Discovered in the lineage of Deuterostomes, sialic acids (Sias) are α-keto acids that belong to a major family of carbohydrates named nonulosonic acids. Unlike the other sugars found in glycan chains of vertebrate glycoconjugates, that are composed of five or six carbon atoms, the Sias family has a characteristic nine-carbon backbone and several other components that can be found in one molecule, including a 3-carbon exocyclic side chain, one or more acylated amino groups and a carboxylic acid. Due to their ability of carrying different molecular groups in a single monosaccharide, Sias are subject to several modifications, resulting in a structurally diverse family of more than 50 carbohydrates, that can be found frequently linked via their C-2 anomeric carbon in α-configuration to the C-3 or C-6 positions of galactose or to another sialic acid at the positions of carbons 8 or 9. The structural diversity of Sias is what makes these molecules capable of playing important modulatory and structural roles in cell pathology and biology. The study of the structure of sialic acids and their biological role can be done through the molecular modeling of these structures. Because of their flexibility, complex carbohydrates adopt different conformations in solution, representing a challenging class of molecules in terms of describing their 3D structure with computational methods. Molecular dynamics (MD) is a computational method that describes the variation of the molecular behavior as a function of the time, which approximates MD to experimental methods,such as Nuclear Magnetic Resonance (NMR). While MD configures an example of unbiased method, metadynamics involves the use of a biased potential that can force the system to leave local minima and sample states that represent lower probabilities. In this work, MD and metadynamics simulations were applied to promote the understanding of the molecular basis for the activities of this family of molecules and to evaluate the ability of molecular mechanics methods for the conformational ensemble of sialic acids. Unbiased 1 μs MD simulations using the force field GROMOS 53A6GLYC indicated 2C5 as the preferential ring pucker conformation for sialic acids. Biased metadynamics simulations described the unusual behavior of the glycosidic linkages found between Sias and other carbohydrates, or between different molecules of the Sias family of glycans.

Analysis of the conformations of sialic acids and their α-linked glycans

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