Monthly MycetOS meeting - 28 May 2024

wwjvdsande commented 5 months ago

Time: May 23 (8 morning UK) (Timezones)

The Outlook invite can be found https://github.com/OpenSourceMycetoma/Monthly-zoom-meetings/issues/2#issuecomment-1905476888

Location: https://uni-sydney.zoom.us/j/99281549497. In case of failure, use https://ucl.zoom.us/j/99789829423 and in case of double failure use MycetOS meeting teams link

Chair: USyd Minute taker: UCL Previous meeting: here Recording of this meeting: Present: Apologies:

AGENDA

Screening updates

@MA-Jjingyi and/or @marijschippers to report on any new data
@AndreaOtago had a chance to look at the SAR data for Series 5?

Series 1 - Fenarimols

@KlementineJBS has added some compounds to a "Desired compounds" page here. Where can the structures be found?
https://github.com/OpenSourceMycetoma/Series-1-Fenarimols/wiki/Desirable-Compounds-Not-Yet-Synthesised seems to be out of date, can anyone advise if this can be deleted or updated?

Paper update

Mat to report: has paper been circulated to coauthors? has a journal been chosen?

Modelling update

@meh-cyprian to proceed to try to model fenarimol compounds in potential protein target (described https://github.com/OpenSourceMycetoma/Series-1-Fenarimols/issues/68#issuecomment-1546869698 or to clarify what more data are needed. Aim is to better understand the SAR via docking vs homology model of protein. @osmanwa also interested in this area, has been in touch with @wwjvdsande and @mattodd by email, and can report back.

Series 2 - Aminothiazoles

@P-Rayner to report on any aminothiazoles his uni has made
updates from USyd - will likely have new compounds described here and here by next meeting (end of June). Focus is on the thiazole end of the molecule, trying out some dichloro combinations and fused rings. @KlementineJBS will be away from July so probably no compounds after that.
Is Wendy's new PhD student willing to do a sweep of the literature on mechanism of action, with support from chemists? can anyone else volunteer?
@wwjvdsande has created a page to communicate about this more clearly (see here)

Not addressed directly

[ ] All compounds have been evaluated, including from @eloizidou and @Whitgift? Any updates to the current SAR page?
[ ] @eloizidou to complete latest LCMS/NMR characterisation of Whitgift samples. Has one sample been evaluated in vitro?
[ ] Mechanism of Action. Any clues from literature? Volunteers for student project? Should we measure for synergism with itraconazole (which hits Cyp51).
[ ] @dosreic to try to secure samples related to this paper https://github.com/OpenSourceMycetoma/Series-2-Aminothiazoles/issues/11 ?

Series 3: Tricyclics/Phenothiazines

@P-Rayner to update on any phenothiazines sent through, state of student notebooks
Have any more phenothiazines been tested at higher concentrations? @MA-Jjingyi @wwjvdsande
@marijschippers or others to report on repeat toxicity tests and efficacy tests for NEU/Curaxin compounds that had promising early results (MYOS626, 627, 628, 631, 632), see here
4 of these NEU/Curaxin compounds screened for toxicity in vivo by @marijschippers were excellently nontoxic (which myos codes?), with minimal larvae death, while one compound showed some toxicity (which myos code?)

Series 5 - Benzimidazoles

@MA-Jjingyi is drafting results into a paper
Andrea is doing some SAR assessments on the benzoxazoles
One compound was very promising in vitro and will move into toxicity screens soon, two have prolonged larval survival
Question of renaming benzimidazoles series 5a and the benzoxazoles series 5b apparently not yet decided - will need volunteers to edit masterlist
@AndreaOtago to update on new benzoxazoles likely to be incoming.
Are there any other labs with related compounds we should contact?

Series 6: ketoximes

@dmitrij176 was putting together a priority list of what would be most useful to test if possible as he would like a few of the earlier compounds to be tested in vivo as single isomers if there is any space in the schedule
Dmitrij is still working on SAR scheme and will share it later

Other

Global Health Priority Box

any updates on paper?
any updates on analogues from GSK?
data. MMV1804559 both prolonged larval survival and induced morphological changes in the grains (decreasing their size), however at higher concentrations it was toxic too. Tentatively DYRK1 could be the (novel) target, potentially woronin body? Some preliminary discussion https://github.com/OpenSourceMycetoma/Monthly-zoom-meetings/issues/15#issuecomment-1943554945.

Kinase Inhibitor Library

Mickey can update on this being written into a paper/share any new results. in vivo testing has been difficult as many compounds in this library are too toxic, will have to try lower concentrations
KCGS library was screened along with compounds of similar classes that were sent by @bebi78, with 6 hits in total
[ ] ACTION link to data / add to masterlist
[x] ACTION @MA-Jjingyi to update spreadsheet with larval toxicity studies if not already done

Plant Extracts from Nigeria

has @bebi78 succeeded in contacting the relevant people again?

Dundee DMPK Measurements

Mat has shared some results here but not all compounds were tested
[ ] ACTION @dmitrij176 will put together a diagram of results

AOB

Sporotrichosis

@wwjvdsande is collaborating with Melissa Xavier from Brazil and will be sharing some samples

Toxicity column

new column in masterlist gives details on toxicity
[ ] ACTION @wwjvdsande will create a page on the Wiki that describes the methods for determining toxicity
current method is basically to inject larvae and compare death rates to injections with water or PBS

Other

@bebi78 writing up info about niclosamide
CUREID is collecting info about off label drug use
still need a pharmaceutical contact, maybe through the DNDi?

Next meeting

25 June 2024: chair: UCL, minute taker: ErasmusMC Will be 12 PM UK/9 PM Sydney - timezones

wwjvdsande commented 5 months ago

@OpenSourceMycetoma/corecontrib tomorrow we will have a new MycetOS meeting. Remember it is an odd month so the early time! I opened the item. According to the agenda USyd is chair and UCL is taking minutes. Could you fill in the agenda for tomorrow?

dmitrij176 commented 5 months ago

Apologies, but I wont be able to join the meeting tomorrow.

wwjvdsande commented 5 months ago

@OpenSourceMycetoma/corecontrib at ErasmusMC we have two open vacancies linked to the MycetOS project, one for a postdoc (https://www.werkenbijerasmusmc.nl/vacature/98921/post-doc-transcriptomics-and-genetically-manipulating-madurella-mycetomatis-find) and one for a PhD student (https://www.werkenbijerasmusmc.nl/vacature/98922/phd-candidate-using-open-science-build-novel-vitro-models-identify-drugs-which-can). If you know biologists which might be interested please forward these vacancies!

MFernflower commented 5 months ago

@wwjvdsande I do not see any data entered for potency for any of the series 3 batches made at York in the mastersheet?!

@P-Rayner

mattodd commented 5 months ago

Fenarimol Paper Update. I took a final read of the manuscript (Fenarimol Paper March 26 V2.4) Little things remaining: LogD, flexibility and rotational bonds was calculated by @bendndi using which software? This needs to be added to materials/methods. Figure 1 - X-axis legends need changing for A, C and D. Figure 5 - Compound codes need changing to the simplified versions (8, 3, 1 etc). The potency spreadsheet (Supplementary File S1) is ready? Figure 11 - it would be nice to have the tert-butyl group drawn properly in 520. Figure 12 - compound numbers in bold. Would be nice to have this figure in colour. Figure 13 - were 4, 10, 310 known already, or found as part of this campaign? Figure 14 - pozaconazole typo. Acknowledgements section - people need to add people and funders etc. Biblio - who assembles this? Notice that there are some legacy reference numbers, and that Wendy said "Everywhere where there is a PMID and a normal number between brackets. The PMID is the one you should use." Authorship/acknowledgements: "Six compounds were synthesised by students from the Illinois Mathematics and Science Academy (IMSA)" are these people suitably acknowledged? (details of the contributions are apparently available in the Appendix?)

P-Rayner commented 5 months ago

I am on holiday at the moment but will provide an update ASAP. On 27 May 2024, at 09:39, Wendy van de Sande @.***> wrote: Time: May 23 (8 morning UK) (Timezones) The Outlook invite can be found #2 (comment) Location: https://uni-sydney.zoom.us/j/99281549497. In case of failure, use https://ucl.zoom.us/j/99789829423 and in case of double failure use MycetOS meeting teams link Chair: USyd Minute taker: UCL Previous meeting: here Recording of this meeting: Present: Apologies: AGENDA Screening updates

@MA-Jjingyi and/or @marijschippers to report on any new data @AndreaOtago had a chance to look at the SAR data for Series 5?

Series 1 - Fenarimols

@KlementineJBS has added some compounds to a "Desired compounds" page here. Where can the structures be found? https://github.com/OpenSourceMycetoma/Series-1-Fenarimols/wiki/Desirable-Compounds-Not-Yet-Synthesised seems to be out of date, can anyone advise if this can be deleted or updated?

Paper update

Mat to report: has paper been circulated to coauthors? has a journal been chosen?

Modelling update @meh-cyprian to proceed to try to model fenarimol compounds in potential protein target (described OpenSourceMycetoma/Series-1-Fenarimols#68 (comment) or to clarify what more data are needed. Aim is to better understand the SAR via docking vs homology model of protein. @osmanwa also interested in this area, has been in touch with @wwjvdsande and @mattodd by email, and can report back. Series 2 - Aminothiazoles

@P-Rayner to report on any aminothiazoles his uni has made updates from USyd - will likely have new compounds described here and here by next meeting (end of June). Focus is on the thiazole end of the molecule, trying out some dichloro combinations and fused rings. @KlementineJBS will be away from July so probably no compounds after that. Is Wendy's new PhD student willing to do a sweep of the literature on mechanism of action, with support from chemists? can anyone else volunteer? @wwjvdsande has created a page to communicate about this more clearly (see here)

Not addressed directly

All compounds have been evaluated, including from @eloizidou and @Whitgift? Any updates to the current SAR page? Some ideas for compounds to be made next are OpenSourceMycetoma/Series-2-Aminothiazoles#19. @eloizidou to complete latest LCMS/NMR characterisation of Whitgift samples. Has one sample been evaluated in vitro? Mechanism of Action. Any clues from literature? Volunteers for student project? Should we measure for synergism with itraconazole (which hits Cyp51). @dosreic to try to secure samples related to this paper OpenSourceMycetoma/Series-2-Aminothiazoles#11 ?

Series 3: Tricyclics/Phenothiazines

@P-Rayner to update on any phenothiazines sent through, state of student notebooks Have any more phenothiazines been tested at higher concentrations? @MA-Jjingyi @wwjvdsande @marijschippers or others to report on repeat toxicity tests and efficacy tests for NEU/Curaxin compounds that had promising early results (MYOS626, 627, 628, 631, 632), see here 4 of these NEU/Curaxin compounds screened for toxicity in vivo by @marijschippers were excellently nontoxic (which myos codes?), with minimal larvae death, while one compound showed some toxicity (which myos code?)

Series 5 - Benzimidazoles

@MA-Jjingyi is drafting results into a paper Andrea is doing some SAR assessments on the benzoxazoles One compound was very promising in vitro and will move into toxicity screens soon, two have prolonged larval survival Question of renaming benzimidazoles series 5a and the benzoxazoles series 5b apparently not yet decided - will need volunteers to edit masterlist @AndreaOtago to update on new benzoxazoles likely to be incoming. Are there any other labs with related compounds we should contact?

Series 6: ketoximes

@dmitrij176 was putting together a priority list of what would be most useful to test if possible as he would like a few of the earlier compounds to be tested in vivo as single isomers if there is any space in the schedule Dmitrij is still working on SAR scheme and will share it later

Other Global Health Priority Box

any updates on paper? any updates on analogues from GSK? data. MMV1804559 both prolonged larval survival and induced morphological changes in the grains (decreasing their size), however at higher concentrations it was toxic too. Tentatively DYRK1 could be the (novel) target, potentially woronin body? Some preliminary discussion #15 (comment).

Kinase Inhibitor Library

Mickey can update on this being written into a paper/share any new results. in vivo testing has been difficult as many compounds in this library are too toxic, will have to try lower concentrations KCGS library was screened along with compounds of similar classes that were sent by @bebi78, with 6 hits in total ACTION link to data / add to masterlist ACTION @MA-Jjingyi to update spreadsheet with larval toxicity studies if not already done

Plant Extracts from Nigeria

has @bebi78 succeeded in contacting the relevant people again?

Dundee DMPK Measurements

Mat has shared some results here but not all compounds were tested ACTION @dmitrij176 will put together a diagram of results

AOB Sporotrichosis

@wwjvdsande is collaborating with Melissa Xavier from Brazil and will be sharing some samples

Toxicity column

new column in masterlist gives details on toxicity ACTION @wwjvdsande will create a page on the Wiki that describes the methods for determining toxicity current method is basically to inject larvae and compare death rates to injections with water or PBS

Other

@bebi78 writing up info about niclosamide CUREID is collecting info about off label drug use still need a pharmaceutical contact, maybe through the DNDi?

Next meeting Will be 7am for Europe/7 pm for Australia.

—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you were mentioned.Message ID: @.***>

wwjvdsande commented 5 months ago

@wwjvdsande I do not see any data entered for potency for any of the series 3 batches made at York in the mastersheet?!

@P-Rayner

@MFernflower could you specify which compounds (MYOS number) that is easier to find. We tested all compounds in vitro which arrived except the ones from @AndreaOtago which arrived last week. I just updated the last data in the mastersheet. @OpenSourceMycetoma/corecontrib may be also a good idea to add two extra column to the mastersheet with the shipping date and an arrival date so that everyone can see when things are shipped and arrive.

wwjvdsande commented 5 months ago

@OpenSourceMycetoma/corecontrib I can't get in zoom. Did something change? I now entered the UCL zoom meeting link. This one I can enter

mattodd commented 5 months ago

No, it's fine. We're in at https://uni-sydney.zoom.us/j/99281549497

wwjvdsande commented 5 months ago

I can't get in it keeps saying you need a commercial zoom account which we don't have. For some reason I can get in the one from UCL

fantasy121 commented 5 months ago

Acknowledgement needed for IMSA contribution. MYOS_00024 | P4_C_001 | IMSA MYOS_00025 | P4_B_013 | IMSA MYOS_00026 | P4_C_009 | IMSA MYOS_00312 | P4_A_001 | IMSA MYOS_00313 | P4_B_004 | IMSA MYOS_00314 | P4_B_005 | IMSA

MFernflower commented 5 months ago

@p-rayner we got some data back from the first box you gave to Wendy and it likely confirms the suspicion that curaxin 137 basically has the most optimal "tail" section so efforts should now shift to finding a better tricyclic core to replace the diacetylcarbazole head of curaxins

On Mon, May 27, 2024, 4:52 PM P-Rayner @.***> wrote:

I am on holiday at the moment but will provide an update ASAP. On 27 May 2024, at 09:39, Wendy van de Sande @.***> wrote: Time: May 23 (8 morning UK) (Timezones) The Outlook invite can be found #2 (comment) Location: https://uni-sydney.zoom.us/j/99281549497. In case of failure, use https://ucl.zoom.us/j/99789829423 and in case of double failure use MycetOS meeting teams link Chair: USyd Minute taker: UCL Previous meeting: here Recording of this meeting: Present: Apologies: AGENDA Screening updates

@MA-Jjingyi and/or @marijschippers to report on any new data @AndreaOtago had a chance to look at the SAR data for Series 5?

Series 1 - Fenarimols

@KlementineJBS has added some compounds to a "Desired compounds" page here. Where can the structures be found?

https://github.com/OpenSourceMycetoma/Series-1-Fenarimols/wiki/Desirable-Compounds-Not-Yet-Synthesised seems to be out of date, can anyone advise if this can be deleted or updated?

Paper update

Mat to report: has paper been circulated to coauthors? has a journal been chosen?

Modelling update @meh-cyprian to proceed to try to model fenarimol compounds in potential protein target (described OpenSourceMycetoma/Series-1-Fenarimols#68 (comment) or to clarify what more data are needed. Aim is to better understand the SAR via docking vs homology model of protein. @osmanwa also interested in this area, has been in touch with @wwjvdsande and @mattodd by email, and can report back. Series 2 - Aminothiazoles

@P-Rayner to report on any aminothiazoles his uni has made updates from USyd - will likely have new compounds described here and here by next meeting (end of June). Focus is on the thiazole end of the molecule, trying out some dichloro combinations and fused rings. @KlementineJBS will be away from July so probably no compounds after that. Is Wendy's new PhD student willing to do a sweep of the literature on mechanism of action, with support from chemists? can anyone else volunteer? @wwjvdsande has created a page to communicate about this more clearly (see here)

Not addressed directly

All compounds have been evaluated, including from @eloizidou and @Whitgift? Any updates to the current SAR page? Some ideas for compounds to be made next are OpenSourceMycetoma/Series-2-Aminothiazoles#19. @eloizidou to complete latest LCMS/NMR characterisation of Whitgift samples. Has one sample been evaluated in vitro? Mechanism of Action. Any clues from literature? Volunteers for student project? Should we measure for synergism with itraconazole (which hits Cyp51). @dosreic to try to secure samples related to this paper OpenSourceMycetoma/Series-2-Aminothiazoles#11 ?

Series 3: Tricyclics/Phenothiazines

@P-Rayner to update on any phenothiazines sent through, state of student notebooks Have any more phenothiazines been tested at higher concentrations? @MA-Jjingyi @wwjvdsande @marijschippers or others to report on repeat toxicity tests and efficacy tests for NEU/Curaxin compounds that had promising early results (MYOS626, 627, 628, 631, 632), see here 4 of these NEU/Curaxin compounds screened for toxicity in vivo by @marijschippers were excellently nontoxic (which myos codes?), with minimal larvae death, while one compound showed some toxicity (which myos code?)

Series 5 - Benzimidazoles

@MA-Jjingyi is drafting results into a paper Andrea is doing some SAR assessments on the benzoxazoles One compound was very promising in vitro and will move into toxicity screens soon, two have prolonged larval survival Question of renaming benzimidazoles series 5a and the benzoxazoles series 5b apparently not yet decided - will need volunteers to edit masterlist @AndreaOtago to update on new benzoxazoles likely to be incoming. Are there any other labs with related compounds we should contact?

Series 6: ketoximes

@dmitrij176 was putting together a priority list of what would be most useful to test if possible as he would like a few of the earlier compounds to be tested in vivo as single isomers if there is any space in the schedule Dmitrij is still working on SAR scheme and will share it later

Other Global Health Priority Box

any updates on paper? any updates on analogues from GSK? data. MMV1804559 both prolonged larval survival and induced morphological changes in the grains (decreasing their size), however at higher concentrations it was toxic too. Tentatively DYRK1 could be the (novel) target, potentially woronin body? Some preliminary discussion #15 (comment).

Kinase Inhibitor Library

Mickey can update on this being written into a paper/share any new results. in vivo testing has been difficult as many compounds in this library are too toxic, will have to try lower concentrations KCGS library was screened along with compounds of similar classes that were sent by @bebi78, with 6 hits in total ACTION link to data / add to masterlist ACTION @MA-Jjingyi to update spreadsheet with larval toxicity studies if not already done

Plant Extracts from Nigeria

has @bebi78 succeeded in contacting the relevant people again?

Dundee DMPK Measurements

Mat has shared some results here but not all compounds were tested ACTION @dmitrij176 will put together a diagram of results

AOB Sporotrichosis

@wwjvdsande is collaborating with Melissa Xavier from Brazil and will be sharing some samples

Toxicity column

new column in masterlist gives details on toxicity ACTION @wwjvdsande will create a page on the Wiki that describes the methods for determining toxicity current method is basically to inject larvae and compare death rates to injections with water or PBS

Other

@bebi78 writing up info about niclosamide CUREID is collecting info about off label drug use still need a pharmaceutical contact, maybe through the DNDi?

Next meeting Will be 7am for Europe/7 pm for Australia.

—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you were mentioned.Message ID: @.***>

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wwjvdsande commented 5 months ago

@mattodd what is the latest version of the fenarimol paper? The one from 26 march and opened last on 27 may I assume? @OpenSourceMycetoma/corecontrib can I take it of to correct the references?

mattodd commented 5 months ago

@OpenSourceMycetoma/corecontrib - @wwjvdsande has kindly entered the references in the Fenarimol paper. It is on Dropbox and it's on me to tweak to the point we can submit. I will be asking things from people, but please do not edit the paper any further.

wwjvdsande commented 5 months ago

@OpenSourceMycetoma/corecontrib - @wwjvdsande has kindly entered the references in the Fenarimol paper. It is on Dropbox and it's on me to tweak to the point we can submit. I will be asking things from people, but please do not edit the paper any further.

@mattodd any updates on the paper? Is something more required?

wwjvdsande commented 5 months ago

@OpenSourceMycetoma/corecontrib the paper which was written by Ma on the screening of the MMV boxes was just published Ma-2024-IJMS25-6227.pdf

mattodd commented 5 months ago

Paper update.

OK, @wwjvdsande has fixed up the references in the offline copy. Thank you Wendy! There are some things like

"061562898 [pii] 5628 [pii] PONE-D-11-14320 [pii]."

but I'm assuming these are just software artefacts and I can delete.

Things remaining:

[ ] @bendndi to advise which software was used to caldulate LogD, flexibility and rotational bonds. Assuming Stardrop? @mattodd will add this to materials/methods.
[ ] @wwjvdsande @fantasy121 @dmitrij176 forward all original figure files to @mattodd. There are a number of minor changes needed that @mattodd will take care of, including

Figure 5 - Compound codes need changing to the simplified versions (8, 3, 1 etc). Figure 11 - Draw tert-butyl group drawn properly in 520. Figure 12 - compound numbers need to be in bold. Would be nice to have this figure in colour. Figure 14 - pozaconazole typo.

But it will be helpful to have the final list of figure files in one place in any case.

[ ] @mattodd to check that the potency spreadsheet (which will be Supplementary File S1) is ready and includes all relevant compounds in the paper.
[ ] @fantasy121 @dmitrij176 - Figure 13: were 4, 10, 310 known already, or found as part of this campaign?
[ ] Acknowledgements section - LAST CHANCE to add people and funders etc. @fantasy121 can you please ensure that the Sydney team are alerted to the need to finalise this section now?
[ ] @mattodd to deal with the important IMSA authorship/acknowledgements issue, including running this past John Thurmond there: "Six compounds were synthesised by students from the Illinois Mathematics and Science Academy (IMSA)" are these people suitably acknowledged? (details of the contributions are apparently available in the Appendix?). Thanks @fantasy121 for clarifying which compounds, above. Compounds were sent to us in 2021 @dmitrij176 and we carried out LCMS, which I will add to the SI.
[ ] @fantasy121 - on Dropbox Is the file "SAR Supp Info" needed?
[ ] @fantasy121 is the file "Fenarimol writing (SAR citation)" needed in the SI, or was this just something internal and can be archived?
[ ] @fantasy121 @dmitrij176 we need an SI file for the NMR spectra for novel compounds in the paper. At the moment we have two separate files of spectra that are not in the right format for submission. You will both need to get these files ready for submission in a format that looks like the NMR spectra here.
[ ] @mattodd will compose the cover letter.
[ ] If anyone has suggestions for referees, please email @mattodd

dosreic commented 5 months ago

Hi Mat, can you please send me a draft or link to Dropbox/Drive so I can access the manuscript and get that software info? Thanks! Luiza

Luiza Cruz, PhD I Drug Discovery Coordinator Drugs for Neglected Diseases initiative (DNDi) Rua São José 70 – Sala 601 - Centro | ZIP 20010020 Rio de Janeiro | Brazil M: +55 21 96672 9043 | @.**@.> dndi.org

[A close up of orange letters Description automatically generated]

De: Mat Todd @.> Enviada em: terça-feira, 18 de junho de 2024 13:54 Para: OpenSourceMycetoma/Monthly-zoom-meetings @.> Cc: Luiza Cruz @.>; Mention @.> Assunto: Re: [OpenSourceMycetoma/Monthly-zoom-meetings] Monthly MycetOS meeting - 28 May 2024 (Issue #22)

Paper update.

OK, @wwjvdsandehttps://github.com/wwjvdsande has fixed up the references in the offline copy. Thank you Wendy! There are some things like

"061562898 [pii] 5628 [pii] PONE-D-11-14320 [pii]."

but I'm assuming these are just software artefacts and I can delete.

Things remaining:

[ ] @bendndihttps://github.com/bendndi to advise which software was used to caldulate LogD, flexibility and rotational bonds. Assuming Stardrop? @mattoddhttps://github.com/mattodd will add this to materials/methods.
[ ] @wwjvdsandehttps://github.com/wwjvdsande @fantasy121https://github.com/fantasy121 @dmitrij176https://github.com/dmitrij176 forward all original figure files to @mattoddhttps://github.com/mattodd. There are a number of minor changes needed that @mattoddhttps://github.com/mattodd will take care of, including

Figure 5 - Compound codes need changing to the simplified versions (8, 3, 1 etc). Figure 11 - Draw tert-butyl group drawn properly in 520. Figure 12 - compound numbers need to be in bold. Would be nice to have this figure in colour. Figure 14 - pozaconazole typo.

But it will be helpful to have the final list of figure files in one place in any case.

[ ] @mattoddhttps://github.com/mattodd to check that the potency spreadsheet (which will be Supplementary File S1) is ready and includes all relevant compounds in the paper.
[ ] @fantasy121https://github.com/fantasy121 @dmitrij176https://github.com/dmitrij176 - Figure 13: were 4, 10, 310 known already, or found as part of this campaign?
[ ] Acknowledgements section - LAST CHANCE to add people and funders etc. @fantasy121https://github.com/fantasy121 can you please ensure that the Sydney team are alerted to the need to finalise this section now?
[ ] @mattoddhttps://github.com/mattodd to deal with the important IMSA authorship/acknowledgements issue, including running this past John Thurmond there: "Six compounds were synthesised by students from the Illinois Mathematics and Science Academy (IMSA)" are these people suitably acknowledged? (details of the contributions are apparently available in the Appendix?). Thanks @fantasy121https://github.com/fantasy121 for clarifying which compounds, above. Compounds were sent to us in 2021 @dmitrij176https://github.com/dmitrij176 and we carried out LCMS, which I will add to the SI.
[ ] @fantasy121https://github.com/fantasy121 - on Dropbox Is the file "SAR Supp Info" needed?
[ ] @fantasy121https://github.com/fantasy121 is the file "Fenarimol writing (SAR citation)" needed in the SI, or was this just something internal and can be archived?
[ ] @fantasy121https://github.com/fantasy121 @dmitrij176https://github.com/dmitrij176 we need an SI file for the NMR spectra for novel compounds in the paper. At the moment we have two separate files of spectra that are not in the right format for submission. You will both need to get these files ready for submission in a format that looks like the NMR spectra herehttps://pubs.acs.org/doi/suppl/10.1021/acs.jmedchem.1c00313/suppl_file/jm1c00313_si_001.pdf.
[ ] @mattoddhttps://github.com/mattodd will compose the cover letter.
[ ] If anyone has suggestions for referees, please email @mattoddhttps://github.com/mattodd

— Reply to this email directly, view it on GitHubhttps://github.com/OpenSourceMycetoma/Monthly-zoom-meetings/issues/22#issuecomment-2176558905, or unsubscribehttps://github.com/notifications/unsubscribe-auth/A4KDXHRLFTA4XFBZUYJEG53ZIBQ3LAVCNFSM6AAAAABIKWAC6OVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNZWGU2TQOJQGU. You are receiving this because you were mentioned.Message ID: @.***>

wwjvdsande commented 5 months ago

@mattodd the references is a thing from the software I guess, You could delete it. I sent you our original figure files.

eloizidou commented 5 months ago

Action reminder for UCL School of Pharmacy to send MYOS432 (Whitgift compound) for analysis. The other compound made by Whitgift MYOS605 has already been tested in vivo.

fantasy121 commented 4 months ago

[ ] RE: wwjvdsande @fantasy121 dmitrij176 forward all original figure files to @mattodd. There are a number of minor changes needed that @mattodd will take care of, including

Figure 5 - Compound codes need changing to the simplified versions (8, 3, 1 etc). Figure 11 - Draw tert-butyl group drawn properly in 520. Figure 12 - compound numbers need to be in bold. Would be nice to have this figure in colour. Figure 14 - pozaconazole typo.

I have updated these four mentioned figures for you @mattodd. Manuscript figures 5, 7–14 were updated, refer to file version "July 29th MHT HPD" (link). I have also provided original chemdraw files in the Submission Pictures > Draft (link) and the Tiff files in Submission Picture (link). Figures I have provided were Figures 5 and 7–14 (Figure 6 was not created by me).

Re: Colouring Figure 12. I have not coloured in vivo figures (Figures 12 and 13) because we haven't agreed on a colour convention for these data like we did for in vitro data with the traffic light system. If we want to add this in, perhaps we could consult with @wwjvdsande team to see what's the threshold could/should be for "green", "amber" and "red" potencies.

[ ] Re: Figure 13: were 4, 10, 310 known already, or found as part of this campaign? 4 and 10 were from Mycetoma Paper 1; 310 were found as part of this campaign for Mycetoma paper 2
[ ] Re: @mattodd to deal with the important IMSA authorship/acknowledgements issue, including running this past John Thurmond there: "Six compounds were synthesised by students from the Illinois Mathematics and Science Academy (IMSA)" are these people suitably acknowledged? (details of the contributions are apparently available in the Appendix?). Does the "Supplementary File S1" (referenced in manuscript) currently have this information on contribution/donation? If not, I have two appendix tables which I compiled for my thesis and include raw in vitro and in vivo data with details of contributions. I used the Master List to create these tables. Potentially these tables can be used to provide compound contribution details for manuscript.
[ ] Re: on Dropbox Are the files "SAR Supp Info" and Fenarimol writing (SAR citation)" needed? These files are no longer needed. I have now archived them in "Superseded" folder.

fantasy121 commented 4 months ago

[ ] Re: Acknowledgements section - LAST CHANCE to add people and funders etc. @fantasy121 can you please ensure that the Sydney team are alerted to the need to finalise this section now? I have notified Peter and Alice to double check on these. Will also have a catch up with them next Monday 29th Jul. I will update on this matter following this meeting.

fantasy121 commented 4 months ago

[ ] Re: @fantasy121 dmitrij176 we need an SI file for the NMR spectra for novel compounds in the paper. At the moment we have two separate files of spectra that are not in the right format for submission. You will both need to get these files ready for submission in a format that looks like the NMR spectra here. Currently working on this item. I will update once finished.

fantasy121 commented 3 months ago

@mattodd @dmitrij176 I've updated the manuscript to version "July 29th MHT HPD" Link I've updated the SI File NMR spectra to version "July 25th MHT HPD" Link

I will be unavailable for manuscript editing between Wed 31st July to Sun 18th August inclusive, but will be checking updates (Github/email) periodically to respond to any quick questions/clarifications if needed, in order to progress this manuscript.

dmitrij176 commented 3 months ago

I have forwarded the finalised NMR SI version to @mattodd on the 22 of July

OpenSourceMycetoma / Monthly-zoom-meetings