Building predictive models for mechanism-of-action classification from phenotypic assay data sets.

Compound mechanism-of-action information can be critical for drug development decisions but is often challenging for phenotypic drug discovery programs. One concern is that compounds selected by phenotypic screening will have a previously known but undesirable target mechanism. Here we describe a useful method for assigning mechanism class to compounds and bioactive agents using an 84-feature signature from a panel of primary human cell systems (BioMAP systems). For this approach, a reference data set of well-characterized compounds was used to develop predictive models for 28 mechanism classes using support vector machines. These mechanism classes encompass safety and efficacy-related mechanisms, include both target-specific and pathway-based classes, and cover the most common mechanisms identified in phenotypic screens, such as inhibitors of mitochondrial and microtubule function, histone deacetylase, and cAMP elevators. Here we describe the performance and the application of these predictive models in a decision scheme for triaging phenotypic screening hits using a previously published data set of 309 environmental chemicals tested as part of the Environmental Protection Agency's ToxCast program. By providing quantified membership in specific mechanism classes, this approach is suitable for identification of off-target toxicity mechanisms as well as enabling target deconvolution of phenotypic drug discovery hits.

Neuropathy associated with microtubule inhibitors: diagnosis, incidence, and management.

Microtubule inhibitor (MTI)-based chemotherapies used in the treatment of breast cancer--including vinca alkaloids, taxanes, and epothilones--are known to be associated with peripheral neuropathy. The incidence and severity of neuropathy, most frequently sensory in nature, depend on the agent used, absolute and cumulative drug dose, administration schedule, and presence of comorbidities. Although some first-generation vinca alkaloids, such as vincristine, were associated with severe mixed sensory/motor neuropathy, the deficits associated with newer agents in this class (eg, vinflunine) are generally milder and limited to distal sensory signs and symptoms. Among the taxanes, sensory neuropathy is reported more often with administration of paclitaxel and albumin-bound paclitaxel and less frequently with docetaxel. Epothilones, a new class of MTI, may be associated with grade 3/4 peripheral neuropathy; however, the neuropathy associated with ixabepilone, a novel epothilone B analog, is generally mild to moderate and reversible to baseline or grade 1 levels. The neuropathy induced by MTI therapy is best managed with dose adjustments and/or treatment delay. This article provides an overview of the incidence, characteristics, and management of MTI-associated neurotoxicities for known vinca alkaloids and taxanes, as well as newer agents, such as vinflunine and ixabepilone.