Detecting similar binding pockets to enable systems polypharmacology

Miquel Duran-Frigola, Lydia Siragusa, Eytan Ruppin, Xavier Barril, Gabriele Cruciani, Patrick Aloy*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review


In the era of systems biology, multi-target pharmacological strategies hold promise for tackling disease-related networks. In this regard, drug promiscuity may be leveraged to interfere with multiple receptors: the so-called polypharmacology of drugs can be anticipated by analyzing the similarity of binding sites across the proteome. Here, we perform a pairwise comparison of 90,000 putative binding pockets detected in 3,700 proteins, and find that 23,000 pairs of proteins have at least one similar cavity that could, in principle, accommodate similar ligands. By inspecting these pairs, we demonstrate how the detection of similar binding sites expands the space of opportunities for the rational design of drug polypharmacology. Finally, we illustrate how to leverage these opportunities in protein-protein interaction networks related to several therapeutic classes and tumor types, and in a genome-scale metabolic model of leukemia.

Original languageEnglish
Article numbere1005522
JournalPLoS Computational Biology
Issue number6
StatePublished - Jun 2017


FundersFunder number
Seventh Framework Programme614944, 306240


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