Properties of phosphoramide benzoazole oligonucleotides (PABAOs). I. Structure and hybridization efficiency of N-benzimidazole derivatives.

In this work, we for the first time conducted a detailed study on the structure, dynamics, and hybridization properties of N-benzimidazole group-bearing phosphoramide benzoazole oligonucleotides (PABAOs) that we developed recently. By circular dichroism we established that the introduction of the modifications does not disrupt the B conformation of the DNA double helix. The formation of complexes is approximated by a two-state model. Complexes of PABAOs with native oligodeoxriboynucleotides form efficiently, and the introduction of such modifications reduces thermal stability of short duplexes (8-10 bp) by ∼5°Ð¡ per modification. Using UV-spectroscopy analysis, a neutral charge of the phosphate residue modified by the N-benzimidazole moiety in the pH range of 3-9.5 was found. The results confirm possible usefulness of PABAOs for both basic research and biomedical applications.

Phosphoramidate Azole Oligonucleotides for Single Nucleotide Polymorphism Detection by PCR.

Detection of the Kirsten rat sarcoma gene (KRAS) mutational status is an important factor for the treatment of various malignancies. The most common KRAS-activating mutations are caused by single-nucleotide mutations, which are usually determined by using PCR, using allele-specific DNA primers. Oligonucleotide primers with uncharged or partially charged internucleotide phosphate modification have proved their ability to increase the sensitivity and specificity of various single nucleotide mutation detection. To enhance the specificity of single nucleotide mutation detection, the novel oligonucleotides with four types of uncharged and partially charged internucleotide phosphates modification, phosphoramide benzoazole (PABA) oligonucleotides (PABAO), was used to prove the concept on the KRAS mutation model. The molecular effects of different types of site-specific PABA modification in a primer or a template on a synthesis of full-length elongation product and PCR efficiency were evaluated. The allele-specific PCR (AS-PCR) on plasmid templates showed a significant increase in analysis specificity without changes in Cq values compared with unmodified primer. PABA modification is a universal mismatch-like disturbance, which can be used for single nucleotide polymorphism discrimination for various applications. The molecular insights of the PABA site-specific modification in a primer and a template affect PCR, structural features of four types of PABAO in connection with AS-PCR results, and improvements of AS-PCR specificity support the further design of novel PCR platforms for various biological targets testing.

Towards next generation antisense oligonucleotides: mesylphosphoramidate modification improves therapeutic index and duration of effect of gapmer antisense oligonucleotides.

The PS modification enhances the nuclease stability and protein binding properties of gapmer antisense oligonucleotides (ASOs) and is one of very few modifications that support RNaseH1 activity. We evaluated the effect of introducing stereorandom and chiral mesyl-phosphoramidate (MsPA) linkages in the DNA gap and flanks of gapmer PS ASOs and characterized the effect of these linkages on RNA-binding, nuclease stability, protein binding, pro-inflammatory profile, antisense activity and toxicity in cells and in mice. We show that all PS linkages in a gapmer ASO can be replaced with MsPA without compromising chemical stability and RNA binding affinity but these designs reduced activity. However, replacing up to 5 PS in the gap with MsPA was well tolerated and replacing specific PS linkages at appropriate locations was able to greatly reduce both immune stimulation and cytotoxicity. The improved nuclease stability of MsPA over PS translated to significant improvement in the duration of ASO action in mice which was comparable to that of enhanced stabilized siRNA designs. Our work highlights the combination of PS and MsPA linkages as a next generation chemical platform for identifying ASO drugs with improved potency and therapeutic index, reduced pro-inflammatory effects and extended duration of effect.

Chlorophyll f can replace chlorophyll a in the soluble antenna of dinoflagellates.

Chlorophyll f is a new type of chlorophyll isolated from cyanobacteria. The absorption and fluorescence characteristics of chlorophyll f permit these oxygenic-photosynthetic organisms to thrive in environments where white light is scarce but far-red light is abundant. To explore the ligand properties of chlorophyll f and its energy transfer profiles we established two different in vitro reconstitution systems. The reconstituted peridinin-chlorophyll f protein complex (chlorophyll f-PCP) showed a stoichiometry ratio of 4:1 between peridinin and chlorophyll f, consistent with the peridinin:chlorophyll a ratio from native PCP complexes. Using emission wavelength at 712 nm, the excitation fluorescence featured a broad peak at 453 nm and a shoulder at 511 nm confirming energy transfer from peridinin to chlorophyll f. In addition, by using a synthetic peptide mimicking the first transmembrane helix of light-harvesting chlorophyll proteins of plants, we report that chlorophyll f, similarly to chlorophyll b, did not interact with the peptide contrarily to chlorophyll a, confirming the accessory role of chlorophyll f in photosystems. The binding of chlorophyll f, even in the presence of chlorophylls a and b, by PCP complexes shows the flexibility of chlorophyll-protein complexes and provides an opportunity for the introduction of new chlorophyll species to extend the photosynthetic spectral range.

New phosphoramides containing imidazolidine moiety as anticancer agents: An experimental and computational study.

In this study, two new phosphoramides containing imidazolidine; diphenyl (2-imidazolidinone-1-yl)phosphonate (DIOP) and diphenyl (2-Imidazolidinethione -1-yl)phosphonate (DITP) as cytotoxic agents, were synthesized and characterized by using IR, 1H NMR, 13C NMR, 31P NMR, Mass spectroscopy and elemental analysis. The target products were obtained in moderate to good yields (69-86%) by using the time (3 h) and solvent (MeCN). The crystal structure of DIOP was investigated using X-ray crystallography. The main non-covalent intermolecular interactions were also studied by Hirshfeld surface analysis and fingerprint plots. The anticancer and growth inhibitory activities of the synthesized compounds were investigated against human breast cancer cell line MDA-MB-231 using MTT assay; DITP was found to be a better cytotoxic agent than DIOP. The cytotoxicity results were supported by a molecular docking study and in order to know the structure-activity relationship (SAR) of synthesized compounds, the values of HOMO and LUMO energies, dipole moments, hardness, softness, and electrophilicity index were investigated computationally by DFT method. These results were in good accordance with those of in vitro investigation and molecular docking study.

Enantioseparation and dissipation of acephate and its highly toxic metabolite methamidophos in pakchoi by supercritical fluid chromatography tandem mass spectrometry.

Acephate is widely used in crops as racemate. However, the enantioselective dissipation of acephate enantiomers has not been investigated in pakchoi. A sensitive and effective approach was established for determining residues of acephate and its highly toxic metabolite methamidophos enantiomers by supercritical fluid chromatography tandem mass spectrometry. Baseline separations for their enantiomers were achieved by using a Chiralcel OD-H column. The optimal chromatographic conditions were obtained as follows: CO2 /ethanol (95/5) as mobile phase; flow rate, 3.0 mL/min; column temperature, 40°C. The mean recoveries (RSDs) of analytes were in the range of 77-83.1% (6.1-9.9%), 75.4-87.5% (9.3-13.2%), and 81.5-84.2% (7.1-13.4%) at three fortification levels (0.005, 0.05, and 0.5 mg/kg for each enantiomer) for interday assay (n = 18). The method was used to evaluate the enantioselective dissipation of acephate and methamidophos in pakchoi. S-acephate dissipated faster than R-acephate, while the concentration of R-methamidophos was higher than that of S-methamidophos during the entire study period. The results indicated that the R-enantiomer of acephate and methamidophos was preferentially enriched in pakchoi. The established analysis approach and the study data provided useful information for the rational use of acephate in agriculture.

Hazard Assessment of the Effects of Acute and Chronic Exposure to Permethrin, Copper Hydroxide, Acephate, and Validamycin Nanopesticides on the Physiology of Drosophila: Novel Insights into the Cellular Internalization and Biological Effects.

New insights into the interactions between nanopesticides and edible plants are required in order to elucidate their impacts on human health and agriculture. Nanopesticides include formulations consisting of organic/inorganic nanoparticles. Drosophila melanogaster has become a powerful model in genetic research thanks to its genetic similarity to mammals. This project mainly aimed to generate new evidence for the toxic/genotoxic properties of different nanopesticides (a nanoemulsion (permethrin nanopesticides, 20 ± 5 nm), an inorganic nanoparticle as an active ingredient (copper(II) hydroxide [Cu(OH)2] nanopesticides, 15 ± 6 nm), a polymer-based nanopesticide (acephate nanopesticides, 55 ± 25 nm), and an inorganic nanoparticle associated with an organic active ingredient (validamycin nanopesticides, 1177 ± 220 nm)) and their microparticulate forms (i.e., permethrin, copper(II) sulfate pentahydrate (CuSO4·5H2O), acephate, and validamycin) widely used against agricultural pests, while also showing the merits of using Drosophila-a non-target in vivo eukaryotic model organism-in nanogenotoxicology studies. Significant biological effects were noted at the highest doses of permethrin (0.06 and 0.1 mM), permethrin nanopesticides (1 and 2.5 mM), CuSO4·5H2O (1 and 5 mM), acephate and acephate nanopesticides (1 and 5 mM, respectively), and validamycin and validamycin nanopesticides (1 and 2.5 mM, respectively). The results demonstrating the toxic/genotoxic potential of these nanopesticides through their impact on cellular internalization and gene expression represent significant contributions to future nanogenotoxicology studies.

AT-527, a Double Prodrug of a Guanosine Nucleotide Analog, Is a Potent Inhibitor of SARS-CoV-2 In Vitro and a Promising Oral Antiviral for Treatment of COVID-19.

The impact of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the causative agent of COVID-19, is global and unprecedented. Although remdesivir has recently been approved by the FDA to treat SARS-CoV-2 infection, no oral antiviral is available for outpatient treatment. AT-527, an orally administered double prodrug of a guanosine nucleotide analog, was previously shown to be highly efficacious and well tolerated in hepatitis C virus (HCV)-infected subjects. Here, we report the potent in vitro activity of AT-511, the free base of AT-527, against several coronaviruses, including SARS-CoV-2. In normal human airway epithelial cells, the concentration of AT-511 required to inhibit replication of SARS-CoV-2 by 90% (EC90) was 0.47 µM, very similar to its EC90 against human coronavirus (HCoV)-229E, HCoV-OC43, and SARS-CoV in Huh-7 cells. Little to no cytotoxicity was observed for AT-511 at concentrations up to 100 µM. Substantial levels of the active triphosphate metabolite AT-9010 were formed in normal human bronchial and nasal epithelial cells incubated with 10 µM AT-511 (698 ± 15 and 236 ± 14 µM, respectively), with a half-life of at least 38 h. Results from steady-state pharmacokinetic and tissue distribution studies of nonhuman primates administered oral doses of AT-527, as well as pharmacokinetic data from subjects given daily oral doses of AT-527, predict that twice daily oral doses of 550 mg AT-527 will produce AT-9010 trough concentrations in human lung that exceed the EC90 observed for the prodrug against SARS-CoV-2 replication. This suggests that AT-527 may be an effective treatment option for COVID-19.

Synthesis, characterization, cytotoxicity studies, theoretical approach of adsorptive removal and molecular calculations of four new phosphoramide derivatives and related graphene oxide.

In this study, four novel phosphoramide ligands (L1-L4) are synthesized and characterized by 31PNMR, 1HNMR, MASS, and FT-IR spectroscopies. In vitro cell growth inhibition is studied by the MTT assay to evaluate the cytotoxicity of ligands against MCF-7 cell line; the result of the assay demonstrates that all ligands significantly suppress the proliferation of breast cancer cells in a concentration-dependent manner. The calculated IC50 values are in the range of 3.6-10.77 µg ml-1, of which the lowest value is attributed to L1. Then a facile approach was developed to functionalize graphene oxide (GO) surface by L1. The data which are obtained by XRD, FT-IR, and EDX analysis confirmed the deposition of phosphoramide on the surface of GO. The cell viability of GO-L1 compound at different concentrations is investigated in 24 h experiment. Excellent synergistic antitumor effects of GO and L1 lead to a decrease in IC50 value up to 2.13 µg ml-1. The Quantum calculations of compounds are used to study energies and HOMO and LUMO values, dipole moments (µ), global hardness (η), global softness (σ), and electrophilicity index (ω) using DMol3 module in Material studio2017. The docking calculations are performed to describe the mode of the binding to DNA and DNA polymerase IIα. Adsorption calculations of ligands (L1-L4) on GO sheet in the presence of water showed that L1 and L2 were located on GO via π electrons of anisole ring. While, L3 and L4 were located on GO by π - π interactions of aniline ring.

The Role of Brain Methamidophos in Acephate Poisoning in Mice.

We gave mice a 540 mg/kg dose of LD50 acephate, followed by an assessment of acephate, methamidophos (MP), and choline esterase (ChE) activity for up to 4 hours (hr) in order to investigate the time course of acephate intoxication. At 1 hr, the blood acephate and MP levels were 428 ± 90 µg/ml (mean ± SEM) and 4.2 ± 0.4 µg/ ml, respectively. The liver acephate levels were similar to those in the blood, but the liver MP levels were approximately 3.5 times that of the blood at 1 hr. The brain MP level tended to be higher than the blood MP at 1 hr. These levels decreased gradually over 4 hr, but the brain acephate and MP levels surpassed the blood levels significantly at 4 hr, and after 2 hr, respectively. Serum, liver, cerebrum, cerebellum, and brainstem cholinesterase activity (ChE) were inhibited at 1 hr, and remained inhibited in all but the cerebellum until the end of the experiment. The obtained data were applied to previously reported autopsy cases of acephate intake. Experimental data suggest that brain MP is involved in acute acephate-induced poisoning, even after a reduction in blood acephate. In autopsy cases with suspected acephate poisoning, the MP level in the brain should be considered in addition to the ChE activity to diagnose the cause of death.

JNJ-4178 (AL-335, Odalasvir, and Simeprevir) for 6 or 8 Weeks in Hepatitis C Virus-Infected Patients Without Cirrhosis: OMEGA-1.

The combination of three direct-acting antiviral agents (AL-335, odalasvir, and simeprevir: JNJ-4178 regimen) for 6 or 8 weeks demonstrated good efficacy and safety in a phase IIa study in chronic hepatitis C virus (HCV) genotype (GT)-1-infected patients without cirrhosis and has now been evaluated in a larger phase IIb study, OMEGA-1. This multicenter, randomized, open-label study (NCT02765490) enrolled treatment-naïve and interferon (±ribavirin) treatment-experienced patients with HCV GT1, 2, 4, 5, or 6 infection. Patients with HCV GT3 infection and/or liver cirrhosis were excluded. Patients received AL-335 800 mg, odalasvir 25 mg, and simeprevir 75 mg once daily for 6 or 8 weeks. The primary endpoint was sustained virologic response 12 weeks after the end of treatment (SVR12). In total, 365 patients (GT1a, 29.3%; GT1b, 42.5%; GT2, 12.3%; GT4, 14.2%; GT5, 1.4%; GT6, 0%) were randomized to receive 6 weeks (n = 183) or 8 weeks (n = 182) of treatment. SVR12 rates after 6 weeks (98.9%) or 8 weeks (97.8%) of treatment were noninferior to a historical control (98%). Viral relapse occurred in 5 patients (1.4%; 4 with HCV GT2c; 1 with GT1a). With the exception of 4 patients in the 8-week group, including 3 patients with missing data at the SVR24 timepoint, all patients who achieved SVR12 also achieved SVR24. One GT1a-infected patient experienced late viral relapse after achieving SVR18. Most adverse events (AEs) were mild with no treatment-related serious AEs. All randomized patients completed treatment. Conclusion: In HCV-infected patients, 6 and 8 weeks of treatment with JNJ-4178 resulted in SVR12 rates of 98.9% and 97.8%, respectively, and was well tolerated.

Biodegradation of acephate by Bacillus paramycoides NDZ and its degradation pathway.

Acephate is widely used in agriculture, but its poisonous metabolites and poor sorption characteristics make it a serious environmental pollutant and toxicant to human health. To screen novel bacteria for biodegradation of acephate and uncover its degradation pathway, a strain called NDZ that is capable of utilizing acephate as a sole carbon and energy source was isolated from severely contaminated cultivated land. The bacterium was identified as Bacillus paramycoides based on 16S rDNA sequence analyses. The growth and degradation capacities of B. paramycoides NDZ under different conditions were studied using optical density at 600 nm (OD600) and high-performance liquid chromatography (HPLC). The results showed that B. paramycoides NDZ can grow well with acephate as its sole carbon source (OD600 = 0.76), and degraded about 76% of acephate in mineral salt medium with an initial concentration of 500 mg/L within 48 h. The results of response surface methodology revealed the optimal conditions for degradation was 36 ℃ and pH 6.85 with 526 mg/L acephate. Gas chromatography-mass spectrometry showed that methamidophos was the main metabolite of B. paramycoides NDZ, different from the degradation products of high-temperature steam (121 °C, 103 kPa). Based on the detection of this intermediate, we inferred that acephate was degraded to methamidophos through hydrolysis of the amide linkage, after which methamidophos was degraded to some small molecules, which can be metabolized easily by the bacterium. In summary, B. paramycoides NDZ is a potentially useful bacterium for acephate degradation and remediation of contaminated soils.

Qualitative enzymatic detection of organophosphate and carbamate insecticides.

In this study, new polymers containing amides (TrisPS-Ntaa, and TrisPS-Ntaa-Fc) were synthesized by condensation reaction for qualitative identification of insecticides. The synthesized polymers, including amides were investigated by infrared spectroscopy (IR), scanning electron microscopy-energy dispersion X- ray spectrometry (SEM-EDX), and gel permeation chromatography (GPC). Then, acetylcholinesterase enzyme (AChE) was covalently immobilized on these polymers to improve properties (including activity, reusability, and storage stability). Accordingly, organophosphate (malathion, acephate, chlorpyrifos methyl) and carbamate (carbofuran, methiocarb, methomyl), which are used to prevent harmful organisms in some agricultural products were enzymatically determined based on their inhibitory activity on AChE.

Cu-Catalyzed Diastereo- and Enantioselective Reactions of γ,γ-Disubstituted Allyldiboron Compounds with Ketones.

A catalytic diastereo- and enantioselective method for the preparation of complex tertiary homoallylic alcohols containing a vicinal quaternary carbon stereogenic center and a versatile alkenylboronic ester is disclosed. Transformations are promoted by 5 mol % of a readily available copper catalyst bearing a bulky monodentate phosphoramidite ligand, which is essential for attaining both high dr and er. Reactions proceed with a wide variety of ketones and allylic 1,1-diboronate reagents, which enables the efficient preparation of diverse array of molecular scaffolds.

A high-specificity immunoassay for the therapeutic drug monitoring of cyclophosphamide.

Personalized medicine is pushing forward new diagnostic techniques to aid in controlling drug therapeutic levels and their toxic effects. This study aims to develop a high-throughput screening method for therapeutic drug monitoring (TDM) and occupational exposure of cyclophosphamide (CP), an alkylating agent used as a chemotherapeutic and immunosuppressive drug. In order to achieve this goal, an immunizing hapten that exposes the cyclophosphamide moiety has been designed for the first time. Antibodies produced against this hapten have been used to develop an indirect competitive ELISA for the quantification of CP with high specificity and low cross-reactivity with some metabolites and other anticancer drugs. The assay obtained showed a LOD of 22 ± 6 nM in serum samples, with concentrations much below the blood CP levels of patients treated with the drug. A new tool for the detection and quantification of CP is provided which could be relevant for future pharmacokinetic studies and for therapeutic index improvement.

Synthesis, crystal structure and biological evaluation of new phosphoramide derivatives as urease inhibitors using docking, QSAR and kinetic studies.

In an attempt to achieve a new class of phosphoramide inhibitors with high potency and resistance to the hydrolysis process against urease enzyme, we synthesized a series of bisphosphoramide derivatives (01-43) and characterized them by various spectroscopic techniques. The crystal structures of compounds 22 and 26 were investigated using X-ray crystallography. The inhibitory activities of the compounds were evaluated against the jack bean urease and were compared to monophosphoramide derivatives and other known standard inhibitors. The compounds containing aromatic amines and their substituted derivatives exhibited very high inhibitory activity in the range of IC50 = 3.4-1.91 × 10-10 nM compared with monophosphoramides, thiourea, and acetohydroxamic acid. It was also found that derivatives with PO functional groups have higher anti-urease activity than those with PS functional groups. Kinetics and docking studies were carried out to explore the binding mechanism that showed these compounds follow a mixed-type mechanism and, due to their extended structures, can cover the entire binding pocket of the enzyme, reducing the formation of the enzyme-substrate complex. The quantitative structure-activity relationship (QSAR) analysis also revealed that the interaction between the enzyme and inhibitor is significantly influenced by aromatic rings and PO functional groups. Collectively, the data obtained from experimental and theoretical studies indicated that these compounds can be developed as appropriate candidates for urease inhibitors in this field.

In Silico Study of the Resistance to Organophosphorus Pesticides Associated with Point Mutations in Acetylcholinesterase of Lepidoptera: B. mandarina, B. mori, C. auricilius, C. suppressalis, C. pomonella, H. armígera, P. xylostella, S. frugiperda, and S. litura.

An in silico analysis of the interaction between the complex-ligands of nine acetylcholinesterase (AChE) structures of Lepidopteran organisms and 43 organophosphorus (OPs) pesticides with previous resistance reports was carried out. To predict the potential resistance by structural modifications in Lepidoptera insects, due to proposed point mutations in AChE, a broad analysis was performed using computational tools, such as homology modeling and molecular docking. Two relevant findings were revealed: (1) Docking results give a configuration of the most probable spatial orientation of two interacting molecules (AChE enzyme and OP pesticide) and (2) a predicted ΔGb. The mutations evaluated in the form 1 acetylcholinesterase (AChE-1) and form 2 acetylcholinesterase (AChE-2) structures of enzymes do not affect in any way (there is no regularity of change or significant deviations) the values of the binding energy (ΔGb) recorded in the AChE-OPs complexes. However, the mutations analyzed in AChE are associated with a structural modification that causes an inadequate interaction to complete the phosphorylation of the enzyme.

Synthesis and biological evaluation of 6-substituted-5-fluorouridine ProTides.

A new family of thirteen phosphoramidate prodrugs (ProTides) of different 6-substituted-5-fluorouridine nucleoside analogues were synthesized and evaluated as potential anticancer agents. In addition, antiviral activity against Chikungunya (CHIKV) virus was evaluated using a cytopathic effect inhibition assay. Although a carboxypeptidase Y assay supported a putative mechanism of activation of ProTides built on 5-fluorouridine with such C6-modifications, the Hint docking studies revealed a compromised substrate-activity for the Hint phosphoramidase-type enzyme that is likely responsible for phosphoramidate bioactivation through P-N bond cleavage and free nucleoside 5'-monophosphate delivery. Our observations may support and explain to some extent the poor in vitro biological activity generally demonstrated by the series of 6-substituted-5-fluorouridine phosphoramidates (ProTides) and will be of guidance for the design of novel phosphoramidate prodrugs.

Novel Chiral Bis-Phosphoramides as Organocatalysts for Tetrachlorosilane-Mediated Reactions.

The formation of novel chiral bidentate phosphoroamides structures able to promote Lewis base-catalyzed Lewis acid-mediated reactions was investigated. Two different classes of phosphoroamides were synthetized: the first class presents a phthalic acid/primary diamine moiety, designed with the aim to perform a self-assembly recognition process through hydrogen bonds; the second one is characterized by the presence of two phosphoroamides as side arms connected to a central pyridine unit, able to chelate SiCl4 in a 2:1 adduct. These species were tested as organocatalysts in the stereoselective allylation of benzaldehyde and a few other aromatic aldehydes with allyl tributyltin in the presence of SiCl4 with good results. NMR studies confirm that only pyridine-based phosphoroamides effectively coordinate tetrachlorosilane and may lead to the generation of a self-assembled entity that would act as a promoter of the reaction. Although further work is necessary to clarify and confirm the formation of the hypothesized adduct, the study lays the foundation for the design and the synthesis of chiral supramolecular organocatalysts.

Metal-Based PSMA Radioligands.

Prostate cancer is one of the most common malignancies for which great progress has been made in identifying appropriate molecular targets that would enable efficient in vivo targeting for imaging and therapy. The type II integral membrane protein, prostate specific membrane antigen (PSMA) is overexpressed on prostate cancer cells in proportion to the stage and grade of the tumor progression, especially in androgen-independent, advanced and metastatic disease, rendering it a promising diagnostic and/or therapeutic target. From the perspective of nuclear medicine, PSMA-based radioligands may significantly impact the management of patients who suffer from prostate cancer. For that purpose, chelating-based PSMA-specific ligands have been labeled with various diagnostic and/or therapeutic radiometals for single-photon-emission tomography (SPECT), positron-emission-tomography (PET), radionuclide targeted therapy as well as intraoperative applications. This review focuses on the development and further applications of metal-based PSMA radioligands.