Nifty Fifty Presentation 2010
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A presentation to high school students at Chula Vista High School, San Diego as part of nifty-fifty where scientists go into the high schools and try and excite students to a career in science. These slides describe my own particular career path.
![One Scientific Career (Computers in Biology) Philip E. Bourne PhD [email_address] http://www.sdsc.edu/pb http://www.sdsc.edu/~bourne](https://image.slidesharecdn.com/carreer-bourne-110106004059-phpapp02/85/Nifty-Fifty-Presentation-2010-1-320.jpg)
![The Life of One Scientist – The Early Years So That You Might Not Make the Same Mistakes ,[object Object],[object Object],[object Object]](data:image/gif;base64,R0lGODlhAQABAIAAAAAAAP///yH5BAEAAAAALAAAAAABAAEAAAIBRAA7)
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Nifty Fifty Presentation 2010
- 1. One Scientific Career (Computers in Biology) Philip E. Bourne PhD [email_address] http://www.sdsc.edu/pb http://www.sdsc.edu/~bourne
- 4. BSc (Hon) It was About Then I Began to Understand Myself – But I Still Made Mistakes
- 9. Some Things Stay with You Your Whole Life
- 18. The Growth of Data is A Major Driver in Biology Number of released entries Year
- 25. Need to Start with a 3D Drug-Receptor Complex - The PDB Contains Many Examples Computational Methodology Generic Name Other Name Treatment PDBid Lipitor Atorvastatin High cholesterol 1HWK, 1HW8… Testosterone Testosterone Osteoporosis 1AFS, 1I9J .. Taxol Paclitaxel Cancer 1JFF, 2HXF, 2HXH Viagra Sildenafil citrate ED, pulmonary arterial hypertension 1TBF, 1UDT, 1XOS.. Digoxin Lanoxin Congestive heart failure 1IGJ
- 26. A Reverse Engineering Approach to Drug Discovery Across Gene Families Characterize ligand binding site of primary target (Geometric Potential) Identify off-targets by ligand binding site similarity (Sequence order independent profile-profile alignment) Extract known drugs or inhibitors of the primary and/or off-targets Search for similar small molecules Dock molecules to both primary and off-targets Statistics analysis of docking score correlations … Xie and Bourne 2009 Bioinformatics 25(12) 305-312
- 29. SMAP p-value < 1e-5 drugs TB proteins p < 1e-7 p < 1e-6 p < 1e-5
- 31. Motivation
- 33. There Have Been a Few Ah Hah Moments
- 36. Life Is About Balance
Editor's Notes
- Tuberculosis, which is caused by the bacterial pathogen Mycobacterium tuberculosis , is a leading cause of mortality among the infectious diseases. It has been estimated by the World Health Organization (WHO) that almost one-third of the world's population , around 2 billion people, is infected with the disease. Every year, more than 8 million people develop an active form of the disease, which claims the lives of nearly 2 million. This translates to over 4,900 deaths per day , and more than 95% of these are in developing countries. Despite the current global situation, antitubercular drugs have remained largely unchanged over the last four decades. The widespread use of these agents has provided a strong selective pressure for M.tuberculosis, thus encouraging the emergence of resistant strains. Multidrug resistant (MDR) tuberculosis is defined as resistance to the first-line drugs isoniazid and rifampin . The effective treatment of MDR tuberculosis necessitates long-term use of second-line drug combinations , an unfortunate consequence of which is the emergence of further drug resistance. Enter extensively drug resistant (XDR) tuberculosis - M.tuberculosis strains that are resistant to both isoniazid plus rifampin, as well as key second-line drugs . Since the only remaining drug classes exhibit such low potency and high toxicity , XDR tuberculosis is extremely difficult to treat. The rise of XDR tuberculosis around the world imposes a great threat on human health , therefore reinforcing the development of new antitubercular agents as an urgent priority. Very few Mtb proteins explored as drug targets
- Purple circular nodes are TB proteins and green rectangular nodes are drugs Binding site similarity is indicated by connecting lines (‘edges’) between the TB proteins and drugs - proteins that are predicted to have similar binding sites are connected Edges are colored according to SMAP p-value i.e. the significance of the match (green<=1e-5, blue<=1e-6, red<=1e-7) The thickness of the edges corresponds to the number binding sites of a particular drug that match the TB protein, expressed as a proportion of the total no. of different binding sites of that drug Dashed lines indicate that although all drug binding sites were matched, there was only one binding site for that drug anyway