Several frameworks and methodologies have been proposed to ease the design of Multi Agent Systems (MAS), but the vast majority of them is tightly tied to specific implementation platforms. In this paper, we outline a methodology for MAS design and prototyping in the more abstract framework of Bigraphical Reactive Systems (BRS). In our approach, components and elements of the application domain are modelled as bigraphs, and their dynamics as graph rewriting rules. Desiderata can be encoded by means of type systems or logical formulae. Then, the BDI agents (i.e., their beliefs, desires and intentions) are identified and extracted from the BRS. This yield a prototype which can be run as distributed bigraphical system, evolving by means of distributed transactional rewritings triggered by cooperating agents depending on their internal intentions and beliefs.This methodology allows the designer to benefit from the results and tools from the theory of BRS, especially in the requirement analysis and validation phases. Among other results, we mention behavioural equivalences, temporal/spatial logics, visual tools for editing, for simulation and for model checking, etc. Moreover, bigraphs can be naturally composed, thus allowing for modular design of MAS.