The Half Decent Pharmaceutical Chemistry Blog

Last Thursday was Valentine’s day. On Carbon-based Curiosities, a rather grumpy Excimer wrote a particularly appropriate post to describe the spirit of the day: hated, if not ignored, by singles. Reserving my anger and hate for more important things (like junkies and something I will describe soon), I generally opt for the latter, but this doesn’t mean I cannot utilize it for a post.

Unlike Excimer and I, many people all over the world might have thought of something amazing to celebrate this special occasion, when love must be in the air with their partner. Some, that’s for sure, turned to Venice, well-known capital of Romance, for a romantic week-end.

Oh, the sunset on the lagoon, the gondolas, the Ponte dei Sospiri, Rialto bridge, San Marco square. And its famous pigeons. In fact, every so often, the issue of salmonella hit the headlines, ruing the atmosphere. Experts point their finger to the dirty pigeons, the rats of the sky. Last week, despite the approaching Valentine’s day, was no exception.

Still, many tourists didn’t bother and exposed themselves to the risk of salmonellosis. Pigeons are excellent carriers of Salmonella bacteria, the major cause of bacterial enterocolitis.
While romantically feeding pigeons in San Marco square (literally covered by the dirty birds), Salmonella invades ileum and colon, unless they immediately wash their hands after this idiotic operation. Salmonella bacteria are typical invading pathogens, affecting liver and Peyer patches, triggering inflammation and local ulceration in those sensitive areas of the intestine resulting from a swollen lymphoid tissue. Gallbladder is frequently selected as a site to create a bacterial reservoir which leads to a chronic carrier condition.

Most dangerous species might even cause typhoid fever with threatening bacteraemia and splenomegaly as early symptoms.
Otherwise the traditional features of salmonella-related infectious enterocolitis are fever, gastrointestinal pain, fatigue, diarrhea (up to dysentery), until, if not controlled, the infection can spread affecting joints, bones and even meninges.

I’ve meant to write this post since the day I started to work at my graduation thesis, but I have to say my professor, not my supervisor, wondered whether to change my project or not: because of a lack of working-force, he was tempted to concentrate all our strengths (meaning people) on a single project, with the ambitious target of eventually producing an article out of it as soon as possible. However, my supervisor and I have recently solved this problem by making me work on both projects.

So, what am I having to do with these days? Cockayne Syndrome. However, this being meant to be a molecular biology project, I am not spending too much time on the pathology itself, but I only care at the molecular details. Still, a brief presentation of this terrible, rare disease could be fruitful for my thesis, given that the odds are that nearly all the people reading it will be pathologists, pharmacologists and pharmaceutical chemists.

Let’s kick off with an eerie picture of the ultimate, phenotypic manifestations.

As I said, this is a very rare disease. So rare I hadn’t heard of it until my supervisor presented the project and even she did a very short introduction talking about some basic features of this syndrome. And you know how much I like unusual, bizarre diseases, don’t you?
Cockayne syndrome (usually abbreviated CS) is an autosomal, recessive disorder. After almost three months reading papers where no author showed any attempt at coming up with an alternative definition, but, instead, preferred to stick to this formula, I annoyingly know it by heart. Still, although I am fed up with it, I must admit it says a lot about CS.

Unsurprisingly, such an uncommon illness was named after the person, in this case a British physician, who discovered or, at least, studied it most comprehensively. Edward Alfred Cockayne wrote an article where he described a multi-system disorder which bore some resemblance to dwarfism, although, from a molecular point of view, it has more in common with Xeroderma Pigmentosum, with impaired DNA repair and UV hypersensitivity being common characteristic of both pathologies. Unlike Xeroderma Pigmentosum, though, CS patients don’t show an unusually high rate of skin cancer.
As the picture shows, CS has dramatic and evident phenotypic consequences such as the abovementioned dwarfism and photosensitivity, premature aging, microcephaly, facial abnormalities (beaked nose, for instance), retinal atrophy, catastrophic teeth fragility, impaired movements (similar to those sometimes experienced by elderly people) and tremors.
But there’s more: neurological abnormalities and mental retardation are as severe as these outlined physical, exterior signs.

Generally, these symptoms start to appear in the first two years of life, as the foetus grows normally, and life expectancy varies between 10 and 20 years. A second, even rarer form of Cockayne syndrome, however, is hallmarked by immediate onset, which leads to abnormalities detectable at birth and, predictably, life expectancy doesn’t exceed 10 years.

Stay tuned for the molecular, sordid details of how DNA repair is badly altered in CS cells.

A couple of days ago, my supervisor pointed out that, for her, one of signs that most strongly marks the approaching Christmas time is the Star Wars trilogy (or whatever it’s become now) being shown on TV. Generally, the broadcaster schedules the former-trilogy so that the final episode could (sort of) cathartically reach the conclusion of the story on Christmas eve, when children’s impatience to get their present has reached its zenith and, therefore, parents desperately need something to keep them quiet and silent while they go through a seven (!) courses dinner: a couple of starters (where secretly depressed women get instantly drunk and you can foresee, from the beginning, how the dinner is going to end), first course (for example a supper), second (massive) course (any sort of meat prepared in such a way that it’ll certainly take you until New Year’s eve to be completely digested), fruit (which, on this occasion, nobody eats because “C’mon, you only live once! Forget about health!”) and, last but not least, a couple of different deserts (but you’d be a bit disappointed finding out they are only two). This, in a few words, is your average, middle-class, Christmas’s Eve, Italian banquet. Unfortunately, kids don’t eat all that stuff and refuse (how can you blame them?) to sit around a table for hours, pretending to enjoy themselves and, in particular, relatives and in-laws, talking about their jobs, their income, their car, their holidays and so on. What they would normally do is trying to set the house on fire or kill themselves or hung their cousin or look under the girl’s skirts (as daddy does, only in a less spontaneous way). To avoid all this, what’s better than a spectacular, science-fiction film which, despite its age, hasn’t lost its touch yet?
Whenever it comes to sixologies or whatever, you cannot avoid setting up a poll to unquestionably determine which episode is the best one. My current group seem to prefer “The Empire Strikes Back”, although I think it’s the worst. By the way, this is pointless because there’s already a winner in this contest : by a large margin, “Spaceballs”. And that’s the end of it.

Nevertheless, there’s something else which is currently striking back in this country and threatens to ruin our joyful Christmas time, with all those people gathering, those cheers and those shared glasses: meningitis. Looking at the figures, you shouldn’t be scared at all: last year the number of infected patients was almost the same, so it’s absolutely incorrect to claim we are facing an epidemic, although this could, in theory, easily result given that meningococci are involved and they know how to viciously and violently spread the disease. However, we are currently right in the middle of an alarming infection spreading from a party in a pub located in the North East. Worryingly, yesterday saw the fourth death in less than a week and five new cases in five different parts of the country, which means something unusual is undoubtedly going on. Luckily, Italian, though, haven’t gone mad that much yet, as they are too busy complaining about the ridiculously rising prices which are making everyone sad, depressed and disillusioned.

Unsurprisingly, neisseria meningitidis is responsible for this latest infection: meningococci are, in fact, the most common cause of epidemics, as they can easily trigger acute leptomeningitis (which is the proper, scientific term for this disease) primarily in adolescents and adults, the two groups of individuals certainly most likely to have an active, social life, which often includes gathering in crowded rooms and drinking in glasses that may not THAT clean after all. In other kinds of people, such as babies and elderly patients, meningitis could be attributed to other infecting bacteria, such as E. Coli, H. influenzae, Streptococcus pneumoniae, Staphylococcus aureus, etc.

What’s more, albeit bacterial meningitis is, by far, the most frequent type, viruses can lead to a so-called lymphocytic meningitis, while other agents (fungi, for instance), infecting immunocompromised individuals, might turn meningitis from an acute to a chronic form.
Bacterial meningitis is also called “purulent” because of its distinguishing, disgusting exudates in the subarachnoid space. Moreover, the (lepto)meninges are characteristically congested as well, with an awful lot of neutrophils and fibrin clearly detectable microscopically. The cerebrospinal fluid turns turbid, due to a massive concentration of neutrophils and proteins, as the vascular permeability is worryingly enhanced. The spinal cord, too, is often edematous.

Early prognosis is vital: if penicillin (drug of choice in the absence of resistance) isn’t given promptly (even prior to the result of the microbiological culture), there could be few chances for the patient to survive. If resistance appears, a possible alternative is to use third or fourth generation cephalosporins, such as ceftriaxone and cefepime. In fact, generally speaking, cephalosporins show only 5-10 % of cross-resistance with penicillins and most recent cephalosporins are effective against neisseria meningitidis.
So, if you are experiencing headache, neck stiffness, photo- or phono-phobia and everyone is telling you that today you’re incredibly irritable, perhaps, you’d better check in and look back that wild party you went to a couple of nights ago: meningitis is striking back.

This morning I’ve come across a couple of juicy articles during a lunch-time break pubmed session. Yes, I know it sounds ill to spend your free time pretty much doing research while eating but the problem is we usually don’t eat all together, despite being an only 5-people group, for which, theoretically, this sort of thing should be easy to arrange. Unfortunately, working on different projects results in spending most of our breaks on our own with little time to become intimate with your colleagues.

Nevertheless, those things I read were actually very interesting. To start with meaningful and, perhaps, shocking statistics, I didn’t know that HIV-encephalitis (quickly mentioned yesterday) is, by far, the leading cause of dementia among young adults. In fact, not only do neurological complications result from easy to spread opportunistic infections, but HIV itself is prone to seriously affect the nervous system. There are actually many disorders it can cause, both centrally and peripherally: primary encephalopathies, myelopathy, meningitis and vasculitis, as well as demyelinating neuropathies.

It has been noticed that meningitis can be an early symptom of the infection, which therefore implies that the nervous system is likely to be a major centre for the development of the infection. This is also consistent with the catastrophic, late, neurologic progress of AIDS: the so-called AIDS dementia syndrome. This particular complication of the disease is characterized by cognitive and motor disturbances, such as loss of memory, impaired fine motor control and progressive loss of central control of bladder and bowel.
The damages produced by HIV on the brain appear even more evident during autopsies. HIV-encephalitis leads to atrophy of the brain and there are many other histological abnormalities. In particular, a distinctive feature is the presence of products of the fusion of infected macrophages, which yields, in the end, giant, polynucleated cells.
There is plenty of weird people who cry out loudly whenever you mention antiretroviral agents. However, these evil chemicals seem to remarkably slow the development of this dramatic AIDS- related pathology, only when used at very high doses. That’s probably because some these molecule (including AZT) can jump across the blood-brain barrier, reaching the central nervous system.

Sadly, although scientists have revealed the impact of HIV on central nervous system, no one has yet come up with an explanation for how the infection attack this area and what regulates, at an early stage, the onset of this type of encephalitis.

We’re having a bit of a problem with the heating system in the lab. On Monday, the technical office of the university kindly listened to our complains and decided we were freezing sufficiently to turn the heat on in the whole department. Predictably, though, there’s now a sort of tropical climate in the rooms because the heating works very simply: if it’s off, no matter how cold it’s, you’ll carry out your assays wearing your raincoat; when it’s on, it’s simply on, you can’t set a temperature, so the building turns into a fireball.

This seems to be particularly disappointing when you set up a western blotting and, right at the beginning, you prepare your SDS-page. Plainly, yesterday it was so hot that the resolving (a.k.a. running) gel wouldn’t polymerize. First, however, my supervisor told me to make a new acrylamide/bisacrylamide solution, because the one we were using was pretty old and it could be an issue. As it turned out, that wasn’t the problem, because, again, it didn’t polymerized, until we opened the windows in the room (with the heating on…what a great way of saving money and the planet!) and let cold air in to cool down the environment.

While weighing the acrylamide, however, I was warned to be extra-careful. That’s because the monomer, not the acrylate polymer, is a vicious neurotoxin. Acrylamide causes axonopathy, a type of CNS toxicity in which either axon and myelin degenerate, whereas the soma is undamaged and still metabolically active: in fact, it begins to synthesise myofibrils as a response to the injury. Histologically, this gives a bulb onion-shape to the neuron, as myofibrils tend to accumulate upstream the first, damaged site.

Characteristically, the first symptom of an acrylamide axonopathy is the loss of mechanical and thermal sensitivity, at first limited to fingers, but then progressively affecting arms and legs. This is all very worrying, but you may think it’s something that has to do only with chemists and biologists, or some kind of workers (poly-acrylamide is utilized in a pretty wide range of industries, from petroleum industry to water purification). Thing is, acrylamide can be found in carbohydrates-rich foods, cooked at high temperature, such as potatoes and, obviously, pasta.

So, to sum up, most of what you eat contains a substance which has been proved to be a neurotoxin to human beings, a genotoxic carcinogen to rats. The question is: how much of this killing substance do we eat on a daily basis?

Fortunately, not much and, in particular, much less than the so-called NOEL (non-observed effect level), which means children, given the poor activity of their detoxifying enzymes and, if you think about it, the high quantity of backed carbohydrates present in their diet, are immune to the dramatic effects of an exposure to acrylamide. This is a case of ALARA (as low as reasonably achievable): we can’t get rid of acrylamide, but we can determine statistically a level of total safety (which is called, anyhow, virtual safety dose). In this case, the NOEL are (because one is for axonopathy and one for genotoxicity) 0.5 mg/kg and 2 mg/kg. The daily intake for a baby is estimated to be 0.3 – 0.8 μg/kg.
To sum up, we can go on eating our beloved spaghetti and French-fries.
Still, there are a few concerns about the long-term consequences of an exposure to low levels of acrylamide, regarding carcinogenesis. What’s more, although it’s been proposed for acrylamide the same mechanism demonstrated for hexane, which reacts with ammines (yielding pyrroles) and cytoskeleton proteins and yields derivatives (such as 2,5 – hexandione), the exact molecular action of acrylamide is yet to be determined.