The study, published in The Proceedings of the National Academy of Sciences (PNAS), describes the first-ever high-resolution three-dimensional structure of an endogenous reverse transcriptase — specifically human endogenous retrovirus-K (HERV-K) reverse transcriptase (RT). Past research has found a significant portion of the human genome is made up of repetitive elements that are relics of past viral infections, which are associated with a range of serious diseases, including cancer.

According to the study, the structure provides therapeutic opportunities for RT inhibitors-antiretroviral drugs used to treat HIV infection or AIDS, and also hepatitis B-in cancer, autoimmune and neurodegenerative diseases.

“This study marks a significant step forward in our understanding of endogenous retroviruses and how they could be targeted to treat disease,” said Eddy Arnold, resident faculty member at the Rutgers Center for Advanced Biotechnology and Medicine (CABM) and scientific advisory board member of biotechnology company ROME Therapeutics.

“Characterizing the structure of HIV RT was a critical turning point in designing novel medicines to combat that deadly virus,” said Arnold, a Distinguished Professor and Board of Governors Professor of chemistry and chemical biology at Rutgers. “Similarly, deeper insights into human endogenous RT could pave the way toward a new class of therapies for cancer and other serious diseases.”

Repetitive elements in the genome such as HERV-K are frequently overexpressed in cancer and elicit biological viral mimicry responses that can alter the tumor microenvironment, according to past research.

The study was co-authored by researchers from ROME Therapeutics, a biotechnology company that aims to develop novel therapies for cancer and autoimmune diseases by researching the Dark Genome — vast stretches of uncharted genetic material that represent more than 60 percent of the human genome — for drug development.

“In this publication, we describe for the first time the crystal structure of an endogenous reverse transcriptase, one known as HERV-K RT, and show that it has remarkable similarities to HIV reverse transcriptase, a well-known tractable drug target,” said Dennis Zaller, chief scientific officer of ROME. “This achievement is a milestone in the Dark Genome field and sheds light on opportunities for structure-based drug design based on established anti-viral targets present in our human genome. This work is the result of a great collaboration between ROME’s exceptional structural biology team and world-leading crystallographers.”

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Converting petroleum into fuels involves crude chemistry first invented by humans in the 1800s. Meanwhile, bacteria have been producing carbon-based energy molecules for billions of years. Which do you think is better at the job?

Well aware of the advantages biology has to offer, a group of biofuel experts led by Lawrence Berkeley National Laboratory (Berkeley Lab) took inspiration from an extraordinary antifungal molecule made by Streptomyces bacteria to develop a totally new type of fuel that has projected energy density greater than the most advanced heavy-duty fuels used today, including the rocket fuels used by NASA.

“This biosynthetic pathway provides a clean route to highly energy-dense fuels that, prior to this work, could only be produced from petroleum using a highly toxic synthesis process,” said project leader Jay Keasling, a synthetic biology pioneer and CEO of the Department of Energy’s Joint BioEnergy Institute (JBEI). “As these fuels would be produced from bacteria fed with plant matter — which is made from carbon dioxide pulled from the atmosphere — burning them in engines will significantly reduce the amount of added greenhouse gas relative to any fuel generated from petroleum.”

The incredible energy potential of these fuel candidate molecules, called POP-FAMEs (for polycylcopropanated fatty acid methyl esters), comes from the fundamental chemistry of their structures. Polycylcopropanated molecules contain multiple triangle-shaped three-carbon rings that force each carbon-carbon bond into a sharp60-degree angle. The potential energy in this strained bond translates into more energy for combustion than can be achieved with the larger ring structures or carbon-carbon chains typically found in fuels. In addition, these structures enable fuel molecules to pack tightly together in a small volume, increasing the mass — and therefore the total energy — of fuel that fits in any given tank.

“With petrochemical fuels, you get kind of a soup of different molecules and you don’t have a lot of fine control over those chemical structures. But that’s what we used for a long time and we designed all of our engines to run on petroleum derivatives,” said Eric Sundstrom, an author on the paper describing POP fuel candidates published in the journal Joule, and a research scientist at Berkeley Lab’s Advanced Biofuels and Bioproducts Process Development Unit (ABPDU).

“The larger consortium behind this work, Co-Optima, was funded to think about not just recreating the same fuels from biobased feedstocks, but how we can make new fuels with better properties,” said Sundstrom. “The question that led to this is: ‘What kinds of interesting structures can biology make that petrochemistry can’t make?'”

A quest for the ring(s)

Keasling, who is also a professor at UC Berkeley, had his eye on cyclopropane molecules for a long time. He had scoured the scientific literature for organic compounds with three-carbon rings and found just two known examples, both made by Streptomyces bacteria that are nearly impossible to grow in a lab environment. Fortunately, one of the molecules had been studied and genetically analyzed due to interest in its antifungal properties. Discovered in 1990, the natural product is named jawsamycin, because its unprecedented five cyclopropane rings make it look like a jaw filled with pointy teeth.

Keasling’s team, comprised of JBEI and ABPDU scientists, studied the genes from the original strain (S. roseoverticillatus) that encode the jawsamycin-building enzymes and took a deep dive into the genomes of related Streptomyces, looking for a combination of enzymes that could make a molecule with jawsamycin’s toothy rings while skipping the other parts of the structure. Like a baker rewriting recipes to invent the perfect dessert, the team hoped to remix existing bacterial machinery to create a new molecule with ready-to-burn fuel properties.

First author Pablo Cruz-Morales was able to assemble all the necessary ingredients to make POP-FAMEs after discovering new cyclopropane-making enzymes in a strain called S. albireticuli. “We searched in thousands of genomes for pathways that naturally make what we needed. That way we avoided the engineering that may or may not work and used nature’s best solution,” said Cruz-Morales, a senior researcher at the Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark and the co-principal investigator of the yeast natural products lab with Keasling.

Unfortunately, the bacteria weren’t as cooperative when it came to productivity. Ubiquitous in soils on every continent, Streptomyces are famous for their ability to make unusual chemicals. “A lot of the drugs used today, such as immunosuppressants, antibiotics, and anti-cancer drugs, are made by engineered Streptomyces,” said Cruz-Morales. “But they are very capricious and they’re not nice to work with in the lab. They’re talented, but they’re divas.” When two different engineered Streptomyces failed to make POP-FAMEs in sufficient quantities, he and his colleagues had to copy their newly arranged gene cluster into a more “tame” relative.

The resulting fatty acids contain up to seven cyclopropane rings chained on a carbon backbone, earning them the name fuelimycins. In a process similar to biodiesel production, these molecules require only one additional chemical processing step before they can serve as a fuel.

Now we’re cooking with cyclopropane

Though they still haven’t produced enough fuel candidate molecules for field tests — “you need 10 kilograms of fuel to do a test in a real rocket engine, and we’re not there yet,” Cruz-Morales explained with a laugh — they were able to evaluate Keasling’s predictions about energy density.

Colleagues at Pacific Northwest National Laboratory analyzed the POP-FAMEs with nuclear magnetic resonance spectroscopy to prove the presence of the elusive cyclopropane rings. And collaborators at Sandia National Laboratories used computer simulations to estimate how the compounds would perform compared to conventional fuels.

The simulation data suggest that POP fuel candidates are safe and stable at room temperature and will have energy density values of more than 50 megajoules per liter after chemical processing. Regular gasoline has a value of 32 megajoules per liter, JetA, the most common jet fuel, and RP1, a popular kerosene-based rocket fuel, have around 35.

During the course of their research, the team discovered that their POP-FAMEs are very close in structure to an experimental petroleum-based rocket fuel called Syntin developed in the 1960s by the Soviet Union space agency and used for several successful Soyuz rocket launches in the 70s and 80s. Despite its powerful performance, Syntin manufacturing was halted due to high costs and the unpleasant process involved: a series of synthetic reactions with toxic byproducts and an unstable, explosive intermediate.

“Although POP-FAMEs share similar structures to Syntin, many have superior energy densities. Higher energy densities allow for lower fuel volumes, which in a rocket can allow for increased payloads and decreased overall emissions,” said author Alexander Landera, a staff scientist at Sandia. One of the team’s next goals to create a process to remove the two oxygen atoms on each molecule, which add weight but no combustion benefit. “When blended into a jet fuel, properly deoxygenated versions of POP-FAMEs may provide a similar benefit,” Landera added.

Since publishing their proof-of-concept paper, the scientists have begun work to increase the bacteria’s production efficiency even further to generate enough for combustion testing. They are also investigating how the multi-enzyme production pathway could be modified to create polycyclopropanated molecules of different lengths. “We’re working on tuning the chain length to target specific applications,” said Sundstrom. “Longer chain fuels would be solids, well-suited to certain rocket fuel applications, shorter chains might be better for jet fuel, and in the middle might be a diesel-alternative molecule.”

Author Corinne Scown, JBEI’s Director of Technoeconomic Analysis, added: “Energy density is everything when it comes to aviation and rocketry and this is where biology can really shine. The team can make fuel molecules tailored to the applications we need in those rapidly evolving sectors.”

Eventually, the scientists hope to engineer the process into a workhorse bacteria strain that could produce large quantities of POP molecules from plant waste food sources (like inedible agricultural residue and brush cleared for wildfire prevention), potentially making the ultimate carbon-neutral fuel.

Who’s up for some eco-friendly space travel?

This work was supported by the U.S. Department of Energy Office of Science and Office of Energy Efficiency and Renewable Energy. JBEI is an Office of Science Bioenergy Research Center.

The potential drugs are still years away from being tested in cancer patients, but a recently published study in the journal Leukemia highlights their promise and the innovative methods that led to their discovery.

In previous studies, the research groups of Rice biochemist Natasha Kirienko and MD Anderson physician-scientist Marina Konopleva screened some 45,000 small-molecule compounds to find a few that targeted mitochondria. In the new study, they chose eight of the most promising compounds, identified between five and 30 closely related analogs for each and conducted tens of thousands of tests to systematically determine how toxic each analog was to leukemia cells, both when administered individually or in combination with existing chemotherapy drugs like doxorubicin.

“One of the big challenges was to establish optimal conditions and doses for testing on both cancer cells and healthy cells,” said study lead author Svetlana Panina, a researcher at the University of Texas at Austin who conducted the research during her postdoctoral studies at Rice. “The results from our previously published cytotoxicity assay were helpful, but very little is known about these small-molecule compounds. None of them had been thoroughly described in other studies, and we had to essentially start from scratch to determine how much to use, what they do in cells, everything. All the doses and treatment conditions had to be adjusted by multiple preliminary experiments.”

In prior work, Kirienko’s lab had shown the eight compounds targeted energy-producing machinery inside cells called mitochondria. Dozens to thousands of mitochondria are at work every minute in every living cell, and like all machines, they wear out with use. The eight compounds induce mitophagy, the housekeeping routine cells use to decommission and recycle mitochondria that are past their prime.

During times of extreme stress, cells can temporarily forgo mitophagy to get an emergency energy boost. Cancer is notorious for hijacking these sorts of programs to fuel pathological growth. For example, previous research has shown leukemia cells have far more damaged mitochondria than healthy cells and are also more sensitive to mitochondrial damage than healthy cells.

Kirienko and Konopleva reasoned that mitophagy-inducing drugs might weaken leukemia cells and make them more susceptible to chemotherapy.

“We hypothesized that if they activate mitophagy, they may be particularly toxic to leukemia cells,” said Kirienko, the corresponding author of the new study. “And indeed, we found that six of the eight small-molecule compounds were deadly to leukemia cells. We then wanted to study them more in depth. So we looked at closely related molecules, and we looked at combinations.”

When two or more drugs are given in combination, researchers can also administer them individually and compare the effectiveness of each regimen.

“There is a number called synergy coefficient that quantifies interactions between drugs,” Kirienko said. “If the coefficient is negative, the drugs are antagonistic and work against one another. Zero means no effect, and positive numbers indicate positive interactions. Anything above 10 is considered synergistic.”

For example, one currently prescribed drug combination for leukemia — doxorubicin and cytarabine — has a synergy coefficient of 13, Kirienko said. The team’s experiments showed several mitophagy-inducing compounds were significantly more synergistic with doxorubicin. The most synergistic, a compound called PS127B, had a coefficient of 29.

“The point of synergy is that there are concentrations, or dosages, where a single drug doesn’t kill,” Kirienko said. “There is no death of healthy cells or cancer cells. But administering those same concentrations in combination can kill a considerable amount of cancer cells and still not affect healthy cells.”

The team started by testing the toxicity of its mitophagy-inducing compounds and combinations against acute myeloid leukemia (AML) cells, the most commonly diagnosed form of the disease. They then tested the six most effective AML-killing compounds against other forms of leukemia and found five were also effective at killing acute lymphoblastic leukemia (ALL) cells and chronic myelogenous leukemia (CML) cells. Control studies found all the mitophagy-inducing drugs caused far less harm to healthy cells.

In their final experiments, the researchers tested one of the most effective mitochondria-targeting compounds, PS127E, using a cutting-edge technique called a patient-derived xenograft (PDX) model. In PDX, also referred to as a “mouse clinical trial,” mice are implanted with cancer cells from a leukemia patient. Once the cells grow, the mouse is exposed to a drug or combination of drugs as a closer-than-cells test of the treatment’s effect. PDX tests on one compound, PS127E, showed it was effective at killing AML cells in mice.

“Although this is very promising, we’re still some distance from having a new treatment we can use in the clinic,” Kirienko said. “We still have a lot to discover. For example, we need to better understand how the drugs work in cells. We need to refine the dose we think would be best, and perhaps most importantly, we need to test on a wide variety of AML cancers. AML has a lot of variations, and we need to know which patients are most likely to benefit from this treatment and which are not. Only after we’ve done that work, which may take a few years, would we be able to start testing in humans.”

Additional study co-authors include Jingqi Pei and Elissa Tjahjono of Rice, Natalia Baran, Shraddha Patel, Gheath Alatrash and Sergej Konoplev of MD Anderson, and Leonid Stolbov and Vladimir Poroikov of the Institute of Biomedical Chemistry in Moscow.

The research was supported by the Cancer Prevention and Research Institute of Texas (RR150044), the National Institutes of Health (R35GM129294, R01CA231364, P50CA100632) and the Russian Federation Fundamental Research Program (1220301001705).