Diego Sierra, Farrah Hmaidan, and Derek Sung
New Delhi metallo-ß-lactamase-1 (NDM-1) is an important enzyme that makes bacteria resistant to broad spectrum beta-lactam antibiotics. Bacteria that produce these types of enzymes are known as superbugs because bacterial infections that arise from them are difficult to treat. The potential dangers of untreatable disease associated with NDM-1 require urgent action from the drug developing sector in order to overcome bacterial antibiotic resistance. The research presented here combines wet and virtual lab techniques in order to find a new therapeutic drug molecule that would disrupt the function of NDM-1. The virtual component of this research consists of computationally screening a library of compounds for their ability to bind the active site of the crystal structure of the target enzyme NDM-1 as predicted by the GOLD molecular docking program. Initially a set of known binders as controls and random negative controls have been docked to validate the docking method. The libraries will contain a chemically diverse set of compounds from Maybridge Hitfinder (14,400 compounds) and ChemBridge (100,000). The predicted top scoring ligands will be analyzed and potentially acquired for further experiments in wet lab to determine in vitro binding ability and stability. The main wet lab techniques that will be used include: transformation in BL21 cells, expression, nickel-affinity purification, differential scanning fluorimetry (DSF) binding assay, and enzymatic assays. Through these experiments our team hopes to find a novel compound that inhibits the activity of NDM-1 and eliminates the antibiotic resistance that it gives to many organisms.
Comments
Very cool! On projects like this where there’s both a virtual and wet lab component, do y’all specialize in one side or another of the project, or do you get experience with both? —Rob Reichle
Great question! We actually get to experience both virtual and wet lab. They are both critical aspects to our research that complement each other. The idea is to use the results we obtain from virtual screening and test them in wet lab to analyze their viability. We typically focus on the ligands that have higher scores to test within lab to see if they perform the function we want it to (inhibiting the activity of NDM-1). —Farrah Hmaidan