Two synthetic analogs of the heparin-binding domain of heparin/heparan sulfate-interacting protein: Ac-SRGKAKVKAKVKDQTK-NH 2 and the all-D-amino acid version of the same peptide (L-HIPAP and D-HIPAP, respectively) were synthesized and their efficacy as agents for neutralization of the anticoagulant activity of heparin was assayed. The two analog peptides were found to be equally effective for neutralization of the anticoagulant activity of heparin, as measured by restoration of the activity of serine protease Factor Xa by the Coatest Heparin Method. The finding that L-HIPAP and D-HIPAP are equally effective suggests that D-amino acid peptides show promise as proteolytically stable therapeutic agents for neutralization of the anticoagulant activity of heparin. The interaction of L-HIPAP and D-HIPAP with heparin was characterized by 1 H NMR, isothermal titration calorimetry (ITC) and heparin affinity chromatography. The two peptides were found to interact identically with heparin. Analysis of the dependence of heparin-peptide binding constants on Na + concentration by counterion condensation theory indicates that, on average, 2.35 Na + ions are displaced from heparin per peptide molecule bound and one peptide molecule binds per hexasaccharide segment of heparin. The analysis also indicates that both ionic and nonionic interactions contribute to the binding constant, with the ionic contribution decreasing as the Na + concentration increases.Heparin, a linear polysaccharide comprised of highly sulfated 1→4 linked uronic acid-(1→4)-D-glucosamine repeating disaccharide units, has been used clinically as an anticoagulant for more than half a century (1,2). Other biological activities include release of lipoprotein lipase and hepatic lipase (3,4), regulation of complement activation (5), regulation of angiogenesis and tumor growth (6-8), regulation of Burkitt's lymphoma growth (9), modulation of inflammation (10) and antiviral activity (11)(12)(13)(14)(15). The biological activity of heparin results from its interaction with proteins, and hundreds of proteins have been shown to interact with heparin (2,(16)(17)(18).Heparin functions as an anticoagulant by binding to antithrombin III (AT 1 ), a serine protease inhibitor that mediates the coagulation cascade; binding causes a conformational change that accelerates inhibition of serine protease factor Xa by AT (19). In some clinical situations, for example where extracorporeal blood circulation is necessary or when patients experience moderate to severe bleeding, the anticoagulant activity must be neutralized to reduce the risk of hemorrhagic hazard. Protamine, a complex mixture of arginine-rich peptides, is used for this purpose. However, protamine can induce life-threatening side effects, such as hypotension + This work was supported in part by National Institutes of Health Grant HL56588. Funding for the Varian Inova 500 spectrometer was provided in part by NSF-ARI Grant 9601831. ‡ Present address: Momenta Pharmaceuticals, Boston MA. * To whom correspondence shou...