Beyond Triphosphates: Reagents and Methods for Chemical Oligophosphorylation

Monodisperse Chemical Oligophosphorylation of Peptides via Protected Oligophosphorimidazolide Reagents

Protein poly- and oligophosphorylation are recently discovered post-translational modifications that remain poorly characterized due to (1) the difficulty of extracting endogenously polyphosphorylated species without degradation and (2) the absence of synthetic and analytical tools to prepare and characterize poly- and oligophosphorylated species in biochemical contexts. Herein, we report a methodology for the selective oligophosphorylation of peptides with monodisperse phosphate chain lengths (Pn=3-6). A library of oligophosphorimidazolide (oligoP-imidazolide) reagents featuring benzyl and o-nitrophenylethyl protecting groups was synthesized in moderate-to-good yields (65-93 %). These oligoP-imidazolide reagents enabled the selective and simultaneous conjugation of multiple phosphate units to phosphoryl nucleophiles, circumventing tedious iterative processes. The generalizability of this approach is illustrated by a substrate scope study that includes several biologically relevant phosphopeptide sequences, culminating in the synthesis of >60 examples of peptide oligophosphates (Pn=2-6). Moreover, we report the preparation of oligoP-diimidazolides (Pn=3-5) and discuss their application in generating unique condensed phosphate-peptide conjugates. We also demonstrate that human phospho-ubiquitin (pS65-Ub) is amenable to functionalization by our reagents. Overall, we envision the methods described here will enable future studies that characterize these newly discovered but poorly understood phosphorylation modes.

Direct conversion of various phosphate sources to a versatile P-X reagent [TBA][PO2X2] via redox-neutral halogenation

Inorganic phosphates hold significant potential as ideal natural building blocks, forming a fundamental basis for organic and biochemical synthesis. However, their limited solubility, inherent chemical stability, and low reactivity pose substantial challenges to converting phosphates into organophosphates under mild conditions. This study introduces an efficient method for the direct conversion of phosphates into P(V)-X reagents, [TBA][PO2X2] (X = Cl, F), via a redox-neutral halogenation process. This method utilizes cyanuric chloride (or cyanuric fluoride) as the halogenation reagent, in combination with 1-formylpyrrolidine and tetrabutylammonium chloride (TBAC), under ambient conditions. The approach enables effective halogenation conversion for various P(V) sources, including orthophosphates, pyrophosphoric acid, Na3P3O9 and P2O5. Furthermore, we demonstrate the synthetic utility of the P(V)-Cl reagent in the phosphorylation of diverse O-, S-, N- and C-nucleophiles. Key advantages of this conversion process include the use of inexpensive and readily available chemicals, the avoidance of high-energy redox reactions, and the generation of a reactive yet stable P(V)-X reagent.

Structural Insights into Broad-Range Polyphosphate Kinase 2-II Enzymes Applicable for Pyrimidine Nucleoside Diphosphate Synthesis

Polyphosphate kinases (PPK) play crucial roles in various biological processes, including energy storage and stress responses, through their interaction with inorganic polyphosphate (polyP) and the intracellular nucleotide pool. Members of the PPK family 2 (PPK2s) catalyse polyP-consuming phosphorylation of nucleotides. In this study, we characterised two PPK2 enzymes from Bacillus cereus (BcPPK2) and Lysinibacillus fusiformis (LfPPK2) to investigate their substrate specificity and potential for selective nucleotide synthesis. Both enzymes exhibited a broad substrate scope, selectively converting over 85 % of pyrimidine nucleoside monophosphates (NMPs) to nucleoside diphosphates (NDPs), while nucleoside triphosphate (NTP) formation was observed only with purine NMPs. Preparative enzymatic synthesis of cytidine diphosphate (CDP) was applied to achieve an yield of 49 %. Finally, structural analysis of five crystal structures of BcPPK2 and LfPPK2 provided insights into their active sites and substrate interactions. This study highlights PPK2-II enzymes as promising biocatalysts for the efficient and selective synthesis of pyrimidine NDPs.

The P(III)-Amidite Based Synthesis of Stable Isotope Labeled mRNA-Cap-Structures Enables their Sensitive Quantitation from Brain Tissue

The 5' cap structure is crucial to mRNA function, with its diverse methylation patterns depending on the cellular state. Sensitive analytical methods are sought after to quantify this cap variety also referred to as cap epitranscriptome. To address a bottleneck for accurate and precise quantitation, we report a facile and fast access to high-quality synthetic standards via a new route, involving P(III)-amidite chemistry. A range of cap nucleotides and their stable heavy isotopic labeled analogues were derived from nucleoside diphosphates, which themselves were directly prepared in a one-step reaction sequence starting from unprotected nucleosides using a triphosphorylating reagent in combination with ethylenediamine. Considering a wider scope, the route also enables direct access to magic spot nucleotides and diphosphates of isoprenyl-alcohols. Stable-isotope labeled cap nucleotides derived from this route paved the way for the development of a highly sensitive LC-MS/MS method, applied to the characterization of mouse brain cap epitranscriptomes, which turned out to be very different from those of cultured cell lines of widespread use in the life sciences.

Potentiality of Nucleoside as Antioxidant by Analysis on Oxidative Susceptibility, Drug Discovery, and Synthesis

Nucleosides are sensitive sites towards oxidations caused by endogenous and exogenous oxidative resources, and a large number of the produced DNA lesions behave as pathogenesis eventually. We herein analyze oxidative modes of nucleosides and structure- activity relationships of some clinical nucleoside drugs. Together with our previous findings on the inhibitory effects of nucleoside derivatives against DNA oxidation, all these results imply a possibility for nucleoside to be a new member in the family of antioxidants. Then, some novel synthetic routines of nucleoside analogs are collected to reveal the applicability in the construction of nucleoside antioxidants. Therefore, it is reasonable to envision that the nucleoside antioxidant will be a novel topic in the research of both nucleosides and antioxidants.

Chemo-enzymatic production of base-modified ATP analogues for polyadenylation of RNA

Base-modified adenosine-5'-triphosphate (ATP) analogues are highly sought after as building blocks for mRNAs and non-coding RNAs, for genetic code expansion or as inhibitors. Current synthetic strategies lack efficient and robust 5'-triphosphorylation of adenosine derivatives or rely on costly phosphorylation reagents. Here, we combine the efficient organic synthesis of base-modified AMP analogues with enzymatic phosphorylation by a promiscuous polyphosphate kinase 2 class III from an unclassified Erysipelotrichaceae bacterium (EbPPK2) to generate a panel of C2-, N6-, or C8-modified ATP analogues. These can be incorporated into RNA using template independent poly(A) polymerase. C2-halogenated ATP analogues were incorporated best, with incorporations of 300 to >1000 nucleotides forming hypermodified poly(A) tails.

Pentaphosphorylation via the Anhydride of Dihydrogen Pentametaphosphate: Access to Nucleoside Hexa- and Heptaphosphates and Study of Their Interaction with Ribonuclease A

Pentametaphosphate is the little studied cyclic pentamer of the metaphosphate ion, [PO3]5 5-. We show that the doubly protonated form of this pentamer can be selectively dehydrated to provide the anhydride [P5O14]3- (1). This trianion is the well-defined condensed phosphate component of a novel reagent for attachment of a pentaphosphate chain to biomolecules all in one go. Here, we demonstrate by extending adenosine monophosphate (AMP) and uridine monophosphate (UMP) to their corresponding nucleoside hexaphosphates, while adenosine diphosphate (ADP) and uridine diphosphate (UDP) are phosphate chain-extended to the corresponding nucleoside heptaphosphates. Such constructs are of interest for their potential biological function with respect to RNA-processing enzymes. Thus, we go on to investigate in detail the interaction of the polyanionic constructs with ribonuclease A, a model protein containing a polycationic active site and for which X-ray crystal structures are relatively straightforward to obtain. This work presents a combined experimental and quantum chemical approach to understanding the interactions of RNase A with the new nucleoside hexa- and heptaphosphate constructs.

Protecting-Group-Free Synthesis of ADP-Ribose and Dinucleoside Di-/Triphosphate Derivatives via P(V)-P(V) Coupling Reaction

Biomolecules containing adenosine di- or triphosphate (ADP or ATP) are crucial for diverse biological processes. Synthesis of these biomolecules and development of their chemical probes are important to elucidate their functions. Enabling reproducible and high-yielding access to these ADP- and ATP-containing molecules via conventional P(III)-P(V) and P(V)-P(V) coupling reactions is challenging owing to water content in highly polar phosphate-containing substrates. Herein, we report an efficient and reliable method for protecting-group-free P(V)-P(V) coupling reaction through in situ activation of phosphates using hydrolysis-stable 2-[N-(2-methylimidazoyl)]-1,3-dimethylimidazolinium chloride (2-MeImIm-Cl), providing the corresponding electrophilic P(V) intermediates for subsequent nucleophilic attack using their coupling partners. This P(V)-P(V) coupling reaction proceeded even in a wet reaction medium and showed a broad substrate scope, accommodating protecting-group-free synthesis of ADP-ribose and nicotinamide adenine diphosphate analogs, ATP-containing biomolecules, and ADP-ribosyl peptides.

Biocompatible aggregation-induced emission active polyphosphate-manganese nanosheets with glutamine synthetase-like activity in excitotoxic nerve cells

Glutamine synthetase (GS) is vital in maintaining ammonia and glutamate (Glu) homeostasis in living organisms. However, the natural enzyme relies on adenosine triphosphate (ATP) to activate Glu, resulting in impaired GS function during ATP-deficient neurotoxic events. To date, no reports demonstrate using artificial nanostructures to mimic GS function. In this study, we synthesize aggregation-induced emission active polyP-Mn nanosheets (STPE-PMNSs) based on end-labeled polyphosphate (polyP), exhibiting remarkable GS-like activity independent of ATP presence. Further investigation reveals polyP in STPE-PMNSs serves as phosphate source to activate Glu at low ATP levels. This self-feeding mechanism offers a significant advantage in regulating Glu homeostasis at reduced ATP levels in nerve cells during excitotoxic conditions. STPE-PMNSs can effectively promote the conversion of Glu to glutamine (Gln) in excitatory neurotoxic human neuroblastoma cells (SH-SY5Y) and alleviate Glu-induced neurotoxicity. Additionally, the fluorescence signal of nanosheets enables precise monitoring of the subcellular distribution of STPE-PMNSs. More importantly, the intracellular fluorescence signal is enhanced in a conversion-responsive manner, allowing real-time tracking of reaction progression. This study presents a self-sustaining strategy to address GS functional impairment caused by ATP deficiency in nerve cells during neurotoxic events. Furthermore, it offers a fresh perspective on the potential biological applications of polyP-based nanostructures.

Non-Hydrolysable Analogues of Cyclic and Branched Condensed Phosphates: Chemistry and Chemical Proteomics

Studies into the biology of condensed phosphates almost exclusively cover linear polyphosphates. However, there is evidence for the presence of cyclic polyphosphates (metaphosphates) in organisms and for enzymatic digestion of branched phosphates (ultraphosphates) with alkaline phosphatase. Further research of non-linear condensed phosphates in biology would profit from interactome data of such molecules, however, their stability in biological media is limited. Here we present syntheses of modified, non-hydrolysable analogues of cyclic and branched condensed phosphates, called meta- and ultraphosphonates, and their application in a chemical proteomics approach using yeast cell extracts. We identify putative interactors with overlapping hits for structurally related capture compounds underlining the quality of our results. The datasets serve as starting point to study the biological relevance and functions of meta- and ultraphosphates. In addition, we examine the reactivity of meta- and ultraphosphonates with implications for their "hydrolysable" analogues: Efforts to increase the ring-sizes of meta- or cyclic ultraphosphonates revealed a strong preference to form trimetaphosphate-analogue structures by cyclization and/or ring-contraction. Using carbodiimides for condensation, the so far inaccessible dianhydro product of ultraphosphonate, corresponding to P4 O11 2- , was selectively obtained and then ring-opened by different nucleophiles yielding modified cyclic ultraphosphonates.

Dynamic Phosphorus: Thiolate Exchange Cascades with Higher Phosphorothioates

In this study, we introduce phosphorus, a pnictogen, as an exchange center for dynamic covalent chemistry. Cascade exchange of neutral phosphorotri- and -tetrathioates with thiolates is demonstrated in organic solvents, aqueous micellar systems, and in living cells. Exchange rates increase with the pH value, electrophilicity of the exchange center, and nucleophilicity of the exchangers. Molecular walking of the dynamic phosphorus center along Hammett gradients is simulated by the sequential addition of thiolate exchangers. Compared to phosphorotrithioates, tetrathioates are better electrophiles with higher exchange rates. Dynamic phosphorotri- and -tetrathioates are non-toxic to HeLa Kyoto cells and participate in the dynamic networks that account for thiol-mediated uptake into living cells.

Synthesis of nucleoside oligophosphates by electrophilic activation of phosphorothioate

We herein report a new synthetic method for nucleoside oligophosphates based on electrophilic activation of 5'-phosphorothioate nucleotides. The treatment of phosphorothioate with 2,4-dinitrochlorobenzene (DNCB) efficiently afforded the key activated species, electrophilic thioester nucleotides (EPT-Ns), which were coupled with various phosphate reagents to afford the target nucleoside oligophosphates, including an mRNA cap analog.

Stabilized Molecular Diphosphorus Pentoxide, P2O5L2 (L = N-Donor Base), in the Synthesis of Condensed Phosphate-Organic Molecule Conjugates

Commercial phosphorus pentoxide reacts with some N-donor bases to give the adducts P₂O₅L₂ and P₄O₁₀L₃ (L = DABCO, pyridine, 4-tert-butylpyridine). The DABCO adducts were structurally characterized by single-crystal X-ray diffraction. It is proposed that P₂O₅L₂ and P₄O₁₀L₃ undergo interconversion through a "phosphate-walk" mechanism, which was evaluated using DFT calculations. P₂O₅(pyridine)₂ (1) efficiently transfers monomeric diphosphorus pentoxide to phosphorus oxyanion nucleophiles, yielding substituted trimetaphosphates and cyclo-phosphonate-diphosphates (P₃O₈R)^2- (R¹ = nucleosidyl, phosphoryl, alkyl, aryl, vinyl, alkynyl, H, F). Hydrolytic ring-opening of these compounds forms linear derivatives [R¹(PO₃)₂PO₃H]^3-, and nucleophilic ring-opening gives linear disubstituted [R¹(PO₃)₂PO₂R²]^3- compounds.

One-pot chemical pyro- and tri-phosphorylation of peptides by using diamidophosphate in water

Protein (pyro)phosphorylation is emerging as a post-translational modification (PTM) in signalling pathways involved in many cellular processes. However, access to synthetic pyrophosphopeptides that can serve as tools for understanding protein pyrophosphorylation is quite limited. Herein, we report a chemical phosphorylation method that enables the synthesis of pyrophosphopeptides in aqueous medium without the need for protecting groups. The strategy employs diamidophosphate (DAP) in a one-pot sequential phosphorylation-hydrolysis of mono-phosphorylated peptide precursors. This operationally simple method exploits the intrinsic nucleophilicity of a phosphate moiety installed on serine, threonine or tyrosine residues in complex peptides with excellent chemoselectivity and good yields under mild conditions. We demonstrate the installation of the pyrophosphate group within a wide range of model peptides and showcase the potential of this methodology by selectively pyrophosphorylating the highly functionalized Nopp140 peptide fragment. The potential to produce higher (poly)phosphorylated peptides was demonstrated as a proof-of-principle experiment where we synthesized the triphosphorylated peptides using this one-pot strategy.