OpenSourceMalaria:Triazolopyrazine (TP) Series
Open Source Malaria Series 4: The Triazolopyrazine (TP) Series
The Triazolopyrazine series is the newest of the OSM series. It was announced on September 10th 2013 as Series 4.
The series arises from industrial work that cannot be fully disclosed which was followed by some hit-to-lead work funded directly by MMV which can.
There is evidence from parasite ion regulation assays (below) that these compounds may be PfATP4 inhibitors. Such evidence distinguishes Series 4 from Series 1-3 where there was no experimental evidence for a mechanism of action.
As with everything involved in OSM, suggestions can be given in multiple ways.
What is Known at the Start of the Campaign
A briefing document written for MMV constitutes what was known at the start of the open project. The authors made the following summary of their work on the triazolopyrazine series:
"We have made compounds in this series down to 16nM potency. The series also seems to have good in vitro HLM and hHEP stability Clint < 8.1 is compatible with 10nM potency. However, RLM remains stubbornly high, particularly for the more potent analogues translating to short half-lives in rat PK. The series also appears to have little polypharmacology or cytotoxicity. The project has so far not challenged the hypothesis that rat metabolism may not be a great model for human metabolism for this series."
The authors also flagged some concerns regarding the series:
"Although dofetilide binding looks weak or nil, the series has shown activity in a patch clamp assay at Essen (1-10uM) which is quite potent though with a window of >100 fold over Pfal potency. The series shows activity in Kieran Kirk’s PfATP4 assay which goes away for Pfal inactives in the series. In Kip Guy’s resistant mutants the picture is perhaps more mixed, but there is still support for the idea that some members of the series are weaker in the resistant strains. The series has no or weak >>1uM activity against gametocytes, no activity against Winzeler’s Pb liver stage and may have weak activity against ookinetes but the dose-response data has not been completed."
Possible next steps were also suggested for the triazolopyrazine series:
"The series has good potency and" in vivo "efficacy with few toxicity concerns. The biggest issue is metabolic stability, as measured in rat in particular. Some possible future directions include: "1. Small scale changes around the side chains to attempt to balance potency and metabolism. 2. Incorporation of a basic centre to increase volume as a potential fix for half-life. However, this might come at the expense of plasma concentration so would require high potency. In addition of the 29 compounds with a basic centre only one has a measured potency < 100nM. 3. More significant structural changes. Of the changes made to the basic skeleton, the most successful might be the recent evaluation of the substitution position changes (eg MMV670945), possibly in combination with modifying the disposition of the N atoms in the core. Related compounds have been made by others and it would be wise to incorporate the learnings from these series into any plans to explore this substitution pattern further. The first few compounds look similar in terms of metabolic stability.
The series has good potency and in vivo efficacy with few toxicity concerns. The biggest issue is metabolic stability, as measured in rat in particular. Some possible future directions include: Small scale changes around the side chains, particularly phenethyl to attempt to balance potency and metabolism N is tolerated in the ring, hasn’t been explored much recently Is 3,4-diF the best substitution pattern ? Some evidence (eg MMV669848) that the phenethyl side chain can be rigidified, perhaps the iso-indoline of that compound could be improved on with other ring systems and by more optimal substitution of the aromatic benzene ring of the isoindoline. The amide MMV670944 is interesting and shows good RLM stability, but many other amides failed to match its potency.
Incorporation of a basic centre to increase volume as a potential fix for half-life. However, this might come at the expense of plasma concentration so would require high potency. In addition of the 29 compounds with a basic centre only one has a measured potency < 100nM.
More significant structural changes. Of the changes made to the basic skeleton, the most successful might be the recent evaluation of the substitution position changes (eg MMV670945), possibly in combination with modifying the disposition of the N atoms in the core. Related compounds have been made by others and it would be wise to incorporate the learnings from these series into any plans to explore this substitution pattern further. The first few compounds look similar in terms of metabolic stability.'
More contents will gradually become part of this wiki (below) as the project progresses.
The raw data behind the briefing document will be released when it is obtained. New ion regulation assay data has already been received (below).
What Can the Community Do Now?
Those wishing to contribute to OSM Series 4 should in the first instance read the briefing document. The first question is: Which 10 compounds ought to be made in Sept/Oct 2013 for evaluation?
Resources Needed: Chemists to either make new molecules, or help obtain existing compounds that might be relevant to this series.
1. Hit-to-lead synthesis and biological evaluation, to improve potency and drug likeness.
2. Validation of PfATP4 activity.
Current Questions for the Community
Starting-point questions are listed at the end of the briefing document. These translate into the initial question of Which 10 compounds ought to be made first? (also asked here and Does anyone possess compounds that could be relevant to this series already? (asked here and there is a separate section for results below).
Prior Knowledge of the Series
Potency of Hits and Analogs
(Detail will be placed here, but for the moment please browse the briefing document).
Possible PfATP4 Activity Deduced from Parasite Ion Regulation Assays
The following five compounds were evaluated in parasite ion regulation assays in the Kirk Laboratory; the hypothesis is that PfATP4 is a Na+ ATPase that exports Na+ and imports H+ (or equivalent) and that the effects of the compounds on Na+ concentration and pH are attributable to inhibition of this activity. Structures, potency, metabolism/solubility and raw PfATP4 assay data are here.
MMV669000: no (potency: inactive)
MMV669304: yes (potency: 280 nM)
MMV669360: yes (potency: 356 nM)
MMV669542: yes (potency: 185 nM)
MMV669848: yes (potency: 114 nM)
MMV669000 did not dissipate the plasma membrane Na+ gradient or increase the plasma membrane pH gradient consistent with it not inhibiting PfATP4 at the concentration tested.
The other compounds dissipated the plasma membrane Na+ gradient and increased the plasma membrane pH gradient at a concentration of 2 μM, consistent with them being PfATP4 inhibitors.
(i.e. note the correlation: compound inactive in these assays is the inactive analog in the plasmodium screen)
Other Sources of Compounds in this Series
Strings for Google
Use this section to paste strings to make the page more discoverable.
MMV669000: O=C(N1CC(C=CC=C2)=C2C1)C3=CN=CC4=NN=C(C5=CC=C(OC(F)F)C=C5)N43; InChI=1S/C21H15F2N5O2/c22-21(23)30-16-7-5-13(6-8-16)19-26-25-18-10-24-9-17(28(18)19)20(29)27-11-14-3-1-2-4-15(14)12-27/h1-10,21H,11-12H2
MMV669304: FC(F)OC(C=C1)=CC=C1C2=NN=C3C=NC=C(CCCC4=CC=CC=C4)N32; InChI=1S/C21H18F2N4O/c22-21(23)28-18-11-9-16(10-12-18)20-26-25-19-14-24-13-17(27(19)20)8-4-7-15-5-2-1-3-6-15/h1-3,5-6,9-14,21H,4,7-8H2
MMV669360: FC(F)OC(C=C1)=CC=C1C2=NN=C3C=NC=C(COCC4=CC=C(F)C(F)=C4)N32; InChI=1S/C20H14F4N4O2/c21-16-6-1-12(7-17(16)22)10-29-11-14-8-25-9-18-26-27-19(28(14)18)13-2-4-15(5-3-13)30-20(23)24/h1-9,20H,10-11H2
MMV669542: FC(F)OC(C=C1)=CC=C1C2=NN=C3C=NC=C(C(NC4=CC=CC(Cl)=C4)=O)N32; InChI=1S/C19H12ClF2N5O2/c20-12-2-1-3-13(8-12)24-18(28)15-9-23-10-16-25-26-17(27(15)16)11-4-6-14(7-5-11)29-19(21)22/h1-10,19H,(H,24,28)
MMV669848: FC(F)OC(C=C1)=CC=C1C2=NN=C3C=NC=C(CN4CC(C=CC=C5)=C5C4)N32; InChI=1S/C21H17F2N5O/c22-21(23)29-18-7-5-14(6-8-18)20-26-25-19-10-24-9-17(28(19)20)13-27-11-15-3-1-2-4-16(15)12-27/h1-10,21H,11-13H2