PAINS: Relevance to Tool Compound Discovery and Fragment-Based Screening

Abstract

Pan assay interference compounds (PAINS) are readily discovered in any bioassay and can appear to give selective and optimisable hits. The most common PAINS can be readily recognised by their structure. However, there are compounds that closely resemble PAINS that are not specifically recognised by the PAINS filters. In addition, highly reactive compounds are not encoded for in the PAINS filters because they were excluded from the high-throughput screening (HTS) library used to develop the filters and so were never present to provide indicting data. A compounding complication in the area is that very occasionally a PAINS compound may serve as a viable starting point for progression. Despite such an occasional example, the literature is littered with an overwhelming number of examples of compounds that fail to progress and were probably not optimisable in the first place, nor useful tool compounds. Thus it is with great caution and diligence that compounds possessing a known PAINS core should be progressed through to medicinal chemistry optimisation, if at all, as the chances are very high that the hits will be found to be non-progressable, often after a significant waste of resources.

Chemistry: Chemical con artists foil drug discovery

“…It is regrettably easy, in our experience, to get a misleading readout in an animal model that is not related to the anticipated mechanism of action. In fact, real hits -molecules that do interact specifically with the desired protein -often do not show activity in cells until structures are modified to bind more efficiently or to enter cells more readily 7 .…”

Identification of mechanistically distinct inhibitors of HIV-1 reverse transcriptase through fragment screening

“…Anilines (e.g., p-hydroxyaniline 8) and related compounds are known as potentially problematic false-positive compounds and have been identified as pan assay interference compounds (PAINS) (30). Frequently, this problematic activity is a result of redox activity, through oxidation to the corresponding quinonoid compounds and the formation of covalent adducts with proteins.…”

Screening-Based Translation of Public Research Encounters Painful Problems

“…Apparent anomalies such as eltrombopag and others 4 are no longer anomalies with recognition of the clear antecedent SAR. While evidence of pathway selectivity may usefully support the value of such compounds, I do not believe exhaustive selectivity profiling is a prerequisite because obtaining this and in any case knowing exactly what this means may be nontrivial and more suited to subsequent investigation.…”

“…One of our most successful protein−protein interaction inhibitor programs was derived from such a library of 100,000 compounds that yielded, among numerous timewasting PAINS, just a single progressable hit (this was our first, stage 1 library 16 and hence contained PAINS because we had not learned what they were then). There was no cell-based activity, as to be expected from a target-based screening hit, 4 but with around 5−10 years worth of medicinal chemistry optimization, this has gone on to furnish a globally unique and valuable tool to probe Bcl-XL pharmacology.…”

“…Phenotypic screening may allow for some leniency, both in terms of library size and structural scrutiny, but in most cases one would not progress a PAINS-containing phenotypic screening hit unless there is clear and genuine SAR. 3,4 Further, it is possible that some amphiphilic phenotypic screening hits may simply be signaling through membrane perturbation. 21−25 While this may be common knowledge among experienced scientists, on the basis of some recent exchanges, we anticipate a new wave of phenotypic screening publications and patents unintentionally reporting on HTS hits or drugs that are actually signaling amphiphilically and not specifically (Figure 1).…”