Oncogenic KRAS G12D mutation promotes dimerization through a second,phosphatidylserine–dependent interface: a model for KRAS oligomerization

KRAS forms transient dimers and higher-order multimers (nanoclusters) on the plasma membrane, which drive MAPK signaling and cell proliferation. KRAS is a frequently mutated oncogene, and while it is well known that the most prevalent mutation, G12D, impairs GTP hydrolysis, thereby increasing KRAS activation, G12D has also been shown to enhance nanoclustering. Elucidating structures of dynamic KRAS assemblies on a membrane has been challenging, thus we have refined our NMR approach that uses nanodiscs to study KRAS associated with membranes. We incorporated paramagnetic relaxation enhancement (PRE) titrations and interface mutagenesis, which revealed that, in addition to the symmetric ‘α–α’ dimerization interface shared with wild-type KRAS, the G12D mutant also self-associates through an asymmetric ‘α–β’ interface. The ‘α–β’ association is dependent on the presence of phosphatidylserine lipids, consistent with previous reports that this lipid promotes KRAS self-assembly on the plasma membrane in cells. Experiments using engineered mutants to spoil each interface, together with PRE probes attached to the membrane or free in solvent, suggest that dimerization through the primary ‘α–α’ interface releases β interfaces from the membrane promoting formation of the secondary ‘α–β’ interaction, potentially initiating nanoclustering. In addition, the small molecule BI-2852 binds at a β–β interface, stabilizing a new dimer configuration that outcompetes native dimerization and blocks the effector-binding site. Our data indicate that KRAS self-association involves a delicately balanced conformational equilibrium between transient states, which is sensitive to disease-associated mutation and small molecule inhibitors. The methods developed here are applicable to biologically important transient interactions involving other membrane-associated proteins.

Studies of membrane-dependent dimerization of KRAS on nanodiscs using paramagnetic NMR titrations and mutagenesis revealed a novel asymmetric ‘α–β’ interface that provides a potential mechanism for the enhanced assembly of KRAS–G12D nanoclusters.     

A photoresponsive antibody–siRNA conjugate for activatable immunogene therapy of cancer

Tumor-targeted delivery of small-interfering RNAs (siRNAs) for cancer therapy still remains a challenging task. While antibody–siRNA conjugates (ARCs) provide an alternative way to address this challenge, the uncontrollable siRNA release potentially leads to undesirable off-tumor side effects, limiting their in vivo therapeutic efficacy. Here, we report a photoresponsive ARC (PARC) for tumor-specific and photoinducible siRNA delivery as well as photoactivable immunogene therapy. PARC is composed of an anti-programmed death-ligand 1 antibody (αPD-L1) conjugated with a siRNA against intracellular PD-L1 mRNA through a photocleavable linker. After targeting cancer cells through the interaction between αPD-L1 and membrane PD-L1, PARC is internalized and it liberates siPD-L1 upon light irradiation to break the photocleavable linker. The released siPD-L1 then escapes from the lysosome into the cytoplasm to degrade intracellular PD-L1 mRNA, which combines the blockade of membrane PD-L1 by αPD-L1 to boost immune cell activity. Owing to these features, PARC causes effective cancer suppression both in vitro and in vivo. This study thus provides a useful conditional delivery platform for siRNAs and a novel means for activatable cancer immunogene therapy.

A photoresponsive antibody–siRNA conjugate (PARC) enables tumor-targeted siRNA delivery and photoactivatable gene silencing for cancer immunotherapy.     

Docking rings in a solid: reversible assembling of pseudorotaxanes inside a zirconium metal–organic framework

An unprecedented zirconium metal–organic framework featuring a T-shaped benzimidazole strut was constructed and employed as a sponge-like material for selective absorption of macrocyclic guests. The neutral benzimidazole domain of the as-synthesized framework can be readily protonated and fully converted to benzimidazolium. Mechanical threading of [24]crown-8 ether wheels onto recognition sites to form pseudorotaxanes was evidenced by solution nuclear magnetic resonance, solid-state fluorescence, and infrared spectroscopy. Selective absorption of [24]crown-8 ether rather than its dibenzo counterpart was also observed. Further study reveals that this binding process is reversible and acid–base switchable. The success of docking macrocyclic guests in crystals via host–guest interactions provides an alternative route to complex functional materials with interpenetrated structures.

A T-shaped ligand was designed as struts for building a zirconium metal–organic framework. Acid–base switchable docking and releasing a 24-membered crown ether inside crystals was successfully accomplished via post-synthetic modification.     

Peptoid-based reprogrammable template for cell-permeable inhibitors of protein–protein interactions

The development of inhibitors of intracellular protein–protein interactions (PPIs) is of great significance for drug discovery, but the generation of a cell-permeable molecule with high affinity to protein is challenging. Oligo(N-substituted glycines) (oligo-NSGs), referred to as peptoids, are attractive as potential intracellular PPI inhibitors owing to their high membrane permeability. However, their intrinsically flexible backbones make the rational design of inhibitors difficult. Here, we propose a peptoid-based rational approach to develop cell-permeable PPI inhibitors using oligo(N-substituted alanines) (oligo-NSAs). The rigid structures of oligo-NSAs enable independent optimization of each N-substituent to improve binding affinity and membrane permeability, while preserving the backbone shape. A molecule with optimized N-substituents inhibited a target PPI in cells, which demonstrated the utility of oligo-NSA as a reprogrammable template to develop intracellular PPI inhibitors.

A peptoid-based modular approach using oligo(N-substituted alanine) as a reprogrammable template enables independent optimization of N-substituents and facile development of cell-permeable inhibitors of protein–protein interactions.     

Modular synthesis of α-arylated carboxylic acids,esters and amides via photocatalyzed triple C–F bond cleavage of methyltrifluorides

α-Arylated carboxylic acids, esters and amides are widespread motifs in bioactive molecules and important building blocks in chemical synthesis. Thus, straightforward and rapid access to such structures is highly desirable. Here we report an organophotocatalytic multicomponent synthesis of α-arylated carboxylic acids, esters and amides from exhaustive defluorination of α-trifluoromethyl alkenes in the presence of alkyltrifluoroborates, water and nitrogen/oxygen nucleophiles. This operationally simple strategy features a unified access to functionally diverse α-arylated carboxylic acids, esters, and primary, secondary, and tertiary amides through backbone assembly from simple starting materials enabled by consecutive C–F bond functionalization at room temperature. Preliminary mechanistic investigations reveal that the reaction operates through a radical-triggered three-step cascade process, which involves distinct mechanisms for each defluorinative functionalization of the C–F bond.

Here we report an organophotocatalytic synthesis of α-arylated carboxylic acids, esters and amides from exhaustive defluorination of α-trifluoromethyl alkenes in the presence of alkyltrifluoroborates, water and nitrogen/oxygen nucleophiles.     

A host–guest strategy for converting the photodynamic agents from a singlet oxygen generator to a superoxide radical generator

Type-I photosensitizers (PSs) generate cytotoxic oxygen radicals by electron transfer even in a hypoxic environment. Nevertheless, the preparation of type-I PSs remains a challenge due to the competition of triplet–triplet energy transfer with O₂ (type-II process). In this work, we report an effective strategy for converting the conventional type-II PS to a type-I PS by host–guest complexation. Electron-rich pillar[5]arenes are used as an electron donor and macrocyclic host to produce a host–guest complex with the traditional electron-deficient type-II PS, an iodide BODIPY-based guest. The host–guest complexation promotes intermolecular electron transfer from the pillar[5]arene moiety to BODIPY and then to O₂ by the type-I process upon light-irradiation, leading to efficient generation of the superoxide radical (O₂⁻˙). The results of anti-tumor studies indicate that this supramolecular PS demonstrates high photodynamic therapy efficacy even under hypoxic conditions. This work provides an efficient method to prepare type-I PSs from existing type-II PSs by using a supramolecular strategy.

A supramolecular strategy is reported for converting the conventional photodynamic agents from a singlet oxygen generator to a superoxide radical generator by the host–guest interaction enhanced electron transfer.     

Efficacious and sustained release of an anticancer drug mitoxantrone from new covalent organic frameworks using protein corona

Solid porous and crystalline covalent organic frameworks (COFs) are characterized by their higher specific BET surface areas and functional pore walls, which allow the adsorption of various bioactive molecules inside the porous lattices. We have introduced a perylene-based COF, PER@PDA-COF-1, which acts as an effective porous volumetric reservoir for an anticancer drug, mitoxantrone (MXT). The drug-loaded COF (MXT–PER@PDA-COF-1) exhibited zero cellular release of MXT towards cancer cells, which can be attributed to the strong intercalation between the anthracene-dione motif of the drug and the perylene-based COF backbone. Here, we have introduced a strategy involving the serum-albumin-triggered intracellular release of mitoxantrone from MXT–PER@PDA-COF-1. The serum albumin acts as an exfoliating agent and as a colloidal stabilizer in PBS medium (pH = 7.4), rapidly forming a protein corona around the exfoliated COF crystallites and inducing the sustained release of MXT from the COF into tumorigenic cells.

Solid porous and crystalline covalent organic frameworks (COFs) are characterized by their higher specific BET surface areas and functional pore walls, which allow the adsorption of various bioactive molecules inside the porous lattices.     

A pillar[5]arene-based covalent organic framework with pre-encoded selective host–guest recognition

It is highly desirable to maintain both permanent accessible pores and selective molecular recognition capability of macrocyclic cavitands in the solid state. Integration of well-defined discrete macrocyclic hosts into ordered porous polymeric frameworks (e.g., covalent organic frameworks, COFs) represents a promising strategy to transform many supramolecular chemistry concepts and principles well established in the solution phase into the solid state, which can enable a broad range of practical applications, such as high-efficiency molecular separation, heterogeneous catalysis, and pollution remediation. However, it is still a challenging task to construct macrocycle-embedded COFs. In this work, a novel pillar[5]arene-derived (P5) hetero-porous COF, denoted as P5-COF, was rationally designed and synthesized. Featuring the unique backbone structure, P5-COF exhibited selective adsorption of C₂H₂ over C₂H₄ and C₂H₆, as well as significantly enhanced host–guest binding interaction with paraquat, in comparison with the pillar[5]arene-free COF analog, Model-COF. The present work established a new strategy for developing COFs with customizable molecular recognition/separation properties through the bottom-up “pre-porous macrocycle to porous framework” design.

A novel pillar[5]arene-derived (P5) COF was rationally designed and synthesized, which exhibited superior performance in selective gas adsorption and paraquat binding.     

Red aqueous room-temperature phosphorescence modulated by anion–π and intermolecular electronic coupling interactions

Aqueous room temperature phosphorescence (aRTP) from purely organic materials has been intriguing but challenging. In this article, we demonstrated that the red aRTP emission of 2Br–NDI, a water-soluble 4,9-dibromonaphthalene diimide derivative as a chloride salt, could be modulated by anion–π and intermolecular electronic coupling interactions in water. Specifically, the rarely reported stabilization of anion–π interactions in water between Cl⁻ and the 2Br–NDI core was experimentally evidenced by an anion–π induced long-lived emission (λ_Anion–π) of 2Br–NDI, acting as a competitive decay pathway against the intrinsic red aRTP emission (λ_Phos) of 2Br–NDI. In the initial expectation of enhancing the aRTP of 2Br–NDI by inclusion complexation with macrocyclic cucurbit[n]urils (CB[n]s, n = 7, 8, 10), we surprisingly found that the exclusion complexation between CB[8] and 2Br–NDI unconventionally endowed the complex with the strongest and longest-lived aRTP due to the strong intermolecular electronic coupling between the nπ* orbit on the carbonyl rims of CB[8] and the ππ* orbit on 2Br–NDI in water. It is anticipated that these intriguing findings may inspire and expand the exploration of aqueous anion–π recognition and CB[n]-based aRTP materials.

The aqueous room temperature phosphorescence of 2Br–NDI is modulated by long-lived-emitting anion–π interactions and tremendously enhanced by intermolecular electronic coupling interactions with the ISC-boosting carbonyl rims of CB[8] host.     

Force-modulated reductive elimination from platinum(ii) diaryl complexes

Coupled mechanical forces are known to drive a range of covalent chemical reactions, but the effect of mechanical force applied to a spectator ligand on transition metal reactivity is relatively unexplored. Here we quantify the rate of C(sp²)–C(sp²) reductive elimination from platinum(ii) diaryl complexes containing macrocyclic bis(phosphine) ligands as a function of mechanical force applied to these ligands. DFT computations reveal complex dependence of mechanochemical kinetics on the structure of the force-transducing ligand. We validated experimentally the computational finding for the most sensitive of the ligand designs, based on MeOBiphep, by coupling it to a macrocyclic force probe ligand. Consistent with the computations, compressive forces decreased the rate of reductive elimination whereas extension forces increased the rate relative to the strain-free MeOBiphep complex with a 3.4-fold change in rate over a ∼290 pN range of restoring forces. The calculated natural bite angle of the free macrocyclic ligand changes with force, but ³¹P NMR analysis and calculations strongly suggest no significant force-induced perturbation of ground state geometry within the first coordination sphere of the (P–P)PtAr₂ complexes. Rather, the force/rate behavior observed across this range of forces is attributed to the coupling of force to the elongation of the O⋯O distance in the transition state for reductive elimination. The results suggest opportunities to experimentally map geometry changes associated with reactions in transition metal complexes and potential strategies for force-modulated catalysis.

The influence of mechanical force on the rates of model reductive elimination reactions depends on the structure of the force-transducing ligand and provides a measure of geometry changes upon reaching the transition state.     

2′-O-Methyl modified guide RNA promotes the single nucleotide polymorphism (SNP) discrimination ability of CRISPR–Cas12a systems

The CRISPR–Cas12a system has been widely applied to genome editing and molecular diagnostics. However, off-target cleavages and false-positive results remain as major concerns in Cas12a practical applications. Herein, we propose a strategy by utilizing the 2′-O-methyl (2′-OMe) modified guide RNA (gRNA) to promote the Cas12a''s specificity. Gibbs free energy analysis demonstrates that the 2′-OMe modifications at the 3′-end of gRNA effectively suppress the Cas12a''s overall non-specific affinity while maintaining high on-target affinity. For general application illustrations, HBV genotyping and SARS-CoV-2 D614G mutant biosensing platforms are developed to validate the enhanced Cas12a''s specificity. Our results indicate that the 2′-OMe modified gRNAs could discriminate single-base mutations with at least two-fold enhanced specificity compared to unmodified gRNAs. Furthermore, we investigate the enhancing mechanisms of the 2′-OMe modified Cas12a systems by molecular docking simulations and the results suggest that the 2′-OMe modifications at the 3′-end of gRNA reduce the Cas12a''s binding activity to off-target DNA. This work offers a versatile and universal gRNA design strategy for highly specific Cas12a system development.

This study illustrates that 2′-O-methyl modified gRNAs improve the specificity of the CRISPR–Cas12a system (mg-CRISPR) via suppressing the Cas12a''s affinity to off-target DNA and provides an efficient strategy for high-specificity gRNA design.     

Molecularly engineered AIEgens with enhanced quantum and singlet-oxygen yield for mitochondria-targeted imaging and photodynamic therapy

Luminogens characteristic of aggregation-induced emission (AIEgens) have been extensively exploited for the development of imaging-guided photodynamic therapeutic (PDT) agents. However, intramolecular rotation of donor–acceptor (D–A) type AIEgens favors non-radiative decay of photonic energy which results in unsatisfactory fluorescence quantum and singlet oxygen yields. To address this issue, we developed several molecularly engineered AIEgens with partially “locked” molecular structures enhancing both fluorescence emission and the production of triplet excitons. A triphenylphosphine group was introduced to form a D–A conjugate, improving water solubility and the capacity for mitochondrial localization of the resulting probes. Experimental and theoretical analyses suggest that the much higher quantum and singlet oxygen yield of a structurally “significantly-locked” probe (LOCK-2) than its “partially locked” (LOCK-1) and “unlocked” equivalent (LOCK-0) is a result of suppressed AIE and twisted intramolecular charge transfer. LOCK-2 was also used for the mitochondrial-targeting, fluorescence image-guided PDT of liver cancer cells.

Luminogens characteristic of aggregation-induced emission (AIEgens) have been engineered for the development of imaging-guided photodynamic therapeutic (PDT) agents.     

Functionalisation of ethereal-based saturated heterocycles with concomitant aerobic C–H activation and C–C bond formation

With an ever-growing emphasis on sustainable synthesis, aerobic C–H activation (the use of oxygen in air to activate C–H bonds) represents a highly attractive conduit for the development of novel synthetic methodologies. Herein, we report the air mediated functionalisation of various saturated heterocycles and ethers via aerobically generated radical intermediates to form new C–C bonds using acetylenic and vinyl triflones as radical acceptors. This enables access to a variety of acetylenic and vinyl substituted saturated heterocycles that are rich in synthetic value. Mechanistic studies and control reactions support an aerobic radical-based C–H activation mechanism.

Herein we disclose a novel method for the aerobic C–H activation of ethereal-based heterocycles to generate various α-functionalised building blocks.     

Cooperativity as quantification and optimization paradigm for nuclear receptor modulators

Nuclear Receptors (NRs) are highly relevant drug targets, for which small molecule modulation goes beyond a simple ligand/receptor interaction. NR–ligands modulate Protein–Protein Interactions (PPIs) with coregulator proteins. Here we bring forward a cooperativity mechanism for small molecule modulation of NR PPIs, using the Peroxisome Proliferator Activated Receptor γ (PPARγ), which describes NR–ligands as allosteric molecular glues. The cooperativity framework uses a thermodynamic model based on three-body binding events, to dissect and quantify reciprocal effects of NR–coregulator binding (K^I_D) and NR–ligand binding (K^II_D), jointly recapitulated in the cooperativity factor (α) for each specific ternary ligand·NR·coregulator complex formation. These fundamental thermodynamic parameters allow for a conceptually new way of thinking about structure–activity-relationships for NR–ligands and can steer NR modulator discovery and optimization via a completely novel approach.

A cooperativity framework describes the formation of nuclear receptor ternary complexes and deconvolutes ligand and cofactor binding into intrinsic affinities and a cooperativity factor, providing a conceptually new understanding of NR modulation.     

Dibenzocycloheptanones construction through a removable P-centered radical: synthesis of allocolchicine analogues

Dibenzocycloheptanones containing a tricyclic 6–7–6-system are present in numerous biologically active natural molecules. However, the simple and efficient preparation of derivatives containing a dibenzocycloheptanone scaffold remains difficult to date. Herein, we report a versatile strategy for the construction of these challenging seven-membered rings using a 7-endo-trig cyclization which is initiated by a phosphorus-centered radical. This approach provides a step-economical regime for the facile assembly of a wide range of phosphorylated dibenzocycloheptanones. Remarkably, we also have devised a traceless addition/exchange strategy for the preparation of dephosphorylated products at room temperature with excellent yields. Therefore, this protocol allows for the concise synthesis of biorelevant allocochicine derivatives.

Dibenzocycloheptanones containing a tricyclic 6–7–6-system are present in numerous biologically active natural molecules.     

N–H⋯X interactions stabilize intra-residue C5 hydrogen bonded conformations in heterocyclic α-amino acid derivatives

Nature makes extensive and elaborate use of hydrogen bonding to assemble and stabilize biomolecular structures. The shapes of peptides and proteins rely significantly on N–H⋯O C interactions, which are the linchpins of turns, sheets and helices. The C5 H-bond, in which a single residue provides both donor and acceptor, is generally considered too weak to force the backbone to adopt extended structures. Exploiting the synergy between gas phase (experimental and quantum chemistry) and solution spectroscopies to decipher IR spectroscopic data, this work demonstrates that the extended C5-based conformation in 4-membered ring heterocyclic α-amino acid derivatives is significantly stabilized by the formation of an N–H⋯X H-bond. In this synergic system the strength of the C5 interaction remains constant while the N–H⋯X H-bond strength, and thereby the support provided by it, varies with the heteroatom.

In 4-membered ring heterocyclic α-amino acid derivatives, extended conformations based on intraresidue C5 H-bonds can be stabilized by N–H⋯X H-bonds, making the combined C5–C6γ structures prominent in both gas phase and in weakly polar solutions.     

Alchemical absolute protein–ligand binding free energies for drug design

The recent advances in relative protein–ligand binding free energy calculations have shown the value of alchemical methods in drug discovery. Accurately assessing absolute binding free energies, although highly desired, remains a challenging endeavour, mostly limited to small model cases. Here, we demonstrate accurate first principles based absolute binding free energy estimates for 128 pharmaceutically relevant targets. We use a novel rigorous method to generate protein–ligand ensembles for the ligand in its decoupled state. Not only do the calculations deliver accurate protein–ligand binding affinity estimates, but they also provide detailed physical insight into the structural determinants of binding. We identify subtle rotamer rearrangements between apo and holo states of a protein that are crucial for binding. When compared to relative binding free energy calculations, obtaining absolute binding free energies is considerably more challenging in large part due to the need to explicitly account for the protein in its apo state. In this work we present several approaches to obtain apo state ensembles for accurate absolute ΔG calculations, thus outlining protocols for prospective application of the methods for drug discovery.

Molecular dynamics based absolute protein–ligand binding free energies can be calculated accurately and at large scale to facilitate drug discovery.     

Correction: Cu-catalyzed C–C bond formation of vinylidene cyclopropanes with carbon nucleophiles

Correction for ‘Cu-catalyzed C–C bond formation of vinylidene cyclopropanes with carbon nucleophiles’ by Jichao Chen et al., Chem. Sci., 2019, 10, 10601–10606.

We regret that in the original article the structure of compound 1 in Tables 1–3 was incorrect. The correct structure is given below.The Royal Society of Chemistry apologises for these errors and any consequent inconvenience to authors and readers.     

Electrochemical oxidative N–H/P–H cross-coupling with H2 evolution towards the synthesis of tertiary phosphines

Tertiary phosphines(iii) find widespread use in many aspects of synthetic organic chemistry. Herein, we developed a facile and novel electrochemical oxidative N–H/P–H cross-coupling method, leading to a series of expected tertiary phosphines(iii) under mild conditions with excellent yields. It is worth noting that this electrochemical protocol features very good reaction selectivity, where only a 1 : 1 ratio of amine and phosphine was required in the reaction. Moreover, this electrochemical protocol proved to be practical and scalable. Mechanistic insights suggested that the P radical was involved in this reaction.

A facile and novel electrochemical oxidative N–H/P–H cross-coupling method for obtaining tertiary phosphines(iii) was developed.     

Fabrication of graphene-based porous materials: traditional and emerging approaches

The anisotropic nature of ‘graphenic’ nanosheets enables them to form stable three-dimensional porous materials. The use of these porous structures has been explored in several applications including electronics and batteries, environmental remediation, energy storage, sensors, catalysis, tissue engineering, and many more. As method of fabrication greatly influences the final pore architecture, and chemical and mechanical characteristics and performance of these porous materials, it is essential to identify and address the correlation between property and function. In this review, we report detailed analyses of the different methods of fabricating porous graphene-based structures – with a focus on graphene oxide as the base material – and relate these with the resultant morphologies, mechanical responses, and common applications of use. We discuss the feasibility of the synthesis approaches and relate the GO concentrations used in each methodology against their corresponding pore sizes to identify the areas not explored to date.

Due to their anisotropic nature, graphene nanosheets can be used to form 3-dimensional porous materials using template-free and template-directed methodologies. These fabrication strategies are found to influence the properties of the final structure.