Antithrombin binding site

Fondaparinux is a chemically synthesized pentasaccharide that mimics the antithrombin-binding site of heparin and LMWH. Its molecular size (1728Da) is too small to bind to thrombin molecules while it is bound to antithrombin, Therefore, it is a pure anti-Xa inhibitor. It binds very little to platelets, proteins, or endothelium and is excreted in the urine, It does not form a complex with PF4 or other positively charged molecules. It is not neutralizable by protamine sulfate, Recent clinical trials have resulted in FDA approval for prophylaxis of deep vein thrombosis in orthopedic surgery, It has been shown to be effective and safe for the treatment of pulmonary embolism (20,21) and ACS (non-ST-elevation Ml) (OASIS 5—Michelangelo Trial) (17). 

Petitou M, Casu B, Lindahl U (2003). 1976-1983, A critical period in the history of heparin the discovery of the antithrombin binding site. Biochimie. 85 83-89. 

Islam T, Butler M, Sikkander SA, Toida T, Linhardt RJ. Further evidence that periodate cleavage of heparin occurs primarily through the antithrombin binding site. Carbohydr Res 2002 337 2239-2243. 

Affinity chromatography is used in the preparation of more highly purified Factor IX concentrates (53—55) as well as in the preparation of products such as antithrombin III [9000-94-6] (56,57). Heparin [9005-49-6], a sulfated polysaccharide (58), is the ligand used most commonly in these appHcations because it possesses specific binding sites for a number of plasma proteins (59,60). 

A heparin-chain segment longer than its minimal binding site (the pentasaccharide 12) is necessary for enhancing the antithrombin-me-... 

Fig. 11. —Proposed Model for aTemary Complex between Heparin (HEP), Antithrombin (AT), and Thrombin (T), Involving an Octadecasaccharide Sequence of the Heparin Chain.419 [Within the large brace, full circles denote uronic acid residues, the small brace encompassing the minimal binding-site for AT. The thrombin-binding region is presumed to be situated towards the nonreducing end of the AT-binding sequence,933 which is arbitrarily assumed to be in the middle of the heparin chain.]...

Fondaparinux sodium is the first of a new class of direct-acting antithrombin agents. The anticoagulant activity of heparin depends on the binding of ATIII to a critical pentasaccharide sequence within the heparin molecule. This results in a change in the conformation of AITII. This leads to the inhibitory effect of ATIII on factor Xa, which activates the conversion of prothrombin to thrombin. Fondaparinux is a synthetic pentasaccharide identical to the ATIII-binding site of heparin. 

Cesaretti, M., Luppi, E., Maccari, M., and Volpi, N. (2004). Isolation and characterization of a heparin with high anticoagulant activity from the clam Tapes philippinarum. Evidence for the presence of a high content of antithrombin Ill-binding site. Glycobiology 14,1275-1284. 

Another label-free optical detection method—FTIR-ATR—has been applied for detection of thrombin by means of DNA aptamers [73], The antithrombin DNA aptamer previously developed by Tasset et al. [17] was immobilized covalently onto Si surface using UV irradiation method. As a quantitative measure, the area of N-H and CH2 bands was used. This method allowed to detect thrombin with a sensitivity around 10 nmol/L. The specificity of binding of protein to aptamer was also investigated using DNA with no binding site for thrombin. It has been noted that for effective binding study by FTIR-ATR method, the concentration of protein should be kept lower than 100 nmol/L. 

Deficiency of antithrombin predisposes the patient to thrombotic complications. Antithrombin deficiencies can be the result of low protein levels or due to functionally abnormal molecules. Low protein levels can be brought about by reduced synthesis or an increased turnover of the molecule, Functional deficiencies can be brought about by mutations in either the reactive site or heparin binding sites, A number of such mutations have been documented (81,86,87),... 

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