DavidsonX – D001x – Medicinal Chemistry Chapter 10 – Lead Discovery Part 3 – Filtering Hits Pt 1 Video Clip – Visual Inspection

HTS can generate many hits. These hits need to be filtered and ranked. The most promising hits can then be advanced in the drug discovery process. The least promising hits will be discarded. One method for sifting through hits is by visual inspection of the structures. Visual inspection of the hits allows medicinal chemists to identify functional groups that are notorious for causing problems at various stages of the drug discovery process. One problem is that some compounds are known to show activity in many different assays. These compounds have been labeled as PAINS, or pan assay interference compounds.1 PAINS do not interact in a specific manner with any one target. Instead, these compound have a general reactivity. Most often, the reactivity is that PAINS are strongly electrophilic and covalently react with proteins in the assay. Covalent interactions are irreversible. Remember that most drugs bind protein targets reversibly through intermolecular forces, not covalent bonds. Molecules that non-specifically and permanently react with the first protein they encounter tend to make very poor drugs. Functional groups that are frequently found in PAINS include electron-poor alkenes (alkenes bearing electron-withdrawing groups – EWGs) that are readily attacked by nucleophilic R- groups of proteins. Selected examples are shown below. Unfortunately, these types of functional groups are easily made through combinatorial techniques. These functional groups are therefore frequently found in many combinatorial libraries and undermine the utility of the libraries for drug discovery.1 O O EWG EWG Nu Cl Nu EWG then EWG protonate O O CH common EWGs HN 3 O N O CH3 R N amide R ester O O H Br O O Br O O N C N R O O ketone nitro cyano O A different problem with some hits and leads is that they contain functional groups that are known to cause frequent problems in drug metabolism. Problematic functional groups trigger a structural alert, or an awareness that the presence of a particular functional group in a lead can result in toxicity issues. One functional group that regularly triggers a structural alert is an aniline. Anilines undergo phase I oxidation and often form quinone imines, which are highly electrophilic and can damage the liver, the site of the phase I oxidation. Another functional group that triggers a structural alert is an arylacetic acid. Arylacetic acids undergo glucuronidation. The resulting acyl glucuronides can react with proteins and cause either tissue damage or an immune response.2 phase phase I HO I O oxidation oxidation potential liver NH NH NH damage R 2 R 2 R aniline quinone imine Some drugs contain structural elements found in PAINS. Some drugs contain functional groups associated with structural alerts. Regardless, when comparing hits and trying to determine which hits should be advanced as leads, a lead discovery team will favor compounds that do not have these structural issues.

1. Baell, J. B.; Holloway, G. A. New Substructure Filters for Removal of Pan Assay Interference Compounds (PAINS) from Screening Libraries and for Their Exclusion in Bioassays. J. Med. Chem. 2010, 53, 2719-2740. 2. Stepan, A. F.; Walker, D. P.; Bauman, J.; Price, D. A.; Baillie, T. A.; Kalgutkar, A. S.; Aleo, M. D. Structural Alert/Reactive Metabolite Concept as Applied in Medicinal Chemistry to Mitigate the Risk of Idiosyncratic Drug Toxicity: A Perspective Based on the Critical Examination of Trends in the Top 200 Drugs Marketed in the United States. Chem. Res. Toxicol. 2011, 24, 1345-1410.