A team of mechanical engineers at the University of California San Diego has successfully used acoustic waves to move fluids through small channels at the nanoscale. The breakthrough is a first step toward the manufacturing of small, portable devices that could be used for drug discovery and microrobotics applications. The devices could be integrated in a lab on a chip to sort cells, move liquids, manipulate particles and sense other biological components. For example, it could be used to filter a wide range of particles, such as bacteria, to conduct rapid diagnosis.
The researchers detail their findings in the Nov. 14 issue of Advanced Functional Materials. This is the first time that surface acoustic waves have been used at the nanoscale.
The field of nanofluidics has long struggled with moving fluids within channels that are 1000 times smaller than the width of a hair, said James Friend, a professor and materials science expert at the Jacobs School of Engineering at UC San Diego. Current methods require bulky and expensive equipment as well as high temperatures. Moving fluid out of a channel that’s just a few nanometers high requires pressures of 1 megaPascal, or the equivalent of 10 atmospheres.
Researchers led by Friend had tried to use acoustic waves to move the fluids along at the nano scale for several years. They also wanted to do this with a device that could be manufactured at room temperature.
After a year of experimenting, post-doctoral researcher Morteza Miansari, now at Stanford, was able to build a device made of lithium niobate with nanoscale channels where fluids can be moved by surface acoustic waves. This was made possible by a new method Miansari developed to bond the material to itself at room temperature. The fabrication method can be easily scaled up, which would lower manufacturing costs. Building one device would cost $1000 but building 100,000 would drive the price down to $1 each.
The device is compatible with biological materials, cells and molecules.
Researchers used acoustic waves with a frequency of 20 megaHertz to manipulate fluids, droplets and particles in nanoslits that are 50 to 250 nanometers tall. To fill the channels, researchers applied the acoustic waves in the same direction as the fluid moving into the channels. To drain the channels, the sound waves were applied in the opposite direction.
By changing the height of the channels, the device could be used to filter a wide range of particles, down to large biomolecules such as siRNA, which would not fit in the slits. Essentially, the acoustic waves would drive fluids containing the particles into these channels. But while the fluid would go through, the particles would be left behind and form a dry mass. This could be used for rapid diagnosis in the field.
Cancer is a notoriously difficult disease to treat. Not only do a wide variety of cancers exist, requiring specialized treatments for each type, but cancer cells within an individual can morph and render previously potent therapeutics ineffective. Thus, there is a continual need to discover new, effective drugs. Research from Dr. Norihiko Nakazawa in the G0 Cell Unit at the Okinawa Institute of Science and Technology Graduate University (OIST) led by Prof. Mitsuhiro Yanagida, may help make the discovery process easier. This research was published in Genes to Cells.
Cancer cells differ from normal cells in a variety of different ways. Most notably, malignant cells exhibit a much higher rate of replication and proliferation than normal ones. The rapid growth of these cells can result in tumor formation and metastasis, or the spreading of cancer to other parts of the body. Fortunately, scientists have been able to exploit these properties to create new treatments. Since the proteins involved in DNA replication are considerably more active in cancer cells than in normal ones, researchers have discovered that drugs which target these proteins will disproportionately affect the malignant cells. These drugs are designed to only affect active proteins, so that even though the same proteins exist in normal cells, the majority of the normal cells will contain inactive proteins at the time of treatment, and thus be unaffected.
Dr. Nakazawa’s research centered on the use of a specific anti-cancer drug, ICRF-193, which targets a protein called DNA topoisomerase II. As part of his research, Dr. Nakazawa treated fission yeast with ICRF-193 and observed the effects. Typically, during cell reproduction, DNA is copied so that a cell temporarily contains twice the amount of DNA than it normally does. These two copies of chromosomal DNA are pulled to different ends of the cell by a protein structure called the mitotic spindle. Once the chromosomal DNA is separated, the cell begins to divide into two identical daughter cells.
When Dr. Nakazawa treated fission yeast with ICRF-193, he noticed that the cells appeared to have difficulty separating after DNA replication had occurred. Instead of separating normally, the mitotic spindle appeared to continue to lengthen despite failing to fully separate the two copies of DNA, producing an arched shape until eventually snapping in the middle. This “arched and snapped” appearance seemed to be unique to the ICRF-193 treated cells.
Researchers can utilize this “arched and snapped” appearance to look for other drugs that affect fission yeast proteins in the same manner. The replication machinery and DNA-bound proteins of fission yeast are highly conserved and thus remarkably similar to other organisms, including humans. Because of this similarity, drugs that affect these proteins in fission yeast are likely to affect the related highly active proteins in human cancers. This research makes it plausible to use fission yeast in the place of human cells in the discovery process of novel cancer drugs.
There are many disadvantages to using human cells in the initial stages of creating a new therapy. Scientists often have to test a large number of compounds in order to find one that is effective against a particular target. Human cells are costly to take care of and require a lot of time and specific conditions in order to grow. According to Dr. Nakazawa, “fission yeast is a relatively fast, easy to use model system that is low cost,” making it advantageous for use in drug screens. Time and cost are often major hurdles in the process of drug development, so any discoveries that expedite the process can help get the next cancer cure in the hands of patients sooner.
Findings Reveal Human Proteins Are Better Drug Targets than Previously Thought
Scientists at The Scripps Research Institute (TSRI) have developed a powerful new method for finding drug candidates that bind to specific proteins.
The new method, reported in this week’s issue of Nature, is a significant advance because it can be applied to a large set of proteins at once, even to the thousands of distinct proteins directly in their native cellular environment. The TSRI researchers demonstrated the technique to find “ligands” (binding partners) for many proteins previously thought to bind poorly to small molecules that can be used to determine the functions of their protein targets and can serve as starting compounds for the development of drugs.
Among the newly discovered ligands are selective inhibitors of two caspase enzymes, which have key roles in multiple diseases but have largely eluded efforts to target them with drugs.
“Our data suggest that the human proteome is much more broadly targetable with small molecules than has been previously appreciated,” said principal investigator Benjamin F. Cravatt, chair of the Department of Chemical Physiology and member of the Dorris Neuroscience Center and Skaggs Institute for Chemical Biology at TSRI. “That opens up new possibilities for developing scientific probes and ultimately drugs.”
Researchers from Carnegie Mellon University (CMU) have created the first robotically driven experimentation system to determine the effects of a large number of drugs on many proteins, reducing the number of necessary experiments by 70%.
The model, presented in the journal eLife, uses an approach that could lead to accurate predictions of the interactions between novel drugs and their targets, helping reduce the cost of drug discovery.
“Biomedical scientists have invested a lot of effort in making it easier to perform numerous experiments quickly and cheaply,” says lead author Armaghan Naik, a Lane Fellow in CMU’s Computational Biology Department.
“However, we simply cannot perform an experiment for every possible combination of biological conditions, such as genetic mutation and cell type. Researchers have therefore had to choose a few conditions or targets to test exhaustively, or pick experiments themselves. The question is which experiments do you pick?”
Naik says that careful balance between performing experiments that can be predicted confidently and those that cannot is a challenge for humans, as it requires reasoning about an enormous amount of hypothetical outcomes at the same time.
To address this problem, the research team has previously described the application of a machine learning approach called “active learning”. This involves a computer repeatedly choosing which experiments to do, in order to learn efficiently from the patterns it observes in the data. The team is led by senior author Robert F. Murphy, Professor at the Ray and Stephanie Lane Center for Computational Biology, and Head of CMU’s Computational Biology Department.
Nature contains a treasure trove of substances that could help fight human disease. Just this year, the Nobel Prize in Physiology or Medicine honored the development of drugs that fight parasites and malaria based on such “natural products.”
But finding these molecules and discovering new chemical identities represents slow and painstaking work. This week in ACS Central Science, researchers report a new way to greatly speed up that process.
Scientists at Cold Spring Harbor Laboratory (CSHL) and five other institutions have used an unconventional approach to cancer drug discovery to identify a new potential treatment for acute myeloid leukemia (AML).
As reported in Nature online on August 3, the scientists have pinpointed a protein called Brd4 as a novel drug target for AML, an aggressive blood cancer that is currently incurable in 70% of patients. Using a drug compound that inhibits the activity of Brd4, the scientists were able to suppress the disease in experimental models.
“The drug candidate not only displays remarkable anti-leukemia activity in aggressive disease models and against cells derived from patients with diverse, genetic subtypes of AML, but is also minimally toxic to non-cancerous cells,” says CSHL scientist Chris Vakoc, M.D., Ph.D., who led the team. “The drug is currently being developed for therapeutic use for cancer patients by Tensha Therapeutics and is expected to enter clinical trials within two years.”
The protein target identified in the RNAi screen described in the current study, Brd4 — which contains a distinct domain or region known as a bromodomain — is a member of the BET family of proteins, which help regulate gene expression. By “reading” certain epigenetic marks or chemical tags attached to chromatin — the combined package of DNA and proteins around which it is coiled within the cell’s nucleus — Brd4 helps control the pattern of which genes are switched on and how they work.
“Cancer is clearly a genetic disease, but we also appreciate that epigenetic changes in how genes are expressed contribute to the uncontrolled growth of cancer cells,” says Vakoc. Cancer cells exploit this altered epigenetic landscape to drive their cell-growth programs.
Vakoc and other scientists have seized on the idea of interfering with this epigenetic dependency to turn the tables on cancer. “Epigenetic alterations acquired during cancer progression are potentially reversible and therefore susceptible to drug intervention,” he explains. With this insight as the backbone of their strategy to find new therapies for cancer, “we began to systematically search for what the cancer needs to keep itself going, to find a way to shut down that cancer-fueling factor and develop a new therapy.”