Covalent labeling of a chromatin reader domain using proximity-reactive cyclic peptides

Chemical probes for chromatin reader proteins are valuable tools for investigating epigenetic regulatory mechanisms and evaluating whether the target of interest holds therapeutic potential. Developing potent inhibitors for the plant homeodomain (PHD) family of methylation readers remains a difficult task due to the charged, shallow and extended nature of the histone binding site that precludes effective engagement of conventional small molecules. Herein, we describe the development of novel proximity-reactive cyclopeptide inhibitors for PHD3—a trimethyllysine reader domain of histone demethylase KDM5A. Guided by the PHD3–histone co-crystal structure, we designed a sidechain-to-sidechain linking strategy to improve peptide proteolytic stability whilst maintaining binding affinity. We have developed an operationally simple solid-phase macrocyclization pathway, capitalizing on the inherent reactivity of the dimethyllysine ε-amino group to generate scaffolds bearing charged tetraalkylammonium functionalities that effectively engage the shallow aromatic ‘groove’ of PHD3. Leveraging a surface-exposed lysine residue on PHD3 adjacent to the ligand binding site, cyclic peptides were rendered covalent through installation of an arylsulfonyl fluoride warhead. The resulting lysine-reactive cyclic peptides demonstrated rapid and efficient labeling of the PHD3 domain in HEK293T lysates, showcasing the feasibility of employing proximity-induced reactivity for covalent labeling of this challenging family of reader domains.

We describe the development of covalent cyclic peptide ligands which target a chromatin methylation reader domain using a proximity-reactive sulfonyl fluoride moiety.     

Late-stage modification of peptides and proteins at cysteine with diaryliodonium salts

The modification of peptides and proteins has emerged as a powerful means to efficiently prepare high value bioconjugates for a range of applications in chemical biology and for the development of next-generation therapeutics. Herein, we report a novel method for the chemoselective late-stage modification of peptides and proteins at cysteine in aqueous buffer with suitably functionalised diaryliodonium salts, furnishing stable thioether-linked synthetic conjugates. The power of this new platform is showcased through the late-stage modification of the affibody zEGFR and the histone protein H2A.

New operationally simple platform for the chemoselective arylation of cysteine in peptides and proteins to access a variety of high value bioconjugates.     

Controlling cyclization pathways in palladium(ii)-catalyzed intramolecular alkene hydro-functionalization via substrate directivity

We report a series of palladium(ii)-catalyzed, intramolecular alkene hydrofunctionalization reactions with carbon, nitrogen, and oxygen nucleophiles to form five- and six-membered carbo- and heterocycles. In these reactions, the presence of a proximal bidentate directing group controls the cyclization pathway, dictating the ring size that is generated, even in cases that are disfavored based on Baldwin''s rules and in cases where there is an inherent preference for an alternative pathway. DFT studies shed light on the origins of pathway selectivity in these processes.

We report a series of palladium(ii)-catalyzed, intramolecular alkene hydrofunctionalization reactions with carbon, nitrogen, and oxygen nucleophiles to form five- and six-membered carbo- and heterocycles.     

Ruthenium(ii)-catalyzed regioselective 1,6-conjugate addition of umpolung aldehydes as carbanion equivalents

One of the most efficient and reliable approaches to construct C–C bonds involves the conjugate addition of carbon nucleophiles to electron-deficient ketones. Yet, 1,6-conjugate additions of extended conjugated systems largely remain underexplored due to difficulties in controlling the regioselectivity. Herein, we report umpolung aldehydes as carbanion equivalents for highly regioselective 1,6-conjugate addition reactions to unsaturated ketones, with preliminary studies of the enantioselective variant. The synergy of ruthenium(ii) catalyst and electron-rich, bidentate phosphine ligand is essential for the reactivity and selectivity under mild reaction conditions.

Highly regioselective 1,6-conjugate addition was developed using hydrazone as carbanion equivalent catalyzed by ruthenium under mild conditions.     

Chemical synthesis of linear ADP-ribose oligomers up to pentamer and their binding to the oncogenic helicase ALC1

ADP-ribosylation is a pivotal post-translational modification that mediates various important cellular processes producing negatively charged biopolymer, poly (ADP-ribose), the functions of which need further elucidation. Toward this end, the availability of well-defined ADP-ribose (ADPr) oligomers in sufficient quantities is a necessity. In this work, we demonstrate the chemical synthesis of linear ADPr oligomers of defined, increasing length using a modified solid phase synthesis method. An advanced phosphoramidite building block temporarily protected with the base sensitive Fm-group was designed and implemented in the repeating pyrophosphate formation via a P(v)–P(iii) coupling procedure on Tentagel solid support. Linear ADPr oligomers up to a pentamer were successfully synthesized and their affinity for the poly-(ADP-ribose)-binding macrodomain of the human oncogenic helicase and chromatin remodeling enzyme ALC1 was determined. Our data reveal a length-dependent binding manner of the nucleic acid, with larger ADPr oligomers exhibiting higher binding enthalpies for ALC1, illustrating how the activity of this molecular machine is gated by PAR.

We report the synthesis of linear ADPr oligomers of defined length up to a pentamer using an improved solid phase method. Binding study with human oncogenic helicase ALC1 shows that ADPr oligomers bind to ALC1 in a length-dependent manner.     

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.     

Rigidochromism by imide functionalisation of an aminomaleimide fluorophore

Fluorescent dyes that exhibit high solid state quantum yields and sensitivity to the mechanical properties of their local environment are useful for a wide variety of applications, but are limited in chemical diversity. We report a trityl-functionalised maleimide that displays rigidochromic behaviour, becoming highly fluorescent when immobilised in a solid matrix, while displaying negligible fluorescence in solution. Furthermore, the dye''s quantum yield is shown to be sensitive to the nature of the surrounding matrix. Computational studies reveal that this behaviour arises from the precise tuning of inter- and intramolecular noncovalent interactions. This work expands the diversity of molecules exhibiting solid state environment sensitivity, and provides important fundamental insights into their design.

In this study, by systematic tuning of imide substituent a maleimides dye with sensitivity to its solid-state environment was investigated.     

Rigid,biconical hydrogen-bonded dimers that strongly encapsulate cationic guests in solution and the solid state

The octol of a new rigid, tetraarylene-bridged cavitand was investigated for self-assembly behaviour in solution. ¹H and DOSY NMR spectroscopic experiments show that the cavitand readily dimerizes through an unusual seam of interdigitated hydrogen-bonds that is resistant to disruption by polar co-solvents. The well-defined cavity encapsulates small cationic guests, but not their neutral counterparts, restricting the conformation of sequestered tetraethylammonium in solution and the solid state.

A robust, dimeric capsule forms quantitatively in low-polarity solvents via a seam of 8 hydrogen bonds. The resulting electron-rich cavity selectively binds small organic cations over neutral counterparts.     

Desymmetrization of pibrentasvir for efficient prodrug synthesis

A novel and practical desymmetrization tactic is described to access a new class of pibrentasvir prodrugs. The homotopic benzimidazoles of pibrentasvir (PIB) are differentiated via a one-pot di-Boc/mono-de-Boc selective N-Boc protection and formaldehyde adduct formation sequence, both enabled by crystallization-induced selectivity. The first step represents the only known application of the Horeau principle of statistical amplification for C₂-symmetric polyheterocycle regioselective functionalization. The resulting versatile intermediate is employed in the high-yielding preparation of several pibrentasvir prodrug candidates.

Horeau principle statistical amplification and solubility-driven selectivities allow C₂-desymmetrization of pibrentasvir without typically required internal functionalization or steric proximity effects.     

Salicylate metal-binding isosteres as fragments for metalloenzyme inhibition

Metalloenzyme inhibitors typically share a common need to possess a metal-binding pharmacophore (MBP) for binding the active site metal ions. However, MBPs can suffer from physicochemical liabilities, impeding the pharmacological properties and drug-likeliness of inhibitors. To circumvent this, problematic features of the MBP can be identified and exchanged with isosteric replacements. Herein, the carboxylic and hydroxyl group of the salicylic acid MBP were replaced and a total of 27 salicylate metal-binding isosteres (MBIs) synthesized. Of these 27 MBIs, at least 12 represent previously unreported compounds, and the metal-binding abilities of >20 of the MBIs have not been previously reported. These salicylate MBIs were examined for their metal-binding features in model complexes, physicochemical properties, and biological activity. It was observed that salicylate MBIs can demonstrate a range of attractive physicochemical properties and bind to the metal in a variety of expected and unexpected binding modes. The biological activity of these novel MBIs was evaluated by measuring inhibition against two Zn²⁺-dependent metalloenzymes, human glyoxalase 1 (GLO1) and matrix metalloproteinase 3 (MMP-3), as well as a dinuclear Mn²⁺-dependent metalloenzyme, influenza H1N1 N-terminal endonuclease (PA_N). It was observed that salicylate MBIs could maintain or improve enzyme inhibition and selectivity. To probe salicylate MBIs as fragments for fragment-based drug discovery (FBDD), an MBI that showed good inhibitory activity against GLO1 was derivatized and a rudimentary structure–activity relationship was developed. The resulting elaborated fragments showed GLO1 inhibition with low micromolar activity.

Metal-binding isosteres (MBIs) of salicylic acid have been developed for metalloenzyme drug development.     

Regiocontrolled allylic functionalization of internal alkene via selenium-π-acid catalysis guided by boron substitution

The selenium-π-acid-catalysis has received increasing attention as a powerful tool for olefin functionalization, but the regioselectivity is often problematic. Reported herein is a selenium-catalyzed regiocontrolled olefin transpositional chlorination and imidation reaction. The reaction outcome benefits from an allylic B(MIDA) substitution. And the stabilization of α-anion from a hemilabile B(MIDA) moiety was believed to be the key factor for selectivity. Broad substrate scope, good functional group tolerance and generally good yields were observed. The formed products were demonstrated to be valuable precursors for the synthesis of a wide variety of structurally complex organoborons.

The allylic boron substitution results in a regiocontrolled olefin transpositional allylic chlorination and imidation reaction.     

Reversible inhibition of the oxidase-like activity of Fe single-atom nanozymes for drug detection

Mechanism research of nanozymes has always been of great interest since their emergence as outstanding mimics of friable natural enzymes. An important but rarely mentioned issue in mechanism research of nanozymology is the inhibitory effect of nanozymes. And conventional nanozymes with various active sites hinder the mechanism research, while single-atom Fe–N–C nanozymes with similar active sites to natural enzymes exhibit structural advantages. Herein, we synthesized Fe single-atom nanozymes (Fe-SANs) with ultrahigh oxidase-like activity and found that a common analgesic-antipyretic drug 4-acetamidophenol (AMP) had inhibitory effects for the oxidase-like activity of Fe-SANs. We investigated the inhibitory effects in detail and demonstrated that the inhibition type was reversible mixed-inhibition with inhibition constants (K_i and ) of 0.431 mM and 0.279 mM, respectively. Furthermore, we put forward a colorimetric method for AMP detection based on nanozyme inhibition. The research on the inhibitory effects of small molecules on nanozymes expands the scope of analysis based on nanozymes and the inhibition mechanism study may offer some insight into investigating the interaction between nanozymes and inhibitors.

Inhibitory effects of paracetamol on the oxidase-like activity of Fe single-atom nanozymes.     

Harnessing natural-product-inspired combinatorial chemistry and computation-guided synthesis to develop N-glycan modulators as anticancer agents

Modulation of N-glycosylation using human Golgi α-mannosidase II (α-hGMII) inhibitors is a potential anticancer approach, but the clinical utility of current α-hGMII inhibitors is limited by their co-inhibition of human lysosomal α-mannosidase (α-hLM), resulting in abnormal storage of oligomannoses. We describe the synthesis and screening of a small library of novel bicyclic iminosugar-based scaffolds, prepared via natural product-inspired combinatorial chemistry (NPICC), which resulted in the identification of a primary α-hGMII inhibitor with 13.5-fold selectivity over α-hLM. Derivatization of this primary inhibitor using computation-guided synthesis (CGS) yielded an advanced α-hGMII inhibitor with nanomolar potency and 106-fold selectivity over α-hLM. In vitro studies demonstrated its N-glycan modulation and inhibitory effect on hepatocellular carcinoma (HCC) cells. In vivo studies confirmed its encouraging anti-HCC activity, without evidence of oligomannose accumulation.

An integrated strategy of Natural-Product-Inspired Combinatorial Chemistry (NPICC) and Computation-Guided Synthesis is used to develop an α-hGMII inhibitor with 106-fold selectivity over α-hLM, with inhibitory effect on hepatocellular carcinoma.     

In situ lattice tuning of quasi-single-crystal surfaces for continuous electrochemical modulation

The ability to control the atomic-level structure of a solid represents a straightforward strategy for fabricating high-performance catalysts and semiconductor materials. Herein we explore the capability of the mechanically controllable surface strain method in adjusting the surface structure of a gold film. Underpotential deposition measurements provide a quantitative and ultrasensitive approach for monitoring the evolution of surface structures. The electrochemical activities of the quasi-single-crystalline gold films are enhanced productively by controlling the surface tension, resulting in a more positive potential for copper deposition. Our method provides an effective way to tune the atom arrangement of solid surfaces with sub-angstrom precision and to achieve a reduction in power consumption, which has vast applications in electrocatalysis, molecular electronics, and materials science.

We reported a new method capable of adjusting the lattice structure of solid surfaces with sub-angstrom precision and achieved in situ and continuous control over electrochemical activity.     

A bioorthogonal chemical reporter for the detection and identification of protein lactylation

l-Lactylation is a recently discovered post-translational modification occurring on histone lysine residues to regulate gene expression. However, the substrate scope of lactylation, especially that in non-histone proteins, remains unknown, largely due to the limitations of current methods for analyzing lactylated proteins. Herein, we report an alkynyl-functionalized bioorthogonal chemical reporter, YnLac, for the detection and identification of protein lactylation in mammalian cells. Our in-gel fluorescence and chemical proteomic analyses show that YnLac is metabolically incorporated into lactylated proteins and directly labels known lactylated lysines of histones. We further apply YnLac to the proteome-wide profiling of lactylation, revealing many novel modification sites in non-histone proteins for the first time. Moreover, we demonstrate that lactylation of a newly identified substrate protein PARP1 regulates its ADP-ribosylation activity. Our study thus provides a powerful chemical tool for characterizing protein lactylation and greatly expands our understanding of substrate proteins and functions of this new modification.

YnLac is an alkynyl-functionalized l-lactate analogue that is metabolically incorporated into l-lactylated proteins in live cells, enabling the fluorescence detection and proteomic identification of novel l-lactylated proteins.     

Selective covalent targeting of SARS-CoV-2 main protease by enantiopure chlorofluoroacetamide

The coronavirus disease 2019 (COVID-19) pandemic has necessitated the development of antiviral agents against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The main protease (M^pro) is a promising target for COVID-19 treatment. Here, we report an irreversible SARS-CoV-2 M^pro inhibitor possessing chlorofluoroacetamide (CFA) as a warhead for the covalent modification of M^pro. Ugi multicomponent reaction using chlorofluoroacetic acid enabled the rapid synthesis of dipeptidic CFA derivatives that identified 18 as a potent inhibitor of SARS-CoV-2 M^pro. Among the four stereoisomers, (R,R)-18 exhibited a markedly higher inhibitory activity against M^pro than the other isomers. Reaction kinetics and computational docking studies suggest that the R configuration of the CFA warhead is crucial for the rapid covalent inhibition of M^pro. Our findings highlight the prominent influence of the CFA chirality on the covalent modification of proteinous cysteines and provide the basis for improving the potency and selectivity of CFA-based covalent inhibitors.

Chlorofluoroacetamide (CFA) was used as the warhead for covalent targeting of SARS-CoV-2 M^pro. The chirality at CFA showed marked influence on inhibitory activity, suggesting stereospecific activation of CFA for cysteine modification in the protein.     

Room-temperature phosphorescence of a supercooled liquid: kinetic stabilisation by desymmetrisation

Achieving organic room-temperature phosphorescence (RTP) in a solvent-free liquid state is a challenging task because the liquid state provides a less rigid environment than the crystal. Here, we report that an unsymmetrical heteroaromatic 1,2-diketone forms an organic RTP liquid. This diketone exists as a kinetically stable supercooled liquid, which resists crystallisation even under pricking or shearing stresses, and remains as a liquid for several months. The unsymmetrical diketone core is flexible, with eight distinct conformers possible, which prevents nucleation and growth for the liquid–solid transition. Interestingly, the thermodynamically stable crystalline solid-state was non-emissive. Thus, the RTP of the diketone was found to be liquiefaction-induced. Single-crystal X-ray structure analysis revealed that the diminished RTP of the crystal is due to insufficient intermolecular interactions and restricted access to an emissive conformer. Our work demonstrates that flexible unsymmetrical skeletons are promising motifs for bistable liquid–solid molecular systems, which are useful for the further development of stimuli-responsive materials that use phase transitions.

Metal-free, single-component, unsymmetrical 1,2-diketone exhibits liquefaction-induced room-temperature phosphorescence. Desymmetrisation provides the supercooled liquid with notable kinetic stability and phase-dependent phosphorescence properties.     

Transition metal-catalyzed organic reactions in undivided electrochemical cells

Transition metal-catalyzed organic electrochemistry is a rapidly growing research area owing in part to the ability of metal catalysts to alter the selectivity of a given transformation. This conversion mainly focuses on transition metal-catalyzed anodic oxidation and cathodic reduction and great progress has been achieved in both areas. Typically, only one of the half-cell reactions is involved in the organic reaction while a sacrificial reaction occurs at the counter electrode, which is inherently wasteful since one electrode is not being used productively. Recently, transition metal-catalyzed paired electrolysis that makes use of both anodic oxidation and cathodic reduction has attracted much attention. This perspective highlights the recent progress of each type of electrochemical reaction and relatively focuses on the transition metal-catalyzed paired electrolysis, showcasing that electrochemical reactions involving transition metal catalysis have advantages over conventional reactions in terms of controlling the reaction activity and selectivity and figuring out that transition metal-catalyzed paired electrolysis is an important direction of organic electrochemistry in the future and offers numerous opportunities for new and improved organic reaction methods.

Transition metal-catalyzed organic electrochemistry is a rapidly growing research area owing in part to the ability of metal catalysts to alter the selectivity of a given transformation.     

Enantioselective iodolactonization to prepare ε-lactone rings using hypervalent iodine

Despite the rapid growth of enantioselective halolactonization reactions in recent years, most are effective only when forming smaller (6,5,4-membered) rings. Seven-membered ε-lactones, are rarely formed with high selectivity, and never without conformational bias. We describe the first highly enantioselective 7-exo-trig iodolactonizations of conformationally unbiased ε-unsaturated carboxylic acids, effected by an unusual combination of a bifunctional BAM catalyst, I₂, and I(iii) reagent (PhI(OAc)₂:PIDA).

We describe the first highly enantioselective 7-exo-trig iodolactonizations of conformationally unbiased ε-unsaturated carboxylic acids, effected by an unusual combination of a bifunctional BAM catalyst, I₂, and I(iii) reagent (PhI(OAc)₂:PIDA).