Drugs Against Bugs

This paper, from a consortium  of academics in Holland, Belgium, and Switzerland and a UK pharmaceutical company, reports on inhibitors for parasite specific phosphodiesterases (PDE). Trypanosomal disease is a major health obstacle in Africa; if the diseases enters into stage 2 (CNS penetration by the parasite) the patient dies. Trypanosoma brucei has two subspecies: T.b. gambiense and T.b. rhodesiense which makes the search for a pan-anti-trypanosomal agent even harder.  The current treatment options: 

...are limited and suffer from suboptimal dosage regimens and/or severe toxicity. During the second stage of the disease, the only choices are the arsenic-containing drug melarsoprol and the ornithine decarboxylase inhibitor eflornithine, used as monotherapy or in combination with nifurtimox (NECT).  However, eflornithine is not effective against T. b. rhodesiense.

Mapping of the T. brucei genome lead to the identification of trypanosomal PDEs.  Two of these PDEB1 and B2 play a pivotal role in proliferation.  Knocking down one or both TbrPDEB1 andTbrPDEB2 simultaneously leads to an arrest of parasite cell division, lysis of the parasites, and elimination of the infection in vivo (in an infected mouse model). Of supreme interest, the "P-pocket" (found in the crystal structure of  Leishmania major crystal structure) was conserved in their homology model. 

The HTS found compound 1 and in their follow up to chemotypes related to this, the came up with compound 6b.  Rolipram itself was inactive (>100uM) despite fitting nicely in the pocket (according to modeling).  However, the catechol moiety was shown to be the key for activity.  Replacing it with a less "worrisome" moiety led to a significant decrease in potency.  Compound 8d (R1, Obenzyl, R2=cycloheptyl) had 500 nM potency that maintained the same ligand efficiency, which indicates the atoms added were reliably efficient, but not super-efficient.  It also had anti-proliferative effects without cytotoxicity; the authors guess that this is due differences in cell-permeability compared to the cyclopentyl compounds. 

The benzylcatechol chemotype was then chosen for further optimization.  The docking shows that the benzyl moiety is at the entrance of the P-pocket (figure 3a) which should afford access to it through growing.  Table 2 shows the results of their efforts here with both the cycloheptyl and isopropyl (which were more ligand efficient).  The docking suggested that they should be able to grow into the p-pocket from the 4 position (Figure 3a).  Compound 20b (49nM) was the best inhibitor and as shown in the docking (Figure 3b) this is most likely due to interactions in the P-pocket.  Interestingly, they also propose that it may be displacing water from this pocket causing some sort of increase in affinity.  

The cLogP of the cycloheptyl compounds was a real issue affecting solubility and may have affected the antitrypanosomal activity.  20b, with a solubilizing tetrazole group, concentration-dependently worked in the anti-trypanosomal assay with a IC50 of 520nM.  It was also found to be very potent against PDE4A-D enzymes.  It should also be noted that 20b is 40 heavy atoms, which is 0.18LEAN. However, 20b was a good inhibitor of  T. b. rhodesiense (60nM).  It was tolerated by a human fibroblast cell line (250 fold sensitivity index)  Lastly, they were able to show that cAMP accumulated in the cells, indicating the target specific effects.

Often, I am very harsh on academic drug discovery, but this paper is an excellent example of what can be accomplished when it is done right.