The Half Decent Pharmaceutical Chemistry Blog

Tonight is the night...

Hello and welcome to the last episode of Saturday Night Synthesis of this series. Simply looking at tonight’s protagonist you might wonder what makes this antiviral drug so special to be in our grand finale. Well, quite a lot to be honest as this synthesis is basically the only reason why, last year, I thought of  describing a synthesis of a drug on any given Saturday night, despite the fact that I hate this sort of weekly, compulsory posting, that forces you to write something on a certain day, turning a great hobby in a work-like duty.

There is no particular reason, I’ll admit, to like this synthesis so much. But, you know, love is always irrational and illogic. The moment I started to study the chemistry of Vidarabine it was love at first sight. Actually, I doubt love is right expression: it’s more a sort of Sturm und Drang, an explosion inside of me, an erupting ensemble of primeval, hidden passions that all comes out at the same time, a cathartic burst of feelings.

All of sudden I feel like I’m in a Caspar David Friedrich painting and my ears are filled with Felix Mendelssohn’s “Fingal’s Cave”.
So, I don’t care too much how drug works (as many other antiviral drugs it’s a fake nucleotide which, after a cycle of phosphorylations, targets the viral DNA polymerase both inhibiting it or yielding an incorrect DNA strand because Vidarabine is basically an adenine bound to D-Arabinose instead of D-Ribose)  or what its clinical applications are (herpes simplex and varicella Zoster). I just want to see this wonderful, touching, enantioselective synthesis, hoping you’ll like it.

The concerto opens with pentose carbohydrate D-Xylofuranose, whose hydroxyls are not only all protected with benzoyl groups, but also with a spatial orientation which is exactly the opposite of that of D-Arabinose. However, changing the orientations of those substituents is easier than what it may seem. First, bromide is added, in acetic acid, and this yields a mono-brominated intermediate, which reacts with chloro-mercuric adenine in what is, by a large margin, my favourite name reaction: the enantioselective Koenigs-Knorr reaction.
Apparently, the reaction begins carbonyl from the protecting benzoyl group in 2’ promoting the formation of a five-term cyclic ketal through the displacement of bromide from the 1’-position. This is also helped by the HgX-group, which tends to evolve into a stable bi-halogenated derivative compound, leaving a negative charge on the purine, therefore, quickly binding to the sugar.  However, all this amazing orchestration gave us a useless intermediate where the sugar is bound to the wrong part of the purine.
Luckily, the benzoyl group breaks the bond with the nitrogenous base twice, so, we end up, once again, with an alpha-oriented ketal, with a delocalised positive charge. The purine undergoes a rearrangement and, now with the negative charge where it ought to be, stereoselectively (with a beta-oriented linkage) binds to the sugar.
At this stage, the structure has reached a decently nucleotide-like shape. So, it’s time to turn Xylose into Arabinose, by epimerising both 2’ and 3’ hydroxyls. First, the protecting group are removed with gaseous ammonia and methanol.
An alpha-oriented cyclic ketal encompassing the 5’ and 3’ position is yielded by adding acetone and, with this protection in place, methanesulfonyl chloride is added, giving a lovely leaving group to the 2’-OH.
Acetic acid and 100°C will do the job of opening the ketal and sodium methoxide yields a beta-oriented epoxide between 2’ and 3’.
This last structure is finally opened, featuring correctly-oriented products, with sodium benzoate in a mixture of DMF and water, so that, at last, Vidarabine is yielded.

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!

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!

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…

 

Tonight, we tell the amazing story of how you sit in front of a computer and, out of nowhere, a new drug comes out.

Hello and welcome! I think some of you have probably put up an annoyed and disgusted expression reading what drug I’m going to discuss tonight: last year, I tackled H₂-antagonists both pharmacologically (as a class of molecules) and synthetically (in the sense that the synthesis of Cimetidine has been already described). So, you might be led to believe I’ve either run out of ideas or developed some kind of H₂-blockers fetishism. Well, I am actually pretty fond of all the drugs which treats gastrointestinal diseases as they were the theme of my very first lecture on pharmacology and, subsequently, the first thing I studied. Luckily, my intestine and I have always had a wonderful relationship: I don’t stress it and it keeps working efficiently and quietly.
Sure this remains an interesting (and much underestimated) subject of study, but the main reason why I’ve chosen Ranitidine is that it gives me the opportunity to talk about an even cooler aspect of pharmaceutical chemistry which, weirdly, has never covered: QSAR.

These days, nearly every new molecule which may eventually manage to end up as a marketable drug is discovered through one of the many computer-assisted drug design techniques. The Romantic (maverick) scientist who finds some nasty mould from which one can obtain a revolutionary antibiotic has now been replaced with a nerdy geek, who sits in front of an insanely powerful computer in a dark room. Actually, I have always mixed feelings when I think about these guys: most of them prove to be complete idiots when you try to talk with them, but there are brilliant scientists who, thanks to their skills, (will) succeed at solving problems that seems impossible if considered solely from a traditional point of view.
What’s more, because they work at a computer, they are able to visit my blog when want to take a break, so, I must be more polite when refer to them.

QSAR is one of so-called correlative techniques you can use to discover new molecules. The acronym stands for Quantitative Structure-Activity Relationship: self-explanatory, isn’t it? It’s defined correlative comes from the assumption that there is a correlation between the biological activity and chemical-physical properties. This relationship is mathematically (and, therefore, quantitatively) determined as follows: you first define some descriptors (x), that quantify well-known chemical physical properties. These descriptors are applied to a number (n) of molecules with known activity (y). With these two variables (x and y) one creates a matrix and, through regression analysis (least squares) yield a model to calculate the structure-activity relationship.
In a nutshell, you have to work out  the a’s in the equation: y = a₁x₁ + a₂x₂ +…+ a_nx_n.

If you haven’t fallen asleep with my quick lecture of mathematics, that’s great, because you can now see how all this monumental amount of calculations comes to play in the drug-design process. You take a basic, structural backbone and choose two positions. Then, you start to size which substituents would be the best there. The aforementioned descriptors (x) generally have to do with lipophilicity, steric hindrance, electronic properties such as mesomeric and inductive effect of the substituents, etc. On the other hand, to quantify activity (y), pIC₅₀ (concentration of a drug to halve the activity of an enzyme) is often chosen.
Amazingly, this statistical approach gives one the opportunity to predict whether a descriptor would be relevant or irrelevant.
To sum up, the great thing about QSAR is that it gives us a hint on the possible activity of a molecule that hasn’t been designed yet.

You might think: “Yes (yawn),  it’s all fantastic and brilliant but what the Hell has it got to do with Ranitidine!” Well, once Cimetidine (first H₂-blocker to be clinically used to treat peptic ulcer disease, people at Glaxo got excited and asked themselves how they could possibly further improve an already superb drug. So, they set their nerdest drug-designers to work at their ultra sophisticated computers and  they came up with some interesting findings (those damn geniuses…): first, you could replace the imidazole with a furan (a dimethyl-amino-methyl-furan, to be precise); then, it was a reasonable thing to do to preserve the highly flexible, long, side chain, keeping the sulphur but changing the cyano-methylguanidine with a nitroethene-diamine. Thanks to these pure prediction made with a QSAR programme, they had invented Ranitidine, an H₂-blocker 4 to 10-times more potent than Cimetidine, 4 to 10-times less prone to bind to cytochrome P450 and longer half-life.

I’m pretty sure they were listening to an early eighties’ (the year Ranitidine was discovered) big hit such as “Another Brick in The Wall” by Pink Floyd as it would perfectly match with the image of a dark room (only lit by monitors) with many people staring at a computer, in the office of a big, evil, pharmaceutical company. And the Pink Floyd were pioneers in the use of electronics in rock music.

The synthesis of this…synthetic drug starts with an amazing Mannich reaction to introduce the amino alkyl group, thanks to the acidic proton of furan. Thionyl chloride is chosen to get a better leaving group (instead on the primary hydroxyl) so that the flexible chain could be bound to the other end of the furan. Meanwhile, nitromethane and carbon disulfide react (in the presence of two equivalents of potassium hydroxide and dimethyl sulphate) to yield a precursor of the nitroethene-diamine, which easily reacts with the amino terminal of the chain.
Finally, a methanethiolate group is substituted with a methyl amino one by adding methylamine.
Impressive, isn’t it?