Toward an Understanding of Pan-Assay Interference Compounds and Promiscuity: A Structural Perspective on Binding Modes

Pan-assay interference compounds
(PAINS) are promiscuous compound
classes that produce false positive hits in high-throughput screenings.
Yet, the mechanisms of PAINS activity are poorly understood. Although
PAINS are often associated with protein reactivity, several recent
studies have shown that they also mediate noncovalent interactions.
Aiming at a deep understanding of PAINS promiscuity, we performed
an analysis of the Protein Data Bank to characterize the binding modes
of PAINS. We explored the binding mode conservation of 34 PAINS classes
present in 871 ligands and among 517 protein targets. The two major
findings of this work are the following: First, different PAINS classes
exhibit different levels of binding mode conservation. Our novel classification
of PAINS based on binding mode similarity enables a rational assessment
of PAINS from a structural perspective. Second, PAINS classes with
variable binding modes can bind with high affinity. The evaluation
of noncovalent binding modes of PAINS-like compounds sheds light on
the mechanisms of promiscuous binding. Our findings could facilitate
the decisions on how to deal with PAINS and help scientists to understand
why PAINS produce hits in their screenings.