Why are membrane targets discovered by phenotypic screens and genome sequencing in Mycobacterium tuberculosis?

Abstract

High through put screening (HTS) was extensively used in attempts to discover new TB drugs from libraries of pure small molecule compounds many of which complied with the rule of five. Coupled with new methods for determining the target of lead compounds by resistance selection followed by genome sequencing, screening for growth inhibitors led to several recent reports of compounds linked to specific antitubercular targets. This systematic approach to drug discovery appears at present to select for small, hydrophobic molecules affecting the function of essential membrane proteins, for example DprE, MmpL3, AtpE, QcrB, and Pks13. All of these molecules possessed bactericidal activity in vitro. Mutations in GlpK were also selected with hydrophobic compounds identified by screening for growth inhibitors. The chemical properties of the compounds reported are considered in the context of uptake and possible mechanisms of inhibition of membrane bound targets based on other model systems (e.g. cardiovascular drugs affecting voltage-gated L-type calcium channels, daptomycin, telavancin, gramicidin S, and role of boundary lipids). The relationship between hydrophobicity, compound uptake, and mode of action are addressed. Compared to the average calculated logP for approved TB drugs of -1.0, the average for these hydrophobic compounds is 4.0 representing a major shift in hydrophobicity of 5 orders of magnitude. Furthermore several hydrophobic compounds in the Prestwick Chemical Library (FDA approved drugs) inhibit growth of M. tuberculosis at 10 μg/ml or less and have an average calculated logP of 5.7 signaling caution with respect to specificity. Key recommendations are made regarding follow-up of the hydrophobic leads recently discovered using phenotypic screening and target elucidation by genome sequencing. Consideration is also given to the properties of small molecule screening libraries, the types of molecules and targets recently discovered as antitubercular leads and compliance with the rule of 5.

Keywords: Antitubercular drugs; Genetic analysis; High throughput screening; Hydrophobic compounds; Membrane targets.