Prioritization of Therapeutic Targets of Inflammation Using Proteomics, Bioinformatics, and In Silico CellCell Interactomics

Leukocyte extravasation is a multistep process, involving the movement of leukocytes out of the circulatory system, through vascular endothelium and to the site of tissue damage or infection. Protein–protein interactions play key roles in the extravasation process and have been attractive therapeutic targets for inhibiting inflammation using blocking (or neutralizing) antibodies. These targets include protein–protein interactions between cytokines (or chemokines) and their receptors on leukocytes and between adhesions molecules involving leukocyte–endothelium contacts. A number of therapeutics against these targets are currently used in clinic for treatment of inflammatory disorders, however, they are associated with side-effects partly due to the off-target actions (i.e., nonspecific targets). There is a need for novel targets involved in the leukocyte extravasation process that are specific to leukocyte subsets or to individual inflammatory disorder, and are amenable for drug development (i.e., duggable). In this chapter, we describe a methodology to identify novel “druggable” targets involving protein–protein interactions between activated leukocytes and endothelial cells using a combination of proteomics, bioinformatics and in silico interactomics. The result is a prioritized list of protein–protein interactions in a network consisting of leukocyte–endothelial cell communication and contacts. These prioritized targets can be pursued for the development of therapeutics such as neutralizing antibodies and for their validation through preclinical testing. The method described here provides the workflow to identify and clinically target important cell–cell interactions that are specific/selective for particular inflammatory disorders and to improve currently available therapies.