Text

theses

Fragment-based drug discovery (FBDD) is a relatively new approach for discovery of small molecule ligands for subsequent lead development. Here, libraries of relatively small molecules or fragments are screened against a target protein to identify hits with relatively weak binding affinity. Several approaches, which include fragment linking, merging, and expansion, can then be utilized to develop these hits into lead candidates. The intrinsically weak binding affinity of fragments requires screening techniques capable of detecting very weak non-covalent interactions with the protein. Biophysical methods, such as nuclear magnetic resonance (NMR), X-ray crystallography, and surface plasmon resonance (SPR), have been traditionally used for FBDD. X-ray crystallography, in particular, has been underappreciated due to major drawbacks associated with low throughput and labor associated. However, advancements in rapid, automated data collection has improved the throughput and reduced the labor associated with this approach. This thesis reports the development of a high throughput screening method using X-ray crystallography and its successful application as a primary screening tool to identify new compounds for lead development against viral drug targets. Specifically, screening was conducted against HIV-1 reverse transcriptase (RT), the catalytic core domain of HIV-1 integrase (IN CCD), and the cap-snatching endonuclease domain of influenza A. Screening revealed fragment binding to promising, druggable allosteric sites within HIV-1 RT and IN CDD. The availability of a three dimensional structure proved to be highly advantageous as it allowed for structure-based drug design (SBDD) to be pursued. Using this approach, a fragment hit identified to bind to the endonuclease domain of influenza was developed into a new class of endonuclease inhibitors with antiviral activity. This thesis not only details the results from each of the screening campaign but also highlights many key advantages of crystallographic fragment screening.

ETD_5021

Ph.D.

Includes bibliographical references

by Disha Patel

doi:10.7282/T34F1NSC

ETD doctoral

The author owns the copyright to this work.