Using microbes to build better medicines

The Challenge

Despite advances in computational chemistry and structural biology, drug design remains exceedingly difficult. Approximately 90% of proteins in the human proteome remain “undruggable” (i.e., they lack an obvious pocket for a drug to bind), and over 50% contain disordered regions that preclude detailed crystallographic analysis. As a result of these challenges, many entire classes of important proteins lack targeted therapeutics of any kind.

Prevailing Challenges

1.Limited Molecular Search Space

Many compound libraries include molecules chosen for their synthetic accessibility, drug-like attributes (Lipinski's rule of five), or historical origin. Many molecular trajectories remain unexplored simply because they’re different.

2.Protein Motion

Proteins move, and their motion can reveal hidden sites that allow small molecules to control protein function from nonintuitive positions (e.g., a site distal to the active site of an enzyme). These sites, which are promising starting points for drug development, are challenging to find with existing biophysical methods.

3.Complex
Objectives

Small-molecule drugs can function by binding to a single protein, multiple proteins, or, perhaps, a protein in a special biophysical state. Screens for molecules that achieve these multifaceted objectives are challenging to assemble.

4.Scale Up

Once discovered, promising molecules must be synthesized in quantities sufficient for biochemical analysis, optimization, formulation, and clinical evaluation. For many interesting molecules, this synthesis is time-consuming and expensive.

Think Bioscience is using synthetic biology to address these challenges. With the aid of engineered microbial systems, we are developing therapeutics against elusive targets.

Platform Advantages

Molecular Diversity

Use biosynthetic machinery to explore a novel molecular search space in drug discovery.

Undruggable Targets

Discover small-molecule modulators of proteins that lack crystal structures, sample multiple conformations, or contain highly disordered regions.

Encoded Complexity

Design microbial systems to find bioactive compounds with improved efficacy and specificity.

Rapid Scale Up

Generate large quantities of promising molecules through simple fermentation.

Targets of Interest

Protein Tyrosine Phosphatases

PTPs catalyze the hydrolytic dephosphorylation of tyrosine residues and, together with protein tyrosine kinases (PTKs), contribute to a striking variety of diseases (e.g., diabetes, cancer, autoimmunity, neurological disorders, deafness, and heart disease). The human genome contains approximately 90 PTKs and over 100 PTPs. PTKs are targets of over 30 FDA-approved drugs. PTPs, which have charged, highly conserved active sites, lack targeted therapeutics of any kind.

Viral Proteases
& Deubiquitinases

Proteases catalyze the hydrolytic breakdown of proteins into smaller peptides and amino acids. They are centrally important to many physiological processes (e.g., digestion, blood clotting, and apoptosis), and contribute to numerous diseases (e.g., cancer, autoimmunity, and viral infections). Despite their success as therapeutic targets, proteases remain an important class of proteins for building new medicines.

Transcription
Factors

Transcription factors regulate the transcription of DNA into RNA. Anomalously regulated—or assembled—transcription factors contribute to autoimmune diseases and several types of cancer. Although approximately 10% of prescribed drugs target the nuclear receptor class of TFs, most promising TF targets have no approved therapeutics.

Other Undruggable
Targets

Our platform is target-agnostic. We are drawn to difficult targets, particularly those with ill-defined (e.g., disordered) structures, suboptimal (e.g., charged) binding sites, or conditional deleterious effects.

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