David's New Book

Sunday, November 4, 2012

Writing Grants - Antimicrobial Screening



So, you are considering writing a grant around an antimicrobial discovery project.  I actually review a fair number of these.  Mostly I work with NIH (I’m on the Drug Discovery and Resistance study section), but I also review occasional grant requests from Canada and Europe to review.  I find that, mostly, those of you in academia are hopelessly lost when it comes to starting out in antimicrobial discovery and the translation of results through preclinical development and on into the clinic.

To save us both time, I thought I’d write this blog in hopes that those of you who are actually considering getting into this area would read it.  This way you would get at least one viewpoint from an experienced reviewer and drug hunter-developer.  I realize that mine is not the only point of view out there and I’m sure there will be some that take issue with what follows – but here goes anyway . . .

This first installment is dedicated to grants around Screening for antimicrobials

If you are going to undertake a screening program – please assure that you have the appropriate chemistry and biology expertise to do this.  You can’t just count on some central screening facility to provide you with an appropriate choice of molecules to move forward nor can such a facility provide you with the most appropriate secondary assays to use as a second step. If you do have such expertise among your key personnel – make sure you describe what role each one of them will play in the screening process. Most of the screening grants I see fail because of the failure to provide this expertise or the kind of information required.

Even if you have the appropriate expertise in your grant request and you have spelled out what each individual will do within the screening program – please provide a fairly detailed screening flow chart.  This flow diagram should tell how the various hits will be eliminated or moved forward according to prespecified criteria.  A hint – just because a compound inhibits your enzyme or binds to your protein in vitro and when you expose bacteria to the compound,  bacterial growth is inhibited – you cannot conclude that the compound is a bona fide hit.  To prove this you must actually show that the growth inhibition you observe is occurring by the mechanism postulated. This can be accomplished by showing accumulation of appropriate intermediates in the cell, by using over expressing and underexpressing strains to show MIC difference or by selecting mutants with mutations occurring in the correct target genes.  The latter is fraught with difficulty since many such mutations in bacteria arise through efflux and other non-specific non-target-based mechanisms.

If you are screening an enzyme or a protein in a cell free system – what are the chances that the compound will actually enter the bacterial cell – especially a Gram negative one?  Not great!  Consider cell-based screens as either the primary screen or as a secondary assay.  Also – consider the library you are screening.  Screening old drugs is great – but the physiciochemical properties of these drugs are not well aligned with what is needed in an antibiotic. The same is true for most chemical libraries.  Think about this before you start.

On the antiviral side of things – most compounds that seem to inhibit viral replication are actually subtle (or sometimes not so subtle) cytotoxins.  Virus replication is a much better indicator of cytotoxicity than standard cytotoxicity assays in many cases. Once again – make sure you have viral assays that prove that viral growth inhibition is going through the appropriate mechanism and not something non-specific or off target.

Next we will get into what a screening paradigm might look like and finally we will talk about early and late preclinical development.