Sankaranarayanan, N. V. | bioRxiv Science

bioRxiv2020

Preferential recognition and antagonism of SARS-CoV-2 spike glycoprotein binding to 3-O-sulfated heparan sulfate

The COVID-19 pandemic caused by SARS-CoV-2 is in immediate need of an effective antidote. Although the Spike glycoprotein (SgP) of SARS-CoV-2 has been shown to bind to heparins, the structural features of this interaction, the role of a plausible heparan sulfate proteoglycan (HSPG) receptor, and the antagonism of this pathway through small molecules remain unaddressed. Using an in vitro cellular assay, we demonstrate HSPGs modified by the 3-O-sulfotransferase isoform-3, but not isoform-5, preferentially increased SgP-mediated cell-to-cell fusion in comparison to control, unmodified, wild-type HSPGs. Computational studies support preferential recognition of the receptor-binding domain of SgP by 3-O-sulfated HS sequences. Competition with either fondaparinux, a 3-O-sulfated HS-binding oligopeptide, or a synthetic, non-sugar small molecule, blocked SgP-mediated cell-to-cell fusion. Finally, the synthetic, sulfated molecule inhibited fusion of GFP-tagged pseudo SARS-CoV-2 with human 293T cells with sub-micromolar potency. Overall, overexpression of 3-O-sulfated HSPGs contribute to fusion of SARS-CoV-2, which could be effectively antagonized by a synthetic, small molecule.

biochemistry↗

bioRxiv2019

Molecular Dynamics Simulations of Glycosaminoglycan Oligosaccharide Using Newer Force Fields

Heparin/heparan sulfate (H/HS) are ubiquitous biopolymers that interact with many proteins to induce myriad biological functions. It is critical to understand conformational properties of H/HS in solution so as to identify their preferred protein targets. Unfortunately, the massive heterogeneity of H/HS precludes the use of solution-based experimental techniques for the thousands of sequences that occur in nature. Computational simulations offer an attractive alternative and several all-atom force fields have been developed to understand their conformational properties. Recently, CHARMM36 carrying parameters for N-sulfamate was developed. This work compares molecular dynamics simulations of a hexasaccharide (HS06) using two all-atom force fields - CHARMM36 and GLYCAM06. We also introduce two new straightforward parameters, including end-to-end distance and minimum volume enclosing ellipsoid, to understand the conformational behavior of HS06. In addition, we analyzed inter- and intra-molecular hydrogen bonds and intermediate water bridges formed for HS06 using both force fields. Overall, CHARMM36 and GLYCAM06 gave comparable results, despite few, small differences. The MD simulations show that HS06 samples a range of conformations in solution with more than one nearly equivalent global minima, which contrasts with the assumed single conformation conclusion derived on the basis of 1HPN structure. A key reason for the stability of multiple low energy conformations was the contribution of intermediate water bridges, which is usually not evaluated in most MD studies of H/HS.

biophysics↗