Mechanisms Involved in Resistance to Antibiotics: Wall Teichoic Acids and Biofilms as Molecular Targets

• Grant number: 17/18173-0
• Support Opportunities: Regular Research Grants
• Start date: February 01, 2018
• End date: January 31, 2020
• Field of knowledge: Biological Sciences - Biophysics - Molecular Biophysics
• Principal Investigator: Alessandro Silva Nascimento
• Grantee: Alessandro Silva Nascimento
• Host Institution: Instituto de Física de São Carlos (IFSC). Universidade de São Paulo (USP). São Carlos , SP, Brazil

Abstract

The emergence of antibiotic resistant bacterial strains represents an important risk for human health. Infection diseases represent the third cause of death worldwide, according to the World Health Organization, and surveillance data taken from hospitals in US indicate that about 50% of the tested Staphylococcus aureus strains found in central line bloodstream infections are already resistant to b-lactam antibiotics. The same report found about 80% of the Enterococcus faecalis strains found in surgical site infections were resistant to vancomycin. These data highlight the urgency of deeper understanding of the mechanisms used by bacteria for the acquisition of antibiotic resistance and the identification of new molecular targets for the design of new antibiotic candidates. In this proposal, we aim to investigate the structure-function relationship of three enzymes previously showed to be involved in the acquisition of antibiotic resistance. The first enzyme is an UDP-N-acetylglucosamine 2-epimerase (MnaA) from S. aureus, involved in the interconversion of UDP-N-acetylglucosamine and UDP-N-acetylmannosamine. These saccharides are used in the synthesis of the wall teichoic acids (WTA), and when the enzyme is inactivated or deleted the minimum inhibitory concentration (MIC) for several ²-lactam antibiotics is reduced, indicating the sensibilization of the strain. The other enzymes are two glycosyltransferases (GTs) from E. faecalis recently showed to be involved in the decoration of the biofilm matrix. The loss of function of these genes, named epaI and epaOX, was shown to result in decreased biofilm formation and increased susceptibility to antibiotics. Here we propose an investigation of the dynamics of MnaA opening/closing during catalysis in order to identify the most probable structural state for the binding of an inhibitor. This task involves precise free energies evaluation of the opening of the enzyme using the metadynamics approach in molecular dynamics simulations. The most probable state will be further be used for the screening of binding candidates using the ligand docking approach. The compounds identified in this stage will be purchased and experimentally tested to characterize the binding and their ability to inhibit the enzyme activity. The genes for the GTs from E. faecalis will be cloned and used for heterologous expression in E. coli. The purified enzymes will be used for protein crystallization and crystal structure determination. The crystal structures, once obtained, will be used for the screening of inhibitor candidates using ligand docking. (AU)

Scientific publications

(8)

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

BARRA, ANGELICA LUANA C.; DANTAS, LIVIA DE OLIVEIRA C.; MORAO, LUANA GALVAO; GUTIERREZ, RAISSA F.; POLIKARPOV, IGOR; WRENGER, CARSTEN; NASCIMENTO, ALESSANDRO S.. Essential Metabolic Routes as a Way to ESKAPE From Antibiotic Resistance. FRONTIERS IN PUBLIC HEALTH, v. 8, FEB 28 2020. (15/13684-0, 17/18173-0, 15/26722-8)

SONODA, MILTON T.; GODOY, ANDRE S.; PELLEGRINI, VANESSA O. A.; KADOWAKI, MARCO A. S.; NASCIMENTO, ALESSANDRO S.; POLIKARPOV, IGOR. Structure and dynamics of Trichoderma harzianum Cel7B suggest molecular architecture adaptations required for a wide spectrum of activities on plant cell wall polysaccharides. BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, v. 1863, n. 6, p. 1015-1026, JUN 2019. (14/06565-2, 15/13684-0, 17/18173-0)

MINARI, KARINE; DE AZEVEDO, ERIKA CHANG; RODRIGUES KIRALY, VANESSA THOMAZ; HELENO BATISTA, FERNANDA APARECIDA; DE MORAES, FABIO ROGERIO; DE MELO, FERNANDO ALVES; NASCIMENTO, ALESSANDRO SILVA; GAVA, LISANDRA MARQUES; INACIO RAMOS, CARLOS HENRIQUE; BORGES, JULIO CESAR. Thermodynamic analysis of interactions of the Hsp90 with adenosine nucleotides: A comparative perspective. International Journal of Biological Macromolecules, v. 130, p. 125-138, JUN 1 2019. (15/26722-8, 13/25646-0, 17/18173-0, 11/23110-0, 14/07206-6, 12/50161-8, 09/53989-4, 17/07335-9)

SARTORI, GERALDO RODRIGUES; NASCIMENTO, ALESSANDRO S.. Comparative Analysis of Electrostatic Models for Ligand Docking. FRONTIERS IN MOLECULAR BIOSCIENCES, v. 6, JUL 3 2019. (15/13684-0, 17/18173-0, 15/26722-8)

DE AZEVEDO, ERIKA CHANG; NASCIMENTO, ALESSANDRO S.. Energy landscape of the domain movement in Staphylococcus aureus UDP-N-acetylglucosamine 2-epimerase. Journal of Structural Biology, v. 207, n. 2, p. 158-168, AUG 1 2019. (15/13684-0, 17/18173-0, 15/26722-8)

FERNANDES, ADRIANO DE FREITAS; LEONARDO, DIEGO ANTONIO; CAVINI, ITALO AUGUSTO; ROSA, HIGOR VINICIUS DIAS; VARGAS, JHON ANTONI; PEREIRA, HUMBERTO D'MUNIZ; NASCIMENTO, ALESSANDRO S.; GARRATT, RICHARD CHARLES. Conservation and divergence of the G-interfaces of Drosophila melanogaster septins. CYTOSKELETON, v. N/A, p. 16-pg., 2023-01-03. (14/15546-1, 19/22000-9, 20/03983-9, 17/18173-0, 20/02897-1, 18/19992-7, 21/08158-9)

DE SOUZA, JOAO VICTOR; NOGUEIRA, VICTOR H. R.; NASCIMENTO, ALESSANDRO S.. Ligand binding free energy evaluation by Monte Carlo Recursion. COMPUTATIONAL BIOLOGY AND CHEMISTRY, v. 103, p. 12-pg., 2023-02-20. (17/18173-0, 20/03983-9, 14/06565-2, 10/15376-8, 14/01751-2, 15/01709-9, 15/26722-8)

DE AZEVEDO, ERIKA CHANG; NASCIMENTO, ALESSANDRO S.. The beta-lactam ticarcillin is a Staphylococcus aureus UDP-N-acetylglucosamine 2-epimerase binder. Biochimie, v. 197, p. 8-pg., 2022-02-03. (17/18173-0, 15/26722-8, 15/13684-0, 20/03983-9)