Drug target discovery by magnetic nanoparticles coupled mass spectrometry

Abstract

Drug target discovery is the basis of drug screening. It elucidates the cause of disease and the mechanism of drug action, which is the essential of drug innovation. Target discovery performed in biological systems is complicated as proteins are in low abundance and endogenous compounds may interfere with drug binding. Therefore, methods to track drug-target interactions in biological matrices are urgently required. In this work, a Fe₃O₄ nanoparticle-based approach was developed for drug-target screening in biofluids. A known ligand-protein complex was selected as a principle-to-proof example to validate the feasibility. After incubation in cell lysates, ligand-modified Fe₃O₄ nanoparticles bound to the target protein and formed complexes that were separated from the lysates by a magnet for further analysis. The large surface-to-volume ratio of the nanoparticles provides more active sites for the modification of chemical drugs. It enhances the opportunity for ligand-protein interactions, which is beneficial for capturing target proteins, especially for those with low abundance. Additionally, a one-step magnetic separation simplifies the pre-processing of ligand-protein complexes, so it effectively reduces the endogenous interference. Therefore, the present nanoparticle-based approach has the potential to be used for drug target screening in biological systems.

Keywords: Drug-target discovery; Mass spectrometry; Nanoparticle.

Graphical abstract

Fig. 1

TEM images of 100 nm nanoparticles (NPs) with (A) 50 nm scale and (B) 100 nm scale; (C) chemical structure of obeticholic acid (OCA); (D) UV absorption of OCA, NPs and OCA-NPs (100 nm).

Scheme 1

Ligand-target discovery by designed Fe₃O₄ NP-based strategy. NP: nanoparticle; UV: ultraviolet; RT: room temperature; lC-MS/MS: liquid chromatography-tandem mass spectrometry.

Fig. 2

(A) Identification and relative quantification of proteins obtained from supernatant or decomposed from OCA-NPs/NPs; and (B) LBD sequence coverage results of each sample. OCA-NP-S: supernatant of OCA-NP treated cell lysate; OCA-NP-P: proteins decomposed from OCA-NPs; NP-S: supernatant from NP treated cell lysate; NP-P: proteins decomposed from NPs; OCA: obeticholic acid; NP: nanoparticle.

Fig. 3

Immunoblotting of proteins obtained from supernatant or decomposed from OCA-NPs/NPs (15 nm). NP-P: proteins decomposed from NPs; OCA-NP-P: proteins decomposed from OCA-NPs; NP-S: supernatant from NP treated cell lysate; OCA-NP-S: supernatant of OCA-NP treated cell lysate; OCA: obeticholic acid; NP: nanoparticle.