PhD Defense – Tatiana Vieira

Many congratulations to Tatiana F. Vieira for successfully defending her PhD thesis in Biomedicine (University of Porto, FMUP) with the title “New Drugs against biofilm formation and development: a computational and experimental approach” (28th June, Porto). Tatiana’s PhD thesis was developed under the supervision of Sérgio Sousa (FMUP/BioSIM), with the co-supervision of Manuel Simões (LEPABE, FEUP) and Nuno S. Cerqueira (FMUP, BioSIM).

Resistance to antibiotics is an increasing threat in global health and strategies to develop or find new drugs are of the utmost importance. Pseudomonas aeruginosa is a Gram-negative pathogen that shows resistance to therapeutics and that leads to high morbidity and mortality rates. It can form biofilms, sessile structures that are known to confer physical stability, increased virulence, and work as a protective armour against antimicrobial compounds. P. aeruginosa can control the expression of genes, population density, and biofilm formation through a process called quorum sensing (QS), a rather complex and hierarchical system of communication. Quorum sensing inhibitors are compounds that are able to block bacterial communication, hence, decreasing bacterial virulence and, when used in combination, potentiating the effect of the antibiotics.

In this thesis, a combined multi‐level computational approach was developed, optimized and applied to find possible inhibitors against P. aeruginosa Pqs system regulator protein MvfR (also known as PqsR) and against PqsD, an anthraniloyl-CoA anthraniloyltransferase involved in the synthesis of the secondary metabolites essential to the formation of Pseudomonas Quinolone Signal (PQS) inducer molecules. Using molecular docking and structured-based virtual screening protocols, five databases of compounds were screened for both PqsR and PqsD (FDA approved subset of the ZINC database, Chimiothèque Nationale, Mu.Ta.Lig. Virtual Chemotheca, Interbioscreen (IBS), and Comprehensive Marine Natural Products Database (CMNPD), representing a total of 221,146 molecules. The top five to ten compounds of each database were selected to be further analysed using molecular dynamics simulations. Binding affinity was validated using free energy calculations, prioritizing compounds for experimental testing. Additionally, two compounds retrieved from the virtual screening of the FDA approved database against PqsR, were selected for experimental testing on the PAO1-L strain of P. aeruginosa, to confirm the docking predictions. The activity of montelukast and cefoperazone was evaluated on QS signal inhibition, pyocyanin synthesis, and prevention and eradication of P. aeruginosa biofilms.

This work reinforces the power of computer-aided drug design tools in speeding up the drug discovery process, whether by using drug repurposing strategies or screening large databases of compounds.

We all wish you all the best for your future endeavors.