One of the fundamental reactions we teach in organic chemistry is “nucleophilic substitution” in which an atom or group of atoms in a molecule is exchanged for another one. Quite logically, the substituted atom or group is known as a “leaving group.” The ease with which a leaving group can be displaced by the substituting species, or “nucleophile,” is variable and depends on several factors including the strength of the bond with which the leaving group is attached to the rest of the molecule. For example, a carbon-fluorine bond is stronger than a carbon-chlorine bond so that a chlorine atom is more readily replaced by a nucleophile than a fluorine atom.
Why do we torture students by making them learn such apparent nuances? Because such nuances can have significant practical applications! For example, an improvement in the treatment of glioblastoma, the most aggressive form of brain tumour with an average survival time of 10-13 months after diagnosis.
The onset of cancer and its treatment make for complicated science that is not easy to simplify. Nevertheless, I’m going to give it a shot. Time to buckle up because you may be in for a bumpy ride! Some of you may immediately conclude that this discussion is “over your head,” but cancer is a topic that is worth struggling with because the disease affects almost everyone in some way. I know that very well, having had to confront my wife’s losing battle with glioblastoma. That obviously increased my interest in this dreadful disease. So, let’s get going. Try to stick with me even though it may be a bit painful.
The basic challenge in the treatment of any form of cancer is the destruction of cancer cells without harming normal cells. Unfortunately, there are no truly effective drugs to treat glioblastoma, but “temozolomide” can extend survival in some cases by disrupting the cancer cell’s DNA, the giant molecule that carries instructions for everything a cell does, including how it divides.
DNA is found inside the nucleus of a cell and is composed of two strands that twist into the shape of a spiral ladder called a double helix. It is made up of four building blocks called nucleotides: adenine (A), thymine (T), guanine (G), and cytosine (C). The nucleotides attach to each other (A with T, and G with C) to form bonds called base pairs that connect the two DNA strands. All the instructions carried by DNA are encoded in short fragments of DNA called “genes,” in which the four possible “nucleotides” are linked in a specific sequence.
All life is based on cells that form our tissues and organs and on their ability to multiply as needed for growth as well as for the replacement of aging or damaged cells that are destined to die. The division of a cell to form two new identical cells requires its DNA to separate into two strands, each of which then becomes a template for the formation of double-stranded DNA in the new cells.
A cell becomes cancerous when a “mutation,” which is an alteration in the sequence of nucleotides that make up a gene, occurs. This can be the result of an accidental error when a cell divides, or can be caused by exposure to ultraviolet light, radiation or exposure to some carcinogenic chemical such as the polycyclic aromatic hydrocarbons (PAHs) found in smoke. Cells with such damaged genes no longer behave as a normal cell and exhibit altered behaviour that can include out-of-control multiplication, the ability to avoid the immune system, ignorance of signals to stop dividing, and aggregation to form tumours.
DNA can also be damaged by a process known as “methylation” in which a “methyl group,” consisting of a carbon and three hydrogen atoms (CH3) gets attached to one of the nucleotides in DNA. This “methylated” nucleotide disrupts the helical structure of DNA and prevents it from dividing properly. Methylation can happen due to natural biochemical reactions or due to exposure to chemicals such as N-nitroso compounds, found in foods like bacon, sausages or cold cuts that are preserved with nitrites.
Methylation can also be carried out on purpose, such as with the use of temozolomide. This gums up the ability of DNA to reproduce, which is desirable when trying to eliminate cancer cells. Unfortunately, the drug will also methylate the DNA in healthy cells, potentially damaging these as well. Fortunately normal cells are equipped with an enzyme (O6-methylguanine methyltransferase (MGMT)) that can repair damage to DNA if given enough time. But about 50% of glioblastoma cells lack this enzyme, so that treatment with temozolomide will damage them and keep them from dividing. There is a problem, though. With time, tumours adapt and evolve various ways to prevent methylation by temozolomide, causing resistance to the drug.
When such resistance develops, researchers play a little molecular roulette and experiment with slight variations in molecular structure to produce a novel drug that avoids resistance. Lomustine, instead of attaching a methyl group to DNA like temozolomide, attaches a “chloroethyl group” made of two carbons and a chlorine atom (ClCH2CH2-). This triggers a subsequent internal nucleophilic substitution reaction in the chloroethylated nucleotide that changes the structure of DNA and prevents it, and consequently cells that contain it, from dividing properly. Still, we have the problem that this also happens in a healthy cell. But were the substitution reaction slowed down, researchers thought, it would give more time for a healthy cell’s MGMT to reverse the chloroethylation and prevent damage. Glioblastoma cells, lacking MGMT, would still be prevented from multiplying.
Knowing that fluorine is less readily displaced than chlorine, researchers turned to a drug that instead of introducing a chloroethyl group introduced a “fluoroethyl group (FCH2CH2-).” KL-50, as the drug was tentatively called, did indeed slow down the substitution reaction that leads to DNA damage. It took about five hours for the cancer cells to be damaged to an extent that they were prevented from multiplying and that gave enough time for the MGMT in healthy cells to reverse the fluoroethylation reaction and prevent damage. As a result, cancer cells were destroyed but healthy cells survived.
Of course, clinical studies will be needed to determine if KL-50 works in glioblastoma patients, but studies have shown that it shrinks tumours in mice. That is encouraging. Whether the drug eventually turns out to increase the life expectancy of victims of this awful disease remains to be seen, but it is clear that knowledge of nucleophilic substitution and leaving groups played an important role in its development. And now you have an example of why we torment organic chemistry students with the nuances of nucleophiles and leaving groups.
