Applied structural biology involved in the biosynthesis of natural products: biotechnolgical aplications and study of unusual molecular reactions

• Grant number: 18/00351-1
• Support Opportunities: Regular Research Grants
• Start date: September 01, 2018
• End date: February 28, 2021
• Field of knowledge: Biological Sciences - Biophysics - Molecular Biophysics
• Principal Investigator: Marcio Vinicius Bertacine Dias
• Grantee: Marcio Vinicius Bertacine Dias
• Host Institution: Instituto de Ciências Biomédicas (ICB). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• Associated scholarship(s): 19/07651-3 - Purification and crystallization of proteins involved in the biosynthesis of antibiotics, BP.TT

Abstract

Soil microorganisms are responsible for the production of a large number of antibiotics due to the highly competitive environment for space and nutrients. In addition, we can also use such molecules in the treatment of various illness, including infectious diseases and cancer. Several groups of antibiotics, such as aminoglycosides, changed completely the Medicine because to the benefits of these molecules in the treatment of diseases. However, the way of how the microorganisms produce these compounds has become an important field in biological chemistry, as by the biotechnological potential that the involved enzymes have, as by the unusual catalytic mechanisms and structures. Our research group has put efforts to understand the biosynthesis of some of such molecules. In this project, we intend to deep our structural studies in the biosynthesis of two classes of aminoglycosides, including gentamicins and butirosin. Additionally, we expect to structurally characterize enzymes involved in the closure of rings in two polyethers ionophore antibiotics, tetronasin and tetronomycin. For the biosynthesis of gentamicin, a set of four PLP dependent enzymes (GenB1-GenB4) are involved in the production of gentamicin C complex. However, although these enzymes have sequential similarity, they perform unique reactions and act as aminotransferases, epimerases, and dehydratases. We have as an objective, to determine the structure of these enzymes, understand their structural mechanisms of catalysis and the specificity for substrates. On the other hand, butirosin is an aminoglycoside that has an (S)-4-amino-2-hydroxybutyrate (AHBA) moiety linked to one of its aminosugars. This group provides for the butirosin to be less susceptible to the enzymatic mechanisms of resistance. Thus, we expect to structurally characterize two enzymes that have non-conserved sequences: one involved in the biosynthesis of the AHBA moiety and another involved in the transference of the AHBA moiety to the ribostamycin to produce butirosin. With these results, we expect to obtain structural insights that may provide biotechnological applications in the production of new derivatives of antibiotics. Finally, the closure of two rings in tetronasin and tetronomycin seems to be catalyzed by enzymes denominated Diels-Alderases and, in this project, we still intend to start the structural studies of hypothetical Diels-Alderases from the biosynthesis of these compounds, characterize their active sites and the interaction with substrate analogs. Thus, these results might provide insights about their catalytic mechanisms. In general, we expect structurally study different problems about natural product biosynthesis that might be biotechnologically useful for the production of new derivatives of antibiotics as well as to understand the peculiarity of Nature in their unusual enzymes. (AU)

Scientific publications

(12)

(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)

DE PAIVA, FERNANDA C. R.; CHAN, KAREN; SAMBORSKYY, MARKIYAN; SILBER, ARIEL M.; LEADLAY, PETER F.; DIAS, MARCIO V. B.. The crystal structure of AjiA1 reveals a novel structural motion mechanism in the adenylate-forming enzyme family. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, v. 76, n. 12, p. 1201-1210, DEC 1 2020. (16/06034-2, 18/00351-1)

RIBEIRO, JOAO AUGUSTO; CHAVEZ-PACHECO, SAIR MAXIMO; DE OLIVEIRA, GABRIEL STEPHANI; SILVA, CATHARINA DOS SANTOS; PIMENTA GIUDICE, JOAO HENRIQUE; LIBREROS-ZUNIGA, GERARDO ANDRES; BERTACINE DIAS, MARCIO VINICIUS. Crystal structures of the closed form of Mycobacterium tuberculosis dihydrofolate reductase in complex with dihydrofolate and antifolates. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, v. 75, n. 7, p. 682-693, JUL 2019. (13/15906-5, 15/09188-8, 18/00351-1, 14/24486-2, 16/18721-4)

LITTLE, RORY; PAIVA, FERNANDA C. R.; JENKINS, ROBERT; HONG, HUI; SUN, YUHUI; DEMYDCHUK, YULIYA; SAMBORSKYY, MARKIYAN; TOSIN, MANUELA; LEEPER, FINIAN J.; DIAS, MARCIO V. B.; et al. Unexpected enzyme-catalysed [4+2] cycloaddition and rearrangement in polyether antibiotic biosynthesis. NATURE CATALYSIS, v. 2, n. 11, p. 1045-1054, NOV 2019. (15/09188-8, 17/50140-4, 18/00351-1)

DE PAIVA, FERNANDA C. R.; CHAN, KAREN; SAMBORSKYY, MARKIYAN; SILBER, ARIEL M.; LEADLAY, PETER F.; DIAS, MARCIO V. B.. The crystal structure of AjiA1 reveals a novel structural motion mechanism in the adenylate-forming enzyme family. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, v. 76, p. 10-pg., 2020-12-01. (18/00351-1, 16/06034-2)

RIBEIRO, JOAO AUGUSTO; CHAVEZ-PACHECO, SAIR MAXIMO; DE OLIVEIRA, GABRIEL STEPHANI; SILVA, CATHARINA DOS SANTOS; PIMENTA GIUDICE, JOAO HENRIQUE; LIBREROS-ZUNIGA, GERARDO ANDRES; BERTACINE DIAS, MARCIO VINICIUS. Crystal structures of the closed form of Mycobacterium tuberculosis dihydrofolate reductase in complex with dihydrofolate and antifolates. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, v. 75, p. 12-pg., 2019-07-01. (13/15906-5, 18/00351-1, 15/09188-8, 14/24486-2, 16/18721-4)

TORMET-GONZALEZ, GABRIELA D.; WILSON, CAROLINA; DE OLIVEIRA, GABRIEL STEPHANI; DOS SANTOS, JADEMILSON CELESTINO; DE OLIVEIRA, LUCIANA G.; DIAS, MARCIO VINICIUS BERTACINE. An epoxide hydrolase from endophytic Streptomycess hows unique structural features and wide biocatalytic activity. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, v. 76, p. 8-pg., 2020-09-01. (19/10564-5, 18/00351-1, 15/09188-8, 11/06209-3, 14/50249-8, 10/15971-3, 13/26242-0, 14/12727-5)

RIBEIRO, JOAO A.; HAMMER, ALEXANDER; LIBREROS-ZUNIGA, GERARDO A.; CHAVEZ-PACHECO, SAIR M.; TYRAKIS, PETROS; DE OLIVEIRA, GABRIEL S.; KIRKMAN, TIMOTHY; EL BAKALI, JAMAL; ROCCO, SILVANA A.; SFORCA, MAURICIO L.; et al. Using a Fragment-Based Approach to Identify Alternative Chemical Scaffolds Targeting Dihydrofolate Reductase from Mycobacterium tuberculosis. ACS INFECTIOUS DISEASES, v. 6, n. 8, p. 2192-2201, AUG 14 2020. (10/15971-3, 13/15906-5, 18/00351-1)

LI, SICONG; BURY, PRISCILA DOS SANTOS; HUANG, FANGLU; GUO, JUNHONG; SUN, GUO; REVA, ANNA; HUANG, CHUAN; JIAN, XINYUN; LI, YUAN; ZHOU, JIAHAI; et al. Mechanistic Insights into Dideoxygenation in Gentamicin Biosynthesis. ACS CATALYSIS, v. 11, n. 19, p. 12274-12283, OCT 1 2021. (14/07843-6, 15/09188-8, 10/15971-3, 18/00351-1)

DE OLIVEIRA, GABRIEL S.; ADRIANI, PATRICIA P.; RIBEIRO, JOAO AUGUSTO; MORISSEAU, CHRISTOPHE; HAMMOCK, BRUCE D.; DIAS, MARCIO VINICIUS B.; CHAMBERGO, FELIPE S.. The molecular structure of an epoxide hydrolase from Trichoderma reesei in complex with urea or amide-based inhibitors. International Journal of Biological Macromolecules, v. 129, p. 653-658, MAY 15 2019. (13/15906-5, 16/12859-4, 15/03329-9, 15/09188-8, 18/00351-1, 14/24107-1, 17/25705-8)

ADRIANI, PATRICIA P.; DE PAIVA, FERNANDA C. R.; DE OLIVEIRA, GABRIEL S.; LEITE, AMANDA C.; SANCHES, ADRIANA S.; LOPES, ADRIANA RIOS; DIAS, MARCIO V. B.; CHAMBERGO, FELIPE S.. Structural and functional characterization of the glutathione peroxidase-like thioredoxin peroxidase from the fungus Trichoderma reesei. International Journal of Biological Macromolecules, v. 167, p. 93-100, JAN 15 2021. (18/00351-1, 17/25705-8, 19/05227-0, 14/24107-1)

RIVAS ARENAS, LAURA A.; DE PAIVA, FERNANDA C. R.; ROSSINI, NICOLAS DE O.; LI, YANYAN; SPENCER, JONATHAN; LEADLAY, PETER; DIAS, MARCIO V. B.. Crystal structure of BtrK, a decarboxylase involved in the (S)-4-amino-2-hydroxybutyrate (AHBA) formation during butirosin biosynthesis. Journal of Molecular Structure, v. 1267, p. 10-pg., 2022-06-30. (18/00351-1)

BILYK, OKSANA; OLIVEIRA, GABRIEL S.; DE ANGELO, RAFAELA M.; ALMEIDA, MICHELL O.; HONORIO, KATHIA MARIA; LEEPER, FINIAN J.; DIAS, MARCIO V. B.; LEADLAY, PETER F.. Enzyme-Catalyzed Spiroacetal Formation in Polyketide Antibiotic Biosynthesis. Journal of the American Chemical Society, v. 144, n. 32, p. 9-pg., 2022-08-03. (18/00351-1, 20/03850-9)