2016 Conference on Computational Modelling with COPASI
Manchester Institute of Biotechnology, 12th – 13th May, 2016

Insight for anti-parasitic drug design — From comparative pocketome analysis to computational modeling of a parasitic folate & biopterin pathway

Ina Pöhner1, Joanna Panecka1, Francesca Spyrakis2, Talia Zeppelin1, Maria Paola Costi2, Rebecca C. Wade1,3

1 - Heidelberg Institute for Theoretical Studies (HITS) gGmbH, Germany; 2 - University of Modena and Reggio Emilia, Italy; 3 - Heidelberg University, Germany

Keywords: Neglected tropical diseases, Folate pathway, dihydrofolate reductase, DHFR, pteridine reductase 1, PTR1, pocket analysis, pathway modeling


Trypanosomatid parasites are the etiological agents of several neglected tropical diseases (NTD) including sleeping sickness, Chagas' disease and leishmaniasis which collectively affect nearly 10 million people worldwide. The few available therapeutics are characterized by toxicity, poor efficacy and emerging parasite resistance, implying a need for new, safe and effective drugs. Drug discovery for NTD often involves target-based approaches, for example focusing on the folate pathway as an established target pathway in the treatment of bacterial infections and some parasitic diseases, such as malaria. Validated key targets include dihydrofolate reductase (DHFR), which is the target of classical antifolate drugs like methotrexate (MTX). MTX is however ineffective against Trypanosomatids due to pteridine reductase 1 (PTR1), an enzyme mostly responsible for the salvage of pterins. PTR1, which has in part overlapping activity with DHFR, can provide a metabolic bypass supplying reduced folates necessary for parasite survival in the case of DHFR inhibition.

Consequently, PTR1, which is unique to the parasite, is considered a promising target for the development of improved therapies. However, many PTR1 inhibitors alone seem incapable of parasite growth inhibition and drug design efforts focus on the development of dual inhibitors targeting both PTR1 and DHFR as well as combination therapies with MTX, which was shown to improve the efficacy and the potency of PTR1 inhibitors.

Aiming at the identification of binding site features common to PTR1 and DHFR to be utilized in the design of dual inhibitors, we carried out an extensive comparison of the structural and physico-chemical properties of folate pathway enzyme binding pockets. We found a surprisingly low similarity of the molecular binding features of PTR1 and DHFR, despite their overlapping substrate pool. DHFR binding pockets were clearly more hydrophobic than PTR1 pockets. As a consequence, the parasitic DHFR appears more druggable than the key target PTR1, but its closely related human homolog complicates efforts to achieve dual inhibition. Our analysis pinpoints both potential sites for optimization towards the parasitic targets and differences to allow for off-target selectivity.

Beyond the well-studied examples of PTR1 and DHFR, the parasites utilize a complex network involving many additional overlapping enzyme functionalities. Therefore, we expanded our initial studies focused on the experimentally best characterized proteins to involve the full pocketome of the Leishmania major folate/biopterin pathway. Mathematical modeling of the parasitic folate and biopterin metabolism will supplement the structure-based studies by simplifying the identification of potential additional promising points of attack in the network, allowing the estimation of minimum levels of enzyme inhibition, and adding to our understanding of target-crosstalk and the effects observed in combination therapy by PTR1 and known DHFR inhibitors.

Conference Program