Investigation of Enzyme Mechanisms with Nucleoside Phosphorothioates

Nucleoside phosphorothioates are modified nucleotides in which an oxygen atom bound to a phosphorus atom has been replaced by a sulfur atom. These compounds are suitable for the investigation of enzyme mechanisms because, although they are bound by enzymes in many cases just as well as the natural substrate, the enzymatic reactions very often proceed considerably more slowly. Since nucleoside thiophosphate O-esters exist as diastereomers these compounds can be used in suitable cases for information about the stereochemistry of enzymatic reactions.     

Dinucleoside (5′ → 3′)-O,S-Phosphorodithioates - New Class of Dinucleotide Analogues

Abstract

Nucleoside 3′-0- and 5′-O-phosphorodithioates have been recently described by Caruthers et al.¹ as a new type of nucleotide analogues. These compounds have also been obtained in our Laboratory by one-pot dithiaphospholane approach.² We now report on the transformation of some of these derivatives into new class of dinucleotide analogues. We have found that nucleoside 3′-O-phosphorodithioates (1) react in DMF solution with 5′-bromo-5′-deoxythymidine to give in high yield corresponding dinucleoside (5′→3′)-O,S-phosphorodithioates (2) - first examples of a new class of dinucleotide analogues possessing the internucleotide phosphorothioate linkage with one of the sulfur atoms in a 3′-bridging position.     

Synthesis of dinucleoside,di(2′-deoxy-2′-fluoro)nucleoside phosphates and phosphorothioates and their stability to snake venom phosphodiesterase

Dithymidine, di(2′-deoxy-2′-fluoro)-cytidine and -uridine phosphate and phosphorothioate have been synthesized. The stereochemistry of the condensation reaction between 2′-deoxy-2′-fluoronucleoside phosphoramidite and nucleoside was preliminarily investigated. The diastereomer separation of the protected phosphorothioates was performed by silica gel column chromatography. The stability of these compounds to snake venom phosphodiesterase was determined.     

Application of phosphonate and thiophosphate analogues of nucleotides to studies of some enzyme reactions

The enzymatic cleavage of a scissile P O bond can be blocked by recourse to phosphonate analogues of biological phosphate esters. α-Fluorophosphonates have an enhanced electronegativity at the bridging carbon, which, in many cases, makes them superior to simple methylene phosphonates for the study of enzyme reactions. Thus, the β,γ-difluoro-methylene analogue of ATP is a good substrate for the interferon-induced (2→5)A_n synthetase, which converts it into a (2→5)A₄ species having a 5′-β,γ-difluoromethylenetriphosphate. This binds strongly to RNase L but does not activate it. The unsymmetrical Ap₄Aases from Artemia and Lupin are strongly inhibited by P^1,P⁴-dithiophosphate analogues of diadenosyl-5′,5‴-P¹,P⁴-tetraphosphate although nonregiospecific cleavage of certain P²,P³-methylene analogues can be observed. Some of these analogues are remarkably effective inhibitors of platelet aggregation and are effective inhibitors in vivo of arterial blood-clotting in rabbits. Separation of all diastereoisomers of P¹,P⁴-dithiophosphate analogues of Ap₄A is achieved cleanly using reverse-phase hplc chromatography and this provides direct access to β,γ-CHF-bridged analogues of ATP with resolved stereochemistry at the CHF center. Lastly, growing cells of Dictyostelium discoideum not only tolerate a range of substituted methylene bisphosphonates in their growth medium but actually incorporate them into nucleotide analogues of ATP and Ap₄A.     

Isotope effects of steroids during analytical separations by paper- and high-pressure liquid chromatography

Conclusions During HPLC (reversed phase), tritiated steroids elute earlier than the unlabeled and the [4-¹⁴C]-labeled analogues. On formamide impregnated paper [4-¹⁴C]-labeled steroids move faster than the tritiated analogues. Thus, in both systems the ³H-labeled compounds behave as if they were more polar [1]. In the case of sixfold labeled estradiol the highly efficient resolution of the paperchromatographic and HPLC-systems (Fig. 1 A) may be applied to obtain carrier-free steroids with high specific activities. On the other hand the analytical application of these systems may lead to great systematic errors if the isotope effects of tritiated steroids are not taken into consideration.

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Isotopieeffekte von Steroiden bei der Papier- und Hochdruckflüssigkeits-Chromatographie

     

Nucleotide coordination with 14 lanthanides studied by isothermal titration calorimetry

ITC reveals the increasingly importance of entropy for heavier lanthanides binding to nucleotides. The phosphate group forming chelating effect with purine bases but not with pyrimidines.     

3′:5′‐Cyclic nucleotides: two sodium salts of cdTMP

3′:5′‐Cyclic nucleotides play an outstanding role in signal transduction at the cellular level but, in spite of comprehensive knowledge of the biological role of cyclic nucleotides, their structures are not established fully. Two hydrated sodium salts of thymidine 3′:5′‐cyclic phosphate (cdTMP, C₁₀H₁₂N₂O₇P), namely sodium thymidine 3′:5′‐cyclic phosphate heptahydrate, Na⁺·C₁₀H₁₂N₂O₇P⁻·7H₂O or Na(cdTMP)·7H₂O, (I), and sodium thymidine 3′:5′‐cyclic phosphate 3.7‐hydrate, Na⁺·C₁₀H₁₂N₂O₇P⁻·3.7H₂O or Na(cdTMP)·3.7H₂O, (II), have been obtained in crystalline form and structurally characterized, revealing one nucleotide in the asymmetric unit of (I) and eight different nucleotides in (II). All the cyclic nucleotide anions adopt a similar conformation with regard to nucleobase orientation, sugar conformation and 1,3,2‐dioxaphosphorinane ring puckering. In (I), no direct inter‐nucleotide hydrogen bonds are present, and adjacent nucleotide anions interact via water‐mediated and Na⁺‐mediated contacts. In contrast, in (II), direct thymine–phosphate N—H...O inter‐nucleotide hydrogen bonds occur and these are assisted by numerous inter‐nucleotide C—H...O contacts, giving rise to the self‐assembly of cdTMP⁻ anions into three different ribbons. Two of these three ribbons run in the same direction, while the third is antiparallel.     

Synthesis of 3′,5′‐Cyclic Phosphate and Thiophosphate Esters of 2′‐C‐Methyl Ribonucleosides

2′‐C‐Methylnucleosides are known to exhibit antiviral activity against Hepatitis C virus. Since the inhibitory activity depends on their intracellular conversion to 5′‐triphosphates, dosing as appropriately protected 5′‐phosphates or 5′‐phosphorothioates appears attractive. For this purpose, four potential pro‐drugs of 2′‐C‐methylguanosine, i.e., 3′,5′‐cyclic phosphorothioate of 2′‐C‐methylguanosine and 2′‐C,O⁶‐dimethylguanosine, 1 and 2 , respectively, the S‐[(pivaloyloxy)methyl] ester of 2′‐C,O⁶‐dimethylguanosine 3′,5′‐cyclic phosphorothioate and the O‐methyl ester of 2′‐C,O⁶‐dimethylguanosine 3′,5′‐cyclic phosphate, 3 and 4 , respectively, have been prepared.     

Arylation of Axially Chiral Phosphorothioate Salts by Dinuclear PdI Catalysis

S‐aryl phosphorothioates are privileged motifs in pharmaceuticals, agrochemicals, and catalysts; yet, the challenge of devising a straightforward synthetic route to enantioenriched S‐aryl phosphorothioates has remained unsolved to date. We demonstrate herein the first direct C?SP(=O)(OR′)(OR′′) coupling of diverse and chiral phosphorothioate salts with aryl iodides, enabled by an air‐ and moisture‐stable Pd^I dimer. Our mechanistic and computational data suggest distinct dinuclear Pd^I catalysis to be operative, which allows for operationally simple couplings with broad scope and full retention of stereochemistry.     

The thermodynamics of phosphate versus phosphorothioate ester hydrolysis

Phosphorothioate esters are phosphate esters in which one of the nonbridging oxygen atoms has been replaced by sulfur. In the comparative hydrolysis reactions of phosphorothioate and phosphate esters, the sulfur substitution accelerates the rates of the monoesters while slowing the rates of diesters and of triesters. Previously measured enthalpies and entropies of activation for the hydrolysis reactions of the monoesters, p-nitrophenyl phosphate and p-nitrophenyl phosphorothioate, were compared to the activation parameters measured herein for the diesters, ethyl p-nitrophenyl phosphate and ethyl p-nitrophenyl phosphorothioate, and the triesters, diethyl p-nitrophenyl phosphate and diethyl p-nitrophenyl phosphorothioate. A consistent trend of a greater DeltaH++ for the phosphorothioate analogue was found in all three classes of ester. In the monoester case, a more positive DeltaS++ arising from a mechanistic difference (D(N) + A(N) for the phosphorothioate versus A(N)D(N) for the phosphate) compensates, resulting in a lower DeltaG++ for the phosphorothioate monoester. Spectroscopic investigations indicate there is no significant difference in bond order to the leaving group in phosphates, as compared to their phosphorothioate analogues, ruling this out as a contribution to the consistently higher enthalpies of activation.     

New Tripodal, “Supercharged” Analogues of Adenosine Nucleotides: Inhibitors for the Fhit Ap3A Hydrolase

Methanetrisphosphonic acids provide a branch point for synthetic nucleotide analogues which can be exploited either to generate novel tripodal nucleotides or to incorporate additional negative charge into linear analogues relative to the parent nucleotide, as exemplified in the picture for ATP and diadenosine tetraphosphate (Ap₄A). These compounds show valuable discriminatory behavior as competitive inhibitors for the tumor suppressor protein Fhit and a second Ap_nA pyrophosphohydrolase. X=H, Cl, F.     

The Reaction of Organoboranes with Ethyl P-Nitrobenzenesulfonoxy-Carbamate Under Two-Phase Conditions. A Convenient Synthesis of Ethyl N-Alkylcarbamates from Olefins via Hydroboration

Organoboranes readily obtainable from olefins via hydroboration have been shown to be versatile synthetic reagents and intermediates.¹ Many reports have appeared dealing with the syntheses of primary,² secondary,³ and tertiary⁴ amines from organoboranes. On the other hand, there are a few examples of the similar reactions leading to nitrogen compounds possessing substituents other than hydrogen or alkyl groups attached to nitrogen. It was known that the reaction of organoboranes with iron(III) azide in the presence of hydrogen peroxide gives corresponding azidoalkanes,⁵ and N-alkylsulfonamides⁶ are prepared via the reaction of organoboranes with chloramine-T and its analogues.     

Homoallylic Phosphonates: Useful Precursors for 3,4-Epoxyalkanephosphonates

Abstract

Exoxyalkanephosphonates are compounds of interest as potential drugs¹ or intermediates in various synthetic transformations^2. Especially 1,2-epoxyalkanephosphonates and 2,3-epoxyalkanephos-phonates attracted much attention and many preparatively useful routes to these compounds have been reported^3. On the other hand the synthesis of 3,4-epoxyalkanephosphonates has to our knowledge not been described?.     

Polymer solution-filled column for the analysis of antisense phosphorothioates by capillary electrophoresis

A capillary electrophoresis (CE) column filled with 13% poly(ethylene glycol) (PEG) solution is demonstrated to resolve different lengths of antisense phosphorothioates in 100 mM Tris-borate (pH 9.0) buffer containing 30% formamide at 50 degrees C. Two sets of mixtures composed of 15-20 mers of either antisense phosphorothioate or phosphodiester oligonucleotides were synthesized based on a sequence of the antisense orientation directed against DNA-methyltransferase (denoted as MT-AS) and were used as model compounds. It was found that column coating reduced electroosmotic flow, as well as wall adsorption, and led to the separation of both phosphorothioate and phosphodiester molecules. Substantial peak broadening, however, specifically occurred to the phosphorothioates and was reduced statisfactorily by the addition of formamide into the buffer solution, raising the temperature, and raising the pH value. Under experimental conditions, a linear relationship between the migration time and the base number was observed, indicating that no peak compression artifacts existed. Without tedious pretreatment, antisense phosphorothioates were spiked into human serum, followed by water dilution, and then directly injected into the column. Separation of different lengths of phosphorothioates was observed using pressure injection, which did not suffer from injection bias.     

Novel Ortho effects detected in the fast atom bombardment mass spectra of substituted bisaryl phosphate antagonists of platelet-activating factor

A series of substituted bisaryl phosphate compounds, (R¹CH₂)⁺ ArOP = O(O^?)(OArR²R₃), was analyzed and characterized by fast atom bombardment mass spectrometry. Abundant fragment ions were observed and correlated with the proposed structures. From fragmentation pattersn, ‘ortho effect’ reactions were demonstrated to have occurred when the phosphoryl oxygen reacted with the (CH₂R¹)⁺ and C?O(OCH₃) substituents in the ortho position, relative to the phosphate group, and displaced the R¹ and OCH₃ groups, respectively, to produce phosphorus containing six-membered rings fused to the aryl moiety. When the (CH₂R¹)⁺ substituents were in the meta position relative to the phosphate group, the ‘ortho effect’ reactions were not observed. However, when the C?O(OCH₃) substituent was in the meta position relative to the phosphate group, an abundant fragment ion containing a five-membered phosphate ring fused to the aryl ring was detected with the original phosphoryl oxygen ortho to both the phosphate oxygen and a formyl group, formed from the original C?O(OCH₃) substituent. All other fragmentations not involving the ‘ortho effect’ reactions were nearly identical for the different structural isomers of the substituted bisaryl phosphate compounds.     

Frustrated Lewis Pair Chemistry: Searching for New Reactions

Frustrated Lewis pair chemistry has taken a steep development in the recent years. It offers possibilities of developing new variants of known reactions and of finding new chemical transformations. This is demonstrated and described by the recently developed FLP‐formylborane chemistry, which has led to the formation of the unique (η²‐formylborane)FLP adducts and opened a way of preparing a genuine formylborane compound, which shows an interesting follow‐up chemistry. FLPs have helped finding phosphorus analogues of the enamine Stork reaction and the Claisen reaction. These reactions lead to new organophosphorus compounds and they make new phosphane/borane systems available. P/B FLPs add to a variety of small main group element oxides. They undergo 1,2‐addition reactions to CO₂, SO₂ and other heterocumulenes and they feature unique 1,1‐addition reactions to carbon monoxide, to isonitriles and even to nitric oxide (NO), the latter yielding examples of a new class of persistent nitroxide radicals, the FLPNO nitroxyls. Eventually, some remarkable radical reactions of FLPs and related compounds are briefly mentioned.     

Interaction of divalent metal cations and nucleotides: A computational study

In this study, the anionic phosphate group of nucleotides was found to be the best site to bind the divalent metal cations Be²⁺, Mg²⁺, Zn²⁺, Cd²⁺, Hg²⁺ and Pb²⁺ to form the most stable complexes. Molecular orbital calculations at the semiempirical level were performed on nucleotidemetal cation complexes to report energies of complexation reactions, geometrical parameters of complexes and charge distributions on the complexes. In the discussion, complexational preferences of divalent metal cations, the charge transfer involved in the binding of the metal cations to the phosphate anion of the nucleotides and their conformational effects are included.     

Geometrical and vibrational features of phosphate, phosphorothioate and phosphorodithioate linkages interacting with hydrated cations: A DFT study

The effect of hexahydrated monovalent and divalent cations on the geometrical and vibrational features of dimethyl phosphate, dimethyl phosphorothioate and dimethyl phosphorodithioate anions (simple suitable model compounds representing the anionic moieties of natural and some modified nucleic acids) was studied. For this purpose, density functional theory (DFT) calculations were carried out at the B3LYP/6-31++G* level.Our results indicate that only K⁺ and Mg²⁺ prefer to be located in the bisector plane of the PO₂⁻ angle, whereas Li⁺ and Na⁺ deviate from this plane. Monovalent and divalent cations are slightly deviated from the OPS⁻ bisector plane and are found closer to the free oxygen atom. Moreover, the present calculations have shown that in contrast to the general belief, the g⁻g⁻ conformer (with respect to the torsion angles defined around the P–O ester bonds) is not always the energetically most favorable. For instance, the g⁻t conformer presents the lowest energy in the case of dimethyl phosphorothioate. The calculated vibrational wavenumbers obtained for dimethyl phosphate and dimethyl phosphorothioate interacting with hydrated sodium counterion, were compared with those previously recorded by Raman scattering and infrared absorption (IR) in aqueous solutions. It has been evidenced that the use of explicit solvent versus dielectric continuum, considerably improves the agreement between the theoretical and observed characteristic wavenumbers.     

Synthesis of phosphatase-resistant analogues of phytic acid (InsP6)

Phytic acid is enzymatically catabolized to numerous inositol polyphosphates and subsequently to myo-inositol and inorganic phosphate. These conversions are important in energy metabolism, metabolic regulation, and signal transduction pathways. A concise synthesis of phosphatase-resistant analogues of phytic acid (InsP₆) is described in which the P-1 phosphate has been replaced by phosphorothioate, phosphoroselenate, or methylphosphonate moieties. In addition, a new synthesis of P-1 tethered aminoalkyl InsP₆ and the corresponding affinity resin are described.