Deciphering the structure and dynamics of quadruplex DNA and DNA-ligand complexes - PROJECT SUMMARY
The proposed research will improve the selectivity and efficacy of anticancer therapies by contributing new
knowledge about non-canonical G-quadruplex (GQ) DNA structure, and the interactions of GQs with small-
molecule ligands. Bioinformatics studies have identified 370,000 sequences with G-quadruplex-forming
potential in the human genome. There is now convincing biological evidence that GQs form in vivo and that
these structures regulate a variety of cancer-related biological processes, such as telomere protection,
oncogene expression, epigenetic modification, and DNA repair. Thus, GQ DNA has been firmly established as
an important therapeutic target for cancer. Small molecules that bind selectively to GQ DNA have been
identified, and some have been shown to inhibit tumor cells growth; however, exact mechanisms underlying
this inhibition are not known. Such small-molecule ligands may ultimately become lead compounds for the
generation of novel selective cancer drugs superior to conventional mutagenetic therapies. Unfortunately,
DNA-centered drug discovery programs suffer from limited structural information available for GQs, especially
in the presence of ligands. The situation is further complicated by high structural diversity of GQs, their
contradictory biological functions, and our limited ability to target a specific GQ folding topology.
To address these challenges, we propose to perform comprehensive crystallographic investigations
focused on telomeric and oncogene promoter G-quadruplexes, both alone and in complex with a variety of
small-molecule ligands. This work will be accompanied by spectroscopic and calorimetric studies of the
thermodynamic parameters of ligand binding to GQ DNA (e.g., stoichiometry, affinity, selectivity, driving
forces). The static structural view of GQs and GQ-ligand complexes will be complemented by rigorous kinetics
studies of ligand-assisted GQ folding and structural rearrangements. Kinetic information can help us identify
the timescale of G-quadruplex formation and thus biological processes that can be affected by the presence of
these structures. Chemical and structural features of ligands essential for G-quadruplex binding or structural
rearrangements will be identified from kinetics and structural studies. Furthermore, we propose chemical
modification to the scaffold of N-methylmesoporphyrin IX (NMM), which we showed displays unprecedented
selectivity for a parallel GQ fold, yet has modest binding affinity. The modifications should lead to new ligands
that retain this selectivity but have improved binding affinity. Ligands that display selective GQ interactions in
vitro will be tested in vivo for their biological effects, and genomic targets will be identified. Collectively, the
proposed work will enhance our understanding of GQ structural plasticity, supply coordinates for drug
discovery platforms, shed light on the origin of ligand selectivity for a specific DNA target, and guide the design
of novel highly selective anticancer therapies while providing transformative training to Swarthmore
undergraduate students.
