The Promise and Peril of Chemical Probe Negative Controls

Chemical probes are selective modulators that are used in cell assays to link a phenotype to a gene and have become indispensable tools to explore gene function and discover therapeutic targets. Chemical probe off-targets are a confounding factor as the observed phenotype may be driven by inhibition of an unknown off-target instead of the targeted protein. A negative control, a close chemical analog of the chemical probe that is inactive against the intended target, is typically used to verify that the phenotype is indeed driven by the targeted protein. Here, we compare the selectivity profiles of four unrelated chemical probes and their respective negative controls. We find that controls that chemically deviate from the probe by a single heavy atom can be inactive against up to 80% of known off-targets if the chemical modification has a charge-neutralizing effect. In such cases, a loss in phenotype upon treatment with the negative control may be driven by loss of inhibition of an off-target. To expand this analysis, we inspect the crystal structures of 90 pairs of unrelated proteins, where both proteins within each pair is in complex with the same drug-like ligand. We computationally estimate that in 50% of cases, methylation of the ligand (a simple chemical modification often used to generate negative controls) at a position that will preclude binding to one protein (the intended target) will also preclude binding to the other (the off-target). These results emphasize the need to select negative controls with care and profile both chemical probes and negative controls against diverse protein arrays to verify that off-targets of probes are also hit by negative controls. When available, a best practice should be to verify that two unrelated chemical probes targeting the same protein elicit the same phenotype.