The Plasmodium falciparum Malaria M1 Alanyl Aminopeptidase (PfA-M1): Insights of Catalytic Mechanism and Function from MD Simulations

Malaria caused by several species of Plasmodium is major parasitic disease of humans, causing 1-3 million deaths worldwide annually. The widespread resistance of the human parasite to current drug therapies is of major concern making the identification of new drug targets urgent. While the parasite grows and multiplies inside the host erythrocyte it degrades the host cell hemoglobin and utilizes the released amino acids to synthesize its own proteins. The P. falciparum malarial M1 alanyl-aminopeptidase (PfA-M1) is an enzyme involved in the terminal stages of hemoglobin digestion and the generation of an amino acid pool within the parasite. The enzyme has been validated as a potential drug target since inhibitors of the enzyme block parasite growth in vitro and in vivo. In order to gain further understanding of this enzyme, molecular dynamics simulations using data from a recent crystal structure of PfA-M1 were performed. The results elucidate the pentahedral coordination of the catalytic Zn in these metallo-proteases and provide new insights into the roles of this cation and important active site residues in ligand binding and in the hydrolysis of the peptide bond. Based on the data, we propose a two-step catalytic mechanism, in which the conformation of the active site is altered between the Michaelis complex and the transition state. In addition, the simulations identify global changes in the protein in which conformational transitions in the catalytic domain are transmitted at the opening of the N-terminal 8 angstrom-long channel and at the opening of the 30 angstrom-long C-terminal internal chamber that facilitates entry of peptides to the active site and exit of released amino acids. The possible implications of these global changes with regard to enzyme function are discussed.

Acid-catalyzed hydrolysis of cellulose and cellulosic waste using a microwave reactor system

A microwave reactor system was investigated as a potential technique to maximize sugar yield for the hydrolysis of municipal solid waste for ethanol production. Specifically, dilute acid hydrolysis of a-cellulose and waste cellulosic biomass (grass clippings) with phosphoric acid was undertaken within the microwave reactor system. The experimental data and reaction kinetic analysis indicate that the use of a microwave reactor system can successfully facilitate dilute acid hydrolysis of cellulose and waste cellulosic biomass, producing high yields of total sugars in short reaction times. The maximum yield of reducing sugars was obtained at 7.5% (w/v) phosphoric acid and 160 degrees C, corresponding to 60% of the theoretical total sugars, with a reaction time of 5 min. When using a very low acid concentration (0.4% w/v) for the hydrolysis in the microwave reactor, it was found that 10 g of total sugars/100 g dry mass was produced, which is significant considering the low acid concentration. When hydrolyzing grass clippings using the microwave reactor, the optimum conditions were an acid concentration of 2.5% (w/v), 175 degrees C with a 15 min reaction time, giving 18 g/100 g dry mass of total sugars, with xylose being the sugar with the highest yield. It was observed that pentose sugars were more easily formed but also more easily degraded, these being significantly affected by increases in acid concentration and temperature. Kinetic modeling of the data indicated that the use of microwave heating may account for an increase in reaction rate constant, k(1), found in this study in comparison with conventional systems described in the literature.

Alkaline hydrolysis of trinitrotoluene, TNT

The kinetics of the alkaline hydrolysis of trinitrotoluene, TNT, in an aqueous solution is a possible approach to destroying the active agent in unwanted munitions. The kinetics are shown to have a rapid initial step, step A, in which a highly coloured species, X (lambda(max) = 450 nm) is formed via an equilibrium reaction: TNT + OH- double left right arrow X. The bimolecular rate constant for the forward part of this equilibrium process, k(1), is: 0.099 +/- 0.004, 0.32 +/- 0.02 and 1.27 +/- 0.05 dm(3) mol(-1) s(-1), at 25, 40 and 60degreesC, respectively. The activation energy for the forward process is 60 kJ mol(-1). The first-order rate constant for the reverse of this process, k(-1), is: (5.3 +/- 2.6) x 10(-4), (1.2 +/- 1.0) x 10(-3) and (7.7 +/- 2.9) x 10(-3) s(-1) at 25, 40 and 60degreesC, respectively. The activation energy for the overall equilibrium process (k(1)/k(-1)) is ca. -5 kJ mol(-1). The subsequent alkaline hydrolysis of X to form the final product P, i.e. step B, is much slower than step A and appears to comprise two processes coupled in series, i.e. steps B1 (X +2OH(-) --> Z) and B2 (Z+OH- --> P). At 25degreesC, Step B1 appears rate determining throughout the decay process. At 45 degreesC and, more so, at 60degreesC, step B appears increasingly biphasic with increasing alkaline concentrations, as step B2 begins to compete with step B1 for position as the rate determining step. The trimolecular rate constant for step B1 is: 0.017 +/- 0.001, 0.0085 +/- 0.0002 and 0.0011 +/- 0.0001 dm(6) mol(-2) s(-1) at 25, 40 and 60degreesC, respectively, and the process has an activation energy of 64 kJ mol(-1). The transition from uniform kinetics, described by step B1, to mixed kinetics, described by steps B1 and B2, as the reaction temperature and alkali concentration are increased most likely occurs because (a) step B2 has a lower activation energy than B1, although it was not possible to measure the former parameter, and (b) step B2 has a lower (1st) order dependence upon [OH-] compared with that of step B1 (2nd). The bimolecular rate constant for step B2 is 0.0035 +/- 0.03 dm(3) mol(-1) s(-1) at 60degreesC. A brief NMR study of the initial hydrolysis product in water, acetone and chloroform, coupled with UV/visible spectra, provides evidence that species X is a Meisenheimer complex.

Comparison of the efficiences of enzymatic and chemical hydrolysis of (nortestosterone and diethylstilboestrol) glucuronides in bovine urine

Residues of 19-nortestosterone (19-NT) and diethylstilboestrol (DES) are excreted in bovine urine, mainly conjugated to glucuronic acid. Prior to quantification, urine must be deconjugated, which is commonly performed by enzymatic or chemical hydrolysis. The efficiencies of two enzymatic and two chemical deconjugation methods were studied. The range of efficiencies obtained for DES were 51.8% (beta -glucuronidase, incubation at 37 degreesC overnight) and 2.7% (methanolic HCl), respectively. Similarly, efficiencies for NT ranged from 43.1% (beta -glucuronidase, incubation at 55 degreesC for 2 h) to 12.7% (methanolic HCl). The results highlight that within control laboratories significant underestimation of drug residue content in samples may occur, due to poor deconjugation. (C) 2001 Elsevier Science B.V. All rights reserved.

NEUROPEPTIDE-F - A NOVEL PARASITIC FLATWORM REGULATORY PEPTIDE FROM MONIEZIA-EXPANSA (CESTODA, CYCLOPHYLLIDEA)

Using a C-terminally directed pancreatic polypeptide (PP) antiserum and immunocytochemical methods, PP-immunoreactivity (IR) was localized throughout the central (CNS) and peripheral nervous systems (PNS) of the cestode, Moniezia expansa. In the CNS, immunostaining was evident in the paired cerebral ganglia (primitive brain), connecting commissure, and the paired longitudinal nerve cords that are cross-linked by numerous regular transverse connectives. The PNS was seen to consist of a fine anastomosing nerve-net of immunoreactive fibres, many of which were closely associated with reproductive structures. Radioimmunoassay of this peptide IR in acid-alcohol extracts of the worm measured 192.8 ng/g of PP-IR. HPLC analyses of the M. expansa PP-IR identified a single molecular form which was purified to homogeneity. Plasma desorption mass spectrometry (PDMS) of purified parasite peptide resolved a single peptide with a molecular mass of 4599 +/- 10 Da. Automated gas-phase Edman degradation identified a 39-amino acid peptide with a C-terminal phenylalaninamide. Examination of its primary structure shows that it displays significant sequence homology with the vertebrate neuropeptide Y superfamily, suggesting that this platyhelminth-derived peptide is the phylogenetic precursor. Neuropeptide F (M. expansa) is the first regulatory peptide to be fully sequenced from the phylum Platyhelminthes and may represent a member of an important new class of invertebrate neuropeptide.

Importance of the proline residue to the functional activity and metabolic stability of the nematode FMRFamide-related peptide, KPNFIRFamide (PF4)

PF4 has previously been shown to have potent inhibitory effects on myoactivity of somatic muscle strips from the nematode, Ascaris suum. This study examined the bioactivity and metabolic stability of position 2- and position 5-modified analogues of PF4. Although the analogues [Leu(5)] PF4, [Ala(2)]PF4, [Gly(2)]PF4, [Ala(2),Leu(5)]PF4, and [Gly(2),Leu(5)]PF4 all had qualitatively similar inhibitory effects on A. suum somatic muscle strips, their effects were quantitatively distinguishable and had the order of potency: PF4 = [Leu(5)] PF4 >> [Ala(2)]PF4 = [Ala(2),Leu(5)] PF4 >> [Gly(2)] PF4 = [Gly(2),Leu(5)] PF4. Leu(5) for Ile(5) substitutions in PF4 did not alter the activity of this peptide; however, Gly(2)/Ala(2) for Pro(2) substitutions reduced, but did not abolish, peptide activity. Peptide stability studies revealed that [Gly(2)]PF4(2-7) and -(3-7) and [Ala(2)]PF4(2-7), -(3-7), and -(4-7) fragments were generated following exposure to A. suum somatic muscle strips. However, the parent peptide (PF4) was not metabolized and appeared to be resistant to the sequential cleavages of native aminopeptidases. Observed analogue metabolism appeared to be due to the activity of released aminopeptidases as identical fragments were generated by incubation in medium that had been exposed to somatic muscle strips and from which the strips had been removed prior to peptide addition. It was found that the muscle stretching and bath mixing characteristics of the tension assay led to more effective release of soluble enzymes from muscle strips and thus greater peptide degradation. These studies reveal that Pro(2) in PF4 is not essential for the biological activity of this peptide; however, it does render the peptide resistant to the actions of native nematode aminopeptidases. Copyright (C) 1996 Elsevier Science Inc.

Isolation of AF2 (KHEYLRFamide) from Caenorhabditis elegans: Evidence for the presence of more than one FMRFamide related peptide-encoding gene

Numerous FMRF amide-related peptides (FaRPs) have been isolated and sequenced from extracts of free-living and parasitic nematodes. The most abundant FaRP identified in ethanolic/methanolic extracts of the parasitic forms, Ascaris suum and Haemonchus contortus and from the free-living nematode, Panagrellus redivivus, was KHEYLRF amide (AF2). Analysis of the nucleotide sequences of cloned FaRP-precursor genes from C. elegans and, more recently, Caenorhabditis vulgaris identified a series of related FaRPs which did not include AF2. An acid-ethanol extract of Caenorhabditis elegans was screened radioimmunometrically for the presence of FaRPs using a C-terminally directed FaRP antiserum. Approximately 300 pmols of the most abundant immunoreactive peptide was purified to homogeneity and 30 pmols was subjected to Edman degradation analysis and gas-phase sequencing. The unequivocal primary structure of the heptapeptide, Lys-His-Glu-Tyr-Leu-Arg-Phe-NH2 (AF2) was determined following a single gas-phase sequencing run. The molecular mass of the peptide was determined using a time-of-flight mass spectrometer and was found to be 920 (MH(+))(-), which was consistent with the theoretical mass of C-terminally amidated AF2. These results indicate that C. elegans possesses more than one FaRP gene. (C) 1995 Academic Press, Inc.

COMPARATIVE ANALYSES OF THE NEUROPEPTIDE-F (NPF)-RELATED AND FMRFAMIDE-RELATED PEPTIDE (FARP)-IMMUNOREACTIVITIES IN FASCIOLA-HEPATICA AND SCHISTOSOMA SPP

Immunochemical techniques were used to determine the distribution, chemical characteristics and relative abundance of immunoreactivity (IR) to two native platyhelminth neuropeptides, neuropeptide F (NPF) (Moniezia expansa) and the FMRFamide-related peptide (FaRP), GNFFRFamide, in the trematodes, Fasciola hepatica and Schistosoma mansoni; the larger S. margrebowiei was used in the chemical analysis. Extensive immunostaining for the two peptides was demonstrated throughout the nervous systems of both F. hepatica and S. mansoni, with strong IR also in the innervation of muscular structures, including those associated with the egg-forming apparatus. The patterns of immunostaining were similar to those previously described for the vertebrate neuropeptide Y superfamily of peptides and for FMRFamide. Ultrastructurally, gold labelling of NPF- and GNFFRFamide-IRs was localized exclusively to the contents of secretory vesicles in the axons and somatic cytoplasm of neurones. Double-labelling experiments showed an apparent homogeneity of antigenic sites, in all probability due to the demonstrated cross-reactivity of the FaRP antiserum with NPF. Radioimmunoassay of acid-ethanol extracts of the worms detected 8.3 pmol/g and 4.7 pmol/g equivalents of NPF- and FMRFamide-IRs, respectively, for F. hepatica, and corresponding values of 4.9 pmol/g and 4.3 pmol/g equivalents for S. margrebowiei. Gel-permeation chromatography resolved IR to both peptides in discrete peaks and these eluted in similar positions to synthetic NPF (M. expansa) and GNFFRFamide, respectively.