Activity-based probe

Activity-based protein profiling (ABPP) is a chemical proteomic strategy in which active-site-directed covalent probes are used to profile the functional states of enzymes in complex proteomes. Activity-based probes (ABPs) can distinguish active enzymes from their inactive zymogens or inhibitor-bound forms. They contain a reactive group intended to modify enzyme active sites covalently and a reporter group (typically rhodamine or biotin) that assists in detection and identification of protein targets. 

Fig. 6.13. Different designs of FRET sensors. (A) Substrates for hydrolytic enzymes. (B) Sensors for bond formation. (C) Sensors based on conformational or structural change. (D) Environmentally sensitive probes. (E) Quenched activity-based probe to monitor small molecule-enzyme interaction. (F) Small molecule-enzyme interaction using a labeled protein.

Fig. 6.14. Quenched activity based probe for the imaging of cathepsins. Upon covalent binding of the sensor to histidine and serine residues in the active site of the enzyme, the quencher is released and increased fluorescence indicates the now covalently labeled enzyme of interest. 

Blum, G., Mullins, S. R., Keren, K., Fonovic, M., Jedeszko, C., Rice, M. J., Sloane, B. F. and Bogyo, M. (2005). Dynamic imaging of protease activity with fluorescently quenched activity-based probes. Nat. Chem. Biol. 1, 203-209. 

Adam GC, Cravatt BF, Sorensen EJ. Profiling the specific reactivity of the proteome with non-directed activity-based probes. Chem Biol 2001 8 81-95. 

The greatly increased nucleophilicity of the catalytic serine distinguishes it from all other serine residues and makes it an ideal candidate for modification via activity-based probes [58]. Of the electrophilic probe types to profile serine hydrolases, the fluorophosphonate (FP)-based probes are the most extensively used and were first introduced by Cravatt and coworkers [38, 39]. FPs have been well-known inhibitors of serine hydrolases for over 80 years and were first applied as chemical weapons as potent acetylcholine esterase inhibitors. As FPs do not resemble a peptide or ester substrate, they are nonselective towards a particular serine hydrolase, thus allowing the entire family to be profiled. FPs also show minimal cross-reactivity with other classes of hydrolases such as cysteine-, metallo-, and aspartylhydrolases [59]. Furthermore, FP-based probes react only with the active serine hydrolase, and not the inactive zymogen, allowing these probes to interact only with functional species within the proteome [59]. Extensive use of this probe family has demonstrated their remarkable selectivity for serine hydrolases and resulted in the identification of over 100 distinct serine hydrolases... 

Heal WP, Dang TH, Tate EW (2011) Activity-based probes discovering new biology and new drug targets. Chem Soc Rev 40 246-257... 

Tully SE, Cravatt BF (2010) Activity-based probes that target functional subclasses of phospholipases in proteomes. J Am Chem Soc 132 3264-3265... 

Fonovic M, Bogyo M (2007) Activity based probes for proteases applications to biomarker discovery, molecular imaging and drug screening. CurrPharm Des 13 253-261... 

Kato D, Boatright KM, Berger AB et al (2005) Activity-based probes that target diverse cysteine protease families. Nat Chem Biol 1 33-38... 

Saghatelian A, Jessani N, Joseph A et al (2004) Activity-based probes for the proteomic profiling of metalloproteases. Proc Natl Acad Sci USA 101 10000-10005... 

Salisbury CM, Cravatt BF (2007) Activity-based probes for proteomic profiling of histone deacetylase complexes. Proc Natl Acad Sci USA 104 1171-1176... 

Wright AT, Song JD, Cravatt BF (2009) A suite of activity-based probes for human cytochrome P450 enzymes. J Am Chem Soc 131 10692-10700... 

Barglow KT, Cravatt BF (2006) Substrate mimicry in an activity-based probe that targets the nitrilase family of enzymes. Angew Chem Int Ed Engl 45 7408-7411... 

Blum G, von Degenfeld G, Merchant MJ et al (2007) Noninvasive optical imaging of cysteine protease activity using fluorescently quenched activity-based probes. Nat Chem Biol 3 668-677... 

Bogyo et al. [33] developed a set of activity-based probes inspired by the natural product E-64 for global analysis of activity patterns of the papain family of cysteine proteases. Instead of the agmatine moiety, the first generation of ABPP probes... 

Fig. 27 [S-Lactam activity-based probes inspired by commercial drugs...

Yee M-C, Fas CF, Stohlmeyer MM, Wandless TJ, Cimprich KA (2005) A cell-permeable, activity base probe for protein and lipid kinases. J Biol Chem 280 29053-29059... 

Keywords Activity-based probes Activity-based protein profiling Antibiotic resistance Catalomics Clostridium difficile Host-pathogen interactions Infectious disease Malaria MRSA Pathogens Virulence factors... 

Fig. 6 Structures of epoxide-based inhibitors and activity-based probes used in the study of falcipain 1...

Puri AW, Lupardus PJ, Deu E, Albrow VE, Garcia KC, Bogyo M, Shen A (2010) Rational design of inhibitors and activity-based probes targeting Clostridium difficile virulence factor TcdB. Chem Biol 17 1201... 

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