Synthesis of oligopeptide chloromethanes to investigate extended binding regions of proteinases: application to the interaction of fibrinogen with thrombin

Thrombin: An Approach to Developing a Higher-Order Reference Material and Reference Measurement Procedure for Substance Identity, Amount, and Biological Activities

Thrombin, the proteolytic enzyme that catalyzes the transformation of soluble fibrinogen to the polymerized fibrin clot, participates in multiple reactions in blood coagulation in addition to the clotting reaction. Although reference materials have existed for many years, structural characterization and measurement of biological activity have never been sufficient to permit claims of clear metrological traceability for the thrombin preparations. Our current state-of-the-art methods for protein characterization and determination of the catalytic properties of thrombin now make it practical to develop and characterize a metrologically acceptable reference material and reference measurement procedure for thrombin. Specifically, α-thrombin, the biologically produced protease formed during prothrombin activation, is readily available and has been extensively characterized. Dependences of thrombin proteolytic and peptide hydrolytic activities on a variety of substrates, pH, specific ions, and temperature are established, although variability remains for the kinetic parameters that describe thrombin enzymatic action. The roles of specific areas on the surface of the thrombin molecule (exosites) in substrate recognition and catalytic efficiency are described and characterized. It is opportune to develop reference materials of high metrological order and technical feasibility. In this article, we review the properties of α-thrombin important for its preparation and suggest an approach suitable for producing a reference material and a reference measurement procedure that is sensitive to thrombin’s catalytic competency on a variety of substrates.

Potential opportunity in the development of new therapeutic agents based on endogenous and exogenous inhibitors of the proprotein convertases

The proprotein convertases (PCs) are responsible for the endoproteolytic processing of various protein precursors (e.g., growth factors, receptors, adhesion molecules, and matrix metalloproteinases) implicated in several diseases such as obesity, diabetes, atherosclerosis, cancer, and Alzheimer disease. The potential clinical and pharmacological role of the PCs has fostered the development of various PC‐inhibitors. In this review we summarized the recent findings on PCs inhibitors, their mode of actions and potential use in the therapy of various diseases. © 2006 Wiley Periodicals, Inc. Med Res Rev, 27, No. 5, 631–648, 2007

Endo/exo-proteolysis in neoplastic progression and metastasis

Biological control of individual cells, organs, and organisms is achieved through interplay of a host of specific interactions that involve various peptidic molecules as modulators or effectors. In tumor cells, these processes may result in uncontrolled growth as a consequence of autocrine and/or paracrine actions. In recent years, growing evidence has accumulated for the important role of proprotein convertases (PCs) and peptide alpha-amidation enzymes in these processes. The widespread belief that these enzymes are involved in the major features of tumor progression, namely, invasiveness and metastasis, has taken place because of their capacity to process and activate many protein precursors involved in the neoplastic progression and metastasis. This includes degrading extracellular matrix proteases, growth promoting factors, and adhesion molecules. Usually, when the processing of these precursor proteins is achieved by one or more of the known PC family members within the general motif (K/R)-(X)n-(K/R) downward arrow, where n=0, 2, 4, or 6, and X, any amino acid except Cys, the accomplishment of the maturation of these molecules is attained by various posttranslational modifications, including the carboxy-terminal alpha-amidation. This review article summarizes recent findings on the role of these enzymatic systems in multiple cellular functions that impact on the invasive/metastatic potential of cancer cells and highlight the potential use of their inhibitors in the treatment of multiple cancers.

Identification of potential activators of proteinase-activated receptor-2

In order to identify physiological activators of proteinase-activated receptor-2 (PAR-2), a peptide chloromethane inhibitor (biotinyl-Ser-Lys-Gly-Arg-CH2Cl) based on the cleavage site for activation of PAR-2 was synthesised and tested with 12 trypsin-like serine proteinases. The second-order rate constant (ki/Ki) for the formation of the covalent proteinase-inhibitor complex varied by 2 x 10(5)-fold between the proteinases. Biotinyl-Ser-Lys-Gly-Arg-CH2Cl reacted very rapidly with trypsin, acrosin from sperm and tryptase from mast cells: the ki/Ki values with these proteinases were greater than 10(5) M(-1) x s(-1). Thus, the specificity of these proteinases matched the sequence of the activation site of PAR-2 and it can be concluded that these proteinases are potential physiological activators of PAR-2.

Allosteric modulation of the activity of thrombin

Substrates containing a P3 aspartic residue are in general cleaved poorly by thrombin. This may be partly due to an unfavourable interaction between the P3 aspartate and Glu192 in the active site of thrombin. In Protein C activation and perhaps also thrombin receptor cleavage, binding of ligands at the anion-binding exosite of thrombin seems to improve the activity of thrombin with substrates containing a P3 aspartate. To investigate the importance of Glu192 and exosite-binding in modulating thrombin's interactions with a P3 aspartate, peptidyl chloromethanes based on the sequence of the thrombin receptor (containing a P3 aspartate) have been synthesized and the kinetics of their inactivation of alpha-thrombin and the mutant Glu192-->Gln determined. The values of the inactivation rate constant (ki) for the chloromethanes containing a P3 aspartate were about two-fold higher with the Glu192-->Gln mutant. A peptide based on the sequence of hirudin (rhir52 65), which binds to the anion-binding exosite of thrombin, was an allosteric modulator of the amidolytic activity of the Glu192-->Gln mutant; a 5-fold decrease in the K(m) value for the substrate D-Phe-pipecolyl-Arg-p-nitroanilide was observed in the presence of saturating concentrations of rhir52-65. This exosite-binding peptide also increased the ki values of chloromethanes containing a P3 aspartate with both alpha-thrombin and the Glu192-->Gln mutant. However, the increases in the ki values were greater with the Glu192-->Gln mutant (5-fold compared with 2-fold for alpha-thrombin). Thus exosite binding does not seem to mitigate putative unfavourable interactions between Glu192 and the P3 aspartate. Moreover, increases in the ki caused by exosite binding were not unique to chloromethanes containing a P3 aspartate; increases of the same magnitude were also observed when the P3 position was occupied by the favourable D-phenylalanine in place of the unfavourable aspartate. The results obtained were consistent with exosite binding's causing changes in the conformation of the S2 and/or S1 site of thrombin.

Synthesis of peptide p-nitroanilides mimicking fibrinogen- and hirudin-binding to thrombin. Design of slow reacting thrombin substrates

The design and synthesis of 20 peptide p-nitroanilides is described. The nitroanilides are used as thrombin substrates that share uncommon properties. These substrates are tested for their applicability to measure thrombin generation in activated plasma. This technique requires substrates that must slowly but selectively be hydrolyzed by thrombin. To ensure selectivity, thrombin's natural substrate and its most potent inhibitor were used as lead compounds. Eighteen peptide p-nitroanilides were synthesized using human fibrinogen A alpha [7-16] decapeptide as lead structure since this fragment constitutes the minimal sequence which binds to thrombin with high affinity. Two other chromogenic substrates were designed using 5-amino-2-nitrobenzoic acid as the chromophore. A peptide giving subsite interactions with the fibrinogen recognition exosite was coupled to the carboxylic function. As the peptide segment, the carboxyl terminal part of hirudin (residues 50-65) was chosen to ensure highly specific thrombin recognition. From the 20 nitroanilides synthesized, we indeed obtained a number of compounds which can be used as substrate in the thrombin generation assay.

Inhibition of thrombin by arginine-containing peptide chloromethyl ketones and bis chloromethyl ketone-albumin conjugates

Arg-containing peptide chloromethyl ketones including D-Phe-Pro-Arg-CH2Cl derivatives have been synthesized and tested as inhibitors for thrombin and several blood coagulation enzymes. The parent compound, D-Phe-Pro-Arg-CH2Cl is still the best thrombin inhibitor in the series with kobs/[I] value of 10(7) M-1s-1. Extension by one amino acid (Phe or Gly), or a peptide moiety (ClCH2-Arg < -Pro < -D-Phe < -CO-CO-, ClCH2-Arg < -Pro < -D-Phe < -CO-(CH2)3-CO-, where < -indicates a reversed amino acid residue, -CO-CHR-NH-) on the N-terminus of D-Phe-Pro-Arg-CH2Cl reduces the inhibition constant by 1-2 orders of magnitude, which indicates the importance of a free amino group at the N-terminus. The tripeptide D-Phe-Pro-Arg-CH2Cl and related tetrapeptide inhibitors inhibit thrombin more potently than factor IXa and plasma kallikrein by 2-5 orders of magnitude. Z-Arg-CH2Cl and Phe-Phe-Arg-CH2Cl which contain a large hydrophobic group at the P2 site inhibit thrombin poorly. All the peptide chloromethyl ketones inhibit plasma kallikrein moderately with kobs/[I] values of 10(2)-10(3) M-1s-1 but inhibit factor IXa poorly (kobs/[I] < 20 M-1s-1). Conjugates of albumin with the bis chloromethyl ketones [(CO-D-Phe-Pro-Arg-CH2Cl)2, (CH2)3-(CO-D-Phe-Pro-Arg-CH2Cl)2] were prepared and are potent thrombin inhibitors. These conjugates are model compounds for developing specific thrombus-bound thrombin inhibitors which may have therapeutic application in the treatment of coagulation disorders.