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Inhibition of the trehalose-P synthase of mycobacteria by various antibiotics.

A number of antibiotics were tested as potential inhibitors of the purified trehalose-P synthase of Mycobacterium smegmatis. Of about 30 compounds tested, 4 (cathomycin, circulin, diumycin, and moenomycin) were active against this enzyme. Thus each of these compounds inhibited the formation of trehalose-P by the purified trehalose-P synthase when either UDP-glucose or GDP-glucose was used as the glucosyl donor. However, preincubation of the synthase with heparin, a polyanion activator of the enzyme when UDP-glucose is used as the substrate, prevented the inhibition by these various antibiotics. Fifty percent inhibition by diumycin and moenomycin occurred at a concentration of about 50 microg/ml (Ki of about 1 x 10(-5) M), but 50% inhibition by cathomycin and circulin required substantially higher concentrations (about 50 to 200 microg/ml). The inhibition by cathomycin, diumycin, and moenomycin was of the competitive type, whereas that by circulin was noncompetitive in nature. However, the inhibition was of a complex nature and the data suggest two different binding sites for these inhibitors. Photoaffinity labeling of the synthase with an azido-UDP-[32P]glucose probe was effectively blocked by diumycin, moenomycin, or cathomycin indicating that these inhibitors do interact at the substrate binding site. These antibiotics also inhibited the growth of M. smegmatis when added to cells innoculated into trypticase soy broth. The inhibition of growth was concentration-dependent and directly proportional to the size of the bacterial innoculum. These antibiotics, however, did not inhibit protein synthesis nor did they inhibit the incorporation of mannose into lipid-linked saccharides.

Anti-Bacterial Agents↗

Refined structure and metal binding site of the kalata B1 peptide.

The cyclic polypeptide kalata B1 from the African plant Oldenlandia affinis DC consists of 29 amino acid residues with three disulfide linkages. In this study we used two-dimensional NMR spectroscopy to investigate the three-dimensional structure of the peptide and to determine the disulfide connectivities. Nuclear Overhauser effects (NOEs) between neighboring beta-protons of the cysteines detected at 750 MHz provided evidence for the disulfide connectivity pattern 5-13, 17-29, and 22-27. These disulfide linkages were confirmed by three-dimensional structures calculated from input constraints derived solely from NOEs without explicit disulfide connectivities. Kalata B1 is insoluble in aqueous solution above pH 3.5, but in a 50-50 water-methanol mixture, it was possible to use natural abundance two-dimensional (15)N-(1)H heteronuclear single quantum coherence spectroscopy to study the hydrophobic peptide from pH 2 to 10. The addition of methanol resulted in no significant structural changes. Although the peptide contains three prolyl residues, no evidence of multiple conformers was detected at any pH. The addition of Mn(2+) to kalata B1 resulted in selective broadening of resonances from Asn 23, Thr 24, and Glu 15; these results suggest that these three residues are involved in a specific metal binding site.

Binding Sites↗

Analysis of the disulfide linkage pattern in circulin A and B, HIV-inhibitory macrocyclic peptides.

Circulin A and B are members of a family of macrocyclic peptides, originally isolated from the tropical tree Chassalia parvifolia, that have been shown to display anti-HIV activity. Complete structural elucidation of these highly constrained peptides was difficult due to their cyclic amide backbone and the presence of six disulfide-linked cysteines. In the present study, the disulfide pairing motif of circulin A and circulin B was determined. Since the circulins were resistant to enzymatic proteolysis, cysteine residue pairings were identified by analysis of the complex mixture of cleavage products that resulted from partial acid hydrolysis of the native peptides. Combined utilization of HPLC, fast atom bombardment mass spectrometry and peptide recognition software ("F-MASS" and "F-LINK" programs) were employed to identify the cleavage products. Thus, we were able to unambiguously identify the disulfide linkage pattern in circulin A and circulin B as Cys1-Cys4, Cys2-Cys5 and Cys3-Cys6, where the numbers on the cystine residues refer to their respective order in the peptides.

Amino Acid Sequence↗

Solution structure of PMP-C: a new fold in the group of small serine proteinase inhibitors.

The solution structure and the disulfide pairings of a 36-residue proteinase inhibitor isolated from the insect Locusta migratoria have been determined using NMR spectroscopy and simulated annealing calculations. The peptide, termed PMP-C, was previously shown to inhibit bovine alpha-chymotrypsin as well as human leukocyte elastase, and was also found to block high-voltage-activated Ca2+ currents in rat sensory neurones. PMP-C has a prolate ellipsoid shape and adopts a tertiary fold hitherto unobserved in the large group of small "canonical" proteinase inhibitors. The over-all fold consists mainly of three strands arranged in a right-handed twisted, antiparallel, beta-sheet that demarcates a cavity, together with a linear amino-terminal segment oriented almost perpendicular to the three strands of the beta-sheet. Inside the cavity a phenyl ring constitutes the centre of a hydrophobic core. The proteinase binding loop is located in the carboxy-terminal part of the molecule, between two cysteine residues involved in disulfide bridges. Its conformation resembles that found in other small canonical proteinase inhibitors. A comparison of PMP-C structure with the recently published solution structure of the related peptide PMP-D2 shows that the most significant differences are complementary changes involved in the stabilization of similar folds. This comparison led us to review the structure of PMP-D2 and to identify two salt bridges in PMP-D2.

Amino Acid Sequence↗

Solution structure by NMR of circulin A: a macrocyclic knotted peptide having anti-HIV activity.

The three-dimensional solution structure of circulin A, a 30 residue polypeptide from the African plant Chassalia parvifolia, has been determined using two-dimensional 1H-NMR spectroscopy. Circulin A was originally identified based upon its inhibition of the cytopathic effects and replication of the human immunodeficiency virus. Structural restraints consisting of 369 interproton distances inferred from nuclear Overhauser effects, and 21 backbone dihedral and nine chi1 angle restraints from spin-spin coupling constants were used as input for simulated annealing calculations and energy minimisation in the program X-PLOR. The final set of 12 structures had mean pairwise rms differences over the whole molecule of 0.91 A for the backbone atom, and 1.68 A for all heavy atoms. For the well-defined region encompassing residues 2-12 and 18-27, the corresponding values were 0.71 and 1.66 A, respectively. Circulin A adopts a compact structure consisting of beta-turns and a distorted segment of triple-stranded beta-sheet. Fluorescence spectroscopy provided additional evidence for a solvent-exposed Trp residue. The molecule is stabilised by three disulfide bonds, two of which form an embedded loop completed by the backbone fragments connecting the cysteine residues. A third disulfide bond threads through the centre of this loop to form a "cystine-knot" motif. This motif is present in a range of other biologically active proteins, including omega-contoxin GVIA and Cucurbita maxima trypsin inhibitor. Circulin A belongs to a novel class of macrocyclic peptides which have been isolated from plants in the Rubiaceae family. The global fold of circulin A is similar to kalata B1, the only member of this class for which a structure has previously been determined.

Amino Acid Sequence↗

Structural characterization of an unusually stable cyclic peptide, kalata B2 from Oldenlandia affinis.

Kalata peptides are isolated from an African medicinal plant, Oldenlandia affinis, an aqueous decoction of which can be ingested to accelerate uterine contraction during childbirth. The closely packed disulfide core of kalata peptides confers unusual stability against thermal, chemical, and enzymatic degradation. The molecular arrangement may hamper NMR-assisted disulfide connectivity assignment. We have combined NMR with high-resolution mass spectrometry (MS) and MS/MS of native and chemically derivatized kalata B2 to determine its amino acid sequence and disulfide connectivity. Infrared multiphoton dissociation establishes the disulfide bond linkages in kalata B2 as I-IV, II-V and III-VI.

Amino Acid Sequence↗

Novel forms of chemical protein diversity -- in nature and in the laboratory.

Novel chemical variants of proteins have been found in nature, including potent 'microprotein' natural products and folded protein molecules that contain a cyclic polypeptide chain. Researchers have used chemical synthesis and genetic methods to make these proteins and more: protein catenanes, neoglycoproteins, and artificial protein molecules with novel architectures or made from novel building blocks. De novo design has taken a big step forward with the accurate design and construction of proteins with complex molecular structure. A variety of non-coded amino acids and other building blocks has been used to make increasingly sophisticated protein molecular devices for use as biosensors and for the study of signal transduction inside living cells.

Cyclotides↗

Evaluation and improvement of the properties of the novel cystine-knot microprotein McoEeTI for oral administration.

Cystine-knot microproteins exhibit several properties that make them highly interesting as scaffolds for oral peptide drug delivery. It was therefore the aim of the study to evaluate the novel clinically relevant cystine-knot microprotein McoEeTI regarding its potential for oral delivery. Additionally, based on the gained results, important features of McoEeTI were improved. Enzymatic degradation was caused by chymotrypsin, trypsin and porcine small intestinal juice whereas McoEeTI was stable towards elastase, membrane bound proteases, pepsin and porcine gastric juice. Only minor McoEeTI degradation was observed during a 24h incubation period in rat plasma. In the presence of various physiological ions about 50% of McoEeTI formed di- and/or trimers. P(app) value of McoEeTI was determined to be (7.4+/-0.4)x10(-6)cm/s. Sodium caprate and polycarbophil-cysteine (PCP-Cys) had no beneficial effect on McoEeTI permeation, whereas the utilization of a chitosan-thiobutylamidine (Chito-TBA) system improved McoEeTI permeation 3-fold. Enzymatic stability could be strongly improved by the utilization of Bowman-Birk-Inhibitor (BBI) as well as PCP-Cys. In conclusion, this study indicates that McoEeTI represents a promising candidate as a novel scaffold for oral peptide drug delivery.

Acrylic Resins↗

pPSX: a novel vector for the cloning and heterologous expression of antitumor antibiotic gene clusters.

A cosmid cloning vector has been constructed that demonstrates high levels of segregational stability in Escherichia coli K12. pPSX is a 14-kilobase vector derived from the IncW plasmid pR388. pPSX is highly stable in E. coli in the absence of antibiotic selection, even while expressing the toxic indolocarbazole antitumor antibiotic violacein. The incorporation of the lambdacos sequence enables construction of cosmid libraries with inserts ranging from 24 to 36kb. The inclusion of a lacZalpha multiple cloning site (MCS) allows blue/white screening. pPSX cosmids can be extracted from the host cell with commercial plasmid extraction kits facilitating downstream analysis, sequencing and sub-cloning. pPSX can be transferred to a variety of heterologous hosts by either electroporation or mobilization from E. coli S17-1. While it is unstable in non-E. coli hosts without antibiotic selection, heterologous host strains such as Rhodobacter sphaeroides and Pseudomonas stutzeri will maintain the plasmid under antibiotic selection to allow screening of expressed inserts. pPSX provides the benefits of large insert sizes with high stability to allow cloning of chemotherapeutic gene clusters in E. coli and a range of other heterologous hosts.

Antibiotics, Antineoplastic↗

Improved high-performance liquid chromatographic method for polypeptide antibiotics and its application to study the effects of treatments to reduce microbial levels in bacitracin powder.

Improvements were made in the high-performance liquid chromatographic (HPLC) method to obtain baseline separation of chromatographic peaks of structurally similar polypeptide components in bacitracin. The improved method uses a 30-cm-long stainless-stell column packed with muBondapak C18. The theoretical plates of the column are approximately 140,000 per meter for the bacitracin A peak. The resolution function between bacitracins B1 and B2 and that between bacitracins A and B2 have been improved 418 and 225%, respectively. The components of bacitracin, bacitracins A, B, C, D, E, F, and G, were fractionated by the countercurrent distribution technique. These components, together with Compound X, a compound separated on a carboxymethylcellulose column, and bacitracin F, obtained by degrading bacitracin A sample at neutral pH, were used to identify peaks in the HPLC chromatogram. Effects of processing methods used to reduce microbial contamination levels in bacitracin powders were evaluated. Heat treatment caused a significant loss of antimicrobial activity (35% reduction), bacitracins A, B1, and B2 were reduced by 37, 22, and 21%, respectively. A significant increase (2.8 times) of bacitracin F, an oxidative degradation compound, was show. Irradiation by 60Co at 1.8 Mrad caused no loss of potency nor change in any of the bacitracin components. Ethylene oxide treatment, on the other hand, caused considerable (46%) reduction of potency. Substantial reduction of areas under the peak of bacitracins A, B1, and B2 (50, 24 and 37%, respectively) were noted. The chromatograms showed numerous unresolved peaks around bacitracins A, B1 and B2,; however, no significant increase in the bacitracin F peak, nor appearance of non-UV absorbing peaks were observed. Peptide antibiotics of the polymyxin group, circulin, colistin, and polymyxin, were also analyzed using the muBondapak C18 column with a linear-gradient elution. A UV monitor was used for polymyxin. A moving-wire flame ionization detector was used to monitor circulin and colistin. A sample of polymyxin, circulin, and colistin may be analyzed in less than 20 min of chromatographic time.

Anti-Bacterial Agents↗

Inhibition of neuronal high voltage-activated calcium channels by insect peptides: a comparison with the actions of omega-conotoxin GVIA.

The whole cell variant of the patch clamp technique was used to investigate the actions of two novel insect peptides on high voltage-activated Ca2+ currents in cultured dorsal root ganglion (DRG) neurones. The insect peptides (PMP-D2 and PMP-C) were isolated originally from insect brains and fat bodies, and have been found to have similar three-dimensional structures to the N-type Ca2+ channel inhibitor omega-conotoxin GVIA (omega-CgTx GVIA). High voltage-activated Ca2+ currents were activated from a holding potential of -90 mV by depolarizing step commands to 0 mV. Extracellular application of synthetic PMP-D2 or PMP-C (1 microM) attenuated high voltage-activated Ca2+ currents. The effects of PMP-C were strongly dependent on the frequency of current activation, but inhibition was apparent and reached a steady state after 20 steps when currents were evoked for 30 msec at 0.1 Hz. The actions of the two insect peptides overlapped both with each other and with omega-CgTx GVIA, suggesting that N-type Ca2+ current was predominantly sensitive to these peptides. Low voltage-activated T-type current and 1,4-dihydropyridine sensitive L-type Ca2+ currents were insensitive to 1 microM PMP-D2 and PMP-C, which indicates a degree of selectivity. The presence of a fucose group on PMP-C abolished the ability of this peptide to attenuate high voltage-activated Ca2+ currents, which may reflect a mechanism by which peptide function could be regulated in insects. The electrophysiological data are supported by studies on 45Ca2+ influx into rat cerebrocortical synaptosomes. Both PMP-D2 (10 microM), PMP-C (10 microM) and omega-CgTx GVIA (1 microM) attenuated a proportion of 45Ca2+ influx into the synaptosomes, but additive effects of these peptides were not observed. We conclude that these naturally occurring peptides obtained from invertebrate preparations have inhibitory effects on N-type Ca2+ channels. Although the peptides have related three-dimensional structures, they have distinct amino acid sequences and appear to have different mechanisms of action to produce inhibition of mammalian neuronal high voltage-activated Ca2+ channels.

Amino Acid Sequence↗

Oldenlandia affinis (R&S) DC. A plant containing uteroactive peptides used in African traditional medicine.

A review of the geographical distribution, clinical use, biological activity and phytochemistry of Oldenlandia affinis (R&S) DC. is presented. During an inventory of medicinal plants in northern Congo/Brazzaville and south-western Central African Republic in 1962, 196 different species were registered, one of which was O. affinis used for the facilitation of childbirth. A medical team working in Luluabourg (Kananga) in Congo during the troubled period in 1960, discovered also the traditional use of the same plant as an oxitocic agent during labour. The plant was collected and the uterotonic substances isolated. Cyclic peptides (called Kalata-peptides) were described, and the main peptide, B1, was subjected to pharmacological and chemical investigations. Later the three-dimensional structure of the peptide was determined. Similar cyclic peptides have been isolated also from other plants in the Rubiaceae family like Chassalia pasvifoloia and Psychotria longipes, and from Viola species: Viola tricolor L. and Viola arvensis Murray. Some of these peptides, included Kalata-peptide B1, have been shown to hold antimicrobial activity. They have recently been synthesized, and they may represent a starting point for the design of new peptide antibiotics.

Animals↗

Structural and functional properties of a novel serine protease inhibiting peptide family in arthropods.

Recently, several arthropod peptides that belong to a new serine protease inhibitor family were discovered. Three members (HI, PMP-D2=LMCI-1 and PMP-C=LMCI-2) were isolated from the migratory locust, Locusta migratoria. Five additional members (SGPI-1-5) were identified in the desert locust Schistocerca gregaria, and a heterodimeric serine protease inhibitor (pacifastin) was isolated from the hemolymph of the crayfish Pacifastacus leniusculus. The light chain of pacifastin constitutes the inhibitory subunit that has nine cysteine-rich domains (PLDs) that are homologous with the locust inhibitors. These locust inhibitors and PLDs share a conserved array of six cysteine residues (Cys-Xaa(9-12)-Cys-Asn-Xaa-Cys-Xaa-Cys-Xaa(2-3)-Gly-Xaa(3-4)-Cys-Thr-Xaa(3)-Cys), which are involved in an identical disulfide bridge pattern (Cys(1)-Cys(4), Cys(2)-Cys(6), Cys(3)-Cys(5)). The solution structures of LMCI-1 and LMCI-2 showed a similar, compact, globular folding, which is unique within the group of the small 'canonical' inhibitors. Moreover, the reactive site, including the P1-P'1 bond was thoroughly investigated by means of synthetic variants. However, the biological function(s) of the locust inhibitors is (are) not fully understood. LMCI-1 and LMCI-2 were shown to inhibit the endogenous proteolytic activating cascade of prophenoloxidase. Northern blot analysis indicated that the genes encoding the SGPI precursors are differentially expressed in a time-, stage- and hormone-dependent manner.

Amino Acid Sequence↗

Elucidation of the primary and three-dimensional structure of the uterotonic polypeptide kalata B1.

The amino acid sequence and structure of a uterotonic polypeptide extracted from the African plant Oldenlandia affinis DC have been determined. The peptide, kalata B1, consists of 29 amino acid residues and is rich in cysteine (6), threonine (5), and glycine (5). Enzyme cleavage studies show that the polypeptide backbone is cyclic. The three-dimensional solution structure has been determined using two-dimensional nuclear magnetic resonance (NMR) spectroscopy and distance-restrained simulated annealing. Kalata B1 is composed mainly of beta-strands connected by tight turns, forming regions of beta-sheet, except in the case of one section which forms a longer, less structured loop. The tertiary fold, together with the disulfides that form a sulfur core, produces a striking and unusual surface in which the majority of the hydrophobic residues form a solvent-exposed patch. The hydrophobic side of kalata B1 is flanked by two diametrically opposed and opposite-charged residues. The structure calculations have been used to predict the previously unknown disulfide bond connectivities using two approaches. In the first, a family of structures was calculated on the basis of NOE constraints without the assumption of a specific disulfide connectivity. The resultant structures were examined to determine whether the calculated position of the sulfur atoms suggested that one set of disulfide connectivities was more likely than the other, theoretically possible, sets. In the second approach, a separate family of structures (50 per set) was calculated for each of the 15 possible disulfide-bonded molecules. The resultant families of structures were compared to see whether one was favored over the others. Both approaches led to the same global fold, and the most likely disulfide connectivity is predicted to be 5-22, 13-27, and 17-29. In the calculated structure the cyclic peptide backbone is folded back onto itself and braced with disulfide pairs across diagonally opposed beta-strands. This structure involves one of the disulfide bonds (5-22) threading through the eight amino acid loop formed by the other two disulfide bonds and the peptide fragments connecting them.

Amino Acid Sequence↗

Solution structure of PMP-D2, a 35-residue peptide isolated from the insect Locusta migratoria.

The three-dimensional solution structure of PMP-D2, a 35 amino acid peptide isolated from the insect Locusta migratoria, has been determined from two-dimensional 1H NMR spectroscopy data. The structure calculations were performed from 222 NOE-derived interproton distances and 11 dihedral angles calculated from the JHN-H alpha coupling constants, using either a combination of distance geometry and restrained simulated annealing or by restrained simulated annealing alone. PMP-D2 contains three disulfide bridges that have been assigned from NMR data and structure calculations and independently confirmed using chemical and enzymatic methods. The core region of PMP-D2 adopts a compact globular fold, stabilized by hydrophobic interactions, which consists of a short three-stranded antiparallel beta-sheet involving residues 8-11, 15-19, and 25-29. Back-calculation of the NOESY spectra was used to validate the final structures. Analysis of the CD spectra of PMP-D2 under various conditions of ionic strength and in the presence of organic solvents demonstrates the high stability of this molecule. PMP-D2 was recently shown to inhibit Ca2+ currents. This activity is discussed based on the comparison of PMP-D2 three-dimensional structure with the recently established three-dimensional structure of the Ca2+ channel blocker omega-conotoxin GVIA.

Amino Acid Sequence↗

Solution structure of the squash trypsin inhibitor MCoTI-II. A new family for cyclic knottins.

The "knottin" fold is a stable cysteine-rich scaffold, in which one disulfide crosses the macrocycle made by two other disulfides and the connecting backbone segments. This scaffold is found in several protein families with no evolutionary relationships. In the past few years, several homologous peptides from the Rubiaceae and Violaceae families were shown to define a new structural family based on macrocyclic knottin fold. We recently isolated from Momordica cochinchinensis seeds the first known macrocyclic squash trypsin inhibitors. These compounds are the first members of a new family of cyclic knottins. In this paper, we present NMR structural studies of one of them, MCoTI-II, and of a beta-Asp rearranged form, MCoTI-IIb. Both compounds display similar and well-defined conformations. These cyclic squash inhibitors share a similar conformation with noncyclic squash inhibitors such as CPTI-II, and it is postulated that the main effect of the cyclization is a reduced sensitivity to exo-proteases. On the contrary, clear differences were detected with the three-dimensional structures of other known cyclic knottins, i.e., kalata B1 or circulin A. The two-disulfide cystine-stabilized beta-sheet motif [Heitz et al. (1999) Biochemistry 38, 10615-10625] is conserved in the two families, whereas in the C-to-N linker, one disulfide bridge and one loop are differently located. The molecular surface of MCoTI-II is almost entirely charged in contrast to circulin A that displays a well-marked amphiphilic character. These differences might explain why the isolated macrocyclic squash inhibitors from M. cochinchinensis display no significant antibacterial activity, whereas circulins and kalata B1 do.

Amino Acid Sequence↗

Selective inhibition of trypsins by insect peptides: role of P6-P10 loop.

PMP-D2 and HI, two peptides from Locusta migratoria, were shown to belong to the family of tight-binding protease inhibitors. However, they interact weakly with bovine trypsin (K(i) around 100 nM) despite a trypsin-specific Arg at the primary specificity site P1. Here we demonstrate that they are potent inhibitors of midgut trypsins isolated from the same insect and of a fungal trypsin from Fusarium oxysporum (K(i) <or= 0.02 nM). Therefore, they display a selectivity not existing for the parent chymotrypsin inhibitor PMP-C. By NMR, we demonstrate that HI possesses a highly rigid structure similar to the crystal structure of a variant of PMP-D2 in complex with bovine alpha-chymotrypsin. The main difference with PMP-C is located in the region from residues 20 to 24 (positions P6-P10) that interacts with the loop containing Gly173 in chymotrypsin. The corresponding residue in mammalian trypsins is always a proline that may generate a steric clash with the inhibitor. The residues thought to confer selectivity were mutated with PMP-C as a model. The resulting analogue PMP-D2(K10W,P21A,W25A) loses some activity toward insect and fungal trypsins but is a more potent inhibitor of mammalian trypsins, corresponding to a decrease of selectivity. This work represents a first attempt in tuning the selectivity of natural peptidic serine protease inhibitors by mutating residues out of the reactive loop (P3-P'3).

Amino Acid Sequence↗