Drug discovery against leishmaniasis : Bio- and chemoinformatic guided strategies for target evaluation and hit identification

Abstract: Leishmaniasis is a neglected tropical disease mainly affecting poor people in developing countries. It is caused by infections of flagellated protozoa belonging to genus Leishmania. The few available drugs are associated with problems such as low effectiveness, severe side effects and resistance development. The overall aim of this thesis is to aid in drug discovery against leishmaniasis – primarily using bio- and chemoinformtic approaches.In the first part of the thesis potential drug targets in Leishmania parasites were identified and hits against these targets were thereafter suggested. In paper I bioinformatics together with experimental work were used to evaluate lateral gene transfer (LGT) in genus Leishmania. LGTs of prokaryote origin often lack human homologs, and are therefore hypothesized to be valuable drug targets. LGT in genus Leishmania is shown to be a dynamic process in which some acquired genes are conserved in the recipient genomes and others are degraded and eventually lost. Some LGTs have also undergone pseudogenization. It is thus important to evaluate LGT products before exploring them as potential drug targets.In paper II ligand-based virtual screening and molecular docking were used to suggest potential hits against the LGT product pteridine reductase 1 (PTR1) and the two-domain enzyme dihydrofolate reductase-thymidylate synthase (DHFR-TS) both involved in folate metabolism. DHFR-TS is not encoded by an LGT but it has been hypothesised that several enzymes in the folate pathway need to be inhibited to affect the viability of Leishmania parasites. One potential hit compound against PTR1 and the DHFR-domain and four hit compounds against PTR1 and the TS-domain were identified and tested on Leishmania tropica promastigotes. The suggested PTR1/TS inhibitors had no effect in the promastigote assay, however one of them enhanced the effect of the PTR1/DHFR inhibitor, which also had effect on its own.In the second part of the project, focus shifted towards predictions of targets for compounds with known anti-leishmanial activity but unknown mechanisms of actions. In paper III a ligand-based-target fishing (LBTF) method was developed. The reference compounds were metabolites to metabolic enzymes and similarities were assessed with Euclidean distance calculations in chemical property space. The LBTF approach was used to suggest potential targets to a set of anti-leishmanial agents retrieved from ChEMBL-database. The theory behind the LBTF method developed in paper III was also used in paper IV to predict targets of two sponge-derived alkaloids that where shown to have anti-leishmanial activity.