1. Quantifying the Stability of Acridines to Ribosomal G-Quadruplexes
Billy Nicholson1, Adam Green1,3, Samuel S. Cho1,2
Wake Forest University Dept. of Physics1 and Computer Science2
University of Tennessee Dept. of Chemistry3
Central Question
How can computational methods guide
rational drug design?
The Problem?
No G4 stabilizing drugs have been successful.
Need to understand drug:G4 interactions
Conclusions
(1) The antiparallel topology was determined to adopt a disordered
configuration due to the lack of planarity in the quartets after
simulation.
(2) Putative ribosomal G4s with shorter loops were found to be more
stable than those with long loops.
(3) We identified several acridines with amino groups, and the natures
of their specificities and relative stabilities were found to depend on the
rDNA G-quadruplex loop structures.
Abstract
G-quadruplexes (G4s) are involved in fundamental regulatory processes,
including those associated with cancer. G4s found in ribosomal DNA or
RNA (rDNA or rRNA) are a potential anticancer drug target through the
inhibition of RNA polymerase in ribosome biogenesis.
To quantify the stability of acridine drugs to putative ribosomal G4s, we
(A) modeled putative ribosomal G4s previously predicted using a
bioinformatics algorithm and CD spectra indicating parallel topologies,
(B) performed molecular docking and molecular dynamics (MD)
simulations of acridines to these putative ribosomal G4s, and
(C) quantified the stability of G4s using a novel approach that asses
planarity and base-base distances within G4 quartets and assessed
relative binding energies using NAMD energy.
We observed that ANO and AOO ligands stabilize parallel G4s better
than antiparallel G4s while the ANN ligand stabilized both topologies.
Ribosomal G-Quarduplexes
Guanine-rich single-stranded DNA may form a secondary structure
called a G-quadruplex (G4). G4s are temporary and are fundamental to
the cell’s regulation of gene expression. Stabilizing G4s found in
ribosomal DNA regions via drug binding may impair RNA polymerase
activity and inhibit ribosome biosynthesis.
G4s consist of stacked, square, and planar guanine quartets with cations
in the center channel. They are highly polymorphic.
Acridines
Acridines feature a polyaromatic face that stack on the outermost
tetrad. Amino or carboxyl side-chains selectively optimize the shape
and electrostatic complementarity of binding.
Computational Biophysics
Mathema cs
Physics Computer Hardware
Computer So ware
Chemistry
Biology
Molecular Docking & MD Simulations
:Molecular docking is a high-throughput method of generating binding
modes of acridines onto G4s. It ranks binding modes by stability using a
scoring function, but modes must be visually inspected for approval.
MD Simulations predict molecular interactions. The potential energies of
each atom are calculated and used to determine resulting trajectories.
Experiments
?
Unfolded Folded
Simula ons
Unfolded FoldedUnfolded Folded
Mode
Affinity
(kcal/mol)
1 -6.1
2 -6.1
3 -5.8
4 -5.8
5 -5.8
6 -5.8
7 -5.8
8 -5.8
9 -5.7
References
Rao, L., et. Al. “Interactions of Platinum-Modified Perylene Derivative with the Human
Telomeric G-Quadruplex.” J. Phys. Chem. B 115 (2011):13701-13712. Print.
Future Studies
(1) The stabilities of Acridines with shorter side-chains to ribosomal
G4s is currently being investigated.
(2) The stabilities of other putative ribosomal G4s and corresponding
acridine:G4 complexes are currently being investigated.
(3) Acridines that stabilize the most in silico will be tested in vitro by
the Bierbach Group, WFU Dept. Chemistry.
Novel Quantification of Stability
The torsional angles were measured to quantify planarity. The free
Energy of each angle was calculated to determine native state.
The base-base distances were measured as well. The free
Energy of each angle was calculated to determine native state.
Relative Binding Energies
To quantify and compare the binding strengths of each ligand to the G4,
the relative binding energies were calculated as follows
𝐸 𝑏𝑖𝑛𝑑𝑖𝑛𝑔 = 𝐸 𝐺4 𝑆𝑦𝑠𝑡𝑒𝑚 − 𝐸𝐴𝑐𝑟𝑖𝑑𝑖𝑛𝑒:𝐺4 𝑆𝑦𝑠𝑡𝑒𝑚
Where EG4 System and EAcridine:G4 System represent the energies of the entire
systems containing either the G4 or the Acridine:G4 complex as
measured by the program NAMD Energy.
Acknowledgments
Thank you to my mentor, Dr. Samuel Cho, for his continued guidance
and support. Thank you to Adam Green and Rongzhong Li.
Thank you to the WFU Center for Molecular Communication and
Signaling, which provided funding for this study.