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Bioinformatics

Bioinformatics. Ayesha M. Khan Spring 2013. Phylogenetic software. PHYLIP http://evolution.genetics.washington.edu/phylip.html. In silico drug design Help in identifying and analyzing drug targets via bioinformatics tools. Computer aided drug design (CADD)

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Bioinformatics

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  1. Bioinformatics Ayesha M. Khan Spring 2013

  2. Phylogenetic software PHYLIP http://evolution.genetics.washington.edu/phylip.html

  3. In silico drug design • Help in identifying and analyzing drug targets via bioinformatics tools. • Computer aided drug design (CADD) • Specialized discipline that uses computational methods to simulate drug interactions • Dependent on bioinformatics tools, applications and databases.

  4. Structural Bioinformatics • Bioinformatics offers a means to obtain a structure through sequencewhile structure aided drug design offers a means to get a drug through structure. • In particular bioinformatics and structure based drug design are providing important information about the structure, function and pharmaceutical potential of many earlier unknown or uncharacterized proteins and ligands. • “Structural bioinformatics” (SBI) • A subset of bioinformatics concerned with the use of biological structures-proteins, DNA, RNA, ligands, etc., and complexes thereof to strengthen our understanding of biological systems.

  5. SBI in Drug Design and Discovery • SBI can be used to examine: • drug targets (usually proteins) • binding of ligands ↓ “rational” drug design (benefits = saved time and $$$)

  6. Traditional Methods of Drug Discovery natural (plant-derived) treatment for illness/ailments ↓ isolation of active compound (small, organic)

  7. synthesis of compound ↓ manipulation of structure to get better drug (greater efficacy, fewer side effects) Aspirin

  8. Modern Drug Discovery Process • Drug discovery process begins with a disease(rather than a treatment) • Use disease model to pinpoint relevant genetic/biological components (i.e. possible drug targets) • If little known about the disease  test procedures usually depend on animal models.

  9. Modern Drug Discovery Process disease→genetic/biological target ↓ discovery of a “lead” molecule - design assay to measure function of target - use assay to look for modulators of target’s function ↓ high throughput screen (HTS) - to identify “hits” (compounds with binding in low nM to low μM range)

  10. Modern Drug Discovery Process small molecule hits ↓ manipulate structure to increase potency ↓ optimization of lead molecule into candidate drug fulfillment of required pharmacological properties: potency, absorption, bioavailability, metabolism, safety ↓ clinical trials

  11. Interesting facts • Over 90% of drugs entering clinical trials fail to make it to market • The average cost to bring a new drug to market is estimated at $770 million

  12. Impact of Structural Bioinformaticson Drug Discovery Speeds up key steps in DD process by combining aspects of bioinformatics, structural biology, and structure-based drug design

  13. human genome “druggable genome” = subset of genes which express proteins capable of binding small drug-like molecules polysaccharides nucleic acids proteins lipids proteins with binding site

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