Enzymatic degradation of microbial biofilm exopolisacharides: structural biophysics, molecular biotechnology and synthetic biochemistry of CAZymes in search for new enzymatic tools for antimicrobial treatments

• Grant number: 21/08780-1
• Support Opportunities: Research Projects - Thematic Grants
• Start date: March 01, 2023
• End date: February 29, 2028
• Field of knowledge: Biological Sciences - Biophysics - Molecular Biophysics
• Principal Investigator: Igor Polikarpov
• Grantee: Igor Polikarpov
• Host Institution: Instituto de Física de São Carlos (IFSC). Universidade de São Paulo (USP). São Carlos , SP, Brazil
• Associated researchers: Ana Carolina Migliorini Figueira ; André Luis Souza dos Santos ; Camila Alves de Rezende ; Cristina Kurachi ; Eduardo Ribeiro de Azevedo ; Fernando Segato ; Francisco Eduardo Gontijo Guimaraes ; Marcos Pileggi ; Mario de Oliveira Neto ; Natalia Mayumi Inada
• Associated research grant(s): 24/00533-3 - Biorefining hemicelluloses and lignin from sugarcane bagasse, AP.R
• Associated scholarship(s): 23/18441-5 - Degradation of extracellular matrix of biofilms from pathogenic microorganisms, BP.DR; 23/13115-2 - Structural and biochemical studies of Saccharum officinarum glycosil hydrolases involved in arabinoxylan degradation in the aerenchyma formation process, BP.DR; 23/12553-6 - Cloning and expression and crystallization of proteins involved in the degradation of complex carbohydrates found in exopolysaccharides from microbial biofilms, BP.TT; 23/10037-0 - Characterization and application of bacterial glycosyl hydrolases for Destruction of the Streptococcus mutans biofilm., BP.IC; 23/07897-8 - Biochemical and structural studies of CAZymes with potential in the degradation of exopolysaccharides from microbial biofilms, BP.PD

Abstract

The consequences of microbial resistance to antibiotics may represent a catastrophe for public health in the near future with an estimated 700,000 deaths per year, in addition to prolonged hospitalizations and potentially intractable diseases. Considering only antimicrobial resistance, the estimated number of deaths will increase to more than 10 million deaths/year by 2050, if this situation is not controlled. Hospital infections are already an extremely serious public health problem in Brazil and worldwide, causing thousands of deaths every day in addition to the steady increase in medical treatment costs valued at $ 33 billion per year in the United States and E 13 to E 24 billion per year in the European Union.It is estimated that 99% of the microorganisms on Earth live in biofilms. The formation of bacterial biofilms can increase antibiotic resistance by 10 to 1,000 times. Biofilms have a complex structure that aggregates microbial cells within an extracellular matrix, composed mainly of exopolysaccharides, extracellular DNA and proteins, where exopolysaccharides represent the main fraction. Within the scope of this project, we are proposing to conduct systematic studies of enzymes active in complex carbohydrates (CAZymes) with potential in the degradation and prevention of the bacterial biofilm formation, using Structural Biophysics, Molecular Biotechnology and Synthetic Biochemistry techniques. Biochemical and structural characterizations of enzymes from recent and still poorly explored CAZymes families will be conducted and the enzymes with high specific activities for exopolysaccharides degradation will be identified. CAZymes with activities against different extracellular matrix biopolymers will be combined to achieve greater levels of degradation and prevention of biofilm formation. The enzymatic action will also be enhanced by the combined use with the existing antibiotics and/or photodynamic therapy. In addition, following Synthetic Biochemistry approaches, the enzymatic circuits will be developed and tested in order to interfere with the formation of biofilms. The enzymatic degradation of biofilms can strengthen our arsenal of antimicrobial therapy and provide important information for the development of revolutionary strategies for the treatment of persistent infections. (AU)

Scientific publications

(11)

(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)

SAMANIEGO, LORGIO VICTOR BAUTISTA; HIGASI, PAULA MIWA RABELO; CAPETTI, CAIO CESAR DE MELLO; CORTEZ, ANELYSE ABREU; PRATAVIEIRA, SEBASTIAO; PELLEGRINI, VANESSA DE OLIVEIRA ARNOLDI; DABUL, ANDREI NICOLI GEBIELUCA; SEGATO, FERNANDO; POLIKARPOV, IGOR. Staphylococcus aureus microbial biofilms degradation using cellobiose dehydrogenase from Thermothelomyces thermophilus M77. International Journal of Biological Macromolecules, v. 247, p. 12-pg., 2023-07-15. (21/08780-1)

NAKAMURA, ALINE MINALI; GODOY, ANDRE SCHUTZER; KADOWAKI, MARCO ANTONIO SEIKI; TRENTIN, LUCAS N.; GONZALEZ, SINKLER E. T.; SKAF, MUNIR S.; POLIKARPOV, IGOR. Structures of BlEst2 from Bacillus licheniformis in its propeptide and mature forms reveal autoinhibitory effects of the C-terminal domain. FEBS Journal, v. 291, n. 22, p. 21-pg., 2024-07-27. (19/17373-0, 13/08293-7, 21/08780-1, 19/17371-8)

CORTEZ, ANELYSE ABREU; DE QUEIROZ, MATEUS XAVIER; DE OLIVEIRA ARNOLDI PELLEGRINI, VANESSA; PELLEGRINI, VANESSA OLIVEIRA ARNOLDI; DE MELLO CAPETTI, CAIO CESAR; DABUL, ANDREI NICOLI GEBIELUCA; LIBERATO, MARCELO VIZONA; PRATAVIEIRA, SEBASTIAO; RICOMINI FILHO, ANTONIO PEDRO; POLIKARPOV, IGOR. Recombinant Prevotella melaninogenica α-1,3 glucanase and Capnocytophaga ochracea α-1,6 glucanase as enzymatic tools for in vitro degradation of S. mutans biofilms. WORLD JOURNAL OF MICROBIOLOGY & BIOTECHNOLOGY, v. 39, n. 12, p. 12-pg., 2023-12-01. (20/15092-1, 21/08780-1)

CAPETTI, CAIO CESAR DE MELLO; PELLEGRINI, VANESSA DE OLIVEIRA ARNOLDI; VACILOTTO, MILENA MOREIRA; CURVELO, ANTONIO APRIGIO DA SILVA; FALVO, MAURICIO; GUIMARAES, FRANCISCO EDUARDO GONTIJO; ONTANON, ORNELLA M.; CAMPOS, ELEONORA; POLIKARPOV, IGOR. Evaluation of Hydrothermal and Alkaline Pretreatment Routes for Xylooligosaccharides Production from Sugar Cane Bagasse Using Different Combinations of Recombinant Enzymes. Food and Bioprocess Technology, v. 17, n. 7, p. 13-pg., 2023-10-18. (19/10942-0, 21/08780-1)

HIGASI, PAULA M. R.; POLIKARPOV, IGOR. Cellulose degradation by lytic polysaccharide monooxygenase fueled by an aryl-alcohol oxidase. Cellulose, v. N/A, p. 9-pg., 2023-10-04. (21/08780-1)

KANE, AISSATA OUSMANE; CORTEZ, ANELYSE ABREU; PELLEGRINI, VANESSA OLIVEIRA ARNOLDI; NGOM, BALLA DIOP; FILGUEIRAS, JEFFERSON G.; DE AZEVEDO, EDUARDO R.; POLIKARPOV, IGOR. Combined liquid hot water and sulfonation pretreatment of sugarcane bagasse to maximize fermentable sugars production. INDUSTRIAL CROPS AND PRODUCTS, v. 201, p. 13-pg., 2023-05-23. (15/13684-0, 21/08780-1)

DE ARAUJO, EVANDRO ARES; CORTEZ, ANELYSE ABREU; PELLEGRINI, VANESSA DE OLIVEIRA ARNOLDI; VACILOTTO, MILENA MOREIRA; CRUZ, AMANDA FREITAS; BATISTA, PAULO RICARDO; POLIKARPOV, IGOR. Molecular mechanism of cellulose depolymerization by the two-domain BlCel9A enzyme from the glycoside hydrolase family 9. Carbohydrate Polymers, v. 329, p. 18-pg., 2024-01-13. (21/08780-1)

SEPULCHRO, ANA GABRIELA VEIGA; VACILOTTO, MILENA MOREIRA; DIAS, LUCAS D.; PELLEGRINI, VANESSA O. A.; VELASCO, JOSMAN; INADA, NATALIA M.; SEGATO, FERNANDO; POLIKARPOV, IGOR. Light-driven Lytic Polysaccharide Monooxygenase Catalysis Mediated by Type I Photosensitizers. CHEMBIOCHEM, v. N/A, p. 14-pg., 2024-11-11. (21/08780-1, 24/00533-3, 19/13569-8, 13/07276-1, 14/50857-8)

MATEUS XAVIER-QUEIROZ; PEDRO RICARDO VIEIRA HAMANN; HEIDI AARØ ÅMDAL; IGOR POLIKARPOV; FERNANDA CRISTINA PETERSEN; ANTÔNIO PEDRO RICOMINI-FILHO. Absence of inhibitory effects of two new glucanases on streptococcus mutans growth. Braz. J. Oral Sci., v. 23, 2025-01-10. (23/07897-8, 20/15092-1, 21/08780-1)

KANE, AISSATA OUSMANE; SCOPEL, EUPIDIO; CORTEZ, ANELYSE ABREU; ROSSI, BRUNO ROBERTO; PELLEGRINI, VANESSA OLIVEIRA ARNOLDI; REZENDE, CAMILA ALVES; POLIKARPOV, IGOR. Enzyme-assisted production of cellulose nanofibers from bleached and bleached/sulfonated sugarcane bagasse: impact of sulfonation on nanocellulose properties and yields. Cellulose, v. 30, n. 18, p. 16-pg., 2023-11-18. (19/19360-3, 21/08780-1, 15/13684-0, 21/12071-6, 18/23769-1)

BRIGANTI, LORENZO; MANZINE, LIVIA R.; CAPETTI, CAIO CESAR DE MELLO; ARAUJO, EVANDRO ARES DE; PELLEGRINI, VANESSA DE OLIVEIRA ARNOLDI; GUIMARAES, FRANCISCO EDUARDO GONTIJO; NETO, MARIO DE OLIVEIRA; POLIKARPOV, IGOR. Unravelling biochemical and structural features of Bacillus licheniformis GH5 mannanase using site-directed mutagenesis and high-resolution protein crystallography studies. International Journal of Biological Macromolecules, v. 274, p. 16-pg., 2024-06-25. (21/08780-1)