Fragment-based screening (FBS), also known as fragment-based drug discovery (FBDD), is a strategy used in the pharmaceutical industry to identify new therapeutic compounds. This approach finds small molecular building blocks that can be developed into novel medicines. Its goal is to efficiently explore chemical space to discover molecules that interact with specific disease-related proteins.
What Are Fragments
Fragments in drug discovery are small organic molecules, typically composed of 10 to 20 atoms, with a molecular weight generally less than 300 Daltons. These molecules are designed to be simple yet diverse in their chemical structure, often adhering to the “rule of three,” which suggests a molecular weight under 300, a partition coefficient (ClogP) under 3, and fewer than three hydrogen bond donors or acceptors. Their small size provides an advantage, as it increases the likelihood of them fitting into various binding pockets on a target protein, enabling a more thorough exploration of potential interaction sites.
While fragments bind weakly to their target proteins, typically with millimolar (mM) to micromolar (µM) affinities, their simplicity means that each atom contributes significantly to the binding interaction. This “atom-efficient” binding quality allows for greater flexibility in modifying their physicochemical properties later in the drug development process. In contrast, traditional drug-like molecules are larger and more complex, generally weighing around 500 Daltons, and are screened for stronger nanomolar affinities.
How Fragment Screening Works
Fragment screening involves testing a library of small fragments against a specific biological target, such as a protein implicated in a disease. The aim is to identify fragments that bind to the target, even if the binding is initially weak. These fragment libraries are considerably smaller than those used in traditional high-throughput screening, often containing a few thousand compounds instead of millions.
Due to the weak binding affinities of fragments, highly sensitive biophysical techniques detect their interactions with the target protein. Common methods include Nuclear Magnetic Resonance (NMR) spectroscopy, which detects fragment binding and characterizes the binding mode, and Surface Plasmon Resonance (SPR), a label-free technique that measures binding kinetics. X-ray crystallography is also used to validate hits by determining the precise binding mode of the fragment within the protein’s structure.
Developing Fragment Hits
Once initial fragment “hits” are identified, the process shifts to “fragment evolution” or “fragment growth.” This involves modifying or linking these small fragments to create more potent and specific drug candidates. This iterative process aims to improve the binding strength and overall drug-like properties. Structural information about how the fragments bind to the target protein, often obtained through techniques like X-ray crystallography, guides these modifications.
Scientists can grow a fragment by adding chemical groups, or link two or more weakly binding fragments that bind to adjacent or overlapping sites on the target protein. This merging or linking strategy creates a larger molecule with increased affinity due to more numerous binding interactions. The goal is to optimize properties like binding strength, solubility, and metabolic stability, ensuring the resulting compounds are synthesizable and retain favorable drug-like characteristics.
Why Fragment-Based Screening Matters
Fragment-based screening offers several advantages over traditional high-throughput screening (HTS) of larger molecules. One benefit is its efficiency; fragment libraries are much smaller, often a few hundred to a few thousand compounds, compared to millions in HTS libraries. This reduced library size allows for a more extensive exploration of chemical space because smaller fragments can fit into a wider variety of binding pockets.
FBS also yields higher “hit rates,” meaning it is more likely to identify initial binders to a target protein. While these initial interactions are weak, they are often of higher quality, with each atom in the fragment contributing meaningfully to the binding. This approach has been instrumental in discovering novel chemical scaffolds that might be overlooked by other methods, accelerating drug discovery, and enabling the development of treatments for challenging targets, including those previously considered “undruggable.”