Download full PDF Article (PDF, 1.1 MB)
Identifying a polypharmacological profile for phenothiazines
Selectivity is a traditional criterion in choosing lead compounds as it helps to avoid potential side effects. However, most traditional drugs act on more than one target, exhibiting a complex, multifaceted pharmacological profile. Their therapeutic action in several cases is probably explained by this polypharmacological behavior.
To facilitate comparisons of bioactivity data from different publications and assay types, all the data points in Reaxys Medicinal Chemistry have pX values. These are normalized values assigned to the data to enable straightforward quantification of compound–target affinity, regardless of the origin of the data.
Taking advantage of the vast amount of experimental data already extracted, structured and available in the Reaxys Medicinal Chemistry database, in silico profiling of a classical medicinal chemistry scaffold was performed to assess the polypharmacology of phenothiazine.
Phenothiazines are very simple substructures. They were among the first dopamine D2 antagonist structures to be discovered. Historically, this scaffold has been used for various therapeutic applications, in particular as an antischizophrenic.
A substructure search for phenothiazine (Figure 1) in Reaxys Medicinal Chemistry retrieved 22,266 compounds with the phenothiazine ring scaffold. These 22,266 compounds are involved in 33,152 reactions, have 32,614 bioactivities associated with them, show activity against 942 targets and were extracted from 7,914 citations.
Understanding the structure–target interactions of phenothiazines
To facilitate comparisons of bioactivity data from different publications and assay types, all the data points in Reaxys Medicinal Chemistry have pX values. They are calculated by transforming EC50, IC50, Ki, etc. into pEC50 = -LogEC50, pIC50= -LogIC50, pKi = -LogKi, etc. These are normalized values assigned to the data to enable straightforward quantification of compound–target affinity regardless of the origin of the data.
The activity profile for all phenothiazines found in Reaxys Medicinal Chemistry can be viewed in the Heatmap (Figure 2). This visualizes the relationships between compounds and their targets in terms of key parameters, allowing rapid identification of relevant compound– target interactions.
In the Heatmap, biological affinities or activities are quantified with the aforementioned pX values which range from 1, indicating low activity and displayed in blue, to 15, indicating high available; white cells indicate a lack of data.
The Heatmap displays all the phenothiazines for which in vitro biological data has been mined from the literature and the target proteins associated with them. In this case, there are 2,074 phenothiazine substances active against 474 targets.
The thumbnail provides an overview of the entire Heatmap with a panel highlighting the section of the map currently displayed on your screen and the data density display showing the number of molecules retrieved per target.
A similar Heatmap could be produced for the most potent substances having a pX value of 5.0 (10 mM) in light green to 15.0 (1 fM, most active) in red (Figure 3). There were 1,174 substances with a pX above 5.0 and they were were active against 250 targets.
A multitude of key parameters can be explored to aid understanding of the compound–target interactions, such as the bioassay types, species, therapeutic effects, biological parameters measured and cell lines. For example, using the side filters, a detailed study can be done using the Heatmap to distinguish binding profiles for human (Figure 4) and rat (Figure 5).
Alternative targets and therapeutics
The following analysis shows how the number of phenothiazole ring structures and biological targets with quantitative bioactivity data varies depending on the pX activity threshold (Figure 6). Most of the phenothiazines with bioactivity data have a pX value between 5.0 and 5.9. These compounds show activity against 175 targets.
Narrowing Focus Further
Examining the data further we can see that 1,174 compounds have biological activity against 250 targets with pX values above 5.0 (Figure 7). Activity against targets such as ataxia telangiectasia mutated protein (ATM), which is a key kinase involved in the DNA damage response-signaling pathway, could provide a new avenue for anticancer research using phenothiazines as the scaffold.
Therapeutic effects of phenothiazine compounds
Extracting data from the Heatmap enables the exploration of the therapeutic effect of phenothiazine compounds with a pX value higher than 5.0 (Figure 8). Phenothiazine scaffolds could have potential as cytotoxic and antineoplastic agents.
This study demonstrates that in silico profiling using Reaxys Medicinal Chemistry is an efficient and rapid method to assess the polypharmacology of compounds, as shown here with the example of phenothiazine compounds. This method could be used to investigate the mechanism of action or act as a starting point for research into new indications for a compound.