In silico activity profiling reveals the mechanism of action of antimalarials discovered in a high-throughput screen

Abstract

The growing resistance to current first-line antimalarial drugs represents a major health challenge. To facilitate the discovery of new antimalarials, we have implemented an efficient and robust highthroughput cell-based screen (1,536-well format) based on proliferation of Plasmodium falciparum (Pf) in erythrocytes. From a screen of Ϸ1.7 million compounds, we identified a diverse collection of Ϸ6,000 small molecules comprised of >530 distinct scaffolds, all of which show potent antimalarial activity (<1.25 M). Most known antimalarials were identified in this screen, thus validating our approach. In addition, we identified many novel chemical scaffolds, which likely act through both known and novel pathways. We further show that in some cases the mechanism of action of these antimalarials can be determined by in silico compound activity profiling. This method uses large datasets from unrelated cellular and biochemical screens and the guilt-by-association principle to predict which cellular pathway and/or protein target is being inhibited by select compounds. In addition, the screening method has the potential to provide the malaria community with many new starting points for the development of biological probes and drugs with novel antiparasitic activities.antifolates ͉ cheminformatics ͉ high-throughput screening ͉ Plasmodium falciparum

Reprogramming of murine fibroblasts to induced pluripotent stem cells with chemical complementation of Klf4

“…To obtain the Ϸ10 9 cells needed to screen large chemical libraries required expansion of OSMtransduced NL-MEFs for 3 passages before screening. At passage 4, OSM-transduced NL-MEFs were seeded into 1,536-well plates at 500 cells/well in mouse ES cell growth media supplemented with leukemia inhibitory factor (LIF; 20 ng/mL) and screened against a large (500,000 compounds), chemically diverse small-molecule library (30). Compounds were added at a final concentration of 2.2 M (20 nL of 1 mM stock solutions in 9 L of media) immediately after plating, and Nanog-driven luciferase expression was assayed 10 days later (Fig.…”

Identification and Mechanistic Evaluation of Hemozoin-Inhibiting Triarylimidazoles Active against Plasmodium falciparum

“…Recently, in phenotypic screens carried out by GSK and Novartis several triarylimidazoles were discovered to have activity against the 3D7 strain of P. falciparum, 1,20 and three triarylimidazoles in the MMV Malaria Box were reported as inhibitors of βH formation. 21 Consequently, this scaffold was selected as interesting for investigating Hz inhibition of this class owing to the novelty of the chemotype.…”

Lead Optimization of Imidazopyrazines: A New Class of Antimalarial with Activity on Plasmodium Liver Stages

“…11 From a previous phenotypic screening effort on Pf blood stages, we selected imidazopyridine 1 as a starting point despite its relatively weak activity (Figure 1). 12 Early hit-to-lead chemistry on the two distal aromatic rings resulted in the identification of 2, a compound that showed a greater than 50-fold increase in potency. Although compound 2 was active on blood stages, it was still relatively inactive on Py schizonts and Pc and suffered from poor physicochemical properties, presumably due to the high lipophilicity (cLogP = 4.3).…”