Virtual Drug Screening Stream (a.k.a. Virtual Cures)

Conducting basic research for the development of new therapeutics

Fig 1. Potential ligands arrayed around the active site of an enzyme as represented

with PyMol (Image courtesy of Kate Kavanagh, Ph.D.)

About:

Virtual Drug Screening (VDS) is the use of computational resources to more effectively and efficiently find compounds that may act as drugs. Virtual screening can be applied to discovering potential inhibitors of enzymes that are involved many different types of disease ranging from cancer, heart disease, diabetes, or epilepsy, to bacterial, viral or parasitic infection.

• • VDS is one of the many streams that make up the Freshman Research Initiative (FRI)

  • The original course was developed by Dr. Kate Kavanagh and the stream was originated by Dr. Jon Robertus but is now led by Dr. Fast. http://sites.utexas.edu/fast/

Motivation:

Proteins (and particularly enzymes) are at the heart of most disease processes. The ability to effectively target and inhibit their function within the cell provides an opportunity to mitigate the deleterious outcomes of disease states in humans. End point assessments of an inhibitor's potency through in vitro or in vivo wet lab methods is the true indicator of efficacy, however, these are very time consuming and expensive assays. Progressing a drug though initial binding assays, animal models and eventual human clinical trials can take 10-15 years and upwards of 800 million dollars. The VDS stream aims to implement a more efficient approach by using software programs to first understand the structural and chemical bonding relationships between the potential inhibitor drug and protein target. From these virtual arrangements, predictions can be made as to which molecules will bind the best while those with low scores are screened out. This method can be easily replicated and scaled up on the computer to analyze hundreds of thousands of molecules. Then the most likely drugs can be purchased and taken to the wet lab to validate their ability to inhibit the protein. In the VDS Stream, these experiments are done with absorbance and fluorescent based enzyme assays.

Current drug targets in the VDS stream:

Fig 2. Comparison of two binding architectures to a protein target (ribosome inhibiting protein - ricin). On the left is an adenine within the binding pocket of ricin. This adenine on ribosomes is the natural substrate for the ricin toxin. On the right is shown a protein molecule which acts as a potent inhibitor of the ricin toxicity due to its structural and chemical similarity to the natural substrate.

This course includes both wet labs and computational/computer-based labs. You will be learning basic techniques that are important in a research lab environment as well as the specific skills that are needed for this project.

Computer labs will initially be spent learning how to visualize and analyze protein structures and protein-ligand interactions. These will primarily use the program PyMol (http://www.pymol.org/)

Spring Labs Schedule

Week 1: Introduction and Literature assignment

Week 2: Buffer and reagent preparation with lab safety

Week 3: Analyzing structure: Pymol lab 1

Week 4: Light absorbance assay (Beer's Law)

Week 5: Analyzing structure: Pymol lab 2

Week 6: Buffer titration with pH

Week 7: Analyzing homologous structure: Pymol lab 3

Week 8: Virtual screening lab 1 (validation dock)

Week 9: Spring Break

Week 10: Bacterial protein expression

Week 11: Virtual screening Phosphatase Lab

Week 12: Protein purification

Week 13: Protein characterization

Week 14: Target Discovery

Week 15: Target Discovery con't

We spend about half of the spring course on virtual techniques and half on wet lab procedures. In the summer and fall, this ratio changes to about 80% wet lab and 20% virtual.