It’s not enough to design new drugs.
For drugs to be effective, they have to be delivered safely and intact to affected areas of the body. And drug delivery, much like drug design, is an immensely complex task. Cutting-edge research and development like that conducted at the U.S. Department of Energy’s Oak Ridge National Laboratory can help solve some of the challenges associated with drug delivery.
In fact, ORNL researchers and collaborators at Wayne State University recently used a unique combination of experimentation and simulation to shed light on the design principles for improved delivery of RNA drugs, which are promising candidates in the treatment of a number of medical conditions including cancers and genetic disorders. Specifically, the research team discovered that the motions of a tRNA (or transfer RNA) model system can be enhanced when coupled with nanodiamonds, or diamond nanoparticles approximately 5 to 10 nanometers in size.
Nanodiamonds are good delivery candidates due to their spherical shape, biocompatibility and low toxicity. And because their surfaces can be easily tailored to facilitate the attachment of various medicinal molecules, nanodiamonds have tremendous potential for the delivery of a vast range of therapies.
The discovery involved ORNL’s Spallation Neutron Source, which provides the most intense pulsed neutron beams in the world for scientific research and industrial development, and ORNL’s Titan supercomputer, the nation’s most powerful for open science -- a one-two punch for illuminating the physical properties of potential drugs that inform new design principles for safer, improved delivery platforms.
By comparing the SNS neutron scattering data with the data from the team’s molecular dynamics simulations on Titan, the researchers have confirmed that nanodiamonds enhance the dynamics of tRNA when in the presence of water. This cross-disciplinary research was profiled in Journal of Physical Chemistry B.
The best of both worlds
The project began when ORNL’s P. Ganesh and Xiang-Qiang Chu of Wayne State University wondered how the water-phobic surfaces of nanoparticles alter the dynamics of biomolecules coated with water, and if it might be something that they could eventually control. They then formed a team including Gurpreet Dhindsa, Hugh O’Neill, Debsindhu Bhowmik and Eugene Mamontov of ORNL and Liang Hong of Shanghai Jiao Tong University in China to observe the motions of hydrogen atoms from the model system, tRNA, in water using SNS’s BASIS neutron backscattering spectrometer, SNS beam line 2.
Hydration is essential for biomolecules to function, and neutrons are excellent at distinguishing between the motions of hydration water molecules and the biomolecule they are surrounding. Therefore, by measuring the atoms’ neutron scattering signals, the team was able to discern the movement of tRNA in water, providing valuable insight into how the large molecule relaxes in different environmental conditions.
After comparing the results of the individual atoms, it was clear that the nanodiamonds were having a profound effect on their companion RNA molecules. The results were somewhat baffling because similar experiments had demonstrated that companion solid materials (such as nanodiamonds) tended to dampen biomolecule dynamics. Surprisingly however, nanodiamonds did the opposite for tRNA.
“Scientists are always interested in the bio-nano interactions,” said Chu. “While the interfacial layer of the bio-nano systems has very distinctive properties, it is very hard to study this mysterious zone without neutron scattering, which only sees hydrogen.”
To realize the potential of nanodiamonds in the delivery of biomolecules using tRNA as a model, the team turned to Titan to shed a much-needed light on the underlying physics.
“Molecular dynamics simulation can really tell those stories that current experimental advancement might not be able to,” said Bhowmik of ORNL’s Computational Science and Engineering Division, who set up and conducted the simulations alongside Monojoy Goswami of the laboratory’s Computer Science and Mathematics Division and Hong of Shanghai Jiao Tong University. “By combining these two techniques, you can enter a whole new world.”
These simulations revealed that the “weak dynamic heterogeneity” of RNA molecules in the presence of nanodiamonds was responsible for the enhanced effect. In other words, the reactions among the nanodiamonds, water and the RNA molecule forms a water layer on the nanodiamond surface, which then blocks it and prevents strong RNA contact to the nanodiamond.
Since RNA is hydrophilic, or “likes water,” the molecules on the nanodiamond surface swell with excess hydration and weaken the heterogeneous dynamics of the molecules.
“You can fine-tune these dynamics with chemical functionalization on the nanodiamond surface, further enhancing its effectiveness,” said Goswami.
The findings will likely guide future studies not only on the potential of nanodiamonds in drug delivery but also on fighting bacteria and treating viral diseases.
Building the bridge
Using simulation to confirm and gain insight into experiments is nothing new. But mimicking large-scale systems precisely is often a challenge, and the lack of quantitative consistency between the two disciplines makes data comparison difficult and answers more elusive to researchers.
This lack of precision, and by extension lack of consistency, is largely driven by the uncertainty surrounding force-field parameters or the interaction criteria between different particles. The exact parameters are scarce for many macromolecules, often forcing researchers to use parameters that closely, but not exactly, match the experiment.
Miscalculating the precision of these parameters can have major consequences for the interpretation of the experimental results.
To ensure the calculations were correct, Goswami worked with Jose Borreguero and Vickie Lynch, both of ORNL’s Neutron Data Analysis and Visualization Division and Center for Accelerated Materials Modeling, to develop a workflow optimization technique known as Pegasus. This method compares molecular dynamics simulations with neutron scattering data and refines the simulation parameters to validate the results with the proper experimental precision.
“Using the Pegasus workflow to run simulations sampling, the force-field parameter space saved time and eliminated input errors,” said Lynch.
These parameters also helped researchers better characterize the nanodiamond-water interactions and tRNA dynamics in the presence of nanodiamonds.
The researchers then developed an automated system capable of optimizing parameters across a wide spectrum of simulation systems and neutron experiments, an effort that will be of great worth to similar experiments going forward. This new workflow is also compatible with the laboratory’s Compute and Data Environment for Science (CADES), which assists experimentalists with the analysis of vast quantities of data.
“Users of the CADES infrastructure can carry the optimization of the simulations within the Bellerophon Environment for the Analysis of Materials, in active development at ORNL,” said Borreguero. The Bellerophon Environment for the Analysis of Materials (BEAM) is an end-to-end workflow software system, developed at ORNL, enabling user-friendly, remote access to robust data storage and compute capabilities offered at CADES and the Oak Ridge Leadership Computing Facility, home of Titan, for scalable data analysis and modeling.
It’s these in-house resources that make ORNL a world leader in experimentation, modeling and the nexus in between and that make discoveries like this possible.
Image: Water is seen as small red and white molecules on large nanodiamond spheres. The colored tRNA can be seen on the nanodiamond surface. Credit: Michael Mattheson, OLCF, ORNL