In this article, the van der Waals interaction potential between two ground-state atoms in the presence of magnetoelectric media, previously obtained via fourth-order perturbation theory, is obtained from second-order perturbative calculation, by introducing an effective interaction Hamiltonian based on linear response theory. This, makes a considerable reduction in complexity and length of the calculation and may be useful, for example, in obtaining the van der Waals interaction potential between chiral molecules, which possess more complexities in comparison to achiral ones.