Human brain microvascular endothelial cell lines (HBMECs) could be used to assess BBB permeability incase you do not have a trans-well system or microfluidic BBB models. SHSY5Y are not directly suitable for assessing blood-brain barrier (BBB) permeability.
Unfortunately, none of the cultured human brain EC models are tight enough to simulate in vivo flux of a small molecule. Use the permeability coefficient from one of the standard cell (MDCK, Caco-2) monolayer models. It is also important to determine whether the compound is a P-glycoprotein substrate and how bound the compound is in plasma. Ideally, measuring a 'calculated free' brain conc. after oral dosing is the best guesstimate.