For Better or Worse

Vavylonis uses the methods of physics to study, analyze and model the physical properties of these biological materials. He wants to decipher their mechanical properties, how they move and multiply, in the hope of finding a weakness that will help other scientists develop better therapeutic options.

“My background is in theoretical physics, working on polymer properties. But I was always interested in biology. At some point, I went to a conference on biophysics and was just fascinated,” said Vavylonis, professor of physics.

He began studying biopolymers and discovered a seemingly endless supply of questions to investigate.

Vavylonis has been collaborating with researchers both at Lehigh and internationally to understand the physics involved as cells move in the body. In collaboration with researchers at Kyoto University, he is investigating the mechanism of cell movement by modeling the kinetics of the cell. The project combines mathematical modeling, image analysis and experimental biology to study actin filaments, abundant cellular protein that regulates cellular shape and motion.

All eukaryotic cells have actin, which forms long fibers that span the distance of the cell and crosslink to make a gel-like network. This network provides the cell’s mechanical properties and can drive changes in cell shape, a constant process of assembly and disassembly.

Vavylonis and his team are interested in understanding how cells use these mechanisms to establish monopolar and bipolar growth patterns and how these patterns contribute to cell shape. He and his collaborators anticipate that acquiring biophysical knowledge about how cells move, change shape and divide can be the basis for explaining fundamental disease mechanisms such as cell metastasis or malignant tumor growth. While his study with Kyoto University uses frog cell lines, Vavylonis separately studies yeast cell remodeling, which uses its actin filaments in a very different way. Yeast cells don’t move, but they grow by remodeling their outer walls with the help of actin filaments. And when a yeast cell divides during mitosis, its actin filaments first assemble a narrow ring shape in the middle of the cell in a perfectly coordinated dance of expansion and compaction.

“Normal cells do this successfully each time. But certain mutant cells have a specific problem with assembly of the ring. We showed that our models can predict how ring failure occurs in these mutant cells. We generated actin filament patterns that were verified by our experimental collaborators studying those yeast cells that cannot divide,” Vavylonis says.

The team was also able to model how another type of mutant yeast cell could survive the ring failure by using a backup pathway to redistribute their actin filaments through an aggregate structure. They recently created a complex model of this behavior to analyze the physical interactions of cellular proteins. He speculates that this information may be useful to researchers hoping to stop cancer cells from multiplying.

“Many forms of chemotherapy are based on preventing cells from dividing,” he says. “This may give insight for the making of a drug that prevents the division of certain cell types.”

Vavylonis published two papers in 2016 in Current Biology about his yeast cell research. More recently, his partnership with Kyoto University received a new NIH grant to continue studying actin dynamics in cell motility and cell mechanics. Among his developing projects is a collaboration with Lehigh chemical engineering professor Jeetain Mittal to model actin polymerization using Mittal’s expertise in methods of molecular simulation.

Together with Mittal and Damien Thévenin, assistant professor of chemistry, they organized the Pennsylvania branch of the Biophysical Society meeting that brought together more than 100 scientists with a quantitative perspective on biological phenomena at Lehigh.

“Biology is moving toward a more quantitative look at life’s processes,” says Vavylonis. “There is a big need to quantify and model all this information, because a model helps to organize it all. Several people at Lehigh are working on modeling, using mathematical, biophysical and quantitative approaches.”

Modeling the perfect cell to test antibiotics

Cellular function can also be dramatically impacted by infections, and harmful bacteria have been living the good life for the past 30 years. All bacteria adapt new survival techniques against existing drugs, but research on new antibiotics isn’t keeping up. Some strains, such as MRSA and Streptococcus pneumonia, have taken on superbug status, multiplying into new, truly deadly strains.

 “Of greater concern is the fact that nearly all antibiotics brought to market over the past 30 years have been variations on existing drugs,” according to The PEW Charitable Trusts, which plans to establish a consortium of academics and industry experts to fight superbugs more aggressively.

Research in the academic setting is gaining momentum. Lehigh University’s strength in biomolecular studies is fueling a movement that is drawing together the best minds in academia, industry and policy, in a race against the evolution of superbugs. In November 2016, leading experts in research and policy to accelerate antibiotic drug development converged at Lehigh for the “Workshop to Take Aim at Bacteria” This event that was organized by Wonpil Im, professor of biological sciences and bioengineering and Presidential Endowed Chair in Health Science and Engineering at Lehigh, included talks by several Lehigh researchers about new avenues of research that could benefit the fight against superbugs.

Without radical new approaches to eradicating these harmful bacteria, says Im, it’s going to get increasingly harder to stay ahead of their natural evolutionary curve.

“Otherwise, it’s like going back to the pre-penicillin era,” says Im.

While some companies are doing antibacterial work, technological challenges and fewer research dollars mean the work remains largely stunted. Worldwide, superbugs cause about 700,000 deaths each year. The UK-based Review on Antimicrobial Resistance estimates that by 2050, more people could die of drug-resistant infections than from cancer.

Im is one of select group of researchers seeking fresh solutions to antibiotic resistance. His decade of work to model bacterial cells has come to fruition with a publicly available biomolecular tool that simulates the complex membrane of lethal pathogens. It’s the first crucial step toward understanding how to penetrate bacterial cells and target and destroy the machinery inside. Antibiotics work because they penetrate the outer membrane of bacterial cells, but when cells mutate to develop tougher exteriors, existing antibiotics are useless.

While gram-positive bacteria have a single membrane barrier that is relatively easy to penetrate, gram-negative bacteria, such as E. coli, have a tough double membrane, as well as other mechanisms that help push unwanted compounds like drugs out of their cells. The problem still remains that researchers don’t really know the mechanics of how molecules penetrate the outer bacterial membrane, Im says. By understanding this process thoroughly, researchers could more easily predict what kinds of molecular structures could target specific bacterial proteins and kill the cell.

After six months of work, Im’s group figured out how to use lipopolysaccharide, a simple phospholipid, to mimic the outer membrane of E. coli, which causes serious food poisoning. It was the first major step for his lab to simulate a gram-negative pathogen for drug discovery.

Im’s CHARMM GUI can model lipopolysaccharide structures’ various bacteria in less than 10 minutes. He hopes the free graphical user interface will allow researchers worldwide to model any number of bacterial cells efficiently.

“Our goal is to get not just one LPS structure, but to also load it into CHARMM-GUI Membrane Builder this year to allow researchers to build various bacterial outer membranes,” Im says.

His ultimate goal is to model complex biomolecular systems that will further scientific understanding of the structure and functions of 10 different superbugs. Im is also working with other Lehigh researchers to create a center for membrane study at the university.

Investigating bacterial immunotherapy

Lehigh’s Marcos Pires is looking for an altogether different approach to beat gram-negative superbugs. He believes in harnessing the body’s natural defenses to do the job without traditional drugs. Despite tremendous efforts and investment toward the discovery of new antibiotics, no new class has been unveiled during the past 30 years. He believes that a nontraditional avenue may be just what the field needs.

The solution sounds like a simple fix: Design a molecular marker for the bad bacteria that mimics a compound the immune system naturally eliminates. Once the marker is attached to the bacteria, immune cells should seek out and destroy the cell, like a torpedo homing in on a target.

“This is immunotherapy, and it’s already a reality for beating some cancers and for fighting HIV. Even in the case of more complex types of cells, such as HIV and certain cancer cells, immunotherapy has proven to be a powerful new mode of combating diseases. So why not design a similar strategy with the idea of having the immune system inactivate disease-causing bacteria? This was still not happening for bacteria until we came into this area,” says Pires, assistant professor of chemistry.

Bacteria have evolved many tricks to avoid the immune system, so Pires wants to provide a hint that would trigger a boost in the immune response.

His research team took advantage of a unique cell wall bacterial building block, amino acids called D-amino acids. He and his students designed synthetic D-amino acids that bacteria incorporated onto their surfaces when growing and dividing. Pires tagged the synthetic D-amino acids with antibody recruiting markers that stuck to the exterior walls of the bacteria. When immune cells floating encountered the markers, they zoomed in and eliminated the cells. After initial success with single-walled gram-positive pathogens, Pires’ team designed an antibody tag that could perform similarly with gram-negative bacteria. The team could watch the activity inside the flask because they designed the antibody markers with fluorescent tags, allowing them to verify that the antibodies were coating the bacterial cells.

“Now we’re on the verge of the next step. Our compounds are working, and we are finalizing and getting ready to publish again,” he says.

His team is also trying to bypass the use of antibodies by looking for a new type of antigen tag that would engage immune cells directly, therefore removing a layer of steps required for the immune system to activate. Theoretically, the immune cells will be triggered to act against the bacterial infection in their vicinity if they notice the tags floating around.

When it comes to antibacterial immunotherapy, there are other, larger hurdles to cross. Success in a flask is but the first step toward proving the technique in an infected human body.

“There’s a lot we still don’t understand about the immune system. If we had an artificial immune system to test, it would be a great advantage,” Pires says. “It feels for us like swimming upstream, but unless we see data showing this will not work, we’ll stick with it. In fact, all evidence shows this should be easy for the immune system, considering how different bacteria are to our own cells.”

Pires feels that this type of work is a race against the clock. Bacterial strains will always keep finding ways to get around standard drugs and become superbugs, he says.

            “We were very spoiled in the past. We treated bacteria as a second thought because we had so many drugs to fight them,” he says. “But now, a standard medical operation comes with the added caveat that you have to think about the tradeoff between the operation’s success and the possibility of lethal infection. It’s on our doorstep.”