Unrestrained conformational characterization of Stenocereus eruca saponins in aqueous and nonaqueous solvents.

Saponins are secondary metabolites that have a plethora of biological activities. However, the absence of knowledge of their 3D structures is a major drawback for structural-based strategies in medicinal chemistry. To address this problem, the current work presents structural models of Stenocereus eruca saponins, named erucasaponin A and stellatoside B. These compounds were constructed on the basis of a combination of unrestrained molecular dynamics (MD) simulations and NOESY data, in both pyridine and water. The models obtained in this way offer a robust description of the saponin dynamics in solution and support the use of submicrosecond MD simulations in describing and predicting glycoconjugate conformations.