The Tinder of Medicines – Basic Science

By Murilo Bomfim

In the jungle of biodiversity, scientists are looking for connections that match diseases

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Regardless of where you live, it is quite possible that there is at least one pharmacy near you. Brazil is one of the countries with the most drug stores in the world: According to the consulting company IQVIA, we have 2,700 inhabitants. In Argentina, a pharmacy supplies 3,200 people; in India 2 million

Brazil does not only stand out in the everyday drugstore, but also stands out in terms of “pharmacies of the future”: From the immense and unknown biodiversity of its flora, molecules can be obtained for the formulation of new drugs. But unlike the establishment on the corner, biodiversity doesn’t have a password or a switch attendant – digging for molecules that are present in every biome is a more complex task.

Daniela Trivella is one of those scientists who immerse themselves in nature looking for compounds with pharmacological activity. In her daily life, she hunts molecules in samples that have been collected in places as diverse as the Amazon or the ocean floor, for example, where a decaying whale carcass with possible connections was found around 4,000 meters below ground.

The scientist holds a degree in biology, a master’s degree in biotechnology, a doctorate in biomolecular physics and a post-doctoral degree in chemistry and pharmacology. Such a diversified academic career enabled him to develop techniques that target the interaction of proteins and bioactive compounds with a view to creating new drugs. It is common for proteins to be involved in disease mechanisms; for example, some antidepressants work on proteins to increase levels of the hormone norepinephrine. For an active ingredient to be able to interact with a protein, they have to be compatible. And this adaptation depends on the shape and the atoms present in the compound: this conformation can stimulate or inhibit protein activity.

Trivella coordinates a team from the National Biosciences Laboratory (LNBio), in Campinas, where plant and bacterial samples are sent that have been collected by specialized partners who venture to different corners of the country – which guarantees the diversity in the natural product library that LNBio compiles has, currently with 6 thousand registered samples. The point is that each sample contains several bioactive compounds, only a few of which are relevant to inspire new drugs. Then how can one identify the specific compound that interacts with a particular protein?

Researchers use two techniques. One of them is protein crystallography, which works like fishing: the protein (in crystal form) is the bait, and the sample to be examined is the sea. When the sample compound binds to the protein, the two form a complex that is later analyzed by Sirius, the particle accelerator that opened in Campinas in 2018. At the end of the process, there is the three-dimensional structure of the protein with the associated compound.

The strategy is complemented by mass spectrometry, which provides the fingerprint of the compound and from which it is possible to know the atoms that make up the bioactive molecule. Armed with the information gleaned from both techniques, the team crosses data and identifies the molecule in question from which the long-awaited drugs can emerge.

However, these crossovers take time and are prone to error and frustration – the molecule may already be known or even irrelevant to the manufacture of a drug. To speed up the process, Trivella is now devoting itself to setting up a computer interface that takes care of these interfaces. It’s like tindering medication: the information is entered and the program shows who suits whom and which couples are most fertile.

The team of chemists, pharmacists and biologists also needed a computer scientist and a mathematician to develop the idea. This diversity of knowledge is essential to combine high technology and Brazilian biodiversity. If all goes well, new drugs will hit the market. Pharmacies will not be missing.

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Murilo Bomfim is a journalist.

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