Activity-based proteomics

Activity-based proteomics, or activity-based protein profiling (ABPP) is a functional proteomic technology that uses chemical probes that react with mechanistically related classes of enzymes.^[1]

Fluorophosphonate-rhodamine (FP-Rhodamine) activity-based probe for profiling of the serine hydrolase superfamily. In this probe the fluorophosphonate is the reactive group (RG) as it binds irreversibly to the active-site serine nucleophile of serine hydrolases and the tag is rhodamine, a fluorophore for in-gel visualization.

Description

The basic unit of ABPP is the probe, which typically consists of two elements: a reactive group (RG, sometimes called a "warhead") and a tag. Additionally, some probes may contain a binding group which enhances selectivity. The reactive group usually contains a specially designed electrophile that becomes covalently-linked to a nucleophilic residue in the active site of an active enzyme. An enzyme that is inhibited or post-translationally modified will not react with an activity-based probe. The tag may be either a reporter such as a fluorophore or an affinity label such as biotin or an alkyne or azide for use with the Huisgen 1,3-dipolar cycloaddition (also known as click chemistry).^[2]

Advantages

A major advantage of ABPP is the ability to monitor the availability of the enzyme active site directly, rather than being limited to protein or mRNA abundance. With classes of enzymes such as the serine hydrolases^[3] and metalloproteases^[4] that often interact with endogenous inhibitors or that exist as inactive zymogens, this technique offers a valuable advantage over traditional techniques that rely on abundance rather than activity. Furthermore, ABPP could be used to target specific proteins which were previously viewed as undruggable targets.^[5]

Multidimensional protein identification technology

In-gel ABPP using probes with different fluorophores in the same lane to simultaneously profile differences in enzyme activities

In recent years ABPP has been combined with tandem mass spectrometry enabling the identification of hundreds of active enzymes from a single sample. This technique, known as ABPP-MudPIT (multidimensional protein identification technology) is especially useful for profiling inhibitor selectivity as the potency of an inhibitor can be tested against hundreds of targets simultaneously.^{[citation needed]}

ABPP were first reported in the 1990s in the study of proteases.^[6][7]

See also

• Mass spectrometry
• Proteomics
• Related inhibitors MAFP and DIFP
• Chemoproteomics

References

1. Berger AB, Vitorino PM, Bogyo M (2004). "Activity-based protein profiling: applications to biomarker discovery, in vivo imaging and drug discovery". American Journal of Pharmacogenomics. 4 (6): 371–81. doi:10.2165/00129785-200404060-00004. PMID 15651898. S2CID 18637390.
2. Speers AE, Adam GC, Cravatt BF (April 2003). "Activity-based protein profiling in vivo using a copper(i)-catalyzed azide-alkyne [3 + 2] cycloaddition". Journal of the American Chemical Society. 125 (16): 4686–7. doi:10.1021/ja034490h. PMID 12696868.
3. Liu Y, Patricelli MP, Cravatt BF (December 1999). "Activity-based protein profiling: the serine hydrolases". Proceedings of the National Academy of Sciences of the United States of America. 96 (26): 14694–9. Bibcode:1999PNAS...9614694L. doi:10.1073/pnas.96.26.14694. PMC 24710. PMID 10611275.
4. Saghatelian A, Jessani N, Joseph A, Humphrey M, Cravatt BF (July 2004). "Activity-based probes for the proteomic profiling of metalloproteases". Proceedings of the National Academy of Sciences of the United States of America. 101 (27): 10000–5. Bibcode:2004PNAS..10110000S. doi:10.1073/pnas.0402784101. PMC 454150. PMID 15220480.
5. Deng, Hui; Lei, Qian; Wu, Yangping; He, Yang; Li, Weimin (2020). "Activity-based protein profiling: Recent advances in medicinal chemistry". European Journal of Medicinal Chemistry. 191. doi:10.1016/j.ejmech.2020.112151. PMID 32109778.
6. Kam CM, Abuelyaman AS, Li Z, Hudig D, Powers JC (1993). "Biotinylated isocoumarins, new inhibitors and reagents for detection, localization, and isolation of serine proteases". Bioconjugate Chemistry. 4 (6): 560–7. doi:10.1021/bc00024a021. PMID 8305526.
7. Abuelyaman AS, Hudig D, Woodard SL, Powers JC (1994). "Fluorescent derivatives of diphenyl [1-(N-peptidylamino)alkyl]phosphonate esters: synthesis and use in the inhibition and cellular localization of serine proteases". Bioconjugate Chemistry. 5 (5): 400–5. doi:10.1021/bc00029a004. PMID 7849068.