OpenSourceMalaria:Triazolopyrazine (TP) Series
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===Pyrazine side-chain modifications - amides===
===Pyrazine side-chain modifications - amides===
Revision as of 00:38, 16 January 2014
Open Source Malaria Series 4: The Triazolopyrazine (TP) Series
(How to respond/input is described in the Landing Page under "Join the Team")
The Triazolopyrazine Series is the newest of the OSM series. It was announced on September 10th 2013 and is sometimes referred to as the TP Series, or OSM 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 and performed by a CRO which can.
A great deal of exploration of the series has been done, with significant diversity in the core and pendant groups. The series includes many potent compounds.
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.
Start of the Campaign
A briefing document written for MMV was the initial knowledgebase. This was accompanied by a PDF summary of pharmacokinetics and efficacy. This is being folded into the sections below, then supplemented.
The aim of the campaign at the outset was to improve the metabolic stability and the pharmacokinetic properties of this series in rat so as to meet the once-dosing criteria (TCP1) set by MMV. New chemistry directed towards blocking the putative metabolic sites was a major part of the research prior to the data being contributed to OSM.
Sources of Data on the TP Series
Initial briefing document (A minor error in the briefing document referring to the amides has been clarified.) Briefing document mostly folded into the below.
PDF summary of pharmacokinetics and efficacy. Needs folding into the below.
The current synthetic lab notebook
Raw Data Spreadsheet on Compounds Prior to Donation to OSM including available quantities of original samples
Summary of Data on Amides in the Series
1. Lead optimisation, to improve solubility and metabolic stability while maintaining potency.
2. Validation of PfATP4 activity.
Last updated: Dec 20th 2013
1. Which compounds to make next? - see two most recent meetings (here and here) for links to the discussions on these points. (Also asked here In particular: evaluation of recent sol/metabolism/MetID results in analog design.
2. Does anyone possess compounds that could be relevant to this series already? ( and there is a separate section for results below).
3. Compounds currently being synthesised may be viewed - some compounds may be on older series.
4. Resources Needed Now: a) Chemists to either make new molecules, b) people to digest the data on this wiki and suggest new compounds to make and c) suggestions for where existing similar/relevant compounds may be obtained (asked here originally), though the series appears different from anything else in PubChem.
Notable Points about the TP Series
- Compounds in this series have been identified down to 16 nM potency.
- Seems to have good in vitro HLM and hHEP stability Clint < 8.1 is compatible with 10 nM potency.
- RLM remains stubbornly high, particularly for the more potent analogues translating to short half-lives in rat PK.
- Series appears to have little polypharmacology or cytotoxicity.
- Not so far challenged the hypothesis that rat metabolism may not be a great model for human metabolism for this series.
- The series shows activity in Kieran Kirk’s PfATP4 assay which goes away for Pfal inactives in the series.
Concerns about the TP Series
- Although dofetilide binding looks weak or nil, the series has shown activity in a patch clamp assay at Essen (1-10 uM) which is quite potent though with a window of >100 fold over Pfal potency.
- In Kip Guy’s resistant mutants the picture is 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.
Project Strands of Current Interest
The biggest issue is metabolic stability, as measured in rat in particular. There are few toxicity concerns. Thus possible future directions:
- Small scale changes around the side chains, particularly phenethyl to attempt to balance potency and metabolism. Other possibilities: a) N is tolerated in the ring, hasn’t been explored much recently. b) Is 3,4-diF the best substitution pattern? c) 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. d) 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. Of the 29 compounds with a basic centre only one (MMV670437, below) has a measured potency < 100 nM (actually 44 nM).
- 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 (e.g., 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.
Cycloaliphatic Triazole Substituent
Attempts at lowering the lipophilicity of the TP compounds by replacing the triazole aryl substituent with a cyclo(hetero)aliphatic group, linked either by the heteroatom or otherwise (e.g. piperidine, tetrahydropyran, indoline or isoindoline) lowered the potency against PfNF54, as did an aniline substituent.
Core Modification of Pyrazine Ring
Based on an assumption that the pyrazine moiety of the TP could undergo AO metabolism at positions alpha- to the nitrogen a few compounds were made with different R groups (Cl, Me, NH2, NEt2). However, all these compounds lost potency against PfNF54.
Core Modification of Triazole Ring
Two compounds based on imadazopyrazines were made (MMV669846 and MMV670250, below). Both showed reduced potency against PfNF54 vs. the corresponding TP compound. The RLM stability of one was found to be poor. Approx 20 structures were made with variations to the 6,5 core system. MMV669846 was the most potent. As most of the analogues were >1 μM potency, fewer were tested in RLM (quite a few in HLM). Of the 4 tested in RLM, the greatest stability had a Clint of 109, (HLM 9.5), several had HLM Clint 8 or less, particularly after moving or removing the N from the pyrazine ring.
(Note - original briefing document contained two entries for MMV669846 at this point with different potencies - need check of original spreadsheet, to verify the above is correct)
Transposing the Pyrazine side-chain
The side-chain on the pyrazine ring was shifted to the adjacent carbon. The chain length was varied (n= 0,1,2) and linked through either O or N.
Among the ethers, the phenethyl ether (X = O, n =2) showed good potency (Pfal IC50 33 nM) but a poor stability in RLM (Cl 100 mL/min/Kg)/
Pyrazine side-chain modifications - non amides
The phenethyl ether side-chain on the pyrazine ring was flagged as a metabolic hot-spot and so several strategies were adopted to mitigate this risk. The following findings were observed:
- Changing the length of the side-chain to anything other than 3 atoms severely lowers potency against PfNF54
- The linker atom to the pyrazine ring is crucial (O>>C>N)
- Heteroatoms in the side-chain lowered potency with the exception of MMV669848 (featuring an isoindolino-methyl group on the pyrazine ring) although this compound had poor RLM stability.
- Constraining the linear side-chain into ring systems (e.g, azetidines, pyrrolidines, pyrazoles) severely reduced potency.
A 2-naphthol substituent on the pyrazine ring showed reasonable potency against Pfal (IC50 114 nM) but suffered from poor RLM stability. Several hetero-analogs of 2-naphthol e.g. indole, indazole, quinoline, chroman, benzisoxazole, quinazoline, etc were made but all lost potency against the parasite.
The phenyethyl chain was replaced by an aromatic group in an attempt to mitigate the potential metabolism of the ethyl chain. Several compounds with a phenol substituent on the pyrazine ring were made. Some substituted phenolates were metabolically more stable in vitro as well as in vivo in rat, although with reduced potency against Pfal.
Considering that the benzylic position in the phenethyl side-chain is prone to metabolic oxidation, several compounds having mono- and di-substitution in the benzylic position were made. Di-Substitution lowered the potency considerably whereas mono-substitution with OMe, OCHF2, CH2OH, NMe2 groups retained good potency. Additional substitution alpha- to the ether oxygen led to complete loss of potency. The alpha-OCHF2 compound MMV670652, with a p-CN-phenyl group on the triazole ring, showed better RLM stability (cLogP effect).
Pyrazine side-chain modifications - amides
A small library of amides (including the m-Cl benzylamide, MMV668958) showed promising potency. However, other amides (derived from aliphatic or anilines) either showed lower potency or were inactive. The RLM of MMV668958 was poor - perhaps due to benzylic oxidation. Alpha-substitution at the benzylic position or constraining the benzylamine into an aminoindane did not improve potency.
The p-Cl benzanilide MMV670246, although not active against PfNF54, showed good RLM stability perhaps due to lack of benzylic metabolism. However, its rat PK showed high clearance. The m-Cl (MMV669542) had poor RLM stability.
Several attempts to make aniline-amides with improved potency against Pfal failed:
- Loading the aniline ring with lipophilic substituents marginally improved potency but led to poor RLM stability.
Only one compound in this Series first made at the CRO was measured in rat PK and that was the relatively weak amide MMV670246. The curve is shown for oral & IV legs & parameters are below.
IMAGE + chart
One of the compounds with better in vitro balance is MMV670652 with potency at 17 nM, HLM Clint < 8 ul/min/mg and RLM Clint at 30 ul/min/mg. This compound has not been in rat PK. Additionally it may be possible to improve potency by synthesis of the more potent enantiomer.
As would be expected HLM vs. RLM shows a general correlation with approx 4-fold shift on average. However, for most of the more potent analogs, this increases to over 10-fold. The figure below shows the 4 sub 30nM compounds with HLM & RLM measured.
IMAGE + chart
Lipophilicity & lipophilic efficiency Few compounds achieve a lipophilic efficiency (as measured by pIC50 – AlogP) of greater than 4.0
IMAGE + chart
Potential next steps - suggested in original pre-OSM briefing document
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.
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)
Solubility is low and improvement should be one of the goals for lead optimisation. The metabolic stability is not a mouse specific event and needs to be improved to deliver a candidate. Met ID data may help in the design of new analogs with improved stability, but we could also look at correlations with Log D etc. to drive new target design)
Other Sources of Compounds in this Series
Strings for Google
Use this section to paste strings to make the page more discoverable.
MMV668955 FC(F)OC(C=C1)=CC=C1C2=NN=C3N2C(CCO)CNC3; InChI=1S/C14H16F2N4O2/c15-14(16)22-11-3-1-9(2-4-11)13-19-18-12-8-17-7-10(5-6-21)20(12)13/h1-4,10,14,17,21H,5-8H2
MMV668958 FC(F)OC(C=C1)=CC=C1C2=NN=C3N2C(C(NCC4=CC(Cl)=CC=C4)=O)=CN=C3; InChI=1S/C20H14ClF2N5O2/c21-14-3-1-2-12(8-14)9-25-19(29)16-10-24-11-17-26-27-18(28(16)17)13-4-6-15(7-5-13)30-20(22)23/h1-8,10-11,20H,9H2,(H,25,29)
MMV668960 FC(F)OC(C=C1)=CC=C1C2=NN=C3N2CCNC3; InChI=1S/C12H12F2N4O/c13-12(14)19-9-3-1-8(2-4-9)11-17-16-10-7-15-5-6-18(10)11/h1-4,12,15H,5-7H2
MMV668962 FC(F)OC(C=C1)=CC=C1C2=NN=C3N2CCN(C(CN)=O)C3; InChI=1S/C14H15F2N5O2/c15-14(16)23-10-3-1-9(2-4-10)13-19-18-11-8-20(12(22)7-17)5-6-21(11)13/h1-4,14H,5-8,17H2
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
MMV669025 FC1=C(F)C=CC(CCOC2=CNC(C3=NN=C(C4=CC=C(OC(F)F)C=C4)N32)=O)=C1; InChI=1S/C20H14F4N4O3/c21-14-6-1-11(9-15(14)22)7-8-30-16-10-25-19(29)18-27-26-17(28(16)18)12-2-4-13(5-3-12)31-20(23)24/h1-6,9-10,20H,7-8H2,(H,25,29)
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
MMV669310 FC(F)OC(C=C1)=CC=C1C2=NN=C3N2C(CCCC4=CC=CC=C4)CNC3; InChI=1S/C21H22F2N4O/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/h1-3,5-6,9-12,17,21,24H,4,7-8,13-14H2
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)
MMV669846 FC1=C(F)C=CC(CCOC2=CN=CC3=NC=C(C4=CC=C(Cl)C=C4)N32)=C1; InChI=1S/C20H14ClF2N3O/c21-15-4-2-14(3-5-15)18-10-25-19-11-24-12-20(26(18)19)27-8-7-13-1-6-16(22)17(23)9-13/h1-6,9-12H,7-8H2
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
MMV670246 FC(F)OC(C=C1)=CC=C1C2=NN=C3N2C(C(NC4=CC=C(Cl)C=C4)=O)=CN=C3; InChI=1S/C19H12ClF2N5O2/c20-12-3-5-13(6-4-12)24-18(28)15-9-23-10-16-25-26-17(27(15)16)11-1-7-14(8-2-11)29-19(21)22/h1-10,19H,(H,24,28)
MMV670250 FC1=C(F)C=CC(CCOC2=CN=CC3=CN=C(C4=CC=C(Cl)C=C4)N32)=C1; InChI=1S/C20H14ClF2N3O/c21-15-4-2-14(3-5-15)20-25-11-16-10-24-12-19(26(16)20)27-8-7-13-1-6-17(22)18(23)9-13/h1-6,9-12H,7-8H2
MMV670437 FC(F)OC(C=C1)=CC=C1C2=NN=C3C=NC=C(OC[C@H](N(C)C)C4=CC(F)=C(F)C=C4)N32; InChI=1S/C22H19F4N5O2/c1-30(2)18(14-5-8-16(23)17(24)9-14)12-32-20-11-27-10-19-28-29-21(31(19)20)13-3-6-15(7-4-13)33-22(25)26/h3-11,18,22H,12H2,1-2H3/t18-/m0/s1
MMV670945 FC(F)OC(C=C1)=CC=C1C2=NN=C3N2C=C(OCCC4=CC=C(F)C(F)=C4)N=C3; InChI=1S/C20H14F4N4O2/c21-15-6-1-12(9-16(15)22)7-8-29-18-11-28-17(10-25-18)26-27-19(28)13-2-4-14(5-3-13)30-20(23)24/h1-6,9-11,20H,7-8H2
MMV670946 FC(F)OC(C=C1)=CC=C1C2=NN=C3N2C=C(OCC4=CC=C(F)C(F)=C4)N=C3; InChI=1S/C19H12F4N4O2/c20-14-6-1-11(7-15(14)21)10-28-17-9-27-16(8-24-17)25-26-18(27)12-2-4-13(5-3-12)29-19(22)23/h1-9,19H,10H2
MMV670949 FC(F)OC(C=C1)=CC=C1C2=NN=C3N2C=C(NCC4=CC=C(F)C(F)=C4)N=C3; InChI=1S/C19H13F4N5O/c20-14-6-1-11(7-15(14)21)8-24-16-10-28-17(9-25-16)26-27-18(28)12-2-4-13(5-3-12)29-19(22)23/h1-7,9-10,19,24H,8H2
MMV671655 FC(F)OC(C=C1)=CC=C1C2=NN=C3N2C=C(NC4=CC=C(F)C(F)=C4)N=C3; InChI=1S/C18H11F4N5O/c19-13-6-3-11(7-14(13)20)24-15-9-27-16(8-23-15)25-26-17(27)10-1-4-12(5-2-10)28-18(21)22/h1-9,18,24H
MMV671926 FC(F)OC(C=C1)=CC=C1C2=NN=C3N2C=C(OC4=CC=C(F)C(F)=C4)N=C3; InChI=1S/C18H10F4N4O2/c19-13-6-5-12(7-14(13)20)27-16-9-26-15(8-23-16)24-25-17(26)10-1-3-11(4-2-10)28-18(21)22/h1-9,18H
MMV671927 FC(F)OC(C=C1)=CC=C1C2=NN=C3N2C=C(NCCC4=CC=C(F)C(F)=C4)N=C3; InChI=1S/C20H15F4N5O/c21-15-6-1-12(9-16(15)22)7-8-25-17-11-29-18(10-26-17)27-28-19(29)13-2-4-14(5-3-13)30-20(23)24/h1-6,9-11,20,25H,7-8H2
MMV672619 FC(F)OC(C=C1)=CC=C1C2=NN=C3N2C=C(O[C@@H]4C(N(C5CC5)[C@@H]4C6=CC(F)=C(F)C=C6)=O)N=C3; InChI=1S/C24H17F4N5O3/c25-16-8-3-13(9-17(16)26)20-21(23(34)33(20)14-4-5-14)36-19-11-32-18(10-29-19)30-31-22(32)12-1-6-15(7-2-12)35-24(27)28/h1-3,6-11,14,20-21,24H,4-5H2/t20-,21+/m1/s1
MMV672939 FC(F)OC(C=C1)=CC=C1C2=NN=C3C=CC(OCCC4=CC(F)=C(F)C=C4)=NN32; InChI=1S/C20H14F4N4O2/c21-15-6-1-12(11-16(15)22)9-10-29-18-8-7-17-25-26-19(28(17)27-18)13-2-4-14(5-3-13)30-20(23)24/h1-8,11,20H,9-10H2
MMV672942 FC(F)OC(C=C1)=CC=C1C2=NN=C3C=CC(NCCC4=CC=C(F)C=C4)=NN32; InChI=1S/C20H16F3N5O/c21-15-5-1-13(2-6-15)11-12-24-17-9-10-18-25-26-19(28(18)27-17)14-3-7-16(8-4-14)29-20(22)23/h1-10,20H,11-12H2,(H,24,27)
MMV672990 FC(F)OC(C=C1)=CC=C1C2=NN=C3N2C=C(NC(CC4=CC=CC(Cl)=C4)=O)N=C3; InChI=1S/C20H14ClF2N5O2/c21-14-3-1-2-12(8-14)9-18(29)25-16-11-28-17(10-24-16)26-27-19(28)13-4-6-15(7-5-13)30-20(22)23/h1-8,10-11,20H,9H2,(H,25,29)
MMV672992 N#CC(C=C1)=CC=C1C2=NN=C3C=CC(NCCC4=CN=CC=C4)=NN32; InChI=1S/C19H15N7/c20-12-14-3-5-16(6-4-14)19-24-23-18-8-7-17(25-26(18)19)22-11-9-15-2-1-10-21-13-15/h1-8,10,13H,9,11H2,(H,22,25)