ABSTRACT
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has created a global pandemic. Viral entry into host cells is mediated by spike glycoprotein (SGP) interactions with angiotensin-converting enzyme 2 (ACE2) and heparan sulfate glycosaminoglycans on the cell surface. Carbohydrate small molecules were found to bind to the receptor binding domain (RBD) of SGP, which also interacts with ACE2, forming a ternary complex. Moreover, glycans isolated from sea cucumber and red alga species exhibited anti-SARS-CoV-2 activities, presumably by blocking viral entry mediated through SGP-heparan sulfate interactions. Here we report a collection of computational studies conducted as part of a collaborative effort to investigate the effects of marine natural products (NPs) on the wild-type and N501Y mutant SGP RBD. Starting from an X-ray crystal structure of the RBD-ACE2 complex, a model of SGP RBD was built. To investigate the static and dynamic behavior of RBD-NP interactions, blind and site-targeted molecular docking using diverse docking programs (Glide, AutoDock Vina or ClusPro) was carried out, followed by extensive molecular dynamics simulations with two force fields (CHARMM36 or Glycam06) and binding free energy calculations. Predicted conformations of the NPs varied considerably when modeled in water or in complex with RBD. Five NP binding sites on the RBD were studied. NP binding specificities towards SARS-CoV-2 variants were explained and important RBD residues were identified. Statistical analyses of the stability of various protein-NP complexes during molecular dynamics simulations helped to differentiate pseudo-vs. real-binding sites. Our results provide significant insights into the importance of extensive molecular dynamics calculations in order to move beyond the limitations of molecular docking.