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Molecule (6/13)



  1. https://doi.org/10.1002/chem.201101163 I am working on synthetic routes to a glucoside. The beta-trimethylsilylethoxymethyl (SEM) group has some attractive features (particularly in regards to deprotection), but I have only found one paper in which four SEM groups were used to protect the oxygen atoms at carbons 2-4 and 6 of a glycoside conjugated with a steroid. They did not deprotect to the best of my knowledge, but I assume that one would use a standard recipe. I did find a paper in which a glycoside was protected with several different groups, including one SEM. Are there disadvantages to using the SEM group as the protecting group? Are there reasons why it has been used more in carbohydrate chemistry? Should I be favoring other protecting groups instead?
  2. You might be able to do it using what is called the specific activity of the enzyme. Specific activity is given as units per milligram of protein. The denominator is a mass, not a concentration.
  3. Does anyone know of a web-based program for estimating retention times that is simple to use? I found one, but I struggled a bit with the output.
  4. Our interest is in LC/MS of the peptides, and we plan to work in water/acetonitrile/formic acid. We found a number of protocols for C-18 on line (I can provide links to these), and we are focusing on those protocols that specify formic acid (not TFA). Our Zip Tips use C-18. (1) Are Zip Tips necessary? (2) Given their capacity, does one obtain enough for material for one or for several LC/MS runs? (3) Are Zip Tips reusable? (4) Does anyone have a paper or protocol that is especially informative? Thank you very much.
  5. We are synthesizing the next generation of inhibitors, and they have increased water solubility.
  6. I don't know the answer to your question, but I am inclined to say that we will try to optimize the compounds. With regard to these compounds, we have in vitro data against a validated target enzyme. They are irreversible inhibitors with ligand binding efficiencies greater than 0.3. The second generation inhibitors that we are currently synthesizing were designed with transport across membranes as a consideration.
  7. Our collaborators used only volatile organic solvents to dissolve the compounds prior to the preparation of the disks. I am not sure whether or not this information is useful.
  8. I asked my institution to file a provisional patent, but I have not yet heard back.
  9. The enzyme has been shown to be essential in some pathogenic bacterial strains and also in Candida albicans. We are in the process of revising our first manuscript on our inhibitors. For the best compounds in this series, the ratios of binding energies to molecular weights are promising, among other possibly favorable properties. We envision either an antifungal or antibacterial compound, although at the moment we are more fungal-focused. What sort of near-term commercial applications do you mean?
  10. That is a helpful reference; thank you. We synthesized a family of compounds that are good inhibitors of an essential microbial enzyme. As a whole they are not very water-soluble, although there is variation in the group. One of the more hydrophilic ones is one of two that showed growth inhibition. Therefore, we are synthesizing the next generations of inhibitors that might be more water-soluble and thinking about what are the meanings of various test results.
  11. One other issue occurs to me. As the compound diffuses, the microorganisms are growing. So it is possible that the compound arrives at a certain place with a particular concentration only after growth has ceased for other reasons, such as buildup of waste or consumption of nutrients.
  12. "VAERS cannot prove that a vaccine caused a problem. Specifically, a report to VAERS does not mean that a vaccine caused an adverse event. But VAERS can give CDC and FDA important information. If it looks as though a vaccine might be causing a problem, FDA and CDC will investigate further and take action if needed." "In some cases, multiple reports are submitted for the same adverse event." "VAERS data alone cannot determine if the vaccine caused the reported adverse event. This specific limitation has caused confusion about the publicly available data, specifically regarding the number of reported deaths. In the past there have been instances where people misinterpreted reports of death following vaccination as death caused by the vaccines; that is a mistake." These three quotes about the vaccine adverse events reporting system come from the CDC. https://www.cdc.gov/vaccinesafety/ensuringsafety/monitoring/vaers/index.html Politifact or some other fact-checking organization also had an article about this kind of erroneous interpretation, if I recall correctly. The Economist magazine calculated an estimate of worldwide excess deaths, of 10 million people. The CDC has a table broken down by age at this link. https://www.cdc.gov/coronavirus/2019-ncov/covid-data/investigations-discovery/hospitalization-death-by-age.html "Sample interpretation: Compared with 5—17-year-olds, the rate of death is 45 times higher in 30—39-year-olds and 8,700 times higher in 85+-year-olds."
  13. One more thing for protein helices. I would ask what are the values of the dihedral angles, phi and psi, and whether or not they fall into the allowed region of the Ramachandran diagram.
  14. I don't know the answer to this question, but the kinds of questions I would ask about any helix would be handedness, hydrogen bonding patterns, and translation of the helix per unit residue.
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