PAINS (pan assay interference compounds) filters have exerted a hold over the drug discovery community ever since the BH2010 study appeared over 15 years ago. Initially I didn’t take much notice of PAINS filters and, in any case, I’d already moved on from analysis of high-throughput screening (HTS) output by that point (I might add ‘thankfully’ because looking at too much HTS output is a sure-fire route to the funny farm). I started analysing HTS output from about 1993 at what was then Zeneca. I used the Daylight toolkit to create the Struct_Anal SMARTS-based chemical structure profiler in 1995 and, at that time, we were already using in house software named Flush (even at that stage it was clear that much of the HTS output being generated was going to disappear round the S-bend and our friends at what was then Rhône-Poulenc Rorer developed HARPick to ensure that nothing remained stuck to the porcelain).
Something that had always worried me was that it was very easy to opine that a compound looked nasty but it was much more difficult to demonstrate objectively that the compound was indeed nasty. Late in 2014 a blog post, which fell well short of the standards that the drug discovery community has come to expect from Practical Fragments, prompted me to take a more forensic look at PAINS filters. What I found was that PAINS filters were based on the output from screening compounds in just six AlphaSceen assays (if a panel of six assays that all use the same read-out strikes you as suboptimal design of an experiment to detect pan-assay interference then you’re not alone). After blogging periodically about PAINS filters for a couple of years I wrote a Perspective on the topic (as noted in this blog post: from time to time, every blogger should write a journal article “pour encourager les autres”).
Nevertheless, doubts about the correctness of my position started to creep in when I was denounced for being insufficiently thoughtful in my published comments on PAINS by the authors, one of whom is a former colleague, of the seminal, insightful and Nobel-worthy ‘Seven Year Itch’ article (BN2017) which oozes wisdom and penetrating insight. Although stung by the criticism and wracked by self-doubt to the extent that I considered therapy, it was a recent study led by the world-renowned expert on tetrodotoxin pharmacology, Prof. Angelique Bouchard-Duvalier of the Port-au-Prince Institute of Biogerontology, working in collaboration with the Budapest Enthalpomics Group (BEG), that removed any lingering doubts about the sublime elegance and extreme predictivity of PAINS filters. The manuscript has not yet been made publicly available although I was able to access it with the help of my associate ‘Anastasia Nikolaeva’ (not sure exactly what she’s doing these days although I understand that she’s currently visiting Port-au-Prince for a medication review with Prof. Bouchard-Duvalier). There is no doubt that this genuinely disruptive study will comprehensively reshape the predictive biochemistry landscape, enabling drug discovery scientists to accurately, meaningfully and robustly predict assay interference using only chemical structures as input for the very first time.
Prof. Bouchard-Duvalier’s seminal study clearly demonstrates that singlet oxygen quenching is actually a conserved feature for all known and unknown mechanisms of interference with assay read-outs and that PAINS filters dramatically outperform all other methods for prediction of assay interference. The math is truly formidable (the rudimentary nature of my understanding of Haitian patois didn’t help either) and involves first projecting the atomic isothermal compressibility matrix into the quadrupole-normalized polarizability tensor before applying the Barron-Samedy transformation, followed by hepatic eigenvalue extraction using a the elegant algorithm devised by E. V. Tooms (a reclusive Baltimore resident and connoisseur of liver pâté whose illustrious thought leadership of the analytic topology field unravelled almost 32 years ago after he failed to comply with the safety instructions for an escalator). The incisive analysis of Prof. Bouchard-Duvalier shows without a shadow of doubt that singlet oxygen quenching as quantified by the AlphaScreen assay read-out is a fundamental principle in biomolecular assay science. Furthermore, ‘Anastasia Nikolaeva’ was also able to ‘liberate’ a prepared press release in which the grinning BEG director Prof. Kígyó Olaj explains:
Possibilities are limitless now that we can accurately and robustly predict the assay interference that compounds will exhibit directly from their chemical structures and we can safely consign experimental biochemical assays to the dustbin of history. Surely the Journal of Medicinal Chemistry Editors will now finally recognize the colossal impact that PAINS filters have made on real world drug discovery and development when they make their FIFA Prize nominations later this year.
