David's New Book

Wednesday, November 28, 2012

Writing Grants - Antimicrobial Screening - 2

 Guest Blogger Lynn Silver of LL Silver Consulting, LLC 

Thanks to Dave Shlaes for the opportunity to contribute to his blog with an entry on grant-writing-and-screening-paradigms.  I have some familiarity with the subject as I worked in antibacterial discovery for 21 years at Merck, including the development and deployment of numerous screens, and I have since been consulting in the pre-clinical discovery sphere.  But, more to the point, I, too, have been doing antibacterial drug discovery peer review for NIH and the EU as well as reviewing for journals. And, in my humble opinion, there is a need for a remedial course in antibacterial screening (and drug discovery in general). Let me emphasize that this is indeed all my opinion – you and others may disagree.

My remit here is to discuss screening paradigms.  I’m not sure if that includes target choice – but I’ll start with a few words on that particular tough nut.  Numerous reviews have covered the various points important for selecting and qualifying targets.  But each author has his or her own POV and will emphasize personal favorites. 

My set: 
1) The target should be essential to the growth, and better, to the survival, of the pathogen [preferably under conditions that can be measured in vitro but that also approximate in vivo conditions].  Genetic proof, preferably with conditional mutants or constructs, is optimum – but demonstration of inviability of knock-outs can suffice.  Don’t pick a target whose product can be supplied by nutrients in the host. I.e. avoid auxotrophic targets in most cases [but there are exceptions].   Anti-pathogenesis targets are a different area; they are interesting – but so far not much has come of them.  Reviewers will be skeptical of them – so if this is your bailiwick, prepare to explain how such an inhibitor would be developed [as a therapeutic? A prophylactic? In combination with a standard antibacterial?]

2) The target should be present in a useful spectrum of pathogens with homologs being structurally and mechanistically closely related.

3) The target should have no human homolog – or there should be a good reason to believe that selectivity [kill pathogen not host] can be achieved.

4) Inhibition of the target should not lead to rapid selection of resistance.  Anl hypothesis to consider: inhibitors of a single-gene encoded target will select for pre-existing resistant mutants in the infecting population.  If the frequency is high enough and the mutants fit enough, then such resistant mutants may compromise therapy.  I have been a proponent of the idea that good monotherapeutic antibacterials target the products of multiple genes or structures produced by multiple gene products (Silver, LL. 2007. Nat.Rev. Drug Disc. 6:41-55) and, as such, select much less frequently for single step, high level target-based resistance than do single-targeted agents.  If you choose a single-gene encoded target, be prepared to defend the choice. 
5) Having ways of measuring the activity of the target or function in vitro as well as the phenotype of inhibiting the target in the intact cell are important for screening and/or follow-up. 

6) Ability to produce the target in quantity for structural studies and eventual iterative optimization is a plus - but not a big enough plus to substitute for meeting the other necessary criteria.

7) Druggability.  Does the target have a deep enough, well-defined enough binding site for selective inhibitory ligands?  Does your chemical library contain likely ligands?

8) Read Payne. et al. (2007. Nat. Rev. Drug Disc. 6:29-40) and note that they ran 70 HTS antibacterial campaigns with very little to show for it.  Why will you succeed when GSK failed?

OK – you’ve got a target.  Consider the chemicals to be screened.  Be warned, chemical libraries are often filled with aggregators, detergents, alkylating agents – compounds that will interfere with many types of screens.  Read Babaoglu et al. (2008, J. Med. Chem.51:2502-2511).   And, similarly, the detergents and alkylators and many other types of toxic compounds will have uninteresting, non-specific antibacterial activity.  It is easy to kill bacteria, even multi-drug resistant bacteria, with chemicals.  It is hard to find novel antibacterials that are highly selective for pathogen over host.

Stay Tuned for Part 3 in this series and - coming very soon - FDA and Nosocomial Pneumonia.