This is part 4 of a series of posts delving into the fundamental scientific challenges in drug discovery. Here are the other parts: 1, 2, 3.

After a short digression into the fundamental laws of physics and the role of falsification in science, we now return to our series of posts on the complexities of drug discovery. In the past posts we looked at three reasons why drug discovery is hard: firstly, because finding a protein implicated in a disease is not easy; secondly, because finding a small molecule that will "drug" this protein is not easy; and thirdly, because getting small molecules inside cells is pretty hard.

But let's say that we have now achieved these three goals. We have a protein which seems to be a key target for small molecule binding in a particular disease, we have actually raided the haystack and found a small molecule that can bind to this protein, and we have even managed to get our molecule inside cells, past the watchful gaze of the lipid bilayer and guardian proteins like PgP. Our drug is now a denizen of the bloodstream.

This is where the fun begins. The next phase of the story concerns one of the most important - possible the most important - aspect of drug development: pharmacokinetics. As the name indicates, pharmacokinetics is the study of the "kinetics" of pharmaceutical compounds. In a nutshell, it deals with what the body does to the drug. The meaning of "kinetics" here is quite broad but it gets to the heart of the issue: we want to find out how fast or slow the drug is absorbed, distributed, metabolized and excreted out of the body. A more comprehensive moniker for pharmacokinetics is thus ADME - Absorption, Distirbution, Metabolism and Excretion. While separately studies for convenience, these four functions are actually simultaneous and linked.

Let's deal with absorption. We already saw how one barrier to absorption arises from the nature of the cell wall and the presence of proteins which are designed to eject drugs out of the cell. The second and third phases, distribution and metabolism, are also more challenging than they seem. In one sense distribution is easy, however, since once your drug is in the blood the natural blood flow of the body can automatically transport it to various organs. But before it can do this the drug has to deal with a formidable organ that's truly the alpha male in the pack: your liver. No orally ingested drug can make it to any other part of the body unless it makes it through the liver. The liver is truly a gift from heaven. Not only does it play a critical role in metabolizing food through the action of various enzymes but it plays an even more critical role in guarding the body against the entry of foreign molecules. Malfunctioning of the liver is the cause of many very serious and often fatal diseases, ranging from cirrhosis to liver cancer. And unlike PgP this role is not passive; the liver actually performs chemical reactions on molecules to detoxify them. If PgP is an Orc, then the liver is Sauron himself.

The liver sports an extraordinary series of enzymes that recognize and react with almost every molecule of food or drug that we ingest. These enzymes are collectively called the cytochrome P450s, abbreviated as CYPs. They account for about 75% of all the reactions that a drug will undergo in the body. In the heart of every CYP is an iron atom that catalyzes the reaction of organic molecules with oxygen. The primary function of the CYPs is thus the oxidation of drug molecules. Why oxidation and not reduction? Because in most cases oxidation makes the molecule less hydrophobic, more water soluble and more like to be excreted through water-rich kidneys; in general kidneys like polar compounds while the liver like nonpolar ones.

The CYPs thus function as primary metabolizing enzymes. A drug that is oxidized by the CYPs can have several fates. It can suddenly become so polar that it is rapidly excreted through the urine, diminishing its ability to reach its target organ and perform its functions. Sometimes the metabolites of the drug - the molecules that it changes into after it is oxidized - are themselves as powerful as the drug. More commonly they are less powerful. Sometimes they may even be toxic. In rare cases the liver can literally save your life by converting a toxic molecule to a non-toxic one. Consider, for instance, the infamous example of the anti-allergy drug terfenadine. Terfenadine is metabolized by the liver to a similar molecule called fexofenadine. It turns out that terfenadine causes an imbalance in the rhythms of the heart (more on this in another post), a serious condition called cardiac arrhythmia which can quite certainly be fatal. Terfenadine displays the effect, fexofenadine does not. The liver, while efficient, does not metabolize all of terfenadine to fexofenadine, and when people started dying from taking terfenadine the FDA quickly withdrew the drug. But it's chilling to think about what would have happened had not terfenadine been metabolized to fexofenadine at all.

Doctors and pharmaceutical scientists thus have to calculate the correct dosage of a drug by correcting for the amount that might be wasted through metabolism by the liver. Researchers can sometimes cleverly take advantage of the CYPs' hunger for organic molecules by administering two drugs, one of which engages the CYPs and keeps it busy so that the other can get across into the bloodstream. Practically this means that you can get away with administering a lower dosage of the second drug than what you usually would; this is beneficial for a variety of reasons, including reduced risk of side effects. An amusing, important and serendipitously discovered example of this effect is the increased effectiveness of statin drugs - which are the world's best-selling heart disease medicines - upon the drinking of grapefruit juice. What happens is that certain compounds in the grapefruit juice bind to the CYP enzymes and keep them busy while the statins can safely get across. It's the classic case of using a diversion to get your troops across the gate. But what this story of the liver demonstrates is another hurdle on the way to drug discovery: it is difficult to know how your molecule is going to be metabolized by the liver unless you actually do the experiment, either in a human or in a simplified test tube model.

Even after drugs have made it past the liver they still have a variety of hurdles to navigate before they can get uniformly distributed throughout the body and do their magic. Other enzymes and organs in the blood can cleave specific bonds and render the drug inactive. So-called secondary metabolizing enzymes attach highly polar groups like sugars to drugs. These groups act like tags which rapidly shuttle the drugs out of the body through the kidneys. Another simple obstacle is the ubiquitous presence of the protein albumin which can tightly bind to drugs and keep them from getting to their target. Cases where 98% of the drug is bound to albumin and only 2% is actually available as a drug are not uncommon. In addition getting to target organs again presents many physical and chemical barriers.

Drugs against neurological disorders are especially hard to engineer since they have to pass through an additional hurdle called the blood-brain barrier. The BBB is a gnarled network of capillaries and cells, sensibly put in place by nature to avoid exposing our all-important brain to harmful molecules. But just like with the liver and the cell membrane, the BBB often does its job too well, blocking important medicines from getting into the brain. It has been found that small, nonpolar compounds are the best candidates for getting across the BBB, but this limitation on size and physicochemical properties puts yet another constraint on what is already a very hard, multiple variable optimization problem.

This concludes the fourth part of the series. Even when a drug gets across the cell membrane there is a variety of enzymes and barriers - especially in the liver - that are poised to tear it apart, change it into something else and quickly get it out of the body. All these mechanisms are sensible defense mechanisms set in place by evolution but they work against the body when you are trying to get a useful drug into it. Because of these pharmacokinetic problems, often you may have a drug that works great in a test tube but is simply not stable enough or doesn't hang around long enough in the body to do its job. And remember, it has to do this job without sacrificing the potency and binding against a protein target that made you pick it to begin with. No wonder pharmacokinetic problems loom large in the development of any drug, and studying blood levels of a molecule and the rate of its clearance from the body are standard parameters in any drug experiment that has advanced beyond the test tube stage. One can study these problems in rats and mice and monkeys, but none of these studies can truly tell you how these issues will look like when the drug is ingested by tens of thousands of people around the world and makes its way to the shelves of your local pharmacy. As usual, prediction is difficult, especially about the future.

Reason 1: Drugs work by modulating the function of proteins. It’s difficult to find out exactly which proteins are involved in a disease. Even if these proteins are found, it is difficult then to know if their activity can be controlled by a small molecule drug.

Reason 2: Since nature has not really optimized its proteins for binding to drugs, it is very difficult to find a hit for a protein even after searching through millions of molecules, either natural or artificial. And even when a hit is discovered, we don’t know for sure how to turn it into a drug with favorable properties.

Reason 3: It is very difficult to get drugs into cells, partly on the basis of fundamental chemical properties and partly because nature has conspired to create specific proteins whose job is to keep drugs out. What’s worse is that we still have little idea exactly what kinds of drugs are kept out by these proteins, so that we have to work on the basis of trial and error to find those that escape their clutches and get in.

Reason 4: A variety of enzymes and processes can adversely affect the absorption, distribution, metabolism and excretion of a drug - a gamut of processes referred to as 'pharmacokinetics'. It is very difficult to predict beforehand the details of these processes, and to modify the structure of your drug so that it can safely navigate this treacherous terrain and stay intact while still retaining its original potency and specificity for a target protein.