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UBC Theses and Dissertations

Developing bioinformatics tools and analyses on protein indels and protein-protein interactions : novel applications for drug discovery in Staphylococcus aureus Hsing, Michael


Infectious diseases caused by bacterial pathogens continue to be major public health concerns affecting millions of human lives annually, as conventional treatment via antibiotics has lost its effectiveness due to growing problems of drug resistance. Recent advancements in systems biology, high-throughout sequencing, protein interaction study and computer-aided drug development can offer possible solutions to antibiotic resistance through discovery of novel antimicrobials. The thesis describes several bioinformatics approaches that focus on protein interaction network (PIN) studies, analyses of targetable protein indels (insertions and deletions) and virtual compound screening for new antibacterial candidates – approaches integrated into an antibiotic discovery pipeline for methicillin-resistant Staphylococcus aureus (MRSA252). In the course of the described work we identified new drug targets corresponding to highly interacting proteins (hubs) through comprehensive PIN analysis in MRSA252. The advantage of using hub proteins as targets is established by their essentiality, non-replaceable PIN position and lower rate of mutation, all of which can help to counter bacterial resistance. To accelerate these studies hub predicting tools have been developed to assist proteomics experiments for PIN discovery and to facilitate drug target identification in pathogens. Because some bacterial proteins are conserved in humans, we applied the indel (insertion or deletion) concept to locate unique compound-binding sites that enabled us to specifically target conserved and essential bacterial hubs. We demonstrated associations between the presence of sizable indels in proteins with their essentiality and network rewiring capability, which established indels as potential markers for drug targets. To provide the research community a fast and user-friendly web portal for identification and characterization of indel-bearing drug targets, the Indel PDB database has been developed to characterize the functional and structural features of 117,266 indel sites across numerous species. Finally, combining the above bioinformatics methodologies with a rapid and efficient procedure of virtual screening allowed discovery of compounds that effectively inhibited MRSA252 cell growth with no signs of human toxicity. We anticipate that the drug discovery pipeline along with established MRSA PIN resource, hub prediction tools and indel database will provide a framework for the development of next-generation antibiotics in other existing or emerging pathogens.

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