The emergence and understanding of new design principles that exploit flow-induced mechanical instabilities for propulsion require robust and accurate flow-structure interaction numerical models. In this contribution, we report the development of an algorithm that combines Vortex Particles Mesh (VPM) method and Multi-Body System (MBS) solver for the simulation of actuated swimming structures in fluids. The hydrodynamic efforts are recovered through an innovative approach based on the penalization and projection steps performed within the VPM method. The resulting method avoids time consuming computation of the stresses at the wall to recover the force distribution on the surface of complex deforming shapes. This feature crucially distinguish the proposed approach from other VPM formulations and opens the door for the development of control frameworks for bio-inspired and autonomous robotic swimmers. As a first illustration towards this goal, this paper reports a swimming agent stabilizing its gait in the wake of a cylinder. Illustrating the dynamic features of our framework, we report the energy saved by swimming behind this cylinder as compared to a stationary gait in an induced flow. We also compared this result to the energy saved by following the wake of a moving cylinder.