In Silico Identification and in Vitro Activity of Novel Natural Inhibitors of Trypanosoma brucei Glyceraldehyde-3-phosphate-dehydrogenase

Abstract

As part of our ongoing efforts to identify natural products with activity against pathogens causing neglected tropical diseases, we are currently performing an extensive screening of natural product (NP) databases against a multitude of protozoan parasite proteins. Within this project, we screened a database of NPs from a commercial supplier, AnalytiCon Discovery (Potsdam, Germany), against Trypanosoma brucei glyceraldehyde-3-phosphate dehydrogenase (TbGAPDH), a glycolytic enzyme whose inhibition deprives the parasite of energy supply. NPs acting as potential inhibitors of the mentioned enzyme were identified using a pharmacophore-based virtual screening and subsequent docking of the identified hits into the active site of interest. In a set of 700 structures chosen for the screening, 13 (1.9%) were predicted to possess significant affinity towards the enzyme and OPEN ACCESSMolecules 2015, 20 16155 were therefore tested in an in vitro enzyme assay using recombinant TbGAPDH. Nine of these in silico hits (69%) showed significant inhibitory activity at 50 µM, of which two geranylated benzophenone derivatives proved to be particularly active with IC50 values below 10 µM. These compounds also showed moderate in vitro activity against T. brucei rhodesiense and may thus represent interesting starting points for further optimization.

Applications of the Pharmacophore Concept in Natural Product inspired Drug Design

“…This work aimed at the identification of natural inhibitors of Trypanosoma brucei Glyceraldehyde‐3‐phosphate‐dehydrogenase ( Tb GAPDH) [27] . Trypanosoma brucei is a protozoan parasite which can cause human African trypanosomiasis (HAT), also known as “sleeping sickness”.…”

The Potential of Secondary Metabolites from Plants as Drugs or Leads against Protozoan Neglected Diseases—Part III: In-Silico Molecular Docking Investigations

“…In another study, the guaianolide sesquiterpenoid lactupicrin (Figure 10) docked strongly to L. major PTR1 [375]. Herrmann and co-workers have carried out an in-silico screening of a natural products library of 700 structures against T. brucei glyceraldehyde-3-phosphate dehydrogenase (TbGAPDH) [399]. These investigators were able to identify 13 "hits" based on the molecular docking and of these, five compounds (three geranylated benzophenones, flavaspidic acid AB, and a bis-resorcinyl tetradecene derivative, Figure 11) showed significant in vitro inhibitory activity against recombinant TbGAPDH as well as T. brucei rhodesiense.…”

“…Four compounds were found to have particularly promising docking characteristics, (15:2)-anacardic acid, 3,18-diacetoxy-1-octadecene-4,6-diyne-8-ol, aculeatin D, and vismione D (Figure 12). Herrmann and co-workers have carried out an in-silico screening of a natural products library of 700 structures against T. brucei glyceraldehyde-3-phosphate dehydrogenase (TbGAPDH) [399]. These investigators were able to identify 13 "hits" based on the molecular docking and of these, five compounds (three geranylated benzophenones, flavaspidic acid AB, and a bis-resorcinyl tetradecene derivative, Figure 11) An in-silico analysis of a dataset of 683 flavonoids for molecular docking to L. mexicana pyruvate kinase found that 3-glycosylated flavonoids (seven compounds), 6,8-diglycosyl flavonoids (one compound), and biflavonoids (four compounds) were the most promising ligands [400].…”

Molecular basis for covalent inhibition of glyceraldehyde‐3‐phosphate dehydrogenase by a 2‐phenoxy‐1,4‐naphthoquinone small molecule

“…The unusual compartmentalization of glycolysis inside the specialized organelle glycosome in Trypanosoma and Leishmania suggested the development of GAPDH inhibitors for the treatment of Trypanosomatidae diseases . The identification of several small‐molecule inhibitors, together with genetic validation by RNAi experiments, has confirmed its druggability. In parallel, human GAPDH ( h GAPDH) has emerged as an appealing target for anticancer therapy .…”