and nucleic acids, have recently dominated the drug market and comprise seven out of the top 10 best-selling drugs. Biologics are usually polar, heat sensitive, membrane impermeable and subject to enzymatic degradation and thus require systemic routes of administration and delivery. Coordination-based delivery vehicles, which include nanosized extended metal–organic frameworks (nMOFs) and discrete coordination cages, have gained a lot of attention because of their remarkable biocompatibility, in vivo stability, on-demand biodegradability, high encapsulation efficiency, easy surface modification and moderate synthetic conditions. Consequently, these systems have been extensively utilized as carriers of biomacromolecules for biomedical applications. This review summarizes the recent applications of nMOFs and coordination cages for protein, CRISPR–Cas9, DNA and RNA delivery. We also highlight the progress and challenges of coordination-based platforms as a promising approach towards clinical biomacromolecule delivery and discuss integral future research directions and applications.

SACs can be efficiently used to load biologics such as proteins, CRISPR–Cas9, DNA and RNA and release them on-demand.     

Nonspecific interactions between SpCas9 and dsDNA sites located downstream of the PAM mediate facilitated diffusion to accelerate target search

RNA-guided Streptococcus pyogenes Cas9 (SpCas9) is a sequence-specific DNA endonuclease that works as one of the most powerful genetic editing tools. However, how Cas9 locates its target among huge amounts of dsDNAs remains elusive. Here, combining biochemical and single-molecule fluorescence assays, we revealed that Cas9 uses both three-dimensional and one-dimensional diffusion to find its target with high efficiency. We further observed surprising apparent asymmetric target search regions flanking PAM sites on dsDNA under physiological salt conditions, which accelerates the target search efficiency of Cas9 by ∼10-fold. Illustrated by a cryo-EM structure of the Cas9/sgRNA/dsDNA dimer, non-specific interactions between DNA ∼8 bp downstream of the PAM site and lysines within residues 1151–1156 of Cas9, especially lys1153, are the key elements to mediate the one-dimensional diffusion of Cas9 and cause asymmetric target search regions flanking the PAM. Disrupting these non-specific interactions, such as mutating these lysines to alanines, diminishes the contribution of one-dimensional diffusion and reduces the target search rate by several times. In addition, low ionic concentrations or mutations on PAM recognition residues that modulate interactions between Cas9 and dsDNA alter apparent asymmetric target search behaviors. Together, our results reveal a unique searching mechanism of Cas9 under physiological salt conditions, and provide important guidance for both in vitro and in vivo applications of Cas9.

Nonspecific interactions between DNA ∼8 bp downstream of the PAM and lysines within residues 1151–1156 of Cas9 mediate one-dimensional diffusion and cause asymmetric target search regions flanking the PAM.     

Photocontrol of CRISPR/Cas9 function by site-specific chemical modification of guide RNA

The function of CRISPR/Cas9 can be conditionally controlled by the rational engineering of guide RNA (gRNA) to target the gene of choice for precise manipulation of the genome. Particularly, chemically modified gRNA that can be activated by using specific stimuli provides a unique tool to expand the versatility of conditional control. Herein, unlike previous engineering of gRNA that generally focused on the RNA part only but neglected RNA–protein interactions, we aimed at the interactive sites between 2′-OH of ribose in the seed region of gRNA and the Cas9 protein and identified that chemical modifications at specific sites could be utilized to regulate the Cas9 activity. By introducing a photolabile group at these specific sites, we achieved optical control of Cas9 activity without disrupting the Watson–Crick base pairing. We further examined our design through CRISPR-mediated gene activation and nuclease cleavage in living cells and successfully manipulated the gene expression by using light irradiation. Our site-specific modification strategy exhibited a highly efficient and dynamic optical response and presented a new perspective for manipulating gRNA based on the RNA–protein interaction rather than the structure of RNA itself. In addition, these specific sites could also be potentially utilized for modification of other stimuli-responsive groups, which would further enrich the toolbox for conditional control of CRISPR/Cas9 function.

The CRISPR/Cas9 function is optically controlled in living cells by the site-specifically caged guide RNA based on the RNA–protein interaction.     

Access to P-chiral sec- and tert-phosphine oxides enabled by Le-Phos-catalyzed asymmetric kinetic resolution

The synthesis of P-stereogenic building blocks is extremely difficult. Herein we report an efficient kinetic resolution of secondary phosphine oxides via a Le-Phos-catalyzed asymmetric allylation reaction with Morita–Baylis–Hillman carbonates. This method provides facile access to enantioenriched secondary and tertiary P-chiral phosphine oxides with broad substrate scope, both of which could serve as P-stereogenic synthons, and can be rapidly incorporated into a given scaffold bearing a P-stereocenter. The highly desirable late stage modifications demonstrate the practicability of our method and can be a critical contribution to obtaining optimal P-chiral catalysts and ligands.

Herein we report an efficient kinetic resolution of secondary phosphine oxides via a Le-Phos-catalyzed asymmetric allylation reaction with Morita–Baylis–Hillman carbonates.     

CHIP-mediated hyperubiquitylation of tau promotes its self-assembly into the insoluble tau filaments

The tau protein is a highly soluble and natively unfolded protein. Under pathological conditions, tau undergoes multiple post-translational modifications (PTMs) and conformational changes to form insoluble filaments, which are the proteinaceous signatures of tauopathies. To dissect the crosstalk among tau PTMs during the aggregation process, we phosphorylated and ubiquitylated recombinant tau in vitro using GSK3β and CHIP, respectively. The resulting phospho–ub-tau contained conventional polyubiquitin chains with lysine 48 linkages, sufficient for proteasomal degradation, whereas unphosphorylated ub-tau species retained only one–three ubiquitin moieties. Mass-spectrometric analysis of in vitro reconstituted phospho–ub-tau revealed seven additional ubiquitylation sites, some of which are known to stabilize tau protofilament stacking in the human brain with tauopathy. When the ubiquitylation reaction was prolonged, phospho–ub-tau transformed into insoluble hyperubiquitylated tau species featuring fibrillar morphology and in vitro seeding activity. We developed a small-molecule inhibitor of CHIP through biophysical screening; this effectively suppressed tau ubiquitylation in vitro and delayed its aggregation in cultured cells including primary cultured neurons. Our biochemical findings point to a “multiple-hit model,” where sequential events of tau phosphorylation and hyperubiquitylation function as a key driver of the fibrillization process, thus indicating that targeting tau ubiquitylation may be an effective strategy to alleviate the course of tauopathies.

Multiple-hit model for tau aggregation, where sequential events of tau phosphorylation and hyperubiquitylation function as a key driver of the fibrillization process.     

Rational design of a “dual lock-and-key” supramolecular photosensitizer based on aromatic nucleophilic substitution for specific and enhanced photodynamic therapy

Photosensitizing agents are essential for precise and efficient photodynamic therapy (PDT). However, most of the conventional photosensitizers still suffer from limitations such as aggregation-caused quenching (ACQ) in physiological environments and toxic side-effects on normal tissues during treatment, leading to reduced therapeutic efficacy. Thus, integrating excellent photophysical properties and accurate carcinoma selectivity in a photosensitizer system remains highly desired. Herein, a “dual lock-and-key” supramolecular photosensitizer BIBCl–PAE NPs for specific and enhanced cancer therapy is reported. BIBCl–PAE NPs are constructed by encapsulating a rationally designed glutathione (GSH)-activatable photosensitizer BIBCl in a pH-responsive diblock copolymer. In normal tissues, BIBCl is “locked” in the hydrophobic core of the polymeric micelles due to ACQ. Under the “dual key” activation of low pH and high levels of GSH in a tumor microenvironment, the disassembly of micelles facilitates the reaction of BIBCl with GSH to release water-soluble BIBSG with ideal biocompatibility, enabling the highly efficient PDT. Moreover, benefiting from the Förster resonance energy transfer effect of BIBSG, improved light harvesting ability and ¹O₂ production are achieved. In vitro and vivo experiments have demonstrated that BIBCl–PAE NPs are effective in targeting and inhibiting carcinoma. BIBCl–PAE NPs show superior anticancer efficiency relative to non-activatable controls.

The “dual lock-and-key” supramolecular photosensitizers enable specific and enhanced photodynamic therapy (PDT).     

Phosphinoborylenes as stable sources of fleeting borylenes

Base-stabilised borylenes that mimic the ability of transition metals to bind and activate inert substrates have attracted significant attention in recent years. However, such species are typically highly reactive and fleeting, and often cannot be isolated at ambient temperature. Herein, we describe a readily accessible trimethylphosphine-stabilised borylborylene which was found to possess a labile P–B bond that reversibly cleaves upon gentle heating. Exchange of the labile phosphine with other nucleophiles (CO, isocyanide, 4-dimethylaminopyridine) was investigated, and the binding strength of a range of potential borylene “ligands” has been evaluated computationally. The room-temperature-stable PMe₃-bound borylenes were subsequently applied to novel bond activations including [2 + 2] cycloaddition with carbodiimides and the reduction of dichalcogenides, revealing that PMe₃-stabilised borylenes can effectively behave as stable sources of the analogous fleeting dicoordinate species under mild conditions.

A room-temperature stable phosphinoborylene provides a source of a reactive two-coordinate borylene via dissociation of a labile phosphine upon gentle heating. Ligand exchange, the capture of unsaturated molecules, and oxidation have been explored.     

Biomimetic nanochannels for the discrimination of sialylated glycans via a tug-of-war between glycan binding and polymer shrinkage

Sialylated glycans that are attached to cell surface mediate diverse cellular processes such as immune responses, pathogen binding, and cancer progression. Precise determination of sialylated glycans, particularly their linkage isomers that can trigger distinct biological events and are indicative of different cancer types, remains a challenge, due to their complicated composition and limited structural differences. Here, we present a biomimetic nanochannels system integrated with the responsive polymer polyethyleneimine-g-glucopyranoside (Glc-PEI) to solve this problem. By using a dramatic “OFF–ON” change in ion flux, the nanochannels system achieves specific recognition for N-acetylneuraminic acid (Neu5Ac, the predominant form of sialic acid) from various monosaccharides and sialic acid species. Importantly, different “OFF–ON” ratios of the conical nanochannels system allows the precise and sensitive discrimination of sialylated glycan linkage isomers, α2–3 and α2–6 linkage (the corresponding ion conductance increase ratios are 96.2% and 264%, respectively). Analyses revealed an unusual tug-of-war mechanism between polymer-glycan binding and polymer shrinkage. The low binding affinity of Glc-PEI for the α2–6-linked glycan caused considerable shrinkage of Glc-PEI layer, but the high affinity for the α2–3-linked glycan resulted in only a slight shrinkage. This competition mechanism provides a simple and versatile materials design principle for recognition or sensing systems that involve negatively charged target biomolecules. Furthermore, this work broadens the application of nanochannel systems in bioanalysis and biosensing, and opens a new route to glycan analysis that could help to uncover the mysterious and wonderful glycoworld.

A glycan-responsive polymer-modified nanochannels system enables the precise discrimination of sialylated glycan linkage isomers via the different “OFF–ON” changes resulting from a “tug-of-war” between polymer-glycan binding and polymer shrinkage.     

Three-component three-bond forming cascade via palladium photoredox catalysis

A highly modular radical cascade strategy based upon radical cyclisation/allylic substitution sequence between alkyl/aryl bromides, 1,3-dienes and nucleophiles ranging from sulfinates to amines, phenols and 1,3-dicarbonyls is described (>80 examples). Palladium phosphine complexes – which merge properties of photo- and cross coupling-catalysts – allow to forge three bonds with complete 1,4-selectivity and stereocontrol, delivering highly value added carbocyclic and heterocyclic motifs that can feature – inter alia – vicinal quaternary centers, free protic groups, gem-difluoro motifs and strained rings. Furthermore, a flow chemistry approach was for the first time applied in palladium–photocatalysed endeavors involving radicals.

Highly modular three-bond three-component cascade featuring palladium as dual photoredox/cross coupling catalyst.     

Counterintuitive solvation effect of ionic-liquid/DMSO solvents on acidic C–H dissociation and insight into respective solvation

How would acidic bond dissociation be affected by adding a small quantity of a weakly polar ionic liquid IL (the “apparent” or “measured” dielectric constant ε of the IL is around 10–15) into a strongly polar molecular solvent (e.g., ε of DMSO: 46.5), or vice versa? The answer is blurred, because no previous investigation was reported in this regard. Toward this, we, taking various IL/DMSO mixtures as representatives, have thoroughly investigated the effects of the respective solvent in ionic–molecular binary systems on self-dissociation of C–H acid phenylmalononitrile PhCH(CN)₂via pK_a determination. As disclosed, in this category of binary media, (1) no linear correspondence exists between pK_a and molar fractions of the respective solvent components; (2) only ∼1–2 mol% of weakly polar ILs in strongly polar DMSO make C–H bonds even more dissociative than in neat DMSO; (3) a small fraction of DMSO in ILs (<10 mol%) can dramatically ease acidic C–H-dissociation; and (4) while the DMSO fraction further increases, its acidifying effect becomes much attenuated. These findings, though maybe counterintuitive, have been rationalized on the basis of the precise pK_a measurement of this work in relation to the respective roles of each solvent component in solvation.

The dependence of PhCH(CN)₂ pK_a on the molar fraction of ionic liquids in ionic–molecular binary mixtures showed a nonlinear three-fragment plot, which was rationalized for the first time by the respective roles of each solvent component for solvation.     

How bulky ligands control the chemoselectivity of Pd-catalyzed N-arylation of ammonia

Steric bulk has been recognized as a central design principle for supporting ligands in the widely utilized Buchwald–Hartwig amination. In a recent example, it was shown that a Pd-catalyst carrying a phosphine ligand can successfully aminate aryl halides using ammonia as the nitrogen source. Interestingly, the chemoselectivity of this reaction was found to depend on the steric demand of the phosphine ligand. Whereas a sterically less demanding phosphine affords diphenylamine as the major product, it was shown that the amination reaction can be stopped after the first amination to give aniline if a sterically more encumbering phosphine ligand is used. Density functional theory calculations were carried out to examine the relationship between the steric demand of the phosphine ligand and the chemoselectivity. It was found that the key feature that leads to the chemoselectivity is the ability of the phosphine ligand to rotate the biaryl moiety of the ligand away from the Pd-center upon amine addition to release some of the steric crowding from the Pd-coordination site.

Steric bulk has been recognized as a central design principle for ligands in the widely utilized Buchwald–Hartwig amination. This mechanistic study reveals how this steric effect manipulates the reaction pathway and determines the chemoselectivity.     

3-Bromotetrazine: labelling of macromolecules via monosubstituted bifunctional s-tetrazines

We report the synthesis and first characterisation of the novel chemical probe 3-bromotetrazine and establish its reactivity towards nucleophiles. This led to the synthesis of several novel classes of 3-monosubstituted s-tetrazines. A remarkable functional group selectivity is observed and is utilised to site-selectively functionalise different complex molecules. The stability of 3-bromotetrazine under the reaction conditions facilitated the development of a protocol for protein functionalisation, which enabled a “minimal”, bifunctional tetrazine unit as a bio-orthogonal handle for inverse electron demand Diels–Alder reactions. Additionally, a novel tetrazine-based chemical probe was developed and its application in the context of thiol-targeted natural product isolation and labelling of mammalian cells is demonstrated.

3-Bromotetrazine selectively labels small and macromolecules up to proteins and can then be used as a fluorophore or as a bio-orthogonal handle for downstream functionalisation.     

Mechanistic insights into copper-catalyzed aerobic oxidative coupling of N–N bonds

Catalytic N–N coupling is a valuable transformation for chemical synthesis and energy conversion. Here, mechanistic studies are presented for two related copper-catalyzed oxidative aerobic N–N coupling reactions, one involving the synthesis of a pharmaceutically relevant triazole and the other relevant to the oxidative conversion of ammonia to hydrazine. Analysis of catalytic and stoichiometric N–N coupling reactions support an “oxidase”-type catalytic mechanism with two redox half-reactions: (1) aerobic oxidation of a Cu^I catalyst and (2) Cu^II-promoted N–N coupling. Both reactions feature turnover-limiting oxidation of Cu^I by O₂, and this step is inhibited by the N–H substrate(s). The results highlight the unexpected facility of the N–N coupling step and establish a foundation for development of improved catalysts for these transformations.

Mechanistic studies provide valuable insights into Cu-catalyzed N–N coupling reactions relevant to energy conversion and pharmaceutical synthesis.     

trans-Hydroboration–oxidation products in Δ5-steroids via a hydroboration-retro-hydroboration mechanism

Herein, we report for the first time a “trans-hydroboration–oxidation product” isolated and characterized under traditional hydroboration–oxidation conditions using cholesterol and diosgenin as substrates. These substrates are excellent starting materials because of the rigidity and different structural environments around the double bond. Further investigations based on experimental evidence, in conjunction with theoretical studies, indicate that the formation of this trans-species occurs via a retro-hydroboration of the major product to generate the corresponding Δ⁶-structure and the subsequent hydroboration by the β-face. Besides, the corresponding Markovnikov type products have been isolated in synthetically useful yields. The behavior of the reaction under a range of temperatures is also investigated.

A trans-product is isolated and characterized under traditional hydroboration–oxidation conditions using Δ⁵-steroids as substrates. Experimental and theoretical studies indicate that the trans-species occurs via a retro-hydroboration mechanism.     

Synthesis and mechanistic investigations of pH-responsive cationic poly(aminoester)s

The synthesis and degradation mechanisms of a class of pH-sensitive, rapidly degrading cationic poly(α-aminoester)s are described. These reactive, cationic polymers are stable at low pH in water, but undergo a fast and selective degradation at higher pH to liberate neutral diketopiperazines. Related materials incorporating oligo(α-amino ester)s have been shown to be effective gene delivery agents, as the charge-altering degradative behavior facilitates the delivery and release of mRNA and other nucleic acids in vitro and in vivo. Herein, we report detailed studies of the structural and environmental factors that lead to these rapid and selective degradation processes in aqueous buffers. At neutral pH, poly(α-aminoester)s derived from N-hydroxyethylglycine degrade selectively by a mechanism involving sequential 1,5- and 1,6-O→N acyl shifts to generate bis(N-hydroxyethyl) diketopiperazine. A family of structurally related cationic poly(aminoester)s was generated to study the structural influences on the degradation mechanism, product distribution, and pH dependence of the rate of degradation. The kinetics and mechanism of the pH-induced degradations were investigated by ¹H NMR, model reactions, and kinetic simulations. These results indicate that polyesters bearing α-ammonium groups and appropriately positioned N-hydroxyethyl substituents are readily cleaved (by intramolecular attack) or hydrolyzed, representing dynamic “dual function” materials that are initially polycationic and transform with changing environment to neutral products.

The synthesis and degradation mechanisms of a class of pH-sensitive, rapidly degrading cationic poly(α-aminoester)s are described.     

Hydrogen and proton exchange at carbon. Imbalanced transition state and mechanism crossover

A recent remarkable study of the C–H oxidation of substituted fluorenyl-benzoates together with the transfer of a proton to an internal receiving group by means of electron transfer outer-sphere oxidants, in the noteworthy absence of hydrogen-bonding interactions, is taken as an example to uncover the existence of a mechanism crossover, making the reaction pass from a CPET pathway to a PTET pathway as the driving force of the global reaction decreases. This was also the occasion to stress that considerations based on “imbalanced” or “asynchronous” transition states cannot replace activation/driving force models based on the quantum mechanical treatment of both electrons and transferring protons.

Using the remarkable study of C–H oxidation of substituted fluorenyl-benzoates as an example, we have shown that a mechanism crossover takes place upon decreasing the driving force, from a CPET pathway to a PTET pathway.     

A 2,2′-diphosphinotolane as a versatile precursor for the synthesis of P-ylidic mesoionic carbenes via reversible C–P bond formation

A metal-templated synthetic route to cyclic (aryl)(ylidic) mesoionic carbenes (CArY-MICs) featuring an endocyclic P-ylide is presented. This approach, which requires metal templates with two cis-positioned open coordination sites, is based on the controlled cyclisation of a P,P′-diisopropyl-substituted 2,2′-diphosphinotolane (1) and leads to chelate complexes coordinated by a phosphine donor and the CArY-MIC carbon atom. The C–P bond formation involved in the former partial cyclisation of 1 proceeds under mild conditions and was shown to be applicable all over the d-block. In the presence of a third fac-positioned open coordination site, the P–C bond formation was found to be reversible, as shown for a series of molybdenum complexes. DFT modelling studies are in line with an interpretation of the target compounds as CArY-MICs.

A metal-templated synthesis of cyclic (aryl)(ylidic)mesoionic carbene complexes (CArY-MICs) is presented. In the case of molybdenum carbonyls, the crucial P–C bond formation, which occurs during CArY-MIC formation, was found to be reversible.     

Efficient alkene hydrosilation with bis(8-quinolyl)phosphine (NPN) nickel catalysts. The dominant role of silyl-over hydrido-nickel catalytic intermediates

A cationic nickel complex of the bis(8-quinolyl)(3,5-di-tert-butylphenoxy)phosphine (NPN) ligand, [(NPN)NiCl]⁺, is a precursor to efficient catalysts for the hydrosilation of alkenes with a variety of hydrosilanes under mild conditions and low catalyst loadings. DFT studies reveal the presence of two coupled catalytic cycles based on [(NPN)NiH]⁺ and [(NPN)NiSiR₃]⁺ active species, with the latter being more efficient for producing the product. The preferred silyl-based catalysis is not due to a more facile insertion of alkene into the Ni–Si (vs. Ni–H) bond, but by consistent and efficient conversions of the hydride to the silyl complex.

A cationic nickel complex of the bis(8-quinolyl)(3,5-di-tert-butylphenoxy)phosphine (NPN) ligand, [(NPN)NiCl]⁺, is a precursor to efficient catalysts for the hydrosilation of alkenes with hydrosilanes under mild conditions and low catalyst loadings.