Author response:
The following is the authors’ response to the original reviews.
Public Reviews:
Reviewer #1 (Public review):
Summary:
The authors' goal was to advance the understanding of metabolic flux in the bradyzoite cyst form of the parasite T. gondii, since this is a major form of transmission of this ubiquitous parasite, but very little is understood about cyst metabolism and growth. Nonetheless, this is an important advance in understanding and targeting bradyzoite growth.
Strengths:
The study used a newly developed technique for growing T. gondii cystic parasites in a human muscle-cell myotube format, which enables culturing and analysis of cysts. This enabled the screening of a set of anti-parasitic compounds to identify those that inhibit growth in both vegetative (tachyzoite) forms and bradyzoites (cysts). Three of these compounds were used for comparative Metabolomic profiling to demonstrate differences in metabolism between the two cellular forms.
One of the compounds yielded a pattern consistent with targeting the mitochondrial bc1 complex and suggests a role for this complex in metabolism in the bradyzoite form, an important advance in understanding this life stage.
Weaknesses:
Studies such as these provide important insights into the overall metabolic differences between different life stages, and they also underscore the challenge of interpreting individual patterns caused by metabolic inhibitors due to the systemic level of some of the targets, so that some observed effects are indirect consequences of the inhibitor action. While the authors make a compelling argument for focusing on the role of the bc1 complex, there are some inconsistencies in the patterns that underscore the complexity of metabolic systems.
We agree with reviewer #1 that metabolic fingerprints are complex to interpret and we did try to approach this problem by including mock treatment and non-metabolic inhibitors as controls. We address specific concerns below.
Reviewer #2 ( Public review):
Summary:
A particular challenge in treating infections caused by the parasite Toxoplasma gondii is to target (and ultimately clear) the tissue cysts that persist for the lifetime of an infected individual. The study by Maus and colleagues leverages the development of a powerful in vitro culture system for the cyst-forming bradyzoite stage of Toxoplasma parasites to screen a compound library for candidate inhibitors of parasite proliferation and survival. They identify numerous inhibitors capable of inhibiting both the disease-causing tachyzoite and the cyst-forming bradyzoite stages of the parasite. To characterize the potential targets of some of these inhibitors, they undertake metabolomic analyses. The metabolic signatures from these analyses lead them to identify one compound (MMV1028806) that interferes with aspects of parasite mitochondrial metabolism. The authors claim that MV1028806 targets the bc1 complex of the mitochondrial electron transport chain of the parasite, although the evidence for this is indirect and speculative. Nevertheless, the study presents an exciting approach for identifying and characterizing much-needed inhibitors for targeting tissue cysts in these parasites.
Strengths:
The study presents convincing proof-of-principle evidence that the myotube-based in vitro culture system for T. gondii bradyzoites can be used to screen compound libraries, enabling the identification of compounds that target the proliferation and/or survival of this stage of the parasite. The study also utilizes metabolomic approaches to characterize metabolic 'signatures' that provide clues to the potential targets of candidate inhibitors, although falls short of identifying the actual targets.
Weaknesses:
(1) The authors claim to have identified a compound in their screen (MMV1028806) that targets the bc1 complex of the mitochondrial electron transport chain (ETC). The evidence they present for this claim is indirect (metabolomic signatures and changes in mitochondrial membrane potential) and could be explained by the compound targeting other components of the ETC or affecting mitochondrial biology or metabolism in other ways. In order to make the conclusion that MMV1028806 targets the bc1 complex, the authors should test specifically whether MMV1028806 inhibits bc1-complex activity (i.e. in a direct enzymatic assay for bc1 complex activity). Testing the activity of MMV1028806 against other mitochondrial dehydrogenases (e.g. dihydroorotate dehydrogenase) that feed electrons into the ETC might also provide valuable insights. The experiments the authors perform also do not directly measure whether MMV1028806 impairs ETC activity, and the authors could also test whether this compound inhibits mitochondrial O2 consumption (as would be expected for a bc1 inhibitor).
We thank the reviewer for highlighting this important aspect. To further investigate the effect of MMV1028806 on the mETC, we adapted a commercial oxygen consumption assay and demonstrated that MMV1028806, like Atovaquone and Buparvaquone, inhibits the ETC, leading to reduced oxygen consumption similar to Antimycin A, which inhibits the bc1-complex. These results are now included in the revised manuscript (Methods, lines 210–233; Results, lines 460–468).
(2) The authors claim that compounds targeting bradyzoites have greater lipophilicity than other compounds in the library (and imply that these compounds also have greater gastrointestinal absorbability and permeability across the blood-brain barrier). While it is an attractive idea that lipophilicity influences drug targeting against bradyzoites, the effect seems pretty small and is complicated by the fact that the comparison is being made to compounds that are not active against parasites. If the authors are correct in their assertion that lipophilicity is a major determinant of bradyzoicidal compounds compared to compounds that target tachyzoites alone, you would expect that compounds that target tachyzoites alone would have lower lipophilicity than those that target bradyzoites. It would therefore make more sense to (statistically) compare the bradyzoicidal and dual-acting compounds to those that are only active in tachyzoites (visually the differences seem small in Figure S2B). This hypothesis would be better tested through a structure-activity relationship study of select compounds (which is beyond the scope of the study). Overall, the evidence the authors present that high lipophilicity is a determinant of bradyzoite targeting is not very convincing, and the authors should present their conclusions in a more cautious manner.
Thank you for raising this excellent point. We performed a statistical test of tachyzoidal and both bradyzoidal and dually active compounds and find indeed no significant difference (P = 0.06). We altered the results text line 367-368 and the figure S2B caption to explicitly mention this.
(3) Page 11 and Figure 7. The authors claim that their data indicate that ATP is produced by the mitochondria of bradyzoites "independently of exogenous glucose and HDQ-target enzymes." The authors cite their previous study (Christiansen et al, 2022) as evidence that HDQ can enter bradyzoites, since HDQ causes a decrease in mitochondrial membrane potential. Membrane potential is linked to the synthesis of ATP via oxidative phosphorylation. If HDQ is really causing a depletion of membrane potential, is it surprising that the authors observe no decrease in ATP levels in these parasites? Testing the importance of HDQ-target enzymes using genetic approaches (e.g. gene knockout approaches) would provide better insights than the ATP measurements presented in the manuscript, although would require considerable extra work that may be beyond the scope of the study. Given that the authors' assay can't distinguish between ATP synthesized in the mitochondrion vs glycolysis, they may wish to interpret their data with greater caution.
We thank the reviewer for addressing this important point. The enzymatic assay used in our study cannot distinguish whether ATP is produced via glycolysis or mitochondrial respiration. However, we minimized glycolytic ATP production in bradyzoites by starving them for one week without glucose. After this period, amylopectin stores are depleted, forcing the parasites to utilize glutamine via the GABA shunt to fuel the TCA cycle and generate ATP predominantly through respiration. While minor ATP production via gluconeogenic fluxes cannot be excluded, the main ATP supply under these conditions is expected to originate from the mitochondrial electron transport chain. Indeed, ATP levels are lower in HDQ-treated bradyzoites, which we attribute to the compound’s impact on electron-supplying enzymes upstream of the bc1 complex, although this inhibition is not sufficient to fully abolish ATP production as observed with Atovaquone treatment.
Reviewer #3 (Public review):
Summary:
The authors describe an exciting 400-drug screening using a MMV pathogen box to select compounds that effectively affect the medically important Toxoplasma parasite bradyzoite stage. This work utilises a bradyzoites culture technique that was published recently by the same group. They focused on compounds that affected directly the mitochondria electron transport chain (mETC) bc1-complex and compared them with other bc1 inhibitors described in the literature such as atovaquone and HDQs. They further provide metabolomics analysis of inhibited parasites which serves to provide support for the target and to characterise the outcome of the different inhibitors.
Strengths:
This work is important as, until now, there are no effective drugs that clear cysts during T. gondii infection. So, the discovery of new inhibitors that are effective against this parasite stage in culture and thus have the potential to battle chronic infection is needed. The further metabolic characterization provides indirect target validation and highlights different metabolic outcomes for different inhibitors. The latter forms the basis for new studies in the field to understand the mode of inhibition and mechanism of bc1-complex function in detail.
The authors focused on the function of one compound, MMV1028806, that is demonstrated to have a similar metabolic outcome to burvaquone. Furthermore, the authors evaluated the importance of ATP production in tachyzoite and bradyzoites stages and under atovaquone/HDQs drugs.
Weaknesses:
Although the authors did experiments to identify the metabolomic profile of the compounds and suggested bc-1 complex as the main target of MMV1028806, they did not provide experimental validation for that.
In our updated manuscript we performed additional experiments such as oxygen consumption assay to further qualify the bc1 complex as the target. We also toned down some of our statements to make sure that no false claims are made.
Recommendations for the authors:
Reviewer #1 (Recommendations for the authors):
Introduction: It would be helpful to briefly describe what the pathogen Box is, what compounds are in it, and the rationale for using a drug screen to better understand mitochondrial function in cysts.
Thank you for this suggestion, we added an introduction of the MMV pathogen box and outlined our rationale for our experimental approach in lines 90 to 99.
Please explain why dual-active drugs were useful for understanding differences, rather than just seeking drugs that might target bradyzoites alone.
We focused on dually active compounds for two reasons. First, these are the most promising and potent targets to develop drugs against. Both stages might occur simultaneously and these dually active drugs may eliminate the need for treatment with a drug combination. Second, we speculated that monitoring the responses to inhibition of the same process in both parasite stages would reveal its functional consequences. Dually active compounds enable this direct comparison. Bradyzoite-specific compounds may be interesting from a developmental perspective but may require a reverse genetic follow-up to compare differences between stages. The lack of a well-established inducible expression system in bradyzoites that allows short term and synchronized knock-down makes metabolomic approaches difficult. We added these two points in brief to the results section (line 378 – 381).
Figure 4: this is a very important figure in understanding the significance of the work, but it is not well described in the legend. Even if these graphics have been used in other manuscripts, it would be helpful to provide better annotation in the figure legend.
Thank you for pointing this out. We expanded the figure legend to explain the isotopologues data in more detail. Line 793 to 802.
B,D: Explain what the three columns for each drug category represent.
Addressed
C,E: Explain what isotopologues are, what the M+ notation means, and what the pie charts represent. Other main figures have suitable legends.
Addressed
Discussion: there are several places where the reasoning is a bit hard to follow, and rearrangement to provide a clear logical flow would be helpful. In particular, the reasoning for why HDQ impairs active but non-essential processes could be laid out more clearly.
We added additional clarifications to the discussion section and re-wrote the HDQ paragraph. We hope that our reasoning is now easier to follow.
Abbreviations: A list of abbreviations for the entire manuscript would be helpful.
This is a good idea and we now provide an abbreviations list.
Minor typos:
P12, 2d paragraph: sentence beginning with: Consistent with this hypothesis... "cysts" is used twice
Corrected
P15, top of the second paragraph: "nano" and "molar" should be one word
Corrected
Reviewer #2 (Recommendations for the authors):
Major comments (not already covered in the weaknesses section of the public review)
(1) Figure 2 and the related description of these experiments in the methods section (page 3). The approach for calculating IC50 values for the compounds against tachyzoites is unclear. How did the authors determine the time point for calculating IC50 vacuoles? Was this when the DMSO control wells reached maximum fluorescence? This could be described in a clearer manner. A concern with calculating IC50 values on different days is that parasites will have undergone more lytic cycles after 7 days compared to 4 days, which means that the IC50 values for fast- vs slow-acting compounds might be quite different between these days. As a more minor comment on these experiments, the methods section does not describe whether the test compound was removed after 7 days, as the experimental scheme in Figure S1A seems to imply. Please clarify in the methods section.
This is a very good point and we clarified this in the methods section, line 157–160. In brief, we choose the latest time point when exponential growth could be observed in the fastest growing cultures, generally this was in mock treated cultures and at day 4 post infection. We also clarified that we changed media and removed treatment after 7 days.
Minor Comments
(2) Page 2. "we employed a recently developed human myotube-based culture system to generate mature T. gondii drug-tolerant bradyzoites". What makes these bradyzoites 'drug-tolerant' or to which drugs are they tolerant? This isn't clear from the description.
We added these details in the introduction (line 94 to 96) and state that these cysts develop resistance against anti-folates, bumped kinase inhibitors and HDQ, a Co-enzyme Q analog.
(3) Figure 1E. The number of compounds in this pie chart adds up to 384, whereas the methods describe that 371 compounds were tested. What explains this discrepancy in numbers?
We understand the confusion. We now updated the pie chart to reflect only compounds that were included in the primary screen (371) as reflected in Supplementary Table S1. We separately analysed 29 compounds that were previously tested against tachyzoites by Spalenka et al., and found an additional 13 compound, that were originally included in the pie chart. In a secondary test the activity of 10 of these 13 compounds could be confirmed. All in all we found the 16 compounds shown in Fig. 2 E-G.
(4) Page 3. The resazurin assays for measuring host cell viability could be explained in a clearer manner. What host cells were used? Were the host cells confluent when the drug was added (and the assay conducted) or was the drug added when the host cells were first seeded? How long were the host cells cultured in the candidate inhibitors before the assays were performed? What concentration (or concentration range) were the compounds tested? The host inhibition data are not easily accessible to the reader - the authors might consider including these data as part of Table S2D.
The necessary information was added to the methods section (line 145 to 153). We tested for host toxicity in both HFF and KD3 myotubes during the primary screen at 10 µM in triplicates. The colorimetric assay was performed after tachyzoite growth assays in HFFs 7 days post infection and after completion of the 4 week re-growth phase of bradyzoites in myotubes. The resulting data is already part of Supplementary File 1. In addition, we performed concentration dependent resazurin assays after secondary concentration dependent growth inhibition assays and also included data in Supplementary File 1. For the bradyzoite growth assay we performed visual inspection after drug exposure for one week and before tachyzoite re-growth to detect missing or damaged monolayer. Also, this data is included in the Supplementary File 1. We also included the cytotoxicity data as suggested into Table S2D.
(5) Page 7. "Except for four compounds (MMV021013, MMV022478, MMV658988, MMV659004), minimal lethal concentrations were higher in bradyzoites". The variation in these data seems quite large to be making this claim. Consider a statistical analysis of these data to compare potencies in tachyzoites vs bradyzoites.
With this sentence we aimed to describe the results and not to make a statement. We toned down the sentence to “… minimal lethal concentrations appear generally higher in bradyzoites… “ line 344 to 347. We also added a line 1 µM in the charts to facilitate easier comparison of compound efficacies.
(6) It would be helpful to readers to include the structures of hit compounds in the figures (perhaps as part of Figure 3).
This is a good idea and would improve the manuscript. To not overburden figure 3 we added structures to Fig S3.
(7) Page 8. "Infected monolayers were treated for three hours with a 3-fold of respective IC50 concentrations". 3-fold higher than IC50 concentrations? This isn't clear.
Thank you for noticing this: We clarified the sentence and also corrected the concentration, corresponding to five times their IC50s as stated in the methods section: “Infected monolayers were treated for three hours with compound concentrations five times their respective IC50 values or the solvent DMSO.” Line 374 - 376
(8) Page 9. "buparvaquone, which we found to be dually active against T. gondii tachyzoites and bradyzoites, targets the bc1-complex in Theileria annulata (McHardy et al. 1985) and Neospora caninum (Müller et al. 2015) and was recently found active against T. gondii tachyzoites (Hayward et al. 2023)." The latter paper showed that buparvaquone targets the bc1 complex in T. gondii tachyzoites as well.
Yes, it was found to inhibit O2 consumption rate in tachyzoites. We changed the sentence accordingly. Line 407 to 411.
(9) Page 9. "Anaplerotic substrates were also affected by all three treatments, most notably a strong accumulation of aspartic acid." It is interesting that the M+3 isotopologue of aspartate (presumably synthesised from pyruvate) is the predominant form (rather than the M+2 and M+4 isotopologues that would derive from the TCA cycle, and as the diagram in Figure 4A seems to suggest). Given that aspartate is a precursor of pyrimidine biosynthesis that is upstream of the DHODH reaction, it is conceivable that its accumulation is related to the depletion of pyrimidine biosynthesis (so would tie into the point about the accumulation of DHO and CarbAsp noted earlier in the paragraph).
Yes, we assume the same. We altered the text and summarized the changes in Asp as a result of DHOD inhibition, as we also already do in the next paragraph using 15N-glutamine labelling. Line: 416 - 418
(10) Figure 6 and Page 10. Regarding the metabolomic experiments that show increased levels of acyl-carnitines. The authors note that "Since [beta-oxidation] is thought to be absent in T. gondii, we attribute these changes to inhibition of host mitochondria". This is conceivable, although the T. gondii genome does encode homologs of the proteins necessary for beta-oxidation (e.g. see PMID 35298557). If the carnitine is coming from host mitochondria, is host contamination a concern for interpreting the metabolomic data? Or do the authors think that parasites are scavenging carnitine from host cells? It is curious that the carnitine accumulation is observed in parasites treated with buparvaquone (and MMV1028806) but not atovaquone, even though buparvaquone and atovaquone (and possibly MMV1028806) target the same enzyme. Do the authors have any thoughts on why that might be the case?
Yes, thank you for raising this point. We changed the discussion elaborating on this and included the debated presence of beta-oxidation: line 640: “We also detect elevated levels of acyl-carnitines in BPQ and MMV1028806 treated bradyzoites. These molecules act as shuttles for the mitochondrial import of fatty acids for β-oxidation. However, this pathway has not been shown to be active and is deemed absent in T. gondii (35298557, 18775675). The presence of acyl-carnitines in bradyzoites might reflect import from the host. It is conceivable that their elevation in response to buparvaquone and MMV1028806 indicates compromised functionality of the host bc1-complex and subsequently accumulating β-oxidation substrates. Indeed, BPQ has a very broad activity across Apicomplexa (Hudson et al. 1985) and kinetoplastids (Croft et al. 1992).“ Regarding the existence of beta-oxidation: some potential enzymes might be conserved, but those could in part take part in branched chain amino acid degradation pathways. On a separate note: we looked extensively on beta-oxidation using stable isotope labelling and became convinced that any activity occurred in the host cell only but not in the parasite (unpublished).
(11) Page 11. "the mitochondrial [electron] transport chain in bradyzoites".
Corrected.
(12) Figure S6B. Were these optimization experiments performed in tachyzoites or bradyzoites? If the former, and given that bradyzoites have apparently smaller amounts of ATP per parasite (Figure 7C), are these values in the linear range for 10^5 bradyzoites?
Yes, we do think that the assay remains linear for these lower concentrations. Tachyzoites give a linear response starting from 10^3 parasites per sample. In the actual experiment we used 10^5 parasites, both tachyzoites and bradyzoites. Under the tested conditions bradyzoites maintain 10% of the ATP pools of tachyzoites, which should be well within the linear range of the assay. Also in Atovaquone-treated bradyzoites ATP concentration could be lower to 10% and still remain in the linear range of the assay. For practical reasons, we simply acknowledge this limitation and consider it acceptable within the scope of this study.
Reviewer #3 (Recommendations for the authors):
Major comments
(1) The authors should provide a negative control for the experiment on Figure 5. I would suggest doing the same experiment with an inhibitor that has no effect on mitochondrial potential.
We addressed this criticism by repeating the assay on tachyzoites and additionally including inhibitors that do not have the mitochondrial electron transport chain as their primary target (Pyrimethamine, Clindamycin, 6-Diazo-5-oxo-L-norleucin). The results are summarized in the supplementary Fig S5, line 445 – 449) and show that there is no effect of these inhibitors on the mitochondrial membrane potential. This supports the specificity of the assay and suggests that MMV1028806 and BPQ indeed target a mitochondrial process in this stage. Also, in this repetition ATQ, BPQ and MMV1028806 did significantly deplete the Mitotracker signal.
(2) Figure 5 - Did the authors perform this experiment in 3 biological replicates? This requires clarification of the figure legend.
No, we did not perform the experiment in 3 biological replicates. After establishing the assay thoroughly, we performed it once on tachyzoites and bradyzoites. The sampling was done on every vacuole we encountered during microscopy going through the slide from left to right. That is the reason the sample size varies from treatment to treatment. The sample size is mentioned in the caption of figure 5. However, we repeated the experiment with additional controls (see Fig. S5), which showed that the Mitotracker signals were significantly depleted in a very similar manner in ATQ, BPQ and MMV1028806 treated parasites.
(3) The authors identify that MMV1028806 has bc1-complex as the main target. I suggest that they should perform a complex III activity assay to affirm this. Also, it would be good to test if other mETC complexes are affected by this compound to prove its specificity. There is only one paper showing complex III activity in tachyzoites (PMID:37471441) and no papers in bradyzoites. So if the authors cannot do this assay, I suggest that they should change the text indicating that bc-1 complex could be the main target of the compound but more experimental validation is needed.
We hope to have satisfied the reviewer’s request by performing an oxygen consumption assay on tachyzoites. Together with metabolic profiling and labelling data, this shows that both upstream and downstream processes are impacted by MMV1028806 and strongly suggest the bc1-complex as a target (Fig 5E).
(4) Figure S5 - Are the differences shown in the EM experiment statistically supported?
We analyzed 28 images and measured the areas in 12 to 26 images. We substituted the table of means in Fig S6B by a graph showing individual values. These areas are indeed statistically different between DMSO and ATQ / MMV treated parasites. We changed the wording in the results section accordingly “Analysis by thin section electron microscopy revealed a largely unaffected sub-mitochondrial ultrastructure but the areas of mitochondrial profiles were changed in comparison to control after exposure with ATQ and MMV1028806 but not with BPQ (Fig. S6)“. The description of Fig S6B was changed to “(B) Measured areas of mitochondrial profiles from 21, 12, 15 and 26 images showing DMSO, ATQ, BPQ and MMV1028806 treated parasites (* denotes p < 0.05 in Mann-Whitney tests)”.
Minor comments:
(1) What was the criteria to choose the example compounds in Figure 1B and 1D? The authors should clarify this in the text.
These graphs are shown for illustrative purposes and were chosen based on their display of different drug efficacies. We considered this helpful for interpreting the screening data.
(2) Figure 2G - add statistical analysis.
We added Mann-Whitney tests and updated the figure legend and results text accordingly in line 344 – 347.
(3) The authors should provide more insights in the discussion about why this new compound is the next step in drug discovery compared to atovaquone or burvaquone - for example, do you expect better availability in the brain, etc.
We used MMV1028806 and the other hits ATQ and BPQ to make the point that the bc1-complex is a good target in bradyzoites that allows curative treatment. We do not suggest that the compound itself is a good starting point. We point to other actively developed candidates such as ELQ series in the discussion, line 719.
(4) Scale bars in Figure 5 should be aligned and have equal thickness.
We re-formatted the scale bars and aligned them when not obscuring parasites.
(5) The authors should be consistent with font sizes and styles in all the figures.
We adjusted the font styles to match each other.
