The Impact of Activity‐Based Protein Profiling in Malaria Drug Discovery

Abstract

Activity‐based protein profiling (ABPP) is an approach used at the interface of chemical biology and proteomics that uses small molecular probes to provide dynamic fingerprints of enzymatic activity in complex proteomes. Malaria is a disease caused by Plasmodium parasites with a significant death burden and for which new therapies are actively being sought. Here, we compile the main achievements from ABPP studies in malaria and highlight the probes used and the different downstream platforms for data analysis. ABPP has excelled at studying Plasmodium cysteine proteases and serine hydrolase families, the targeting of the proteasome and metabolic pathways, and in the deconvolution of targets and mechanisms of known antimalarials. Despite the major impact in the field, many antimalarials and enzymatic families in Plasmodium remain to be studied, which suggests ABPP will be an evergreen technique in the field.

Strategies for Competitive Activity‐Based Protein Profiling in Small Molecule Inhibitor Discovery and Characterization

“…The ability to characterize small molecule activity against an enzyme class in native biological conditions can accelerate hit‐to‐lead and lead optimization [6a] . Since its initial introduction, the platform for competitive ABPP has been extended to encompass multiple detection strategies including optical, mass spectrometry, and qPCR [6a,11,39] . With limited throughput (compared to HTS), ABPP is not a practical strategy for screening diversity or other large compound collections; however recent applications demonstrate real promise for ABPP as a primary screen for focused libraries [12f] .…”

“…The third ABP building block is either a fluorescent reporter for detection of bound proteins or an affinity handle to enable biochemical enrichment of the target protein family. These can be included directly on the ABP (e. g., biotin) or in the form of a latent bioorthogonal group (e. g., alkyne) [6a,11] . As shown in Figure 1B, ABPs elaborated with a fluorescent reporter are readily used in gel‐based workflows, whereby proteins labeled in cellular extracts are separated by SDS‐PAGE followed by in‐gel fluorescence detection [26] .…”

“…Detection was initially based on visualization of gel‐separated proteins, with mass spectrometry (MS)‐based detection implemented not long thereafter [9–10] . ABPP has proven sufficiently powerful in ligand target identification and elucidating protein function that researchers have expanded on the original platform to include multiple activity probes and numerous detection schemes [6a,11] . Herein we provide an overview of competitive ABPP for profiling small molecule inhibitors.…”

Activity‐Based Protein Profiling of Oxidases and Reductases

“…In order to address these limitations, activity-based protein profiling (ABPP) was introduced by Cravatt, [7] which aims to measure only the catalytically active proteins within certain enzyme classes. ABPP has become a very valuable tool in chemical proteomics, [8][9][10][11][12][13] for the investigation of the mode of action and selectivity profile of drugs [14][15][16][17][18] and natural products. [19][20] It has been used to determine the activity profile of proteins in fields ranging from microbiology [21][22] to plant sciences.…”

Glutaraldehyde modified red blood cells delivering artesunate to the liver as a dual therapeutic and prophylactic antimalaria strategy

“…In malaria-free countries, precaution has also been taken through the use of malaria vaccines, vector control, research and diagnosis to prevent malaria recurrence. 3 There are four types of plasmodium that cause human malaria: Plasmodium ovale, Plasmodium falciparum, Plasmodium vivax, and Plasmodium malariae. 4 Plasmodium vivax is the most common species, and Plasmodium falciparum causes the most severe cases with high mortality rates.…”