Using Docking as a Driver of Hypothesis Formation in an Undergraduate Biochemistry Lab Course
Mentor:blake gillespie, Associate Professor of Chemistry, CSU Channel Islands
Enzyme inhibition is a staple component of the undergraduate biochemistry lab curriculum. We are augmenting what is often a 'canned' exercise by building in a hypothesis-driven component. Biochemistry students rank potential inhibitors of Gallus gallus Lactate Dehydrogenase A (LDH-A) by docking a small set of target molecules into a known LDH-A structure using the widely available molecular graphics software package ICM. The small molecule ligand with the highest score is predicted to be the strongest competitive inhibitor; the lowest score is predicted to be the weakest. These rankings are then tested empirically in the laboratory section of the course. We have observed that Ki for a series of oxamic acid derivatives, mimicking the natural substrate pyruvate, show that the inhibitors' Ki's increase with derivative volume. This correlates with binding energies calculated from docking simulations, and suggests that inhibition becomes weaker as inhibitors get bulkier. While positive results support and augment the course's learning objectives, unexpected results are often also 'teachable', revealing misconceptions about potential competitive inhibitors. Though the current work focuses on a single enzyme system, the method may be applied to many instructional-laboratory targets.