Phenotypic Drug Discovery Forum/SIG Sept 28, 2012

1. Phenotypic Drug Discovery SIG
Results from Survey Monkey
September 28, 2012

2. About the Survey
The Phenotypic Drug Discovery LinkedIN group has grown to over 350 members
since its start in Mid May and is composed of a diverse population representing
scientists, service/technology providers, and bio-entrepreneurs. With the help
of Lynn Valastyan and Francis Willard two surveys were developed to provide
general information about the PDD SIG membership in general and to better
estimate the use and impact of phenotypic approaches by scientists.
Survey responses have hit a plateau so it is probably time to publicize the
complete results of both surveys. The data from the survey cannot be
statistically significant with less than 10% of the PDD SIG membership
responding. Although the response was initially disappointing, Nan Hallock
(Director of Publishing for SLAS) indicated that surveys were like letters to the
editors….not too many people actively participate, but many are interested.
Hopefully members of the PDD SIG will find the results interesting…..
Jonathan Lee
September 28, 2012

3. PHENOTYPIC ASSAY SURVEY-1: ALL
LINKEDIN PDD SIG MEMBERS

10. How can the Phenotypic Drug Discovery SIG
LinkedIn site better serve your needs?
• Discussion forum is very helpful to follow progress in the area
• Networking and leads to capital investors.
• Keep the discussion going
• Exchange ideas and promote concept
• Understand hurdles identified by others. Sharing of practical
implementation techniques. Progression of phenotypic-based projectsinto
the clinic.
• By somehow getting more coal-face medchemists to join in!
• I was impressed with excellent discussions posted by finest scientists in
the field. Adding presentations that highlight the PSA if any would be
interesting.
• The set of very good and relevant topics that were raised up recently. It
provided very useful sharing of information and stimulated interesting
discussion.
• A section or catalog of PSA resources, e.g. service providers, pre-
competitive consortia, academic core labs, would be helpful.

11. How can the Phenotypic Drug Discovery SIG
LinkedIn site better serve your needs?
• The discussions on the site are extremely useful to me as a young
scientist in academia. The site would be better if we had some sort
of member directory so that we may more easily find people of
certain expertise and network (if one wishes to be involved in such
a network).
• Monthly or weekly compilation of all relevant papers in the area of
PDD
• Provide catalogue of available phenotypic capabilities and assays
with contact names
• It's too late to serve my personal needs, but for the needs of many
others, it we should discuss new business models (including funding
sources) to reintegrate PDD into mainstream drug discovery. This
may not seem natural for the primarily scientific bent of this
group, but if scientists don't get more savvy and assertive in the
business, satisfactory change can not occur.

13. PHENOTYPIC ASSAY SURVEY-2: RESEARCH
SCIENTISTS (PAST AND PRESENT)

21. What significant achievements and or obstacles have
been encountered when using phenotypic approaches
for target identification or si/shRNA screening?
• Uniformity across the board for acceptable bioassays. Harmonization of
protocols for PSA in target discovery and validation.
• The quality of libraries have been questionable (especially Qiagen). Off
target effects are troublesome and require several individual oligos per
gene. The cellular response is variable and population-based analysis is
required. Transfecting some cell types can be challenging. There is no real
negative control in siRNA screens, since all oligo will have some sort of
effect. Obtaining a good base line is difficult, probably the best is the
mode or median of the entire library screen omitting positive controls.
• reproducible results
• Not all responses are direct effects - both mechanistic and siRNA
nonspecificity issues.
• Obstacle: disconnect between mammalian cells and yeast genetic screens
for small molecule TID.
• Translation os siRNA results into shRNA results for stable cell generation in
target validation studies

22. • Achievements: always found known genes in the list of potential functional genes.
Obstacles: -Very low confirmation rate for the whole list of genes in functional screen.
-Never sure that the siRNA against target will work and demonstrate effect significant
to produce detectable phenotype. - Problem with the selection of the hits from the
list to follow up on.
• Obstacle: relative cost and need for larger collaborations Acheivement: proof of
concept on modification of a key pathway cells/tissues specifically mimicking human
disease phenotypes.
• We are just starting target identification work, however a strategy using genetic
methods are already in place.
• Challenges: library preperation and throughput across assays formats, Validation of
hits. Achievement validated novel targets identified.
• Target identification in phenotypic settings is not a trivial exercise - there's always
concern that interactions seen are not actually those which are relevant to the
observed phenotype.
• Achievements: many novel, useful targets or pathways discovered. Useless targets
eliminated. Novel compound-target pairings discovered that were developed into
biological probes and new screens that couldn't have been developed any other way.
Obstacles: 1, managerial/investor resistance to starting program without predefined
target(s) and screen(s) specifically directed at the predefined target(s); 2,
managerial/investor resistance to doing what looks to them like "just tool
development

23. What significant achievements and or obstacles have been
encountered when using phenotypic approaches for drug
discovery?
• Achievement- whole cell activity obtained Obstacle- deciphering of biological target has been cumbersome for
biology colleagues.
• Acceptance for peer-review funding. If you have specific NIH study sections that are interested in promoting PSA,
it will be much appreciated.
• Processing time for a thorough image analysis is challenging, requires powerful computer clusters. Statistical
analysis of objects within populations is challenging from a computational point of view as files comprising
several billion lines need to be processed. This requires computers with either large RAM or much free disk space
for temp files. Visualisation of data is complex (how to display population distributions of various phenotypes?).
Statistic methods to derive probabilities of phenotypes and test of population results.
• just getting started, target deconvoltion is currently our largest concern
• Acheivement = small molecule with novel MOA Obstacle = chemist
• Hard task to convince managers that PSA could be valuable and successfull for finding drugs with new MOA.
Mentalities are still target oriented !
• Identifying the molecular target. Of course, there is not agreement if this is necessary, but it is very helpful for
publication in a highend journal (this is a University).
• Identified 4 compounds from Prestwick library as non-DA symptomatic augmentation therapy for Parkinson's
disease
• Achievements: identification of small molecules with cellular activity producing desired pheontype made cell
target validation and in vivo relevance more convincing, plus delivered valid tool compounds and cellular
systems to feed into the DD program. Obstacles: The chemical matter used in the the phenotype screen was not
of good drug discovery quality (i.e. chemotypes unsuitable for development) necessitating a follow up to
discover better chemcial matter against the target. This was because as an academic group we did not have
access to good pharma collections but rather just the (cheap) off the shelf combichem library.

24. • Achievements: new target and biology were found for anti-TB drug discovery. New scaffolds in characterization for
HCV drug discovery. Two completed successful phenotypic siRNA screening discovered new functional genes.
Obstacles: secondary assays are not ready after primary assay is done mostly because potential mechanisms and
targets are not known
• Obstacle: timing and throughput issues; longer learn and confirm med. chem. cycle AChievement: bettwr
understanding of pre-ADME issues and enablement of a proof of concept and proof of relevance in patient derived
tissues i.e. a clinical trial in a test-tube on modulation of the disease phenotype.
• Assays of sufficient quantitative quality have been set up so as to perform SAR using phenotypic assays
• Achievements: Identified molecules which modulated in vitro and in vivo biology and easily differentiated from
standard of care. Identified cellular processes not previously associated with therapeutic biology. Demonstrated
that phenotypic assays can provide evidence of compound SAR, can successfully utilize chemoinformatics mining
methods, and can be statistically validated. Phenotypic assays can be as operationally robust as biochemical assays
yet interrogate multiple molecular targets in a native context and without preconceptions of target validation.
Obstacles: Compound drug-ability and metabolism issues encountered (like biochemical approaches). Compound
prioritization can be difficult. Phenotypic approaches may lead to unexpected findings relevant to the biology
resulting in flow scheme modification and timeline delays.
• Obstacles: Flat in vitro SAR; Low hit rate; High hit rate; Lack of a experience/strategy/knowledge for prosecuting
hits. Target-directed mindsets that are inherently biased against PDD- both in bench scientists and the
management. Overselling of the concept by senior management. Achievements: novel mechanistically
differentiated compounds for therapeutically relevant assays. Often the comparable 'target-based' projects have
major druggability issues.
• Challenges: Implementation of informatics workflows to collate multiparametric high-content data. Throuput for
screening compound and combinations across multiple assay formats/cell models. Development of bespoke image
analysis algorithms to extract quantitative data from novel (3D, co-culture) assay formats.
• Target identification can be difficult to do rapidly, which puts pressure on the team as a whole.
• Achievements: discovering novel chemical scaffolds with a desirable balance of pharmacological properties acting
on previously undiscovered or intractable targets. Obstacles: 1, managerial/investor resistance to advancing leads
without a defined or fashionable mechanism of action. 2, managerial/investor resistance to starting programs not
predicated on screening against fashionable target(s).