SARS-CoV-2 infects human cells through its surface spike glycoprotein (SgP), which relies on host cell surface heparan sulfate (HS) proteoglycans that facilitate interaction with the ACE2 receptor. Targeting this process could lead to inhibitors of early steps in viral entry. Screening a microarray of 24 HS oligosaccharides against recombinant S1 and receptor-binding domain (RBD) proteins led to identification of only eight sequences as potent antagonists; results that were supported by detailed dual-filter computational studies. Competitive studies using the HS microarray suggested almost equivalent importance of IdoA2S–GlcNS6S and GlcNS3S structures, which were supported by affinity studies. Exhaustive virtual screening on a library of >93 000 sequences led to a novel pharmacophore with at least two 3- O -sulfated GlcN residues that can engineer unique selectivity in recognizing the RBD. This work puts forward the key structural motif in HS that should lead to potent and selective HS or HS-like agents against SARS-CoV-2.

The insulin-like growth factor-1 receptor (IGF-1R) is a receptor tyrosine kinase (RTK) that plays critical roles in cancer. Microarray, computational, thermodynamic, and cellular imaging studies reveal that activation of IGF-1R by its cognate ligand IGF1 is inhibited by shorter, soluble heparan sulfate (HS) sequences (e.g., HS06), whereas longer polymeric chains do not inhibit the RTK, a phenomenon directly opposed to the traditional relationship known for GAG-protein systems. The inhibition arises from smaller oligosaccharides binding in a unique pocket in the IGF-1R ectodomain, which competes with the natural cognate ligand IGF1. This work presents a highly interesting observation on preferential and competing inhibition of IGF-1R by smaller sequences, whereas polysaccharides are devoid of this function. These insights will be of major value to glycobiologists and anti-cancer drug discoverers.

The insulin‐like growth factor‐1 receptor (IGF‐1R) is a receptor tyrosine kinase (RTK) that plays critical roles in cancer. Microarray, computational, thermodynamic, and cellular imaging studies reveal that activation of IGF‐1R by its cognate ligand IGF1 is inhibited by shorter, soluble heparan sulfate (HS) sequences (e.g., HS06), whereas longer polymeric chains do not inhibit the RTK, a phenomenon directly opposed to the traditional relationship known for GAG‐protein systems. The inhibition arises from smaller oligosaccharides binding in a unique pocket in the IGF‐1R ectodomain, which competes with the natural cognate ligand IGF1. This work presents a highly interesting observation on preferential and competing inhibition of IGF‐1R by smaller sequences, whereas polysaccharides are devoid of this function. These insights will be of major value to glycobiologists and anti‐cancer drug discoverers.

Despite decades of research, glycosaminoglycans (GAGs) have not been known to interact with sialyl transferases (STs). Using our in-house combinatorial virtual library screening (CVLS) technology, we studied seven human isoforms, including ST6GAL1, ST6GAL2, ST3GAL1, ST3GAL3, ST3GAL4, ST3GAL5, and ST3GAL6, and predicted that GAGs, especially heparan sulfate (HS), are likely to differentially bind to STs. Exhaustive CVLS and molecular dynamics studies suggested that the common hexasaccharide sequence of HS preferentially recognized ST6GAL1 in a site overlapping the binding site of the donor substrate CMP-Sia. Interestingly, CVLS did not ascribe any special role for the rare 3-O-sulfate modification of HS in ST6GAL1 recognition. The computational predictions were tested using spectrofluorimetric studies, which confirmed preferential recognition of HS over other GAGs. A classic chain length-dependent binding of GAGs to ST6GAL1 was observed with polymeric HS displaying a tight affinity of ~65 nM. Biophysical studies also confirmed a direct competition between CMP-Sia and an HS oligosaccharide and CS polysaccharide for binding to ST6GAL1. Overall, our novel observation that GAGs bind to ST6GAL1 with high affinity and compete with the donor substrate is likely to be important because modulation of sialylation of glycan substrates on cells has considerable physiological/pathological consequences. Our work also brings forth the possibility of developing GAG-based chemical probes of ST6GAL1.

SARS‐CoV‐2 remains a prominent threat to human lives despite the recent approval of vaccines and antibodies across the world. There is also a growing concern of mutations in the virus that demand effective strategies to combat infection. SARS‐CoV‐2 infects cells via its surface Spike glycoprotein (SgP), a homo‐trimeric assembly of S1 and S2 subunits, that binds to cell surface angiotensin‐converting enzyme 2 (ACE2), thereby gaining viral entry. SgP also utilizes the cell surface bound heparan sulfate proteoglycans (HSPGs) to enhance the efficiency of viral entry. The receptor‐binding domain (RBD) in the S1 subunit interacts with both the ACE2 receptor as well as the heparan sulfate (HS) chains of HSPGs. HS is a type of glycosaminoglycan (GAG) that has been recognized as a crucial factor in the infectivity of numerous viruses. Our early work suggested that of the numerous structural possibilities, 3‐O‐sulfated (3‐OS) sequences of HS may be involved in better recognition of SgP (bioRxiv (2020) DOI:10.1101/2020.10.08.331751). Large‐scale computational analysis based on our in‐house developed genetic algorithm‐based dual filtering strategy indicated that HS more favorably interacts with the RBD compared to other electropositive regions in the SgP trimer. The results suggested that the RBD of SgP prefers to recognize optimal three‐dimensional factors governed by chain length and sulfation pattern of HS sequences. Microarray screening of 24 distinct HS sequences against the S1 and RBD domains resulted in only eight sequences displaying reasonable affinity for the RBD, which were significantly weaker for the S1 subunit. Of these, two containing 3‐O­S sequences exhibited some of the highest signals on the array. Competition studies using the same microarray in the presence of fondaparinux (a 3‐OS‐containing pentasaccharide) and HS06 (a non‐3‐OS variant of a HS hexasaccharide) led to the observation that HS06 is a more efficient competitor than fondaparinux. Advanced computational experiments indicated that RBD tends to bind more effectively with 3‐OS‐containing HS chains when more than one 3‐OS groups is present. In conclusion, our work provides additional insight into the structural requirements within HS for mediating efficient viral entry, while also offering new avenues for developing potential inhibitors of SARS‐CoV‐2 infection.