Laboratory investigates bacterial proteins in the search for new antibiotics

Research study conducted under the program São Paulo Excellence Chairs.

By Karina Toledo

Agência FAPESP – Discovering the biological mechanisms that bacteria use to infect humans and avoid attack by the immune system and studying target proteins for the development of new antibiotics. These are the main objectives of a project coordinated by Brazilian researcher Andrea Dessen de Souza e Silva of the Structural Biology Institute (IBS) of Grenoble, France.

The study has been underway for roughly a year at the Brazilian Biosciences National Laboratory (LNBio) in Campinas under the auspices of the São Paulo Excellence Chairs (SPEC), an FAPESP pilot program that seeks to establish collaboration between São Paulo institutions and high-level researchers living abroad.

Last week, the LNBio partnership with France was formalized through an agreement with the National Scientific Research Center (CNRS), which created the International Associated Laboratory (LIA), a laboratory without borders that brings together researchers and resources from two countries.

Bacwall, the name of the project, aims to study the virulence mechanisms that are dependent on the bacterial cell wall using x-ray crystallography, biochemistry, molecular biology and electron microscopy.

Dessen’s group at the IBS has already collaborated with other European institutions, such as the Pasteur Institute (Paris) and Utrecht University (Holland), allowing for the formation of a broad network that includes LNBio and the Brazilian Nanotechnology National Laboratory (LNNano) – both belonging to the Brazilian Center for Energy and Materials Research (CNPEM).

“The collaboration with Brazil allows us to be bold and pursue more ambitious objectives. In France, the financial situation is not good, and we must fight to fund the hiring of students. The fellowships last only three years, and there is no possibility for renewal,” explained Dessen.

After earning a degree in chemical engineering from Universidade do Estado do Rio de Janeiro (Uerj) in 1987, Dessen has been working outside Brazil for 25 years. Before settling in France, she completed her doctorate at New York University and post-doctoral research at Albert Einstein College of Medicine and later at Harvard University. She specialized in the study of protein structure using biochemistry and crystallography techniques.

In the last few years, Dressen has been dedicated to the study of a class of proteins known as penicillin-binding proteins (PBPs), which are essential for forming the bacterial cell wall.

“By inhibiting cell wall synthesis, the bacteria literally explode because the cell wall becomes fragile and is incapable of supporting the cell’s internal pressure. This is the action mechanism of penicillin and its synthetic analogs; however, due to mutations, many bacteria have become resistant,” said the researcher.

According to Dessen, there is a group of infectious diseases – caused by Staphylococcus aureus in particular – that kills more people than AIDS and tuberculosis combined. “We have a population that is aging and a growing number of transplant and cancer patients. People are getting more sensitive to microbes. For this reason, this research topic interests us,” Dessen said.

International hub

Dessen, under SPEC requirements, will spend 10 weeks in Brazil per year for the duration of the project (at least four years). In addition to her, research at LIA is being coordinated by Brazilian David Neves, Dessen’s research assistant and former post-graduate student in Grenoble.

The team also includes doctoral student Mayara Mayele Miyachiro, an FAPESP fellow, and master’s student Paulo Madeira. In August, the team will welcome French post-doctoral student Samira Zouhir of the University of Paris, who will come to Brazil with FAPESP’s support.

“Zouhir was selected from among 30 candidates from several countries. We intend to broaden the number of post-doctoral students in the group and will publicize them internationally when new positions become available. The goal is for the laboratory to be an international hub,” said Dessen.

First results

To date, the group has published a commentary on the factors of bacterial virulence in the journal Nature Chemical Biology.

Two other articles resulting from studies coordinated by Neves should be published soon, with work on the macroglobulin protein appearing in the journal mBio of the American Society for Microbiology.

“This protein exists in the human immunological system, and a homolog in bacteria was discovered in 2004. Our research showed that the structure of bacterial macroglobulin is similar to the human protein, which led us to believe that the protein has the function of protecting bacteria from the immune system” stated Dessen.

The article to be published in Journal of Molecular Biology covers a family of proteins called internalins expressed by Listeria monocytogenes, a bacterium that causes food poisoning. It is thought that internalins are part of a bacterial strategy to avoid attack by the immune system.

At present, Neves is dedicated to research on a Staphylococcus aureus surface protein that resides in the cell membrane of the pathogen. The function of this protein is to recruit another protein of the human immune system, so-called factor H, which inhibits the attack of the invader.

“We intend to better understand how this interaction between bacteria and the immune system occurs by studying the structure of the two proteins,” said the researcher.

Madeira’s master’s thesis is focused on investigating the structure of a phospholipase secreted by the opportunistic bacterium Pseudomonas aeruginosa that helps to penetrate the cell membrane of the host to facilitate infection.

Meanwhile, Miyachiro has been dedicated to the study of the bacterium Thermotoga maritima and the enzymes that are essential for synthesis of its cell wall. “The mechanisms of action of these enzymes could inspire a new type of antibiotic,” said Dessen.

The group also intends to test a collection (a ‘library’) of more than 30,000 chemical compounds that LNBio purchased from the National Institutes of Health in the U.S. to identify any potential drugs that can inhibit the synthesis of target proteins that are essential to bacteria.

“As of January 2012, LNBio will also have a library of compounds based on Brazilian biodiversity, with roughly 10,000 strains of bacteria and fungi. If the tests with the chemical compounds are successful, we also intend to evaluate the molecules from Brazilian biodiversity in collaboration with researchers from the LNBio Bioexperiment Laboratory,” commented Dessen.

International collaboration in research

During the inauguration ceremony for LIA, FAPESP’s Scientific Director Brito Cruz stressed that promoting international collaboration opportunities for São Paulo researchers is an important part of the Foundation’s strategy.

“Andrea Dessen was the first researcher chosen for the SPEC program, and we are happy to see the results of the project that we are financing through CNPEM,” affirmed Brito Cruz.

Gilles Bloch, director of the Division of Life Sciences at the French Commission of Alternative Energy and Atomic Energy (CEA), noted that IBS is one of the best and most attractive laboratories in the area of biology.

“We are very proud of Dessen’s initiative to create this bridge with Brazil. This project is a good example of integrated structural biology. This study is based on the structure of biomolecules and is therefore capable of dealing with problems at the cellular level, likely resulting in clinical applications. It is a major opportunity for us to develop strong ties with Brazil,” affirmed Bloch.

Also present at the ceremony were Kleber Franchini, leader of the Brazilian side of LIA and director of LNBio; Carlos Alberto Aragão, General Director of CNPEM; Renaud Blaise, Director of International Relations at CEA; Serge Perez, Counsel at France’s Nuclear Service in Brasília; Jean-Pierre Briot, representative of the CNRS in Brazil; Yassine Lakhnech, Vice-President of Research at Joseph Fourier University; and Gérard Chuzel, Science and Technology Attaché at France’s Consulate General in São Paulo. The CNRS, CEA and Joseph Fourier University are French public agencies responsible for the oversight of IBS.