Innovative method for synthesizing this chemical compound will allow virology research and demonstrates the unique advances resulting from interdisciplinary science
A group researching synthetic chemistry at the Brazilian Center for Research in Energy and Materials (CNPEM) has developed an unprecedented method for obtaining a substance considered essential to some virological studies. This molecule, 7DMA (7-deaza-2’-methyladenosine), has been difficult to import, since it is not offered in significant volumes and is extremely expensive: just one gram costs roughly 130,000 reais. The discovery was published in Frontiers in Chemistry.
Chemistry laboratory within the Brazilian Center for Research in Energy and Materials (CNPEM), a private, non-profit organization overseen by the Ministry of Science, Technology, and Innovation
At the same time, a different substance that appeared as a byproduct of experiments to synthesize 7DMA was examined using the Sirius particle accelerator, and was the first “small” molecule (compared to macromolecules like proteins, for example, which the equipment was designed for) to be completely detailed using the Manacá research station. This type of analysis is being fine-tuned on this beamline, and soon the fourth-generation synchrotron will also be available to the small molecule community.
Why 7DMA?
Originally, 7DMA was developed to combat the hepatitis C virus, but its clinical trials in humans were unsuccessful. Nevertheless, it is still being used in other research involving treatment for viral diseases. The virology team at the CNPEM tried to import 7DMA but had trouble accessing the quantities required; they instead went to the synthetic chemistry group for help.
The chemists, led by researcher Marjorie Bruder, responded by adapting a protocol described on the SciFinder platform (a fundamental tool in the world of chemical research) and discovered a new way to obtain 7DMA in sufficient quantities for the study’s needs at a fraction of the market price. “Without this achievement in the area of chemistry, we would not have been able to make our own advance in virology,” said Rafael Elias Marques, who studies viral biology and helps look for treatments for diseases like dengue, Zika, yellow fever, and other less widely known infections (such as the Mayaro and Usutu viruses).
Once they had the 7DMA, the CNPEM virologists were able to create a test for the Usutu virus; this emerging disease has not yet been studied in detail, but has attracted attention from global health agencies after spreading to Africa to Europe with the potential for complicated symptoms. The researchers found that the molecule successfully stopped the virus from replicating in vitro, justifying further research in this area. Marques explained that although real treatment is still far-off, the initial steps are essential in the process of developing an actual pharmaceutical.
He said that testing chemical compounds is part of the scientific process; 7DMA still shows promise for research, especially when it involves collaboration. “This substance makes these studies possible. With these studies, there are inevitably greater chances that we will find treatments for diseases that today have none,” he added.
Sirius and the unexpected byproduct
During the reaction to synthesize the 7DMA molecule, the CNPEM team was surprised by the unexpected (and undesired) formation of a secondary compound. The chemist Fabrício Naciuk, who was working on the project, investigated the mysterious substance with the usual techniques for determining the structure of chemical compounds, like mass spectrometry and nuclear magnetic resonance (NMR). Even though these provided useful data, the team opted to look farther with the x-ray equipment at Sirius, the CNPEM’s fourth-generation particle accelerator.
The results from the x-ray crystallography analysis conducted with the Manacá beamline at Sirius decisively confirmed what the researchers had suspected: in the words of the chemist Marjorie Bruder, “nothing is so direct and leaves as little doubt as an x-ray analysis.”
Sample positioning in the Manacá beamline at Sirius
Laboratories most commonly use a device called an x-ray diffractometer in similar situations, but not all small molecules can be successfully examined in these devices; in these cases, the synchrotron is the best option.
According to Manacá beamline coordinator Andrey Nascimento, using a synchrotron to investigate the structure of small molecules is much more than an alternative solution. He explained that Sirius generates extremely precise results while also providing something very important for researchers who wish to use the facilities: it saves precious experimentation time.
“It can take only minutes from the collection of diffraction data from a small molecule in Sirius to the initial resolution of its structure,” said Nascimento, and added that the preparation and search for crystals suitable for this generation synchrotron is much less complicated and faster than for diffractometer.
The combined use of the various analytical techniques available at the CNPEM allowed the researchers to deduce and propose a molecular structure, as well as the mechanism by which it was thought to be formed. The mysterious compound resulted from an intermediary’s reaction to the solvent used in the key stage of producing 7DMA. “This was very surprising, since normally the main role of solvents is to dissolve reagents, and they tend to be inert to the reaction conditions,” added Bruder.
Left: molecular structure of the byproduct formed unexpectedly during the process of synthesizing 7DMA obtained from x-ray crystallography in ORTEP using the Manacá beamline at the Sirius synchrotron light source (a). Right: chemical structures for the byproduct and for 7DMA (b)
After the resulting byproduct was identified, the reaction could be adjusted to eliminate it from the process and obtain just 7DMA, which was the initial objective. The researchers noted that when they work together in a multidisciplinary effort, their perspectives on how they understand the same object complement each other. In this case, they had the “what” (the micro-level view of the molecules) and the “why” (the macro-level vision of the virus and disease), and can now move on to the “how” with investigations into the interaction between a potential drug (an antiviral) and a pharmacological target (the virus).
About CNPEM
A sophisticated and effervescent environment for research and development, unique in Brazil and present in few scientific centers in the world, the Brazilian Center for Research in Energy and Materials (CNPEM) is a private non-profit organization, under the supervision of the Ministry of Science, Technology and Innovation (MCTI). The Center operates four National Laboratories and is the birthplace of the most complex project in Brazilian science – Sirius – one of the most advanced synchrotron light sources in the world. CNPEM brings together highly specialized multi-thematic teams, globally competitive laboratory infrastructures open to the scientific community, strategic lines of investigation, innovative projects in partnership with the productive sector and training of researchers and students. The Center is an environment driven by the search for solutions with impact in the areas of Health, Energy and Renewable Materials, Agro-environment, and Quantum Technologies. As of 2022, with the support of the Ministry of Education (MEC), CNPEM expanded its activities with the opening of the Ilum School of Science. The interdisciplinary higher course in Science, Technology and Innovation adopts innovative proposals with the aim of offering excellent, free, full-time training with immersion in the CNPEM research environment. Through the CNPEM 360 Platform, it is possible to explore, in a virtual and immersive way, the main environments and activities of the Center, visit: https://pages.cnpem.br/cnpem360/.
