Protocol to identify drug-binding sites in proteins using solution NMR spectroscopy

Dusquetide is a next-generation IDR (innate defense regulator) targeting the ma-jor autophagy receptor protein SQSTM1/p62 and modulating the innate immune response. Here, we describe a protocol for determining dusquetide-binding sites of p62 by solution NMR spectroscopy. Step-by-step technique details were pro-vided, including sample preparation, NMR experiment setup, data processing, and binding site analysis. This protocol could be applied to characterize other small molecules targeting the ZZ domain of p62 (9 kDa) or other proteins contain-ing ZZ domains.For complete details on the use and execution of this protocol, please refer to Zhang et al. (2022).