Classifying compound mechanism of action for linking whole cell phenotypes to molecular targets

Abstract

Drug development programs have proven successful when performed at a whole cell level, thus incorporating solubility and permeability into the primary screen. However, linking those results to the target within the cell has been a major set-back. The Phenotype Microarray system, marketed and sold by Biolog, seeks to address this need by assessing the phenotype in combination with a variety of chemicals with known mechanism of action (MOA). We have evaluated this system for usefulness in deducing the MOA for three test compounds. To achieve this, we constructed a database with 21 known antimicrobials, which served as a comparison for grouping our unknown MOA compounds. Pearson correlation and Ward linkage calculations were used to generate a dendrogram that produced clustering largely by known MOA, although there were exceptions. Of the three unknown compounds, one was definitively placed as an anti-folate. The second and third compounds’ MOA were not clearly identified, likely due to unique MOA not represented within the commercial database. The availability of the database generated in this report for S. aureus ATCC 29213 will increase the accessibility of this technique to other investigators. From our analysis, the Phenotype Microarray system can group compounds with clear MOA, but distinction of unique or broadly acting MOA at this time is less clear.

High-Throughput Screening of a Diversity Collection Using Biodefense Category A and B Priority Pathogens

“…We have also assessed the phenotypic effect of one of the benzene sulfonamides using the phenotype microarray system (Biolog), which provided an inconclusive MOA and indicated it is not likely acting against DHPS. 26 …”

Phenotype MicroArrays as a complementary tool to next generation sequencing for characterization of tree endophytes

“… Bochner (2009) states that technically one cell per well would be adequate, but recommends 100 cells per 100 μL for the inoculum. For bacterial cells, a concentration of approximately 10 6 cells/mL is a common standard (e.g., Bourne et al, 2012 ). For fungi, Atanasova and Druzhinina (2010) recommend an adjusted cell density ranging from 1.25 × 10 5 to 5 × 10 5 spores/mL, depending on the tested fungus to guarantee repeatable OD measurements.…”

The application of phenotypic microarray analysis to anti-fungal drug development

“…Metabolic fingerprinting provides information on the metabolic pathways employed by a microbe in the presence of exogenous compounds (2,3). PM technology has improved knowledge of bacterial growth inhibitors, strain phenotypes, phenotypes of pathway mutations, drug targets and sensitivity to chemicals (1,4,7,14,15). To date, however, no study has applied PM analysis to investigate the real-time effects of exogenous compounds on the growth characteristics of clinical fungal isolates.…”