The thermodynamics of polyamide-DNA recognition: hairpin polyamide binding in the minor groove of duplex DNA

Crescent-shaped synthetic ligands containing aromatic amino acids have been designed for specific recognition of predetermined DNA sequences in the minor groove of DNA. Simple rules have been developed that relate the side-by-side pairings of Imidazole (Im) and Pyrrole (Py) amino acids to their predicted target DNA sequences. We report here thermodynamic characterization of the DNA-binding properties of the six-ring hairpin polyamide, ImImPy-gamma-PyPyPy-beta-Dp (where gamma = gamma-aminobutyric acid, beta = beta-alanine, and Dp = dimethylaminopropylamide). Our data reveal that, at 20 degrees C, this ligand binds with a relatively modest 1.8-fold preference for the designated match site, 5'-TGGTA-3', over the single base pair mismatch site, 5'-TGTTA-3'. By contrast, we find that the ligand exhibits a 102-fold greater affinity for its designated match site relative to the double base pair mismatch site, 5'-TATTA-3'. These results demonstrate that the energetic cost of binding to a double mismatch site is not necessarily equal to twice the energetic cost of binding to a single mismatch site. Our calorimetrically measured binding enthalpies and calculated entropy data at 20 degrees C reveal the ligand sequence specificity to be enthalpic in origin. We have compared the DNA-binding properties of ImImPy-gamma-PyPyPy-beta-Dp with the hairpin polyamide, ImPyPy-gamma-PyPyPy-beta-Dp (an Im --> Py "mutant"). Our data reveal that both ligands exhibit high affinities for their designated match sites, consistent with the Dervan pairing rules. Our data also reveal that, relative to their corresponding single mismatch sites, ImImPy-gamma-PyPyPy-beta-Dp is less selective than ImPyPy-gamma-PyPyPy-beta-Dp for its designated match site. This result suggests, at least in this case, that enhanced binding affinity can be accompanied by some loss in sequence specificity. Such systematic comparative studies allow us to begin to establish the thermodynamic database required for the rational design of synthetic polyamides with predictable DNA-binding affinities and specificities.

Synthesis and biological evaluation of novel cryptophycin analogs with modification in the beta-alanine region

Structure modification of the beta-alanine region (fragment C) of the potent antimitotic agent cryptophycin was investigated. This includes: (1) introduction of substituents at the previously unsubstituted C7 position of the macrolide ring and (2) replacement of the (2R)-3-amino-2-methyl-propanoic acid (beta-alanine) with various (1)-amino acids to give the corresponding 15-membered unnatural cryptophycin analogs.

Volatile components formed from reaction of sugar and beta-alanine as a model system of cookie processing

Volatile components formed from the reaction of monosaccharides or disaccharides with beta-alanine were investigated in a dry condition as a model system of cookie processing. Maltol is a common compound formed in the Maillard reaction, but it was very difficult to detect it in previous experiments using actual cookie materials. In this work, we investigated the principal compounds and maltol formation from the reaction of monosaccharides or disaccharides with beta-alanine at 150 degrees C for 10 min. Neither the reaction of monosaccharides nor the disaccharides with beta-alanine resulted in the formation of maltol. 2,3-Dihydro-3,5-dihydroxy-6-methyl-4(H)-pyran-4-one (DDMP) was detected as a principal product from the reaction of monosaccharides with beta-alanine. 5-Hydroxymethyl-2-furfural was also confirmed as being a major product in both reactions.

Identification and initial structure-activity relationships of a novel class of nonpeptide inhibitors of blood coagulation factor Xa

The discovery and some of the basic structure-activity relationships of a series of novel nonpeptide inhibitors of blood coagulation Factor Xa is described. These inhibitors are functionalized beta-alanines, exemplified by 2a. Docking experiments placing 2a in the active site of Factor Xa implied that the most expeditious route to enhancing in vitro potency was to modify the group occupying the S3 site of the enzyme. Increasing the hydrophobic contacts between the inhibitor and the enzyme in this region led to 8, which has served as the prototype for this series. In addition, an enantioselective synthesis of these substituted beta-alanines was also developed.

Changes in the starvation response through covalent cell attachment

Covalent attachment of Candida utilis cells, possibly simulating natural microbial immobilizations, stimulated stable and significant enhancement of extracellular production of alkaline protease, specifically induced by four different starvation conditions. The enzyme analysis confirmed the identity of the proteases released under all conditions of starvation and no parallel production of other proteolytic enzyme. The enhancement phenomenon as a uniform and stable effect of the whole cell immobilization is discussed in relation to the effect of multipoint, cell-solid surface contact, potentially bringing positive modulations of complex, cellular functions.

Design, synthesis, and in vitro activities of benzamide-core glycoprotein IIb/IIIa antagonists: 2,3-diaminopropionic acid derivatives as surrogates of aspartic acid

In an effort to discover novel nonpeptide glycoprotein IIb/IIIa (GPIIb/IIIa, alpha IIb/beta 3) inhibitors, we investigated RGD mimetics featuring a 3-substituted benzoic acid as the core, benzamidine as the basic moiety, and a series of beta- and alpha-substituted beta-alanine derivatives as aspartic acid surrogates. It was found that the use of beta-methyl beta-alanine slightly improved the anti-aggregant potency in human platelet-rich plasma over the unsubstituted beta-alanine compound, while beta-substitution with a trifluoromethyl group resulted in considerable loss in activity. Significant enhancement (up to 100-fold) in potency was obtained when the beta-alanine was replaced with N2-substituted 1-2,3-diaminopropionic acid derivatives. Among the three types of alpha-substituents (carbamate, amide, and sulfonamide) investigated, no apparent preference was observed with respect to in vitro potency. However, alkyl groups were more favorable than arylalkyl groups (Cbz) in the carbamate analogues. We also investigated piperidine, piperazine, and N-formamidinopiperidine as replacements for the benzamidine moiety. The former two replacements led to a drop in potency while the latter replacement resulted in maintenance of activity as compared with the corresponding benzamidine analogue.

Biodegradation and aquatic toxicity of beta-alaninediacetic acid (beta-ADA)

The aquatic toxicity and biodegradability of the new chelating agent beta-alaninediacetic acid (beta-ADA) were investigated. There is no inhibition effect of beta-ADA in the daphnia magna 24 h test up to a concentration of 1000 mg/L. The algal growth inhibition test resulted in an EC 50 of 19.7 mg/L. An EC 20 of 740 mg/L was determined in the luminescent bacteria test. An EC 50 was not obtained in this test up to a concentration of 2000 mg/L beta-ADA. The degree of biodegradation of beta-ADA was determined in a static and a continuous test. The beta-ADA removal reached 98% at the end of the test after eight weeks in the continuous test which was carried out with laboratory activated sludge units simulating a waste water treatment plant. Further, biodegradation and toxicity tests were coupled, i.e. the effluents of the laboratory activated sludge units were applied in the toxicity tests. A higher toxicity of the effluents of the test units in comparison with the control unit was not observed.

Simultaneous gas chromatographic-mass spectrophotometric determination of alpha-fluoro-beta-alanine and 5-fluorouracil in plasma

A gas chromatographic-mass spectrometric (GC-MS) method is reported for simultaneous determination of alpha-fluoro-beta-alanine (FBA), the major end metabolite of 5-fluorouracil (5-FU), and 5-FU in plasma samples isolated from cancer patients. 5-Chlorouracil (5-CIU, 1 micrograms/ml) is added to samples as an internal standard. The method relies on protein precipitation of the plasma sample followed by derivatisation with pentafluorobenzyl bromide. Following sample purification with Sep-pak C18 columns the derivatives are analysed by GC-MS, with FBA, 5-FU and 5-CIU being determined at 36.96-37.03, 46.91-46.98 and 51.99-52.13 min, respectively. The ions measured in each case had m/z of 390, 490 and 506, respectively. The method showed good reproducibility with coefficients of variation between 3 and 10%, with a detection limit of < 1 ng/ml for 5-FU and < 5 ng FBA/ml plasma. The possibility of sensitive determination of FBA without the use of radioisotopes should permit routine estimation of rates of 5-FU metabolism in individual patients.

The mechanism of high-yielding chiral syntheses catalysed by wild-type and mutant forms of aspartate aminotransferase

The ability of aspartate aminotransferase to catalyse beta-elimination of alpha-amino acids that have a good leaving group at C beta has been exploited in the synthesis of novel amino acids by the inclusion of appropriate nucleophiles as co-substrates. Two compounds, L-serine O-sulphate and 3-chloro-L-alanine, were used as beta-elimination substrates. Nucleophiles used successfully as co-substrates were thiosulphate, 2-mercaptoethanol, mercaptoacetate and aminoethylthiopseudourea. The synthesis achieved using serine O-sulphate and thiosulphate was found to produce sulphocysteine with a yield of 70%. Circular dichroism demonstrated that the compound was a single enantiomer and, therefore, that nucleophilic addition had taken place on the enzyme. The initial rate of synthesis was 10% of the rate at which the enzyme catalyses its normal transamination reaction. The synthetic reaction was accompanied by minor side reactions that led to small amounts of additional amino acid and oxo acid products through partitions of the main reaction at two stages in the mechanism. By mutating Arg292, which is the residue that binds the distal carboxyl group of natural substrates, the wild-type enzyme was converted to a form that could discriminate completely between serine O-sulphate and chloroalanine as beta-eliminating substrate. Similar alterations in nucleophile cosubstrate specificity were also observed. Whereas, for example, the wild-type enzyme catalysed syntheses between 3-chloroalanine and either mercaptoethanol or mercaptoacetate with equal facility, the Arg292Asp enzyme showed complete preference for mercaptoethanol. The system should be of general use in the synthesis of novel amino acids as single enantiomers with potentially interesting biological activities.

Multipin solid-phase synthesis of acyl 2, 3-diaminopropionic acid oligomers

A modular approach for the synthesis of sets of diverse organic molecules is described. N-alpha-Fmoc-N-beta-Alloc-D-2,3-diaminopropionic acid (Fmoc-D-Dpr(Alloc)-OH) was prepared in four steps from Boc-D-asparagine and used as a scaffold for attachment of sidechains. Using the Multipin approach, a number of model acyl trimers were rapidly prepared by sequential coupling of Fmoc-D-Dpr(Alloc)-OH and acylation of the beta-amino group with a range of activated carboxylic acids.

19F-[1H] nuclear Overhauser effect and proton decoupling of 5-fluorouracil and alpha-fluoro-beta-alanine

19F-[1H] magnetic double-resonance experiments were performed on model solutions of the antitumor drug 5-fluorouracil (5-FU) and of alpha-fluoro-beta-alanine (FBAL) in order to improve 19F NMR sensitivity for the application in pharmacokinetic studies in vivo. Upon driving the proton spins into saturation, a fluorine signal enhancement (nuclear Overhauser effect) was observed on the order of the theoretical NOE maximum gamma H/2 gamma F = 53% for purely dipolar coupled 19F-1H spin systems in extreme narrowing. The dependence of the effect on proton excitation frequency and temporal parameters was measured and cross-relaxation rate constants of 0.07 s-1 (5-FU) and 0.19 s-1 (FBAL) were determined. Irradiation of the proton spin system by a broad pulse during the 19F signal detection period removed FBAL multiplet splittings completely and narrowed the linewidth of this resonance band by a factor of six. Application of proton presaturation in the 19F NMR examination of a patient undergoing 5-FU chemotherapy enhanced the signal-to-noise ratio of the major 5-FU catabolite FBAL detected noninvasively in the liver.

Synthesis and use of a new bromoacetyl-derivatized heterotrifunctional amino acid for conjugation of cyclic RGD-containing peptides derived from human bone sialoprotein

A new amino acid derivative, N alpha-(tert-butyloxycarbonyl)-N beta-(bromoacetyl)diaminopropionic acid (BBDap), has been synthesized as a reagent for introducing side-chain bromaocetyl groups into any position of a peptide sequence during solid-phase peptide synthesis. By using minor modifications to the protocol of the automated peptide synthesizer and a two-step in situ neutralization procedure, the syntheses of (bromoacetyl)diaminopropionic acid (BDap) in Arg-Gly-Asp-containing peptides from human bone sialoprotein were optimized and completed. Following HPLC purification, the BDap-derivatized peptides were cyclized or/and conjugated to carrier protein or to glass cover slips. In addition, a new procedure for site-specific conjugation of cyclic peptides to protein carriers or to glass was developed. The cell attachment activity of the peptide derivatives and conjugates was tested in cell adhesion assays with human osteoblasts, and the specificity of the binding was confirmed by competition with linear and/or cyclic forms of GRGDS. The results show that conjugates containing the linear and cyclic derivatives of the peptide EPRGDNYR supported cell attachment and spreading in a dose-dependent manner when the peptides were immobilized as described. Cell attachment to the intact bone sialoprotein and to conjugates containing the linear peptides was abolished by competition with linear and cyclic RGD-containing peptides, whereas the attachment to conjugates containing the cyclic peptide was inhibited only partially, and the cell spreading was preserved even in the presence of RGD-peptides.

A possible prebiotic synthesis of pantetheine, a precursor to coenzyme A

The involvement of coenzyme A in many enzyme reactions suggests that it acted in this capacity very early in the development of life on Earth. Particularly relevant in this regard is its role in the activation of amino acids and hydroxy acids in the biosynthesis of some peptide antibiotics--a mechanism of peptide synthesis that forms the basis for the proposal that a thioester world could have preceded the RNA world. The components of coenzyme A have been shown to be probable prebiotic compounds: beta-alanine, pantoyl lactone and cysteamine and possibly adenosine. We show here that the pantetheine moiety of coenzyme A (which also occurs in a number of enzymes) can be synthesized in yields of several per cent by heating pantoyl lactone, beta-alanine and cysteamine at temperatures as low as 40 degrees C. These components are extremely soluble and so would have been preferentially concentrated in evaporating bodies of water, for example on beaches and at lagoon margins. Our results show that amide bonds can be formed at temperatures as low as 40 degrees C, and provide circumstantial support for the suggestion that pantetheine and coenzyme A were important in the earliest metabolic systems.

Constrained search of conformational hyperspace of inactivators of glucosamine-6-phosphate synthase

Glucosamine-6-phosphate (GlcN-6-P) synthase (EC 2.6.1.16) is a key enzyme in amino sugar metabolism in micro-organisms and its selective and irreversible inhibitors can become valuable antifungal drugs. We performed a constrained search of the conformational hyperspace of glutamine and of the set of specific inactivators of the enzyme, as well as of some non-specific inhibitors of many cysteine containing enzymes. From these calculations we obtained spatial relationships of functional groups, the presence and specific orientation of which in the active site of the enzyme is important for effective and selective action of the inhibitor. Subsequent quantum chemical calculations confirmed the correctness of the pharmacophore conformation we obtained. Pharmacophore conformation of FMDP molecule, the most potent inhibitor in the selective inhibitors group, is placed close to the energy minimum on the conformational energy map.

Alterations of specific and nonspecific binding of monoclonal antibody by introduction of acidic and hydrophobic groups

AB-6 monoclonal antibody (mAb) against bovine serum albumin (BSA) was coupled with beta-alanine or n-propylamine using a heterobifunctional cross-linking reagent, N-(epsilon-maleimidocaproyloxy)succinimide (EMCS) and a linker, poly-L-cysteine to introduce acidic or hydrophobic groups into the mAb. The mAb molecules coupled with beta-alanine at lower than 1:16 molar ratios and those coupled with n-propylamine at 1:14 retained the original reactivity to BSA but modification with higher amounts of beta-alanine or n-propylamine decreased the reactivity. In contrast, nonspecific bindings of AB-6 mAb to a plastic culture plate and tumor (MDA-MB-453) cells were decreased by modification with beta-alanine and increased by n-propylamine. These results suggested that introduction of acidic groups, and hydrophobic groups to antibody leads to fluctuations in the non-specific binding of antibody.

NMR determination of the structures of peroxycobalt(III) bleomycin and cobalt(III) bleomycin, products of the aerobic oxidation of cobalt(II) bleomycin by dioxygen

The oxidation of Co(II) bleomycin A2 by dioxygen leads to two products, HO2-Co(III) bleomycin A2 (form I) and Co(III) bleomycin A2 (form II). 1H NMR chemical shift assignments for protons of both forms have been made by two-dimensional NMR spectral techniques. The chemical shifts of protons throughout forms I and II differ from each other and from apobleomycin A2. NOESY spectra reveal a number of intermediate and long-range 1H-1H couplings within the metal-binding domain, between the metal-binding domain and the peptide linker, which connects it and the DNA-binding region of the molecule, and, in form I, between the DNA- and metal-binding domains. Molecular dynamics calculations were carried out based on the NOESY results and an adjustable square pyramidyl ligand geometry around Co(III) composed of nitrogen atoms of the primary and secondary amine groups, pyridine (N5), and amide and imidazole (N1) of the hydroxyhistidine residue. In form I, the bithiazole group folds back across the square pyramid forming a compact structure. Although this conformational feature was not observed in form II, the peptide linker between the metal- and DNA-binding domains in both species shows extensive folding based on a large number of intramolecular interactions.

First characterization at atomic resolution of the C-activating groups in a peptide synthesis acid chloride, acid azide and carboxylic-carboxylic mixed anhydride

The X-ray diffraction structures of three N alpha-protected, C alpha-activated MeAib derivatives are reported. They are Tos-MeAib-Cl, Tos-MeAib-N3 and Tos-MeAib-O-Piv. The geometry and conformation of these classical carboxyl activating groups, which have been characterized at atomic resolution for the first time, are discussed.

beta-Alanine containing peptides: gamma-turns in cyclotetrapeptides

In the present paper we describe the synthesis, purification, single-crystal x-ray analysis, solution conformational characterization, and conformational energy calculations of the cyclic tetrapeptide cyclo-(beta-Ala-L-Pro-beta-Ala-L-Val). The peptide was synthesized by classical solution methods and the cyclization of the free tetrapeptide was accomplished in good yields in diluted methylene chloride solution using N,N-dicyclohexyl-carbodiimide. The compound crystallizes in the monoclinic space group P2(1) from ethanol with two independent molecules in the unit cell. All peptide bonds are trans. The nmr molecular conformation in the acetonitrile solution as well as that derived from the molecular dynamic simulation in vacuo is quite different from those observed in the solid state and is very similar to that previously observed for the parent compound cyclo- (beta-Ala-L-Pro-beta-Ala-L-Pro).

Chemical properties of the natural neurotoxin of Lathyrus sativus 3-N-oxalyl-2,3-diamino-propanoic acid (beta-ODAP), its nontoxic 2-N-oxalyl isomer, and its hydrolysis product 2,3-diamino-propanoic acid (DAPRO) by 1H- and 13C-NMR spectroscopy

The 1H and 13C NMR data of DAPRO, alpha- and beta-ODAP were measured at varying pH values and the physical relevance of these data was studied. As a potential way to detoxify the neurotoxin beta-ODAP, its isomerization was studied at room temperature and at 60 degrees C. An unknown hydrolysate is identified as DAPRO.

3-(Phenylamino)alanine, a novel aniline-derived amino acid associated with the eosinophilia-myalgia syndrome: a link to the toxic oil syndrome?

The eosinophilia-myalgia syndrome (EMS) is an inflammatory disease that occurred in epidemic proportions in the United States during 1989. Cases of EMS were also reported in Europe and elsewhere. Clinically, EMS resembles the Spanish toxic oil syndrome. EMS has been associated with ingestion of manufactured L-tryptophan and, more specifically, with lots of tryptophan that contained the trace contaminant 1,1'-ethylidenebis(tryptophan) (EBT). Another trace contaminant ("peak UV-5") has been reported, but the strength of its association with EMS has not been demonstrated. Herein we report independently that peak UV-5 is 3-(phenylamino)alanine (PAA). Patients with EMS ingested significantly greater amounts of both PAA and EBT than did control tryptophan users. PAA is chemically similar to 3-phenylamino-1,2-propanediol, an aniline derivative isolated from samples of oil that were consumed by persons in whom the toxic oil syndrome developed. The discovery of an aniline-derived contaminant in tryptophan raises the possibility that EMS and toxic oil syndrome may have a common etiologic trigger.

Investigation of the inhibition pathway of glucosamine synthase by N3-(4-methoxyfumaroyl)-L-2,3-diaminopropanoic acid by semiempirical quantum mechanical and molecular mechanics methods

Glucosamine synthase (E.C. 2.6.1.16) is a promising target in antifungal drug design. It has been reported that its potent inhibitor, N3-(4-methoxyfumaroyl)-L-2,3-diaminopropanoic acid (FMDP), inactivates the enzyme by the Michael addition of the S-H group to the FMDP molecule followed by cyclisation reactions. In this study we have investigated, by means of semiempirical MNDO, PM3 and molecular mechanics methods, the energetics and kinetic possibility of the formation of various stereoisomers of the products of cyclisation of the Michael addition products detected experimentally. It was found that the substituted 1,4-thiazin-3-one can be formed in one step under alkaline conditions; the stereoisomers of this compound predicted to be the most stable on the basis of theoretical calculations are also the dominant ones in reality.

Monomer units for the beta-bend ribbon structure: MeAib peptides

A conformational analysis in CDCl3 solution by using i.r. absorption and 1H nuclear magnetic resonance spectroscopy was performed on the fully blocked dipeptides Z-MeAib-Aib-NHMe, Z-MeAib-L-Ala-NHMe, Z-Aib-MeAib-NHMe, and Z-L-Ala-MeAib-NHMe, representing repeating units of the beta-bend ribbon spiral (an approximate 3(10)-helix, with an intramolecular H-bonding donor every two residues), where Z represents benzyloxycarbonyl, MeAib alpha-methylaminoisobutyric acid, and NHMe methylamino. The molecular and crystal structures of the first three compounds were also assessed by X-ray diffraction. While the -MeAib-Aib-, -MeAib-L-Ala-, and -Aib-MeAib- sequences give stable beta-bend structures, the preferred conformation of the -L-Ala-MeAib- sequence is open. These results indicate that the MeAib residue is a good beta-bend promoter, but less efficient than its unmethylated counterpart at position i + 2.

Carboxylic acid replacement structure-activity relationships in suosan type sweeteners. A sweet taste antagonist. 1

N-(4-Cyanophenyl)-N'-(2-carboxyethyl)urea (2), an analogue of suosan [1,N-(4-nitrophenyl)-N'-(2-carboxyethyl)urea], is a known high-potency sweetener derived from beta-alanine. Sulfonic and phosphonic acid analogues of 2 were prepared to develop structure-activity relationships through modification of the carboxylic acid region of this family of sweeteners. Neither of the carboxylic acid replacements resulted in sweet analogues. However, we found that N-(4-cyanophenyl)-N'-[(sodiosulfo)methyl]urea (7) is an antagonist of the sweet taste response. The bitter taste response to caffeine, quinine, and naringin was also antagonized. Antagonist 7 was found to inhibit the sweet taste perception of a variety of sweeteners. Antagonist 7 had no effect on the sour or salty taste response.

Beta-alanine containing peptides: a novel molecular tool for the design of gamma-turns

In the present paper we describe the synthesis, purification, single crystal x-ray analysis, and solution conformational characterization of the cyclic tetrapeptide cyclo-(L-Pro-beta-Ala-L-Pro-beta-Ala). This peptide was synthesized by classical solution methods and the cyclization of the free tetrapeptide was accomplished in good yields in diluted methylene chloride solution using N,N-dicyclohexyl-carbodiimide (DCCI). The compound crystallizes in the orthorombic space group P2(1)2(1)2(1) from ethyl acetate. All peptide bonds are trans. The molecular conformation is stabilized by two intramolecular hydrogen bonds between the CO and NH groups of the two beta-alanine residues. These hydrogen bonds take place in a C7 structure in which both proline residues occupy the 2 position of an inverse gamma-turn. The two beta-alanine residues have a typical folded conformation (around the C alpha-C beta bond) observed in other cyclic peptides containing this residue. A detailed 1H-nmr analysis in CD3CN solution has been carried out. The molecule assumes a twofold symmetry in solution with a molecular conformation consistent with that observed in the solid state.