Background: The antimalarial drug discovery pipeline, despite its modest success, is constrained in its ability to adequately define drug target information and allow novel compounds to advance to clinical translation. Accurate and precise drug target ID requires combining multiple experimental approaches to deconvolute the correct target. Many clinically promising drugs fail due to poor efficacy, toxicity, or swiftly developed resistance, often as a result of overlooked or unclear drug mechanism of action during preclinical development. Novel pharmaceutics often require tailored approaches for drug target ID, as not every tool fits the job, and highlights why a library of experimental approaches are needed for drug target ID. Recent proteomics approaches provide unbiased, efficient methods for identifying drug targets, essential for deconvoluting drug mechanisms for clinical development.
Objective: To develop and apply multiple contemporary proteomics approaches for drug target identification and validation in malaria parasite drug development.
Methods and Results: We have applied new proteomics approaches in malaria parasites to contribute to the existing pool of methodology to confirm drug target ID. Specifically, we have established: (PELSA) protein local stability analysis: Identifies drug-protein interactions by observing differential proteolysis sensitivity in the proteome. (ABPP) Activity Based Proteome Profiling Chemo-proteomics: Using chemical probes that compete with drug binding we can interrogate drug binding sites by comparing enriched peptides of drug binding sites. (SEC-MS) Size-exclusion chromatography mass spectrometry: Employs chromatographic separation of the proteome with drugs and their targets and performs single fraction split proteomic and metabolomic profiling to infer drug binding interactions. These approaches have then been confirmed by the recently developed technique for antimalarial drug target ID (SPP) Solvent-Induced Proteome Profiling: Uses MS-based proteomics to identify molecular targets by observing drug-induced stabilization of target proteins. The above methods, coupled with the Orbitrap Astral MS, enhance target ID accuracy and bandwidth by adding to the pool of experimental techniques to confirm target ID and have successfully identified drug targets for various novel antimalarial compounds.
Conclusion: This study contributes significantly to techniques for drug target identification in malaria research using a range of omics-based approaches, supporting the characterization and development of novel drug candidates.