The Half Decent Pharmaceutical Chemistry Blog

Tonight, you are invited to a masquerade ball.

Good evening and welcome to a secret episode of Saturday Night Synthesis. Totally inspired by my recent watching of Kubrick’s last film, Eyes Wide Shut, tonight we talk of a drug whose action could be briefly explained with its characteristic of being masqueraded as a thymidine and then perform its synthesis, all dressed up like it was still carnival and Jocelyn Pook’s “Masked Ball” casts an spell of mystery, decadence and sin upon the scene. It is thanks to this mask, in fact, that Brivudine (aka BVDU) exerts an effect against viruses such as varicella zoster and, above all, herpes simplex 1. Both major targets, thus, belong to the Herpesviridae family: therefore, they present a double-stranded, linear DNA, a broad host spectrum and a relatively quick replication cycle.

While polymerases are replicating the viral DNA, nucleoside analogues tend to be incorporated into the growing strand with predictable dramatic consequences. Virus-encoded thymidine kinase selectively activates the drug phosphorylating it to its 5 '-diphosphate derivative.
After this step, cellular enzymes continue phosphorylating the molecule, until it becomes a 5'-triphosphate, which is finally capable of acting as an alternative substrate against the viral DNA polymerase. This, in turn, leads to a block of this incredibly active enzyme, on which both HSV-1 and VZV rely massively for their replication cycle.
To sum up, this drug is recognized as a normal thymidine by the enzymes which phosphorylate it, despite having a bigger substituent instead of a methyl. This, though, is the sole difference between the two and this striking similarity makes Brivudine so effective.

To achieve this impressive level of effectiveness, you don’t need to go through a particularly complicated pathway, though. The synthesis starts from a Uracil with a vinyl group in 5, brominated in DMF. Both carbonyls are subsequently protected with sylil chloride in HMDS.
Now, everything is in place for the main event: a rather protected 1-chloro-deoxyribose reacts with the Uracil derivative in, sadly, a non-stereoselective reaction (see below), yielding in turn both enantioforms.
Before the therapeutically useful product could be isolated (namely, the 2R), all the protection are removed by adding sodium methylate.
Important news: this edition of Saturday Night Synthesis will finish next Saturday (8th). Stay tuned: we are preparing our grand finale!

No, it’s not the name of some new, trendy, innovative anti retroviral drug ready for the market. VBP stands for Very-Busy-Person and it’s what I turning into. Let’s make a brief recap: your group leader is on holiday in Germany doing meditation (that’s just an unconfirmed rumour, although from an informed and reliable source), the said reliable source (my direct supervisor) has gone home on Thursday, the other PhD student has no willingness to work and no sense of duty, so, predictably, has literally just dropped in to say hello, the other guy usually working in your group is in the middle of the writing of his graduation thesis. Plainly, you are all alone in the lab, but far from being unemployed.

I’ve completed an old ChIP (chromatin immunoprecipitation, for all the chemists reading) with a second series of RT-PCR, prepared some buffers I’ll need on Monday, started a new ChIP and looked after my supervisor’s cells. Not bad.
None of these things, though, really matters when compared to a couple of other major events, which have turned me into a VBP.

This morning I have had my very first real conference/business call (something I’ll be able to describe more in detail later) at 12:30. Throughout the working day (which isn’t yet over as a VBP’s working day is never really over) I received gratifying emails that are giving me the great chance of complaining about the huge number of (refunded) flights I’ll have to book in the next month (see above).

I can go one better, though. Before heading north, my group leader made me an offer you cannot refuse: to help him in correcting written tests. Usually a (punishment) for PhDs or even PostDocs, my red pen is going to judge whether second-year students of my same degree course have any idea what a polymerase is.
To complete this task I have occupied the luxurious office of the boss, with its human-leather chair (if you aren’t Italian you can’t get this reference, sorry) and much more. Plainly, the ideal position for business calls.

For what concerns the exams, I am going to complete their correction on Sunday. It’s a multiple choice test: so, I completed it to get the right answers and this has speed up the process. I am also considering going scientific plotting the results and publishing everything here.

Oh, the power!

Tonight, we reaffirm our genuine hate for Mr. Watson by destroying DNA (or, at least, undermining it).

Hello and welcome to the show. Last Thursday was not only my 24th birthday, but people might have celebrated the anniversary of the discovery of the structure of DNA. Back in 1953, Adolf Watson and Crick came up with their hugely important finding and subsequently went for a pint of ale at the Eagle Pub in Cambridge. This will always remain a milestone in the history of science and mankind, despite the men who gave it to the World. In fact, (if you haven’t lived on the Moon during the last 4 months, you can skip this part) Herr Watson seems particularly keen of expressing narrow-minded, idiotic, racist, fascist views I’ve already commentated here.
On that occasion I realised nearly all of my readers agrees with Watson’s ideas: I respect everybody’s opinions and, therefore, always published whatever comment one wants to make (the only reason why comments are moderate is to prevent this blog to be full of spam). This, though, doesn’t mean at all that, to meet reader’s demands I am going to take everything I said and believe in back (as Watson apparently did). Thus, this will always remain an anti-Watson zone.

On S.N.S, I’ve already tried to make him losing his temper by giving an example of gay-lesbian-transgender piece of synthetic work, when describing testosterone. Today, despite my undeniable love for molecular biology, I celebrate Watson’s achievements by targeting DNA metabolism and showing how to effectively tackle biology using nothing but pure chemistry. So, tonight’s show is a little bit about anger: I suggest listening to Blur’s “Song 2” while performing these two, incredibly short syntheses.

Our target, ladies and gentlemen, is the biosynthesis of folic acid, a fundamental substance for the replication of DNA. In particular, a fruitful target to inhibit the biosynthesis of DNA (in mammals as well as bacteria) is tetrahydrofolic acid, a functional derivative of folic acid, which basically acts as a methylene donor.

In bacteria, tetrahydrofolic acid is synthesised from pteridine. The reaction requires two molecules of ATP, para-aminobenzoic acid and glutamate. In mammals, instead, you go straight from dihydrofolic to tetrahydrofolic acid.
Two enzymes play key roles here: first, dihydropteroate synthetase, which catalyses the formation of the covalent bond between phosphorylated pteridine and PABA, and dihydrofolate reductase, which yields the final product. While the former is found exclusively in bacteria, the latter represents a target for the design of both antibacterial and anticancer drugs.
And here is where chemistry come to play. Both Trimethoprim and Pyrimethamine are non-classic dihydrofolate inhibitors, in the sense that they retain only a small portion that mocks the structural motif of dihydrofolic acid, the substrate of the enzyme. This structure has proved to be just what it takes to efficiently interact with the active site of the reductase, actually preventing it from doing its job, through three hydrogen bonds: exactly those dihydrofolic acid forms.

Despite a similar structure and synthesis, Trimethoprim and Pyrimethamine are used in two, completely different contexts: while the former is an effective bactericidal (in association with sulfamethoxazole), the latter (as well as all the other non-classic inhibitors) is useful in the treatment of malaria.

Trimethoprim targets an enzyme present in both bacterium and mammalian host, but is quicker at acting on the former type, so, despite possible plasmid-related resistance strategies (reduce cell permeability, reductase overproduction, etc.), it is a reliable weapon against K. pneumoniae, Moraxella caterrhalis, P. pneumonia, Enterobacter, Serratia and Salmonella.
Its synthesis begins with ethoxypropanenitrile and trimethoxybenzaldehyde reacting in a condensation which occurs with some help from sodium ethanolate. Then, guanidine is added and, through a double nucleophilic attack, we directly obtain Trimethoprim.
Pyrimethamine is remarkably prone to react with the protozoal version of dihydrofolate reductase. As a result, it’s able to provide a good treatment against merozoites, with P. falciparum often mutating its enzyme to survive the exposure to this drug. Nevertheless, when in association with Chloroquine, it can serve as a highly effective prophylactic treatment and, in association with sulfadoxine, a cheap alternative to Chloroquine when this has become useless because of resistance.
This synthesis is rather short, too: all you need is ethyl propionate to react with phenylacetonitrile in a Claisen condensation. The carbonyl is subsequently methylated with diazomethane and strong nucleophile guanidine is added to complete the reaction and free methanol to yield the aromatic ring.
Live with that, Watson!

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.

Tonight, we wait for a response from the coroner.

Good evening and welcome to this hypnotic episode of Saturday Night Synthesis. Following the death of Hollywood’s next iconic actor Heath Ledger for what seems to be an accidental overdose of prescription benzodiazepines mixed with opiates (so Mr. Ledger was another depressed and hopeless junky), a lot of attention turned to drugs such as diazepam (whose commercial name is very iconic and popular, too: Valium). I was kind of disappointed when I read both excellent Kyle’s posts on this tragic episode (because, no matter what’s your opinion on someone, death is always a tragedy. End of the story…) and realised I hadn’t felt the need to link to any of my posts. How can you blog about drugs and not quote any half-decent post?! How is this legally possible?

Well, it doesn’t really matter because that made me reflect on one thing: I’ve talked about benzos from different points of view but, strangely, never described the synthesis of one of them. Generally speaking, they all start with the same synthesis of a crucial bit: the phenyl-methanone.
Therefore, once you’ve seen the synthesis of one of them, you’ve seen everything. I mean, each benzodiazepine might have unquestionably cool steps in its synthesis, but the overall process is rather conserved. Diazepam, though, serves as the ideal molecule to describe some general features of these glamorous drugs. In fact, it’s the typical benzodiazepine: great in relieving anxiety state and reliable to promote the onset of sleep.
It’s the most lipid-soluble and, as a result, the quickest to reach the central nervous system. It undergoes the classic biotransformation pathway: metabolised by hepatic enzymes, it’s dealkylated and hydroxylated during the so-called phase I, and the resulting metabolite is turned into a glucuronide, easily excreted in the urine. On the other hand, phase I yields two metabolites which retain activity: Desmethyl-diazepam and Oxazepam.
Benzodiazepines are remarkably safer than barbiturates, but, although you won’t die, their (ab)use isn’t trouble-free at all. First, there is physical dependence, which often leads to abstinence syndrome, characterised by anxiety, insomnia, excitability and convulsions. Then, there is the usual list of adverse effects, which is far from being reassuring: impaired judgement, lethargy, loss of self-control and, eventually, coma. Theoretically, one could even choose benzos to commit suicide, but, in that case, my opinion about junkies and drug-abusers will just be confirmed: it’s stupid to select benzodiazepines (unless enhancing their central, sedative effect with alcohol, but that’s a different story), because this would require a jolly massive amount of tablets even the most depressed individual would be unable to swallow.
The (relative) safety of these molecules helps explain why they have quickly and entirely replaced barbiturates as sedative-hypnotic drugs of choice in clinical practice.

Let’s go back to the synthesis: is it any good? It is. It begins with the nicest Friedel-Crafts acylation I’ve ever seen on this weekly show: it involves two moles of each substrate (4-chlorobenzamine and benzoyl chloride) and yields unstable Schiff bases, easily hydrolysed by the addition of acid.

 

This is the common step in the synthesis of any benzodiazepine. The proper mechanism to obtain diazepam (to be performed while listening to The Who’s “My Generation”: “I hope I die before I get old”) begins with the activation of the primary amine with tosyl chloride and continues with the methylation of this function in the presence of sodium and, predictably, dimethyl sulphate.
To add the extra carbons required for the cycloheptane, an amide is formed by adding a reactive chloroacetyl chloride.
Hexamine is finally used to slowly release ammonia and yield our benzodiazepine.

Rest in peace…