Design, synthesis, and in vitro biological activity of benzimidazole based factor Xa inhibitors.

Inhibitors based on the benzimidazole scaffold showed subnanomolar potency against Factor Xa with 500-1000-fold selectivity against thrombin and 50-100-fold selectivity against trypsin. The 2-substituent on the benzimidazole ring had a strong impact on the FXa inhibitory activity. Crystallography studies suggest that the 2-substituent may have a conformational effect favoring the extended binding conformation.

Conformations of trypsin-bound amidine inhibitors of blood coagulant factor Xa by double REDOR NMR and MD simulations.

Double rotational-echo double resonance (double REDOR) has been used to investigate the bound conformations of (13)C,(15)N,(19)F-labeled factor Xa inhibitors to bovine trypsin. Carbon-fluorine dipolar couplings were measured by (13)C{(19)F} REDOR with natural-abundance background interferences removed by (13)C{(15)N} REDOR. The conformations of the bound inhibitors were characterized by molecular dynamics (MD) simulations of binding restrained by double REDOR-determined intramolecular C-F distances. A symmetrical bisamidine inhibitor and an asymmetrical monoamidine-monoamine inhibitor of the same general shape had distinctly different conformations in the bound state. According to the MD models, these differences arise from specific interactions of the amidine and amine groups with the active-site residues of trypsin and nearby water molecules.

Synthesis, characterization, and structure-activity relationships of amidine-substituted (bis)benzylidene-cycloketone olefin isomers as potent and selective factor Xa inhibitors.

Factor Xa (FXa) is a trypsin-like serine protease that plays a key role in blood coagulation linking the intrinsic and extrinsic pathways to the final common pathway of the coagulation cascade. During our initial studies, we observed facile photochemical conversion of the known FXa/tPA inhibitor, BABCH ¿(E,E)-2, 7-bis(4-amidinobenzylidene)cycloheptan-1-one, 1a, to the corresponding (Z,Z) olefin isomer, 1c (FXa K(i) = 0.66 nM), which was over 25,000 times more potent than the corresponding (E,E) isomer (1a, FXa K(i) = 17 000 nM). In order to determine the scope of this observation, we expanded on our initial investigation through the preparation of the olefin isomers in a homologous series of cycloalkanone rings, 4-substituted cyclohexanone analogues, and modified amidine derivatives. In most cases the order of potency of the olefin isomers was (Z,Z) > (E,Z) > (E,E) with the cycloheptanone analogue (1c) showing the most potent factor Xa inhibitory activity. In addition, we found that selectivity versus thrombin (FIIa) can be dramatically improved by the addition of a carboxylic acid group to the cycloalkanone ring as seen with 8c (FXa K(i) = 6.9 nM, FIIa K(i) > 50,000 nM). Compounds with one or both of the amidine groups substituted with N-alkyl substituents or replaced with amide groups led to a significant loss of activity. In this report we have demonstrated the importance of the two amidine groups, the cycloheptanone ring, and the (Z,Z) olefin configuration for maximum inhibition of FXa within the BABCH template. The results from this study provided the foundation for the discovery of potent, selective, and orally active FXa inhibitors.

Modeling of a Diode-Side-Pumped Nd:YAG Laser.

We have developed a unique numerical laser model by use of a commercial physical optics software package. The experimentally measured lasing threshold, slope efficiency, power output distribution, and phase front have been derived. This model is particularly powerful for monitoring the effects caused by thermal distortions encountered in power scaling lasers. Extrapolations have been made through parametric studies to predict changes required in the laser design that would optimize the performance of the laser.

Demonstration and characterization of a multibillion-shot, 2.5-mJ, 4-ns, Q-switched Nd:YAG laser.

We have demonstrated and characterized a Q-switched Nd:YAG laser under continuous operation for over 7 billion shots. Through periodic monitoring of the laser's vital signs, the system dynamics were decoupled to identify the sources of degradation. The initial and the final pump-laser diode wavelengths and powers were measured and compared. No evidence of an accumulative effect leading to optical damage at a fluence lower than the single-shot threshold was observed.

Efficient, diode-laser-pumped, diode-laser-seeded, high-peak-power Nd:YLF regenerative amplifier.

Optical amplification of 11 orders of magnitude in a microlens-collimated, diode-laser-pumped regenerative amplifier has been demonstrated. The amplifier was seeded with 20-ps pulses from an FM mode-locked oscillator and with 0.9-ns pulses from a modulated diode laser. Seed pulses from both sources were amplified to energies exceeding 2.5 mJ. With the thermoelectric coolers and the Pockels cell electronics neglected, the diode-seeded system exhibited an electrical-to-optical efficiency of 2.2%.

Frequency-modulation mode-locking performance for four Nd(3+)-doped laser crystals.

To determine an optimum host for simultaneous short-pulse-width and large-slope-efficiency generation, the performance of Nd:YAG, Nd:YLF, Nd:YVO(4), and Nd(3+):Sr(5)(VO(4))(3)F [Nd:strontium fluorovanadate (S-VAP)] was characterized under a variety of end-pumped and frequency-modulation mode-locking conditions. The slope efficiency, threshold pump power, and pulse width were recorded for each laser and compared with theory. A figure of merit was defined, yielding Nd:YLF and Nd:YVO(4) as the experimentally determined crystals of choice.

In vitro attachment of bilins to apophycocyanin. III. Properties of the phycoerythrobilin adduct.

Addition of phycoerythrobilin (PEB) to apophycocyanin at pH 7.0 resulted in covalent adduct formation. The adduct showed absorbance maxima at 575 and 605 nm and fluorescence emission maxima at 582 and 619 nm. Analysis of bilin peptides obtained upon tryptic digestion of the adduct showed residues alpha-Cys-84 and beta-Cys-82 to be the sites of bilin addition. The product of PEB addition at the alpha-Cys-84 site was shown by 1H NMR analysis to be a dihydrobiliviolinoid peptide-linked pigment differing in structure from that of the naturally occurring PEB-adduct by the presence of a double bond in between C2 and C3 of ring A. At the beta-Cys-82 site both a dihydrobiliviolinoid and a PEB adduct were obtained. Biliverdin also formed a covalent adduct with apophycocyanin with a lambda max of 669 nm. These results show that the spontaneous in vitro addition of bilins to apophycocyanin does not exhibit the site selectivity of bilin addition observed in vivo. This offers the opportunity to form novel semisynthetic phycobiliproteins.

In vitro attachment of bilins to apophycocyanin. II. Determination of the structures of tryptic bilin peptides derived from the phycocyanobilin adduct.

In vitro reaction of phycocyanobilin (PCB) with apophycocyanin results in the specific addition of the bilin to two of the cysteinyl residues, alpha-Cys-84 and beta-Cys-82, which normally function in PCB attachment (Arciero, D. M., Bryant, D. A., and Glazer, A. N. (1988) J. Biol. Chem. 263, 18343-18349). These bilin binding sites are designated alpha-1 and beta-1, respectively. Tryptic digestion of the apophycocyanin-PCB adduct releases two major bilin peptides, alpha-1 mesobiliverdin (MBV) and beta-1 MBV, which encompass the two bilin-binding sites. These peptides were examined by 1H NMR and fast atom bombardment mass spectroscopies. The NMR spectra show that the bilin is attached to each peptide through a thioether linkage identical to the linkage observed in the corresponding tryptic peptides, alpha-1 PCB and beta-1 PCB, derived from the natural product, C-phycocyanin. However, the NMR spectra of the adduct peptides lack the resonances corresponding to protons at positions C2 and C3 of ring A seen in the spectra of the alpha-1 PCB and beta-1 PCB peptides. Fast atom bombardment mass spectroscopy shows the masses of the alpha-1 MBV and beta-1 MBV peptides to be 2 atomic mass units lower than those of the alpha-1 PCB and beta-1 PCB peptides, respectively. Comparison of the bilin portion of the NMR spectra of the alpha-1 MBV and beta-1 MBV peptides to the NMR spectra of PCB and mesobiliverdin confirms that the bilin of the two adduct peptides resembles mesobiliverdin in having an extra double bond in the C2-C3 position of ring A. These results show that the major bilin products arising from the reaction of PCB with apophycocyanin differ from the bilins present in C-phycocyanin. The relevance of these results to the biosynthetic pathway for the attachment of tetrapyrroles to phycobiliproteins is discussed.

Exclusive A-ring linkage for singly attached phycocyanobilins and phycoerythrobilins in phycobiliproteins. Absence of singly D-ring-linked bilins.

Previous spectroscopic studies on the phycocyanobilin-containing peptide beta-2T from Synechococcus sp. 6301 C-phycocyanin and the phycoerythrobilin-containing peptide beta-2TP from Porphyridium cruentum B-phycoerythrin indicated a different single thioether mode of attachment, postulated to be through the D-ring of the tetrapyrrole, in contrast to the A-ring linkage established for the other singly linked bilins in these proteins (Bishop, J.E., Lagarias, J.C., Nagy, J. O., Schoenleber, R.W., Rapoport, H., Klotz, A.V., and Glazer, A.N. (1986) J. Biol. Chem. 261, 6790-6796; Klotz, A.V., Glazer, A.N., Bishop, J.E., Nagy, J.O., and Rapoport, H. (1986) J. Biol. Chem. 261, 6797-6805). The crystal structure of Agmenellum quadruplicatum C-phycocyanin at 2.5-A resolution (Schirmer, T., Bode, W., and Huber, R. (1987) J. Mol. Biol., 196, 677-695) supports an A-ring linkage for all three phycocyanobilins. Consequently we have re-evaluated our proposed structural assignments by further 1H NMR studies. Two-dimensional homonuclear correlated and nuclear Overhauser enhancement spectroscopic data presented here show that all three bilins in Synechococcus 6301 C-phycocyanin are attached solely through the A-ring, complementary to the crystallographic data. The evidence from the NMR data for all bilin peptides examined includes the dipoledipole interactions of the 5-H with the 3-H, 3'-H, and a pyrrole methyl group (7-CH3); the corresponding interactions would not be possible in a D-ring-linked bilin. The 5-H also consistently exhibits allylic J-coupling to the 3-H, supporting A-ring linkage assignment. These data are inconsistent with the alternative D-ring linkage assignment since this would involve J-coupling through five bonds. Examination of the phycoerythrobilin beta-2 position in B-phycoerythrin also reveals an A-ring type of attachment by similar criteria. We conclude that all singly linked bilins are attached through the A-ring.

trans-4-Hydroxy-2-hexenal: a reactive metabolite from the macrocyclic pyrrolizidine alkaloid senecionine.

The toxicity of macrocyclic pyrrolizidine alkaloids in the livers of man and animals has been attributed to the formation of reactive pyrroles from dihydropyrrolizines. Now a novel metabolite, trans-4-hydroxy-2-hexenal, has been isolated from the macrocyclic pyrrolizidine alkaloid senecionine, in an in vitro hepatic microsomal system. Other alkenals such as trans-4-hydroxy-2-nonenal have previously been isolated from microsomal systems when treated with halogenated hydrocarbons or subjected to lipid peroxidation. The in vivo pathology caused by trans-4-hydroxy-2-hexenal appears to be identical to that previously attributed to reactive pyrroles. There are similarities between the toxic effects of this alkenal and those of centrilobular hepatotoxins such as CCl4 and other alkenals formed during lipid peroxidation.

Two dihydropyrrolizine alkaloid metabolites isolated from mouse hepatic microsomes in vitro.

The in vitro mouse hepatic microsomal metabolism of the macrocyclic pyrrolizidine alkaloid senecionine was studied for additional metabolites. Using previously developed HPLC systems plus a preparative system, two additional dihydropyrrolizine metabolites have been identified from the microsomal enzyme system of mice. The metabolites 1-hydroxymethyl-7-methoxy-6,7-dihydro-5H-pyrrolizine (methoxydehydroretronecine) and 1-formyl-7-hydroxy-6,7-dihydro-5H-pyrrolizine (hydroxydanaidal) have not been heretofore isolated from mouse microsomal enzyme systems. The metabolite dehydroretronecine which had previously been isolated from rat hepatic microsomes, was not detected while senecic acid, 19-hydroxysenecionine, and senecionine N-oxide were again present.

Mg-2,4-divinyl pheoporphyrin a5: the product of a reaction catalyzed in vitro by developing chloroplasts.

The major product of an aerobic reaction mixture containing developing chloroplasts, Mg-protoporphyrin IX, S-adenosylmethionine, and other cofactors was isolated and purified. Structural studies using nuclear magnetic resonance confirmed earlier reports, based on fluorescence and absorption spectra, that this compound is Mg-2,4-divinyl pheoporphyrin a5. The molecular weight determined by secondary-ion mass spectroscopy further confirmed the assigned structure. Absorption and fluorescence spectra indicate that this compound is identical to that reported previously by various workers in less-purified biological extracts. The nuclear magnetic resonance spectrum of the Mg-free base also supports the assigned structure.

Identification of a key structural feature of cobalt(III)-bleomycins: an exogenous ligand (e.g. hydroperoxide) bound to cobalt.

A series of cobalt(III) complexes of the anticancer antibiotic bleomycin has been prepared. Mass spectrometry and enzymatic analysis show that the green cobalt-bleomycin complex contains a hydroperoxide (-OOH) group bound to cobalt with unusual stability. Under appropriate conditions, cobalt-bleomycins containing other monodentate ligands to cobalt can be formed; fast-atom bombardment mass spectra of such complexes show peaks for cobalt-bleomycin at the expected mass, and also peaks for the intact complexes at the required higher mass.

High-field 1H NMR studies of synthetic analogs of somatostatin. Structural features involving aromatic residues in an active eight-membered ring analog.

360 MHz 1H-NMR data are presented for somatostatin and an analog whose primary structure is cyclo(-Gaba-Asn5-Phe6-Phe7-DTrp8-Lys9-Thr10-Phe11-). This report focuses on the aromatic portion of the spectrum, and this region for the analog is unambiguously assigned, using two experimental approaches: selective deuteration and photo-induced CIDNP. The most prominent feature of the analog aromatic spectrum is a two-proton resonance which exhibits a pronounced upfield shift. Significantly, this feature is also present for somatostatin and other active analogs (unpublished data). Assignments show that this resonance derives from the ortho hydrogens of the Phe6 and that aromatic resonances of Phe6 shift markedly upfield as temperature is decreased. In contrast, the aromatic resonances of Phe7,11 and DTrp8 reveal generally much smaller temperature coefficients and shift primarily downfield as temperature is decreased. Ring-current analysis shows that simple pair-wise parallel pi-stacking alone cannot give rise to the observed data. However, a simple hypothesis involving only two phenylalanine residues is totally consistent with the data if they maintain a time-averaged co-perpendicular orientation. Indirect evidence is offered which implicates only one phenylalanine stacking partner for Phe6, which we tentatively identify as Phe11.

Periodate inactivation of ovotransferrin and human serum transferrin.

Azari and Phillips (Azari, P., and Phillips, J. L. 1970 Arch. Biochem. Biophys. 138, 32-38) reported that periodate treatment of iron-free ovotransferrin causes a rapid loss of iron-binding activity and an oxidation of 3 to 5 tyrosines and 1 tryptophan. Rapid inactivation and loss of tyrosine in ovotransferrin has been confirmed, and the work extended to human serum transferrin and effects of denaturing concentrations of urea. Extensive (> 80%) inactivations of both ovotransferrin and human serum transferrin were observed when approximately 4 tyrosines were destroyed. Amino acid analysis and 360-MHz 1H NMR spectra confirmed that tyrosines are the only residues rapidly oxidized; the correlation of tyrosine loss with the loss of iron-binding activity suggests strongly that the tyrosines involved are those that function as ligands to metal ions bound to the protein. NMR spectra also showed that periodate oxidation causes local changes of structure in ovotransferrin (presumably at the metal-binding sites) but does not grossly alter the conformation. The addition of 5 to 8 M urea greatly retarded the inactivation and losses of tyrosine.

Carbon-13 N.M.R. study of bleomycin-A2 protonation.

The acid-base titration of bleomycin-A2 in D2O solution at 35 +/- 5 degrees has been monitored by 13C n.m.r. spectroscopy at 67.89 MHz. The following pKDa values were obtained: 3.68 +/- 0.05 (secondary amine), 5.29 +/- 0.03 (imidazole), and 8.23 +/- 0.19 (primary amine), where KDa is the dissociation constant in D2O solution. The equilibrium isotope effects (pKDa--pKa in H2O) are: 0.70 +/- 0.06 (secondary amine), 0.28 +/- 0.04 (imidazole), and 0.85 +/- 0.19 (primary amine). Titration of the imidazole group of Bleo-A2 occurs at Npi, i.e. only Ntau is protonated in basic solution. Significant protonation shifts are almost completely limited to carbons of the N-terminal tetrapeptide, suggesting that the C-terminal tripeptide extends into the solvent and interacts to a minimal extent with the rest of the molecule. Long range protonation shifts associated with titration of the imidazole and secondary amine groups indicate that protonation of one or both of these sites is probably accompanied by significant conformational changes. The observed protonation shifts generally fail to correlate with Zn(II) complexation shifts reported by Dabrowiak et al. (1973, Biochemistry 17., 4090) indicating that ligation sites cannot unambiguously be determined from these complexation shifts. The complexation shifts previously attributed to coordination of the imidazole and carbamoyl groups probably result from conformational changes.