Chemical proteomic profling with photoaffinity labeling strategy identifies antimalarial targets of artemisinin

Present research on the antimalarial mechanisms of artemisinin(ART)is mainly focused on covalent drug binding targets alkylated by free radicals,while non-covalent binding targets have rarely been reported.Here,we developed a novel photoaffinity probe of ART to globally capture and identify the antimalarial target proteins of ART through chemical proteomics.The results demonstrated that ART can bind to par-asite proteins by both covalent and non-covalent modification,and these may jointly contribute to the antimalarial effects.Our work enriches the research on the antimalarial targets of ART,and provides a new perspective for further exploring the antimalarial mechanism of ART.

A clickable photoaffinity probe of betulinic acid identifies tropomyosin as a target

Target identification of bioactive compounds is important for understanding their mechanisms of action and provides critical insights into their therapeutic utility. While it remains a challenge,unbiased chemoproteomics strategy using clickable photoaffinity probes is a useful and validated approach for target identification. One major limitation of this approach is the efficient synthesis of appropriately substituted clickable photoaffinity probes. Herein, we describe an efficient and consistent method to prepare such probes. We further employed this method to prepare a highly stereo-congested probe based on naturally occurring triterpenoid betulinic acid. With this photoaffinity probe, we identified tropomyosin as a novel target for betulinic acid that can account for the unique biological phenotype on cellular cytoskeleton induced by betulinic acid.

Chemical Synthesis of diSUMO Photoaffinity Probes for the Identification of PolySUMO Chain-Specific Interacting Proteins

Small ubiquitin-like modifiers(SUMOs)are protein modifiers that can form polymeric chains.They are important signals in cellular processes,and their study and profiling require the development of molecular tools.Herein,the authors have reported an efficient chemical protein synthesis approach for the generation of dimeric SUMO-2-based photoaffinity probes through the ligation of four readily synthesizable peptides.Proteomic studies using this diSUMO-2 probe on HeLa cell nuclear lysate found it to capture a significantly different selection of proteins compared with its monoSUMO counterparts.This resulted in the identification of several previously unknown SUMO chain-specific interacting proteins such as 40S ribosomal protein S3,which showed a significantly higher affinity for polySUMO chains than monomeric SUMO.Collectively,these results emphasize the need to develop SUMO chain-based probes in other species,and to shed light on the important role of polySUMOylation in diseases.

Analysis of receptor-ligand binding by photoaffinity cross-linking

Photoaffinity cross-linking is a fast developing technology for biomolecular interactions,including receptor-ligand binding.The chemical mechanisms of the most commonly used photoactivatable probes and their respective photochemistry are summarized.This review focuses on the expanding utilities of this technology as a result of recent advances in the(i)identification of receptor contact sites,(ii)monitoring ligand-induced receptor conformational changes,(iii)identification of global binding surfaces,(iv)binding mode analysis using bifunctional photo-probes,(v)application of biosynthetic photo-probes,and(vi)examples of novel target discovery using this technology.Limitations and future potential of this approach are also discussed.

Design and Synthesis of Photoaffinity Probe Candidates for the GABA-gated Chloride Channel

In order to characterize binding sites of insecticidal compounds on GABA gated chloride channel, new photoaffinity probe candidates based on 5e-t-butyl-2e-[4-（substituted-propynyl）phenyl]-1,3-dithiane for the noncompetitive blocker （NCB） site of the γ-aminobutyric acid （GABA）-gated chloride channel were designed and synthesized, and their potency as an inhibitor on NCB was measured by 4＇-ethynyl-4-n-[2,3-^3H2]-propylbicycloorthobenzoate （^3H EBOB） assay. The synthesized compounds showed high inhibition activities with half maximum inhibition concentrations （IC50） of lower than 35 nmol/L and were very stable in binding conditions as well photoreacted quickly at 300 nm light. These new compounds are expected to be good photoaffinity labeling probes if radioisotope iodine is incorporated.

Discovery and identification of EIF2AK2 as a direct key target of berberine for anti-inflammatory effects

Using chemoproteomic techniques,we first identified EIF2AK2,eEF1A1,PRDX3 and VPS4B as direct targets of berberine(BBR)for its synergistically anti-inflammatory effects.Of them,BBR has the strongest affinity with EIF2AK2 via two ionic bonds,and regulates several key inflammatory pathways through EIF2AK2,indicating the dominant role of EIF2AK2.Also,BBR could subtly inhibit the dimerization of EIF2AK2,rather than its enzyme activity,to selectively modulate its downstream pathways including JNK,NF-κB,AKT and NLRP3,with an advantage of good safety profile.In EIF2AK2 gene knockdown mice,the inhibitory IL-1β,IL-6,IL-18 and TNF-a secretion of BBR was obviously attenuated,confirming an EIF2AK2-dependent anti-inflammatory efficacy.The results highlight the BBR's network mechanism on anti-inflammatory effects in which EIF2AK2 is a key target,and inhibition of EIF2AK2 dimerization has a potential to be a therapeutic strategy against inflammationrelated disorders.

Capture and Identification of Dual Specificity Mitogen-Activated Protein Kinase Kinase 7 as a Direct Proteomic Target of Berberine to Affect the c-JunN-Terminal Kinase Pathway

Seven photoaffinity-based and sixteen biotin-based berberine(BBR)probes were constructed and screened for their effects on c-Jun N-terminal protein kinases(JNK)phosphorylation(p-JNK)suppression at the cellular level.Taking active-photoaffinity probe 7c as a chemical tool,we first identified mitogen-activated protein kinase 7(MAP2K7),an upstream protein on the JNK/stress activated protein kinase(SAPK)pathway,as a direct proteomic target of BBR using activity-based protein profiling(ABPP)and other chemical proteomic techniques.Furthermore,BBR’s inhibitory effect on p-JNK was significantly attenuated in both the MAP2K7-knockdown and models,indicating a MAP2K7-dependent inhibition on the JNK signaling pathway.For the first time,we demonstrate the unique mechanism of BBR that directly targets MAP2K7 to inhibit p-JNK rather than JNK activity with the advantages of multiple activities and a good safety profile.

Chemical proteomics reveals ligustilide targets SMAD3,inhibiting collagen synthesis in aortic endothelial cells

Atherosclerosis is a persistent inflammatory state,while vascular endothelial fibrosis is one of the primary causes of atherosclerosis development.Although ligustilide(Lig) was shown to exert obvious antiatherogenic effects in previous studies,its precise mechanism has not been deeply discussed.In this paper,we designed a Lig-derived photoaffinity labelling(PAL) probe to identify potential therapeutic targets of Lig via chemical proteomics approach.Mothers against decapentaplegic homologue 3(SMAD3),a signal transmitter of transforming growth factor-β(TGF-β) which promotes the development of vascular fibrosis,was identified as a potential target of Lig.Lig suppressed the phosphorylation and nuclear translocation of SMAD3 by blocking the interaction between SMAD3 and TGF-β receptor 1,thereby inhibiting the collagen synthesis process.Hence,developing a novel SMAD3 inhibitor may present a promising therapeutic option for preventing vascular fibrosis.

Chemical proteomics combined with metabonomics reveals berberine targets NDUFV1 of complex Ⅰ in the respiratory chain to regulate energy metabolism

Berberine(BBR) is the primary alkaloid compound of the heat-clearing traditional Chinese medicine Huanglian(Coptis chinensis) and exerts regulatory effects on energy metabolism. However, the specific targets and molecular mechanisms are not clear. In this paper, the BBR-affected energy metabolism pathway was screened by nontargeted metabolomics, and a BBR-derived photoaffinity labeled(PAL) probe was designed to identify potential targets via a chemical proteomics approach. NDUFV1, a subunit of complex Ⅰ on mitochondria, was identified as a potential target of BBR. In the respiratory chain, BBR suppressed the activity of complex Ⅰ, reduced the electrochemical potential in the mitochondrial intermembrane and inhibited the generation of ATP and heat via competitive binding with NDUFV1. The results illustrated the underlying mechanism of BBR in the downregulation of energy metabolism.