The fast development of Cloud-based services and applications have a significant impact on Service Oriented Computing as it provides an efficient support to share data and processes. The de-perimeterised vision involved by these Intelligent Service Clouds lead to new security challenges: providing a consistent protection depending on the business environment conditions and on the deployment platform specific threats and vulnerabilities. To fit this context aware protection deployment challenge, we propose a MDS@run.time architecture, coupling Model Driven Security (MDS) and Models@run.time approaches. By this way, security policies (that can be generated via a MDS process) are interpreted at runtime by a security mediator depending on the context. This proposition is illustrated thanks to a proof of concept prototype plugged on top of the FraSCAti middleware.