Fig 1.
MMV007384 is a bilayer-modifying compound.
Fluorescence quench traces showing the effects of 5,5'-Methylenebis [2- (4-methoxyphenyl)-1H-benzimidazole] or MMV007384 [5]) in the gramicidin-based fluorescence assay (GBFA). The panel left shows the results over 1 s. In the presence of 5 or 10 μM of the Malaria Box compound, the quench rate normalized to control (in the absence of the compound) increased to 1.8 (q5) and 2 (q10), respectively. The difference is statistically significant (p < .0001). The right panel shows the average trace for a single run at higher time resolution.
Fig 2.
Four Malaria Box compounds have statistically significant bilayer effects.
80 Malaria Box compounds were tested at 5 μM, the order of the compounds is A2 … A11, B2 … B11, etc. The four Malaria Box compounds that perturb the bilayer are MMV007384 (red bar, q5 = 1.79, p<0.01), and from L to R (amber bars): N-{4-[(4-methyl-1-piperidinyl)methyl]phenyl}-1H-pyrrolo[3,2-h]quinoline-2-carboxamide, MMV020549, q5 = 1.3, p<0.05); N-{4-[(4-ethyl-1-piperazinyl)methyl]phenyl}-1H-pyrrolo[3,2-h]quinoline-2-carboxamide, MMV020548, q5 = 1.27, p < .05); and 2-{[1-(2,4-dimethoxyphenyl)-1H-imidazol-2-yl]sulfanyl}-N-(2,5-dimethylphenyl)acetamide MMV019258, q5 = 1.32, p < .05). Error bars depict S.E.M. Unpaired, two-tailed t-tests were performed in comparison to control.
Fig 3.
The Malaria Box compounds’ estimated hydrophobicity (clogP) is not correlated with lipid bilayer effects.
Plot of the quench rate (relative to control) vs. cLogP, which was calculated using the ALOGP algorithm [44] as implemented by Collaborative Drug Discovery, Inc. (http://collaborativedrug.com, Burlingame, CA). MMV007384 (red dot cLogP = 6.37); from L to R (amber dots): MMV020548, cLogP = 3.39; MMV020549, cLogP = 4.16; and MMV019258, cLogP = 4.01.
Fig 4.
QED does not correlate with bilayer-mediated off-target effects.
Plot of the quench rate (relative to control) vs. the weighted QED [43]. There is some clustering of the Malaria Box compounds toward the “attractive” QED value. MMV007384 (red dot, weighted QED = .292) is an unattractive complex compound. From L to R (amber dots): MMV020548 (weighted QED = .523) and MMV020548 (weighted QED = .527) are unattractive complex compounds; and MMV019258 (weighted QED = .605) is at the cusp of attractive and unattractive simple compounds. Vertical dotted lines represent reported averages of, from L to R: unattractive (complex); unattractive (simple); and attractive QED values. QED was calculated using Pipeline Pilot (Accelrys Inc., San Diego, CA). (Weighted QED did not differ substantially from unweighted QED, not shown).