We report experimental and theoretical studies on the magnetoelastic interactions in MnPS$_3$. Raman scattering response measured as a function of temperature shows a blue shift of the Raman active modes at 120.2 and 155.1 cm$^{-1}$, when the temperature is raised across the antiferromagnetic-paramagnetic transition. Density functional theory (DFT) calculations have been performed to estimate the effective exchange interactions and calculate the Raman active phonon modes. The calculations lead to the conclusion that the peculiar behavior with temperature of the two low energy phonon modes can be explained by the symmetry of their corresponding normal coordinates which involve the virtual modification of the super-exchange angles associated with the leading antiferromagnetic (AFM) interactions.