Towards the identification of unknown neuropeptide precursor-processing enzymes: Design and synthesis of a new family of dipeptidyl phosphonate activity probes for substrate-based protease identification.

Specific proteolytic processing of inactive precursors is an exquisite cellular mechanism that triggers the activation of numerous physiologic peptides and proteins. This process ensures the generation of biologically active peptides, such as many neuropeptides and peptide hormones, in the appropriate cellular compartments at the right time, and its failure leads to several pathological conditions. Identification of the proteases involved in this limited proteolysis is, therefore, an essential step for the subsequent establishment of new therapeutic targets. As a first effort along this line, we synthesized eight new dipeptidyl phosphonate activity-based probes and used them to explore the soluble proteome from mouse brain and pituitary gland for substrate-based protease identification both by in-gel analysis and mass spectrometry.