Multi-Agent Motion Planning (MAMP) is a problem that seeks collision-free dynamically-feasible trajectories for multiple moving agents in a known environment while minimizing their travel time. MAMP is closely related to the well-studied Multi-Agent Path-Finding (MAPF) problem. Recently, MAPF methods have achieved great success in finding collision-free paths for a substantial number of agents. However, those methods often overlook the kinodynamic constraints of the agents, assuming instantaneous movement, which limits their practicality and realism. In this paper, we present a three-level MAPF-based planner called PSB to address the challenges posed by MAMP. PSB fully considers the kinodynamic capability of the agents and produces solutions with smooth speed profiles that can be directly executed by the controller. Empirically, we evaluate PSB within the domains of traffic intersection coordination for autonomous vehicles and obstacle-rich grid map navigation for mobile robots. PSB shows up to 49.79% improvements in solution cost compared to existing methods.