Joanna Panecka-Hofman1, Ina Pöhner2, Francesca Spyrakis3, Talia Zeppelin2, Flavio Di Pisa4, Lucia Dello Iacono4, Alessio Bonucci4, Antonio Quotadamo5, Alberto Venturelli5, Stefano Mangani4, Maria Paola Costi6, Rebecca C Wade7. 1. Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, Heidelberg 69118, Germany; Centre of New Technologies (CeNT), University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland. Electronic address: j.panecka@cent.uw.edu.pl. 2. Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, Heidelberg 69118, Germany. 3. Department of Drug Science and Technology, University of Turin, Via P. Giuria 9, Turin 10125, Italy; Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, Modena 41121, Italy. 4. Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via Aldo Moro 2, Siena 53100, Italy. 5. Tydock Pharma srl, Strada Gherbella 294/B, Modena 41126, Italy. 6. Department of Life Sciences, University of Modena and Reggio Emilia, Via Campi 103, Modena 41121, Italy. 7. Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies (HITS), Schloß-Wolfsbrunnenweg 35, Heidelberg 69118, Germany; Center for Molecular Biology (ZMBH), DKFZ-ZMBH Alliance, Heidelberg University, Im Neuenheimer Feld 282, Heidelberg 69120, Germany; Interdisciplinary Center for Scientific Computing (IWR), Heidelberg University, Im Neuenheimer Feld 205, Heidelberg 69120, Germany. Electronic address: rebecca.wade@h-its.org.
Abstract
BACKGROUND: Multi-target approaches are necessary to properly analyze or modify the function of a biochemical pathway or a protein family. An example of such a problem is the repurposing of the known human anti-cancer drugs, antifolates, as selective anti-parasitic agents. This requires considering a set of experimentally validated protein targets in the folate pathway of major pathogenic trypanosomatid parasites and humans: (i) the primary parasite on-targets: pteridine reductase 1 (PTR1) (absent in humans) and bifunctional dihydrofolate reductase-thymidylate synthase (DHFR-TS), (ii) the primary off-targets: human DHFR and TS, and (iii) the secondary on-target: human folate receptor β, a folate/antifolate transporter. METHODS: We computationally compared the structural, dynamic and physico-chemical properties of the targets. We based our analysis on available inhibitory activity and crystallographic data, including a crystal structure of the bifunctional T. cruzi DHFR-TS with tetrahydrofolate bound determined in this work. Due to the low sequence and structural similarity of the targets analyzed, we employed a mapping of binding pockets based on the known common ligands, folate and methotrexate. RESULTS: Our analysis provides a set of practical strategies for the design of selective trypanosomatid folate pathway inhibitors, which are supported by enzyme inhibition measurements and crystallographic structures. CONCLUSIONS: The ligand-based comparative computational mapping of protein binding pockets provides a basis for repurposing of anti-folates and the design of new anti-trypanosmatid agents. GENERAL SIGNIFICANCE: Apart from the target-based discovery of selective compounds, our approach may be also applied for protein engineering or analyzing evolutionary relationships in protein families.
BACKGROUND: Multi-target approaches are necessary to properly analyze or modify the function of a biochemical pathway or a protein family. An example of such a problem is the repurposing of the known human anti-cancer drugs, antifolates, as selective anti-parasitic agents. This requires considering a set of experimentally validated protein targets in the folate pathway of major pathogenic trypanosomatid parasites and humans: (i) the primary parasite on-targets: pteridine reductase 1 (PTR1) (absent in humans) and bifunctional dihydrofolate reductase-thymidylate synthase (DHFR-TS), (ii) the primary off-targets: humanDHFR and TS, and (iii) the secondary on-target: humanfolate receptor β, a folate/antifolate transporter. METHODS: We computationally compared the structural, dynamic and physico-chemical properties of the targets. We based our analysis on available inhibitory activity and crystallographic data, including a crystal structure of the bifunctional T. cruziDHFR-TS with tetrahydrofolate bound determined in this work. Due to the low sequence and structural similarity of the targets analyzed, we employed a mapping of binding pockets based on the known common ligands, folate and methotrexate. RESULTS: Our analysis provides a set of practical strategies for the design of selective trypanosomatid folate pathway inhibitors, which are supported by enzyme inhibition measurements and crystallographic structures. CONCLUSIONS: The ligand-based comparative computational mapping of protein binding pockets provides a basis for repurposing of anti-folates and the design of new anti-trypanosmatid agents. GENERAL SIGNIFICANCE: Apart from the target-based discovery of selective compounds, our approach may be also applied for protein engineering or analyzing evolutionary relationships in protein families.
Authors: Ina Pöhner; Antonio Quotadamo; Joanna Panecka-Hofman; Rosaria Luciani; Matteo Santucci; Pasquale Linciano; Giacomo Landi; Flavio Di Pisa; Lucia Dello Iacono; Cecilia Pozzi; Stefano Mangani; Sheraz Gul; Gesa Witt; Bernhard Ellinger; Maria Kuzikov; Nuno Santarem; Anabela Cordeiro-da-Silva; Maria P Costi; Alberto Venturelli; Rebecca C Wade Journal: J Med Chem Date: 2022-06-08 Impact factor: 8.039