Biological Evaluation of Compounds

 

Data derived from pre-OSM work on Series 4 amides. Was originally posted here, but posted here again as may be more suitable grouped with biological data.

Original spreadsheet:

Wiki summary here.

Chemdraw file

Picture file

 

 

Strings:

MMV668958    N1=CC2=NN=C(N2C(=C1)C(=O)NCc1cc(ccc1)Cl)c1ccc(cc1)OC(F)F
MMV669000    N1=CC2=NN=C(N2C(=C1)C(=O)N1Cc2c(cccc2)C1)c1ccc(cc1)OC(F)F
MMV669001    N1=CC2=NN=C(N2C(=C1)C(=O)NCc1ccc(cc1)Cl)c1ccc(cc1)OC(F)F
MMV669002    N1=CC2=NN=C(N2C(=C1)C(=O)NCc1ccccc1Cl)c1ccc(cc1)OC(F)F
MMV669003    N1=CC2=NN=C(N2C(=C1)C(=O)NCC1CCOCC1)c1ccc(cc1)OC(F)F
MMV669010    N1=CC2=NN=C(N2C(=C1)C(=O)N1CCN(c2ncccc2)CC1)c1ccc(cc1)OC(F)F
MMV669011    N1=CC2=NN=C(N2C(=C1)C(=O)NCCN1CCOCC1)c1ccc(cc1)OC(F)F
MMV669022    N1=CC2=NN=C(N2C(=C1)C(=O)N1CCCC1)c1ccc(cc1)OC(F)F
MMV669104    N1(CCCC1c1ccccc1)C(=O)C1=CN=CC2=NN=C(N12)c1ccc(cc1)OC(F)F
MMV669023    N1(CCN(CC1)S(=O)(=O)C)C(=O)C1=CN=CC2=NN=C(N12)c1ccc(cc1)OC(F)F
MMV669020    N1(CCOCC1)C(=O)C1=CN=CC2=NN=C(N12)c1ccc(cc1)OC(F)F
MMV669024    N([C@H](c1ccccc1)C)C(=O)C1=CN=CC2=NN=C(N12)c1ccc(cc1)OC(F)F
MMV669021    N([C@@H](c1ccccc1)C)C(=O)C1=CN=CC2=NN=C(N12)c1ccc(cc1)OC(F)F
MMV669026    n1c(cccc1)NC(=O)C1=CN=CC2=NN=C(N12)c1ccc(cc1)OC(F)F
MMV669027    N(CCc1ccccc1)C(=O)C1=CN=CC2=NN=C(N12)c1ccc(cc1)OC(F)F
MMV669105    Clc1cc(ccc1)CN(C)C(=O)C1=CN=CC2=NN=C(N12)c1ccc(cc1)OC(F)F
MMV669543    n12c(cncc1nnc2c3ccc(cc3)OC(F)F)C(=O)NCc4ccc(c(c4)F)F
MMV669542    n12c(cncc1nnc2c3ccc(cc3)OC(F)F)C(=O)Nc4cccc(c4)Cl
MMV670246    c1ncc2nnc(n2c1C(Nc1ccc(cc1)Cl)=O)c1ccc(cc1)OC(F)F
MMV669849    c1ncc2nnc(n2c1C(Nc1ccc(cc1)F)=O)c1ccc(cc1)OC(F)F
MMV669850    c1ncc2nnc(n2c1C(Nc1ccc(c(c1)F)F)=O)c1ccc(cc1)OC(F)F
MMV670767    c1ncc2n(c1C(=O)Nc1ccc(c(c1)Cl)F)c(nn2)c1ccc(cc1)OC(F)F
MMV670944    c1ncc2n(c1C(=O)Nc1ccnc(c1)C(F)(F)F)c(nn2)c1ccc(cc1)OC(F)F
MMV670768    c1ncc2n(c1C(=O)N1CCc3c1ccc(c3)F)c(nn2)c1ccc(cc1)OC(F)F
MMV671654    c1ncc2n(c1C(=O)Nc1ccc(cc1Cl)F)c(nn2)c1ccc(cc1)OC(F)F
MMV671676    c1c(c(ccc1Cl)Cl)CNC(c1cncc2n1c(nn2)c1ccc(cc1)OC(F)F)=O
MMV671677    c1c(c(c(cc1)C(F)(F)F)Cl)CNC(c1cncc2n1c(nn2)c1ccc(cc1)OC(F)F)=O

Ion regulation assays to be performed by Kiaran Kirk on representative compounds from early series of OSM project. Relevant consultation:

https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/77

Draft Chemdraw of structures posted here. Require addition of potencies and molecular weights and then re-posting, partly as reference for Kirk Lab when doing testing.

Part of launch of Series 4. Five compounds were originally evaluated in ion regulation assays by Kiaran Kirk since this could indicate the compounds are inhibiting PfATP4.

Data sheet from MMV on the compounds is attached:

Structures of the compounds:

 

Ion regulation activity (vs potency):

MMV669000: no (potency: inactive)

MMV669304: yes (potency: 280 nM)

MMV669360: yes (potency: 356 nM)

MMV669542: yes (potency: 185 nM)

MMV669848: yes (potency: 114 nM)

(Note the correlation: compound inactive in ion regulation assay is the inactive Pf analog)

The experiments were done by Adelaide Dennis, then a Research Assistant and now a PhD student in the Kirk lab. 

 

Compound Strings
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

Biological evaluation of OSM-S-96 through 105 performed by Vicky Avery's lab by Sabine Fletcher.

Structures:

PDF summarising data:

Excel sheet of raw data:

Comments from Sabine:
Unfortunately, none of the cpds was active enough on 3D7 to obtain an
IC50 curve (only cpd OSM-S-103 showed 61% inhibition at the highest dose).

Slight solubility issues etc. after thorough vortexing were as follows:

OSM-S-100: very few, tiny undissolved crystals
OSM-S-101: few floating specks that looked like dust / cotton wool
OSM-S-104: few floating specks of different colour: white (cotton
wool?) large black 'chip' (plastic from lid?) and tiny orange specks (undissolved crystals?)
OSM-S-105: had cotton wool in lid. I 'flushed' the cotton wool
thoroughly with DMSO to dissolve all compound on the cotton wool and
then discarded the wool.

Places where these results are discussed:
G+


InChIs:
(need to insert)

Yeas-based genetic sensitivity assay performed by the Nislow Lab at The University of Toronto. Data acquired by Marinella Gebbia and subsequent gene set analysis performed by Anna Lee.

Relevant Compounds:

The Excel file contains the log2 intensity ratios (control/treatment) which are proportional to the strains sensitivity to the compound. It also has a list of sensitive genes for all compound tested and a description of the cellular compartment, the metabolic process and the gene function for each strain.

The Spotfire file contains all the data plots.

The enrichment maps show the GO biological processes that are enriched amongst the genes associated with compound-sensitivity. Maps are *not* provided for compounds that did not yield any significant enrichment (FDR<= 0.1).

The Word document contains a more detailed description of the enrichment maps, and details about how they were generated.

Marinella also kindly provided the Spotfire plots (Powerpoint file):

and said: "on the Y axis you have the log2ratios (control/treatment) and on the X axis the genes."

Associated discussion of these data: GHI20

Update. Additional data sent 18th Feb. File attached "Dataset S35 Nislow4". Excel file of the fitness defect scores for all deletion strains.

File lists the significantly sensitive strains derived from Tag4 microarray hybridizations as described in Lee AY, St.Onge RP, Proctor MJ, et al. Mapping the Cellular Response to Small Molecules Using Chemogenomic Fitness Signatures. Science2014;344(6180):208-211. doi:10.1126/science.1250217.

 
Raw data normalization and removal of problematic tags Each probe on the Genflex tag16k array (Affymetrix, Santa Clara, CA), i.e. the Tag4 array, is represented by 5 replicate features. These replicates allow the removal of outliers that may for example, arise from small debris in the hybridization solution. To identify and remove probes defined as outliers, we used a previously described masking algorithm. We next defined the ‘raw average’ of each tag as the average of all remaining probe replicates for a particular tag. We then removed all tags corresponding to the control strain. For each array, uptags and downtags were normalized separately, as were heterozygous and homozygous strains, creating 4 sets: uptag/het, uptag/hom, downtag/het, downtag/hom. To simplify our dataset, we removed strains where the deletions no longer correspond to valid genes according to the Saccharomyces Genome Database (SGD).

 
The fitness defect (FD) score We devised a fitness defect (FD) score that quantifies the sensitivity of each deletion strain to a chemical perturbation by comparing the signal of a strain following chemical treatment to the signal of the strain from control samples (i.e. DMSO-treated samples). Specifically, log2ratios were calculated for each strain as follows: log2ratio = log2[ / ]

 
Identification of significant chemical-genetic interactions: We defined significant chemical-genetic interactions by identifying FD scores that deviated significantly from other FD scores in a given screen (heterozygous and homozygous strains were considered separately). This approach is based on the assumption that, at chemical concentrations that only minimally inhibit growth of the pool, most strains will not exhibit a fitness defect.

Forward link to PRR Assay performed to verify these data.