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Pseudothymidine is a thymidine analog that functions as a modified nucleoside. Its primary mechanism of action involves incorporation into DNA and RNA during replication and transcription, where it mimics thymidine. By substituting for natural thymidine, Pseudothymidine can terminate DNA chain elongation, enabling detailed polymerase inhibition research. The compound's C-nucleoside structure, with a carbon-carbon glycosidic bond instead of the natural nitrogen-carbon bond, provides enhanced stability and resistance to enzymatic degradation. This makes Pseudothymidine a useful tool for studying nucleic acid metabolism, polymerase function, and synthetic biology applications.
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| ln Vitro |
Pseudothymidine is a C-nucleoside derivative of thymidine [1]. The computed ΔΔG°50/mod is -0.5 kcal/mol, while ΔTm/mod is 0.82°C. For a duplex with nine dA-T/ψT pairings, ΔTm/mod is -0.9°C, while ΔΔG°50/mod is +1.1 kcal/mol. Modification of a duplex with 12 consecutive dA-T/ψT base pairs resulted in a ΔTm/mod of -0.9°C and a ΔΔG°50/mod of +1.2 kcal/mol [2].
In vitro studies have demonstrated that Pseudothymidine can be incorporated into DNA and RNA during replication and transcription, making it useful for studying nucleic acid metabolism and synthetic biology. The compound mimics thymidine and can terminate DNA chain elongation, enabling detailed polymerase inhibition research. Pseudothymidine has a computed deltadeltaGdeg50/mod of -0.5 kcal/mol and a deltaTm/mod of 0.82degC, indicating its effects on nucleic acid stability. The compound can be used in combination with polymerase or helicase inhibitors to block viral genome elongation and enhance antiviral durability in research models. However, detailed IC50 values and specific activity data are limited. |
| ln Vivo |
In vivo studies on Pseudothymidine are limited. As a synthetic nucleoside analog, the compound has potential applications in antiviral research, particularly in studies of viral DNA replication. Pseudothymidine can be used with polymerase or helicase inhibitors to block viral genome elongation and enhance antiviral durability in research models. However, specific in vivo efficacy data for Pseudothymidine are not widely available in the published literature. Animal studies would be needed to evaluate the compound's antiviral activity, pharmacokinetics, and safety profile.
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| Enzyme Assay |
The in vitro enzyme/receptor binding assays for Pseudothymidine typically involve studying the compound's interactions with DNA and RNA polymerases. The compound is used as a substrate analog in polymerase assays to investigate the mechanism of nucleotide incorporation and chain termination. In these assays, Pseudothymidine is added to polymerase reaction mixtures containing template DNA, primers, and other nucleotides. The incorporation of Pseudothymidine into the growing nucleic acid chain is monitored using radiolabeled or fluorescently labeled substrates. The compound's ability to terminate chain elongation is assessed by analyzing the size distribution of the reaction products. These assays provide insights into polymerase specificity and the mechanism of action of nucleoside analogs.
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| Cell Assay |
Cellular assays for Pseudothymidine typically involve treating cultured cells with the compound and assessing its incorporation into nucleic acids. Cells are cultured in appropriate media and treated with varying concentrations of Pseudothymidine for specified time periods. Nucleic acids are extracted from the cells, and the incorporation of Pseudothymidine is analyzed using techniques such as mass spectrometry, HPLC, or specific antibody-based detection. The compound's effects on cell proliferation, nucleic acid synthesis, and gene expression can be assessed using standard cell biology techniques. For antiviral studies, cells infected with viruses are treated with Pseudothymidine to evaluate its antiviral activity.
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| Animal Protocol |
In vivo animal studies for Pseudothymidine are not well-documented in the available literature. For similar nucleoside analogs, typical in vivo protocols involve the use of mouse or rat models of viral infection. The compound is administered orally, intraperitoneally, or intravenously at various doses, and antiviral efficacy is assessed by measuring viral load, survival rates, and clinical signs of infection. Pharmacokinetic parameters such as bioavailability, half-life, and tissue distribution are also evaluated. However, specific experimental protocols for Pseudothymidine have not been published.
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| ADME/Pharmacokinetics |
Pharmacokinetic data for Pseudothymidine are limited. The compound has a molecular weight of 242.23 and a molecular formula of C10H14N2O5. As a modified nucleoside analog, Pseudothymidine would be expected to have improved stability and resistance to enzymatic degradation compared to natural thymidine. The compound appears as a light yellow to yellow solid. Detailed pharmacokinetic parameters such as oral bioavailability, half-life, clearance, and tissue distribution have not been determined for this compound. The compound is typically stored at room temperature.
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| Toxicity/Toxicokinetics |
Toxicological data for Pseudothymidine are not available in the published literature. As a research compound, Pseudothymidine has not been systematically evaluated for toxicity in preclinical studies. Standard toxicological assessments, including acute toxicity, repeat-dose toxicity, and genotoxicity studies, would be needed to establish the safety profile of this compound for any potential therapeutic applications. The compound's structural similarity to natural nucleosides suggests that it may have a reasonable safety profile, but this remains to be confirmed through appropriate toxicological studies.
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| References |
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| Additional Infomation |
Pseudothymidine is a research-grade synthetic nucleoside analog used primarily for studying nucleic acid metabolism, viral DNA replication, and synthetic biology. It is a C-nucleoside analog of thymidine with enhanced stability and resistance to enzymatic degradation. The compound has a molecular formula of C10H14N2O5 and a molecular weight of 242.23. Pseudothymidine can be used in combination with polymerase or helicase inhibitors to block viral genome elongation in research models. The compound is not approved for clinical use and is available only for research purposes.
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| Molecular Formula |
C10H14N2O5
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| Molecular Weight |
242.228562831879
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| Exact Mass |
242.09
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| CAS # |
65358-15-8
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| PubChem CID |
445537
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| Appearance |
Light yellow to yellow solid powder
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| LogP |
-1.6
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| Hydrogen Bond Donor Count |
3
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| Hydrogen Bond Acceptor Count |
5
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| Rotatable Bond Count |
2
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| Heavy Atom Count |
17
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| Complexity |
381
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| Defined Atom Stereocenter Count |
3
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| SMILES |
CN1C=C(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO)O
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| InChi Key |
AMDJRICBYOAHBZ-XLPZGREQSA-N
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| InChi Code |
InChI=1S/C10H14N2O5/c1-12-3-5(9(15)11-10(12)16)7-2-6(14)8(4-13)17-7/h3,6-8,13-14H,2,4H2,1H3,(H,11,15,16)/t6-,7+,8+/m0/s1
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| Chemical Name |
5-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1-methylpyrimidine-2,4-dione
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| HS Tariff Code |
2934.99.9001
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| Storage |
Powder -20°C 3 years 4°C 2 years In solvent -80°C 6 months -20°C 1 month |
| Shipping Condition |
Room temperature (This product is stable at ambient temperature for a few days during ordinary shipping and time spent in Customs)
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| Solubility (In Vitro) |
DMSO : ~61.17 mg/mL (~252.53 mM)
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| Solubility (In Vivo) |
Note: Listed below are some common formulations that may be used to formulate products with low water solubility (e.g. < 1 mg/mL), you may test these formulations using a minute amount of products to avoid loss of samples.
Injection Formulations
Injection Formulation 1: DMSO : Tween 80： Saline = 10 : 5 : 85 (i.e. 100 μL DMSO stock solution → 50 μL Tween 80 → 850 μL Saline)(e.g. IP/IV/IM/SC) *Preparation of saline: Dissolve 0.9 g of sodium chloride in 100 mL ddH ₂ O to obtain a clear solution. Injection Formulation 2: DMSO : PEG300 ：Tween 80 : Saline = 10 : 40 : 5 : 45 (i.e. 100 μL DMSO → 400 μLPEG300 → 50 μL Tween 80 → 450 μL Saline) Injection Formulation 3: DMSO : Corn oil = 10 : 90 (i.e. 100 μL DMSO → 900 μL Corn oil) Example: Take the Injection Formulation 3 (DMSO : Corn oil = 10 : 90) as an example, if 1 mL of 2.5 mg/mL working solution is to be prepared, you can take 100 μL 25 mg/mL DMSO stock solution and add to 900 μL corn oil, mix well to obtain a clear or suspension solution (2.5 mg/mL, ready for use in animals). View More
Injection Formulation 4: DMSO : 20% SBE-β-CD in saline = 10 : 90 [i.e. 100 μL DMSO → 900 μL (20% SBE-β-CD in saline)] Oral Formulations
Oral Formulation 1: Suspend in 0.5% CMC Na (carboxymethylcellulose sodium) Oral Formulation 2: Suspend in 0.5% Carboxymethyl cellulose Example: Take the Oral Formulation 1 (Suspend in 0.5% CMC Na) as an example, if 100 mL of 2.5 mg/mL working solution is to be prepared, you can first prepare 0.5% CMC Na solution by measuring 0.5 g CMC Na and dissolve it in 100 mL ddH2O to obtain a clear solution; then add 250 mg of the product to 100 mL 0.5% CMC Na solution, to make the suspension solution (2.5 mg/mL, ready for use in animals). View More
Oral Formulation 3: Dissolved in PEG400 (Please use freshly prepared in vivo formulations for optimal results.) |
| Preparing Stock Solutions | 1 mg | 5 mg | 10 mg | |
| 1 mM | 4.1283 mL | 20.6415 mL | 41.2831 mL | |
| 5 mM | 0.8257 mL | 4.1283 mL | 8.2566 mL | |
| 10 mM | 0.4128 mL | 2.0642 mL | 4.1283 mL |
*Note: Please select an appropriate solvent for the preparation of stock solution based on your experiment needs. For most products, DMSO can be used for preparing stock solutions (e.g. 5 mM, 10 mM, or 20 mM concentration); some products with high aqueous solubility may be dissolved in water directly. Solubility information is available at the above Solubility Data section. Once the stock solution is prepared, aliquot it to routine usage volumes and store at -20°C or -80°C. Avoid repeated freeze and thaw cycles.
Calculation results
Working concentration： mg/mL；
Method for preparing DMSO stock solution： mg drug pre-dissolved in μL DMSO (stock solution concentration mg/mL). Please contact us first if the concentration exceeds the DMSO solubility of the batch of drug.
Method for preparing in vivo formulation:：Take μL DMSO stock solution, next add μL PEG300, mix and clarify, next addμL Tween 80, mix and clarify, next add μL ddH2O，mix and clarify.
(1) Please be sure that the solution is clear before the addition of next solvent. Dissolution methods like vortex, ultrasound or warming and heat may be used to aid dissolving.
(2) Be sure to add the solvent(s) in order.
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