Rute da Fonseca
Early work: protein modelling
Here is a short summary of my PhD results. My supervisor was Maria João Ramos @UPorto.
Models of cytochromes P450
During my PhD I explored some aspects of the chemistry and biology of Cytochromes p450 (CYPs). CYPs constitute a superfamily of enzymes involved in the oxidative metabolism of a wide range of compounds. Their role in the disposal of xenobiotics interferes with human health in both positive and negative ways, with some of its members being accounted for the controlled biotransformation of pharmaceutical drugs and others taking part in the activation of carcinogenic compounds.
The initial approach focused on exploring protein structure and function. Homology models were built for human and rat CYP1A2 [1], an enzyme involved in the activation of carcinogenic heterocyclic amines present in cooked red meat.
Flavones as CYP inhibitors
The following step involved the study of the interaction of human CYP1A2 with known inhibitors, two groups of naturally occurring flavonoids [2, 3]. The physicochemical characteristics of these molecules were compared and related to the differential inhibitory character they exhibited towards human CYP1A2.
This was accompanied by a thorough analysis of the specific interactions established by the flavonoids inside the active site, with the correspondent quantification by calculation of ligand/receptor binding energies.
The evolution of CYPs
I used various computational genomics methods to analyse the functional divergence of CYP2 enzymes, largely involved in the metabolism of different pharmaceutical agents [4]. Phylogenetic studies were carried out together with statistical analyses of detection of functional divergence and positive selection using both amino acid and nucleotide sequences.
The sites under positive selection in CYP2s were located in the substrate binding areas, while the areas related to maintaining the highly conserved catalytic mechanism (close to the heme prosthetic group) show signatures of negative selection. We have therefore proposed that the broadening in substrate specificity that we observe in this group of enzymes is being driven by natural selection.