化学蛋白质组学在天然产物分子靶标鉴定中的应用

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

摘要/Abstract

摘要：

绿色新农药的开发和利用有利于农业的可持续发展，基于天然产物进行活性先导发现及作用机制研究是重要的新农药创制策略，然而其作用靶标和作用机制难以确定，阻碍了其在新农药中的应用。因此发现化合物新靶点对于新农药创制来说是一项既重要又艰巨的任务。化学蛋白质组学作为后基因组时代的新技术，目前已经成为研究药物靶点的重要手段之一。本文对基于化学蛋白组学的化合物作用分子靶点发现方法和典型案例进行探析，介绍这些技术的主要原理、应用以及各自的优点和局限性，旨在阐述基于化学蛋白质组学发现药物作用靶标的最新方法，并为天然产物靶点及新农药创制研究提供参考。

关键词: 化学蛋白组学, 药物靶点鉴定, 化学标记法, 非化学标记法, 天然产物

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

周璐祺, 崔婷茹, 郝楠, 赵雨薇, 赵斌, 刘颖超. 化学蛋白质组学在天然产物分子靶标鉴定中的应用[J]. 生物技术通报, 2023, 39(9): 12-26.

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.

图/表 7

图1 CCCP和ABPP化学蛋白质组比较

Fig. 1 Comparison of CCCP and ABPP chemical proteome

图2 基于亲和蛋白质组分析策略 A：与生物素偶联结合；B：基于生物正交反应基团（炔基）的探针；C：基于光亲和基团的生物探针

Fig. 2 Analysis strategies based on affinity proteomic A: Conjugated with biotin. B: Probes based on the bioorthogonal reactive groups（alkynyl）. C: Biological probes based on photoaffinity groups

图3 DTB 标签的分子结构

Fig. 3 Molecular structure of DTB label

表1 生物素探针用于小分子化合物的靶点鉴定实例

Table 1 Examples of biotin probes used for the target identification of small molecular compounds

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

表2 生物正交化学反应用于小分子化合物的靶点鉴定实例

Table 2 Examples of bioorthogonal chemistry for target identification of small molecular compounds

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

表3 光亲和探针用于小分子化合物的靶点鉴定实例

Table 3 Photoaffinity probe for the target identification of small molecular compounds

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

图4 非标记法识别药物靶标蛋白策略 A：药物亲和反应的靶点稳定性；B：蛋白质热稳定性分析；C：热蛋白质组分析；D：氧化蛋白稳定性

Fig. 4 Schematics of label-free target identification methods A: Drug affinity responsive target stability（DARTS）. B: Cellular thermal shift assay（CETSA）. C: Thermal proteome profiling（TPP）. D: Stability of proteins from rates of oxidation（SPROX）

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