Selective conversion of fructose to 5-hydroxymethyl-furfural (HMF) involves the participation of high-boiling solvents like dimethyl sulfoxide (DMSO). In order to replace DMSO with low-boiling solvents, it is imperative that we understand the effect of DMSO solvation in protecting (i) HMF from rehydration and humins formation reactions and (ii) fructose from side reactions, other than its dehydration to HMF. In the present work, molecular dynamics simulations of HMF and fructose in water and in water-DMSO mixtures are carried out using the OPLS-AA force field. Radial pair distribution functions, coordination numbers and the hydrogen-bond network between the HMF/fructose molecule and the solvent molecules are analysed. The local 3-dimensional picture of the arrangement of solvent molecules around the solute, which cannot be accessed from pair distribution functions, is also computed. We show preferential coordination of DMSO around HMF and explain how this could provide a shielding effect to the HMF molecule, thus protecting it from further rehydration to levulinic acid and formic acid and from humins formation. In the case of fructose, the presence of DMSO also reduces the number of water molecules in the immediate vicinity of fructose. Though fewer water molecules coordinate around fructose, they are bound strongly to it. Analysis of the local 3-dimensional arrangement of DMSO molecules suggests that it protects the fructose molecule from side reactions that would lead to condensation or reversion products. However, the presence of DMSO molecules does not hamper the water molecules coming into contact with the oxygen atom of the hydroxyl groups of fructose, which is required for a proton transfer from water to fructose, to initiate the dehydration reaction to HMF.