Enantiodivergent Formation of C−P Bonds: Synthesis of P‑Chiral Phosphines and Methylphosphonate Oligonucleotides

Phosphorus Incorporation (PI, abbreviated Π) reagents for the modular, scalable, and stereospecific synthesis of chiral phosphines and methylphosphonate nucleotides are reported. Synthesized from translimonene oxide, this reagent class displays an unexpected reactivity profile and enables access to chemical space distinct from that of the Phosphorus−Sulfur Incorporation reagents previously disclosed. Here, the adaptable phosphorus(V) scaffold enables sequential addition of carbon nucleophiles to produce a variety of enantiopure C−P building blocks. Addition of three carbon nucleophiles to Π, followed by stereospecific reduction, affords useful P-chiral phosphines; introduction instead of a single methyl group reveals the first stereospecific synthesis of methylphosphonate oligonucleotide precursors. While both Π enantiomers are available, only one isomer is requiredthe order of nucleophile addition controls the absolute stereochemistry of the final product through a unique enantiodivergent design

Serine-Selective Bioconjugation.

This Communication reports the first general method for rapid, chemoselective, and modular functionalization of serine residues in native polypeptides, which uses a reagent platform based on the P(V) oxidation state. This redox-economical approach can be used to append nearly any kind of cargo onto serine, generating a stable, benign, and hydrophilic phosphorothioate linkage. The method tolerates all other known nucleophilic functional groups of naturally occurring proteinogenic amino acids. A variety of applications can be envisaged by this expansion of the toolbox of site-selective bioconjugation methods

Synthetic Elaboration of Native DNA by RASS (SENDR)

The controlled, site-specific ligation of molecules to native DNA remains an unanswered challenge. Herein, we report a simple solution to achieve this ligation through the tactical combination of two recently developed technologies: One for the manipulation of DNA in organic media, and another for the chemoselective labeling of alcohols. Reversible Adsorption of Solid Support (RASS) is employed to immobilize DNA and facilitate its transfer into dry acetonitrile. Subsequent ligation with P(V)-based Ψ reagents takes place in high yield with exquisite selectivity for the exposed 3’ or 5’ alcohols on DNA. This two-stage process, dubbed SENDR for Synthetic Elaboration of Native DNA by RASS, can be applied to a multitude of DNA conformations and sequences with a variety of functionalized Ψ reagents to generate useful constructs. Such entities can address numerous longstanding challenges, including the selective single coupling of DNA to proteins, ASOs, and functional small molecules, and also can allow the synthesis of doubly-labeled congeners for novel probe constructs including ones of potential interest to COVID-19 research. Finally, a prototype for the industrialization of SENDR in a kit format is presented

Enantiodivergent Formation of C–P Bonds: Synthesis of P-Chiral Phosphines and Methyl-phosphonate Oligonucleotides

A simple limonene-derived P(V)-based reagent for the modular, scalable, and stereospecific synthesis of chiral phosphines and methyl-phosphonate oligonucleotide (MPO) building blocks is presented. Built on a translimonene oxide (TLO) core, this formally triply electrophilic reagent class displays starkly differing reactivity from the cis-limonene oxide derived reagents reported previously [dubbed phosphorus-sulfur incorporation reagents or Ψ (PSI) for short]. These new phosphorus-incorporation reagents (PI, abbreviated as Π) access distinctly different chemical space than Ψ. The P(V)-manifold disclosed herein permits the stereochemically controlled sequential addition of carbon-based nucleophiles (from one to three) to produce a variety of enantiopure C–P bearing building blocks. When three carbon nucleophiles are added, useful P-chiral phosphines can be accessed after stereospecific reduction. When a single methyl group is added, the remaining nucleophiles can be nucleosides thus opening the door to the first stereospecific access to MPO-based oligonucleotide building blocks. Although both enantiomers of Π are available, only one isomer is required as the order of nucleophile addition controls the absolute stereochemistry of the final product through a unique enantiodivergent design.</p

Diverted Total Synthesis of Promysalin Analogs Demonstrates That an Iron-Binding Motif Is Responsible for Its Narrow-Spectrum Antibacterial Activity

Promysalin is a species-specific <i>Pseudomonad</i> metabolite with unique bioactivity. To better understand the mode of action of this natural product, we synthesized 16 analogs utilizing diverted total synthesis (DTS). Our analog studies revealed that the bioactivity of promysalin is sensitive to changes within its hydrogen bond network whereby alteration has drastic biological consequences. The DTS library not only yielded three analogs that retained potency but also provided insights that resulted in the identification of a previously unknown ability of promysalin to bind iron. These findings coupled with previous observations hint at a complex multifaceted role of the natural product within the rhizosphere

A P(V)-Platform for Oligonucleotide Synthesis

The early promise of gene-based therapies is currently being realized at an accelerated pace with over 155 active clinical trials for antisense compounds and multiple FDA-approved oligonucleotide therapeutics. Fundamental advances in this area are vital and present an unprecedented opportunity to both address disease states that have been resistant to other common modalities and improve the significant sustainability challenges associated with production of these complex molecules on a commercial scale. The advent of phosphoramidite coupling chemistry and solid-phase synthesis 40 years ago democratized oligonucleotide synthesis to the scientific community, paving the way for many of these stunning developments. The reliability and generality of this approach for the preparation of native phosphate-diesters is attributed to the high reactivity of phosphorus when in the P(III)-oxidation state versus the desired P(V), as it enables rapid P-heteroatom bond formation. However, the growing demand for more diverse phosphorus-based linkages has challenged the limits of this technology. For example, the phosphorothioate (PS) linkage, which stabilizes oligonucleotides towards nuclease cleavage, is universally employed in current oligonucleotide therapeutics but is generally incorporated in racemic form. Stereodefined PS oligonucleotides may have desirable biological and physical properties but are accessed with difficulty using phosphoramidite chemistry. Here we report a flexible and efficient [P(V)]-based platform that can install a wide variety of phosphate linkages at will into oligonucleotides. This approach uses readily accessible reagents and can efficiently install not only stereodefined or racemic thiophosphates, but can install any combination of (S, R or rac)-PS with native phosphodiester (PO2) and phosphorodithioate (PS2) linkages into DNA and other modified nucleotides. Importantly this platform easily accesses this diversity under a standardized coupling protocol with sustainably prepared, stable, P(V) reagents.</div

Electrochemically Driven, Ni-Catalyzed Aryl Amination: Scope, Mechanism, and Applications

C–N cross-coupling is one of the most valuable and widespread transformations in organic synthesis. Largely dominated by Pd- and Cu-based catalytic systems, it has proven to be a staple transformation for those in both academia and industry. The current study presents the development and mechanistic understanding of an electrochemically driven, Ni-catalyzed method for achieving this reaction of high strategic importance. Through a series of electrochemical, computational, kinetic, and empirical experiments the key mechanistic features of this reaction have been unraveled, leading to a second generation set of conditions that is applicable to a broad range of aryl halides and amine nucleophiles, including complex examples on oligopeptides, medicinally-relevant heterocycles, natural products, and sugars. Full disclosure of the current limitations as well as procedures for both batch and flow scale-ups (100 gram) are also described. </div

Phase 2 of extracellular RNA communication consortium charts next-generation approaches for extracellular RNA research.

The extracellular RNA communication consortium (ERCC) is an NIH-funded program aiming to promote the development of new technologies, resources, and knowledge about exRNAs and their carriers. After Phase 1 (2013-2018), Phase 2 of the program (ERCC2, 2019-2023) aims to fill critical gaps in knowledge and technology to enable rigorous and reproducible methods for separation and characterization of both bulk populations of exRNA carriers and single EVs. ERCC2 investigators are also developing new bioinformatic pipelines to promote data integration through the exRNA atlas database. ERCC2 has established several Working Groups (Resource Sharing, Reagent Development, Data Analysis and Coordination, Technology Development, nomenclature, and Scientific Outreach) to promote collaboration between ERCC2 members and the broader scientific community. We expect that ERCC2\u27s current and future achievements will significantly improve our understanding of exRNA biology and the development of accurate and efficient exRNA-based diagnostic, prognostic, and theranostic biomarker assays