Structure-Activity Relationships

As you've probably noticed by now, I've changed the background of my blog a bit to *hopefully* make it easier to read. (My eyes were getting tired really quickly when I was trying to read over my posts, but my eyesight has always been pretty shitty. I blame genetics. Let's just ignore the fact that I spend waaaaaaaay too much time on computers and waaaaaaaay too little time inside.)

This post is going to be a bit different from the other ones, in that we're focusing more on the structure of the drugs themselves and how improving the structure can improve efficacy and decrease toxic effects. Yay!

1) Demonstrate understanding of the “structure-activity relationship” and its importance during the search for better, safer drugs.

The "structure-activity relationship," as the name states, is the relationship between the structure of a drug and its activity in the body. The structure-activity relationship is all to do with drugs having to be a certain shape to fit into the receptor of interest. The better a drug fits the receptor of interest, the more likely it is to bind and have an effect. Another area of concern is that a drug might be able to fit into multiple receptors and have unwanted side-effects at the other receptors: so-called "off-target side effects." Tweaking the structure of a drug may be able to prevent this from happening.

2) Show awareness for methods used to change the structure of a drug to make it a better ligand for its target receptor.

There are several different methods used to change the structure of drugs:

• Varying the substituents so that the drug has a better "fit" with its receptor
• Adding substituents that can interact with other binding sites
• Changing the length of the "linker" (the part of the drug between the bits that actually bind to the target) so that the binding groups can bind more effectively
• Changing the size of rings- for the same reason as changing the length of the "linker"
• Rigidifying areas with moveable bonds so as to "lock in" a particular structure, and therefore also "lock in" affinity with a certain receptor

Now it's time for an example of where this knowledge has been used!

Aspirin (acetylsalicylic acid) is a very useful anti-inflammatory (Nonsteroidal Anti-Inflammatory Drug for long, NSAID for short). However, it can also cause gastric issues, especially if used long-term. It was later discovered (by a Prof John Vane, who won a Nobel Prize for his work) that aspirin has an inhibitory effect on the production of prostaglandins, which function as signalling molecules in the body. Prostaglandins are produced by the oxidation of arachidonic acid by COX-1 (cyclo-oxygenase-1), a enzyme that is inhibited by aspirin.

Later on, it was discovered that aspirin actually induced its beneficial effects by acting on COX-2, an isoform of COX-1. (Aspirin can bind to both COX-1 and COX-2.) As the binding site for COX-2 is larger than that for COX-1, the logical solution was to add extra substituents to aspirin so that the resulting drug can fit into the COX-2 binding site, but would be too large to fit into the COX-1 binding site. Hence the "Coxibs," or COX-2 selective NSAIDs, were born. Conveniently enough, their names all end with "-coxib." The coxibs have been found to induce fewer gastric ulcers than NSAIDs that block both COX-1 and COX-2.

3) Show how structure-activity knowledge helps improve the pharmacokinetic and toxicological properties of drugs.

The structure of drugs can also affect pharmacokinetic parameters such as absorption and half-life. As I've alluded to in my post about absorption and distribution, one of the factors affecting absorption is the lipophilicity and hydrophilicity of drugs. These parameters can be manipulated by adding or removing substituents. As for half-life, this can be altered by protecting oxidation-prone groups (by adding bulky "steric shields") or by removing them altogether. Another way of extending half-life is to replace hydrogen atoms with deuterium (i.e. hydrogen with one neutron), which our bodies cannot break down as quickly.

Some substituents are notorious for toxic properties, and so knowledge of structure can also pinpoint which groups may need to be removed or replaced in order to improve a drug's toxic profile. Currently studies manipulating the structure of valproate, an anticonvulsant drug with possible hepatotoxic and teratogenic effects, are being done. So far, strong differences in teratogenicity have been found across different analogues of valproate. In the future, perhaps many more drugs will be improved just by tweaking their structure a little.

Toxicity to the Unborn

Moving on with toxicology, now I'm going to cover a topic that is especially important to pregnant women: namely, how certain teratogens can harm their babies. After all, it would be a real bummer (to say the least) to have to carry around an embryo/foetus for a while... only to have them die of a preventable cause.

1) Demonstrate understanding of the meaning of key terms such as teratology, developmental toxicology, embryolethality, teratogenicity.

• Teratology- I had to Google this one, because it wasn't in the lecture slides, but apparently it's the study of abnormalities of physical development.
• Developmental toxicology- The study of substances that are toxic to the conceptus (i.e. the embryo and placenta) during prenatal development.
• Embryolethality- The death of the embryo.
• Teratogenicity- The ability of a substance to produce structural alterations in the conceptus, but not embryolethality.

2) Show awareness of factors that govern the susceptibility of the unborn to chemicals.

One of the major factors that governs the susceptibility of the unborn is age. In the embryonic period (roughly the first 8 weeks), the embryo is still developing organs (organogenesis), so exposure at this stage can disrupt the development of the organs. Hence, a lot of teratogens are at their most toxic during the embryonic stage. During the foetal period, organ development and growth are occurring. Toxicity at this stage can stunt growth, which is still pretty nasty, but not quite as nasty as not developing the organs in the first place.

A second factor is the ability of the drug to cross the placenta. This, in turn, is influenced by several other factors. One of these is molecular weight. Similar to absorption the GI tract, the lower the molecular weight, the more likely it is that the drugs are able to cross the placenta. Another factor is the size of the embryo. As the embryo grows, so too does the placenta and the number of vessels supplying it. As the number of vessels grows, blood flow to the embryo increases, and thus the amount of drug that gets to the embryo likewise increases.

A third point of interest is that the unborn have a very limited ability to metabolise drugs. CYP450 only begins appearing at around 6-7 weeks, and doesn't reach adult levels until around one year after birth. The placenta also contains some CYP450 enzymes, but they generally only have a minor role unless the mother has been exposed to CYP-inducing agents. Conjugative metabolism also occurs very little in the foetus, and there are also low levels of antioxidant enzymes so that foetuses are prone to oxidative stress.

3) Understand the main toxic outcomes accompanying in utero exposure to major human teratogens such as phenytoin, ethanol, and thalidomide.
4) Demonstrate knowledge of mechanism of action of 3 major human teratogens.

Phenytoin is a drug used to treat epilepsy, but it also has a risk of causing "foetal hydantoin syndrome" in foetuses. This syndrome is characterised by malformations, such as cleft lip, a low birth weight and mental defects. However, epilepsy could also have adverse effects on the foetus, so the poor woman is caught between a rock and a hard place. Bummer.

Phenytoin is thought to have its teratogenic effects via bioactivation into reactive epoxides. It undergoes two main bioactivation pathways. In the first pathway, CYP450 converts it into a reactive epoxide, which can damage proteins and DNA if it is not first detoxified by epoxide hydrolase to form a nontoxic diol metabolite. In the second pathway, foetal peroxidases convert phenytoin into phenytoin hydroperoxide, which can form reactive oxygen radicals. This second pathway can be blocked by antioxidants.

Ethanol is probably the teratogen of greatest concern nowadays as it's so readily available. It can cause Foetal Alcohol Syndrome (FAS) which is characterised by the FAS "triad" of symptoms: growth retardation, craniofacial abnormalities and a low IQ. It is not always easy to diagnose because there are other teratogens that have similar symptoms; however, it can be tested in the meconium (the first few stools passed by the baby after birth). These "meconium markers" include ethyl glucuronide, ethyl sulfate and fatty acid ethyl esters, which are metabolites of ethanol.

Aside from FAS, ethanol exposure can have somewhat milder effects in the form of ARND, or Alcohol-Related Neurodevelopmental Disorders. ARND doesn't have visible structural effects like FAS, though it does have CNS impairments. It is important to note that even mild alcohol use during pregnancy can affect the CNS. This might be particularly problematic in the early stages, when the woman might not even know that she's pregnant.

Once again, ethanol has several routes through which it can exert its teratogenic effects. In one route, ethanol is oxidised by alcohol dehydrogenase to form acetaldehyde, which is a protein and DNA adduct (protein/DNA adducts are mentioned in my previous post). In a second route, it can be oxidised by CYP2E1 to form hydroxyethyl radicals, which then form oxygen radicals, which then start destroying lipid membranes and may have roles in forming reactive aldehydes.

The third main teratogen that I'm going to cover is thalidomide, which is infamous for having caused birth defects all over the developed world and was a major impetus for the development of modern toxicology. It was originally developed to treat nausea and insomnia in pregnancy, and was well tolerated in mothers. However, babies who had been exposed to this in the first trimester of pregnancy were found to be prone to birth defects, most notably phocomelia (reduction or absence of limbs).

Unfortunately, I can't tell you how thalidomide exerts its teratogenic effects, because the scientific community doesn't know for sure either. It doesn't help that thalidomide has around 12 metabolites either. Here are some possible reasons:

• It blocks angiogenesis in rabbits, so maybe it blocks vascularisation in growing limb buds
• It inhibits integrin beta 1 and beta 2 which mediate attachment to the ECM, so maybe cell migration is inhibited
• Pro-apoptotic effects?
• Disruption of various metabolic processes?
• Binds to CRBN (cereblon), which is an E3 ubiquitin ligase. CRBN may have roles in limb development, as CRBN-deficient zebrafish have been found to have fin abnormalities.

Target Organ Toxicity

Now I'm going to continue on with toxicology!

Oh, and by the way, a quick word about the 2nd lab for those of you who haven't done it yet. It's a great lab- very fun and relaxing. You'll be disappointed when it ends.

*cough*

Anyway, target organ toxicity. Here we go...

1) Demonstrate an awareness of the significance of “local” versus “systemic” toxic exposures.

This is fairly self-explanatory. Some chemicals can injure the site of exposure- hence "local" exposure. Others need to get into the systemic circulation- hence "systemic" exposure.

2) Understand why the toxicity of particular chemicals is expressed in just a handful of “target” organs.

Often, toxic responses occur in only a handful of "target" organs. This may be because there is preferential delivery to that target tissue. For example, the liver is often at risk because it's the first place that drugs go after being taken up via the GI tract. Another reason for target organ toxicity is that enzymes that break down the drug into its toxic metabolites may only be present in certain organs. Once again, the liver is often particularly vulnerable as it contains a lot of these enzymes.

3) Be able to define the term “bioactivation” and show awareness of its toxicological significance.

"Bioactivation" is basically the breakdown of a drug into a more toxic metabolite. Often this results in a drug becoming more electrophilic (i.e. contains electron-deficient sites that "love electrons"). Electrophilic sites can interact with nucleophilic sites in proteins or DNA, which obviously isn't too desirable. These toxic, electrophilic metabolites are sometimes also known as protein or DNA "adducts." It's not all doom and gloom, though, as the body often has ways of getting rid of these toxic metabolites before they become a huge problem.

4) Understand mechanistic basis for the classic toxicological responses that accompany paracetamol overdose and exposure to MPTP.

Paracetamol (known as acetaminophen in the US) is a drug that is pretty useful for relieving headaches in low doses, but can wreak havoc on your liver in high doses. It is an intrinsic hepatotoxicant, which means that its toxic effects are predictable and dose-related. (Other types of hepatotoxicants include idiosyncratic hepatotoxicants, which are less predictable and probably require prior exposure, and cholestatic hepatotoxicants, which inhibit the formation and flow of bile.)

Paracetamol can undergo three different routes of metabolism. It can undergo sulfation via sulfotransferases, which produces a safe, water-soluble metabolite that is more readily excreted by the kidneys. It can also undergo glucuronidation via UDP-glucuronosyltransferase, which again produces a water-soluble metabolite for easy excretion. The third pathway is a bit more problematic. Around 2% of paracetamol is bioactivated by CYP450 enzymes, particularly CYP2E1, CYP3A4 and CYP1A2. This forms a toxic metabolite known as NAPQI, which can go around using its electrophilicity to destroy proteins and cells. (Rude.) (And no, I'm not sure what NAPQI stands for, aside from that the QI bit probably stands for "quinone imine" because the slide says "toxic electrophilic quinone imine metabolite.")

But again, it's not all gloom and doom, as our bodies have ways of getting rid of NAPQI. NAPQI can be metabolised via glutathione conjugation, due to the action of a very nice enzyme called glutathione-S-transferase.

Unfortunately, at really high doses of paracetamol (much higher than regular doses), this might not be enough. Administering N-acetylcysteine may help, as it helps to replenish the body's supplies of glutathione and thus helps the body to get rid of NAPQI. The sooner this is done, the better. It takes several days to die from paracetamol poisoning, but by the time symptoms start to show, it might already be too late.

Another interesting point to make is the effects of alcohol on paracetamol hepatotoxicity. Ethanol is actually a competitive inhibitor of the CYP450 enzymes that bioactivate paracetamol (particularly CYP2E1). Hence, if you have normal levels of CYP450 enzymes (as do people who drink rarely), downing paracetamol with ethanol is actually decreasing your susceptibility to paracetamol toxicity. People who drink heavily don't get to experience this protective effect, though, as they have higher expression of CYP2E1 in their livers. Instead, they are more susceptible to paracetamol toxicity.

NOTE: If you are thinking of committing suicide, please call Lifeline on 13 11 14. And definitely don't try to go by overdosing on paracetamol, because that several day window is more than enough time for you to change your mind- and by then it might be too late. So yeah, call Lifeline, and if you don't like talking they also have a web chat function- as does Kids Helpline and eheadspace.

Alright, now time to talk about MPTP. Firstly, I'm going to answer the question that's probably on your mind right now- what is MPTP? Well, another drug known as MPPP (meperidine opioid) was found to induce Parkinson's-like symptoms in drug addicts. It was soon found that it wasn't so much MPPP that was the problem, though. You see, MPTP could be formed as a by-product of the reactions that make MPPP.

MPTP can cross the blood-brain barrier, where it is activated by the MAO-B enzyme located in astrocytes. It forms a toxic metabolite known as MPP+, which actually ends up affecting dopaminergic neurons, particularly in the substantia nigra, as MPP+ is a substrate for dopamine reuptake pathways. Aside from interfering with the distribution of dopamine in vesicles, MPP+ is also capable of forming reactive oxygen radicals. Further issues arise when MPP+ is sequestered by mitochondria, where it inhibits the electron transport chain and produces shitloads of oxygen radicals. This, in turn, oxidises DNA and activates apoptosis (cell death). This means that there's less dopamine to go around, which in turn causes many of the symptoms of Parkinson's.

As for how MPTP was found to cause neurotoxicity via oxidative stress? Well, that's a bit complicated, so you can probably afford to skip over this bit. One bit of evidence that MPTP causes toxicity in this manner is that Nrf2-knockout mice are more susceptible to MPTP toxicity. Nrf2 is usually bound to another protein called Keap-1, but during oxidative stress, it is released. When released, it acts as a transcription factor which regulates genes containing ARE (Antioxidant Response Element). Without Nrf2, mice are more susceptible to issues relating to oxidative stress.

5) Show understanding of the emerging role of HLA phenotypes in idiosyncratic hepatotoxicity

I mentioned idiosyncratic hepatotoxicity earlier on in this post. In case you've forgotten, idiosyncratic hepatotoxicity is unpredictable and rare, and may require prior exposure. Idiosyncratic responses may also be gene-related. Some variations of HLA (human leucocyte antigen) genes have found to be associated with hepatotoxicity; however, there is still a lot of work that is being done in this area.

Introduction to Toxicology

Now we move onto toxicology, which looks more at the adverse effects of not just drugs, but all kinds of substances.

1) Demonstrate an introductory knowledge of the scope and history of the discipline of toxicology.

Oh joy, the history stuff. Now I'm not a history buff, so I'm just going to give the bare bones here.

There's been some interest in toxic substances for a long time, which is why the ancient Greeks were able to poison Socrates. (After all, they wouldn't have been able to poison him without knowing what substances were poisonous.) The ancient Egyptians also had recipes for poisons. There was also some guy called Mithridates VI who lived in Pontus (which according to my quick Google search was located in what is now northeastern Turkey). This Mithridates VI chap wasn't one you'd want to cross, because apparently he would test poisons and antidotes on prisoners. (Somehow, I don't think that would pass an ethics board today.)

Moving over a millennium later to the year 1490, in Basel, Switzerland, the medieval physician Paracelsus suggested a very important concept. He suggested that "the dose makes the poison," a phrase that you might have heard before. Basically it means that everything is poisonous to some degree but it is the amount that largely determines toxicity. For example even water can become toxic if you consume too much of it.

Another important figure was Mathieu JB Orfila, the Spanish "Founder of Modern Toxicology" hailing from the year 1787. He made quite a few contributions, including publishing a "Treatise of General Toxicology" when he was only 26 years old. He refined methods for detecting poisons in the body, which was helpful in forensics as well.

Skipping forward to today, the thalidomide disaster of the 1960s spurred renewed interest in toxicology. There are now journals and societies dedicated to it. The end. (Or not, because toxicology, just like any other discipline, is still developing. But writing "the end" gives me satisfaction because I'm pretty shallow.)

2) Show an awareness of the unique opportunities for exposure to chemical substances in our modern world.

As I mentioned when I spoke about Paracelsus, pretty much everything is toxic at certain doses. And "everything" actually includes quite a lot of substances given the variety of things we are exposed to in our everyday lives. Aside from industrial chemicals and environmental pollutants, we are also exposed to a variety of household chemicals, drugs, food additives and so on.

3) Display an understanding of the “dose-response relationship” and its foundational importance to toxicology.

The dose-response relationship is literally just relating the dose to the percentage of patients that experience an effect (i.e. a response). It can be plotted on a graph, which are usually sigmoidal (S-shaped): at lower doses there is little to no effect, but as the dose enters the therapeutic range, the response increases quite steadily until the therapeutic range is exceeded, at which point the graph flattens out again.

Similar curves can be drawn for the toxicity of drugs. At low concentrations, there is little to no effect. The suggested dose at which an effect begins to occur is the "threshold." After the threshold dose, the toxicity increases steadily until pretty much everyone has succumbed to the toxic effects, at which point the graph flattens out again. Patients who respond at lower doses are considered to be "susceptible individuals," whereas patients who don't respond until very high doses are considered to be "non-susceptible individuals."

There are different kinds of susceptibility to drugs. Some responses, the "hypersensitivity responses," basically encompass things such as allergic reactions to drugs. These often require prior priming of the immune system. The other category of susceptibility, "idiosyncratic responses," are generally thought to arise from genetic traits.

4) Demonstrate understanding of the importance of exposure route, exposure frequency/duration, and toxic latency as determinants of toxic effects to foreign chemicals.

Exposure route- Sometimes the route of exposure influences the magnitude of the toxic response. For example, IV drugs can be more toxic than oral drugs. This is because while IV drugs are administered directly into the systemic circulation, oral drugs have to bypass the gut wall and the liver. Inhaled toxicants are also of great concern because it is harder to control your exposure (for example, being stuck in a cloud of secondhand smoke while waiting for the bus).

Exposure frequency/duration- The frequency and duration of exposure can also influence the toxic effects. Exposure duration can be roughly categorised into four categories: acute (< 24hr), subacute (1-30 days), subchronic (1-3 months) and chronic (3+ months). An example in which the toxic effects may vary according to the duration of exposure is benzene. Under acute conditions, benzene causes depression of the central nervous system. However, chronic exposure can lead to bone marrow toxicity and leukaemia.

A related point is that sometimes a drug may be less toxic if administered in smaller doses over a longer time (a process known as "dose fractionation"), but carcinogens and other kinds of mutagens may be exceptions to this rule.

Latency- Latency is essentially how long it takes for a toxic response to appear. Some toxicants show their toxic effects immediately, while others take weeks or even generations to appear.

Basic Principles of Pharmacokinetics

(I notice that my overall page views seem to have dropped off quite a bit since the test yesterday. Good job, guys.)

(EDIT 17/6/16: I noticed that there were some errors with regards to the half-life equations. I have fixed them up, and hopefully they should be correct now.)

1) Show awareness of how plasma drug concentration versus time curves provide valuable insight into the pharmacokinetic properties of any drug

Plasma drug concentration versus time curves are a great way to show trends in plasma concentrations of drugs (well, that's pretty much what they're meant to do, by definition). Also, if you calculate the area under the curve, by integration or otherwise, you can find out the patient's total exposure to a drug over a given time. A larger area under a curve would suggest that the drug is better absorbed. As well as this, you can also use the area under a curve to calculate other pharmacokinetic parameters, such as clearance: more on this in a bit.

2) Show an understanding of the concept of “clearance” and how it is determined for a given drug

Clearance is the volume of blood cleared of the drug per unit of time (and is hence measured in units such as L/hr or mL/min). It is also the constant that relates the plasma drug concentration with the rate of elimination. "Total body clearance" refers to the overall clearance, whereas "renal clearance" and "hepatic clearance" refer to clearance by the kidneys and liver, respectively. To determine the clearance, you first need to give the patient a single IV dose of the drug. (Oral won't work, because there are too many confounding factors surrounding the absorption of oral drugs.) After that, you need to take blood samples at various time points and work out the plasma drug concentration at each time point. These points can then be plotted onto a curve and the area under the curve calculated. Finally, to work out the clearance, simply divide the dose by the area under the curve.

Clearance is important in determining drug concentration at "steady state." Steady state is the state in which the rate of drug administration is equal to the rate of drug elimination.

Now, as I've mentioned before, clearance is the constant that relates the plasma drug concentration with the rate of elimination. Hence:

Clearance * Plasma drug concentration = elimination rate

However, when the plasma drug concentration = steady state drug concentration, elimination rate = rate of drug administration. Hence:

Clearance * Steady state drug concentration = Rate of drug administration

Again, this gets a bit more complicated during oral dosing. There isn't really a "steady state drug concentration" in oral dosing as the drug isn't being constantly infused- rather, it is taken over several intervals. However, to my understanding, this equation is still somewhat applicable, but you have to replace "steady state drug concentration" with "average drug plasma concentration between dosing intervals," which is a bit of a mouthful.

3) Show an appreciation of the “volume of distribution” and how it is estimated together with an awareness of how this value reveals the behaviour of drugs within the human body

I feel like I've already spoken about this before. Oh wait, I have, on an earlier post: Drug Absorption and Distribution.

Now I'm going to go a bit further and talk about how the volume of distribution is estimated. It's best estimated using the plasma drug concentration at zero time, as you know that no drug could have been metabolised by that point. Once again, IV dosing is used so as to avoid the confounding variables of absorption by the gut and so forth. Blood samples are collected at various intervals, and then the curve is extrapolated back to find the plasma drug concentration at t = 0. The original dose is then divided by this plasma drug concentration to give the volume of distribution.

Why is the volume of distribution important? Volume of distribution can be useful for helping us determine how to achieve a therapeutic drug concentration in a short period of time. As the volume of distribution = (dose)/(plasma drug concentration), then the dose required to reach a particular plasma concentration can be calculated by dose = (volume of distribution)*(plasma drug concentration).

4) Be able to provide a simple sketch to show an appreciation of the concept of drug “half-life” together with an awareness of how it is estimated in human subjects.

Okay well screw the "simple sketch" part because I'm too lazy to draw a diagram. Half-life is probably a concept that you've encountered before, though: it's simply the time that it takes for the plasma concentration of a drug to drop by 50%. Half-life is not considered to be a fundamental pharmacokinetic parameter (as opposed to clearance and volume of distribution) as it is determined by clearance and volume of distribution.

Plasma drug concentrations can also be described using a nice little exponential equation:

C_t = C₀ e^(-kt)
where C_t = concentration at time t, C₀ = concentration at time 0, k = the elimination rate constant (which is the proportion of drug removed in an hour, or whatever time units you're using) and t = time.

This can then be used to determine half-life. You see, after the first half life, C_t = 0.5C₀. Hence the equation can be rearranged to directly link k and t:

0.5C₀ = C₀ e^(-kt)
0.5 = e^(-kt)
ln 0.5 = -kt
-k = (ln 0.5)/t
-k = (ln 2^(-1))/t
-k = (-ln 2)/t
k = (ln 2)/t

You may also see this equation written as k = 0.693/t. It's the same thing really: 0.693 is the natural log of 2.

As I mentioned before, half-life is determined by clearance and volume of distribution. Naturally, there's an equation linking these three variables:

t = (0.693*V)/CL (where t = time at the first half-life).

Hence, half-life is increased by an increased volume of distribution, but decreased with an increased clearance. This makes sense: the more of the drug that's "filling up" your body, the more time you'll need to get rid of it. Also, if clearance (which is constant for a particular drug and a particular patient) is high, then it'll be cleared pretty quickly and so half-life will be low.

5) Define the concept of “oral bioavailability,” showing a basic awareness of the factors that influence it together with how it is determined experimentally.

Bioavailability, sometimes denoted by the letter F (presumably B was already taken up, or "bioavailability" starts with the letter F in some weird language), is essentially the proportion of drug that reaches the systemic circulation. IV drugs pretty much all have a bioavailability of 1 as they are taken directly into the bloodstream. Oral drugs are a bit different, however: they must first be absorbed by the gut, and then passed through the liver. Not all of a drug will make it through the liver, as some of it will be metabolised there. The overall bioavailability for an oral drug can be calculated by multiplying the percentage that was absorbed via the gut by the percentage that makes it through the liver in its original form.

There are other ways of calculating bioavailability, again using the area under a curve. Bioavailability can be calculated by dividing the area under a curve for the oral dose by the area under a curve for the IV dose. If the oral and IV doses are different, just use this nifty formula:

F = (AUC(oral)*DOSE(IV))/(AUC(IV)*DOSE(oral))
where F = bioavailability and AUC = area under the curve

Aaaaaaaaaaand I think that's pretty much it for this lecture! (At some point I need to revise my Research and Communications Exercise, though. I wrote a helluva lot of bullshit on steady state concentrations and stuff in there, and it's probably not very accurate. This unit coordinator is pretty merciless- and he's going to be the one marking the assignment. Ah well, I still have over a month to fix it up :) )

Intrinsic Postvertebral Muscles

Okay, I should probably stop soon and focus on cramming for those embryo slides, since that's what the test is going to be focused on. But oh well.

Vertebral Ligaments

First, I'm going to touch on the vertebral ligaments. I've touched on the annulus fibrosus, the outer layers of which join the endplates of adjacent vertebrae together. Here's a list of some others:

• Anterior longitudinal ligament- runs all the way up the anterior side of the vertebral bodies. Multisegmental (i.e. crosses many segments).
• Posterior longitudinal ligament- runs all the way up the posterior side of the vertebral bodies. Multisegmental.
• Ligamentum flavum- joins the laminae of adjacent vertebrae. "Flavum" means "yellow," and it refers to the yellow-looking elastic tissue that makes up this ligament. The elasticity means that it doesn't buckle into the spinal cord, which is pretty important.
• Intertransverse ligament- connects the transverse processes of adjacent vertebrae.
• Capsular ligament of zygapophysial joints- surrounds the joints I guess?
• Interspinous ligament- joins the spinous processes of adjacent vertebrae.
• Supraspinous ligament- runs along the tips of the vertebrae. Multisegmental.

Unisegmental

The three unisegmental muscles are, as their name suggests, muscles that only run between one segment. The intertransverse muscle pretty much runs along with the intertransverse ligament and the interspinous muscle pretty much runs along with the interspinous ligament. The third unisegmental muscle, the levatores costarum, lifts the ribs.

Transversospinales

Transversospinales are muscles that run from a transverse process UP to a spinous process of a vertebra above it. There are three main types.

Rotatores muscles, found only in the thoracic region, run from a transverse process to the spinous process of a vertebra 1 or 2 segments above the first. Their fibres are almost horizontal. As their name suggests, they are good at rotating things.

Multifidus muscles are found everywhere in the vertebral column, but are less important in the thorax. They cross 3 or 4 segments.

Finally, semispinalis muscles, found only in the upper back, cross 5 or 6 segments.

Erector spinae

The erector spinae muscles run longitudinally up the spine. They all begin inferiorly as the sacrospinalis tendon, and each fibre runs 6 segments before "passing the baton" to another fibre which runs up another 6 segments. Spinalis muscles attach to the spinous processes, longissimus muscles attach to the transverse processes and iliocostalis muscles attach to the ribs (costalis = ribs).

Before I move on, I'm just going to quickly mention a few more points. All of the muscles that I have spoken about so far are known as the intrinsic postvertebral muscles. They are all derived from the epimere, and therefore their nerve supply is from the dorsal rami.

There is one more muscle that is derived from the epimere. It's not part of the erector spinae, but I don't know where else to put it so I'm going to put it here. It's called the splenius. The splenius, in contrast to the transversospinales, is a spinotransverse muscle. That means that it runs from the spinous process of a vertebra UP to the transverse processes. They arise from the upper thoracic and cervical spinous processes. The splenius cervicis, which is the lower part, inserts on the transverse processes of C1 to C4. The splenius capitus, which is the upper part, goes up to the nuchal line of the skull.

Other muscles derived from hypomere

Aside from the above muscles derived from the epimere, there are several muscles derived from the hypomere. Some of the deeper ones include the serratus posterior superior and serratus posterior inferior. These go from the upper 4 or lower 4 thoracic spinous processes to the upper 4 or lower 4 ribs, respectively. Of course, there are many other muscles involved, like the obliques and stuff, but I won't go into those now.

The thoracolumbar fascia

The thoracolumbar fascia is a sheet of connective tissue that encloses the intrinsic postvertebral muscles in the thoracic and lumbar regions (hence "thoraco" and "lumbar"). In the thorax, the fascia is thin and stretchy to accommodate breathing, but in the lumbar region it's tougher (in order to provide stability) and has three layers. The posterior layer attaches to the spinous processes, the middle layer attaches to the transverse processes and the anterior layer attaches to the vertebral bodies. The three layers all meet laterally to the vertebrae, and then continue on to form the transversus abdominus, which is one of the muscles of the abdominal wall. The muscles I have talked about so far (well, aside from the serratus posterior) are enclosed within the middle and posterior layers. Between the anterior and middle layers lie two more muscles: the anterior one is the psoas, whereas the posterior one is the quadratus lumborum.

Aaaaand now I should take a break from stressing about muscles! (Now I'm just going to stress about something else instead... bugger.)

Regions of the Vertebral Column

Now the study's getting a bit more panicky, because the test is tomorrow :( On the upside, they did say that we'd only be tested on limited vertebral column stuff. On the downside, EMBRYO SLIDES. Ugh.

Evolution of regions

To examine the evolution of different regions of the spine, we're going to have a look at living creatures.

First we'll start off with fish. Fish have thoracic vertebrae (and therefore ribs), as well as caudal vertebrae (vertebrae past the anus). That's it. They don't have necks, because they can just swim onto their food.

Next we'll look at amphibians, because they spend some time in the water (like fish) and some time on the land (unlike fish). Amphibians also have thoracic and caudal vertebrae, but they also have sacral vertebrae because their hindlimbs need a firm attachment. And yes, they still have no neck. Instead, they have other specialisations for gaining food (maybe this is why frogs have long tongues? Who knows).

Reptiles are the next group of interest. They're a bit like amphibians, but they spend more time on the land. This is the first group to have a neck! Yay! This cervical (neck) region seems pretty important for land animals, but not for aquatic animals. Mammals that have returned to the sea, such as dolphins and whales, retain their cervical vertebrae, but they're flattened and quite rudimentary. Although reptiles are more advanced with their fancy-pants necks and all, they still move a lot like fish, with side-to-side undulations of their bodies.

Movement starts to become more developed with the addition of the lumbar region in mammals. This is kinda important because the alignment of the limbs of mammals (rotated under the body) isn't very conducive to the whole side-to-side undulations thing. Instead their lumbar regions allow them to have flex-extend locomotion, which allows for galloping and so forth. Mammals that return to the sea also have lumbar vertebrae, and also move by flex-extend locomotion.

The relative size of the thoracic and lumbar regions can also give a clue as to the preferred locomotion of the animal. You see, while the lumbar region is good for flexion and extension, the thoracic region is for axial rotation. Hence, terrestrial animals that need to run and gallop a lot have a more developed lumbar region, whereas arboreal (i.e. tree-dwelling) animals have a more developed thoracic spine, allowing them to swing from branch to branch.

Oh, and one last quick note before moving on. Birds have all of the main spinal regions (cervical, thoracic, lumbar, sacral and caudal). However, all of these regions, with the exception of the neck, are fused to some degree.

The motion segment

The motion segment, to my understanding, is a collective name for all the bits and pieces in the spine that allow for motion. Another way of looking at it is that the motion segment refers to two vertebrae plus the joints in between. The motion segment can be divided up into two sections: anterior elements and posterior elements. Anterior elements are more load-bearing (carrying 80% of the weight) and are comprised of the intervertebral discs and the vertebral bodies themselves. Posterior elements, on the other hand, are more responsible for the movement. Posterior elements include the bony bits (spinous processes, transverse processes and laminae) along with associated ligaments and zygapophyseal joints. (Yup, that's a longish word- I'll cover more on this later, I promise.)

The Intervertebral Disc (IVD)

In my previous post, I alluded to the development of the intervertebral disc. Time to go back into that topic with more gusto!

So, a recap plus a bit of expansion on what I talked about before. In my previous post, I mentioned that the notochord gets "pinched off" into the region between somites. The significance of this is that they begin to form the nucleus pulposus, which makes up the middle of the intervertebral discs. The notochordal cells themselves begin to degenerate at around 6 months gestation as they are replaced by acellular material derived from the annulus fibrosus (yes, yes, I'll get to that later), but some cells do remain until adulthood. The nucleus pulposus is eventually made up of a hydrophilic mixture made up of collagen fibrils, hyaluronic acid and proteoglycans, allowing it to retain water easily. (This water can be squeezed out during our everyday activities, which is why we're generally slightly shorter at night than in the morning.) As we age, the nucleus is gradually replaced with fibrous tissue and contains less water.

Alright, so you might be wondering what the annulus fibrosus is. It is made up of many layers of fibrocartilage that run in rings around the nucleus pulposus. Well, actually, pretty much only the inner layers run in rings around the nucleus pulposus- the outer layers just join the two endplates of adjacent vertebrae to each other.

This overall structure of a hydrophilic core surrounded by fibrocartilage is quite useful. Intervertebral discs are capable of transmitting loads and allowing movement. The "envelope" formed by the annulus fibrosus provides tensile strength which maintains the pressure in the nucleus pulposus, keeps the vertebrae apart and allows the vertebrae to move. However, this can go wrong: if the envelope is weak in any way, the nucleus can escape or the annulus can bulge and press on other structures.

Control of movement – Zygapophysial joints

The zygapophysial joints exist mainly between the inferior articular facet of one vertebra and the superior articular facet of the next. The angles of motion available depends to a large extent on the angles of the facets. In the thoracic region, the facets are set on the arc of a circle- very conducive to rotation. In the lumbar region, however, the facets are "radial" which means that rotation is not possible. Cervical region facets are oblique which allows for a wider range of movement.

The intervertebral discs also play roles in movement. In the lumbar and thoracic vertebrae, the joints are perpendicular to the plane of the disc so that some rotation occurs in the disc. In the cervical vertebrae, however, some translation occurs instead.

Regions and Ribs

Finally, I'm going to give a quick guide to how to tell the different vertebral regions apart.

Cervical vertebrae are somewhat easy, as they have transverse foraminae (i.e. little holes in the transverse processes).

Thoracic vertebrae can either be easy or hard to tell apart, depending on what you're provided with. Thoracic vertebrae are attached to ribs, so if there are ribs present, it's really easy. However, if there aren't, then you have to look for the rib facets (little bumps where the ribs attach). Sometimes the rib facets are really subtle and hard to see. Also, one point of interest is that most thoracic vertebrae actually have two demifacets- one at the top and one at the bottom. (Most ribs attach to two demifacets from adjacent vertebrae.) The exception is T12 which only has one rib facet.

I'm going to skip lumbar and go straight to sacral. Sacral are really easy, as they're all fused together.

Finally, lumbar is basically the "none of the above" category.