Paper draft and discussion

[MFernflower]

1. Should the paper be worked on now or should we all wait for more data to come in?
2. What journal do we want to publish this work into?? Journal of Antimicrobial Chemotherapy perhaps?

[danaklug]

Hey @MFernflower thanks for getting this started. I have actually started to put together a draft of the paper in Google docs that anyone can now edit. A few things to keep in mind:

• The author list is tentative and I know I've left people out - please add the names of people that should be included!
• There is now a repository for paper files such as schemes, figures, experimental, supplementary files, etc. Please try to keep this up to date as much as possible! (Quick guide to GH repositories here for those that need it.)

• For experimental write up of compound synthesis, please have a look at Alvaro's experimental document and try to keep as similar to his formatting as possible to make it easier to put everything together.

  I think the journal is TBD as we're still waiting to see how the MoA and tox sections will shape up but happy to have suggestions/discussion in this issue.

[danielgedder]

Dear @danaklug I have started to organize all the NMRs data, mass, synthetic route, etc of my compounds and I will update the google file as soon as I get it ready. I can help you to draw SARs figures and schemes, just let me know in case you need any help. Best regards!

[danaklug]

@danielgedder Amazing!!

[mattodd]

Thanks all, great to get this going. Just a very general note about open data associated with this paper. Our submission is going to consist of 1) The paper 2) The usual SI - descriptions of procedures, protocols, dead PDF scans of 1H/13C of novel compounds etc, as is usual for a medchem paper 3) As much open data as we can share - meaning raw NMR data files, Excel sheets, and so on. This needs to be gathered together and uploaded somewhere like UCL's e-repository, since most journals aren't interested in hosting data like this. I would also like to include all relevant offline ("snapshot") copies of lab notebooks that have been used in the syntheses, where we have them.

It's point 3 that distinguishes open projects like this one from most other published projects - all data, available for re-analysis and re-use. I'm not sure how best to assemble all this stuff in advance of the paper submission, but I would guess that the best place would be someone's ELN.

[jarvist]

I've found https://zenodo.org/ very useful for hosting (computational) data, particularly as you can get it to archive + version a GitHub 'release', after editing it as normal in a git repository. (Zenodo then instantly generates a DOI for linking from your paper.)

[mattodd]

Some quick To Do's on the paper to get us to the next stage.

• [x] @danielgedder to write up compounds he's made for this paper in the same style as @edwintse 's experimental section. We're not yet sure which compounds will be in the final paper (most, I'd expect) but we know we need the data
• [x] @danielgedder to take a look at the paper's SAR sections (written by Dana thus far) and add any comments onto the manuscript. Please check that all the original picture/chemdraw files can be accessed somewhere.
• [ ] @edwintse similarly to read/check the synthetic chemistry section and ensure everything is accurate. Please check all the original picture/chemdraw files can be accessed somewhere.
• [ ] @mattodd to read through the intro and annotate the manuscript directly.

[danielgedder]

Hi @mattodd, I have added my experimental section and made some comments/updates to the main manuscript.

[lferrins]

Just a short update from the NU side - we have a near complete experimental of all the NU compounds and will share shortly. When looking at the spreadsheet of compounds that @danaklug compiled here we noticed that there are DNDi compounds so I am writing to Ben Perry and Peter Sjo to confirm how to handle these (there is an existing publication that I will cross-check with also).

A quick question about the general experimental that we would like your input on... Due to a series of unfortunate circumstances, we have acquired data on 3 (or 4) different LCMS instruments. On 1 of the setups we had to replace the detector (Waters Micromass ZQ detector (electrospray ionization), or Waters Micromass QDA detector) would you like us to separate the data that came from each of these separately? Excerpt below in case that helps.

LCMS analysis was performed using either a: 1 Waters Alliance reverse phase HPLC (columns Waters SunFire C18 4.6 × 50 mm, 3.5 μm, or Waters SunFire C8 4.6 × 50 mm, 3.5 μm), using a multiwavelength photodiode array detector from 210 to 600 nm and either a Waters Micromass ZQ detector (electrospray ionization), or Waters Micromass QDA detector. 2 Waters Alliance reverse phase HPLC (2695; Xbridge C18 4.6 × 50 mm, 3.5 μm), using a multi-wavelength photodiode array detector from 210 nm to 600 nm and Waters Micromass QDA detector. 3 Agilent 1260 Infinity HPLC (Agilent SB-C18 column (1.8 um, 2.1 x 50 mm), using a multiwavelength photodiode array detector monitoring 210 nm, 230 nm, 254 nm, and 280 nm coupled to an Agilent 6120 single quad MS (ESI [source]).