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10th December 2014 @ 14:10

Biological activities of OSM-S-106 and PT-22-C1 performed at the Dundee Drug Discovery Unit by Irene Hallyburton.

OSM-S-106 was resynthesised in Edinburgh (PT-23-C1) and found to have an activity of 150 nM, consistent with that reported as TCMDC 135294 but a little lower than the Avery results. Adding a methyl group to improve solubility by introducing an axial twist gave PT-22-C1, which was inactive.





OSM-S-106 and PT-22-C1.pdf

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17th November 2014 @ 17:48

A set of 12 compounds were sent to Syngene for evaluation against blood stage asexual NF54 strain of Plasmodium falciparum.

Samples sent for in vitro efficacy evaluation against Plasmodium falciparum asexual blood stage

Data were received (via the ScienceCloud portal at MMV) on October 10th. Data for one compound was missing, and subsequently received on Oct 23rd. Data:

Syngene Data Oct 2014


1. CF3 tolerated as a replacement for CHF2 in northeast, which may make synthesis simpler. Impact of using Me looks to be to reduce potency.

Impact of CH3 vs CF3 vs CHF2

(Note - need analysis along similar lines for impact of Cl and CN)

2. High sensitivity to changes in northwest ring. Compare MMV675951 and MMV675950


3. Pyridyl is a bad substitution. Compare MMV675963 with MMV675961, MMV675962. Also compare MMV675949 with OSM-S-189.

4. Benzylic in northwest not bad, but deleterious compared to phenethyl (MMV639565, 38 nM).


This post originally authored by Mat Todd

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16th November 2014 @ 22:57

Context: 12 compounds were sent for evaluation for metabolic clearance by aldehyde oxidase (Discussion, Compounds sent:

Which Compounds to Send for Aldehyde Oxidase Assay?

Assay performed by: Christine Orozco, Scott Obach, Pfizer, Groton CT.


Aldehyde Oxidase Results OSM Series 4


The compounds were incubated in 1 mg/mL cytosol out to 3 hours. Controls: carbazeran, zoniporide and zaleplon were assayed in each incubation plate to represent high, moderate and low AO clearance respectively. The Open Source Malaria compounds were assayed along with the controls and compared using a relative yardstick approach.

The test compounds had a range of clearances. There was one high clearance compound similar to carbazeran, three moderate clearance compounds similar to zoniporide, two compounds with moderate to low clearance, and the remaining four compounds were stable/low clearance with no turnover within 3 hours.

Two compounds were not included for technical reasons. Compound MMV670250 was not detected under the analytical methods used so new LC/MS methods are being developed for this compound. For MMV672939, there was variability in the later time points of both replicates. These two compounds can be repeated in the future.

More detail on the data, protocol, assay notes and conditions is in the attached spreadsheet.

OpenSource Malaria_Cytosol_Results_Protocol_CCO.xlsx

This post originally authored by Mat Todd

MMV668956 FC(F)OC(C=C1)=CC=C1C2=NN=C(N32)C=NC=C3OC4CN(C5=CC(F)=C(F)C=C5)C4 InChI=1S/C21H15F4N5O2/c22-16-6-3-13(7-17(16)23)29-10-15(11-29)31-19-9-26-8-18-27-28-20(30(18)19)12-1-4-14(5-2-12)32-21(24)25/h1-9,15,21H,10-11H2 FFDOLPKXJUAFAH-UHFFFAOYSA-N
MMV669784 FC(F)OC(C=C1)=CC=C1C2=NN=C3C=NC=C(OC4=CC=C(Cl)C=C4)N32 InChI=1S/C18H11ClF2N4O2/c19-12-3-7-13(8-4-12)26-16-10-22-9-15-23-24-17(25(15)16)11-1-5-14(6-2-11)27-18(20)21/h1-10,18H WXNPYOXFQUYIOI-UHFFFAOYSA-N
MMV669844 FC(C=C1)=C(F)C=C1[C@@H](OC)COC2=CN=CC3=NN=C(C4=CC=C(C#N)C=C4)N32 InChI=1S/C21H15F2N5O2/c1-29-18(15-6-7-16(22)17(23)8-15)12-30-20-11-25-10-19-26-27-21(28(19)20)14-4-2-13(9-24)3-5-14/h2-8,10-11,18H,12H2,1H3/t18-/m0/s1 PERKBMZWWUEZNJ-SFHVURJKSA-N
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 MQHQNFQVEXYAMO-UHFFFAOYSA-N
MMV670947 FC(F)OC(C=C1)=CC=C1C2=NN=C(N32)C=NC=C3OCC(CO)C4=CC=C(F)C(F)=C4 InChI=1S/C21H16F4N4O3/c22-16-6-3-13(7-17(16)23)14(10-30)11-31-19-9-26-8-18-27-28-20(29(18)19)12-1-4-15(5-2-12)32-21(24)25/h1-9,14,21,30H,10-11H2 MKSKANAVVSFYNL-UHFFFAOYSA-N
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) CAFUHAVOTBMKAN-UHFFFAOYSA-N
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 JHORUMGXLQTHAD-UHFFFAOYSA-N
MMV670944 FC(F)OC(C=C1)=CC=C1C2=NN=C3N2C(C(NC4=CC=NC(F)=C4)=O)=CN=C3 InChI=1S/C18H11F3N6O2/c19-14-7-11(5-6-23-14)24-17(28)13-8-22-9-15-25-26-16(27(13)15)10-1-3-12(4-2-10)29-18(20)21/h1-9,18H,(H,23,24,28) UEOZBGRWGZEYED-UHFFFAOYSA-N
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 PPYIQNQWTQZDBZ-UHFFFAOYSA-N
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 GVXYAEXVJYZTBB-UHFFFAOYSA-N
MMV672727 FC(F)OC(C=C1)=CC=C1C2=NN=C(N32)C=NC=C3OCC(F)(C)C4=CC=C(F)C(F)=C4 InChI=1S/C21H15F5N4O2/c1-21(26,13-4-7-15(22)16(23)8-13)11-31-18-10-27-9-17-28-29-19(30(17)18)12-2-5-14(6-3-12)32-20(24)25/h2-10,20H,11H2,1H3 MHMDPQOWBHVFHN-UHFFFAOYSA-N
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 POGWIRSWBGSGTG-UHFFFAOYSA-N

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25th September 2014 @ 09:00

Six "Near Neighbour" compounds in OSM Series 1 were synthesised by an undergraduate cohort at Lawrence University supervised by Stefan Debbert. The compounds have been evaluated for potency by Julie Clark in Kip Guy's lab. The results are summarised below and may be found in full in the attached spreadsheet. Julie said "I ran 2 independent experiments with a data analysis for each experiment, then I re-ran the data analysis for both runs together (combined analysis)." The data will be folded into the first OSM paper that is being written.

Debbert Guy Data

Two of the compounds (OSM-S-37 and OSM-S-111) have been evaluated for potency before. The new numbers matche very well in one case, and not so well in the other. One compound (OSM-A-2 note that the "A" stands for Appleton, where the compounds were made) appears to be unstable, given the difference in the values obtained between the two measurements. Two of the other compounds (OSM-A-1 and OSM-A-4) display low activity. One new compound of the six (OSM-A-3) displays good potency, in fact the best of the set.

At the time of writing, this series is parked, but can be pursued further by anyone. Compounds are potent and synthetically accessible.

(A note from the OSM team to the students who made these compounds - way to go, guys)


Julie Clark provided the attached Word file as a description of the protocol used in the assay.


(This entry authored by Mat)


OSM-S-111, SJ000849514-1, 

OSM-A-2, SJ000849515-1, 

OSM-A-1, SJ000849516-1, 

OSM-A-4, SJ000849517-1, 

OSM-S-37, SJ000849518-1, 

OSM-A-3, SJ000849519-1, 

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22nd September 2014 @ 04:02


A selection of Series 4 compounds were sent for evaluation again the hERG ion channel using a  "medium-throughput electrophysiology-based hERG assay using IonWorksTM HT" at AstraZeneca.

The compounds were selected from compounds synthesised at The University of Sydney (biological data here) and also those inherited from MMV following online discussion (see GitHub Issue #211).



(updated by Mat, original file still attached below. Reason for update: units provided in AZ assay were micromolar, as an IC50. These have been converted into the more standard pIC50, which is -log of the IC50 when expressed in Molar and is unitless)


Updated hERG AZ results


Graphical Representation of ClogP vs -p(IC50) and LogP vs -log10(IC50)

(updated by Mat, original file still attached below)

plot of herg vs pIC50

Excel Data
(updated by Mat, original file still attached below)

MMV_-OSD_hERG results from AZ with calcs.xlsx


Preliminary Conclusions

Initial examination of the new data suggests that amides/amines show problematic hERG activity whereas ethers are tolerated. However, it is also possible that the Para OCHF2 ether is the problem. One of the original two data points (for MMV669844) shows that a compound lacking both is still active in the assay, so the answer is more subtle. There is little correlation between CLogP and hERG activity, but clogp is an approximation to actual solubility.

Future Work

The team need to synthesise some amides containing the para-nitrile aromatic group (or pyridyl) on the 'right-hand-side' in order to determine whether amides containing different aryl groups show hERG activity. Despite these data, only compounds possessing lower LogP values should be synthesised in the next round to aid solubility, and this will provide more data for the hERG/logP correlation. Following the next two rounds of synthesis and evaluation, more compounds will be evaluated in this assay.

General Assay Principle

"The hERG-expressing Chinese hamster ovary K1 (CHO) cells described by Persson, Carlsson, Duker, and Jacobson (2005) were grown to semi-confluence at 37 °C in a humidified environment (5% CO2) in F-12 Ham medium containing L-glutamine, 10% foetal calf serum (FCS) and 0.6 mg/ml hygromycin (all Sigma- Aldrich). Prior to use, the monolayer was washed using a pre- warmed (37 °C) 3 ml aliquot of Versene 1:5000 (Invitrogen). After aspiration of this solution the flask was incubated at 37 °C in an incubator with a further 2 ml of Versene 1:5000 for a period of 6 min. Cells were then detached from the bottom of the flask by gentle tapping and 10 ml of Dulbecco's phosphate-buffered saline containing calcium (0.9 mM) and magnesium (0.5 mM) (PBS; Invitrogen) was then added to the flask and aspirated into a 15 ml centrifuge tube prior to centrifugation (50×g, for 4 min). The resulting supernatant was discarded and the pellet gently re- suspended in 3 ml of PBS. A 0.5 ml aliquot of cell suspension was removed and the number of viable cells (based on trypan blue exclusion) was determined in an automated reader (Cedex; Innovatis) so that the cell re-suspension volume could be adjusted with PBS to give the desired final cell concentration. It is the cell concentration at this point in the assay that is quoted when referring to this parameter. CHO-Kv1.5 cells, which were used to adjust the voltage offset on IonWorksTM HT, were maintained and prepared for use in the same way."


Bridgland-Taylor MH, Hargreaves AC, Easter A, Orme A, Henthorn DC, Ding M, Davis AM, Small BG, Heapy CG, Abi-Gerges N, Persson F, Jacobson I, Sullivan M, Albertson N, Hammond TG, Sullivan E, Valentin J-P,  Pollard CE (2006) Optimisation and validation of a medium-throughput electrophysiology-based hERG assay using IonWorksTMHT. Journal of Pharmacological and Toxicological Methods 54: 189–199 (10.1016/j.vascn.2006.02.003)

 Post originally authored by Alice E Williamson

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