Human thrombin

Jones-Hertzog D K and W L Jorgensen 1997. Binding Affinities for Sulphonamide Inhibitors witl Human Thrombin Using Monte Carlo Simulations with a Linear Response Method. Journal o Medicinal Chemistry 40 1539-1549. 

This is a dry sponge of human fibrin prepared by elotting a foam of human fibrinogen solution with human thrombin. It is then freeze-dried, cut into shapes and sterilized by dry heat at 130°C for 3 hours. Before use, it is saturated with thrombin solution. Blood coagulation occurs in contact with the thrombin in the interstices of the foam. 

Wakselman, M. Mazaleyrat, J.-P. Lin, R. C. Xie, J. Vigier, B. Vilain, A. C. Fesquet, S. Boggetto, N. Reboud-Ravaux, M. Design, synthesis and study of a selective cyclopeptidic mechanism-based inhibitor of human thrombin. In Peptides Chemistry, Structure... 

Bock L. C., Griffin L. C., Latham J. A., et al. Selection of single-stranded DNA molecules that bind and inhibit human thrombin. Nature 1992 355,564-6. 

Jones-Hertzog, D.K. Jorgensen, W.L., Binding affinities for sulfonamide inhibitors with human thrombin using Monte Carlo simulations with a linear response method, J. Med. Chem. 1997, 40, 1539-1549... 

Computational modelling of inhibitor binding to human thrombin, Eur. J. Pharm. Sci. 14 441 (2001). 

The great potential of QM/MM calculations has attracted much attention in the past decade and the number of studies published in recent years is now so large that it is not possible to cover them all here. Among recent QM/MM applications at different levels are para-hydroxybenzoate hydrolase [56, 74], citrate synthase [4-6, 52], uracil-DNA glycosylase [88], neuraminidase [89, 90], aldose reductase [91], human thrombin [92], glutathione S-transferases [57], and HIV protease [93]. 

Fig. 13 Fluorescent spectra of (a) polymer 1, (b) human thrombin/Xl aptamer/ polymer 1, (c) human thrombin/X2 aptamer/ polymer 1 mixture, and (d) Xl/polymer 1 complex in water, measured at 50°C [24]...

Banner, D.W. and Hadvary, P. Crystallographic analysis at 3.0 angstroms resolution of the binding to human thrombin of four active site-directed inhibitors./. Biol. Chem. 1991, 266, 20085-20090. 

A series of 3,4-dihydro-177-pyrido[2,3- ]pyr3zine-2-ones were found to be very potent receptor antagonists of corticotropin-releasing factor-1 among them, 768 has ICso = 0.7 nM <2004JME5783>. Polysubstituted hexahydro-pyrido[3,4- ]pyrazinone derivatives 769 inhibit human thrombin with Ki <0.1 nM <1999USP5869487>. 

Human thrombin complex with Hirudin variant PDB ID IHXF... 

Peptide chimeras of this type have proven extremely valuable for the examination of an array of recognition events. In conjunction with molecular modeling, peptidomimetic substrates and inhibitors of human thrombin were designed and synthesized to evaluate our proposed structure for the thrombin-bound conformation of fibrinopeptide A (Scheme 2i)J%]... 

Electrochemical indicator methods are based on the application of redox probe that undergoes oxidation and reduction transition due to electron transfer from electrode surface to a probe. In 2005, several studies that used methylene blue (MB) as an electrochemical indicator were published. MB is positively charged low-molecular-weight compound that can be reduced by two electrons to a leucomethylene blue (LB). The reduction process can be effectively monitored, e.g., by differential pulse voltammetry or coulometry. In presence of redox probe Fe(CN)6, the LB is oxidized to MB and the system is regenerated [44,45]. In papers by Hianik et al. [31,46], MB was used as the indicator of detection of interaction of human thrombin with DNA aptamer. The method of detection is schematically shown in Fig. 33.3B. MB binds both to DNA and to the protein. For charge transfer from electrode to MB, i.e., for MB reduction, it is important that MB should be close to the electrode surface. Therefore, the charge transfer from the electrode... 

Kubik, M.F., Stephens, A.W., Schneider, D., Marlar, R.A. and Tasset, D. (1994) High-affinity RNA ligands to human -thrombin. Nucleic Acids Res., 22, 2619-2626. 

A THEORETICAL MODEL OF THE HUMAN THROMBIN RECEPTOR (PAR-1), THE FIRST KNOWN PROTEASE-ACTIVATED G-PROTEIN-COUPLED RECEPTOR... 

Figure 1. Diagram of the human thrombin receptor, viewed edge-on, showing the sequence around the proteolytic cleavage site (LDPR-SFLLRN) in the long extracellular amino-terminus and the seven transmembrane domains (TM1-TM7).

Initially, we attempted to build a 3-D homology model of the transmembrane regions of the human thrombin receptor from the structure of IBRD, which is available from the Brookhaven Protein Database. Unfortunately, the suboptimal placement of several amino acid side chains resulted in severe deviations from structural standards for membrane-bound receptors with a seven-helix bundle topology (Figure 2). For example, carboxylate and ammonium groups on amino acid side chains at a mid-helix location were directed into the membrane, rather than toward the inside of the helix bundle, and the hydrophobic packing between some helices was either poor or nonexistent. 

Figure 3. Key hydrogen-bonding network between side chains of the GPCR-con-served amino acids Asn-120 (TM1), Asp-148 (TM2), and Asp-367 (TM7) for human thrombin receptor.

SFLLRN.15 The cleaved human thrombin receptor has an extracellular N-terminus of approximately 55 amino acids (before the beginning of TM1 and up to the SFLLRN motif). Given also the key role of the extracellular epitopes in other peptide-ligand GPCRs, we were interested in examining the role of the N-terminus of the thrombin receptor, in addition to its extracellular loops. 

At this point, we had assembled a preliminary model of the human thrombin receptor that contained all three extracellular loops linked to the seven TM domains, as well as the N-terminus out to residue 75. Docking studies with agonist peptide SFLLRN, and additional mutagenesis experiments, were carried out in parallel. Measurement of the effects of site-specific mutations in human PAR-1 identified several key amino acids of the receptor as being important for activation (Table 1),... 

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