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1.
Eur Rev Med Pharmacol Sci ; 28(8): 3268-3274, 2024 Apr.
Article En | MEDLINE | ID: mdl-38708485

BACKGROUND: We describe the first case of a pediatric patient with acute intermittent porphyria and severe chronic porphyric neuropathy treated with givosiran, a small-interfering RNA that drastically decreases delta-aminolevulinic acid production and reduces porphyric attacks' recurrence. CASE REPORT: A 12-year-old male patient with refractory acute intermittent porphyria and severe porphyric neuropathy was followed prospectively for 12 months after givosiran initiation (subcutaneous, 2.5 mg/kg monthly). Serial neurological, structural, and resting-state functional magnetic resonance imaging (MRI) evaluations were performed, including clinical scales and neurophysiological tests. Delta-aminolevulinic acid urinary levels dropped drastically during treatment. In parallel, all the administered neurological rating scales and neurophysiological assessments showed improvement in all domains. Moreover, an improvement in central motor conduction parameters and resting-state functional connectivity in the sensory-motor network was noticed. At the end of the follow-up, the patient could walk unaided after using a wheelchair for 5 years. CONCLUSIONS: A clear beneficial effect of givosiran was demonstrated in our patient with both clinical and peripheral nerve neurophysiologic outcome measures. Moreover, we first reported a potential role of givosiran in recovering central motor network impairment in acute intermittent porphyria (AIP), which was previously unknown. This study provides Class IV evidence that givosiran improves chronic porphyric neuropathy.


Acetylgalactosamine/analogs & derivatives , Porphyria, Acute Intermittent , Humans , Male , Porphyria, Acute Intermittent/drug therapy , Child , Acetylgalactosamine/therapeutic use , Aminolevulinic Acid/analogs & derivatives , Aminolevulinic Acid/urine , Magnetic Resonance Imaging , Pyrrolidines/therapeutic use , Uridine/analogs & derivatives , Uridine/therapeutic use , Uridine/administration & dosage , Recovery of Function , Chronic Disease , Treatment Outcome
2.
J Agric Food Chem ; 72(20): 11405-11414, 2024 May 22.
Article En | MEDLINE | ID: mdl-38717990

This study investigated the multiple herbicide resistance (MHR) mechanism of one Echinochloa crus-galli population that was resistant to florpyrauxifen-benzyl (FPB), cyhalofop-butyl (CHB), and penoxsulam (PEX). This population carried an Ala-122-Asn mutation in the acetolactate synthase (ALS) gene but no mutation in acetyl-CoA carboxylase (ACCase) and transport inhibitor response1 (TIR1) genes. The metabolism rate of PEX was 2-fold higher, and the production of florpyrauxifen-acid and cyhalofop-acid was lower in the resistant population. Malathion and 4-chloro-7-nitrobenzoxadiazole (NBD-Cl) could reverse the resistance, suggesting that cytochrome P450 (CYP450) and glutathione S-transferase (GST) contribute to the enhanced metabolism. According to RNA-seq and qRT-PCR validation, two CYP450 genes (CYP71C42 and CYP71D55), one GST gene (GSTT2), two glycosyltransferase genes (rhamnosyltransferase 1 and IAAGLU), and two ABC transporter genes (ABCG1 and ABCG25) were induced by CHB, FPB, and PEX in the resistant population. This study revealed that the target mutant and enhanced metabolism were involved in the MHR mechanism in E. crus-galli.


Cytochrome P-450 Enzyme System , Echinochloa , Herbicide Resistance , Herbicides , Mutation , Plant Proteins , Herbicide Resistance/genetics , Herbicides/pharmacology , Herbicides/metabolism , Echinochloa/genetics , Echinochloa/drug effects , Echinochloa/metabolism , Echinochloa/growth & development , Plant Proteins/genetics , Plant Proteins/metabolism , Cytochrome P-450 Enzyme System/genetics , Cytochrome P-450 Enzyme System/metabolism , Acetyl-CoA Carboxylase/genetics , Acetyl-CoA Carboxylase/metabolism , Plant Weeds/drug effects , Plant Weeds/genetics , Plant Weeds/metabolism , Acetolactate Synthase/genetics , Acetolactate Synthase/metabolism , Butanes , Nitriles , Sulfonamides , Uridine/analogs & derivatives
3.
Anal Chem ; 96(21): 8674-8681, 2024 May 28.
Article En | MEDLINE | ID: mdl-38712815

Messenger RNA (mRNA) can be sequenced via indirect approaches such as Sanger sequencing and next generation sequencing (NGS), or direct approaches like bottom-up mass spectrometry (MS). Direct sequencing allows the confirmation of RNA modifications. However, the conventional bottom-up MS approach involves time-consuming in-solution digestions that require a large amount of sample, and can lead to the RNase contamination of the LC-MS system and column. Here, we describe a platform that enables online nucleotide mapping of mRNAs via the use of immobilized RNase cartridges and 2D-LC-MS instrumentation. The online approach was compared to conventional offline digestion protocols adapted from two published studies. For this purpose, five model mRNAs of varying lengths (996-4521 nucleotides) and chemistries (unmodified uridine vs 5-methoxyuridine (5moU)) were analyzed. The profiles and sequence coverages obtained after RNase T1 digestion were discussed. The online nucleotide mapping achieved comparable or slightly greater sequence coverage for the 5 mRNAs (5.8-51.5%) in comparison to offline approaches (3.7-50.4%). The sequence coverage was increased to 65.6-85.6 and 69.7-85.0% when accounting for the presence of nonunique digestion products generated by the RNase T1 and A, respectively. The online nucleotide mapping significantly reduced the digestion time (from 15 to <5 min), increased the signal intensity by more than 10-fold in comparison to offline approaches.


RNA, Messenger , RNA, Messenger/analysis , RNA, Messenger/genetics , Nucleotide Mapping/methods , Mass Spectrometry , Chromatography, Liquid , Uridine/analogs & derivatives , Uridine/chemistry , Humans , Ribonuclease T1/metabolism
4.
Org Biomol Chem ; 22(22): 4568-4573, 2024 06 05.
Article En | MEDLINE | ID: mdl-38771639

Wavelength-shifting molecular beacons were prepared from L-DNA. The clickable anchor for the two dyes, Cy3 and Cy5, was 2'-O-propargyl-L-uridine and was synthesized from L-ribose. Four clickable molecular beacons were prepared and double-modified with the azide dyes by a combination of click chemistry on a solid support for Cy3 during DNA synthesis and postsynthetic click chemistry for Cy5 in solution. Cy3 and Cy5 successfully formed a FRET pair in the beacons, and the closed form (red fluorescence) and the open form (green fluorescence) can be distinguished by the two-color fluorescence readout. Two molecular beacons were identified to show the greatest fluorescence contrast in temperature-dependent fluorescence measurements. The stability of the L-configured molecular beacons was demonstrated after several heating and cooling cycles as well as in the cell lysate. In comparison, D-configured molecular beacons showed a rapid decrease of fluorescence contrast in the cell lysate, which is caused by the opening of the beacons, probably due to degradation. This was confirmed in cell experiments using confocal microscopy. The L-configured molecular beacons are potential intracellular thermometers for future applications.


Click Chemistry , DNA , Uridine , DNA/chemistry , Uridine/chemistry , Uridine/analogs & derivatives , Humans , Fluorescent Dyes/chemistry , Fluorescent Dyes/chemical synthesis , Fluorescence Resonance Energy Transfer , Carbocyanines/chemistry , Temperature
5.
Mol Biol Rep ; 51(1): 502, 2024 Apr 10.
Article En | MEDLINE | ID: mdl-38598020

BACKGROUND: Thyroid cancer, originating in the neck's thyroid gland, encompasses various types. Genetic mutations, particularly in BRAF and RET genes are crucial in its development. This study investigates the association between BRAF (rs113488022) and RET (rs77709286) polymorphisms and thyroid cancer risk in the Khyber Pakhtunkhwa (KP) population. METHODS: Blood samples from 100 thyroid cancer patients and 100 healthy controls were genotyped using ARMS-PCR followed by gel electrophoresis and statistical analysis. RESULTS: Analysis revealed a significant association between the minor allele T of BRAF (rs113488022) and thyroid cancer risk (P = 0.0001). Both genotypes of BRAF (rs113488022) showed significant associations with thyroid cancer risk (AT; P = 0.0012 and TT; P = 0.045). Conversely, the minor allele G of RET (rs77709286) exhibited a non-significant association with thyroid cancer risk (P = 0.2614), and neither genotype showed significant associations (CG; P = 0.317, GG; P = 0.651). Demographic and clinical parameters analysis using SPSS showed a non-significant association between BRAF and RET variants and age group (P = 0.878 and P = 0.536), gender (P = 0.587 and P = 0.21), tumor size (P = 0.796 and P = 0.765), or tumor localization (P = 0.689 and P = 0.727). CONCLUSION: In conclusion, this study emphasizes the significant association between BRAF polymorphism and thyroid cancer risk, while RET polymorphism showed a less pronounced impact. Further validation using larger and specific datasets is essential to establish conclusive results.


Proto-Oncogene Proteins B-raf , Sulfones , Thyroid Neoplasms , Uridine/analogs & derivatives , Humans , Proto-Oncogene Proteins B-raf/genetics , Thyroid Neoplasms/epidemiology , Thyroid Neoplasms/genetics , Alleles , Proto-Oncogene Proteins c-ret/genetics
6.
Biomed Res Int ; 2024: 5924799, 2024.
Article En | MEDLINE | ID: mdl-38590385

This study accessed the potential antimalarial activity of triterpene glycoside of H. atra through targeting orotidine 5-monophosphate decarboxylase protein (PfOMPDC) in P. falciparum by molecular docking. Nine triterpene glycosides from H. atra extract modeled the structure by the Corina web server and interacted with PfOMPDC protein by using Hex 8.0.0. The docking results were visualized and analyzed by Discovery Studio version 21.1.1. 17-Hydroxyfuscocineroside B showed the lowest binding energy in PfOMPDC interaction, which was -1,098.13 kJ/mol. Holothurin A3, echinoside A, and fuscocineroside C showed low binding energy. Nine triterpene glycosides of H. atra performed interaction with PfOMPDC protein at the same region. Holothurin A1 posed interaction with PfOMPDC protein by 8 hydrogen bonds, 3 hydrophobic interactions, and 8 unfavorable bonds. Several residues were detected in the same active sites of other triterpene glycosides. Residue TYR111 was identified in all triterpene glycoside complexes, except holothurin A3 and calcigeroside B. In summary, the triterpene glycoside of H. atra is potentially a drug candidate for malaria therapeutic agents. In vitro and in vivo studies were required for further investigation.


Carboxy-Lyases , Cardiac Glycosides , Triterpenes , Uridine/analogs & derivatives , Molecular Docking Simulation , Glycosides/chemistry , Triterpenes/chemistry
8.
Bioorg Chem ; 147: 107379, 2024 Jun.
Article En | MEDLINE | ID: mdl-38643567

Coronaviruses are a group of enveloped viruses with non-segmented, single-stranded, and positive-sense RNA genomes. It belongs to the 'Coronaviridae family', responsible for various diseases, including the common cold, SARS, and MERS. The COVID-19 pandemic, which began in March 2020, has affected 209 countries, infected over a million people, and claimed over 50,000 lives. Significant efforts have been made by repurposing several approved drugs including antiviral, to combat the COVID-19 pandemic. Molnupiravir is found to be the first orally acting efficacious drug to treat COVID-19 cases. It was approved for medical use in the UK in November 2021 and other countries, including USFDA, which granted approval an emergency use authorization (EUA) for treating adults with mild to moderate COVID-19 patients. Considering the importance of molnupiravir, the present review deals with its various synthetic strategies, pharmacokinetics, bio-efficacy, toxicity, and safety profiles. The comprehensive information along with critical analysis will be very handy for a wide range of audience including medicinal chemists in the arena of antiviral drug discovery especially anti-viral drugs against any variant of COVID-19.


Antiviral Agents , COVID-19 Drug Treatment , COVID-19 , Cytidine , Hydroxylamines , SARS-CoV-2 , Humans , Antiviral Agents/pharmacology , Antiviral Agents/chemistry , Antiviral Agents/therapeutic use , Antiviral Agents/chemical synthesis , Hydroxylamines/therapeutic use , Hydroxylamines/chemistry , Hydroxylamines/pharmacology , COVID-19/virology , SARS-CoV-2/drug effects , Cytidine/analogs & derivatives , Cytidine/therapeutic use , Cytidine/pharmacology , Cytidine/chemistry , Cytidine/chemical synthesis , Uridine/pharmacology , Uridine/analogs & derivatives , Uridine/chemical synthesis , Uridine/chemistry , Uridine/therapeutic use , Pandemics , Betacoronavirus/drug effects , Coronavirus Infections/drug therapy , Pneumonia, Viral/drug therapy
9.
Lancet Haematol ; 11(4): e276-e286, 2024 Apr.
Article En | MEDLINE | ID: mdl-38452788

BACKGROUND: Hypomethylating agents combined with venetoclax are effective regimens in patients with acute myeloid leukaemia who are ineligible for intensive chemotherapy. Decitabine and cedazuridine (ASTX727) is an oral formulation of decitabine that achieves equivalent area-under-curve exposure to intravenous decitabine. We performed a single centre phase 2 study to evaluate the efficacy and safety of ASTX727 plus venetoclax. METHODS: This study enrolled patients with newly diagnosed (frontline treatment group) acute myeloid leukaemia who were ineligible for intensive chemotherapy (aged ≥75 years, an Eastern Cooperative Oncology Group [ECOG] performance status of 2-3, or major comorbidities) or relapsed or refractory acute myeloid leukaemia. Being aged 18 years or older and having an ECOG performance status of 2 or less were requirements for the relapsed or refractory disease treatment cohort, without any limits in the number of previous lines of therapy. Treatment consisted of ASTX727 (cedazuridine 100 mg and decitabine 35 mg) orally for 5 days and venetoclax 400 mg orally for 21-28 days in 28-day cycles. The primary outcome was overall response rate of ASTX727 plus venetoclax. Living patients who have not completed cycle one were not evaluable for response. Safety was analysed in all patients who started treatment. This study was registered on ClinicalTrials.gov (NCT04746235) and is ongoing. The data cutoff date for this analysis was Sept 22, 2023. FINDINGS: Between March 16, 2021, and Sept 18, 2023, 62 patients were enrolled (49 frontline and 13 relapsed or refractory) with a median age of 78 years (IQR 73-82). 36 (58%) were male; 53 (85%) were White, 4 (6%) Black, 2 (3%) Asian and 3 (5%) other or did not answer. 48 (77%) of 62 patients were European LeukemiaNet 2022 adverse risk, 24 (39%) had antecedent myelodysplastic syndromes, 12 (19%) had previously failed a hypomethylating agent, ten (16%) had therapy-related acute myeloid leukaemia, and 11 (18%) had TP53 mutations. The median follow-up time was 18·3 months (IQR 8·8-23·3). The overall response rate was 30 (64%) of 47 patients (95% CI 49-77) in frontline cohort and six (46%) of 13 patients (19-75) in relapsed or refractory cohort. The most common grade 3 or worse treatment-emergent adverse events were febrile neutropenia in 11 (18%) of 62 patients, pneumonia in eight (13%), respiratory failure in five (8%), bacteraemia in four (6%), and sepsis in four (6%). Three deaths occurred in patients in remission (one sepsis, one gastrointestinal haemorrhage, and one respiratory failure) and were potentially treatment related. INTERPRETATION: ASTX727 plus venetoclax is an active fully oral regimen and safe in most older or unfit patients with acute myeloid leukaemia. Our findings should be confirmed in larger multicentric studies. FUNDING: MD Anderson Cancer Center Support Grant, Myelodysplastic Syndrome/Acute Myeloid Leukaemia Moon Shot, Leukemia SPORE, Taiho Oncology, and Astex Pharmaceuticals.


Bridged Bicyclo Compounds, Heterocyclic , Drug Combinations , Leukemia, Myeloid, Acute , Respiratory Insufficiency , Sepsis , Sulfonamides , Uridine/analogs & derivatives , Humans , Male , Aged , Aged, 80 and over , Female , Decitabine/adverse effects , Treatment Outcome , Leukemia, Myeloid, Acute/diagnosis , Antineoplastic Combined Chemotherapy Protocols/adverse effects , Respiratory Insufficiency/chemically induced , Respiratory Insufficiency/drug therapy , Sepsis/chemically induced , Sepsis/drug therapy
10.
J Oncol Pharm Pract ; 30(4): 721-736, 2024 Jun.
Article En | MEDLINE | ID: mdl-38509812

OBJECTIVE: To review the pharmacokinetic (PK)-pharmacodynamic (PD) profiles, disease setting, dosing, and safety of oral and parenteral hypomethylating agents (HMAs) for the treatment of myelodysplastic syndromes/neoplasms (MDS) and acute myeloid leukemia (AML), and to provide a multidisciplinary perspective on treatment selection and educational needs relating to HMA use. DATA SOURCES: Clinical and real-world data for parenteral decitabine and azacitidine and two oral HMAs: decitabine-cedazuridine (DEC-C) for MDS and azacitidine (CC-486) for AML maintenance therapy. DATA SUMMARY: Differences in the PK-PD profiles of oral and parenteral HMA formulations have implications for their potential toxicities and planned use. Oral DEC-C (decitabine 35 mg and cedazuridine 100 mg) has demonstrated equivalent systemic area under the concentration-time curve (AUC) exposure to a 5-day regimen of intravenous (IV) decitabine 20 mg/m2 and showed no significant difference in PD. The AUC equivalence of oral DEC-C and IV decitabine means that these regimens can be treated interchangeably (but must not be substituted within a cycle). Oral azacitidine has a distinct PK-PD profile versus IV or subcutaneous azacitidine, and the formulations are not bioequivalent or interchangeable owing to differences in plasma time-course kinetics and exposures. Clinical trials are ongoing to evaluate oral HMA combinations and novel oral HMAs, such as NTX-301 and ASTX030. CONCLUSIONS: Treatment with oral HMAs has the potential to improve quality of life, treatment adherence, and disease outcomes versus parenteral HMAs. Better education of multidisciplinary teams on the factors affecting HMA treatment selection may help to improve treatment outcomes in patients with MDS or AML.


Azacitidine , Decitabine , Leukemia, Myeloid, Acute , Myelodysplastic Syndromes , Humans , Myelodysplastic Syndromes/drug therapy , Leukemia, Myeloid, Acute/drug therapy , Administration, Oral , Azacitidine/pharmacokinetics , Azacitidine/administration & dosage , Azacitidine/analogs & derivatives , Azacitidine/therapeutic use , Decitabine/pharmacokinetics , Decitabine/administration & dosage , Antimetabolites, Antineoplastic/pharmacokinetics , Antimetabolites, Antineoplastic/administration & dosage , Antimetabolites, Antineoplastic/therapeutic use , Uridine/pharmacokinetics , Uridine/analogs & derivatives , Uridine/administration & dosage , Uridine/therapeutic use , Uridine/pharmacology
11.
Molecules ; 29(5)2024 Feb 29.
Article En | MEDLINE | ID: mdl-38474577

While numerous Fabaceae seeds are a good nutritional source of high-quality protein, the use of some species is hampered by toxic effects caused by exposure to metabolites that accumulate in the seeds. One such species is the faba or broad bean (Vicia faba L.), which accumulates vicine and convicine. These two glycoalkaloids cause favism, the breakdown of red blood cells in persons with a glucose-6-phosphate dehydrogenase deficiency. Because this is the most common enzyme deficiency worldwide, faba bean breeding efforts have focused on developing cultivars with low levels of these alkaloids. Consequently, quantification methods have been developed; however, they quantify vicine and convicine only and not the derivatives of these compounds that potentially generate the same bio-active molecules. Based on the recognition of previously unknown (con)vicine-containing compounds, we screened the fragmentation spectra of LC-MS/MS data from five faba bean cultivars using the characteristic fragments generated by (con)vicine. This resulted in the recognition of more than a hundred derivatives, of which 89 were tentatively identified. (Con)vicine was mainly derivatized through the addition of sugars, hydroxycinnamic acids, and dicarboxylic acids, with a group of compounds composed of two (con)vicine residues linked by dicarboxyl fatty acids. In general, the abundance profiles of the different derivatives in the five cultivars mimicked that of vicine and convicine, but some showed a derivative-specific profile. The description of the (con)vicine diversity will impact the interpretation of future studies on the biosynthesis of (con)vicine, and the content in potentially bio-active alkaloids in faba beans may be higher than that represented by the quantification of vicine and convicine alone.


Alkaloids , Fabaceae , Glucosides , Pyrimidinones , Uridine/analogs & derivatives , Vicia faba , Vicia faba/chemistry , Liquid Chromatography-Mass Spectrometry , Chromatography, Liquid , Tandem Mass Spectrometry , Plant Breeding
12.
Lancet Haematol ; 11(3): e186-e195, 2024 Mar.
Article En | MEDLINE | ID: mdl-38316133

BACKGROUND: Hypomethylating agents are approved in higher-riskmyelodysplastic syndromes. The combination of a hypomethylating agent with venetoclax is standard of care in acute myeloid leukaemia. We investigated the safety and activity of the first totally oral combination of decitabine plus cedazuridine and venetoclax in patients with higher-risk-myelodysplastic syndromes and chronic myelomonocytic leukaemia. METHODS: We did a single-centre, dose-escalation and dose-expansion, phase 1/2, clinical trial. Patients with treatment-naive higher-risk-myelodysplastic syndromes or chronic myelomonocytic leukaemia (risk level categorised as intermediate-2 or higher by the International Prognostic Scoring System) with excess blasts (>5%). Treatment consisted of oral decitabine 35 mg plus cedazuridine 100 mg on days 1-5 and venetoclax (variable doses of 100-400 mg, day 1 to 14, 28-day cycle). The primary outcomes were safety for the phase 1 part and the overall response for the phase 2 part of the study. The trial is ongoing and this analysis was not prespecified. This study is registered with ClinicalTrials.gov, NCT04655755, and is currently enrolling participants. FINDINGS: Between Jan 21, 2021, and Jan 20, 2023, we enrolled 39 patients (nine in phase 1 and 30 in phase 2). The median age was 71 years (range 27-94), 28 (72%) patients were male, and 11 (28%) were female. The maximum tolerated dose was not reached, and the recommended phase 2 dose was established as oral decitabine 35 mg plus cedazuridine 100 mg for 5 days and venetoclax (400 mg) for 14 days. The most common grade 3-4 adverse events were thrombocytopenia (33 [85%] of 39), neutropenia (29 [74%]), and febrile neutropenia (eight [21%]). Four non-treatment-related deaths occurred on the study drugs due to sepsis (n=2), lung infection (n=1), and undetermined cause (n=1). The median follow-up time was 10·8 months (IQR 5·6-16·4). The overall response rate was 95% (95% CI 83-99; 37/39). 19 (49%) patients proceeded to hematopoietic stem-cell transplantation. INTERPRETATION: This early analysis suggests that the combination of oral decitabine plus cedazuridine with venetoclax for higher-risk-myelodysplastic syndromes and chronic myelomonocytic leukaemia is safe in most patients, with encouraging activity. Longer follow-up will be needed to confirm these data. FUNDING: MD Anderson Cancer Center, MDS/AML Moon Shot, Genentech/AbbVie, and Astex Pharmaceuticals.


Bridged Bicyclo Compounds, Heterocyclic , Leukemia, Myeloid, Acute , Leukemia, Myelomonocytic, Chronic , Myelodysplastic Syndromes , Sulfonamides , Uridine/analogs & derivatives , Humans , Male , Female , Adult , Middle Aged , Aged , Aged, 80 and over , Decitabine , Treatment Outcome , Leukemia, Myelomonocytic, Chronic/drug therapy , Leukemia, Myeloid, Acute/drug therapy , Myelodysplastic Syndromes/drug therapy
14.
Phys Chem Chem Phys ; 26(11): 8761-8766, 2024 Mar 13.
Article En | MEDLINE | ID: mdl-38419552

5-Fluorouracil is now routinely used in chemo- and radiotherapy. Incorporated within DNA, the molecule is bound to the sugar backbone, forming the 5-fluorouridine sub-unit investigated in the present work. For the clinical usage of the latter, no information exists on the mechanisms that control the radiosensitizing effect at the molecular level. As low energy (< 12 eV) electrons are abundantly produced along the radiation tracks during cancer treatment using beams of high energy particles, we study how these ballistic secondary electrons damage the sensitizing molecule. The salient result from our study shows that the N-glycosidic bonds are principally affected with a cross-section of approximately two orders of magnitude higher than the canonical thymidine, reflecting to some degree the surviving factor of radiation-treated carcinoma cells with and without 5-fluorouracil incorporation. This result may help in the comprehension of the radiosensitizing effect of the fluoro-substituted thymidine in DNA.


Electrons , Radiation-Sensitizing Agents , Uridine/analogs & derivatives , DNA/chemistry , Radiation-Sensitizing Agents/chemistry , DNA Damage , Thymidine , Fluorouracil
15.
Curr Protoc ; 4(2): e984, 2024 Feb.
Article En | MEDLINE | ID: mdl-38327099

A simple, reliable, and efficient method for the gram-scale chemical synthesis of pyrimidine nucleosides functionalized with C5-carboxyl, nitrile, ester, amide, or amidine, starting from unprotected uridine and cytidine, is described. The protocol involves the synthesis of 5-trifluoromethyluridine and 5-trifluoromethylcytidine with Langlois reagent (CF3 SO2 Na) in the presence of tert-butyl hydroperoxide and subsequent transformation of the CF3 group to the C5-C 'carbon substituents' under alkaline conditions. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Synthesis and characterization of 5-trifluoromethyluridine (5-CF3 U) and 5-trifluoromethylcytidine (5-CF3 C) Basic Protocol 2: Conversion of 5-CF3 U and 5-CF3 C to several C5-substituted ribonucleosides.


Chemistry, Organic , Pyrimidine Nucleosides , Cytidine/analogs & derivatives , Pyrimidine Nucleosides/chemical synthesis , Pyrimidine Nucleosides/chemistry , Ribonucleosides/chemistry , Uridine/analogs & derivatives , Chemistry, Organic/methods
16.
Bioorg Med Chem ; 100: 117616, 2024 Feb 15.
Article En | MEDLINE | ID: mdl-38295488

Herein, we report the synthesis of 2'-O-alkyl/2'-fluoro-N3-methyluridine (2'-O-alkyl/2'-F-m3U) phosphoramidites and their incorporation in DNA and RNA oligonucleotides. The duplex binding affinity and base discrimination studies showed that all 2'-O-alkyl/2'-F-m3U modifications significantly decreased the thermal stability and base-pairing discrimination ability. Serum stability study of dT20 with 2'-O-alkyl-m3U modification exhibited excellent nuclease resistance when incubated with 3'-exonucleases (SVPD) or 5'-exonucleases (PDE-II) as compared to m3U, 2'-F, 2'-OMe modified oligonucleotides. MD simulation studies with RNA tetradecamer duplexes illustrated that the m3U and 2'-O-methyl-m3U modifications reduce the duplex stabilities by disrupting the Watson-Crick hydrogen bonding and base-stacking interactions. Further molecular modelling investigations demonstrated that the 2'-O-propyl-m3U modification exhibits steric interactions with amino acid residues in the active site of 3'- and 5'-exonuclease, leading to enhanced stability. These combined data indicate that the 2'-modified-m3U nucleotides can be used as a promising tool to enhance the stability, silencing efficiency, and drug-like properties of antisense/siRNA-based therapeutics.


Nucleic Acids , Uridine , Exonucleases/metabolism , Nucleic Acid Conformation , Oligonucleotides/chemistry , RNA/chemistry , RNA, Small Interfering/chemistry , Uridine/analogs & derivatives , Uridine/chemistry , Uridine/pharmacology
17.
Molecules ; 27(19)2022 Sep 23.
Article En | MEDLINE | ID: mdl-36234824

The faba bean is one of the earliest domesticated crops, with both economic and environmental benefits. Like most legumes, faba beans are high in protein, and can be used to contribute to a balanced diet, or as a meat substitute. However, they also produce the anti-nutritional compounds, vicine and convicine (v-c), that when enzymatically degraded into reactive aglycones can potentially lead to hemolytic anemia or favism. Current methods of analysis use LC-UV, but are only suitable at high concentrations, and thus lack the selectivity and sensitivity to accurately quantitate the low-v-c genotypes currently being developed. We have developed and fully validated a rapid high-throughput LC-MS method for the analysis of v-c in faba beans by optimizing the extraction protocol and assessing the method of linearity, limit of detection, limit of quantitation, accuracy, precision and matrix effects. This method uses 10-times less starting material; removes the use of buffers, acids and organic chemicals; and improves precision and accuracy when compared to current methods.


Favism , Vicia faba , Glucosides , Pyrimidinones , Uridine/analogs & derivatives , Vicia faba/chemistry
18.
Bioorg Med Chem ; 73: 117002, 2022 11 01.
Article En | MEDLINE | ID: mdl-36170759

A synthetic scheme was developed to derive a modified ribothymidine bearing a 3-(N-methylsulfamoyl)propyl group on 2'-oxygen (TMSP). For synthesis initiation, a nucleophilic attack of 1,2-ethanediol on 5'-protected 2,2'-anhydro-ribothymidine was performed to selectively modify the 2'-position. After protection of the 3'-hydroxy group, the hydroxyethyl group was oxidized to the aldehyde, which was coupled with isobutyl (diethoxyphosphinyl)methanesulfonate through the Horner-Wadsworth-Emmons reaction to yield the sulfonate intermediate. The intermediate was further converted to the desired TMSP. Using the phosphoramidite units derived from nucleosides, we synthesized oligonucleotides incorporating TMSP. Oligonucleotides modified with TMSP were found to have duplex stability, resistance toward 3'-exonuclease digestion, and antisense activity comparable to that of the oligonucleotide modified with a previously reported 2'-O-methylcarbamoylethyl group. Based on these results and the generality of the synthetic scheme, 2'-O-sulfamoylalkyl modification is expected to be used for the modulation of the properties of oligonucleotides by changing the substituents on the nitrogen, enabling the oligonucleotides to possess suitable properties for antisense oligonucleotides.


Nucleosides , Oligonucleotides, Antisense , Aldehydes , Ethylene Glycol , Mesylates , Nitrogen , Oligonucleotides , Oxygen , Uridine/analogs & derivatives
19.
Environ Mol Mutagen ; 63(6): 296-307, 2022 07.
Article En | MEDLINE | ID: mdl-36054159

The harmful effects of pesticides can be extended beyond the exposure time scale. Appraisals combining exposure and long-term post-exposure periods appear as an unavoidable approach in pesticide risk assessment, thus allowing a better understanding of the real impact of agrochemicals in non-target organisms. This study aimed to evaluate the progression of genetic damage in somatic and germ tissues of the crayfish Procambarus clarkii, also seeking for gender-specificities, following exposure (7 days) to penoxsulam (23 µg L-1 ) and a post-exposure (70 days) period. The same approach was applied to the model genotoxicant ethyl methanesulfonate (EMS; 5 mg L-1 ) as a complementary mean to improve knowledge on genotoxicity dynamics (induction vs. recovery). Penoxsulam induced DNA damage in all tested tissues, disclosing tissue- and gender-specificities, where females showed to be more vulnerable than males in the gills, while males demonstrated higher susceptibility in what concerns internal organs, that is, hepatopancreas and gonad. Crayfish were unable to recover from the DNA damage induced by EMS in gills and hepatopancreas (both genders) as well as in spermatozoa. The genotoxicity in the hepatopancreas was only perceptible in the post-exposure period. Oxidative DNA lesions were identified in hepatopancreas and spermatozoa of EMS-exposed crayfish. The spermatozoa proved to be the most vulnerable cell type. It became clear that the characterization of the genotoxic hazard of a given agent must integrate a complete set of information, addressing different types of DNA damage, tissue- and gender-specificities, as well as a long-term appraisal of temporal progression of damage.


Pesticides , Water Pollutants, Chemical , Agrochemicals , Animals , Astacoidea/genetics , Astacoidea/metabolism , DNA Damage , Ethyl Methanesulfonate/toxicity , Female , Germ Cells , Male , Sulfonamides , Uridine/analogs & derivatives , Water Pollutants, Chemical/metabolism , Water Pollutants, Chemical/toxicity
20.
Pestic Biochem Physiol ; 187: 105211, 2022 Oct.
Article En | MEDLINE | ID: mdl-36127055

Penoxsulam is an important herbicide for the control of Echinochloa crus-galli (L.) P. Beauv. Two resistant populations 17GA (R1) and 16NXB (R2) showed 17- and 3-fold resistance to penoxsulam, respectively. A known resistance mutation of Trp-574-Leu in ALS gene and enhanced rates of penoxsulam metabolism likely involving GST contribute to penoxsulam resistance in R1 population. This population had resistance to the ALS-inhibitors pyribenzoxim and bispyribac­sodium and the auxin herbicide quinclorac, but was susceptible to ACCase-inhibitors quizalofop-p-ethyl and cyhalofop-butyl. No known mutations in the ALS gene conferring target site resistance to ALS-inhibiting herbicides were presented in R2 population. However, penoxsulam metabolism in R2 plants was about 4-fold greater than in susceptible population 14YC (S0) plants. The enzyme inhibitors piperonyl butoxide, malathion and 4-chloro-7-nitrobenzoxadiazole reversed penoxsulam resistance in this population. GST and P450 enzyme activities and the genes of GST1-1, GST1-2, GST1-3, CYP81A18, CYP81A12, CYP81A21 were increased significantly in R2 population. These results indicate that multiple resistance mechanisms had occurred in E. crus-galli populations in central China and resistance needs to be managed effectively by diverse chemical and non-chemical methods.


Echinochloa , Herbicides , Cytochrome P-450 Enzyme System/metabolism , Enzyme Inhibitors/pharmacology , Herbicide Resistance/genetics , Herbicides/metabolism , Herbicides/pharmacology , Indoleacetic Acids/metabolism , Malathion/pharmacology , Piperonyl Butoxide/pharmacology , Sulfonamides , Uridine/analogs & derivatives
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