Nuisance Compounds I Have Known
Drug discovery practitioners are painfully familiar with “nuisance” compounds. These compounds may be screening hits that start out as promising actives but then are later discovered to be artifacts or working through unwelcome mechanisms. Jayme Dahlin along with an international team from the US, Germany, the UK, Australia, and China have nicely summarized the features of nuisance compounds in this recent article, “Nuisance Compounds in Cellular Assays”. The authors also describe various prescriptions for dealing with these trashy mischief-makers.
Nuisance compounds are defined in the paper as “undesirable compounds whose apparent bioactivities are due to assay technology-related and non-technology-related interferences.” For practical purposes, we find it useful to further divide “non-technology-related interferences” into two categories (1) compounds that are non-selective, interfering with multiple targets and (2) compounds that are selective, but with mechanisms associated with adverse effects in vivo. We can describe these as nuisance compounds and nuisance mechanisms.
Non-selective nuisance compounds interact with multiple targets, often with increased numbers of targets at higher concentrations. As more targets are engaged, the probability of interfering with cell health related pathways increases. Thus, these compounds are typically found to cause cytotoxicity to cells at higher concentrations and when tested in vivo exhibit narrow therapeutic windows. Such compounds are problematic as drug candidates. With a limited therapeutic window, many patients either won’t get sufficient drug to achieve benefit or they will get too much drug and experience side effects.
Nuisance mechanisms include genotoxins (e.g., DNA intercalators), inhibitors of lysosomal function, tubulin inhibitors and inhibitors of mitochondrial function. These mechanisms are important for cell and tissue health. While compounds with these mechanisms can be successful drugs, their use is typically restricted to oncology indications or limited to selected routes of exposure (e.g., topical or inhaled). Exposure to compounds with these mechanisms is associated with toxicity to different organs including the GI tract, immune system, liver and CNS, with adverse effects more pronounced in humans than animals.
Nuisance mechanisms can also arise as an unexpected secondary activity unrelated to the primary target. These mechanisms are often not easy to detect as they can contribute to drug efficacy for certain indications. For example, inhibition of lysosomal function contributes to anti-viral activity, inhibition of mitochondria contributes to autoimmune efficacy, and inhibition of tubulin contributes to efficacy in cancer indications. If these mechanisms go undetected during drug discovery, they can confuse SAR studies, misinform target validation efforts, and confound interpretation of in vivo efficacy studies.
Fortunately, many nuisance compounds and mechanisms exhibit characteristic features when profiled in phenotypic platforms, for example, the broad panel of human primary cell based assays, BioMAP® Systems. Some nuisance mechanisms can be identified by profile similarity to reference compounds (see here and here). More recently, specific assays within the broad panel have been shown to be useful for screening out certain of these mechanisms. These assays may be helpful when incorporated as a generic screening funnel for compound triage in early discovery (when compound amounts are low and compound numbers are high).
Non-selective nuisance compounds can also be identified by characteristic behaviors in the broad assay panel. Profiles of these compounds feature sharp concentration-response properties and exhibit cytotoxicity to primary human cell types at high compound concentrations. We’ve used the term dose resistance to describe concentration-response characteristics. Dose-resistant compounds generate mathematically similar profiles over multiple concentrations. Dose resistance can be quantified by the concentration range over which compound profiles are similar to neighbor concentrations. Approved drugs and target-selective compounds are more dose resistant than early stage discovery and non-selective nuisance compounds.
The use of phenotypic assays and platforms across the stages of drug discovery continues to rise (discussed previously here). As these approaches become more integrated into drug discovery workflows it will be easier to identify nuisance compounds at earlier stages. A side benefit of applying phenotypic platforms more broadly in drug discovery will be the generation of useful data sets for developing more in silico predictive tools. In the future, it will be easier to consign these bad actors to the dustbin before wasting precious resources and time.
Photo by Juli Kosolapova on Unsplash.
