Chemical Genetics and Drug Target Discovery

Jay Yang
Singer Instruments, Roadwater, TA23 0RE.


Chemical genetics is the study of genes through small-molecule perturbation. Chemical genetic screening is a phenotypic screening methodology that systematically tests the efficacy of thousands of small molecules simultaneously.  It is superior to  target-based screening methodology for drug discovery because chemical genetic screening  is unbiased and screens chemicals directly in complex cellular environment. Therefore, chemical genetic screening is an efficient way to discover and validate new drugable targets and identify potentially efficacious therapeutics.

The theory behind chemical genetic screening

Chemical probes are cell permeable small molecules which potently inhibit protein function. Modern methods for identifying chemical probes rely on the screening of thousands of chemicals against a target(s) of interest in vitro (Figure 1A).  However, this approach is ineffective, and the number of approved new drugs for treating human diseases has been in steady decline over the past decade.  This is because in  target-based screening where the target is pre-defined and drug-target interactions are conducted in vitro, the potency of the chemical in vitro rarely translates to low-dosage and high specificity efficacy in vivo.  It also limits our ability to discover other drug targets (1).

A: The target-based approach begins with the selection of a protein target based on its relevance to a disease state. Then, a high-throughput screen is set up to look for chemicals that modulate target protein activities. Interesting hits are then validated and modified to
improve its efficacy.

B: On the other hand, with the chemical genetics approach, a large chemical library is screened in a cell-based assay to find bioactive molecules for a disease state. After validation and modification, most interesting hits are subject to subsequent assays to identify cellular targets.

Phenotypic screening in model organisms is an alternative approach for discovering new small-molecule therapeutics which address the aforementioned shortfalls of current methodologies (Figure 1B).  Phenotypic screening is a method for the systematic, unbiased, and parallel testing of thousands of molecules for a desired cellular phenotype.  Employing cell-based phenotypic screening addresses two drawbacks specifically associated with the conventional target-based screening methods.  Firstly, screening using a cell-based assay directly measures drug potency in a complex cellular environment, which allows for the early assessment of the biological activities and off-target potential of a drug candidate.  Secondly, screening for chemicals that alter the entire cellular pathway bypasses the bias of target pre-selection, leading to the unbiased discovery of new druggable targets (2).

Principles of chemical genetics in drug discovery

Two criteria must be met in a drug discovery process (3).  Firstly, large chemical libraries must be screened to identify biologically active compounds that elicit the desired phenotype.  Secondly, once the compounds are found, the relevant protein targets need to be identified.  Chemical genetics can specifically address these two areas in drug discovery (Figure 2)

A cell-based assay is established to screen for chemicals that induce a particular cellular phenotype. Once the hits from the primary screen are validated, the cellular targets of the most interesting hits are then identified using various genetic assays.

Compound screening

In a typical screen to identify bioactive compounds, a diverse library of compounds is applied to the cells that mimic a particular disease state, causing perturbations to different cellular pathways and resulting in phenotypic responses.  Compounds that specifically elicit desired phenotypes will be identified and subjected to follow-up studies to identify their protein targets (4).