June 2012 update on two potential drug candidates from the Todd group

21 Jun
Published by JimCronshaw
chlorinationscheme.png10.33 KB
JRC12-1.png10.05 KB
TSLthienopyrimidineclosure.PNG14.23 KB
JRC16-1.PNG6.5 KB

Jim Cronshaw from the Todd group at the University of Sydney here again. It’s been quite some time since I made an update on my research on The Synaptic Leap. This post is intended to give an overview of what problems have been hounding me over the intervening two months.

Previously I reported that the sulfonyl chloride – used in the synthesis of the ‘triazolourea singleton’ – was succesfully synthesised through an oxidative chlorination reaction (Figure 1). H-NMR and mass spec. indicated that this was indeed the case.

Figure 1: Oxidative chlorination

The next step in the synthetic plan towards the singleton used this sulfonyl chlorine in a coupling reaction with a secondary amine (in this case, 4-chloro-N-methylaniline) to afford a sulfonamide. The reaction is carried out at 50 °C, in acetonitrile, with potassium carbonate as a base (Figure 2).

Figure 2: Sulfonamide synthesis

Fairly standard chemistry, right? This reaction was performed three times – with subtle differences in the workup and reaction conditions – which all failed to afford the desired sulfonamide. DMAP, varying temperatures and different isolation procedures (of the sulfonyl chloride) all failed to synthesise the sulfonamide.

 Given the propensity of sulfonyl chlorides reacting with water, it was reasoned that perhaps this sulfonyl chloride was hydrolysing during workup or the subsequent reaction. To eliminate this possibility, all workup steps were eliminated and the solvents from the oxidative chlorination reaction were removed promptly following this reaction to once again afford the desired sulfonyl chloride (as shown by H-NMR and mass spec.) in relatively pure form.

Next, I investigated whether the amine I was using was unreactive. I compared the reactivity of benzylamine with 4-chloro-N-methylaniline. Table 1 summarises these results.

Table 1: Sulfonamide synthesis

The H-NMR’s for the benzylamine reactions are difficult to interpret but since benzylamine is more reactive than 4-chloro-N-methylaniline I assume that the relative sulfonamide is present in small quantities. In any case, the problem with this reaction is clear: Scrappy yield. At present there is 116 mg of sulfonamide available for biological testing, but it would be nice to get this reaction working better.

At this stage I have another sulfonamide coupling reaction, using 4-chloro-N-methylaniline in refluxing chloroform (triethylamine as a base) to see if this procedure works any better. I also want to investigate how readily the sulfonyl chloride is hydrolysed by performing a reaction in water. Still, two obvious issues remain: How do I get this sulfonamide coupling reaction to give good yields? And, why is this reaction proving to be so difficult?


The other compound I am working on - the 'thienopyrimidine lead' - has been progressing far better than I reported previously. The thienopyrimidine bi-heterocyclic compound fully cyclised by heating the reaction to 140 °C. My happiness with this discovery was boosted by working out that the thienopyrimidine bi-heterocycle could be synthesised in one step – avoiding the aldehyde ‘intermediate’ – by combining the reactants in stoichiometric amounts and allowing them to reflux at 140 °C (summary in Figure 3).

Figure 3: Thienopyrimidine core synthesis

Following this, a reaction with POCl3 replaced the alcohol group on the thienopyrimidine core with a chlorine atom easily enough. The plan after this step was to react this chlorinated compound with ammonium hydroxide. Refluxing the chlorinated compound with ammonium hydroxide at standard atmospheric pressure did not lead to synthesis of the amine, but utilising a sealed tube at ~95 psi did. The next step was to remove the proton at the α position on the thiophene ring with n-butyllithium, and to react the resultant carbanion with iodine (Figure 4).

Figure 4: Replacing the alpha proton with an iodine atom

This reaction did not occur and starting material was recovered. An investigation on what protons were being removed with various butyllithiums in varying conditions is summarised below in Table 2.

Table 2: Butyllithium Reactions

Removing a proton from the α position on a thiophene ring is well known chemistry, but it is not occurring in this case. There are two explanations for this result: The first is that the compound is wet, leading the butyllithium to react with the water present. This possibility was investigated by using 7 equiv. of sec-buthyllithium. The H-NMR spectrum of this reaction was not shimmed well so the result is forthcoming. The other possibility is that the α proton is simply not acidic enough to be removed. I doubt this is the case, given that this is well known chemistry. This possibility is being investigated by replacing the secondary amine with a morpholine group. This eliminates the possibility of the protons on the amine being removed, meaning that only this α proton, or the proton between the two nitrogen atoms on the pyrimidine ring may be removed. I will perform this investigation shortly. The question at this stage is why is the α proton on the thiophene ring proving to be so difficult to remove?

Once the target molecules from these two series are synthesised they will be sent for testing. The' triazolourea singleton' is under high vacuum as I type this, and will be sent for its first round of biological testing tomorrow. We have a list of commercially available compounds with structural similarity to both the 'triazolourea singleton' and the 'thienopyrimidine core'. In the coming weeks, we will request samples of these compounds from the relevant sources and once we obtain these compounds they will be sent for biological testing as well. The ultimate aim is to ascertain what structural motifs in these molecules gives rise to anti-malarial activity so that I can begin synthesising more analogues.

Hopefully I'll have completed these tasks when the time for my next update comes around. Feedback is wanted! (as is always the case with my updates)