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OpenSourceMycetoma / Series-1-Fenarimols

Open Source Mycetoma's First Series of Molecules
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paper writing #55

Open wwjvdsande opened 3 years ago

wwjvdsande commented 3 years ago

@mattodd @dmitrij176 @fantasy121 @Wilson-Lm To keep track of the writing, wilson had prepared a google docs for the paper. We added the last analysis in but the chemistry is lacking. I know we did not finish all experiments yet but it might be handy to put everything we have already in the manuscript file. The file can be found here: https://docs.google.com/document/d/13iRAEGrZfuupZUADGE5y_iJuicfP5jI0eFRFbVPGOLc/edit?usp=sharing

mattodd commented 3 years ago

As @wwjvdsande mentioned in the June meeting #58 it'd be very useful to start the process of making sure that the paper contains adequate descriptions of the synthetic chemistry. We can reference procedures that are already published, but we need to add in characterisation data, particularly regarding the purity of novel compounds that were biologically evaluated. I guess most of the heavy lifting here will fall on @fantasy121 and @dmitrij176.

fantasy121 commented 3 years ago

@mattodd @dmitrij176. Here's the link to the SAR dropbox. The main file is the word document and the excel spreadsheet. All raw data are available in the other folders as well. Please have a look and let me know if you have any suggestion/thought/idea. I'm keen to have another catchup on Zoom with you guys to talk more about this too.

https://www.dropbox.com/sh/ppueyu7sen8wy8r/AAAwBulBTKjdbD4VTPnzMZQ0a?dl=0

Re: Structural consistency when presenting these compounds for the manuscript, I think the most time-efficient way to do this is for us to decide, in our final draft of the content, which compounds will be included in the manuscript and then I will work on making sure those are consistently presented. It will take too much time otherwise to work on all of them as there are many in the master list.

fantasy121 commented 3 years ago

Follow-up from previous comment here, @mattodd @dmitrij176 I want to meet with you to discuss the SAR result and and find a direction to make the SAR concise and paper-ready. Will you be free sometime this week or next, maybe for about up to 1 hour? Let me know.

Alice and Peter and also in the process of reviewing this SAR for feedback as well.

dmitrij176 commented 3 years ago

Follow-up from previous comment here, @mattodd @dmitrij176 I want to meet with you to discuss the SAR result and and find a direction to make the SAR concise and paper-ready. Will you be free sometime this week or next, maybe for about up to 1 hour? Let me know.

Alice and Peter and also in the process of reviewing this SAR for feedback as well.

Sure Hung. I am available any time and think it would be useful for us to discuss this. @mattodd would you please let us know which day/time is more suitable to your schedule.

mattodd commented 3 years ago

Wed Oct 6th at 10 a.m. London would work - I think that's 8pm your time @fantasy121 ? They key is in the prep work - in this case folding in the new data to the existing diagrams, then grouping relevant structures and colour coding them by activity (for example).

fantasy121 commented 3 years ago

@mattodd @dmitrij176 Ok sounds good. I have sent a calendar invite for 8PM Sydney time (10 am London) for the 6th October. We will use the same Zoom link as our monthly meeting (https://uni-sydney.zoom.us/j/99281549497) and record this session for everyone's convenience.

If the calendar invite times messes up, just turn up at the agreed time and I think we should be okay. I can't send the invite to Dmitrij because I don't have your email but if Mat can add Dmitrij in, or if one of you give me Dmitrij's email then I can do that. Otherwise, just join the meeting at the agreed time. Hope this works out okay for everyone.

In the mean time, I will add SAR for 25 uM and see if anything else interesting comes up.

fantasy121 commented 2 years ago

@mattodd Re: structures for SAR, please use the chemdraw files on Dropbox (link below). I put the compound structures for each of the motifs into separate chemdraw files. The word doc/excel sheet file still contains the main info/analysis.

Link updated: https://www.dropbox.com/sh/1uyd2rjpgsqty14/AACZ6EUcqF2equgGtd9SdmjZa?dl=0

fantasy121 commented 2 years ago

@dmitrij176 @mattodd On the Dropbox, there will be:

Can you work on Motif C? @dmitrij176

All structure data for compounds in Motif C will be in the chemdraw file in the folder Motif C. There will be a tab "Motif C" in the excel file which contain tabulated data for these compounds. My analysis so far for this motif can be accessed in the word doc (just scroll down towards the end).

Might be beneficial to split Motif C into two subgroups (1-piperadyl and 5-piperadyl subgroups) then do any further division as appropriate.

As discussed (meeting recording), we will be looking for a mix of general trends (for summary diagram purposes) as well as interesting exemplars of what works/doesn't work, and specific case comparison of any obvious/interesting observation (could be 1 v 1 comparison, or 1 group of compounds vs another group).

Hope this helps. If anything is not clear, let me know and I see if I can show you where things are.

dmitrij176 commented 2 years ago

@dmitrij176 @mattodd On the Dropbox, there will be:

  • Folders for chemdraw files of each Motif A to D
  • An excel spreadsheet (Stats and Tables for SAR)
  • A word doc (SAR Analysis.docx)
  • Chemdraw files for Motif General Structures (the two chemdraw files: Motif Overview and Motif Structures)

Can you work on Motif C? @dmitrij176

All structure data for compounds in Motif C will be in the chemdraw file in the folder Motif C. There will be a tab "Motif C" in the excel file which contain tabulated data for these compounds. My analysis so far for this motif can be accessed in the word doc (just scroll down towards the end).

Might be beneficial to split Motif C into two subgroups (1-piperadyl and 5-piperadyl subgroups) then do any further division as appropriate.

As discussed (meeting recording), we will be looking for a mix of general trends (for summary diagram purposes) as well as interesting exemplars of what works/doesn't work, and specific case comparison of any obvious/interesting observation (could be 1 v 1 comparison, or 1 group of compounds vs another group).

Hope this helps. If anything is not clear, let me know and I see if I can show you where things are.

Thanks @fantasy121

wwjvdsande commented 2 years ago

I uploaded the google dox document in word in the dropbox The link is: https://www.dropbox.com/sh/972i5u4cxcm65xy/AAD7_42VnlGPdxWmsWTClhPza?dl=0

wwjvdsande commented 2 years ago

@kym834 can you give @Wilson-Lm also access to the dropbox? I couldn't add him

dmitrij176 commented 2 years ago

@wwjvdsande the online word editor in dropbox is not formatting schemes correctly again. I am going to add experimental on my computer and reupload the updated manuscript version on dropbox. Would that be ok?

wwjvdsande commented 2 years ago

@dmitrij176 that would be ok. I just added new parts from Wilson in the manuscript. Could you copy that in the new version as well? Wilson did not have access to the dropbox so I had to upload his adjustments in the document as well.

dmitrij176 commented 2 years ago

@dmitrij176 that would be ok. I just added new parts from Wilson in the manuscript. Could you copy that in the new version as well? Wilson did not have access to the dropbox so I had to upload his adjustments in the document as well.

Yes, no problem.

kym834 commented 2 years ago

@wwjvdsande - Bugger. I tried to set it up so that everyone could share it but it seems it is just that everyone can view it.. I've made you the owner of the folder now so you should be able to share it.

wwjvdsande commented 2 years ago

@kym834 @Wilson-Lm I added Wilson now.

wwjvdsande commented 2 years ago

@fantasy121 @mattodd: @Wilson-Lm and I updated and merged the paper in the dropbox. Not sure if I understood the SAR correctly but is it correct that in the first SAR figure you mention the lead compounds with in vivo activity in the larvae? If so, only MYOS00001, MYOS00004, MYOS00008, MYOS00016 and MYOS00167 prolonged larval survival.

Wilson-Lm commented 2 years ago

Hi all, Is anyone planning to work on the manuscript this weekend? I am asking because I will be doing some editing in the manuscript on dropbox this weekend. I am unable to directly make changes in the document on dropbox via browser, so I will have to download it, edit and the reupload.

Just FYI, please let me know if you are planning to work on it and we can plan it out.

MFernflower commented 2 years ago

When will this paper be uploaded to googledocs? I don't have a dropbox

Wilson-Lm commented 2 years ago

I believe there was an issue with googledocs and we had to put it in dropbox, not sure if that still applies. Will need to have a look at this. It is more accessible with googledocs.

wwjvdsande commented 2 years ago

@mattodd @fantasy121 @dmitrij176 @Wilson-Lm @MFernflower @MA-Jjingyi @kym834 I have uploaded the version @Wilson-Lm worked on in dropbox. You can find it here: https://www.dropbox.com/scl/fi/fi6viozy057abhymgq1f3/Fenarimols-4-20220404.docx?dl=0&rlkey=rz3izx2asuqjqdl6g4ogxgk15

mattodd commented 2 years ago

Hi @OpenSourceMycetoma/corecontrib I've taken a look at the first half of the paper, up to the point where the SAR analysis starts. File is "Fenarimols 4 (20220613)"

I'm not clear on the split between the experimental section in the manuscript (which is short) and the experimental section for the SI (which is presumably much longer). Is there a plan to put everything in one place? There are still lots of little things that need correcting, so am I looking at the right version?

The file on Dropbox for in vivo compound experimental is currently empty - again, what was the plan for this?

There are some duplicate references. Can someone volunteer to check this and elminate those?

There needs to be consistency of active/passive voice in the writing - again, could someone volunteer to check that throughout?

I'd encourage people to look at the manuscript and try to clear some of the many comments that remain. If you change anything minor you can probably get away with saving the file with its existing name, particularly if you're only editing for a few minutes. If you change anything major, save the file with a new file name. We're at risk of conflicting edits in this phase.

I will move on to looking at the rest of the SAR section next.