Determining the Degree of Promiscuity of Extensively Assayed Compounds

Abstract

In the context of polypharmacology, an emerging concept in drug discovery, promiscuity is rationalized as the ability of compounds to specifically interact with multiple targets. Promiscuity of drugs and bioactive compounds has thus far been analyzed computationally on the basis of activity annotations, without taking assay frequencies or inactivity records into account. Most recent estimates have indicated that bioactive compounds interact on average with only one to two targets, whereas drugs interact with six or more. In this study, we have further extended promiscuity analysis by identifying the most extensively assayed public domain compounds and systematically determining their promiscuity. These compounds were tested in hundreds of assays against hundreds of targets. In our analysis, assay promiscuity was distinguished from target promiscuity and separately analyzed for primary and confirmatory assays. Differences between the degree of assay and target promiscuity were surprisingly small and average and median degrees of target promiscuity of 2.6 to 3.4 and 2.0 were determined, respectively. Thus, target promiscuity remained at a low level even for most extensively tested active compounds. These findings provide further evidence that bioactive compounds are less promiscuous than drugs and have implications for pharmaceutical research. In addition to a possible explanation that drugs are more extensively tested for additional targets, the results would also support a "promiscuity enrichment model" according to which promiscuous compounds might be preferentially selected for therapeutic efficacy during clinical evaluation to ultimately become drugs.

Fig 1. Assay frequency.

Reported is the distribution of compounds tested in increasing numbers of (a) primary and (b) confirmatory assays. In (c), both assay categories are combined. In each case, the mean and median number of assays in which a compound was tested is provided.

Fig 2. Inactive compounds.

Reported is the distribution of compounds that were consistently inactive in increasing numbers of (a) primary and (b) confirmatory assays.

Fig 3. Exemplary inactive compounds.

Shown are nine compounds that were consistently inactive in all assays. For each compound, the number of primary and confirmatory assays it was tested in is reported in blue and red, respectively.

Fig 4. Assay and target promiscuity.

Reported are the percentages of compounds with increasing degrees of (a) assay and (b) target promiscuity. In addition, average and median degrees of assay and target promiscuity are reported.

Fig 5. Assay frequency vs. assay promiscuity.

For increasing numbers of (a) primary and (b) confirmatory assays, the distribution of assay promiscuity is reported in a box plot format. The plot gives the smallest degree of assay promiscuity (bottom line), first quartile (lower boundary of the box), median value (thick line), third quartile (upper boundary of the box), and largest degree of assay promiscuity (top line).

Fig 6. Assay frequency vs. target promiscuity.

For increasing numbers of (a) primary and (b) confirmatory assays, the distribution of target promiscuity is reported in box plots according to Fig 5.

Fig 7. Highly promiscuous compounds.

Shown are five exemplary highly promiscuous compounds. For each compound, the number of assays it was tested in and its assay and target promiscuity are reported. Four of these five compounds contain PAINS substructures (red).