Just about anyone who’s ever been in a GNC knows melatonin by now. People know it best as a sleep aid. However, it is responsible for a diverse range of biological processes, and you might be surprised to know that it is a sufficiently ancient compound that it seems to be found in quite a wide range of species.

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This is one of those boring-seeming ones: cysteine. However, biochemistry really wouldn’t work without it. Cysteine is the sulfur analogue of the amino acid serine. I say “sulfur analogue” because oxygen and sulfur are in the same group (column) of the periodic table. They are in group 6B, also known as the “chalcogens”, from the greek for “ore formers.” (Oxygen and sulfur, as well as, to a lesser extent, selenium and tellurium being ubiquitous in ores of metals). Many oxygen compounds have a sulfur analogue. In many ways members of the same group are very similar to each other, because their electrons are configured in analagous ways.

Oxygen can form a structure called a peroxide. R-OH (R representing something else attached to the oxygen) is an alcohol that has a peroxide brother in R-O-O-R. Peroxides are potent oxidizers (witness hydrogen peroxide and benzoyl peroxide’s use as disinfectants in low concentrations). At very high concentrations, they can be initiators for explosives (or explosives themselves!).

The sulfur analogue of a peroxide is a disulfide. This is a dimer of R-SH (a “thiol”), or R-S-S-R. This is an oxidized compound as well, but R-S-S-R is a much milder oxidant than R-O-O-H. Mild is the name of the game in biochemistry, since you only have cells, enzymes, blood, etc. to hold these things in. Peroxides are a bit much outside of our glass and plastic vessels. So it’s fortunate we have something mild and easily reversed, like disulfide bonds. Cysteine is what forms just about every disulfide bond in your body. The disulfide oxidized cysteine dimer is called cystine:

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This drug is one that really has had a profound effect on the medical landscape, but you don’t hear much about it in popular culture. Naloxone, commercial name Narcan, is an opioid antagonist. An antagonist is a drug that binds to a receptor, without activating it. Contrast an agonist, which binds a receptor and activates it. Opioid agonists are drugs like heroin, morphine, codeine, etc. Read the rest of this entry »

PABA, or para-aminobenzoic acid, was used as a sunscreen some time ago. Most sunscreens are simply organic molecules that aren’t too soluble in water (so they don’t wash away) that absorb UV light (and convert it into heat). There are other kinds, like zinc oxide creams, that just provide an opaque/reflective layer. PABA, however, is of the first type.

It is also a biosynthetic precursor to folic acid in many bacteria. This is a profoundly essential nutrient, especially for rapidly dividing cells. This applies to pregnant women (hence the inclusion of extra folate in prenatal vitamins) and most bacteria, which tend to be pretty busy dividing. Since people don’t depend on the PABA-Folate conversion system (because we don’t have it), PABA has been used as a drug target for antibiotics. These are the ancient sulfa drugs, which predate even penicillin. Here is the structure of PABA:

Today, PABA is not in sunscreens because of allergy and carcinogenicity concerns (close analogues are safe and included, though). Sulfa drugs have also fallen by the wayside, largely because of allergy and poor efficacy compared to the modern stuff.

Interestingly, furosemide (Lasix) contains a sulfa-drug like structure, but works on a completely different pathway (it’s a diuretic).

See you tomorrow!

Here’s a quickie, phenolphthalein:

Phenolphthalein is known as an acid-base indicator because it gives a colorimetric change depending on the pH. Above a certain critical pH, called its pKa, phenolphthalein adopts mainly the lower structure shown above . Below this pH, it is mainly the upper structure. The lower structure is pinkish-purple, the upper is colorless.

As you can imagine, molecules like this have all sorts of uses. You can figure out the concentration of an acid or base, using the color as an indicator of whether your solution is acidic or basic (8.2 is sufficiently close to 7, neutral pH, that you can get away with this). It apparently is used to test for the presence of blood. It used to be used as a laxative, but its carcinogenicity has not been completely ruled out. It is also used in Barbie Hollywood Hair (scroll down to “uses”).

The broad class of dyes are used in “pH papers” for lab use; papers soaked with one or more dyes will change color depending on the pH; a series of dyes can give resolution below even 1 pH unit, which is pretty good. “Litmus” paper is the best known of these, containing a dye extracted from lichen.

You can extract your own pH indicator from cabbage. If you never did this, you had a deprived childhood and should try it over the weekend. If you are lazy, you can just use red wine or grape juice; there is a similar pigment with red acidic and blue basic forms. This broad class of pigments is known as anthocyanins. Many of the deep reds and blues in nature are due to this class of pigments, and they make great pH indicators.

In the comments, yesterday, we started talking about other retinoids a bit. We were talking about naturally occuring ones and close pharmaceutical analogues. I was racking my brain today trying to come up with one that didn’t follow the terpenoid/long chain of alternating double bonds pattern. I know of one that a friend targets for his research, but I can never remember the structure. Then I remembered another: adapalene!

Not very like retinoic acid (a vitamin A-related compound):

It is a topical acne drug. Many of the acne drugs, such as Accutane (isotretinoin) and Retin-A (tretinoin, just retinoic acid, above) target Vitamin A (really retinoic acid) receptors.

My favorite part about adapalene is that it has an adamantyl group:

Adamantane is named from Latin, from Greek, from adamas (”diamond,” or “invincible” depending whom you ask). This is because the 3-d structure of that ugly thing is actually very much like diamond. This has led into a bunch of research on diamondoids and molecular diamonds, which are kind of neat. Here, it is just a bulky alkyl group.

I think it’s 4-day weekend time. See you later.

Today’s molecule, canthaxanthin, is a member of the carotenoid family. This includes beta-carotene and lutein. These molecules are all strongly colored. This is a function of the degree of conjugation in the system.

A conjugated system has alternating double and single bonds, as you see in that long central chain. Small conjugated systems like benzene absorb in the UV, and larger conjugated systems, like our carotenes, absorb lower-energy light, yielding a visible color. For more information, see particle in a box (warning to the uninitiated: this ventures into quantum mechanics and gets a bit esoteric). Read the rest of this entry »

I was curious about this one after seeing it in the grocery and drugstore so many times. Docosanol, or Abreva, is apparently an effective treatment for herpes labialis (cold sores). It is one of the most boring structures you can imagine, and probably one of the only drugs to have its IUPAC name as its common generic name:

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I’ve mentioned this in the past as one of the canonical bitter compounds. It was originally extracted from the bark of the cinchona tree. It has been found useful in the treatment of malaria. The scope of malaria’s effects is both broad and amazing. According to a citation in Wikipedia, malaria infects 350-500M individuals annually - for reference, this is roughly 6-8% of the world! The vast majority of infections are in African children.

Antimalarial drugs, then, are a godsend. One of the most famous natural products ever, quinine was extracted from cinchona for years, and finally synthesized by Bob Woodward in 1944. The pharmaceutical and chemical industry would look incredibly different today if this man had never existed. You can see a picture of him at Dylan’s Tenderblog. He is the one on the right, smoking the cigarette next to the flask of the toxic and/or flammable chemicals. Amazingly, RB Woodward’s total synthesis of quinine takes up only one page in a journal. It would be slightly longer today. With more pictures. Here’s a picture:

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Here is one with which many readers will be acquainted first hand: nicotine. Named after Jean Nicot, tobacco booster extraordinaire, nicotine is an alkaloid that occurs in the whole nightshade family, of which tobacco is a member. Typically people will give the structure on the left, below.

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