Molecular Pull-Down Assay

Technical Services

NEORABIO

Technical Services

Molecular Pull-Down Assay
Molecular Pull-Down Assay
Neorabio's molecular pull-down assay service provides a targeted approach for identifying specific protein–small molecule interactions from complex biological samples. By combining affinity enrichment strategies with sensitive mass spectrometry analysis, this technique enables direct capture and characterization of binding partners from natural products, small-molecule libraries, cellular lysates, or tissue proteomes. Molecular pull-down assays are widely used in chemical biology, drug discovery, and mechanism of action studies for lead compound screening, target validation, and interaction network annotation (Hart et al., 2017; Lange et al., 2020).

About Services

Neorabio's molecular pull-down workflow integrates both target-to-drug and drug-to-target strategies to support diverse experimental designs. Purified target proteins or immobilized small molecules are incubated with compounds, natural product extracts, or complex proteomes, followed by affinity enrichment, elution, and high-resolution LC-MS/MS analysis to identify interacting partners. Optimized immobilization chemistries and appropriate controls are applied to minimize non-specific binding, with replicate analyses ensuring data robustness. Resulting spectra are interpreted using advanced bioinformatic tools to generate annotated candidate lists, confidence metrics, and structured reports detailing assay conditions and analytical rationale.

Key Advantages

Dual-mode workflow: Supports both target-to-drug and drug-to-target strategies
Custom affinity enrichment: Multiple immobilization options for diverse chemistries
High-resolution identification: Sensitive LC-MS/MS detection of bound species
Integrated analysis: Combined proteomic identification and data mining
Expert interpretation: Functional annotation and target insight support

Applications

Active compound screening from natural products or chemical libraries
Identification of protein targets for lead molecules
Mechanism of action studies in complex biological systems
Off-target and polypharmacology exploration
Interaction network mapping and tool compound validation

Workflow


Target-to-Drug Approach: Target protein expression & immobilization → Incubation with small molecules/natural product samples → Elution of bound small molecules → LC-MS/MS detection → Data analysis → Delivery of candidate compounds
Drug-to-Target Approach: Small molecule modification & immobilization → Incubation with proteome → Capture of binding proteins → Elution & detection → Data analysis → Delivery of potential targets

References

Hart T., et al. High-throughput profiling of protein–small molecule interactions by affinity enrichment and mass spectrometry. Nature Protocols, 2017, 12(7):1390–1414. DOI: 10.1038/nprot.2017.045
Lange E., et al. Applications of pull-down assays coupled with mass spectrometry in drug discovery. Journal of Proteomics, 2020, 211:103541. DOI: 10.1016/j.jprot.2019.103541
Bantscheff M., et al. Quantitative mass spectrometry in proteomics: A critical review. Annual Review of Analytical Chemistry, 2012, 5:109–130. DOI: 10.1146/annurev-anchem-061011-143114
Savitski M.M., et al. Measuring and managing ratio compression for accurate isobaric quantitative proteomics. Nature Methods, 2014, 11(11):1063–1068. DOI: 10.1038/nmeth.3035

Inquiry Center

Neorabio's molecular pull-down assay services are delivered by teams experienced in affinity enrichment, mass spectrometry, and interaction analysis. Each project begins with experimental design tailored to the molecule class and biological context, followed by controlled enrichment, LC-MS/MS acquisition, and data interpretation. Through rigorous quality controls and structured reporting, Neorabio provides reliable interaction insights that support mechanistic hypotheses and translational research decisions.
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