How to Fix Medical Research in One Law
Posted 8:18 AM

The #1 reason why companies won't research or develop a drug or treatment - even if it works or has proven mechanism - is if they don't think a patent will hold.

If the drug is a pre-existing compound, or was published in research literature by a University... this will often preclude development.

This problem was illustrated quite nicely in a recent Newsweek article, but the author came to a rather backward conclusion.

The right solution is simple. The company that pays for the clinical trials and gets FDA clearance for a drug or treatment should receive an exclusive right to develop or license that precise treatment for several years - even if it is not patentable.

In other words...if you do a trial on Vitamin-C infusion as a cancer cure... and prove it, and get clearance to use that treatment.... then your company becomes the only company allowed to to advertise and sell Vitamin-C cancer treatments for 3 years.

Sure, lots of people will "off label" buy their own Vitamin-C and use it. But a good marketing team with an exclusive on a working treatment is worth its weight in gold.

A simple law like this would be extremely beneficial to the industry. Billions of dollars are wasted every week on developing new, less-effective drugs, when effective solutions already exist... merely because pre-existing drugs aren't patentable.

An incentive for innovative treatments - without needing to develop new drugs, would work wonders. Literally.

Labels: biotech, politics

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Catalytic Antibodies Simply Explained
Posted 1:17 AM

Catalysis is the process of speeding up a chemical reaction by lowering its activation energy - the energy hump a reaction has to go over before it can roll downhill. Efficient catalysts of chemical reactions are extremely commercially valuable and widely researched.

Enzyme Catalysis Basics: Biological enzymes are known to catalyze (speed up) chemical reactions, in part, by stabilizing the transition state (halfway point at the top of the hump) of an otherwise energetically-favorable (downhill) reaction. Some catalysts work by moving chemicals next to each other that would otherwise not randomly meet that often. (1) Some enzymes are known to change their shape (conformation) after binding and during the reaction - driving catalysis (2).

The immune system can be stimulated to respond to a incredibly diverse range of molecules by producing antibodies which bind (cling, stick) to these molecules. The theory of "catalytic antibodies" was that if an antibody was purified that bound to the transition state of a reaction, it would, in the same manner as an enzyme (above), stabilize that state (drag it up the hill) and accelerate the reaction. In order to generate such an antibody, a "transitions state analog" (TSA) - molecule that looks like the known transition state of a reaction - is used. Antibodies that are generated (usually by injection into a mouse) to bind to that TSA are then screened until one is found that catalyzes the reaction. Surprisingly, to me, this works very well. (3)

However, these "abzyme" catalysts are never as efficient as enzymes for many reasons. The abzyme may strongly bind to the product of the reaction (not letting go when it's done), greatly inhibiting its effectiveness. Also there is the difficulty of creating a TSA - they may differ in bond angles or polarity, etc. Many enzymes form strong (covalent) bonds during their catalysis mechanism, but this is not known to be possible with abzymes. Enzymes also employ conformational changes, metals and other cofactors to accelerate catalysis.

Abzymes are being aggressively researched, however. For example, it may be possible to engineer abzymes which bind to prosthetic groups to be used in metal-catalyzed reactions. Abzyme reactions which employ several cofactors have already been demonstrated. (4,5)

(1) "Chemical basis for enzyme catalysis", 2000, TC Bruice, SJ Benkovic
(2) "Catalysis by Enzyme Conformational Change", 2004 Jiali Gao1, Kyoungrim Lee Byun, and Ronald Kluger
(3) "Catalytic antibodies" (Biochem. J.), 1989, G. Michael BLACKBURN,t Angray S. KANG
(4) "Pyridoxal 5?-Phosphate-dependent Catalytic Antibody" (1996) Svetlana I. Gramatikova, Philipp Christen
(5) "A cofactor approach to copper-dependent catalytic antibodies" Kenneth M. Nicholas, Paul Wentworth, Jr

Labels: biotech

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Myoglobin Pov-Ray
Posted 9:34 AM

One of my assignments from biochem class was to play around with VMD and Pov-Ray. It was fun. The red sphere is supposed to be an oxygen.... (I know it's not that big, or shiny, or red and there's no heme prosthetic to bind it with.)

You can click on the image to zoom in.

Labels: biotech

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Caffeine, Cancer and Gray Hair
Posted 3:41 AM

We're exposed to DNA damaging, age-accelerating radiation every day. And caffeine might make it worse... or better. (Click on links for references).

Caffeine can accelerate the division of cells, speeding up repair, but also it appears to inhibit the activation of "ATM", a gene responsible for DNA repair. This makes cells more "radiosensitive" ... in other words, more likely to have damaging mutations.

Caffeine is fully absorbed about 45 minutes after drinking coffee. However, it stays in the body for up to 10 hours (5-10 hours for most of us, but 10-20 or more hours for people over 55, women who are pregnant, children and women taking hormone (oral/patch/etc) contraceptives).

So how does this add up? Basically, it means, don't drink coffee up to 10 hours before you go out in the sun for any extended period of time... unless you want your hair to prematurely gray. (Graying hair, and overall aging, has been directly linked to DNA damage and the mediation of this damage by pathways such as those involving ATM kinase.)

Labels: biotech, science

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Given Molarity and Ka, Solve For PH
Posted 5:08 AM

In water, when [H+] and [A-] are produced, [H+] and [A-] are approx equal (call it x). If Ka is very small compared to M (which it usually is), then you can usually reduce it to sqrt(M*Ka).

x^2/(M-x) = Ka
x = sqrt(M*Ka-Ka^2/4)-Ka/2
ph = -log(x)

Labels: biotech

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