Kinetic characterization of potential inhibitors of DEAH/RHA Family Helicase 36 (DHX36) for the disruption of c-MYC G-Quadruplexes

G-Quadruplexes (G4s) are nucleic acid secondary structures formed in guanine rich sequences. They frequently occur in the promoter regions of human oncogenes and play an important role in regulating gene expression and cancer. c-Myc is a proto-oncogene with a G4 forming sequence in its promoter region, and the stabilization of this G4 has been shown to prevent overexpression of c-Myc that could lead to tumorigenesis. DEAH/RHA family helicase 36 (DHX36) is the dominant G4 resolvase in human cells, and efficiently disrupts G4 structures through a translocating ATP dependent pathway. Inhibiting the ability of DHX36 to bind and disrupt this c-Myc G4 shows promise as an anticancer drug target. 10 small molecule inhibitors were rationally designed and synthesized by collaborating labs using the crystal structure of the c-Myc G4. Utilizing fused cyclic aromatic backbones, these small molecules are proposed to function as inhibitors of G4 and DHX36 interactions by binding to the planar surface at the 3’ or 5’ end of the G4 structure and potentially interfering with the formation of the DHX36-G4 complex. One of these small molecule inhibitors, arbitrarily named JL205, is a previously known inhibitor and is used as a positive control and reference point for inhibition for this project. Interactions between DHX36 and the c-Myc G4 in the presence and absence of each small molecule inhibitor were kinetically characterized in discontinuous enzyme assays to identify the effects of the small molecule on G4 disruption by DHX36. Two assay models with varying order of addition were used to observe the effect of the small molecule inhibitor before versus after the formation of the DHX36-G4 complex. The arbitrarily named small molecule B17 showed the highest level of consistent inhibition out of the nine unknown small molecules, but was found to be much less potent than the known inhibitor JL205. Order of addition had no observed effect on the inhibitory capabilities of B17 and JL205, and the additional eight inhibitors lacked sufficient evidence for inhibition overall.