Nucleoside Puns

referring to: https://en.wikipedia.org/wiki/Nucleoside_analogue

I was wondering, why do these class of drugs affect the virus more than the host? Both replicate their DNA, so shouldn't these drugs also terminate elongation for hosts?

A new industry-academic partnership between the University of Oxford and biopharmaceutical company NuCana as found that chemotherapy drug NUC-7738, derived from Cordyceps sinensis , has 40 times greater potency for killing cancer cells than its parent compound.

The naturally-occurring nucleoside analog known as Cordycepin (a.k.a 3'-deoxyadenosine) is found in the Himalayan fungus Cordyceps sinensis and has been used in traditional Chinese medicine for hundreds of years to treat cancers and other inflammatory diseases. However, it breaks down quickly in the blood stream, so a minimal amount of cancer-destroying drug is delivered to the tumor. In order to improve its potency and clinically assess its applications as a cancer drug, biopharmaceutical company NuCana has developed Cordycepin into a clinical therapy, using their novel ProTide technology, to create a chemotherapy drug with dramatically improved efficacy.

Once inside the body, Cordycepin requires transport into cancer cells by a nucleoside transporter (hENT1), it must be converted to the active anti-cancer metabolite, known as 3'-dATP, by a phosphorylating enzyme (ADK), and it is rapidly broken down in the blood by an enzyme called ADA. Together, these resistance mechanisms associated with transport, activation and breakdown result in insufficient delivery of anti-cancer metabolite to the tumor. NuCana have utilized novel ProTide technology to design a therapy that can bypass these resistance mechanisms and generate high levels of the active anti-cancer metabolite, 3'-dATP, inside cancer cells.

ProTide technology is a novel approach for delivering chemotherapy drugs into cancer cells. It works by attaching small chemical groups to nucleoside analogs like Cordycepin, which are then later metabolized once it has reached the patient's cancer cells, releasing the activated drug. This technology has already been successfully used in the FDA approved antiviral drugs Remsidivir and Sofusbuvir to treat different viral infections such as Hepatitis C, Ebola and COVID-19.

Oxford researchers and their collaborators in Edinburgh and Newcastle are now assessing NUC-7738 in the Phase 1 clinical trial NuTide:701, which tests the drug in patients with advanced solid tumors that were resistant to conventional treatment. Early results from the trial have shown that NUC-7738 is well tolerated by patients and shows encouraging signs of anti-cancer activity.

Further Phase 2 clinical trials of this drug are now

I'm not sure if this is the right sub for this, but I'm looking for some deeper insight into how mRNA synthesis and breakdown works, as well as insight into nucleoside analogs used in the currently available mRNA vaccines.

I don't work in the field, but I do have a solid grasp on the concepts for a layman (I took some biochem in college), so no need to hold anything back or dumb it down.

I've googled this extensively, but I can't find good answers to these questions, and just talking to a biochemist(s) would be incredibly helpful.

Primarily, I'm curious for insight into:

1. What mRNA breaks down into. My understanding is that it breaks down into its component nucleotides. Is that correct?
2. What's known about the nucleoside analogs that are being used in the Pfizer/Moderna modRNA. I think the exact composition of the modRNA is proprietary, because I wasn't able to find it. Wikipedia tells me that 5-methylcytosine and pseudouridine are commonly used analogs, but what else could they use? In general, some nucleoside analogs are known to be harmful, such as in some older HIV drugs which cause bone marrow suppression as a side effect, although those drugs were designed specifically to interact with nucleic acids, so I'm not sure that applies here.
3. Related to 2), my understanding is that your body synthesizes RNA/DNA from free floating nucleotides. Could synthetic nucleoside analogs be incorporated into future RNA/DNA? Or are those analogs also broken down before that could happen? Even if they were incorporated, is that a bad thing that could cause adverse long term effects, or is it unknown?

Thanks for a lot for any help or discussion!

I understand why the phosphate group is good at its function but is there a reason why for example adenosine is used in ATP and not some other triphophorylated molecule?

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7410331/ These results look very good in animal models. Hope this is being worked on still.

https://preview.redd.it/1ui444lc2vs61.jpg?width=847&format=pjpg&auto=webp&s=fb9a2306a102fda130076943fd2175bdec6d5d7b

Hi all, I am curious to hear your opinion regarding potential interactions between the guanosine analog acyclovir, which is used as an antiviral medication in humans, and the intended therapeutic effect of the new mRNA vaccines for SARS-CoV-2.

My understanding is limited, I am a physician and my molecular biology training is somewhat remote, but this is a question that the pharmacists I work with have been unable to answer.

Specifically, I am curious if use of acyclovir during immunization with this or a similar mRNA vaccine would be likely to disrupt protein synthesis by replacing guanosine in RNA? I believe the vaccine works by single use transcription and from there on is protein based, but I am not sure if there is dynamic nucleobase substitution in a formed RNA strand or if there is an additional step that may imply cross reaction.

I apologize in advance if this is a sophomoric question, I just want to be sure I understand before I attempt to discuss the mechanism with colleagues and patients.

Thank you!

From a library of 26 deoxyuridine‐ and deoxycytidine‐derived diarylethenes we identified two high‐performance photoswitches with near‐quantitative, fully reversible back‐and‐forth switching, high reaction quantum yields and no detectable thermal or photochemical deterioration. Incorporated into an oligonucleotide, these nucleotides allowed the optochemical modulation of the activity of T7 RNA polymerase.

Abstract

Nucleosidic and oligonucleotidic diarylethenes (DAEs) are an emerging class of photochromes with high application potential. However, their further development is hampered by the poor understanding of how the chemical structure modulates the photochromic properties. Here we synthesized 26 systematically varied deoxyuridine‐ and deoxycytidine‐derived DAEs and analyzed reaction quantum yields, composition of the photostationary states, thermal and photochemical stability, and reversibility. This analysis identified two high‐performance photoswitches with near‐quantitative, fully reversible back‐and‐forth switching and no detectable thermal or photochemical deterioration. When incorporated into an oligonucleotide with the sequence of a promotor, the nucleotides maintained their photochromism and allowed the modulation of the transcription activity of T7 RNA polymerase with an up to 2.4‐fold turn‐off factor, demonstrating the potential for optochemical control of biological processes.

https://ift.tt/3u83HGm

Discovery of amino/imino ribonucleoside artifacts that are generated during RNA hydrolysis under ammonium‐buffered mild basic conditions. The general approach for discovery uses higher‐energy collisional dissociation‐mass spectrometry (HCD‐MS) and isotope labeling of RNA.

Abstract

Liquid chromatography‐tandem mass spectrometry (LC‐MS/MS) has become the gold‐standard technique to study RNA and its various modifications. While most research on RNA nucleosides has been focused on their biological roles, discovery of new modifications remains of interest. With state‐of‐the‐art technology, the presence of artifacts can confound the identification of new modifications. Here, we report the characterization of a non‐natural mcm5isoC ribonucleoside in S. cerevisiae total tRNA hydrolysate by higher‐energy collisional dissociation (HCD)‐based fingerprints and isotope labeling of RNA. Its discovery revealed a class of amino/imino ribonucleoside artifacts that are generated during RNA hydrolysis under ammonium‐buffered mild basic conditions. We then identified digestion conditions that can reduce or eliminate their formation. These finding and method enhancements will improve the accurate detection of new RNA modifications.

https://ift.tt/2HRMbDg

I was reading a bit of background material on nucleic acids, having not studied any chemistry for 20 years.

I learned that ribose exists in an equilibrium between cyclic and linear forms. However, in diagrams only the cyclic structure is shown. Does the addition of a nitrogenous base somehow make the cyclic form preferable?

Also, why are the positions on the sugar labeled with primes? Why not just call them 1, 2, ..., 5?

γ‐Alkyl‐nucleoside triphosphates were studied as DNA‐polymerase inhibitors. A strong selectivity for HIV reverse transcriptase over DNA polymerases α, β, and γ was observed. γ‐Alkyl‐nucleoside triphosphates proved highly stable in cell extracts in contrast to the parent NTPs. Lipophilic prodrugs were also prepared. High anti‐HIV activity was detected in infected CEM/TK‐deficient cells, making these compounds promising potential antivirals.

Abstract

The development of nucleoside triphosphate prodrugs is one option to apply nucleoside reverse transcriptase inhibitors. Herein, we report the synthesis and evaluation of d4TTP analogues, in which the γ‐phosphate was modified covalently by lipophilic alkyl residues, and acyloxybenzyl prodrugs of these γ‐alkyl‐modified d4TTPs, with the aim of delivering of γ‐alkyl‐d4TTP into cells. Selective formation of γ‐alkyl‐d4TTP was proven with esterase and in CD4+‐cell extracts. In contrast to d4TTP, γ‐alkyl‐d4TTPs proved highly stable against dephosphorylation. Primer extension assays with HIV reverse transcriptase (RT) and DNA‐polymerases α, β or γ showed that γ‐alkyl‐d4TTPs were substrates for HIV‐RT only. In antiviral assays, compounds were highly potent inhibitors of HIV‐1 and HIV‐2 also in thymidine‐kinase‐deficient T‐cell cultures (CEM/TK−). Thus, the intracellular delivery of such γ‐alkyl‐nucleoside triphosphates may potentially lead to nucleoside triphosphates with a higher selectivity towards the viral polymerase that can act in virus‐infected cells.

https://ift.tt/3b9L2Qt

Journal of the American Chemical SocietyDOI: 10.1021/jacs.0c11884

Scott M. Shepard, Hyehwang Kim, Qing Xin Bang, Norah Alhokbany, and Christopher C. Cummins

https://ift.tt/3rIoaRB

Queuosine (Q) is a hypermodified RNA nucleoside that is found in tRNA His , tRNA Asn , tRNA Tyr , and tRNA Asp . It is located at the wobble position of the tRNA anticodon loop, where it can interact both with U or C bases located at the respective position of the corresponding mRNA codons. In higher eukaryotes, including humans, the Q base is for yet unknown reasons further modified in tRNA Tyr and tRNA Asp by the addition of a galactose or mannose sugar, respectively. The reason for this additional modification, and how the sugar modification is orchestrated with Q‐formation and insertion, is unknown. Here, we report a total synthesis of the hypermodified nucleoside galactosyl‐queuosine (galQ). The availability of the compound enabled us to study the absolute levels of the Q‐family nucleosides in six different organs of new‐born and adult mice, and also in human cytosolic tRNA. Our synthesis now paves the way to a more detailed analysis of the biological function of the Q‐nucleoside family.

https://ift.tt/2THSJI6

Does anyone know?

My two guesses would be to use PCR, or maybe grow samples on bacteria/ nutrients containing the analog and then the cells uptake the analog into their DNA when they undergo DNA replication. If you used PCR then you'd essentially have to make the DNA strand yourself? So i dont think its that.

And to make sure that the integration has been successful do you use DNA Probes???

Liquid chromatography‐tandem mass spectrometry (LC‐MS/MS) has become the gold‐standard technique to study RNA and its various modifications. While most research on RNA nucleosides has been focused on studying their biological roles, discovery of new modifications remains of interest. With state‐of‐the‐art technology, the presence of artifacts generated during sample preparation or LC‐MS/MS analysis can confound the identification of new modifications. Here, we report the characterization of a non‐natural mcm5isoC ribonucleoside in S. cerevisiae total tRNA hydrolysate. We demonstrate its discovery and characterization by higher‐energy collisional dissociation (HCD)‐based fingerprints and isotope labeling of RNA. More importantly, its discovery revealed a whole class of amino/imino ribonucleoside artifacts that are generated during RNA hydrolysis under ammonium‐buffered mild basic conditions. We then identified digestion conditions that can reduce or eliminate their formation. The discovery of such a class of artifacts will eliminate their misidentification as naturally occurring ribonucleosides, helping to improve the accurate detection of new RNA modifications.

https://ift.tt/2HRMbDg