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OpenSourceMycetoma / series-5-benzimidazoles

After screening the pandemic response box, two benzidazoles were able to prolong larval survival in Madurella mycetomatis infected larvae. Furthermore all three also showed some acivity against Falciformispora senegalensis, another prominent mycetoma causative agent.
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Benzoxazoles manuscript writing #5

Open MA-Jjingyi opened 2 months ago

MA-Jjingyi commented 2 months ago

Here, the database of Benzoxazoles is updated. 25082024 series5 benzoxazoles database.xlsx

@AndreaOtago, please help us do SAR analysis again in this updated database.

I am writing an manuscript for these database. and the first draft will be uploaded here next week.

MA-Jjingyi commented 2 months ago

https://github.com/OpenSourceMycetoma/series-5-benzimidazoles/issues/5#issue-2521662031 Hi @AndreaOtago, in case you didn't notice the former message, I want to give you a reminder. The SAR analysis using this updated database is needed. Please give us a hand.

AndreaOtago commented 2 months ago

Hi @MA-Jjingyi yes I can have a look at the new compound data over the next week or so. We don't need to redo the analysis but just to add in/adjust for any new trends emerging from the added data. One other thing I want to formalise - will I be an author on this paper? Slightly awkward topic to ask about but I am unsure when this stands / what is usual for the open science field. Another person you/we should loop in early on in MS draft is Charlotte from Imperial, as she/her students made a lot of the compounds, along with Otago students, incl some of the lead ones. She could be involved too as an author/not an author but would be good to have this discussion too. I will be at the meeting tonight :)

MA-Jjingyi commented 2 months ago

Hi @MA-Jjingyi yes I can have a look at the new compound data over the next week or so. We don't need to redo the analysis but just to add in/adjust for any new trends emerging from the added data. One other thing I want to formalise - will I be an author on this paper? Slightly awkward topic to ask about but I am unsure when this stands / what is usual for the open science field. Another person you/we should loop in early on in MS draft is Charlotte from Imperial, as she/her students made a lot of the compounds, along with Otago students, incl some of the lead ones. She could be involved too as an author/not an author but would be good to have this discussion too. I will be at the meeting tonight :)

Yep. we don't want to miss any co-author. thanks for letting us know. and we are welcome to add co-author name in author list. but i am not sure whether we can add the students name. maybe just note them in acknowledgement. we can discuss this in meeting, alone with Wendy. sorry that i can't attend this meeting. however, please let me know who' name I need to add.

We really need your help in writing, for example, what is the difference of benzomidazoles and benzoxazoles( for introduction); chemical synthesized (material); SAR analysis (conclusion). we will upload the first draft in which we noted several places we need help,

AndreaOtago commented 2 months ago

Great sounds good we can discuss tonight (realise you won't be there). Yes agree on students/class group in acknowledgments. Happy to write synthesis, compound characterisation, chem intro etc. Def. will need Charlotte involved as although pretty simple chemistry I think the Imperial students used different coupling conditions, and potentially synthesised materials from a few steps back, so their compounds will likely be made using different methods (although same overall end transformations).

AndreaOtago commented 2 months ago

Hi @MA-Jjingyi I have had a quick-ish look at the new IC50 data, considering the newer Otago 2024 compounds, reflection against first 2 pages/previous SAR done:

Another Q to sort soon - what journal (for chem expt data write up style, prob in SI so doesn’t matter) is this going to? Or at least what publisher?

happy to edit a MS draft.

AV_25082024.series5.benzoxazoles.database.xlsx.zip

Also here is a slightly updated excel sheet - I added structures of the 2024 compounds and I have added the DNDi code to this excel sheet and also into the online spreadsheet.

MA-Jjingyi commented 2 months ago

@AndreaOtago , thanks for your update. I am writing the draft. I hope the draft can be uploaded next week here.

by the way, @wwjvdsande we didn't discuss which journal we want to submit yet. In my experience, maybe the journal like Antimicrobial Agents and Chemotherapy or Journal of Antimicrobial Chemotherapy is our choice,

MA-Jjingyi commented 1 month ago

series 5 Bnezoxazoles screening 02102024.docx Dear Andrea, @AndreaOtago, the first draft of benzoxazoles is uploaded. please check. thanks for your attention.

AndreaOtago commented 1 month ago

Hi @MA-Jjingyi and @wwjvdsande , great thanks for sending the draft, I will work on this over the next week. I think you should email @csuth22 (I think this is her on GitHub) Charlotte at Imperial (https://profiles.imperial.ac.uk/c.sutherell). I am not sure how active she is on this platform. I am happy to help write the text about benzoxazole compound descriptions and SAR but a large number of the compounds in your paper were made by Imperial students and Charlotte, so they need to be looped in, may want to help write as well, and you will need to ask them for the experimental data for those compounds. I can only provide the Otago-made compound analytical data.

csuth22 commented 1 month ago

Hi @MA-Jjingyi, @wwjvdsande and @AndreaOtago

Apologies I've been very out in the loop on this and seem to keep missing notifications about when meetings are happening. Definitely don't understand GitHub as I should! Thanks @AndreaOtago for flagging this to me.

I can look at the draft but not until after 11th October as I am heavily committed because of start of the academic term.

i'm not familiar with the suggested journals regarding their expectations on chemical SI data but will take a look. As for these student labs they aren't given full access to all analytical facilities I'd want to ensure we have everything that is required

Charlotte

AndreaOtago commented 1 month ago

Hi @csuth22 sounds good, we can chat details about chemical compound data in the next month. FYI at Otago we don't have 13C NMR spectra for any of the compounds, 1H NMR, HRMS and analytical HPLC were run by the students are part of their lab. I'm not sure if the journal has been decided - @MA-Jjingyi ?

MA-Jjingyi commented 1 month ago

@csuth22 @AndreaOtago the journal is not selected because Wendy is not available to discuss this topic. I will let you know the journal as soon as possible we have decision. @wwjvdsande

We really need your help in writing, for example, what is the difference of benzomidazoles and benzoxazoles( for introduction); chemical synthesized (material); SAR analysis (conclusion). I leave several notes where we need help. please check. Furthermore, please has no any hesitation to add or modify text, we really need more comments to make this draft more logical.

@AndreaOtago @csuth22 a little notification that please add your information in author list (university, department, city and country).

AndreaOtago commented 1 month ago

@MA-Jjingyi @wwjvdsande @csuth22 , I have uploaded a revised manuscript. I started writing the SAR section in the 'Results' section but then stopped as in the draft there is no SI figure of all compound data. Will this be published in the SI? It doesn't make sense to talk about SAR in the paper if only the 4 lead compound data is published, all compound data (even if in SI) if needed to conclude/report on SAR (including inactive compounds). So once you advise this I can finish writing the SAR section in the results. Also regarding the chemistry in the SI - I am working on writing this up, and will keep doing so in the background to the MS document drafting.

AndreaOtago commented 1 month ago

here is the MS series.5.Bnezoxazoles.screening.02102024_AV2110.docx

MA-Jjingyi commented 1 month ago

here is the MS series.5.Bnezoxazoles.screening.02102024_AV2110.docx

Hi, @AndreaOtago . thanks for your update.

Actually, we don't know how to choose compounds or make a SI figure to explain/discuss the SAR even though we worked together on benzoxazoles data base which maybe include all data this paper needs.

AV_25082024.series5.benzoxazoles.database.xlsx (1).zip

So that, please help us select compounds and make a figure. or the data base can not be used to make a SI figure? then, what we can do for SI figure? sorry, I hope I understand what your mean.

thanks for your nice comments, you know we really need your help in chemists. If you need further talk, please let me know.

AndreaOtago commented 1 month ago

@MA-Jjingyi yes having that excel sheet tidied up/as a PDF/maybe landscape across a few pages would be perfect. Prob OK to discuss SAR in the main paper and refer the reader to comprehensive data in the SI. Depending on the reviewer/journal some do not like that approach but I think we try this on the first submission.

MA-Jjingyi commented 1 month ago

@AndreaOtago That's great! Then, please continue to help writing this draft first. When @wwjvdsande Wendy is available, we can discuss which journal is our choice. @csuth22 Hi, Charlotte. Please don't forget to check this draft after your teaching. Thanks for your attention.

If anyone has any confusion, please leave message here. Nice to work with you all.

AndreaOtago commented 1 month ago

@MA-Jjingyi here is an updated MS with the SAR written. IMPORTANT - FIGURE 2 HAS A COMPOUND ERROR. I believe you have put two of the structures above the wrong compound codes, please see comment boxes in the MS. I can't change this as I do not have the figure/image file.

AndreaOtago commented 1 month ago

MS here series.5.Bnezoxazoles.screening.02102024_AV2310.docx

MA-Jjingyi commented 1 month ago

Hi, @AndreaOtago , thanks for your comments. we really didn't realize the wrong structure linking to wrong compounds code in Figure 2. I will work on them and update this draft as soon as possible.

MA-Jjingyi commented 1 week ago

series.5.Bnezoxazoles.screening 17112024 second draft.docx Dear @AndreaOtago , this is the update draft. thanks for your writing and comments. and if you are available, please help us to finalize this draft. Next, i will send this manuscript to my supervisor to ask for more comments.

@csuth22 Hi Charlotte. Please don't forget to check this draft when you are free. and please write the author information in the beginning.

AndreaOtago commented 1 week ago

Hi @MA-Jjingyi , I have had a quick look and relatively minor comments so it is best I read again properly after it has gone to Wendy and other authors, so I won't make any changes on this version, please proceed. I will have a sentence to add in for the 'funding' but can do that in the later draft too. In the meantime I am chipping away at writing the chemistry experimental for the SI. I won't be able to make the meeting next Tuesday as I have a conference next week.