scholarly journals Ethacrynic Acid Is an Inhibitor of Human Factor XIIIa

2021 ◽  
Author(s):  
Srabani Kar ◽  
Kayla Vu ◽  
Madhusoodanan Mottamal ◽  
Rami A. Al-Horani
Keyword(s):  
Active Site ◽  
Human Factor ◽  
Ethacrynic Acid ◽  
Blood Clot ◽  
Covalent Bond ◽  
Parenteral Administration ◽  
Factor Xiiia ◽  
Bleeding Complications ◽  
Coagulation Process ◽  
Michael Acceptor

Abstract Ethacrynic acid (EA) is a loop diuretic that is approved orally and parenterally to manage edema-associated diseases. Nevertheless, it was earlier reported that it is also associated with bleeding upon its parenteral administration. In this report, we investigated the effects of EA on human factor XIIIa (FXIIIa) of the coagulation process using a variety of techniques. FXIIIa is a transglutaminase that works at the end of the coagulation process to form an insoluble, rigid, and cross-linked fibrin rich blood clot. In fact, inhibition of FXIIIa-mediated biological processes has been reported to result in a bleeding diathesis. Inhibition of FXIIIa by EA was investigated given the nucleophilic nature of the thiol-containing active site of the enzyme and the Michael acceptor-based electrophilicity of EA. In a bisubstrate-based fluorescence trans-glutamination assay, EA inhibited FXIIIa with a moderate potency (IC50 ~ 105 µM) and efficacy (∆Y ~ 66%). In SDS-PAGE experiment, EA appears to significantly inhibit the FXIIIa-mediated polymerization of fibrin(ogen) as well as the formation of fibrin(ogen) – α2-antiplasmin complex which indicates that EA affects the physiological functions of FXIIIa. Interestingly, EA did not affect the clotting times of human plasma in the activated partial thromboplastin time (APTT) or prothrombin time (PT) assays at the highest concentration tested of 2.5 mM suggesting the lack of effects on the coagulation serine proteases and potentially the functional selectivity of EA with respect to the clotting process. Molecular modeling studies demonstrated that the Michael acceptor of EA forms a covalent bond with catalytic residue of Cys314 in the active site of FXIIIa. Overall, our studies indicate that EA inhibits the physiological function of human FXIIIa in vitro which may potentially contribute to the bleeding complications that were reported with the association of the parenteral administration of EA.

scholarly journals 1250. Novel Boronic Acid Transition State Analogs (BATSI) with in vitro inhibitory activity against class A, B and C β-lactamases

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S643-S643
Author(s):  
Maria F Mojica ◽  
Christopher Bethel ◽  
Emilia Caselli ◽  
Magdalena A Taracila ◽  
Fabio Prati ◽  
...  
Keyword(s):  
Active Site ◽  
Inhibitory Activity ◽  
Covalent Bond ◽  
Thiol Group ◽  
Viable Cell ◽  
Free Thiol ◽  
Transition State Analogs ◽  
Cell Counts ◽  
Free Thiol Group

Abstract Background Catalytic mechanisms of serine β-lactamases (SBL; classes A, C and D) and metallo-β-lactamases (MBLs) have directed divergent strategies towards inhibitor design. SBL inhibitors act as high affinity substrates that -as in BATSIs- form a reversible, dative covalent bond with the conserved active site Ser. MBL inhibitors bind the active-site Zn2+ ions and displace the nucleophilic OH-. Herein, we explore the efficacy of a series of BATSI compounds with a free-thiol group at inhibiting both SBL and MBL. Methods Exploratory compounds were synthesized using stereoselective homologation of (+) pinandiol boronates to introduce the amino group on the boron-bearing carbon atom, which was subsequently acylated with mercaptopropanoic acid. Representative SBL (KPC-2, ADC-7, PDC-3 and OXA-23) and MBL (IMP-1, NDM-1 and VIM-2) were purified and used for the kinetic characterization of the BATSIs. In vitro activity was evaluated by a modified time-kill curve assay, using SBL and MBL-producing strains. Results Kinetic assays revealed that IC50 values ranged from 1.3 µM to >100 µM for this series. The best compound, s08033, demonstrated inhibitory activity against KPC-2, VIM-2, ADC-7 and PDC-3, with IC50 in the low μM range. Reduction of at least 1.5 log10-fold of viable cell counts upon exposure to sub-lethal concentrations of antibiotics (AB) + s08033, compared to the cells exposed to AB alone, demonstrated the microbiological activity of this novel compound against SBL- and MBL-producing E. coli (Table 1). Table 1 Conclusion Addition of a free-thiol group to the BATSI scaffold increases the range of these compounds resulting in a broad-spectrum inhibitor toward clinically important carbapenemases and cephalosporinases. Disclosures Robert A. Bonomo, MD, Entasis, Merck, Venatorx (Research Grant or Support)

Role of factor XIII in fibrin clot formation and effects of genetic polymorphisms

Blood ◽  
2002 ◽  
Vol 100 (3) ◽  
pp. 743-754 ◽  
Author(s):  
Robert A. S. Ariëns ◽  
Thung-Shenq Lai ◽  
John W. Weisel ◽  
Charles S. Greenberg ◽  
Peter J. Grant
Keyword(s):  
Genetic Polymorphisms ◽  
Factor Xiii ◽  
Blood Clot ◽  
Site Directed Mutagenesis ◽  
Clot Formation ◽  
Factor Xiiia ◽  
Clotting Factors ◽  
Functional Features

Abstract Factor XIII and fibrinogen are unusual among clotting factors in that neither is a serine protease. Fibrin is the main protein constituent of the blood clot, which is stabilized by factor XIIIa through an amide or isopeptide bond that ligates adjacent fibrin monomers. Many of the structural and functional features of factor XIII and fibrin(ogen) have been elucidated by protein and gene analysis, site-directed mutagenesis, and x-ray crystallography. However, some of the molecular aspects involved in the complex processes of insoluble fibrin formation in vivo and in vitro remain unresolved. The findings of a relationship between fibrinogen, factor XIII, and cardiovascular or other thrombotic disorders have focused much attention on these 2 proteins. Of particular interest are associations between common variations in the genes of factor XIII and altered risk profiles for thrombosis. Although there is much debate regarding these observations, the implications for our understanding of clot formation and therapeutic intervention may be of major importance. In this review, we have summarized recent findings on the structure and function of factor XIII. This is followed by a review of the effects of genetic polymorphisms on protein structure/function and their relationship to disease.

scholarly journals Myoglobin Dynamics Measured With Vibrational Echo Experiments

1999 ◽  
Vol 19 (1-4) ◽  
pp. 19-34 ◽  
Author(s):  
K. D. Rector ◽  
M. D. Fayer
Keyword(s):  
Active Site ◽  
Covalent Bond ◽  
Native Protein ◽  
Vibrational Dephasing ◽  
Pure Dephasing ◽  
Homogeneous Linewidth ◽  
The Fourier Transform ◽  
Vibrational Echo ◽  
Protein Fluctuations ◽  
Dephasing Rate

Ps infrared vibrational echo experiments on myoglobin and myoglobin mutants are presented. The vibrational dephasing experiments examine the influence of protein dynamics on the CO ligand, at the active site of myoglobin, from low temperature to physiologically relevant temperatures. The vibrational echo results are combined with measurements of the CO vibrational lifetime to yield the homogeneous pure dephasing. The pure dephasing is the Fourier transform of the homogeneous linewidth with the lifetime contribution removed. The mutant H64V protein's CO vibrational pure dephasing rate is ∼20% slower (narrower pure dephasing linewidth) than the native protein at all temperatures, although the only difference between the two proteins is the replacement of the native’s polar distal histidine by a non-polar valine. The mutant H93G(N-MeIm) pure dephasing is identical to the native's, despite the severing of the only covalent bond between the heme and the globin. These results provide insights into the mechanisms of the transmission of protein fluctuations to the CO ligand bound at the active site.

scholarly journals Chloroacetone as an active-site-directed inhibitor of the aliphatic amidase from Pseudomonas aeruginosa

1980 ◽  
Vol 191 (3) ◽  
pp. 811-826 ◽  
Author(s):  
M R Hollaway ◽  
P H Clarke ◽  
T Ticho
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Active Site ◽  
Chemical Reactivity ◽  
Covalent Bond ◽  
Order Rate Constant ◽  
Reaction Scheme ◽  
Enzymic Activity ◽  
Adsorption Complex ◽  
Apparent Dissociation Constant ◽  
Kinetic Experiment

1. Chloroacetone (I) was shown to be an active-site-directed inhibitor of the aliphatic amidase (EC 3.5.1.4) from Pseudomonas aeruginosa strain PAC142.2. This inhibitor reacted with the enzyme in two stages: the first involving the reversible formation of an enzymically inactive species, EI, and the second the formation of a species, EX, from which enzymic activity could not be recovered. 3. Different types of kinetic experiment were conducted to test conformity of the reaction to the scheme: E + I k+1 Equilibrium k-1 EI Leads to K+2 EX A computer-based analysis of the results was carried out and values of the individual rate constants were determined. 4. No direct evidence for a binding step before the formation of EI could be obtained, as with [E]0 Less Than [I]0 the observed first-order rate constant for the formation of EI was directly proportional to the concentration of chloroacetone up to 1.2 mM (above this concentration the reaction became too rapid to follow even by the stopped-flow method developed to investigate fast inhibition). 5. The value of k+1 exhibited a bell-shaped pH-dependency with a maximum value of about 3 × 10(3) M-1. S-1 at pH6 and apparent pKa values of 7.8 and about 4.8.6. The values of k-1 and K+2 were similar and changed with the time of reaction from values of about 3 × 10(-3) S-1 (pH8.6) at short times to about one-sixth this value for longer periods of incubation. In this respect the simple reaction scheme is insufficient to describe the inhibition process. 7. The overall inhibition reaction is rapid, whether it is considered in relation to the expected chemical reactivity of chloroacetone, the rate of reaction of other enzymes with substrate analogues containing the chloromethyl group, or the rate of the amidase-catalysed hydrolysis of N-methylacetamide, a substrate that is nearly isosteric with chloroacetone. 8. Acetamide protected the amidase from inhibition by chloroacetone, and the concentration-dependence of the protection gave a value of an apparent dissociation constant similar to the Km value for this substrate. 9. Addition of acetamide to solutions of the species EI led to a slow recovery of activity. Recovery of active enzyme was also observed after dilution of a solution of EI in the absence of substrate. 10. The species EI is considered not to be a simple adsorption complex, and the possibilities are discussed that it may be a tetrahedral carbonyl adduct, a Schiff base (azomethine) or a complex in which the enzyme has undergone a structural change. The species EX is probably a derivative in which there is a covalent bond between a group in the enzyme and the C-1 atom of the inhibitor.

Structure of a backtracked state reveals conformational changes similar to the state following nucleotide incorporation in human norovirus polymerase

2014 ◽  
Vol 70 (12) ◽  
pp. 3099-3109 ◽  
Author(s):  
Dmitry Zamyatkin ◽  
Chandni Rao ◽  
Elesha Hoffarth ◽  
Gabriela Jurca ◽  
Hayeong Rho ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Active Site ◽  
Covalent Bond ◽  
Crystal Form ◽  
Phosphoryl Group ◽  
Nucleoside Triphosphate ◽  
Orthorhombic Crystal ◽  
Crystal Forms ◽  
Terminal Nucleotide ◽  
Thumb Domain

The RNA-dependent RNA polymerase (RdRP) from norovirus (NV) genogroup II has previously been crystallized as an apoenzyme (APO1) in multiple crystal forms, as well as as a pre-incorporation ternary complex (PRE1) bound to Mn2+, various nucleoside triphosphates and an RNA primer-template duplex in an orthorhombic crystal form. When crystallized under near-identical conditions with a slightly different RNA primer/template duplex, however, the enzyme–RNA complex forms tetragonal crystals (anisotropic data,dmin≃ 1.9 Å) containing a complex with the primer/template bound in a backtracked state (BACK1) similar to a post-incorporation complex (POST1) in a step of the enzymatic cycle immediately following nucleotidyl transfer. The BACK1 conformation shows that the terminal nucleotide of the primer binds in a manner similar to the nucleoside triphosphate seen in the PRE1 complex, even though the terminal two phosphoryl groups in the triphosphate moiety are absent and a covalent bond is present between the α-phosphoryl group of the terminal nucleotide and the 3′-oxygen of the penultimate nucleotide residue. The two manganese ions bound at the active site coordinate to conserved Asp residues and the bridging phosphoryl group of the terminal nucleotide. Surprisingly, the conformation of the thumb domain in BACK1 resembles the open APO1 state more than the closed conformation seen in PRE1. The BACK1 complex thus reveals a hybrid state in which the active site is closed while the thumb domain is open. Comparison of the APO1, PRE1 and BACK1 structures of NV polymerase helps to reveal a more complete and complex pathway of conformational changes within a single RdRP enzyme system. These conformational changes lend insight into the mechanism of RNA translocation following nucleotidyl transfer and suggest novel approaches for the development of antiviral inhibitors.

scholarly journals Isolation of a fibrin-binding fragment from blood coagulation factor XIII capable of cross-linking fibrin(ogen)

1988 ◽  
Vol 256 (3) ◽  
pp. 1013-1019 ◽  
Author(s):  
C S Greenberg ◽  
J J Enghild ◽  
A Mary ◽  
J V Dobson ◽  
K E Achyuthan
Keyword(s):  
Active Site ◽  
Factor Xiii ◽  
Polyacrylamide Gel Electrophoresis ◽  
Limited Proteolysis ◽  
Coagulation Factor ◽  
Cysteine Residue ◽  
Factor Xiiia ◽  
Platelet Factor ◽  
Transglutaminase Activity ◽  
A Chain

Purified platelet Factor XIII was radioiodinated and then partially degraded by thrombin or trypsin, and a fibrin-binding fragment was identified by autoradiography and immunoblotting following separation by SDS/polyacrylamide-gel electrophoresis. Limited proteolysis of 125I-Factor XIII by thrombin or trypsin produced an 125I-51 kDa fragment and an unlabelled 19 kDa fragment. The 51 kDa fragment was purified by h.p.l.c. on a TSK-125 gel-filtration column. Partial amino acid sequence analysis of the 51 kDa fragment indicated that it was similar in sequence to the Gly38-Lys513 segment in placental Factor XIII a-chain. More than 70% of the 51 kDa fragment bound to fibrin, whereas the 19 kDa fragment did not bind. The active site was localized to the 51 kDa fragment since this fragment expressed transglutaminase activity, cross-linked fibrin and fibrinogen and incorporated iodo[14C]acetamide into the active-site cysteine residue. Isolation of a fibrin-binding fragment expressing transglutaminase activity demonstrates that each a-chain of the dimeric Factor XIIIa could function independently to cross-link fibrin. The fibrin-binding site could play an important role in localizing Factor XIIIa to the fibrin clot.

scholarly journals The alternatively spliced V region contributes to the differential incorporation of plasma and cellular fibronectins into fibrin clots.

1992 ◽  
Vol 119 (4) ◽  
pp. 923-933 ◽  
Author(s):  
C L Wilson ◽  
J E Schwarzbauer
Keyword(s):  
Blood Clot ◽  
Coagulation Factor ◽  
Factor Xiiia ◽  
Cross Linking ◽  
Asymmetric Distribution ◽  
Alternatively Spliced ◽  
V Region ◽  
Fibrin Clots

During blood clot formation in vivo, plasma fibronectin (pFN) is cross-linked to fibrin by coagulation factor XIIIa. Cellular FN (cFN), which localizes to connective tissue, is distinguished from pFN by the inclusion of alternatively spliced segments. To determine if these two FNs are functionally equivalent in blood clotting, the cross-linking of rat pFN and cFN to fibrin was compared in an in vitro clotting assay. Fibrinogen and FN were incubated at physiological ratios in the presence of thrombin and factor XIIIa. Cross-linking of FN to fibrin was monitored by SDS-PAGE and immunoblotting. Over 24 h, cFN was incorporated at a significantly slower rate than pFN and was not completely cross-linked to fibrin at a temperature that favors this interaction (0 degrees C). This difference was observed with purified fibrinogens from human, rat, and bovine and with rat plasma and was maintained even after incubation of pFN with rat fibroblasts for several days. Using the same assay, purified recombinant V(+)-V0 and V(+)-V+ FN dimers resembling pFN and cFN, respectively, showed a similar difference in cross-linking kinetics. These results suggest that the asymmetric distribution of the V region among pFN dimers plays a role in regulating its incorporation into blood clots. In fibrin clots, cFN was converted into a set of cross-linked intermediates distinct from those of pFN. For example, while pFN was initially cross-linked into a pFN-fibrin alpha heterodimer, this product was not a major intermediate in clots formed with cFN. This finding, in conjunction with evidence for the formation of factor XIIIa-catalyzed cFN-cFN cross-links, indicated that cFN molecules interact with each other, and with fibrin, differently from pFN. Together, these results show an important functional distinction between pFN and cFN.

scholarly journals Relevance of single cell and single molecule studies at different biological and physical length scales

2017 ◽  
Author(s):  
Wenfa Ng
Keyword(s):  
Quantum Mechanics ◽  
Single Cell ◽  
Single Molecule ◽  
Active Site ◽  
Covalent Bond ◽  
The Other ◽  
Quantum Mechanical ◽  
Microfluidic Channels ◽  
Other Hand ◽  
Single Molecule Studies

Scale transcends multiple levels of biological and physical organization, and is the critical factor that determines success of any scientific investigation. Specifically, the scale at which a question is posed plays a crucial role in influencing the type of experiments and apparatuses needed. Single cell and single molecule experiments came to the fore of experiment science due to its capability at addressing a fundamental problem in biology and physical science: does the same behavior in cells and molecules transcend different length and population scales? Thus far, single cell experiments could be achieved with trapping of single cell using optical tweezer traps and microfluidic channels. The same, however, is not true for single molecule studies, which remains in the realm of theoretical and simulation studies. Specifically, single molecule experiment remains at the hundreds to thousands of molecules level, where possible skew in the population of molecules sampled could provide a false depiction of molecular reality of a larger population. But, what do scientists learn from single cell and single molecule studies? Is it the uncovering of mysteries of the probabilistic behavior at the single entity level, guided by perhaps quantum mechanics? The answer is no for single cell studies, given that cellular decision making require the input of tens to hundreds of molecular sensors and effectors within a cell. Hence, single cell behavior is not random, but directed at a nutrient or concentration gradient or signaling source. On the other hand, enzymatic catalysis of a single molecule substrate with the active site involves a quantum mechanical crosstalk. Thus, reaction between the substrate molecule and the active site proceeds if suitable energy levels (i.e., quantum mechanical states) are found for both parties. Given that distribution of quantum mechanical states is probabilistic, stochasticity rules single molecule interaction such as a covalent bond formation reaction between reactant A and B. Thus, single cell and single molecule studies do hold relevance in biological and physical sciences research if the correct experiment tool is used for a pertinent question at an appropriate length and population scale. For example, while tremendous amount of basic understanding could be derived from single cell experiments, single cell perspective is not relevant to questions examining the interactions between two large subpopulations of cells. Single molecule experiments, on the other hand, remains in the theoretical and simulation realm for highlighting the effect of quantum mechanics in guiding the behavior of molecules at the nanoscale.

Enzymatic activity is necessary for thrombin-mediated increase in endothelial permeability

1990 ◽  
Vol 259 (4) ◽  
pp. L270-L275 ◽  
Author(s):  
J. L. Aschner ◽  
J. M. Lennon ◽  
J. W. Fenton ◽  
M. Aschner ◽  
A. B. Malik
Keyword(s):  
Active Site ◽  
Endothelial Permeability ◽  
Covalent Bond ◽  
Catalytic Site ◽  
Irreversible Inhibitor ◽  
Chloromethyl Ketone ◽  
High Concentrations ◽  
Dose Dependent Increase ◽  
Dose Dependent ◽  
Fold Excess

alpha-Thrombin causes a dose-dependent increase in endothelial permeability as measured by the clearance rate of 125I-albumin across a monolayer of bovine pulmonary artery endothelial cells. We determined if an active catalytic site is necessary for the thrombin-mediated increase in endothelial permeability. alpha-Thrombin was reacted with 10-fold excess D-phenylalanyl-prolyl-arginine chloromethyl ketone (PPACK), an irreversible inhibitor that forms a covalent bond with thrombin's active site, producing an enzymatically inactive thrombin. PPACK completely inhibited the alpha-thrombin-mediated increase in 125I-albumin permeability. Similar results were obtained with gamma-thrombin, an enzymatically active alpha-thrombin form with an altered fibrinogen recognition domain. PPACK alone and the active site-inhibited PPACK-alpha-thrombin had no effect on permeability. Diisopropylphospho (DIP)-alpha-thrombin was effective only in very high concentrations (10(-6)M), and this effect was abolished by the addition of PPACK. These studies demonstrate that binding alone is insufficient for the thrombin-mediated increase in endothelial monolayer permeability. Thrombin's active catalytic site is a requirement for the increase in transendothelial albumin permeability.

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