Glycosaminoglycans (GAGs) are sulfated polysaccharides that mediate a variety of extracellular interactions. Heparan sulfate (HS) is one of the most prominent GAGs on human cell surfaces. Both endogenous proteins, such as growth factors, and exogenous proteins, such as pathogen surface proteins, recognize and bind GAGs to gain access to human cells. Oligosaccharides and other structural analogs of HS and GAGs have been evaluated for a variety of therapeutic targets including angiogenesis and infectious diseases. Development of compounds to block HS-protein interactions has primarily focused on optimizing the degree and orientation of anionic substituents on a scaffold, to mimic HS structure, but their utility is diminished by their large size and non-specific interactions with many proteins. To overcome these limitations, it has been demonstrated that replacing N-sulfo groups on heparin with non-anionic N-arylacyl groups increased affinity and selectivity for binding different heparin-binding proteins. However, the heparin-derived compounds in that work were heterogeneous polysaccharides. Strategies to obtain small, structurally-defined and lower charge ligands are needed to ultimately obtain specific bind-and-block antagonists of HS-binding proteins. This study addresses these challenges by synthesizing N-arylacyl O-sulfonated aminoglycosides as small molecule, structurally-defined ligands to identify novel structures that selectively bind to HS-binding proteins. This study details development of new HPLC and LC-MS methods to separate, characterize, and purify amphiphilic oligosaccharides. The development of these methods enabled the synthesis of a panel of N-arylacyl O-sulfonated aminoglycosides. The compounds in this panel were screened for affinity and selectivity in binding with HS-binding proteins. This work demonstrates for the first time the selective binding of small amphiphilic oligosaccharides with HS-binding proteins. Significantly, individual compounds demonstrate heparin-like affinity for binding with select HS-binding proteins. Structural differences between the N-arylacyl O-sulfonated aminoglycosides, including changing the aminoglycoside core or the structure of the N-arylacyl moiety, are shown to impart specificity for these compounds to selectively bind different HS-binding proteins.