Resolving the Ligand Binding Specificity in c-MYC G-quadruplex DNA: Absolute Binding Free Energy Calculations and SPR Experiment

ABSTRACT

We report the absolute binding free energy calculation and surface plasmon resonance (SPR) experiment for ligand binding with the cMYC G-quadruplex DNA. The unimolecular parallel DNA G-quadruplex formed in the c-MYC gene promoter regulates the transcription of c-MYC and is recognized as an emerging drug target for developing cancer therapy. Quindoline derivatives  stabilize the G-quadruplex and inhibit its expression in cancer cells. NMR experiments revealed two ligand-induced binding sites located at the 5’ and 3’ termini of the c-MYC G-quadruplex. Questions about which site is more favored and the basis for the ligand-induced binding site formation remain unresolved. Here, we employ two absolute binding free energy methods, the double decoupling (DDM) and the potential of mean force (PMF) methods, to dissect the ligand binding specificity in the c-MYC G-quadruplex. The calculated absolute binding free energies ranging from -8 kcal/mol to -11 kcal/mol are in general agreement with the experimental value derived from the SPR measurement (-8.94 kcal/mol). The results suggest that the quindoline compound has a small preference for the 5’-end binding site. Furthermore, the simulations show that the flanking residues involved in the two binding sites undergo significant reorganization as the ligand unbinds, which provides evidence for ligand-induced binding pocket formation. This study provides atomistic insights that help interpret experimental data and inform rational design of small molecules targeting the c-MYC G-quadruplex.

Blog #3 Combining Docking, Molecular Dynamics Simulation, and Free Energy Calculation to Improve the Accuracy of Virtual Screening of Drug Candidates Against HIV Integrase

Our group is honored to present a poster at the 38th Annual Meeting of the Society of Fellows on March 9, 2019.

The poster we presented includes an introduction section, graphs to show potential of mean force method (PMF) for computing binding free energy, steps for double decoupling method (DDM) for computing binging free energy, and a conclusion section. Our results suggest that quinoline binds 5′ end with a somewhat higher affinity.

It was an amazing experience to discuss our research with other faculty and student researchers.

Blog #2 Combining Docking, Molecular Dynamics Simulation, and Free Energy Calculation to Improve the Accuracy of Virtual Screening of Drug Candidates Against HIV Integrase

Our research group has done a few AMBER tutorials during the Fall 2018 semester, and we will meet twice a week during winter break to continue the research. These tutorials provided us information about how to use the AMBER software and how to run simulations efficiently. Tutorial B1 is one of them and it prepares our research group well for the future steps.

The goal of AMBER tutorial B1 is to simulate a DNA polyA-polyT Decamer. First we made sure that the required files prmtop, rst7, mdin are set up. Then we performed basic RMSd analysis and visualized the results with VMD. After that we used the Born implicit solvent model to run MD simulation for the DNA model. Last we used TIP3P explicit water to run production simulation.

Combining Docking, Molecular Dynamics Simulation, and Free Energy Calculation to Improve the Accuracy of Virtual Screening of Drug Candidates Against HIV Integrase

In order to be better prepared for the research, our group did Amber tutorial B0 as a start. Amber is the abbreviation for “Assisted Model Building and Energy Refinement.” It is a set of force fields that describe the potential energy function and parameters of the interaction of biomolecules. It also refers to a package of molecular simulation programs which includes source code and demos.

Our group worked on a computer with AmberTools v15, VMD, and xmgrace installed. The AMBER tutorial B0 asks us to run a molecular dynamics simulation and analyze the results. The steps include preparing topology and coordinate files, loading a protein and nucleic acid force field, building alanine dipeptide, solvating alanine dipeptide, minimizing input, running Amber MD sander, running minimization, running heating MD, and running production MD. Completing Amber tutorial enabled our group to become familiar with Linux and the Amber software.