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CoMFA – MFer. March 8, 2007

Posted by thwalls in Blogroll.


 So I’m finishing up some of my work and of course a CoMFA is required since my work centers around the inhibition of a particular transmembrane protein.  Of course, if you’re familiar with medicinal chemistry, you’ll know that every medchem student is entrenched with the thorough understanding that if the computer tells you the analog is good, then obviously…it’s good.  This then leads to your PI telling you to make all 150,000 analogs that could possibly be good since, hey, the in vitro data may be different.

I hate Sybyl, and I think it equally hates me. 

And possibly you too.


Where’s the Spin?? December 20, 2006

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Still nothing new unfortunately.  I’m hoping that after this examination that’s coming up in February I’ll devote a bit more time to the endeavor that this is by bringing up some new and novel chemistry…but at the moment I’m trying to make sure that I have enough sources for my Candidacy Research paper.  I’m hoping to get this done by the end of the week so that I can get some people started on my reviews, but we’ll see how that goes. 

Either way, I’ve found some novel Vanadium chemistry that should yield better results for my cyanation of an aryl ketone.  This is some of the work with the Vanadium triflate catalyst that seems like it can do anything but make you a sandwhich while the reaction is running.  Apparantly you just take some oxo-vanadium sulfate, and impregnate it into a dowex ion exchange column.  You then pass through it a solution of hot 1 M triflic acid and presto chango, you get vanadium triflate out the other side which can then be used directly in your reaction that is high yielding and exceptionally easy to work up.  The vanadium catalyst is actually very water soluble and thus can washed out, leaving only your product and any remaining starting material, so hopefully just two spots on the TLC plate…well actually I’m hoping for one…

Our lab also purchased a new 400 MHz Varian NMR which we’ve been using like crazy, especially after not having access to one for over 3 months.  So for some reason you’ll be using it and the guage that measures your NMR tube spin will spontaneously drop to zero and your nice flat base line turns into thick-sliced bacon as your peaks become uber fat…so not too happy about that.

Second Years Unite December 10, 2006

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It has been at least one full moon since I’ve updated this and I think that I’m totally justified in my absence.  I’ve got about two months now until my Candidacy/Proposal Exam and I’m starting to feel the pressure just a little bit.  Since I am a Med/Synthetic Student I have to know the reactions, which aren’t too bad, along with the medicinal reasoning and biological jargon…which sucks.

 I can understand Chemical Experiments where you combine A and B to get C.  You can then go on to explain why you chose A and B as your starting reagents.  But when trying to figure out how a sodium channel works the biologists won’t tell you why exactly they chose Saxamaxaaflaxataxatoxin Q1 to block the sodium channel in it’s resting state by binding to the outer portion of the S1 subunit.  Or why they used the squeezings of a scorpion to effect something or other in the active transporter of the neuron.  So that seems to be the hold up right now.

I can’t wait for March.

C & EN, November, 20…Vol.2 (Kornberg’s Triumph?) November 23, 2006

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You should have also noted the article, “Complexity to live by.” discussing this years Nobel Prize in Chemistry for the ellucidation of the Pol II crystal structure with co-crystallized DNA as it is being transcribed.  I will have to admit that I love a good crystal structure, especially one as magnitudinous as RNA Polymerase II.



 Sorry for the small pictures (The EMBO Journal (1998) 17, 2353–2358).

Anyway, the article is interesting and I highly suggest that you check it out (Science 2001, 292, 1863-1876) since this kind of work has a tendency to lead to novel drug targets.  Even though SYBYL is excellent if you can’t get the crystal structure, everyone likes to actually see what they’re trying to bind to…not just patches of computationally determined red, green, yellow, and blue space on a screen.  This leads into my complete lack of trust for things such as FlexX and flexible docking in general, but I think that’s a different topic for a different day. 

 More to the point, kudos to the Kornberg lab and all the grad students that slaved over the X-ray crystal data to unlock the first 20% of the structure. 

The one thing that I didn’t like about this article was that it threw a dead rat into the festivities by saying that Robert Roeder at Rockefelller University should have probably shared the award with him – even though it is something that I would whole heartedly agree with.  This is not to say that everyone on your acknowledgements, or everyone who helped advance your research should share in the work, but at least throw in the other guy who “[was] among the first to identify RNA pol II,” and “led the characterization of the activities of the polymerase in regulation of genes for decades.”

This kind of argument is not a new one to say the least, especially in this field.  Everyone should know about the Watson, Crick, and Wilson debacle for their Nobel Prize in “for their discoveries concerning the molecular structure of nucleic acids and its significance for information transfer in living material” (http://nobelprize.org/nobel_prizes/medicine/laureates/1962/).  Rosalind Franklin, a crystallographer who actually performed the crystallography work and appeared with them in Nature, was never mentioned by the Nobel committee.  It’s also interesting to note that neither Watson nor Crick ever received permission from Franklin to use her crystallographic data from which the elucidation of the alpha helical structure of DNA was made.  So even though this is not exactly the same situation, some can definitely see the parallels…at least I can.

 So, congrats to the Kornberg Lab and my sympathies to the Roeder Lab – better luck next year.


C & EN, November, 20… Vol. 1 November 23, 2006

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So I assume that all of you opened up your mailbox and with eager fingers began looking through your latest edition of C&EN news this week.  Lately I’ve been finding the business aspects kind of gloomy, what with certain chemical companies cutting back (Merck, the pharmaceutical industry, etc.) but hey, the Japanese market is booming, so I guess I’ll just have to move. 

Two articles made me think, one concerning the shipment of chemicals and the other concerning the passing of a new “Animal Terrorism” Bill. 

The articles one chlorine containment and shipment and the general shipment of hazardous materals was interesting.  I really have never thought about how they bring me my Ethylacetate and as long as they kept it coming, I didn’t care.  But when you think about it, there’s a lot of “stuff” getting moved around that is pretty nasty and oh so unfriendly.  They referenced the derailing of some chlorine containers spilling gaseous chlorine into the open on a metric ton scale.  That would be pretty bad, especially if it happened to my shipment of chlorine that I needed for a reaction. 

Also, the animal terrorism bill leaves something to be desired since it points out that it is illegal to enter a laboratory and set free the animals, nor is it legal to harass a scientist or the family of a scientist because of his or her research.  Hmmm…I thought that this was already illegal.

 On top of that, several animal activist groups (go online and you shall find many) claim that this is infringement of free speech and parts of first ammendment rights.  I’m all about the humane treatment of animals, in and out, of the lab.  But it’s a shame when specific laws like these need to be addressed because some people can’t see the bigger picture.   Though, I will agree that some animal research is useless, but coming from a med lab, it comes with the territory, so bring on the rats baby.

Hello, is this thing on…? November 22, 2006

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So the holdiay season is upon us and of course, I am alone in the lab.  I don’t know if other people have the same thing happen in there respective laboratories, but it seems that every time there is a holiday weekend, people just take more and more time off around here.  Even the Boss was gone for the entire week. 

Not that I’m at all bothered by it since I get all of the instruments and lab space to myself and can be that guy who plays his music/NPR too loud…hey, I got catch up on my news sometimes.

 Although it is a bit brisk outside today, making the eventual drudge into the outside world an awful thought to think about. I guess it’ll just keep me here longer today.