Screening and hit evaluation of a chemical library against blood-stage Plasmodium falciparum

Abstract

BackgroundIn view of the need to continuously feed the pipeline with new anti-malarial agents adapted to differentiated and more stringent target product profiles (e.g., new modes of action, transmission-blocking activity or long-duration chemo-protection), a chemical library consisting of more than 250,000 compounds has been evaluated in a blood-stage Plasmodium falciparum growth inhibition assay and further assessed for chemical diversity and novelty.MethodsThe selection cascade used for the triaging of hits from the chemical library started with a robust three-step in vitro assay followed by an in silico analysis of the resulting confirmed hits. Upon reaching the predefined requirements for selectivity and potency, the set of hits was subjected to computational analysis to assess chemical properties and diversity. Furthermore, known marketed anti-malarial drugs were co-clustered acting as ‘signposts’ in the chemical space defined by the hits. Then, in cerebro evaluation of the chemical structures was performed to identify scaffolds that currently are or have been the focus of anti-malarial medicinal chemistry programmes. Next, prioritization according to relaxed physicochemical parameters took place, along with the search for structural analogues. Ultimately, synthesis of novel chemotypes with desired properties was performed and the resulting compounds were subsequently retested in a P. falciparum growth inhibition assay.ResultsThis screening campaign led to a 1.25% primary hit rate, which decreased to 0.77% upon confirmatory repeat screening. With the predefined potency (EC50 < 1 μM) and selectivity (SI > 10) criteria, 178 compounds progressed to the next steps where chemical diversity, physicochemical properties and novelty assessment were taken into account. This resulted in the selection of 15 distinct chemical series.ConclusionA selection cascade was applied to prioritize hits resulting from the screening of a medium-sized chemical library against blood-stage P. falciparum. Emphasis was placed on chemical novelty whereby computational clustering, data mining of known anti-malarial chemotypes and the application of relaxed physicochemical filters, were key to the process. This led to the selection of 15 chemical series from which ten confirmed their activity when newly synthesized sample were tested.

Identification and Deconvolution of Cross-Resistance Signals from Antimalarial Compounds Using Multidrug-Resistant Plasmodium falciparum Strains

“…2A). Compounds 1 and 2 were initially identified as hits on the erythrocytic stage of P. falciparum during the phenotypic screening of a library of more than 250,000 compounds (24). Compound 3 was synthesized while performing the resynthesis of compounds 1 and 2.…”

Imaging-Based High-Throughput Screening Assay To Identify New Molecules with Transmission-Blocking Potential against Plasmodium falciparum Female Gamete Formation

“…Although phenotypic screening has been widely used to identify compounds active against P. falciparum asexual stages (17)(18)(19)(20), it is more laborious to scale up gametocyte-based assays because of the tedious, timedemanding, and expensive production of such stages. As of now, the production of gametocytes is one of the main impediments in the development of large-scale in vitro transmission-blocking assays.…”

New insights into novel inhibitors against deoxyhypusine hydroxylase from plasmodium falciparum: compounds with an iron chelating potential

“…The previously described 40 most active compounds of the Malaria Box (Avery et al 2014) were empirically pre-selected for potential iron complexing agents. This approach resulted in three compounds, i.e., the bis-benzimidazole A03 (MMV666023), the naphthyl azobenzimidazole B08 (MMV007384), and a 1,2,5-oxadiazole C03 (MMV665805).…”