Structural studies and ligand discovery of the enzyme dihydropteroate synthase from Xanthomonas albilineans for the leaf scald treatment

Author(s)

Andrew Albert de Oliveira

• Document type: Doctoral Thesis
• Press: São Carlos.
• Institution: Universidade de São Paulo (USP). Instituto de Física de São Carlos (IFSC/BT)
• Defense date: 2019-09-06

Examining board members

Rafael Victório Carvalho Guido; Luis Eduardo Aranha Camargo; Marcio Vinícius Bertacine Dias; Marcos Vicente de Albuquerque Salles Navarro; Mirela Ines de Sairre

• Advisor: Rafael Victório Carvalho Guido

Abstract

The gram-negative bacterium Xanthomonas albilineans causes one of the substantial diseases found in sugarcane crops: leaf scald. Currently, no chemical or biological product is known to control this plague. Therefore, this severe panorama raises the urgent need for developing new alternatives for pathogen control. Therefore, strategies were drawn for the discovery and development of new bioactive molecules through Phenotypic Screening, Medicinal Chemistry and Structural Biology. The inhibitory potentials of two imidazole series were assessed through bacterial growth analysis, totalizing 41 compounds, that resulted in 11 intermediate capacity inhibitors to stop the bacterium growth. Simultaneously, we have selected two molecular targets based on two X. albilineans essential pathways: i. Folate biosynthesis and ii. Synthesis of albicidin. The enzyme dihydropteroate synthase (XaDHPS) is related to the production of tetrahydrofolate, while the enzyme benzoate coenzyme A ligase (XaBCL) linked to the virulence factor. Over the enzyme XaDHPS, significant advances were obtained, among them: i. Purification; ii. Crystallisation; iii. Collection of more than 300 datasets iv. Resolution of the unpublished 3D structure (in the apoenzyme form and complexes with native substrate and product) and v. Screening, identification, validation and structural detailing of complexed fragments. In detail, the binding modes of 43 molecular fragments bound to diverse protein regions were elucidated. We recognised the presence of a single site, β1, as well as the characterisation of auxiliary pockets and transition states in the movement of the catalytic loops. The presence of nearby compounds facilitates binding into a new molecule with inhibitory potential against XaDHPS. The results of this work will allow planning methods based on the receptor target structure (SBDD) and the fragment (FBDD) to be applied for the construction and development of new bioactive compounds as agrochemicals candidates for sugarcane culture. In addition, the mapping of this enzyme contributes to the development of new antimicrobial agents in the fight against diseases caused by gram-negative bacteria. (AU)

• FAPESP's process: 15/07005-3 - Structural Biology and Medicinal Chemistry studies toward the discovery and design of new agrochemicals
• Grantee: Andrew Albert de Oliveira
• Support Opportunities: Scholarships in Brazil - Doctorate (Direct)