Tuesday, May 20, 2014

Fragment-Based Lead Discovery

After doing some browsing regarding my cancer project, I came across a chemotherapeutic drug used to treat late stage malignant melanoma called Vemurafenib.  This particular targeted drug therapy was found through fragment-based lead discovery.  I had no idea what this drug discovery method entailed.  Fragment-based lead discovery is a new approach developed this decade that is increasingly used in the pharmaceutical industry. 

Previously used high-throughput screening (HTS) relies on the potency as the key component for observing a desired compound.  HTS was the leading operation of small molecule drug discovery until FBLD.  The desired compound is often referred to as the “hit compound”.  In the past, the pharmaceutical industry built large collections of highly functionalized compounds in an attempt to identify a sufficient number of hits.  Biopharmaceutical companies in then invested in liquid handling, robotics and read-out technologies to increase HTS efficiency.  Problems began to arise with HTS when hit compounds were producing drug-unlike properties.  In the past decade, researchers have faced the challenge of ensuring that the correct compounds are screened with HTS.  This method has provided scientist with very large screening libraries, but these libraries fall short of the potential chemistry diversity library.  It became more logical to screen for very small molecules and linking them to high-affinity binders.  Figure 1 represents a good comparison between HTS and FBLD.  First of all, this graph seems to represent a very broad generalization of molecular mass and potency of hit fragments.  Fragment hits will have a molecular mass of 120-380 with a lower potency of 1mM to 30uM.  While HTS hits tend to have a higher molecular mass with a much lower potency.  It seems as though lead molecules tend to be very potent for the actual size of the molecule.   

Figure 1:Range of molecular mass and potency for HTS hits and fragments superimposed on the typical requirement for drug candidates.  
Fragment based lead discovery does not rely on the potency of the compound as the driving force for hit compound selection, rather it emphasizes efficacy.  FBLD depends on the fitting of the hit compound to a binding site on the protein target.  This process starts by identifying small chemical fragments that weakly bind to the chemical target.  Then the small chemical fragments are grown and combined with the chemical targets to produce a lead with higher affinity, which exceed the criteria applied to the previously used HTS hits.  FBLD involves a strong component of target compound and ligand interaction.  Fragments are less likely to contain interfering compounds that block affinity.

Methods involved with identifying and validating weak binding fragments can be very difficult to practice.  The first step is to build a library with fragments typically smaller than HTS compounds.  Then methods like functional or direct bind assays procedures at high concentrations may be used.  Described in this article, a research group isolated a small set of fragments at 1mM with a common linkage group in an attempt to find inhibitors for a particular kinase.  The fragments were joined from the common linkage group using five different linkers and then rescreened to find the most potent inhibitors.  The second approach involved with FBLD is NMR based screening.  NMR stands for nuclear magnetic resonance and provides information regarding the compound by nuclei absorbing and re-emitting energy at a particular frequency.  In regards to FBLD, mass spectrometry has been used to detect the binding of non-covalent weak fragments to RNA.  X-Ray crystallography has been used to identify the complete structure of the small fragment binding to the target ligand.   

Work Cited.
Erlanson, Daniel A., Dr. "Fragment-Based Drug Discovery." Santa Clara University. Journal of Medicinal Chemistry, 11 Feb. 2004. Web. 20 May 2014. <http://pubs.acs.org.libproxy.scu.edu/doi/pdf/10.1021/jm040031v>.

Barker, John, Dr., Thomas Hesterkamp, Dr., and Mark Whittaker, Dr. "Integrating HTS and Fragment-based Drug Discovery. Summer 08."Drug Discovery World. DDW, June-July 2008. Web. 20 May 2014. <http://www.ddw-online.com/screening/p92852-integrating-hts-and-fragment-based-drug-discoverysummer-08.html>.