Using in Vitro Evolution and Whole Genome Analysis To Discover Next Generation Targets for Antimalarial Drug Discovery

Abstract

Although many new anti-infectives have been discovered and developed solely using phenotypic cellular screening and assay optimization, most researchers recognize that structure-guided drug design is more practical and less costly. In addition, a greater chemical space can be interrogated with structure-guided drug design. The practicality of structure-guided drug design has launched a search for the targets of compounds discovered in phenotypic screens. One method that has been used extensively in malaria parasites for target discovery and chemical validation is in vitro evolution and whole genome analysis (IVIEWGA). Here, small molecules from phenotypic screens with demonstrated antiparasitic activity are used in genome-based target discovery methods. In this Review, we discuss the newest, most promising druggable targets discovered or further validated by evolution-based methods, as well as some exceptions.

Open-source discovery of chemical leads for next-generation chemoprotective antimalarials

“…3C and table S4). To further investigate mitochondrial inhibition, and because there are multiple potential targets, we used an in vitro evolution and whole-genome analysis (IViEWGA) approach ( 22 ) to further elucidate the molecular target of several of the compounds, including MMV1454442, MMV1432711, and MMV142795. First, three independent lines resistant to MMV1454442 were isolated after growing in sublethal concentrations of compound.…”

In vitroevolution and whole genome analysis to study chemotherapy drug resistance in haploid human cells

“…Our work using IVIEWGA in pathogens (see (66) for a review) guided our pipeline development: We focused on protein coding alterations that arose in association with a single treatment condition. Overall, our results are similar to what we have observed in eukaryotic pathogens with a mix of CNVs and single nucleotide variants giving rise to resistance.…”

Defeating the trypanosomatid trio: proteomics of the protozoan parasites causing neglected tropical diseases

“…A combination of complementary methods is often required to identify the real target(s) and mode of action. Wyllie et al recently employed quantitative chemical proteomics MS and in vitro evolution combined with whole-genome analysis 67 to identify cyclin dependent kinase 12 (CDK12) (also known as cdc-2-related kinase 12 or CRK12) as the principal molecular target of their preclinical pyrazolopyrimidine compound DDD853651 or GSK3186899 (compound 1 in Fig. 2 ) for visceral leishmaniasis.…”