Identification of protein binding partners of small molecules using label-free methods

ABSTRACT

Introduction: Drug discovery efforts across the globe are chasing new drug targets and novel mechanisms of action. To support the identification of novel mechanisms of action, phenotype-based drug screening has significantly increased over the last decade. Along with the rise in phenotypic screening, methods and technologies that can help to identify drug targets of phenotypically screened ‘hits’ have also evolved significantly.

Areas covered: This article provides an overview of successful examples, limitations and advances in small-molecule target identification methodologies. Primarily, the methods are described, where small-molecules without derivatization are used as test-molecules for identifying their direct binding protein partners, the targets, in detail. A brief discussion of other affinity chromatography coupled mass-spectrometry based target identification methods are also presented for comparative appreciation of label-free methods.

Expert opinion: Label-free methods do not require (a) extensive structure activity analysis of phenotypically screened ‘hits’ and (b) preparation of tool compounds or target capturing probes for target identification. These methods are significantly shortening the time required for the identification and the downstream validation of targets and hence are gaining popularity as the method of choice for target identification.

KEYWORDS:

• Chemical proteomics
• small molecule target identification
• target deconvolution
• phenotypic screening
• chemical biology
• mass spectrometry
• thermal proteome profiling
• DARTS
• SPROX
• UPT
• CETSA

Article highlights

• Phenotypic Screening ‘hits’ needs to go through the Target Identification Process.

• Target Identification processes that require derivatization of Bait Molecule, though successful, are resource and time consuming.

• Several Target Identification methods that use Label-free-bait-molecules such as TPP, DARTS, SPROX and UPT are under development.

• Unique Polymer Technology (UPT) can enrich the target using affinity chromatography workflow and hence is advantageous over other label-free methods.

• Identified Targets using any of the methods should be considered as putative targets only till the functional validation is achieved.

This box summarizes key points contained in the article.

Declaration of interest

C Saxena is the Chief Executive Officer of Shantani Proteome Analytics Pvt. Ltd. He has no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

Additional information

Funding

This manuscript has not been funded.