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Newsletter | Spring 2014 ⋅ Number 61

Education Corner

Dr. Josh Beckham is an Assistant Director and Research Educator with the Freshman Research Initiative in the College of Natural Sciences at The University of Texas at Austin. He teaches computational and molecular biology techniques in the context of drug discovery for infectious diseases while fostering the development of the program and promoting external relations.

The Virtual Drug Screening Stream: research and discovery as undergraduates

by Josh Beckham, Ph.D.

Student researchers in the Virtual Drug Screening stream

Figure 1: A representation of an active site with small molecule
compounds arrayed around the protein to be docked
and scored by a virtual screening program.
Made in PyMol®.

Alyssa and Melissa pipetting in lab

Joshua presenting his research on a virulence phosphatase
in Mycobacterium tuberculosis at the NCUR 2012 conference.

Kathryn presenting her work on a fatty acid synthesis
enzyme (FabI) at the undergraduate poster session at UT-Austin

Imagine the impact of being able to do research in your first years of college. Would it have changed your career path? Would you have understood your coursework better and appreciated your undergraduate experience more? The value of research to an education in the sciences has been documented extensively 1,2 The challenge is being able to implement research on a large scale in a meaningful way for students of all backgrounds.

Students at The University of Texas at Austin that are in the FRI (Freshman Research Initiative) program have this opportunity. The FRI is a novel approach that brings the missions of education and research together. Initiated in 2005 by NSF funding and supported in part by the Howard Hughes Medical Institute (HHMI), the program involves over 800 freshmen and sophomores in research projects under both a tenured faculty member and a non-tenure track 'Research Educator' in courses that we call 'Streams'.

In my FRI class of approximately ~35 students called the Virtual Drug Screening stream, we carry out research in the context of drug discovery for infectious diseases. The challenge of drug discovery to successfully find new lead compounds is well known3. A powerful technique to speed up this process is virtual drug screening where molecular docking programs are used to score and rank the predicted binding interactions of small molecule compounds to a protein receptor. Ideally, the virtual screening software can filter out the low probability compounds and thereby minimize the number necessary to test in the wet lab using biochemical assays for validation and further characterization.

In the spring semester, students learn the fundamental skills of the research (making buffers and solutions, titrations, Beer's Law, molecular graphics software, docking software). In the summer and fall, they work on their individual or small group projects where they have chosen a disease of interest (e.g. Malaria, tuberculosis, African Sleeping sickness, Bubonic plague, Epidemic Typhus) and an enzyme within that organism that is essential for survival or virulence (e.g. fatty acid biosynthesis enzymes 3F9I, dihydrofolate reductases 3DAT, or host-pathogen signaling phosphatases 2Y2F). The students narrow their selection by those enzyme which have an available PDB crystal structure. These structures are then used as the inputs to make the receptors in the virtual screening software. Currently, GOLD4 and ICM5 are implemented on an in-house cluster (Ti-3D) here at UT Austin. The cluster has 64 parallel cores running CentOS with the Sun Grid Engine (SGE) for high throughput screens. Students will screen several thousand small molecule compounds against their target protein along with positive and negative controls ligands, if available. Novel virtual libraries from Chembridge® and Maybridge® are docked as well as the NIH Clinical Collection of compounds that have already been through a phase of clinical trials for other diseases. The chemical compounds with the highest virtual docking scores and that also satisfy Lipinski's Rule of Five 6 are purchased for validation and testing.

In parallel to their computational work, the class members carry out extensive wet lab work in pairs or teams. The coding DNA sequence (CDS) for their enzyme is synthesized via primer overlap PCR and cloned into a plasmid vector (pNIC-Bsa4), the protein expressed using a T7 promoter system, purified via nickel affinity chromatography using a 6xHIS tag, polished up with size-exclusion FPLC, and then assessed for purity and yield on an SDS-PAGE gels. Subsequently, spectrophotometric enzyme assays are performed to assess activity through absorbance of either the substrates or product of the enzyme's chemical reaction. These assays are then used to test whether the compounds from virtual screening will actually inhibit the enzyme activity and validate whether the virtual screening predictions were meaningful.

One of the most profound impacts that this type of research has is the way that students engage in multiple learning styles. With the virtual aspect of the work they are able to visualize protein structure and protein-ligand interactions with software such as PyMol7 and the RCSB PDB's Ligand Explorer viewer. In the wet lab, they are learning abstractly through the hands on experiments where they cannot see the molecular interactions taking place, but instead see the data from a PCR gel or a numerical output of absorbance from a spectrophotometer.

In addition to content learning, this course provides a point of early intervention for the students to become involved in research in a significant manner. Both anecdotally and as cited in many publications of STEM education, an early research experience captures the interest of students and leads to a more enriching environment.8 The sense of ownership that these students have in their projects leads them to be responsible for their own education instead of passively absorbing information in lecture-based classes or checking tasks off in a regular cookbook style lab. As a result of these factors, FRI program has been shown to raise student retention in science majors and increase the numbers that go on to successfully matriculate into graduate and professional schools.9 However, one of the best indicators of success for the program is the enthusiasm by the students when sharing their research.

Freshman Research Initiative
http://www.cns.utexas.edu/fri

REFERENCES

  1. The Boyer Commission on Educating Undergraduates in the Research University, Reinventing Undergraduate Education: A blueprint for America's Research Universities. New York, NY, 1998.
  2. Lopatto, D., Undergraduate research experiences support science career decisions and active learning. CBE Life Sci Educ 2007, 6 (4), 297-306.
  3. Shoichet, B., Virtual screening of chemical libraries. Nature 2004, 432 (7019), 862-5.
  4. Jones, G.; Willett, P.; Glen, R. C., Molecular recognition of receptor sites using a genetic algorithm with a description of desolvation. J Mol Biol 1995, 245 (1), 43-53.
  5. Abagyan, R. A.; Totrov, M. M.; Kuznetsov, D. N., ICM - a new method for protein modeling and design. Applications to docking and structure prediction from the distorted native conformation. J.Comp.Chem. 1994.
  6. Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeney, P. J., Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Deliv Rev 2001, 46 (1-3), 3-26.
  7. Schrödinger, L. The PyMOL Molecular Graphics System, Version 1.5.0.4.
  8. Russell, S. H.; Hancock, M. P.; McCullough, J., The pipeline. Benefits of undergraduate research experiences. Science 2007, 316 (5824), 548-9.
  9. Shear, R. I.; Simmons, S. L. In Teaching through research: Five-year outcome data from the Freshman Research Initiative at the University of Texas at Austin. , 67thSouthwest regional ACS meeting, Austin, TX, Austin, TX, 2011.