Research article
In silico drug re-purposing against African sleeping sickness using GlcNAc-PI de-N-acetylase as an experimental target

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Abstract

Trypanosoma brucei is a protozoan that causes African sleeping sickness in humans. Many glycoconjugate compounds are present on the entire cell surface of Trypanosoma brucei to control the infectivity and survival of this pathogen. These gycoconjugates are anchored to the plasma membrane with the help of glycosyl phosphatidyl inositol (GPI) anchors. This type of anchor is much more common in protozoans than in other eukaryotes. The second step of glycosyl phosphatidyl inositol (GPI) anchor biosynthesis is catalyzed by an enzyme, which is GlcNAc-PI de-N-acetylase. GlcNAc-PI de-N-acetylase has a conserved GPI domain, which is responsible for the functionality of this enzyme. In this study, the three-dimensional structure of the target is modelled by I-TASSER and the ligand is modelled by PRODRG server. It is found that the predicted active site residues of the GPI domain are ultra-conserved for the Trypanosomatidae family. The predicted active site residues are His41, Pro42, Asp43, Asp44, Met47, Phe48, Ser74, Arg80, His103, Val144, Ser145, His147 and His150. Two hydrogen bond acceptors and four hydrogen bond donors are found in the modelled pharmacophore. All compounds of the Drugbank database and twenty three known inhibitors have been considered for structure based virtual screening. This work is focused on approved drugs because they are already tested for safety and effectiveness in humans. After the structure-based virtual screening, seventeen approved drugs and two inhibitors are found, which interact with the ligand on the basis of the designed pharmacophore. The docking has been performed for the resultant seventeen approved drugs and two known inhibitors. Two approved drugs have negative binding energy and their pKa values are similar to the selected known inhibitors. The result of this study suggests that the approved drugs Ethambutol (DB00330) and Metaraminol (DB00610) may prove useful in the treatment of African sleeping sickness.

Section snippets

Background

The protozoa are among the most diverse and ancient group of organisms in the eukaryotic kingdom (Sogin et al., 1989). Many of their members are parasitic, of which some belonging to the family Trypanosomatidae (Trypanosoma brucei, Trypanosoma cruzi, Leishmania Species) cause some of the worst diseases in humans and their domestic livestock. There are two sub species of the genus Trypanosoma, T.brucei gambiense which causes African sleeping sickness in humans and T. brucei brucei which causes

Material and methods

The flowchart of steps of our study of re-purposing of drugs is given in Fig. 1. The drug target, GlcNAc-PI de-N-acetylase, sequence (TTDR00597) for T.brucei has been taken from the Therapeutic Target Database (TTD) (Chen et al., 2002). The Uniprot Id of the target sequence is Q8I8A5. Then BLASTP (Altschul et al., 1990) against RefSeq protein sequence database has been performed to detect homologues of this target protein sequence of T. brucei. A Web-based tool, SMART is used to find the active

Results and discussion

The results, after applying the sequential steps of drug re-purposing, are as follow:

Acknowledgements

MR is thankful to the Council of Scientific & Industrial Research (CSIR), India for the financial support through CSIR Senior Research Fellowship. The authors would also like to acknowledge and thank the two anonymous reviewers, whose valuable and incisive suggestions led to a vast improvement of this paper.

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