Stereocontrolled access to thioisosteres of nucleoside di- and triphosphates.

Nucleoside diphosphates and triphosphates impact nearly every aspect of biochemistry; however, the use of such compounds as tools or medicinal leads for nucleotide-dependent enzymes and receptors is hampered by their rapid in vivo metabolism. Although a successful strategy to address the instability of the monophosphate moiety in oligonucleotide therapeutics has been accomplished by their isosteric replacement with phosphorothioates, no practical methods exist to rapidly and controllably access stereopure di- and triphosphate thioisosteres of both natural and unnatural nucleosides. Here we show how a modular, reagent-based platform can enable the stereocontrolled and scalable synthesis of a library of such molecules. This operationally simple approach provides access to pure stereoisomers of nucleoside α-thiodiphosphates and α-thiotriphosphates, as well as symmetrical or unsymmetrical dinucleoside thiodiphosphates and thiotriphosphates (including RNA cap reagents). We demonstrate that ligand-receptor interactions can be dramatically influenced by P-stereochemistry, showing that such thioisosteric replacements can have profound effects on the potency and stability of lead candidates.

Stereocontrolled Radical Thiophosphorylation.

The first practical, fully stereoselective P(V)-radical hydrophosphorylation is presented herein by using simple, limonene-derived reagent systems. A set of reagents have been developed that upon radical initiation react smoothly with olefins and other radical acceptors to generate P-chiral products, which can be further diversified (with conventional 2e- chemistry) to a range of underexplored bioisosteric building blocks. The reactions have a wide scope with excellent chemoselectivity, and the unexpected stereochemical outcome has been supported computationally and experimentally. Initial ADME studies are suggestive of the promising properties of this rarely explored chemical space.

An electroaffinity labelling platform for chemoproteomic-based target identification.

Target identification involves deconvoluting the protein target of a pharmacologically active, small-molecule ligand, a process that is critical for early drug discovery yet technically challenging. Photoaffinity labelling strategies have become the benchmark for small-molecule target deconvolution, but covalent protein capture requires the use of high-energy ultraviolet light, which can complicate downstream target identification. Thus, there is a strong demand for alternative technologies that allow for controlled activation of chemical probes to covalently label their protein target. Here we introduce an electroaffinity labelling platform that leverages the use of a small, redox-active diazetidinone functional group to enable chemoproteomic-based target identification of pharmacophores within live cell environments. The underlying discovery to enable this platform is that the diazetidinone can be electrochemically oxidized to reveal a reactive intermediate useful for covalent modification of proteins. This work demonstrates the electrochemical platform to be a functional tool for drug-target identification.

Hydrolytic (in)stability of phosphate isosteres.

For decades enzymatic hydrolysis of nucleotides, a cornerstone of life, was studied extensively along with the chemical hydrolytic reaction. The metabolic instability of nucleotides, in contrast with their enormous chemical stability, triggered development of metabolically stable phosphate isosteres. However, their chemical stability has not been reported. Here, we fill this gap by exploring the hydrolytic stability of the thiophosphate (PS) and dithiophosphate (PS2) monoester isostere families. Kinetic experiments with uridine-PS and -PS2 (UMPS and UMPS2) allow to chart their borders of stability. Furthermore, characterization of several chemical and structural features of UMPS and UMPS2 provide insights, which explain the dramatically different stability of PS or PS2 moieties at different positions of the nucleotide phosphate chain. Our conclusions may guide the broad scientific community that applies phosphate isosteres and allow the selection of optimal isosteres.

A Stereodivergent Approach to the Synthesis of gem-Diborylcyclopropanes.

We report a designed stereodivergent strategy for the synthesis of gem-diborylcyclopropanes. The reaction provides a highly modular approach to prepare cyclopropane ring variants bearing gem-(Bpin,Bpin), gem-(Bpin,Bdan), and gem-(Bpin,BF3 K), with outstanding levels of stereocontrol. This was achieved by diastereoselective Pd-catalyzed cyclopropanation reactions of gem-diborylalkenes with α-diazoarylacetates and α-diazoaryl-trifluoromethyl. The key to the success of this general protocol was the diastereoselective trifluorination reaction of gem-diborylcyclopropanes, followed by the stereospecific interconversion of the trifluoroborate salts into the Bdan group.

Chiral Porous Carbon Surfaces for Enantiospecific Synthesis.

Chiral surfaces, developed in the last decade, serve as media for enantioselective chemical reactions. Until today, they have been based mostly on developments in silica templating, and are made mainly from imprints of silicate materials developed a long time ago. Here, a chiral porous activated carbon surface was developed based on a chiral ionic liquid, and the surface chemistry and pore structure were studied to lay a new course of action in the field. The enantioselectivities of surfaces are examined by using variety of methods such as circular dichroism, linear sweep voltammetry and catalysis. These techniques revealed a 28.1% preference for the D enantiomer of the amino acid proline, and linear sweep voltammetry confirmed chirality recognition by another probe. An aldol surface chiral catalytic reaction was devised and allowed to determine the root of the enantiomeric excess. These results affirm the path toward a new type of chiral surface.

The Synthesis of Nucleoside 2',3'-Cyclic Monophosphate Analogs with Regio- and Stereospecificity.

This article presents a new method for the rapid, stereoselective and regioselective synthesis of nucleoside 2',3'-O,O-phosphorothioate and 2',3'-O,O-phosphoroselenoate molecules. The method avoids the use of protection groups, chiral reagents, and chiral metal catalysts, as well as complicated chiral separations. This synthetic method has been applied successfully to all of the natural nucleosides. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Preparation of 2-chloro-1,3,2-dithiophospholane (6) Basic Protocol 2: Preparation of 2-cyanoethoxy-thio-dithiophospholane (8) Basic Protocol 3: Preparation of 2-cyanoethoxy-seleno-dithiophospholane (9) Basic Protocol 4: Preparation of uridine-2',3'-O,O-phosphorothioate (Sp, exo; 1A) Basic Protocol 5: Preparation of uridine-2',3'-O,O-phosphoroselenoate (Sp, exo; 11) Basic Protocol 6: Preparation of adenosine-2',3'-O,O-phosphorothioate (Sp, exo; 12) Basic Protocol 7: Preparation of thymidine-2',3'-O,O-phosphorothioate (Sp, exo; 13) Basic Protocol 8: Preparation of cytosine-2',3'-O,O-phosphorothioate (Sp, exo; 14) Basic Protocol 9: Preparation of guanosine-2',3'-O,O-phosphorothioate (Sp, exo; 15).

Stereoselective Diels-Alder Reactions of gem-Diborylalkenes: Toward the Synthesis of gem-Diboron-Based Polymers.

Although gem-diborylalkenes are known to be among the most valuable reagents in modern organic synthesis, providing a rapid access to a wide array of transformations, including the construction of C-C and C-heteroatom bonds, their use as dienophile-reactive groups has been rare. Herein we report the Diels-Alder (DA) reaction of (unsymmetrical) gem-diborylalkenes. These reactions provide a general and efficient method for the stereoselective conversion of gem-diborylalkenes to rapidly access 1,1-bisborylcyclohexenes. Using the same DA reaction manifold with borylated-dienes and gem-diborylalkenes, we also developed a concise, highly regioselective synthesis of 1,1,2-tris- and 1,1,3,4-tetrakis(boronates)cyclohexenes, a family of compounds that currently lack efficient synthetic access. Furthermore, DFT calculations provided insight into the underlying factors that control the chemo-, regio-, and stereoselectivity of these DA reactions. This method also provides stereodivergent syntheses of gem-diborylnorbornenes. The utility of the gem-diborylnorbornene building blocks was demonstrated by ring-opening metathesis polymerization (ROMP), providing a highly modular approach to the first synthesis of the gem-diboron-based polymers. Additionally, these polymers have been successfully submitted to postpolymerization modification reactions. Given its simplicity and versatility, we believe that this novel DA and ROMP approach holds great promise for organoboron synthesis as well as organoboron-based polymers and that it will result in more novel transformations in both academic and industrial research.

Addressing regio- and stereo-specificity challenges in the synthesis of nucleoside 2',3'-cyclic monophosphate analogs - a rapid and facile synthesis of nucleoside-2',3'-O,O-phosphoro-thioate or -selenoate, and elucidation of the origin of the rare specificity.

A new facile, rapid, stereo- and regio-selective one-pot synthesis of nucleoside-2',3'-O,O-phosphorothioate and selenoate analogs has been developed. This method avoids the need for protection strategies and chiral reagents, chiral metal catalysts, or chiral separations. This synthetic method has been applied to all natural nucleosides (U/A/G/C/T). Furthermore, we have deciphered the origin of the stereo- and regio-selectivity of the reaction.

Enantioselective Crystallization of Chiral Inorganic Crystals of ϵ-Zn(OH)2 with Amino Acids.

Many inorganic materials can form crystals, but little is known about their enantioselective crystallization. Herein, we report on the enantioselective crystallization of ϵ-Zn(OH)2 (Wulfingite) chiral crystals by using amino acids. Crystals of ϵ-Zn(OH)2 were crystallized from supersaturated sodium hydroxide and zinc nitrate aqueous solutions in the presence of l- or d-arginine. All of the chiral measurements, such as selective chiral adsorption by circular dichroism (CD), chiral chromatography, and polarimetry measurements, clearly show chiral discrimination during the crystallization of ϵ-Zn(OH)2 . In addition, a new method has been developed for identifying chirality in crystals by using electron paramagnetic resonance (EPR). Although the values of chiral induction of the ϵ-Zn(OH)2 crystals obtained are somewhat low, these values are still significant because they demonstrate that enantioselectivity during the crystallization of chiral inorganic crystals with chiral additives can be achieved. The method can be applied to many chiral inorganic systems. Understanding and controlling the crystallization of chiral inorganic crystals is important for gaining knowledge on the interaction of chiral molecules with inorganic surfaces. This knowledge can lead to an understanding of basic scientific questions such as the evolution of homochirality in biomolecules and the development of chiral inorganic crystals for a variety of purposes such as asymmetric catalysis and optical applications.

Ultrasonic assisted synthesis of styrylpyridinium dyes: Optical properties and DFT calculations.

The ultrasonic technique has received considerable attention in several fields; in particular, it gained rapid momentum in organic synthesis due to the larger reaction rates, milder reaction conditions, and better yields. We report herein a facile synthesis of a series of styrylpyridinium based dyes under ultrasonic irradiation. Within short reaction time (15 min) under ultrasonic irradiation, compared to normal laboratory conditions, (4-16 h), we can achieve good to excellent yields. The reaction time is shortened because ultrasound can accelerate the generation of the nucleophile of the pyridinium salt and subsequently a nucleophilic addition of an aldehyde followed by dehydration affords the styrylpyridinium dye, (Knoevenagel condensation). The photophysical properties of all compounds are comprehensively investigated in different solvents. All the compounds exhibit negative solvatochromism both in absorption and fluorescence emission spectra. Such behavior is due to the higher dipole moment of these molecules at the ground state. DFT calculations were performed to understand the electronic structure of the molecules. Our results show the high efficacy of sonochemistry over other methods for preparation of styrylpyridinium dyes.

Adenine-(methoxy)-ethoxy-Pα,α-dithio-triphosphate inhibits pathologic calcium pyrophosphate deposition in osteoarthritic human chondrocytes.

Nucleotide pyrophosphatase/phosphodiesterase-1 (NPP1) inhibitors have been suggested as a potential treatment for calcium pyrophosphate dihydrate (CPPD) deposition disease. Here, we targeted the development of improved NPP1 inhibitors based on acyclic mimics of Pα,α-phosphorodithioate-substituted adenine nucleotides, 7-10. The latter were obtained in a facile two-step synthesis from adenine-(methoxy)ethanol. Among analogs 7-10, adenine-(methoxy)ethoxy-Pα,α-dithio-triphosphate, 8, was the most potent NPP1 inhibitor both with purified enzyme (IC50 0.645 µM) and in osteoarthritic human chondrocytes (IC50 0.033 µM). Furthermore, it efficaciously (10-fold vs. control) inhibited ATP-induced CPPD in human articular chondrocytes. Importantly, 8 was a highly selective NPP1 inhibitor which showed only minor inhibition of NPP3, CD39 and CD73, and did not inhibit TNAP (tissue nonspecific alkaline phosphatase) activity in human chondrocytes. Furthermore, 8 did not activate P2Y1,2,6 receptors. Analog 8 was not toxic to cultured chondrocytes at 100 µM. Therefore, 8 may be suitable for further development as a drug candidate for the treatment of CPPD arthritis and other NPP1-related diseases.

Structure-activity relationship study of NPP1 inhibitors based on uracil-N1-(methoxy)ethyl-ß-phosphate scaffold.

Overexpression of ecto-nucleotide pyrophosphatase-1 (NPP1) is associated with diseases such as calcium pyrophosphate dihydrate deposition disease, calcific aortic valve disease, and type 2 diabetes. In this context, NPP1 inhibitors are potential drug candidates for the treatment of these diseases. The present study focuses on the analysis of the structure-activity relationship of NPP1 inhibitors based on acyclic uracil-nucleotides. For this purpose, we synthesized acyclic uridine-monophosphate analogs, 10-11, uridine-diphosphate analogs, 12-14, and uridine-Pα,α-dithio-triphosphate analogs, 15-17. We evaluated their inhibitory activity and selectivity towards NPP1, -3, NTPDase1, -2, -3, and -8, and P2Y2,4,6 receptors. Analogs 16 and 17 were the most selective and potent NPP1 inhibitors (Ki 0.94 and 0.73 µM, respectively) among the tested molecules. Analogs 10-17 had only minute effect on uracil-nucleotide responding P2Y2,4,6 receptors. Analog 17 (100 µM) displayed 96% inhibition of NPPase activity in osteoarthritic human chondrocytes. Analogs 14-17 displayed weak inhibitory effect on alkaline phosphatase activity at equimolar concentrations in human chondrocytes. All tested analogs showed no toxicity at human chondrocytes. We concluded that ribose-ring to chain transformation, as well as the type of the nucleobase, are parameters of minor significance to NPP1 inhibition, whereas the major parameter is Pα-dithio-substitution. In addition, the length of the phosphate chain also significantly affects inhibition. Overall, the experimental results were well reproduced by molecular docking. A correlation was observed between the activities of the compounds and the number of H-bonds and salt bridges formed between the inhibitors and NPP1 binding site residues. Uracil-N1-(methoxy)ethyl-ß-Pα,α-dithio, Pß,γ-methylene tri-phosphate, 17, was identified as the most potent, selective, and non-toxic NPP1 inhibitor among the tested analogs, and may be used as a lead structure for further drug development.

Sonochemically modified ovalbumin enhances enantioenrichment of some amino acids.

As part of our efforts to develop a new method for chiral resolution of amino acids with sonochemically modified proteins, we present result that indicates how ovalbumin microspheres (OAMS) interact specifically with l-amino acids from a racemate in solution, leaving an excess of d-enantiomer in the permeate solution. Among different amino acids that interacted with the OAMS, tryptophan (Trp) was the most successfully resolved with 65% enantiomeric excess. A control experiment with native ovalbumin in solution did not show any chiral resolution of amino acids. Interestingly, when the OAMS were pretreated with racemic lysine (Lys) solution and then used for resolution of tryptophan the enantiomeric enrichment of d-tryptophan was raised to 98%. This unanticipated positive effect is discussed in terms of the structural correlation between Trp and Lys, which is less apparent in other amino acids such as phenylalanine.

Correction to: Identification of adenine-N9-(methoxy)ethyl-ß-bisphosphonate as NPP1 inhibitor attenuates NPPase activity in human osteoarthritic chondrocytes.

The original version of the article unfortunately contained an error.

Aminomethylene-Phosphonate Analogue as a Cu(II) Chelator: Characterization and Application as an Inhibitor of Oxidation Induced by the Cu(II)-Prion Peptide Complex.

Recently, we reported on a series of aminomethylene-phosphonate (AMP) analogues, bearing one or two heterocyclic groups on the aminomethylene moiety, as promising Zn(II) chelators. Given the strong Zn(II) binding properties of these compounds, they may find useful applications in metal chelation therapy. With a goal of inhibiting the devastating oxidative damage caused by prion protein in prion diseases, we explored the most promising ligand, {bis[(1H-imidazol-4-yl)methyl]amino}methylphosphonic acid, AMP-(Im)2, 4, as an inhibitor of the oxidative reactivity associated with the Cu(II) complex of prion peptide fragment 84-114. Specifically, we first characterized the Cu(II) complex with AMP-(Im)2 by ultraviolet-visible spectroscopy and electrochemical measurements that indicated the high chemical and electrochemical stability of the complex. Potentiometric pH titration provided evidence of the formation of a stable 1:1 [Cu(II)-AMP-(Im)2]+ complex (ML), with successive binding of a second AMP-(Im)2 molecule yielding ML2 complex [Cu(II)-(AMP-(Im)2)2]+ (log K' = 15.55), and log ß' = 19.84 for ML2 complex. The CuN3O1 ML complex was demonstrated by X-ray crystallography, indicating the thermodynamically stable square pyramidal complex. Chelation of Cu(II) by 4 significantly reduced the oxidation potential of the former. CuCl2 and the 1:2 Cu:AMP-(Im)2 complex showed one-electron redox of Cu(II)/Cu(I) at 0.13 and -0.35 V, respectively. Indeed, 4 was found to be a potent antioxidant that at a 1:1:1 AMP-(Im)2:Cu(II)-PrP84-114 molar ratio almost totally inhibited the oxidation reaction of 4-methylcatechol. Circular dichroism data suggest that this antioxidant activity is due to formation of a ternary, redox inactive Cu(II)-Prp84-114-[AMP-(Im)2] complex. Future studies in prion disease animal models are warranted to assess the potential of 4 to inhibit the devastating oxidative damage caused by PrP.

Identification of adenine-N9-(methoxy)ethyl-ß-bisphosphonate as NPP1 inhibitor attenuates NPPase activity in human osteoarthritic chondrocytes.

Overproduction of extracellular diphosphate due to hydrolysis of ATP by NPP1 leads to pathological calcium diphosphate (pyrophosphate) dihydrate deposition (CPPD) in cartilage, resulting in a degenerative joint disease that today lacks a cure. Here, we targeted the identification of novel NPP1 inhibitors as potential therapeutic agents for CPPD deposition disease. Specifically, we synthesized novel analogs of AMP (NPP1 reaction product) and ADP (NPP1 inhibitor). These derivatives incorporate several chemical modifications of the natural nucleotides including (1) a methylene group replacing the Pα,ß-bridging oxygen atom to provide metabolic resistance, (2) sulfonate group(s) replacing phosphonate(s) to improve binding to NPP1's catalytic zinc ions, (3) an acyclic nucleotide analog to allow flexible binding in the NPP1 catalytic site, and (4) a benzimidazole base replacing adenine. Among the investigated compounds, adenine-N9-(methoxy)ethyl-ß-bisphosphonate, 10, was identified as an NPP1 inhibitor (Ki 16.3 µM vs. the artificial substrate p-nitrophenyl thymidine-5'-monophosphate (p-Nph-5'-TMP), and 9.60 µM vs. the natural substrate, ATP). Compound 10 was selective for NPP1 vs. human NPP3, human CD39, and tissue non-specific alkaline phosphatase (TNAP), but also inhibited human CD73 (Ki 12.6 µM). Thus, 10 is a dual NPP1/CD73 inhibitor, which could not only be of interest for treating CPPD deposition disease and calcific aortic valve disease but may also be considered for the immunotherapy of cancer. Compound 10 proved to be a promising inhibitor, which almost completely reduces NPPase activity in human osteoarthritic chondrocytes at a concentration of 100 µM.