Cleavage Conditions Research Articles

Stepwise conversion of two pyrrole moieties of octaethylporphyrin to pyridin-3-ones: synthesis, mass spectral, and photophysical properties of mono and bis(oxypyri)porphyrins.

Free-base octaethylporphyrin (OEP) was converted in two steps (beta,beta'-dihydroxylation and oxidative diol cleavage with concomitant aldol condensation) to the corresponding oxypyriporphyrin. This conversion was previously described to be applicable only to the Ni(II) complex of OEP. Modified diol cleavage conditions made this reaction sequence now applicable to free-base OEP. The single-crystal structure of the resulting free-base oxypyriporphyrin was determined, proving its near-perfect planarity. The reaction sequence can also be applied to oxypyriporphyrin itself, generating the unprecedented bacteriochlorin-type bis(oxypyri)porphyrin as two separable isomers. The ground-state (UV/Vis and fluorescence spectroscopies) and excited-state (transient triplet-triplet absorption, triplet lifetimes, and triplet EPR spectroscopy) photophysical properties of all chromophores are compared with those of OEP, chlorins, and oxochlorins. The pyridone-modified porphyrins possess unique spectroscopic signatures that distinguish them from regular porphyrins or chlorins. The presence of the pyridone moiety alters the ESI(+) collision-induced fragmentation properties of these oxypyriporphyrins only to a minor degree when compared with those of OEP or chlorins, confirming their stability.

The splitting of sperm heads from tails in eight mammalian species and the measurement of their sizes.

Ejaculated spermatozoa from man, the Euopean wild boar and the bull, and spermatozoa from the cauda epididymes of the rabbit, rat, mouse, hamster and Guinea pig were treated with a sonic bath, a sonic probe, trypsin with and without prior treatment with a sulphhydryl reagent, pronase and alkalis. The fragments produced were counted and sized in an accurately calibrated Coulter Counter, Model ZB Industrial, before and after Zaponin treatment to lyse accompanying debris and the peripheral cytoplasm. Head and tail fractions were separated on sucrose gradients. Each species required different conditions for cleavage or fragmentation. Rabbit and bull spermatozoa were cleaved by the ultrasonic bath exactly into heads and tails, producing twice the number of particles with two peaks in the size distribution curves butith some 60% loss of total sperm volume which became the soluble fraction. The ultrasonic probe, and for the bull, pronase, produced the same cleavage but these more drastic treatments dissolved a considerable portion of the tail fraction. Rodent spermatozoa, especially the rat, were cleaved perfectly into heads and tails by mild trypsin treatment. All the nonrodent spermatozoa were resistent to trypsin cleavage, although prior treatment with a sulphhydryl reagent caused swelling and subsequent trypsin action caused digestion into miscellaneous pieces. Spermatozoa from the boar and from man could not be cleaved by any of the procedures. The sonic probe produced fragmentation with progressive dissolution of the tail fragments and a single peak in the size distribution curve corresponding to small stripped heads. The soluble fraction always constituted a large proportion of the original whole spermatozoa.

Recombinant chymosin used for exact and complete removal of a prochymosin derived fusion tag releasing intact native target protein

Fusion tags add desirable properties to recombinant proteins, but they are not necessarily acceptable in the final products. Ideally, fusion tags should be removed releasing the intact native protein with no trace of the tag. Unique endoproteinases with the ability to cleave outside their own recognition sequence can potentially cleave at the boundary of any native protein. Chymosin was recently shown to cleave a pro-chymosin derived fusion tag releasing native target proteins. In our hands, however, not all proteins are chymosin-resistant under the acidic cleavage conditions (pH 4.5) used in this system. Here, we have modified the pro-chymosin fusion tag and demonstrated that chymosin can remove this tag at more neutral pH (pH 6.2); conditions, that are less prone to compromise the integrity of target proteins. Chymosin was successfully used to produce intact native target protein both at the level of small and large-scale preparations. Using short peptide substrates, we further examined the influence of P1' amino acid (the N-terminus of the native target protein) and found that chymosin accepts many different, although not all, amino acids. We conclude that chymosin has several appealing characteristics for the exact removal of fusion tags. It is readily available in highly purified recombinant versions approved by the FDA for preparation of food for human consumption. We suggest that one should consider extending the use of chymosin to the preparation of pharmaceutical proteins.

Disulfide and multisulfide antitumor agents and their modes of action

A variety of natural products that contain disulfide or multisulfide bonds were found to display potent biological activities, including antitumor activities. At the center of these biological activities are disulfide or multisulfide moieties. The importance of disulfide or multisulfide groups in the areas of chemistry, biology, and pharmacology has been well recognized. Among these agents, especially noteworthy are mitomycin disulfides, leinamycin, thiarubrines, varacins, calicheamicins, and esperamicins. Their general features, including their biological profiles, peculiar structures, and related chemistries, were summarized and more importantly, their working mechanisms were elucidated in detail in this review. Mechanistic studies of these compounds have provided evidence of the key role of disulfide or multisulfide groups. In general, the cleavage of disulfide or multisulfide bonds produces thiol (or thiolate), which triggers an activation cascade leading to the generation of highly reactive electrophile(s) or cytotoxic species that may cause DNA strand scission. The main concerns with the mode of action are the reactivity and stability of disulfide and multisulfide bonds, their cleavage conditions, and the generation of toxic species. A range of studies for each agent was executed to gather important information on their activation, and the obtained information was gradually integrated to give some clues to the agents' working mechanisms. Such information may be further used to generate biomechanistically designed and more potent derivatives.

DNA Oligonucleotides Containing Stereodefined Phosphorothioate Linkages in Selected Positions

This unit describes a method for the synthesis of DNA chimeric PO/PS-oligonucleotides with a stereodefined phosphorothioate bond in the selected position. Diastereomerically pure 5'-O-DMTr-N-protected-deoxyribonucleoside-3'-O-(2-thio-spiro-4,4-pentamethylene-1,3,2-oxathiaphospholane)s obtained according to the previously described protocol (UNIT 4.17) are transformed via a stereospecific 1,3,2-oxathiaphospholane-ring opening condensation into the corresponding dinucleoside phosphorothioates. Such dimers cannot be introduced into an oligonucleotide chain via the phosphoramidite approach since the unprotected P-S(-) bond is easily oxidized during routine I(2)/Py/water oxidation of the phosphite function. In the methodology described here, the reversible alkylation of the PS function is applied. Subsequently, the 3'-phosphoramidites of such PS-protected dimers prepared in situ are used for routine synthesis of chimeric PO/PS-oligonucleotides according to the phosphoramidite method. The presence of the alkylated PS-function requires modified conditions for oligonucleotide deprotection and cleavage from the solid support. Detailed procedures for the synthesis of PS-dimers and their incorporation into an oligonucleotide chain, as well as deprotection/purification steps are presented.

Expression and Purification of Zinc Finger Antiviral Protein

Ever since the discovery of viruses so many years ago there have been researchers of many different fields racing to find the perfect inhibitor. Any and all discoveries of viral resistance have been taken into a spotlight to discover the mechanisms. Zinc Finger Antiviral Protein (ZAP) is found in the kidney and liver cells of Rattus norvegicus; this protein makes these cells more resistant to viral infection. Gao et al concluded that ZAP facilitates inhibition of the antiviral gene expression, one of the major propagation steps (rather than inhibition of infection ZAP affects viral expression) by binding viral mRNA. Since then ZAP has been shown to increase resistance against Moloney Murine Leukemia virus, Sindbis virus, Ebola virus, and Marburg virus. Activity of ZAP containing four CCCH zinc fingers seems to be dependent on the integrity of the second and fourth CCCH zinc fingers. With HIV in mind, which is also a retrovirus, we have concluded that ZAP will have profound and influential implications.Our goal is to determine the structure of the zinc-binding domain of ZAP using Nuclear Magnetic Resonance. Zap was expressed as a fusion protein in E. coli with several different cleavage conditions and purified using Immobilized Metal Ion Affinity Chromatography (IMAC) were screened and found unsuccessful in that the cleaved ZAP was insoluble. However, we are currently working on the smaller ZAP proteins that only contain two zinc fingers; their constructs show promising results in terms of solubility after cleavage.

Hydrolysis of 3,4-methylenedioxymethamphetamine (MDMA) metabolite conjugates in human, squirrel monkey, and rat plasma

Characterizing the formation of metabolites of 3,4-methylenedioxymethamphetamine (MDMA, "Ecstasy") in different species (rat, squirrel monkey, and human) may provide insight into mechanisms of MDMA neurotoxicity. Two prominent MDMA metabolites, 3,4-dihydroxymethamphetamine (HHMA) and 4-hydroxy-3-methoxymethamphetamine (HMMA), are conjugated with glucuronic or sulfuric acid, but reference standards are not available; therefore, quantification is only possible after conjugate cleavage. Different concentrations of HHMA and HMMA were obtained in human, squirrel monkey, and rat plasma specimens when acid or enzymatic cleavage was performed. Our data document that these differences are due to species-specific influences on conjugate cleavage. Acidic hydrolysis should be used for analyzing free HHMA and HMMA in human or squirrel monkey plasma, while enzymatic hydrolysis with glucuronidase or sulfatase maximizes recovery of free HHMA and HMMA in rat plasma. Optimization of cleavage conditions showed that sulfate conjugates were more readily cleaved by acid hydrolysis and glucuronides by glucuronidase.

Synthesis of 3′-O-(2-cyanoethyl)-2′-deoxythymidine-5′-phosphate as a model compound for evaluation of cyanoethyl cleavage

An essential and challenging task during the development of our sequencing-by-synthesis (SBS) technique is the evaluation of efficient cyanoethyl (CE) cleavage conditions. For this purpose 3′-O-(2-cyanoethyl)-2′-deoxythymidine-5′-phosphate as a model compound as well as a short DNA oligomer bearing the CE function as terminal group were synthesized and used for various deprotection experiments. As it is already known for 2′-O-CE-protected RNA oligonucleotides, the CE function can be cleaved with tetrabutylammonium fluoride (TBAF) in THF. Indeed, by using 3′-O-(2-cyanoethyl)-2′-deoxythymidine-5′-phosphate as a simple model compound for cleavage tests, we found out that the 3′-O-CE function is quantitatively cleaved with 1 M TBAF in THF. However, the CE group is also cleaved by other small bases like hydroxy groups under alkaline conditions. The CE cleavage with TBAF in THF gives the fastest and quantitative removal of the CE group under mild conditions for our sequencing-by-synthesis (SBS) application. The efficient removal of the 3′-CE group is crucial for the proof-of-principle of our SBS approach using dye-labeled 3′-CE-blocked dNTPs, which is currently under investigation. Herein we describe the application of 3′-O-(2-cyanoethyl)-2′-deoxythymidine-5′-phosphate as model compound for the development of reversible terminators for the SBS technique. Furthermore we suggest that nucleoside phosphates bearing any removable 3′-modification might be suitable model compounds for cleavage studies in a heterogeneous environment comparable to an oligonucleotide/ aprotic solvent system.

Diaryl Ether and Diaryl Thioether Syntheses on Solid Supports via Copper (I)-Mediated Coupling

An efficient method to synthesize diaryl ethers and thioethers on solid supports is described. Starting from immobilized phenols or arylhalides, coupling with an access of aryliodides/arylbromides or phenolic/thiophenolic substrates in solution was successful in the presence of CuCl and Cs(2)CO(3) as base. Coupling conditions known from solution-phase syntheses of diaryl ethers have been effectively modified and adapted to solid-phase synthesis. Optimized conditions enabled the coupling of sterically hindered and/or electronically deactivated aryl moieties. After coupling, a newly developed diversity-generating linker based on cinnamic acid allowed the diaryl ethers to be cleaved from the resin either via saponification/transesterification or via ozonolysis. Latter offers the possibility of generating several additional compounds by simple variation of the cleavage conditions. The target substances were generally isolated in good to excellent yields and high purities.

Photoresponsive Surfaces with Two Independent Wavelength-Selective Functional Levels

Two photoremovable protecting groups, namely, nitroveratryloxycarbonyl (NVo) and diethylamino-coumarin-4-yl (DEACM), have been tested for wavelength-selective, independent removal. The chromophores were attached to the amine group of aminopropyltriethoxysilane and used for the modification of silica surfaces. A photolytic experiment on the photosensitive layers allowed us to identify the irradiation conditions for the selective cleavage of the chromophores. UV measurements revealed that the photolabile DEACM group can be cleaved off with UV light at 412 nm without damaging the NVo group. The NVo group could then be removed at 365 nm. Masked irradiation of substrates modified with a 1:1 molar mixture of both silanes allowed the generation of bifunctional patterns after the selective cleavage of DEACM and NVo in a sequential irradiation process. The deprotection reaction was confirmed by coupling two different fluorescent dyes to the liberated amine groups. The expected two-color pattern could be observed by fluorescence microscopy.

Chemistry of α‐hydroxymethylserine: problems and solutions

Further improvements related to the synthesis of peptides containing HmS are presented. Efficient synthetic protocols have been developed to synthesize "difficult" sequences containing a C-terminal HmS residue, MeA-HmS or consecutive HmS. Preparative methods for orthogonal N- and/or C-protected HmS(Ipr) derivatives are described. Their compatibility with standard solution or solid-phase peptide chemistry protocols allows synthetic flexibility toward HmS-containing peptides. In the synthesis of the sterically hindered dipeptides with the C-terminal HmS(Ipr) residue, HATU proves the highest efficiency, as compared with the fluoride and PyBroP/DMAP coupling methods. The HATU method also outperforms the fluoride activation in the solid-phase assembly of HmS homosequence. Specific protocols are described to overcome an undesired cyclization to diketopiperazines that occurs during the removal of Fmoc from dipeptides with the C-terminal HmS(Ipr) or HmS residues, thus precluding their C-->N elongation. The successful protocols involve: (i) the 2+1 condensation using mixed anhydride activation yielding the desired product with the highest optical integrity or (ii) use of the 2-chlorotrityl resin as a solid support sterically suppressing the undesired cleavage due to diketopiperazine formation. The latter approach allows the mild conditions of peptide cleavage from solid support, preserving the isopropylidene protection and minimizing the undesired N-->O-acyl migration that was observed under prolonged acid treatment used for cleaving the HmS peptide from the Wang resin.

Production of recombinant human epidermal growth factor using Ssp dnaB mini-intein system

Chemical-enzymatic synthesis of human Epidermal Growth Factor (hEGF) cDNA has been performed, following by cloning into expression vector pTWIN1 (New England Biolabs). The resulting recombinant fusion protein expressed in Escherichia coli consisted of the N-terminal chitin-binding domain, mini-intein Ssp dnaB domain and hEGF polypeptide at the C-terminus. In this construct, mini-intein Ssp dnaB played a role of catalytically active subunit capable under certain conditions of autocatalytic cleavage resulting in separation of the target protein. As the hybrid protein had several cysteins in its sequence—one in chitin-binding domain, one in mini-intein and six in hEGF, it was necessary to work out optimal scheme for refolding and purification of the recombinant hEGF. As a result of this work, two schemes of the recombinant hEGF purification have been developed: according to the first scheme, the recombinant protein with reduced cysteins is bound to the chitin column, the hEGF is cleaved off and eluted, and then refolded to form appropriate cystein bridges. In the second scheme, the entire hybrid protein is first refolded to form disulfide bonds and then loaded to affinity resin; the recombinant hEGF is cleaved off and eluted in its native state. In spite of the fact that the first scheme is more common and suitable for a variety of recombinant proteins, in case of recombinant hEGF, the second scheme proved to be more productive and cost-effective.

Mechanistic studies of amide bond scission during acidolytic deprotection of Pip containing peptide

Unusual TFA catalyzed cleavage reaction is reported for peptide containing pipecolic acid residues. Although the use of TFA under standard cleavage conditions is sufficiently mild to prevent degradation of the desired products, the amide bond between consecutive pipecolic acid residues is unexpectedly hydrolyzed by standard TFA treatment. The hydrolysis is proposed to proceed via an oxazolinium ion intermediate. This mechanism is supported by H/D exchange as observed by ESI-MS and NMR experiments.

Synthesis and Biological Evaluation of Cruentaren A Analogues

The complex macrolide cruentaren A is a highly selective and potent inhibitor of F-ATPase (F-type adenosine triphosphatase). As it shows some resemblance to benzolactone enamides like apicularen A, it was of interest to perform some structure-activity studies to delineate the key functional groups that are responsible for the activity. Building upon our previously developed route to cruentaren A, which is based on a ring-closing alkyne metathesis reaction (RCAM), several cruentaren analogues were prepared. Replacement of the 3-hydroxy hexanoic part with acids that lack the hydroxy group function resulted in a significant drop in cytotoxicity and F-ATPase inhibition. Furthermore, two enamide analogues 23 and 50 were synthesized. However, these compounds were only cytotoxic in the micromolar range. Under the conditions for cleavage of the C3 aromatic methyl ether, the enamide function was transformed to the corresponding oxazinanone, resulting in analogues 25 and 52.

Chemo-enzymatic synthesis of new ferrocenyl-oxazolidinones and their application as chiral auxiliaries

A chemo-enzymatic synthesis of new chiral ferrocenyl-oxazolidinones has been developed. The key step was the addition of HCN to formylferrocene catalysed by the hydroxynitrile lyase from Hevea brasiliensis, which yielded an enantiomerically pure ferrocenyl-cyanohydrine in excellent yield and ee. The ferrocenyl-oxazolidinones obtained by this strategy were tested as chiral auxiliaries for asymmetric alkylations and aldol reactions and were shown to be effective in terms of yields, stereoselectivities and cleavage conditions.

Efficient cleavage of the N–O bond of 3,6-dihydro-1,2-oxazines mediated by some α-hetero substituted carbonyl compounds in mild conditions

The efficient cleavage of the N-O bond of some nitroso Diels-Alder cycloadducts has been achieved in mild conditions, mediated either by 2,2-dimethyl-1,3-dioxan-5-one or 1,3-dithiolane-2-carboxaldehyde. These new and purely organic conditions allow an excellent tolerance with respect to many functional groups that would have been affected by previous reductive cleavage conditions.

Solid-Supported Nitroso Hetero Diels–Alder Reactions. 1. Acylnitroso Dienophiles: Scope and Limitations

Polymer-supported acylnitroso dienophiles were prepared and used in hetero Diels-Alder (HDA) reactions with a variety of dienes. The transient acylnitroso dienophiles were prepared in situ from immobilized hydroxamates, which were attached to solid supports via several linkers each cleavable by different cleavage reagents, and served for the synthesis of both N-unsubstituted and N-derivatized HDA adducts. Model compounds were used to (i) optimize reaction conditions for solid-supported HDA reactions, (ii) evaluate the outcome of the reactions with various dienes, (iii) compare relative reactivities of dienes, and (iv) assess the stability of HDA adducts toward cleavage conditions typically used in solid-phase syntheses. Cleaved products were submitted to biological assays, and the results are reported. The accompanying paper, focused on complementary arylnitroso HDA reactions, includes a comparison of both HDA reactions.

Solid-Supported Nitroso Hetero Diels–Alder Reactions. 2. Arylnitroso Dienophiles: Scope and Limitations

Immobilized arylnitroso dienophiles were prepared and used in hetero Diels-Alder (HDA) reactions with a variety of dienes. Polymer-supported arylnitroso species were prepared on several linkers cleavable by different cleavage reagents and used for (i) optimization of reaction conditions for HDA reactions, (ii) evaluation of the reaction outcome with various dienes, (iii) comparison of relative reactivities of dienes, and (iv) assessment of the stability of HDA adducts toward cleavage conditions typically used in solid-phase preparation (TFA). The outcome of the HDA reactions has been evaluated for a set of 19 dienes, and the relative reactivities of dienes that yielded the expected HDA adducts were compared. Cleaved products were submitted to biological assays, and the results are reported.

HIV-1 VprB and C RNA Cleavage by Potent 10–23 DNAzymes That Also Cause Reversal of G2 Cell Cycle Arrest Mediated by Vpr Genes

Accessory Vpr protein of HIV-1 is known to influence several key cellular functions that also impacts on the HIV-1 replication cycle. Besides other activities, it alone causes cell cycle arrest at the G2 phase and thus potentially contribute to the overall pathology. We designed several 10-23 catalytic motifs containing DNAzymes (Dzs) against the full-length Vpr gene from subtype B and checked its activity against VprC gene from one of the Indian HIV-1 isolates. Among several Dzs that showed sequence-specific cleavage activities, Dz-94 was very potent and equally efficient in its ability to cleave full-length VprB and C RNA to completion under standard conditions of cleavage. Although Dz-90 target sequence was fully conserved between VprB and C genes, it was more effective on latter genes, suggesting that spatial structures of RNA at other regions of Vpr can also influence the cleavage activity for this Dz. HIV-1 VprB and C encoding genes under the powerful CMV promoter, when cotransfected into mammalian cells with Dz-94, a potent intracellular inhibition, was observed, which also resulted in reversing the G2 cell cycle arrest mediated by VprB and C proteins. Thus, Dz-94 could potentially be developed to prevent Vpr-mediated cytopathic effects caused by HIV-1 subtype B and C isolates.

Elimination and exchange of trifluoroacetate counter‐ion from cationic peptides: a critical evaluation of different approaches

Most synthesized peptides are nowadays produced using solid-phase procedures. Due to cleavage and purification conditions, they are mainly obtained in the presence of trifluoroacetic acid (TFA) and, for cationic peptides, as trifluoroacetate (TF-acetate) salts. However, TF-acetate interferes with physicochemical characterizations using infrared spectroscopy and might significantly affect the in vivo studies. Thus, TF-acetate exchange by another counter-ion is often required. Up to now, the classical procedure has consisted of freeze-drying the peptide several times in the presence of an excess of a stronger acid than TFA (pKa approximately 0): generally HCl (pKa = - 7). This approach means that working at pH < 1 can induce peptide degradation. We therefore tested three different approaches to exchange the tightly bound TF-acetate counter-ion from the dicationic octapeptide lanreotide: (i) reverse-phase HPLC, (ii) ion-exchange resin, and (iii) deprotonation/reprotonation cycle of the amino groups. The first two approaches allow the partial to almost complete exchange of the TF-acetate counter-ion by another ion from an acid weaker than TFA, such as acetic acid (pKa = 4.5), and the third requires a basic solution that permits the complete removal of TF-acetate counter-ion. The efficiency of these three procedures was tested and compared by using different analytical techniques such as 19F-NMR, 1H-NMR and attenuated total reflectance Fourier transformed infrared spectroscopy (ATR FT-IR). We also show that ATR-IR can be used to monitor the TFA removal. The counter-ion exchange procedures described in this study are easy to carry out, fast, harmless and reproducible. Moreover, two of them offer the very interesting possibility of exchanging the initial TF-acetate by any other counter-ion.