Natural Bioactive Compound Target Identification

Knowing the cellular targets of a drug is crucial for the process of drug discovery. Creative Biolabs offers a full spectrum of target identification service associated with bioactive natural compounds.

Two out of three major classes of currently used antifungals/antibacterials are derived from natural products, their derivatives, or mimics. Target identification and validation for natural agents are crucial for determining drug-target interactions and understanding the molecular mechanisms of actions. Our laboratory is devoted to employing a range of target identification strategies to determine compound targets, modes of action, and molecular mechanisms. The process to identify the molecular targets of active hits is also known as target deconvolution. Some chemical proteomics and chemical genetics related strategies can assist target deconvolution, together with conventional techniques.

Several techniques are provided for natural compound target identification:

Computer-Aided Target Identification and Validation

Creative Biolabs uses sophisticated computational software to help identify and confirm targets for a natural compound. We provide both structure-based and ligand-based method for data mining to increase the odds of identifying satisfying targets. Additional information we provide via this platform includes gene expression, proteomics, and transgenic phenotyping.

Affinity Chromatography

Affinity chromatography is a liquid chromatographic technique. It is widely used for purifying or separating biochemical mixtures based on highly specific interaction between two substances, e.g. antigen and antibody, enzyme and substrate, or receptor and ligand. In recent years, this technique has become increasingly important in defining the target proteins of a compound and understanding its mechanism of action. We use affinity selection to “fish” cellular targets from the entire proteome combined with mass spectrometry for protein structure determination.

Gene Expression Profiling

Creative Biolabs' highly qualified molecular biologists, geneticists, and bioinformaticians have significant experience in gene expression profiling. We provide comprehensive solutions for gene expression profiling and validation. This process is supported by technologies of DNA microarrays, transcriptome sequencing, digital PCR, and real-time PCR.

Gene Manipulation

We have exploited chemical-genomic strategies to systematic construct genome-wide clone sets of overexpression and deletion. The drug susceptibility clones related to specific genes can be rapidly mapped by these methods. Two strategies are used in this program:

• Downregulating or upregulating a particular gene.
• Gene conditional expression.

Figure 1. Methods for target identification (Farha and Brown, 2016)

Our natural compound target identification platforms include:

• High Throughput Screening: A target-based approach in which fluorescence-labeled synthetic genome proteins act as the primary source for detecting “yes” or “no” signal.
• High Content Screening: Cell-based screening relies on specific reporter genes.
• RNAi Screening and Antisense RNA-mediate gene downregulation: The reducing of gene product leads to the differential sensitivity to drugs. This platform is designed to screen growth inhibition of target strain.
• Gene Conditional Expression: This approach enables the identification of a set of genes that are essential for fungal pathogens.

Figure 2. Four platforms for natural compound target identification. (Farha and Brown, 2016)

For more detailed information, please feel free to contact us or directly sent us an inquiry.

Reference

1. Farha MA and Brown ED (2016). “Strategies for target identification of antimicrobial natural products”. Nat Prod Rep 33(5): 668-680. doi: 10.1039/c5np00127g.

For Research Use Only.