Metabolomics Provides Good Source of Small Molecule Biomarkers

biomarker methods

By Michael Sullivan, Senior Research Fellow, Worldwide Clinical Trials

Small molecule biomarkers provide insight into metabolic pathways related to therapeutic treatment and can help explain the mechanism of action during drug development for an array of therapeutic areas.


biomarker methods

The research area of metabolomics is a good source of candidates for potential small molecule biomarkers, just as larger molecule biomarkers are found in the proteome. These small molecular weight metabolites and substrate are used as tools to provide insight into the biochemical pathways relating to many different disease areas (see table below).

diseases and their biomarkers

Small molecule bioanalysis is usually performed using liquid chromatographic techniques coupled to mass spectrometric detection (LC-MS). This approach to biomarker analysis addresses the general challenges related to quantifying small molecules and provides low level quantitation, excellent selectivity, and fast separation from other small molecules. However, small molecule biomarkers are often endogenous to the control matrix that would otherwise be used for preparation of calibration samples, adding an additional challenge for quantification.

Pharmacokinetic and Biomarker Assay Development Share Similarities

Small molecule biomarker assay development is approached in a similar way to developing a small molecule pharmacokinetic (PK) assay. The advantages to this approach are:

  • Results tend to be extremely accurate (compared to ligand binding/radio-immunoassays).
  • Detection specificity is high due to mass selectivity (for LC-MS).
  • Detection sensitivity is high due to the elimination of background noise.

Method performance for PK assays are held to a high standard through a method validation process outlined by regulatory agencies (FDA, EMA). Criteria defining accuracy and precision limits of results are the foundation of these method validation standards. Biomarker assays used for the purpose of collecting data for regulatory submissions are commonly held to these same high performance standards. These biomarker data are typically collected during late stages of drug development and help:

  • Assess safety
  • Assess efficacy
  • Support dosing
  • Support other patient treatment (drug interactions, food effects, contraindications)

Biomarker Assay Performance Criteria may Change to Support Internal Decisions

There are situations where small molecule biomarker assay performance requires less stringent performance criteria. This is usually at an early stage of drug development and the purpose of the biomarker data is usually for internal decision making regarding:

  • Proof of concept for the mechanism of action
  • Viability of a drug candidate
  • Candidate screening

Most bioanalytical labs have procedures established for either approach. At Worldwide Clinical Trials there are standard operating procedures (SOPs) in place for method testing (including biomarker methods) to satisfy requirements from early to late stages of drug development.

biomarker methods

Under Fit-For-Purpose Qualifications, a lot of flexibility in assay performance is offered depending on the purpose of the data. In contrast, the SOP for Full Method Validation outlines what is needed for complete compliance with regulatory guidelines for accurate method performance.  

Small molecule biomarker assay development is a good compliment to traditional PK bioanalysis. The tools/instruments are the same across the two areas and the assays perform to very tight standards. Bioanalytical assays that have been developed at Worldwide Clinical Trials that are useful for various drug development programs are listed below.

biomarker methods

Learn More about our Bioanalytical Assay Development Methods

For more information about how our scientific team leverages metabolomics research in various therapeutic areas, or to learn more about biomarker and other small molecule bioanalytical methods available at Worldwide Clinical Trials, contact us here.


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