Application of Chemical Proteomics in Identifying the Molecular Targets of Natural Products

doi:10.13560/j.cnki.biotech.bull.1985.2023-0188

Abstract

Abstract:

The development and utilization of new green pesticides are conducive to the sustainable development of agriculture. Studying active leading discovery and action mechanisms based on natural products is essential for creating new pesticides. However, its target and action mechanism are difficult to determine, which hinders its development in new drug research and development. Therefore, discovering compound new targets is an important and arduous task for creating new pesticides. As a new technology in the post-genomic era, chemical proteomics has become one of the essential means of drug targeting. This paper reviewed the discovery methods and typical cases of molecular targets of chemical compounds based on proteomics and introduced main principles, applications, advantages and limitations of these technologies, aiming to provide references for the research of natural product targets and new pesticide creation by explaining the progress of the latest methods of discovering drug action targets based on chemical proteomics.

Key words: chemical proteomics, target identification, chemical probe, non-chemical probe, natural products

ZHOU Lu-qi, CUI Ting-ru, HAO Nan, ZHAO Yu-wei, ZHAO Bin, LIU Ying-chao. Application of Chemical Proteomics in Identifying the Molecular Targets of Natural Products[J]. Biotechnology Bulletin, 2023, 39(9): 12-26.

Figures/Tables 7

References 87

[1]	Van Emden HF. Crop production and crop protection: estimated losses in major food and cash crops[J]. J Agric Sci, 1996, 127(1): 137.
[2]	吴剑, 宋宝安. 绿色农药创新及靶标研究现状与思考[J]. 中国科学基金, 2020, 34(4): 486-494.
	Wu J, Song BA. Current situation and thinking for the innovation of green pesticide[J]. Bull Natl Nat Sci Found China, 2020, 34(4): 486-494.
[3]	Guo ZR. The modification of natural products for medical use[J]. Acta Pharm Sin B, 2017, 7(2): 119-136. doi: 10.1016/j.apsb.2016.06.003 pmid: 28303218
[4]	邵旭升, 杜少卿, 李忠, 等. 中国绿色农药的研究和发展[J]. 世界农药, 2020, 42(4)16-24.
	Shao XS, Du SQ, Li Z, et al. Research and development of green pesticides in China[J]. World Pestic, 2020, 42(4)16-24.
[5]	Cheng D, Feng MX, Ji YF, et al. Effects of celangulin IV and V from Celastrus angulatus maxim on Na⁺/K⁺-ATPase activities of the oriental armyworm(Lepidoptera: Noctuidae)[J]. J Insect Sci, 2016, 16(1): 59. doi: 10.1093/jisesa/iew051 URL
[6]	Moffat JG, Vincent F, Lee JA, et al. Opportunities and challenges in phenotypic drug discovery: an industry perspective[J]. Nat Rev Drug Discov, 2017, 16(8): 531-543. doi: 10.1038/nrd.2017.111 pmid: 28685762
[7]	Heilker R, Lessel U, Bischoff D. The power of combining phenotypic and target-focused drug discovery[J]. Drug Discov Today, 2019, 24(2): 526-532. doi: S1359-6446(18)30155-7 pmid: 30359770
[8]	Schirle M, Jenkins JL. Identifying compound efficacy targets in phenotypic drug discovery[J]. Drug Discov Today, 2016, 21(1): 82-89. doi: S1359-6446(15)00290-1 pmid: 26272035
[9]	Liu GY, Ju XL, Cheng J, et al. 3D-QSAR studies of insecticidal anthranilic diamides as ryanodine receptor activators using CoMFA, CoMSIA and DISCOtech[J]. Chemosphere, 2010, 78(3): 300-306. doi: 10.1016/j.chemosphere.2009.10.038 URL
[10]	Meissner F, Geddes-McAlister J, Mann M, et al. The emerging role of mass spectrometry-based proteomics in drug discovery[J]. Nat Rev Drug Discov, 2022, 21(9): 637-654. doi: 10.1038/s41573-022-00409-3
[11]	Majumder A, Biswal MR, Prakash MK. One drug multiple targets: an approach to predict drug efficacies on bacterial strains differing in membrane composition[J]. ACS Omega, 2019, 4(3): 4977-4983. doi: 10.1021/acsomega.8b02862
[12]	Strassberger V, Fugmann T, Neri D, et al. Chemical proteomic and bioinformatic strategies for the identification and quantification of vascular antigens in cancer[J]. J Proteom, 2010, 73(10): 1954-1973. doi: 10.1016/j.jprot.2010.05.018 URL
[13]	Fedorov II, Lineva VI, Tarasova IA, et al. Mass spectrometry-based chemical proteomics for drug target discoveries[J]. Biochemistry Moscow, 2022, 87(9): 983-994. doi: 10.1134/S0006297922090103
[14]	Humphrey SJ, James DE, Mann M. Protein phosphorylation: a major switch mechanism for metabolic regulation[J]. Trends Endocrinol Metab, 2015, 26(12): 676-687. doi: 10.1016/j.tem.2015.09.013 URL
[15]	Rix U, Superti-Furga G. Target profiling of small molecules by chemical proteomics[J]. Nat Chem Biol, 2009, 5(9): 616-624. doi: 10.1038/nchembio.216 pmid: 19690537
[16]	Harding MW, Galat A, Uehling DE, et al. A receptor for the immuno-suppressant FK506 is a cis-trans peptidyl-prolyl isomerase[J]. Nature, 1989, 341(6244): 758-760. doi: 10.1038/341758a0
[17]	Bach S, Knockaert M, Reinhardt J, et al. Roscovitine targets, protein kinases and pyridoxal kinase[J]. J Biol Chem, 2005, 280(35): 31208-31219. doi: 10.1074/jbc.M500806200 pmid: 15975926
[18]	Gyenis L, Kuś A, Bretner M, et al. Functional proteomics strategy for validation of protein kinase inhibitors reveals new targets for a TBB-derived inhibitor of protein kinase CK2[J]. J Proteom, 2013, 81: 70-79. doi: 10.1016/j.jprot.2012.09.017 URL
[19]	Faiella L, Piaz FD, Bisio A, et al. A chemical proteomics approach reveals Hsp27 as a target for proapoptotic clerodane diterpenes[J]. Mol BioSyst, 2012, 8(10): 2637-2644. doi: 10.1039/c2mb25171j pmid: 22802135
[20]	Lu LN, Qi ZJ, Zhang JW, et al. Separation of binding protein of celangulin V from the midgut of Mythimna separata walker by affinity chromatography[J]. Toxins, 2015, 7(5): 1738-1748. doi: 10.3390/toxins7051738 URL
[21]	Hu LH, Iliuk A, Galan J, et al. Identification of drug targets in vitro and in living cells by soluble-nanopolymer-based proteomics[J]. Angewandte Chemie Int Ed, 2011, 50(18): 4133-4136. doi: 10.1002/anie.v50.18 URL
[22]	Bantscheff M, Scholten A, Heck AJR. Revealing promiscuous drug-target interactions by chemical proteomics[J]. Drug Discov Today, 2009, 14(21/22): 1021-1029. doi: 10.1016/j.drudis.2009.07.001 URL
[23]	Adam GC, Sorensen EJ, Cravatt BF. Chemical strategies for functional proteomics[J]. Mol Cell Proteom, 2002, 1(10): 781-790. doi: 10.1074/mcp.R200006-MCP200 URL
[24]	Benns HJ, Tate EW, Child MA. Activity-based protein profiling for the study of parasite biology[J]. Curr Top Microbiol Immunol, 2019, 420:155-174. doi: 10.1007/82_2018_123 pmid: 30105424
[25]	Zhou YQ, Xiao YL. Target identification of bioactive natural products[J]. Acta Chim Sinica, 2018, 76(3): 177. doi: 10.6023/A17110484
[26]	杨婉琪, 张崇敬. 基于分子原型和分子探针的药用活性分子蛋白作用靶标研究[J]. 药学学报, 2020, 55(7): 1439-1452.
	Yang WQ, Zhang CJ. Protein targets of medicinally active molecules based on their original structures and molecular probes[J]. Acta Pharm Sin, 2020, 55(7): 1439-1452.
[27]	Wright MH, Tao Y, Drechsel J, et al. Quantitative chemoproteomic profiling reveals multiple target interactions of spongiolactone derivatives in leukemia cells[J]. Chem Commun, 2017, 53(95): 12818-12821. doi: 10.1039/C7CC04990K URL
[28]	Wang C, Chen N. Activity-based protein profiling[J]. Acta Chim Sinica, 2015, 73(7): 657. doi: 10.6023/A15040223
[29]	Zanon PRA, Lewald L, Hacker SM. Isotopically labeled desthiobiotin azide(isoDTB)tags enable global profiling of the bacterial cysteinome[J]. Angewandte Chemie Int Ed, 2020, 59(7): 2829-2836. doi: 10.1002/anie.v59.7 URL
[30]	Kong LM, Deng X, Zuo ZL, et al. Identification and validation of p50 as the cellular target of eriocalyxin B[J]. Oncotarget, 2014, 5(22): 11354-11364. doi: 10.18632/oncotarget.v5i22 URL
[31]	Kwok BHB, Koh B, Ndubuisi MI, et al. The anti-inflammatory natural product parthenolide from the medicinal herb Feverfew directly binds to and inhibits IκB kinase[J]. Chem Biol, 2001, 8(8): 759-766. doi: 10.1016/S1074-5521(01)00049-7 URL
[32]	Yang CR, Peng B, Cao SL, et al. Synthesis, cytotoxic evaluation and target identification of thieno[2, 3-d]pyrimidine derivatives with a dithiocarbamate side chain at C2 position[J]. Eur J Med Chem, 2018, 154: 324-340. doi: 10.1016/j.ejmech.2018.05.028 URL
[33]	Chen ZZ, Jiang ZY, Chen N, et al. Target discovery of ebselen with a biotinylated probe[J]. Chem Commun, 2018, 54(68): 9506-9509. doi: 10.1039/C8CC04258F URL
[34]	Martín-Serrano Á, Gonzalez-Morena JM, Barbero N, et al. Biotin-labelled clavulanic acid to identify proteins target for haptenation in serum: implications in allergy studies[J]. Front Pharmacol, 2020, 11: 594755. doi: 10.3389/fphar.2020.594755 URL
[35]	Zhou W, Chen MM, Liu HL, et al. Dihydroartemisinin suppresses renal fibrosis in mice by inhibiting DNA-methyltransferase 1 and increasing Klotho[J]. Acta Pharmacol Sin, 2022, 43(10): 2609-2623. doi: 10.1038/s41401-022-00898-3 pmid: 35347248
[36]	Dai Z, An LY, Chen XY, et al. Target fishing reveals a novel mechanism of 1,2,4-oxadiazole derivatives targeting Rpn6, a subunit of 26S proteasome[J]. J Med Chem, 2022, 65(6): 5029-5043. doi: 10.1021/acs.jmedchem.1c02210 pmid: 35253427
[37]	Orahoske CM, Afrin M, Li YX, et al. Identification of prazosin as a potential flagellum attachment zone 1(FAZ1)inhibitor for the treatment of human African trypanosomiasis[J]. ACS Infect Dis, 2022, 8(8): 1711-1726. doi: 10.1021/acsinfecdis.2c00331 pmid: 35894227
[38]	Speers AE, Cravatt BF. Profiling enzyme activities in vivo using click chemistry methods[J]. Chem Biol, 2004, 11(4): 535-546. doi: 10.1016/j.chembiol.2004.03.012 URL
[39]	Wang JG, Tan XF, Nguyen VS, et al. A quantitative chemical proteomics approach to profile the specific cellular targets of andrographolide, a promising anticancer agent that suppresses tumor metastasis[J]. Mol Cell Proteom, 2014, 13(3): 876-886. doi: 10.1074/mcp.M113.029793 URL
[40]	Ciepla P, Konitsiotis AD, Serwa RA, et al. New chemical probes targeting cholesterylation of Sonic Hedgehog in human cells and zebrafish[J]. Chem Sci, 2014, 5(11): 4249-4259. pmid: 25574372
[41]	Wang JG, Zhang JB, Zhang CJ, et al. In situ proteomic profiling of curcumin targets in HCT116 colon cancer cell line[J]. Sci Rep, 2016, 6(1): 1-8. doi: 10.1038/s41598-016-0001-8
[42]	Chen B, Long QS, Zhao YL, et al. Sulfone-based probes unraveled dihydrolipoamide S-succinyltransferase as an unprecedented target in phytopathogens[J]. J Agric Food Chem, 2019, 67(25): 6962-6969. doi: 10.1021/acs.jafc.9b02059 URL
[43]	Liang HC, Liu YC, Chen H, et al. In situ click reaction coupled with quantitative proteomics for identifying protein targets of catechol estrogens[J]. J Proteome Res, 2018, 17(8): 2590-2599. doi: 10.1021/acs.jproteome.8b00021 URL
[44]	Tian Y, Wang S, Shang H, et al. The clickable activity-based probe of anti-apoptotic calenduloside E[J]. Pharm Biol, 2019, 57(1): 133-139. doi: 10.1080/13880209.2018.1557699 pmid: 30843752
[45]	Zhang M, Ma XY, Xu HL, et al. A natural AKT inhibitor swertiamarin targets AKT-PH domain, inhibits downstream signaling, and alleviates inflammation[J]. FEBS J, 2020, 287(9): 1816-1829. doi: 10.1111/febs.15112 pmid: 31665825
[46]	Yoo E, Schulze CJ, Stokes BH, et al. The antimalarial natural product salinipostin A identifies essential α/β serine hydrolases involved in lipid metabolism in P.falciparum parasites[J]. Cell Chem Biol, 2020, 27(2): 143-157.e5. doi: 10.1016/j.chembiol.2020.01.001 URL
[47]	Fang MY, Huang KH, Tu WJ, et al. Chemoproteomic profiling reveals cellular targets of nitro-fatty acids[J]. Redox Biol, 2021, 46: 102126. doi: 10.1016/j.redox.2021.102126 URL
[48]	Liu C, Wang L, Sun YJ, et al. Probe synthesis reveals eukaryotic translation elongation Factor 1 Alpha 1 as the anti-pancreatic cancer target of BE-43547A2[J]. Angewandte Chemie, 2022, 134(34): e202206953.
[49]	Cai Q, Li ZQ, Wei JJ, et al. Assembly of indole-2-carboxylic acid esters through a ligand-free copper-catalysed cascade process[J]. Chem Commun, 2009(48): 7581-7583.
[50]	Yan JB, Yao RF, Chen L, et al. Dynamic perception of jasmonates by the F-box protein COI1[J]. Mol Plant, 2018, 11(10): 1237-1247. doi: S1674-2052(18)30241-7 pmid: 30092285
[51]	Eirich J, Orth R, Sieber SA. Unraveling the protein targets of vancomycin in living S. aureus and E. faecalis cells[J]. J Am Chem Soc, 2011, 133(31): 12144-12153. doi: 10.1021/ja2039979 pmid: 21736328
[52]	Lamos SM, Krusemark CJ, McGee CJ, et al. Mixed isotope photoaffinity reagents for identification of small-molecule targets by mass spectrometry[J]. Angewandte Chemie Int Ed, 2006, 45(26): 4329-4333. doi: 10.1002/anie.v45:26 URL
[53]	Li BX, Chen JJ, Chao B, et al. Anticancer pyrroloquinazoline LBL1 targets nuclear lamins[J]. ACS Chem Biol, 2018, 13(5): 1380-1387. doi: 10.1021/acschembio.8b00266 pmid: 29648791
[54]	Gao CL, Hou GG, Liu J, et al. Synthesis and target identification of benzoxepane derivatives as potential anti-neuroinflammatory agents for ischemic stroke[J]. Angewandte Chemie Int Ed, 2020, 59(6): 2429-2439. doi: 10.1002/anie.v59.6 URL
[55]	Kennedy CR, Goya Grocin A, Kovačič T, et al. A probe for NLRP3 inflammasome inhibitor MCC950 identifies carbonic anhydrase 2 as a novel target[J]. ACS Chem Biol, 2021, 16(6): 982-990. doi: 10.1021/acschembio.1c00218 pmid: 34003636
[56]	Zhuo FF, Guo Q, Zheng YZ, et al. Photoaffinity labeling-based chemoproteomic strategy reveals RBBP4 as a cellular target of protopanaxadiol against colorectal cancer cells[J]. ChemBioChem, 2022, 23(13): e202200038.
[57]	Corson TW, Cavga H, Aberle N, et al. Triptolide directly inhibits dCTP pyrophosphatase[J]. ChemBioChem, 2011, 12(11): 1767-1773. doi: 10.1002/cbic.201100007 pmid: 21671327
[58]	Klaić L, Morimoto RI, Silverman RB. Celastrol analogues as inducers of the heat shock response. design and synthesis of affinity probes for the identification of protein targets[J]. ACS Chem Biol, 2012, 7(5): 928-937. doi: 10.1021/cb200539u pmid: 22380712
[59]	Zhao Q, Ding Y, Deng ZS, et al. Natural products triptolide, celastrol, and withaferin A inhibit the chaperone activity of peroxiredoxin I[J]. Chem Sci, 2015, 6(7): 4124-4130. doi: 10.1039/c5sc00633c pmid: 28717468
[60]	Lomenick B, Jung G, Wohlschlegel JA, et al. Target identification using drug affinity responsive target stability(DARTS)[J]. Curr Protoc Chem Biol, 2011, 3(4): 163-180. doi: 10.1002/9780470559277.ch110180 pmid: 22229126
[61]	Zhang X, Xu H, Bi XY, et al. Src acts as the target of matrine to inhibit the proliferation of cancer cells by regulating phosphorylation signaling pathways[J]. Cell Death Dis, 2021, 12(10): 931. doi: 10.1038/s41419-021-04221-6 pmid: 34642304
[62]	Kim Y, Sugihara Y, Kim TY, et al. Identification and validation of VEGFR2 kinase as a target of voacangine by a systematic combination of DARTS and MSI[J]. Biomolecules, 2020, 10(4): 508. doi: 10.3390/biom10040508 URL
[63]	Zhu Z, Li RM, Qin W, et al. Target engagement of ginsenosides in mild cognitive impairment using mass spectrometry-based drug affinity responsive target stability[J]. J Ginseng Res, 2022, 46(6): 750-758. doi: 10.1016/j.jgr.2021.12.003 pmid: 36312734
[64]	Zhao B, Fan SJ, Fan ZJ, et al. Discovery of pyruvate kinase as a novel target of new fungicide candidate 3-(4-methyl-1, 2, 3-thiadiazolyl)-6-trichloromethyl-[1, 2, 4]-triazolo-[3, 4-b][1, 3, 4]-thiadizole[J]. J Agric Food Chem, 2018, 66(46): 12439-12452. doi: 10.1021/acs.jafc.8b03797 URL
[65]	Geng J, Liu W, Gao J, et al. Andrographolide alleviates Parkinsonism in MPTP-PD mice via targeting mitochondrial fission mediated by dynamin-related protein 1[J]. Br J Pharmacol, 2019, 176(23): 4574-4591. doi: 10.1111/bph.v176.23 URL
[66]	Hu HF, Xu WW, Li YJ, et al. Anti-allergic drug azelastine suppresses colon tumorigenesis by directly targeting ARF1 to inhibit IQGAP1-ERK-Drp1-mediated mitochondrial fission[J]. Theranostics, 2021, 11(4): 1828-1844. doi: 10.7150/thno.48698 URL
[67]	Ren YS, Li HL, Piao XH, et al. Drug affinity responsive target stability(DARTS)accelerated small molecules target discovery: principles and application[J]. Biochem Pharmacol, 2021, 194: 114798. doi: 10.1016/j.bcp.2021.114798 URL
[68]	West GM, Tucker CL, Xu T, et al. Quantitative proteomics approach for identifying protein-drug interactions in complex mixtures using protein stability measurements[J]. Proc Natl Acad Sci USA, 2010, 107(20): 9078-9082. doi: 10.1073/pnas.1000148107 pmid: 20439767
[69]	Molina DM, Jafari R, Ignatushchenko M, et al. Monitoring drug target engagement in cells and tissues using the cellular thermal shift assay[J]. Science, 2013, 341(6141): 84-87. doi: 10.1126/science.1233606 pmid: 23828940
[70]	Savitski MM, Reinhard FBM, Franken H, et al. Tracking cancer drugs in living cells by thermal profiling of the proteome[J]. Science, 2014, 346(6205): 1255784. doi: 10.1126/science.1255784 URL
[71]	Islam A, Su AJ, Zeng ZM, et al. Capsaicin targets tNOX(ENOX2)to inhibit G1 cyclin/CDK complex, as assessed by the cellular thermal shift assay(CETSA)[J]. Cells, 2019, 8(10): 1275. doi: 10.3390/cells8101275 URL
[72]	Dziekan JM, Yu H, Chen D, et al. Identifying purine nucleoside phosphorylase as the target of quinine using cellular thermal shift assay[J]. Sci Transl Med, 2019, 11(473): eaau3174. doi: 10.1126/scitranslmed.aau3174 URL
[73]	Wang JJ, Weng QF, Yin F, et al. Interactions of destruxin A with silkworms'arginine tRNA synthetase and lamin-C proteins[J]. Toxins, 2020, 12(2): 137. doi: 10.3390/toxins12020137 URL
[74]	金金, 梁旭俊, 毕武, 等. 基于液相色谱-串联质谱技术鉴定药物靶标的研究进展[J]. 生命科学研究, 2022. DOI: 10.16605/j.cnki.1007-7847.2022.08.0187.
	Jin J, Liang XJ, Bi W, et al. Advances in the identification of drug targets based on liquid chromatography-tandem mass spectrometry[J]. Life Sci Res, 2022. DOI: 10.16605/j.cnki.1007-7847.2022.08.0187.
[75]	Li CH, Zhou Y, Tu PF, et al. Natural carbazole alkaloid murrayafoline A displays potent anti-neuroinflammatory effect by directly targeting transcription factor Sp1 in LPS-induced microglial cells[J]. Bioorg Chem, 2022, 129: 106178. doi: 10.1016/j.bioorg.2022.106178 URL
[76]	Hatstat AK, Quan BY, Bailey MA, et al. Chemoproteomic-enabled characterization of small GTPase Rab1a as a target of an N-arylbenzimidazole ligand's rescue of Parkinson's-associated cell toxicity[J]. RSC Chem Biol, 2022, 3(1): 96-111. doi: 10.1039/D1CB00103E URL
[77]	Ogburn RN, Jin L, Meng H, et al. Discovery of tamoxifen and N-desmethyl tamoxifen protein targets in MCF-7 cells using large-scale protein folding and stability measurements[J]. J Proteome Res, 2017, 16(11): 4073-4085. doi: 10.1021/acs.jproteome.7b00442 URL
[78]	Geer Wallace MA, Kwon DY, Weitzel DH, et al. Discovery of manassantin A protein targets using large-scale protein folding and stability measurements[J]. J Proteome Res, 2016, 15(8): 2688-2696. doi: 10.1021/acs.jproteome.6b00237 pmid: 27322910
[79]	Peng H, Guo HB, Pogoutse O, et al. An unbiased chemical proteomics method identifies FabI as the primary target of 6-OH-BDE-47[J]. Environ Sci Technol, 2016, 50(20): 11329-11336. doi: 10.1021/acs.est.6b03541 URL
[80]	郝海平, 叶慧, 皖宁, 等. 一种基于化学蛋白质组学的小分子靶标筛选方法及其应用:CN112485442A[P]. 2021-03-12.
	Hao HP, Ye H, Wan N. A Chemical proteomics Based Small Mole-cular Target Screening Method and Its Application:CN112485442A[P]. 2021-03-12.
[81]	Zhu YY, Wan N, Shan XN, et al. Celastrol targets adenylyl cyclase-associated protein 1 to reduce macrophages-mediated inflammation and ameliorates high fat diet-induced metabolic syndrome in mice[J]. Acta Pharm Sin B, 2021, 11(5): 1200-1212. doi: 10.1016/j.apsb.2020.12.008 pmid: 34094828
[82]	Deng GL, Zhou LS, Wang BL, et al. Targeting cathepsin B by cycloastragenol enhances antitumor immunity of CD8 T cells via inhibiting MHC-I degradation[J]. J Immunother Cancer, 2022, 10(10): e004874. doi: 10.1136/jitc-2022-004874 URL
[83]	Chan JNY, Vuckovic D, Sleno L, et al. Target identification by chromatographic co-elution: monitoring of drug-protein interactions without immobilization or chemical derivatization[J]. Mol Cell Proteomics, 2012, 11(7): M111.016642.
[84]	Schäkermann S, Wüllner D, Yayci A, et al. Applicability of chromatographic Co-elution for antibiotic target identification[J]. Proteomics, 2021, 21(1): 2000038. doi: 10.1002/pmic.v21.1 URL
[85]	Ramsay RR, Popovic-Nikolic MR, Nikolic K, et al. A perspective on multi-target drug discovery and design for complex diseases[J]. Clin Transl Med, 2018, 7(1): e3. doi: 10.1186/s40169-017-0181-2 URL
[86]	Chen JX, Song BA. Natural nematicidal active compounds: recent research progress and outlook[J]. J Integr Agric, 2021, 20(8): 2015-2031. doi: 10.1016/S2095-3119(21)63617-1 URL
[87]	Croston GE. The utility of target-based discovery[J]. Expert Opin Drug Discov, 2017, 12(5): 427-429. doi: 10.1080/17460441.2017.1308351 URL

小分子化合物 Small molecule compound	基于活性的探针结构 ABPs	靶蛋白 Protein target
Thieno[2,3-d]pyrimidine derivatives^[32]		Tubulin
Ebselen^[33]		β-lactoglobulin A
Clavulanic acid^[34]		Human serum albumin; Ig gamma-1 chain C region human; Haptoglobin human; Ig kappa chain C region human
Dihydroartemisinin^[35]		DNA methyltransferase 1
1,2,4-Oxadiazole derivatives^[36]		Rpn6
Prazosin^[37]		Flagellum Attachment Zone 1

小分子化合物 Small molecule compound	基于活性的探针结构 ABPs	靶蛋白 Protein target
Thieno[2,3-d]pyrimidine derivatives^[32]		Tubulin
Ebselen^[33]		β-lactoglobulin A
Clavulanic acid^[34]		Human serum albumin; Ig gamma-1 chain C region human; Haptoglobin human; Ig kappa chain C region human
Dihydroartemisinin^[35]		DNA methyltransferase 1
1,2,4-Oxadiazole derivatives^[36]		Rpn6
Prazosin^[37]		Flagellum Attachment Zone 1

小分子化合物 Small molecule compound	基于活性的探针结构 ABPs	靶蛋白 Protein target
Catechol estrogens^[43]		Cytochrome c; superoxide dismutase
Calenduloside E^[44]		Hsp90
Swertiamarin^[45]		AKT-PH
Salinipostin A^[46]		Lysophospholipase; exported lipase 2; esterase; a/β hydrolase; BEM4 6-like protein
Nitro-fatty acids^[47]		Extended synaptotagmin 2; signal transducer and activator of transcription 3; toll-like receptor 2; retinoid X receptor alpha; glucocorticoid receptor
Natural product: BE-43547A₂^[48]		Eukaryotic translation elongation factor 1

小分子化合物 Small molecule compound	基于活性的探针结构 ABPs	靶蛋白 Protein target
Catechol estrogens^[43]		Cytochrome c; superoxide dismutase
Calenduloside E^[44]		Hsp90
Swertiamarin^[45]		AKT-PH
Salinipostin A^[46]		Lysophospholipase; exported lipase 2; esterase; a/β hydrolase; BEM4 6-like protein
Nitro-fatty acids^[47]		Extended synaptotagmin 2; signal transducer and activator of transcription 3; toll-like receptor 2; retinoid X receptor alpha; glucocorticoid receptor
Natural product: BE-43547A₂^[48]		Eukaryotic translation elongation factor 1

小分子化合物Small molecule compound	探针结构ABPs	靶蛋白Protein target
Anticancer pyrroloquinazoline: LBL1^[53]		Nuclear lamins
Benzoxepane Derivatives^[54]		PKM2
7-oxocallitrisic acid^[54]		Carnitine palmitoyltransferase 1A
MCC₉₅₀^[55]		Carbonic Anhydrase 2
Protopanaxadiol^[56]		Retinoblastoma Binding Protein 4