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BabcockHall

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Everything posted by BabcockHall

  1. We are synthesizing the next generation of inhibitors, and they have increased water solubility.
  2. 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.
  3. 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.
  4. I asked my institution to file a provisional patent, but I have not yet heard back.
  5. 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?
  6. 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.
  7. 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.
  8. "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."
  9. 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.
  10. 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.
  11. "Two doses of BNT162b2 are highly effective across all age groups (≥16 years, including older adults aged ≥85 years) in preventing symptomatic and asymptomatic SARS-CoV-2 infections and COVID-19-related hospitalisations, severe disease, and death, including those caused by the B.1.1.7 SARS-CoV-2 variant. There were marked and sustained declines in SARS-CoV-2 incidence corresponding to increasing vaccine coverage. These findings suggest that COVID-19 vaccination can help to control the pandemic." From a study of the Pfizer vaccine in Israel, published earlier this month in The Lancet. "This study in a nationwide mass vaccination setting suggests that the BNT162b2 mRNA vaccine is effective for a wide range of Covid-19–related outcomes, a finding consistent with that of the randomized trial." From a study published in April, in the New England Journal of Medicine. There was an article at CNN that quoted some hematologists, all of whom recommended that people get the vaccine.
  12. Hello Everyone, I am making enzyme inhibitors and turning them over to a microbiology laboratory for testing against standard strains of bacteria and fungi. They are performing disk diffusion assays, and seeing a few results that look positive. I would like better to understand the meaning and limitations of this experiment. I would hazard a guess that the compound's concentration falls off at greater distances from the disk, but I don't know how to interpret the diameter of the dead zone in a quantitative way, or even if that is possible. Perhaps there is a good textbook treatment of this subject, for example.
  13. Please show your attempt. If you can, please explain where you got stuck.
  14. I can't say which transition state without knowing the other reactants besides oxygen. Let me limit myself to nucleophilic substitution reactions for the sake of illustration. By an open transition state I mean one in which the leaving group has largely left (the bond order to the central atom might be roughly 0.2) and the nucleophile is only weakly present (bond order also might be around 0.20). The opposite situation (a tight transition state) is one in which the leaving group has just begun to depart (bond order of 0.8 or so) and the nucleophile has largely made a bond to the central atom.
  15. Dissociative or associative might be applied to the nature of the transition state. Dissociative means that the transition state is open (exploded), and associative means the opposite.
  16. Did you try using the Henderson-Hasselbalch equation?
  17. As a general rule B. subtilis does chemotaxis in a different (sometime opposite) way versus E. coli. I never thought about bushings before, but I will ask around.
  18. When an enzyme is saturated with its substrate, its velocity reaches its maximum, notated as Vmax. Because enzymes are catalytic and because one has different purposes, it is not possible to give a general answer about how much enzyme to use in a given experiment. When discussing the quantity of enzyme, one often encounters the word "unit." One unit of an enzyme is the amount that will convert one micromole of substrate to product per minute under a given set of conditions. Often enzymes are sold on the basis of how many units are present.
  19. I am not sure that a transporter in the outer membrane would be needed, owing to the presence of porins in the outer membrane.
  20. Ciak, What if you used a molecule with two different halogens at the 1 and 3 positions?
  21. Is this a homework problem or an exam problem? Can you explain what you were taught and what you do and don't understand at this point?
  22. Structure A could be fixed by adding a formal charge to oxygen. There is a good reason to insist that formal charges should always be written out explicitly and not assumed or inferred.
  23. Have you searched using PubMed? I am not sure that it would pick up dissertations, but it would surely find research articles.
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