Identification of the Binding Site of Chroman-4-one-Based Sirtuin 2-Selective Inhibitors using Photoaffinity Labeling in Combination with Tandem Mass Spectrometry

Shedding light on cellular dynamics: the progress in developing photoactivated fluorophores

Photoactivated fluorophores (PAFs) are highly effective imaging tools that exhibit a removal of caging groups upon light excitation, resulting in the restoration of their bright fluorescence. This unique property allows for precise control over the spatiotemporal aspects of small molecule substances, making them indispensable for studying protein labeling and small molecule signaling within live cells. In this comprehensive review, we explore the historical background of this field and emphasize recent advancements based on various reaction mechanisms. Additionally, we discuss the structures and applications of the PAFs. We firmly believe that the development of more novel PAFs will provide powerful tools to dynamically investigate cells and expand the applications of these techniques into new domains.

Identification of novel α-glucosidase and ACE inhibitory peptides from Douchi using peptidomics approach and molecular docking

In this study, the effect of Douchi extract (DWE) on α-glucosidase and angiotensin-converting enzymes (ACE) were investigated, and several novel peptides with inhibitory activity against α-glucosidase and ACE were identified using peptidomics approach based on UPLC-MS/MS. The average inhibition rates of DWE on α-glucosidase and ACE were 73.75-78.10% and 4.56-27.07%, respectively. In the DWE, a total of 710 peptides were detected. Two novel peptides with potential inhibitory activity against α-glucosidase were identified using the correlation analysis, database alignment and molecular docking methods. They were DVFRAIPSEVL and DRPSINGLAGAN, with the IC50 values of 0.121 and 0.128 mg/mL, respectively. Also, four novel peptides with potential inhibitory activity against ACE were identified: PSSPFTDLWD, EEQDERQFPF, PVPVPVQQAFPF and PSSPFTDL, with IC50 values of 1.388, 0.041, 0.761 and 0.097 mg/mL, respectively. These results indicated that combining peptidomics and molecular docking is an effective alternative strategy for rapidly screening numbers of novel bioactive peptides from foods.

Targeting GDP-Dissociation Inhibitor Beta (GDI2) with a Benzo[a]quinolizidine Library to Induce Paraptosis for Cancer Therapy

Inducing paraptosis, a nonapoptotic form of cell death, has great therapeutic potential in cancer therapy, especially for drug-resistant tumors. However, the specific molecular target(s) that trigger paraptosis have not yet been deciphered yet. Herein, by using activity-based protein profiling, we identified the GDP-dissociation inhibitor beta (GDI2) as a manipulable target for inducing paraptosis and uncovered benzo[a]quinolizidine BQZ-485 as a potent inhibitor of GDI2 through the interaction with Tyr245. Comprehensive target validation revealed that BQZ-485 disrupts the intrinsic GDI2-Rab1A interaction, thereby abolishing vesicular transport from the endoplasmic reticulum (ER) to the Golgi apparatus and initiating subsequent paraptosis events including ER dilation and fusion, ER stress, the unfolded protein response, and cytoplasmic vacuolization. Based on the structure of BQZ-485, we created a small benzo[a]quinolizidine library by click chemistry and discovered more potent GDI2 inhibitors using a NanoLuc-based screening platform. Leveraging the engagement of BQZ-485 with GDI2, we developed a selective GDI2 degrader. The optimized inhibitor (+)-37 and degrader 21 described in this study exhibited excellent in vivo antitumor activity in two GDI2-overexpressing pancreatic xenograft models, including an AsPc-1 solid tumor model and a transplanted human PDAC tumor model. Altogether, our findings provide a promising strategy for targeting GDI2 for paraptosis in the treatment of pancreatic cancers, and these lead compounds could be further optimized to be effective chemotherapeutics.

Visible light-induced radical cascade acylmethylation/cyclization of 2-(allyloxy)arylaldehydes with α-bromo ketones: access to cyclic 1,5-dicarbonyl-containing chroman-4-one skeletons

A novel photocatalytic protocol for effective and efficient synthesis of cyclic 1,5-diketones containing chroman-4-one skeletons in moderate to good yields via radical cascade acylmethylation/cyclization of 2-(allyloxy)arylaldehydes with α-bromo ketones has been described. This reaction features a broad substrate scope, good functional group tolerance, and metal- and oxidant-free conditions. An acylmethyl radical-triggered cascade cyclization was involved.

Identification of photocrosslinking peptide ligands by mRNA display

Photoaffinity labelling is a promising method for studying protein-ligand interactions. However, obtaining a specific, efficient crosslinker can require significant optimisation. We report a modified mRNA display strategy, photocrosslinking-RaPID (XL-RaPID), and exploit its ability to accelerate the discovery of cyclic peptides that photocrosslink to a target of interest. As a proof of concept, we generated a benzophenone-containing library and applied XL-RaPID screening against a model target, the second bromodomain of BRD3. This crosslinking screening gave two optimal candidates that selectively labelled the target protein in cell lysate. Overall, this work introduces direct photocrosslinking screening as a versatile technique for identifying covalent peptide ligands from mRNA display libraries incorporating reactive warheads.

Visible-Light-Mediated Tandem Difluoromethylation/Cyclization of Alkenyl Aldehydes toward CF2H-Substituted Chroman-4-one Derivatives

An efficient and facile visible-light-mediated tandem difluoromethylation/cyclization of alkenyl aldehydes, with easily accessible and air-stable [Ph₃PCF₂H]⁺Br^- as the difluoromethylation reagent, has been established. A range of CF₂H-substituted chroman-4-one skeletons and their derivatives, such as 2,3-dihydroquinolin-4(1H)-ones, chroman, 3,4-dihydronaphthalen-1(2H)-one, 2,3-dihydrobenzofuran, and 2,3-dihydro-1H-inden-1-one, are efficiently produced in moderate to good yields with excellent chemoselectivity under mild reaction conditions.

Light-induced stabilization of microtubules by photo-crosslinking of a Tau-derived peptide

For light-induced stabilization of microtubules (MTs) to manipulate cells, a photo-reactive diazirine group was conjugated to a Tau-derived peptide, a motif binding on the inside of MTs. Ultraviolet (UV) light irradiation induced significant stabilization of MTs via the formation of a covalent bond of the peptide and showed toxicity.

Covalent cannabinoid receptor ligands - structural insight and selectivity challenges

X-ray crystallography and cryogenic electronic microscopy have provided significant advancement in the knowledge of GPCR structure and have allowed the rational design of GPCR ligands. The class A GPCRs cannabinoid receptor type 1 and type 2 are implicated in many pathophysiological processes and thus rational design of drug and tool compounds is of great interest. Recent structural insight into cannabinoid receptors has already led to a greater understanding of ligand binding sites and receptor residues that likely contribute to ligand selectivity. Herein, classes of heterocyclic covalent cannabinoid receptor ligands are reviewed in light of the recent advances in structural knowledge of cannabinoid receptors, with particular discussion regarding covalent ligand selectivity and rationale design.

Visible-Light-Induced Dual Acylation of Alkenes for the Construction of 3-Substituted Chroman-4-ones

Heterocyclic compounds, especially oxygen-containing heterocyclic compounds, are crucial moieties in bioactive compounds and drug leads. Substituted chroman-4-ones are a kind of the most significant structural skeletons. Herein, we report a visible-light-induced dual acylation of alkenes for constructing 3-substituted chroman-4-ones, which undergoes a radical tandem cyclization reaction through carbon-carbon bond cleavage of oxime esters by a nitrogen-centered radical strategy. A series of 3-substituted chroman-4-ones were prepared with up to 86% yield.

Synthesis of 2-alkyl-chroman-4-ones via cascade alkylation-dechlorination of 3-chlorochromones

An efficient and mild synthetic approach for 2-alkyl-substituted chroman-4-ones via zinc-mediated cascade decarboxylative β-alkylation and dechlorination of 3-chlorochromones was developed. This transformation employed commercially available starting materials and was performed under mild conditions without heat, visible light, peroxide or heavy metals. Moreover, various alkyl NHPI esters with functional groups and differently substituted 3-chlorochromones were tolerated, affording the targeted products with moderate to excellent yields. This protocol could be utilized to construct a diverse library of 2-substituted chroman-4-one derivatives, which could be useful in the discovery of lead compounds for drug discovery in the future.

Synthesis, X-ray Structure Determination, and Comprehensive Photochemical Characterization of (Trifluoromethyl)diazirine-Containing TRPML1 Ligands

Potential (trifluoromethyl)diazirine-based TRPML1 ion channel ligands were designed and synthesized, and their structures were determined by single-crystal X-ray diffraction analysis. Photoactivation studies via ¹⁹F NMR spectroscopy and HPLC-MS analysis revealed distinct kinetical characteristics in selected solvents and favorable photochemical properties in an aqueous buffer. These photoactivatable TRPML activators represent useful and valuable tools for TRPML photoaffinity labeling combined with mass spectrometry.

Direct synthesis of 4-hydroxycoumarins and 4-hydroxy-6-methyl-2-pyrone containing chroman-4-ones via a silver catalyzed radical cascade cyclization reaction

A novel AgNO3/K2S2O8 catalyzed radical cascade cyclization reaction of 2-(allyloxy)arylaldehydes with 4-hydroxycoumarins and 4-hydroxy-6-methyl-2-pyrone produces two new series of chroman-2-ones.

Recent advances in the development of histone deacylase SIRT2 inhibitors

Sirtuin 2 (SIRT2) is an important and special member of the atypical histone deacetylase Sirtuin (SIRT) family. Due to its extensive catalytic effects, SIRT2 can regulate autophagy, myelination, immunity, inflammation and other physiological processes. Recent evidence revealed that dysregulation of human SIRT2 activity is associated with the pathogenesis and prognosis of cancers, Parkinson's disease and other disorders; thus SIRT2 is a promising target for potential therapeutic intervention. This review presents a systematic summary of nine chemotypes of small-molecule SIRT2 inhibitors, particularly including the discovery and structural optimization strategies, which will be useful for future efforts to develop new inhibitors targeting SIRT2 and associated target proteins.

This review presents a systematic summarization of nine chemotypes of small-molecule SIRT2 inhibitors, which will be useful for future efforts to develop new inhibitors targeting SIRT2 and associated target proteins.

The Application of Fluorine-Containing Reagents in Structural Proteomics

Structural proteomics refers to large-scale mapping of protein structures in order to understand the relationship between protein sequence, structure, and function. Chemical labeling, in combination with mass-spectrometry (MS) analysis, have emerged as powerful tools to enable a broad range of biological applications in structural proteomics. The key to success is a biocompatible reagent that modifies a protein without affecting its high-order structure. Fluorine, well-known to exert profound effects on the physical and chemical properties of reagents, should have an impact on structural proteomics. In this Minireview, we describe several fluorine-containing reagents that can be applied in structural proteomics. We organize their applications around four MS-based techniques: a) affinity labeling, b) activity-based protein profiling (ABPP), c) protein footprinting, and d) protein cross-linking. Our aim is to provide an overview of the research, development, and application of fluorine-containing reagents in protein structural studies.

Phototriggered labeling and crosslinking by 2-nitrobenzyl alcohol derivatives with amine selectivity

Here we report the use of 2-nitrobenzyl alcohol (NB) as a photoreactive group with amine selectivity and explore its applications for photoaffinity labeling and crosslinking of biomolecules. This work confirms that NB is an efficient photoreactive group and has great potential in drug discovery, chemical biology and protein engineering.

Characterisation of utrophin modulator SMT C1100 as a non-competitive inhibitor of firefly luciferase

Firefly luciferase (FLuc) is a powerful tool for molecular and cellular biology, and popular in high-throughput screening and drug discovery. However, FLuc assays have been plagued with positive and negative artefacts due to stabilisation and inhibition by small molecules from a range of chemical classes. Here we disclose Phase II clinical compound SMT C1100 for the treatment of Duchenne muscular dystrophy as an FLuc inhibitor (K_D of 0.40 ± 0.15 µM). Enzyme kinetic studies using SMT C1100 and other non-competitive inhibitors including resveratrol and NFκBAI4 identified previously undescribed modes of inhibition with respect to FLuc's luciferyl adenylate intermediate. Employing a photoaffinity strategy to identify SMT C1100's binding site, a photolabelled SMT C1100 probe instead underwent FLuc-dependent photooxidation. Our findings support novel binding sites on FLuc for non-competitive inhibitors.

Design and Synthesis of the Diazirine-based Clickable Photo-affinity Probe Targeting Sphingomyelin Synthase 2

Background:

SMS family plays a very important role in sphingolipids metabolism and is involved in the membrane mobility and signaling transduction.

Methods:

SMS2 subtype was related to a variety of diseases and could be regarded as a promising potential drug target. However, the uncertainty of the binding sites and the molecular mechanism of action limited the development of SMS2 inhibitors. Herein, we discovered a photo-affinity probe PAL-1 targeting SMS2.

Results:

The enzyme inhibitory activity and the photo-affinity labeling experiments showed that PAL-1 could be mono-labeled on SMS2.

Conclusion:

In summary, starting from the N-arylbenzamides core structure and the minimalist terminal alkyne-containing diazirine photo-crosslinker, we designed and synthesized a photoaffinity probe PAL-1 targeting SMS2. The enzymatic inhibitory activity study showed that PAL-1 exhibited superior selectivities for SMS2 with an IC50 of 0.37 µM over SMS1.

Recent Applications of Diazirines in Chemical Proteomics

The elucidation of substrate-protein interactions is an important component of the drug development process. Due to the complexity of native cellular environments, elucidating these fundamental biochemical interactions remains challenging. Photoaffinity labeling (PAL) is a versatile technique that can provide insight into ligand-target interactions. By judicious modification of substrates with a photoreactive group, PAL creates a covalent crosslink between a substrate and its biological target following UV-irradiation. Among the commonly employed photoreactive groups, diazirines have emerged as the gold standard. In this Minireview, recent developments in the field of diazirine-based photoaffinity labeling will be discussed, with emphasis being placed on their applications in chemical proteomic studies.

Fishing for Drug Targets: A Focus on Diazirine Photoaffinity Probe Synthesis

Target identification is a high-priority, albeit challenging, aspect of drug discovery. Diazirine-based photoaffinity probes (PAPs) can facilitate the process by covalently capturing transient molecular interactions. This can help identify target proteins and map the ligand's interactome. Diazirine probes have even been incorporated by cellular machinery into proteins. Embarking on the synthesis of customized PAPs, containing either an aliphatic or trifluoromethyl phenyl diazirine, can be a considerable endeavor, particularly for medicinal chemists and chemical biologists new to the field. This review takes a synthetic focus, aiming to summarize available routes, propose new avenues, and illuminate recent advances in diazirine synthesis. Select examples of diazirine photoaffinity labeling applications have been included throughout to provide instructive definition of the advantages and limitations of the technology while simultaneously highlighting how these reagents can be applied in a practical sense.

Transition-metal-free direct C-3 alkylation of quinoxalin-2(1H)-ones with ethers

An efficient protocol for the synthesis of 3-alkyl quinoxalin-2(1H)-ones has been developed via the transition-metal-free cross-coupling reaction of quinoxalin-2(1H)-ones with ethers with moderate to good yields under relatively mild conditions.

Silver-catalyzed decarboxylative cascade radical cyclization of tert-carboxylic acids and o-(allyloxy)arylaldehydes towards chroman-4-one derivatives

A convenient silver-catalyzed decarboxylative cascade radical cyclization of tertiary carboxylic acids and o-(allyloxy)arylaldehydes was developed to synthesize 3-alkyl-substituted chroman-4-one derivatives.

Current advances of carbene-mediated photoaffinity labeling in medicinal chemistry

Photoaffinity labeling (PAL) in combination with a chemical probe to covalently bind its target upon UV irradiation has demonstrated considerable promise in drug discovery for identifying new drug targets and binding sites. In particular, carbene-mediated photoaffinity labeling (cmPAL) has been widely used in drug target identification owing to its excellent photolabeling efficiency, minimal steric interference and longer excitation wavelength. Specifically, diazirines, which are among the precursors of carbenes and have higher carbene yields and greater chemical stability than diazo compounds, have proved to be valuable photolabile reagents in a diverse range of biological systems. This review highlights current advances of cmPAL in medicinal chemistry, with a focus on structures and applications for identifying small molecule–protein and macromolecule–protein interactions and ligand-gated ion channels, coupled with advances in the discovery of targets and inhibitors using carbene precursor-based biological probes developed in recent decades.

Photoaffinity labeling (PAL) in combination with a chemical probe to covalently bind its target upon UV irradiation has demonstrated considerable promise in drug discovery for identifying new drug targets and binding sites.

Thienopyrimidinone Based Sirtuin-2 (SIRT2)-Selective Inhibitors Bind in the Ligand Induced Selectivity Pocket

Sirtuins (SIRTs) are NAD-dependent deacylases, known to be involved in a variety of pathophysiological processes and thus remain promising therapeutic targets for further validation. Previously, we reported a novel thienopyrimidinone SIRT2 inhibitor with good potency and excellent selectivity for SIRT2. Herein, we report an extensive SAR study of this chemical series and identify the key pharmacophoric elements and physiochemical properties that underpin the excellent activity observed. New analogues have been identified with submicromolar SIRT2 inhibtory activity and good to excellent SIRT2 subtype-selectivity. Importantly, we report a cocrystal structure of one of our compounds (29c) bound to SIRT2. This reveals our series to induce the formation of a previously reported selectivity pocket but to bind in an inverted fashion to what might be intuitively expected. We believe these findings will contribute significantly to an understanding of the mechanism of action of SIRT2 inhibitors and to the identification of refined, second generation inhibitors.