A joint effort, involving local and external researchers, validated crystallographic study of small molecules, alongside the usual with proteins
From left to right: Andrey Fabrício Z. Nascimento (Brazilian Center for Research in Energy and Materials, CNPEM), Leopoldo Suescun (University of la República, Uruguay), Alejandro Pedro Ayala (Federal University of Ceará, UFC), Javier Ellena (USP-São Carlos), and Florencia di Salvo (University of Buenos Aires, Argentina).
Manacá, one of the beamlines operating at Sirius, was designed for analysis of the three-dimensional structure of macromolecules, especially proteins. However, in late May, a group of specialists, including physicists and chemists from universities in Brazil and abroad, came to Sirius to validate the current instrumentation in the beamline, so that it would be possible to welcome the research community that studies what are known as small molecules.
These molecules, or micromolecules, have low molecular weight and size on the order of 1nm. Their relevance on pharmacology studies is fundamental, since it is this kind of molecule that can bind to macromolecules like proteins, nucleic acids (DNA and RNA), and polysaccharides, performing functions that can be beneficial or detrimental to biological functioning
In most cases, these molecules can be studied in the lab with a device called a diffractometer, and, therefore, synchrotron light is not necessary to the analyses. However, Manacá beamline coordinator Andrey Nascimento explains that not only does the synchrotron reduce the time needed to analyze diffracted crystals from hours to a few minutes (for very small crystals), it is also recommended in situations where the molecule is difficult to obtain or rare, such as natural metabolites. “In these cases, Sirius will be available to conduct analyses for research that otherwise would not be possible,” he explains.
The first test of the Manacá beamline involving a small molecule was successfully conducted as part of an internal multidisciplinary study by CNPEM researchers. After the initial trial, a specific working group was invited to focus on a more systematic implementation of beamline measurements and softwares, in order to extend the service to the research community of small molecules.
“During this process of validating the Manacá beamline, with the cooperation of the beamline’s technical team and experienced external users, we were able to test the limits with real samples, which served to perfect the protocols and routines that are now available to the entire scientific community,” adds Mateus Cardoso, Head of the Soft and Biological Material Division at the LNLS.
Making this new capability possible required increasing the line’s energy, moving the sample detector closer, and installing a part that repositions the crystals, by turning the sample that receives the beam light. Besides the coordinator of the Manacá beamline, the researchers responsible for thinking, calibrating, and testing the new developments were Florencia di Salvo of the University of Buenos Aires, Javier Ellena of the University of São Paulo-São Carlos, Alejandro Ayala of the Federal University of Ceará, and Leopoldo Suescun of the University of la República. Ayala and Suescun are part of the current LNLS User Committee.
The group of researchers brought samples from their respective laboratories to Sirius to conduct the testing, and according to Andrey Nascimento, “using Manacá they were able to measure crystals they never dreamed of measuring with a laboratory diffractometer.” The group also used the compound produced at the CNPEM as a byproduct from the previous internal study as a model molecule.
At the end of the three days of experiments the researchers reported a few challenges, such as the improvements required in the part that repositions the crystals, the need to reduce the distance between the sample and the detector, and the possibility of using a robot to automatically mount the samples. However, they unanimously declared that, in general, the test was very satisfactory and successful.
“Members of the LNLS user committee knew that the small molecule x-ray crystallography community was interested in using the beamlines at Sirius to collect high-quality data on crystals that are very small or sensitive to radiation. A series of experiments was then proposed so that members of the committee, technical specialists, and the coordinator of the beamline could analyze this difficult problem together and confirm that Manacá could be useful in solving it. Then they could develop an automated procedure so that less experienced users could study these crystals on their own. The procedures that were developed had very positive results, and will expand the reach of Sirius to the community of scientists dedicated to organic and inorganic chemistry and physical chemistry,” says Leopoldo Suescun of the University of la República in Uruguay (UdelaR).
Even though the beamlines at Sirius are always being improved, this is an important landmark for Manacá, which now has made the process easier and automatic for less experienced users and will provide a vast and immeasurable new range of research possibilities.
About the CNPEM
With a sophisticated and vibrant environment for research and development that is the only one of its kind in Brazil and found in only a few scientific centers in the world, the Brazilian Center for Research in Energy and Materials (CNPEM) is a private, non-profit organization overseen by the Ministry of Science, Technology and Innovation (MCTI). The Center operates four national laboratories and is home to Sirius, the most complex project in Brazilian science and one of the world’s most advanced synchrotron light sources. The CNPEM is home to highly specialized multi-thematic teams, globally competitive lab infrastructure that is open to the scientific community, strategic lines of research, innovative projects in partnerships with the productive sector, and training for researchers and students. The Center is an environment driven by research into solutions that impact the areas of health, energy and renewable materials, agri-environmental, and quantum technologies. In 2022, with support from the Brazilian Ministry of Education (MEC), the CNPEM expanded its activities with the opening of the Ilum School of Science. This interdisciplinary undergraduate program in science, technology, and innovation implements innovative ideas to provide a high-quality free and full-time undergraduate program immersed in the research environment at the CNPEM. The CNPEM 360 Platform provides visitors with a virtual immersive visit to the Center’s main environments and activities. Visit at: https://pages.cnpem.br/cnpem360/.
