Glycosaminoglycan (GAG) sequences that selectively target heparin cofactor II (HCII), akey serpin present in human plasma, remain unknown. Using ac omputational strategy on alibrary of 46 656 heparan sulfate hexasaccharides we identified ar are sequence consisting of consecutive glucuronic acid 2-O-sulfate residues as selectively targeting HCII. This and four other unique hexasaccharides were chemically synthesized. The designed sequence was found to activate HCII ca. 250-fold, while leaving aside antithrombin, ac losely related serpin, essentially unactivated. This group of rare designed hexasaccharides will help understand HCII function. More importantly,our results show for the first time that rigorous use of computational techniques can lead to discovery of unique GAGsequences that can selectively target GAG-binding protein(s), which may lead to chemical biology or drug discovery tools.Heparin cofactor II (HCII) is as erine protease inhibitor (serpin) that circulates in human plasma at high levels. Although it has been known to selectively inhibit thrombin for several decades, [1][2][3] its true physiologic function remains to be understood. [4] HCII is known to bind to glycosaminoglycans (GAGs) such as dermatan sulfate (DS) and heparan sulfate (HS), which help mediate its inhibition of thrombin. One of the key reasons for the inability to identify HCIIs biologic role is the lack of knowledge on the specificity of HCII-GAGi nteraction.HCII is an interesting serpin. It bears considerable similarity to antithrombin (AT), another plasma serpin that mediates the anticoagulant action of heparin and fondaparinux, [5,6] two clinically used drugs.A Tand HCII are homologous in primary,secondary and tertiary structure ( Figure S1 in the Supporting Information). Yet, whereas AT binds specifically to fondaparinux sequence in heparin, [7] HCII is considered to bind non-specifically to heparin and HS. Further,a lthough both serpins display at wo-step,i nducedfit, allosteric activation mechanism in inhibiting their target enzymes, [8][9][10] no HS oligosaccharide has been discovered to induce robust activation of HCII.Identifying GAGs equences that selectively target proteins is extremely challenging.Akey reason for this is their structural complexity.H S, ah ighly anionic polymer containing variably sulfated, acetylated and epimerized residues, presents enormous structural diversity that makes comprehensive analysis of all possible sequences difficult. Thus, identifying key "needles" in this haystack, especially with synthesis [11,12] or isolation of oligosaccharides from nature nearly impossible. [13] We had earlier developed ad ual-filter computational algorithm, called combinatorial virtual library screening (CVLS) strategy,torapidly sort HS sequences into "specific" and "non-specific" bins. [14,15] We wondered whether this tool could pinpoint HS sequences that preferentially activate HCII for inhibition of thrombin. Further, we posited that such asequence,ifany,would be different from the pentasaccharide seq...