Site-Specific Activity-Based Protein Profiling Using Phosphonate Handles.

Most drug molecules target proteins. Identification of the exact drug binding sites on these proteins is essential to understand and predict how drugs affect protein structure and function. To address this challenge, we developed a strategy that uses immobilized metal-affinity chromatography-enrichable phosphonate affinity tags, for efficient and selective enrichment of peptides bound to an activity-based probe, enabling the identification of the exact drug binding site. As a proof of concept, using this approach, termed PhosID-ABPP (activity-based protein profiling), over 500 unique binding sites were reproducibly identified of an alkynylated afatinib derivative (PF-06672131). As PhosID-ABPP is compatible with intact cell inhibitor treatment, we investigated the quantitative differences in approachable binding sites in intact cells and in lysates of the same cell line and observed and quantified substantial differences. Moreover, an alternative protease digestion approach was used to capture the previously reported binding site on the epidermal growth factor receptor, which turned out to remain elusive when using solely trypsin as protease. Overall, we find that PhosID-ABPP is highly complementary to biotin-based enrichment strategies in ABPP studies, with PhosID-ABPP providing the advantage of direct activity-based probe interaction site identification.

Phosphonate production by marine microbes: Exploring new sources and potential function.

SignificancePhosphonates are a class of phosphorus metabolites characterized by a highly stable C-P bond. Phosphonates accumulate to high concentrations in seawater, fuel a large fraction of marine methane production, and serve as a source of phosphorus to microbes inhabiting nutrient-limited regions of the oligotrophic ocean. Here, we show that 15% of all bacterioplankton in the surface ocean have genes phosphonate synthesis and that most belong to the abundant groups Prochlorococcus and SAR11. Genomic and chemical evidence suggests that phosphonates are incorporated into cell-surface phosphonoglycoproteins that may act to mitigate cell mortality by grazing and viral lysis. These results underscore the large global biogeochemical impact of relatively rare but highly expressed traits in numerically abundant groups of marine bacteria.

Ultra-Microporous Fe-MOF with Prolonged NO Delivery in Biological Media for Therapeutic Application.

Nitric oxide (NO), a key element in the regulation of essential biological mechanisms, presents huge potential as therapeutic agent in the treatment and prevention of chronic diseases. Metal-organic frameworks (MOFs) with open metal sites are promising carriers for NO therapies but delivering it over an extended period in biological media remains a great challenge due to i) a fast degradation of the material in body fluids and/or ii) a rapid replacement of NO by water molecules onto the Lewis acid sites. Here, a new ultra-narrow pores Fe bisphosphonate MOF, denoted MIP-210(Fe) or Fe(H2O)(Hmbpa) (H4mbpa = p-xylenediphosphonic acid) is described that adsorbs NO due to an unprecedented sorption mechanism: coordination of NO through the Fe(III) sites is unusually preferred, replacing bound water, and creating a stable interaction with the free H2O and P-OH groups delimiting the ultra-narrow pores. This, associated with the high chemical stability of the MOF in body fluids, enables an unprecedented slow replacement of NO by water molecules in biological media, achieving an extraordinarily extended NO delivery time over at least 70 h, exceeding by far the NO kinetics release reported with others porous materials, paving the way for the development of safe and successful gas therapies.

Impact of Single Acyclic Phosphonate Nucleotide (ZNA) Modifications on DNA Duplex Stability.

An acyclic phosphonate-linked nucleic acid backbone (ZNA) demonstrated the capability to support duplex formation and propagate genetic information in vivo, unveiling its potential for evolution into a synthetic genetic system (XNA). To determine the structural impact of such modification, modified Dickerson Drew DNA dodecamers (DDDs) were prepared by solid phase synthesis, each containing either an (R) or (S) isomeric form of a cytosine ZNA nucleotide. While the DDD is known to adopt a stable duplex, both duplex and hairpin forms were simultaneously observed for both modified oligonucleotides by NMR spectroscopy over a broad temperature range (5-65 °C). Diffusion-ordered spectroscopy (DOSY) experiments allowed to separate duplex and hairpin signals based on the different diffusion constants of both conformational states. For the oligomer containing (R)-ZNA, only the duplex form occurred at 5 °C, while it was not possible to determine by NMR a single hairpin conformation at higher temperatures. In the case of the (S)-ZNA nucleoside modified oligomer, both hairpin and duplex forms were observable at 0 °C, while a single hairpin conformation was detected at 37 °C, suggesting a higher destabilizing effect on dsDNA.

Peptide mixed phosphonates for covalent complex formation with thioesterases in nonribosomal peptide synthetases.

Natural macrocyclic peptides derived from microorganisms are medicinal resources that are important for the development of new therapeutic agents. Most of these molecules are biosynthesized by a nonribosomal peptide synthetase (NRPS). The thioesterase (TE) domain in NRPS is responsible for the macrocyclization of mature linear peptide thioesters in a final biosynthetic step. NRPS-TEs can cyclize synthetic linear peptide analogs and can be utilized as biocatalysts for the preparation of natural product derivatives. Although the structures and enzymatic activities of TEs have been investigated, the substrate recognition and substrate-TE interaction during the macrocyclization step are still unknown. To understand the TE-mediated macrocyclization, here we report the development of a substrate-based analog with mixed phosphonate warheads, which can react irreversibly with the Ser residue at the active site of TE. We have demonstrated that the tyrocidine A linear peptide (TLP) with a p-nitrophenyl phosphonate (PNP) enables efficient complex formation with tyrocidine synthetase C (TycC)-TE containing tyrocidine synthetase.

Biosynthesis of fosfomycin in pseudomonads reveals an unexpected enzymatic activity in the metallohydrolase superfamily.

The epoxide-containing phosphonate natural product fosfomycin is a broad-spectrum antibiotic used in the treatment of cystitis. Fosfomycin is produced by both the plant pathogen Pseudomonas syringae and soil-dwelling streptomycetes. While the streptomycete pathway has recently been fully elucidated, the pseudomonad pathway is still mostly elusive. Through a systematic evaluation of heterologous expression of putative biosynthetic enzymes, we identified the central enzyme responsible for completing the biosynthetic pathway in pseudomonads. The missing transformation involves the oxidative decarboxylation of the intermediate 2-phosphonomethylmalate to a new intermediate, 3-oxo-4-phosphonobutanoate, by PsfC. Crystallographic studies reveal that PsfC unexpectedly belongs to a new class of diiron metalloenzymes that are part of the polymerase and histidinol phosphatase superfamily.

Adsorptive stripping voltammetric sensor based on Cd zeolitic imidazole framework-67 for electrochemical detection of sarin simulant.

A selective and reliable modified glassy carbon sensor, based on a 1.0% Cd zeolitic imidazole framework-67 modified glassy carbon sensor (GCS2), has been developed for ultrasensitive detection of dimethyl methyl phosphonate (DMMP) in human biological fluid. The synthesis of porous nanoparticles of Cd zeolitic imidazole framework-67 (Cd ZIF-67) was carried out via the hydrothermal method. The resulting Cd ZIF-67 powder emerges with good crystallinity, a rhombic dodecahedral morphology with particle size in the range 300 ~ 500 nm, and a specific surface area of 1780 m2·g-1. Furthermore, the fabricated sensor exhibited superior performance in the detection of DMMP with two linearity ranges of 0.02-2.0 nM and 2.0-9.0 nM and a limit of detection (LOD) of 0.06 pM. The fabricated sensor exhibited good reliability, long-term stability, and repeatability, which are favourable attributes for electroanalytical detection. In addition, the fabricated sensor displayed superior performance without significant interference during the assay of DMMP in a biological fluid (human serum sample) within two linearity ranges of 0.1-1.0 nM and 1.0-6.0 nM and a LOD of 0.03 nM.

A Novel Organic Phosphonate Additive Induced Stable and Efficient Perovskite Solar Cells with Efficiency over 24% Enabled by Synergetic Crystallization Promotion and Defect Passivation.

Defect passivation is crucial to enhancing the performance of perovskite solar cells (PSCs). In this study, we successfully synthesized a novel organic compound named DPPO, which consists of a double phosphonate group. Subsequently, we incorporated DPPO into a perovskite solution. The presence of a P═O group interacting with undercoordinated Pb2+ yielded a perovskite film of superior crystallinity, greater crystal orientation, and smoother surface. Additionally, the addition of DPPO can passivate defect states and enhance upper layer energy level alignment, which will improve carrier extraction and prevent nonradiative recombination. Consequently, an impressive champion efficiency of 24.24% was achieved with a minimized hysteresis. Furthermore, the DPPO-modified PSCs exhibit enhanced durability when exposed to ambient conditions, maintaining 95% of the initial efficiency for 1920 h at an average relative humidity (RH) of 30%.

Gold and Silver Nanoparticles as Biosensors: Characterization of Surface and Changes in the Adsorption of Leucine Dipeptide under the Influence of Substituent Changes.

Early detection of diseases can increase the chances of successful treatment and survival. Therefore, it is necessary to develop a method for detecting or sensing biomolecules that cause trouble in living organisms. Disease sensors should possess specific properties, such as selectivity, reproducibility, stability, sensitivity, and morphology, for their routine application in medical diagnosis and treatment. This work focuses on biosensors in the form of surface-functionalized gold (AuNPs) and silver nanoparticles (AgNPs) prepared using a less-time-consuming, inexpensive, and efficient synthesis route. This allows for the production of highly pure and stable (non-aggregating without stabilizers) nanoparticles with a well-defined spherical shape, a desired diameter, and a monodisperse distribution in an aqueous environment, as confirmed by transmission electron microscopy with energy-dispersive X-ray spectroscopy (TEM-EDS), X-ray diffraction (XRD), photoelectron spectroscopy (XPS), ultraviolet-visible (UV-VIS) spectroscopy, and dynamic light scattering (DLS). Thus, these nanoparticles can be used routinely as biomarker sensors and drug-delivery platforms for precision medicine treatment. The NPs' surface was coated with phosphonate dipeptides of L-leucine (Leu; l-Leu-C(R1)(R2)PO3H2), and their adsorption was monitored using SERS. Reproducible spectra were analyzed to determine the orientation of the dipeptides (coating layers) on the nanoparticles' surface. The appropriate R2 side chain of the dipeptide can be selected to control the arrangement of these dipeptides. This allows for the proper formation of a layer covering the nanoparticles while also simultaneously interacting with the surrounding biological environment, such as cells, tissues, and biological fluids.

Functionalizing Thiosemicarbazones for Covalent Conjugation.

Thiosemicarbazones (TSCs) with their modular character (thiosemicarbazides + carbonyl compound) allow broad variation of up to four substituents on the main R1R2C=N(1)-NH-C(S)-N(4)R3R4 core and are thus interesting tools for the formation of conjugates or the functionalization of nanoparticles (NPs). In this work, di-2-pyridyl ketone was introduced for the coordination of metals and 9-anthraldehyde for luminescence as R1 and R2 to TSCs. R3 and R4 substituents were varied for the formation of conjugates. Amino acids were introduced at the N4 position to produce [R1R2TSC-spacer-amino acid] conjugates. Further, functions such as phosphonic acid (R-P(O)(OH)2), D-glucose, o-hydroquinone, OH, and thiol (SH) were introduced at the N4 position producing [R1R2TSC-spacer-anchor group] conjugates for direct NP anchoring. Phenyl, cyclohexyl, benzyl, ethyl and methyl were used as spacer units. Both phenyl phosphonic acid TSC derivatives were bound on TiO2 NPs as a first example of direct NP anchoring. [R1R2TSC-spacer-end group] conjugates including OH, S-Bn (Bn = benzyl), NH-Boc (Boc = tert-butyloxycarbonyl), COOtBu, C≡CH, or N3 end groups were synthesized for potential covalent binding to functional molecules or functionalized NPs through amide, ester, or triazole functions. The synthesis of the thiosemicarbazides H2NNH-C(S)-NR3R4 starting from amines, including amino acids, SCCl2 or CS2, and hydrazine and their condensation with dipyridyl ketone and anthraldehyde led to 34 new TSC derivatives. They were synthesized in up to six steps with overall yields ranging from 10 to 85% and were characterized by a combination of nuclear magnetic resonance spectroscopy and mass spectrometry. UV-vis absorption and photoluminescence spectroscopy allowed us to easily trace the dipyridyl imine and anthracene chromophores.