Computational Chemogenomics Drug Repositioning Strategy Enables the Discovery of Epirubicin as a New Repurposed Hit for Plasmodium falciparum and P. vivax

Abstract

Widespread resistance against antimalarial drugs thwarts current efforts for controlling the disease and urges the discovery of new effective treatments. Drug repositioning is increasingly becoming an attractive strategy since it can reduce costs, risks and time-to-market. Herein we have used this strategy to identify novel antimalarial hits. We performed a comparative in silico chemogenomics approach to select Plasmodium falciparum and P. vivax proteins as potential drug targets and analyzed these using a computer-assisted drug repositioning pipeline to identify approved drugs with potential antimalarial activity. Among seven drugs identified as promising antimalarial candidates, the anthracycline epirubicin was selected for further experimental validation. Epirubicin was shown to be potent in vitro against sensitive and multidrug-resistant P. falciparum strains and P. vivax field isolates in the nanomolar range, as well as being effective against an in vivo murine model of P. yoelii. Transmission-blocking activity was observed for epirubicin in vitro and in vivo. Finally, using yeast-based haploinsufficiency chemical genomic profiling, we aimed to get insights on epirubicin's mechanism of action. Beyond the target predicted in silico (a DNA gyrase in the apicoplast), functional assays suggested a GlcNac-1-P-transferase (GPT) enzyme as a potential target. Docking calculations predicted the binding mode of epirubicin with DNA gyrase and GPT proteins. Epirubicin is originally an antitumoral agent and presents associated toxicity. However, its antiplasmodial activity not only against P. falciparum but also P. vivax in different stages of the parasite lifecycle supports the use of this drug as a scaffold for hit-to-lead optimization in malaria drug discovery.

Ex vivo and In vitro antiplasmodial activities of approved drugs predicted to have antimalarial activities using chemogenomics and drug repositioning approach

“…Epirubicin exhibited excellent antiplasmodial activity with a mean IC 50 value of 0.158 μM which was better than that of CQ with a mean IC 50 value of 0.928 μM across all strains of P. falciparum and field isolates. The antiplasmodial activity of epirubicin compares well with other studies [ 23 ], especially to Ferreira and colleagues’ study that used computational chemogenomics and drug repositioning [ 23 ], where epirubicin displayed potent in vitro antiplasmodial activity against three different strains of P. falciparum ; 0.111 μM (3D7), 0.099 (DD2) and 0.069 (W2). Similarly, irinotecan exhibited a mean IC 50 value of 0.468 μM when tested against different strains of P. falciparum and fresh field isolates.…”

“…This was the highest Consurf analysis percentage among all the P. falciparum proteins that are similar to the proteins of the drugs tested in this study. Protein–protein pairwise alignment was performed to determine conserved amino acids in a protein [ 23 ]. This identifies functional amino acid residues shared between P. falciparum proteins and its homologous putative drug targets.…”

Promising antimalarial hits from phenotypic screens: a review of recently-described multi-stage actives and their modes of action

“…Epirubicin is predicted to be an antimalarial hit via computational chemogenomics (Ferreira Letıćia et al, 2020). It demonstrated nanomolar potency against asexual blood stage (TCP-1) P. falciparum and blocked the in vitro conversion from sexual stage P. berghei to ookinetes (IC 50 0.39 µM).…”

“…Epirubicin also reduced 53% of P. vivax oocyst formation (TCP-5) in infected mosquitoes' midguts in membrane feeding assays (Figure 1). P. falciparum Gyr subunit A (PfGyrA) was predicted to be the target of epirubicin by molecular modelling and docking (Ferreira Letıćia et al, 2020). PfGyr is a type II topoisomerase which releases tension in the supercoiled double stranded DNA and hence facilitates DNA replication (Nagano et al, 2014;.…”

“…PfGyrA is also essential for the structural integrity of the apicoplast (Goodman and McFadden, 2013;Nagano et al, 2014;Milton and Nelson, 2016;. Resistance selection for epirubicin in Saccharomyces cerevisiae resulted in downregulation of alg7, which encodes for the dolichol phosphate N-acetylglucosamine-1-phosphotransferase (Ferreira Letıćia et al, 2020). Since P. falciparum has a homologous alg7 gene that is thought to be essential, epirubicin is speculated to interfere with protein glycosylation in P. falciparum (Zhang et al, 2018;Böhme et al, 2019;Chappell et al, 2020).…”