High throughput screening methods: evolution and refinement

416 Pages·2016·12.4 MB·English

by  Joshua A Bittker

High Throughput Screening Methods
Evolution and Refinement
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Chemical Biology Series
Editor-in-Chief:
Tom Brown, University of Oxford, UK
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77 Kira J. Weissman, Lorraine University, France
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62 Sabine Flitsch, University of Manchester, UK
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78 Nick J. Westwood, University of St Andrews, UK
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g | d Titles in the Series:
or 1: High Throughput Screening Methods: Evolution and Refinement
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High Throughput Screening
Methods
01 Evolution and Refinement
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http:// Email: [email protected]
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doi: ChemicalBiologyNo.1
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c.or PrintISBN:978-1-78262-471-4
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p:// ISSN:2055-1975
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20 rTheRoyalSocietyofChemistry2017
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77 Foreword: Transforming
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p:// phaseoftherapeuticdiscoveries.Forexample,analysisofhumangeneticsis
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n revealingallelicseriesofriskandprotectivevariantsofgenesacrossarange
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6 of diseases. These allelic series demonstrate a dose–response relationship
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2 that relates the activity of a gene to its effect on, for example, the risk of a
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b disease. Prior to embarking on the discovery of a drug, we can establish
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ce whether perturbing a target, in the context of human physiology, has the
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5 D intended effect in terms of safety and efficacy. Biochemical mechanistic
n 0 investigations of variant proteins can provide a blueprint for the activities
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s teins in order to be safe and efficacious.
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u Thisisanamazingadvancewiththepotentialtotransformmedicine.We
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hear about this promise frequently, especially from scientists pioneering
these advances. The promise of these advances has led to powerful terms
suchas‘‘precisionmedicine’’beingusedbyPresidentObamaathisStateof
the Union speech in 2015, and these terms have even entered the main-
streamvernacularofthemediaandpublic.However,majorhurdlesexistto
realize this potential, and these hurdles may not be well appreciated by the
advocates of the human biology/patient based approach to drug discovery.
Without recognizing these hurdles and overcoming them, we are at risk of
this potential revolution in medicine being unfulfilled.
Why this pessimism? For one, the activities suggested by these experi-
ments of nature are challenging and often unfamiliar in the context of the
ChemicalBiologyNo.1
HighThroughputScreeningMethods:EvolutionandRefinement
EditedbyJoshuaA.BittkerandNathanT.Ross
rTheRoyalSocietyofChemistry2017
PublishedbytheRoyalSocietyofChemistry,www.rsc.org
v
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vi Foreword:TransformingMedicinebyInnovatingtheScienceofTherapeutics
historicalpathtowardsdrugdiscovery.Forthemostpart,todate,drugsthat
have these suggested mechanisms of action (MoA) do not exist. In order to
realizethepromiseofmodernbiologyinmedicine,wemustinnovateinthe
science of therapeutics.
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0 Chemistryandchemicalbiology,asevidencedbythisimportantnewbook
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F High Throughput Screening Methods: Evolution and Refinement, are offering
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7 new ways to discover compounds with novel (previously unknown) MoA
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2 (nMoA). Novel methods are being developed to discover specific nMoA
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8 compounds suggested by the human biology, patient based concept. Novel
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8 methodsarealsobeingdevelopedtoidentifyvastcollectionsofcompounds
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9/ whereeachmemberhasadistinctMoA—knownandnovel—inanticipation
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10 of their future utility. The range of innovations presented by the authors
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1 is extraordinary and the level of creativity that underlies these advances is
doi: inspiring and makes for exciting reading. The methods described in this
g | bookandtheirdescendants,onceintegratedintothetherapeuticsdiscovery
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c. efforts of laboratories worldwide, offer great promise to bridge the gap
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bs.r betweentheknowledgegainedfromhumanbiologyandthethusfarelusive
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http://p traInnsfaodrdmitaitoivnetmoetdhiecisnpeesctihfiactswcereheonpinegtomdeetrhiovedsf,rotmhisthbeomok. also hints at
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16 future success. Foundational capabilities that enable the translation of
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er 2 insights from human biology to novel therapeutics are in general far easier
mb to share than compounds, targets and biological insights associated with
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c specific drug discovery projects. Innovations in the science of therapeutics
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5 can be developed effectively through collaborations involving scientists in
n 0 the public and private sectors, especially when the participating not-for-
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ed profit and for-profit organizations agree to avoid restrictions in the sharing
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blis of novel innovations. Evidence of this opportunity for interaction and col-
Pu laboration is seen in the contributions from the authors in this book—the
chapter contributors are from both sectors and cover topics important to
each (for example, the importance of novel asymmetric synthetic chemistry
and small-molecule libraries, integrating new techniques into probe and
drug discovery, and proper annotation and sharing of data, among many
others). The individual chapters also reinforce how overcoming the new
challenges of human biology based precision medicine will need the
foundationalcapabilitiestocontinueevolvingandhowresearcherswillneed
to learn from each other as part of this evolution.
Stuart L. Schreiber
Center for the Science of Therapeutics, Broad Institute, Cambridge, USA
Howard Hughes Medical Institute, Department of Chemistry and
Chemical Biology, Harvard University, Cambridge, USA
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77 Preface
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p:// gies. Such reviews, while useful for a brief period of time, are quickly sur-
htt passed by changes in the field. This may be due to the discovery and
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n 0 in a plug and play format (e.g. new fluorophores or luciferase enzyme
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stillrequireimprovement,wehopetoalsoencourageourreaderstoconsider
the philosophy underlying technological change. How and why are im-
provements in technology made? Surely they reflect an underlying demand
from researchers to be able to generate results more quickly and answer
questions more efficiently or more robustly.
Small-molecule activity screening, considered as a specific discipline
practicedinitiallywithinthepharmaceuticalindustry,andnowmorewidely
availabletoacademicsandbiotechnologyfirms,couldbeconsideredtohave
startedinthemid-1900s.Thisinvolvedtheroutineparalleltestingofnatural
product extracts and purified compounds, as well as synthetically available
compounds from related industries, in cellular phenotypic assays such as
microbial viability systems or whole animals.1 It became more robust and
ChemicalBiologyNo.1
HighThroughputScreeningMethods:EvolutionandRefinement
EditedbyJoshuaA.BittkerandNathanT.Ross
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viii Preface
standardized with the shift towards target-based enzymatic assays, large
scale combinatorial synthetic compound collections, and robotic auto-
mationinthe1990s,driveninpartbygenomicstudiesdrasticallyincreasing
the number of putative therapeutic targets.2 This new approach required
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2 izationsofferingHTSasaservice,ademocratizationoccurredinthefieldof
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8 small-moleculediscovery.Thischangeledbothtomoreroutineapplication
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8 of screening to early biological targets as well as to the development of a
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doi: molecule discovery. Why apply automation, previously used in areas such
g | as industrial manufacturing, to increasing the number of measurements
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c. made?Whatdemandsdidthis increase inthroughput haveontherelated
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n technological changes, including the information revolution and political
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mb shortcoming in the existing capabilities, but in turn can lead to its own
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n 0 ponents of HTS: chemical perturbagens, bioassays, data analysis and man-
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ed agement, and organizational infrastructure. For example, with the increase
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blis in throughput of cell free enzymatic and cell based reporter assays, more
Pu compounds were required. These were accessed through new methods in
highthroughputchemicalsynthesis,whichgreatlyincreasedthenumberof
compounds available but did not always consider the optimal chemical di-
versity necessary for a range of biological targets.3 Analysis of the desired
properties of compounds changed,4 with many pharmaceutical companies
paring back their collections by 30% or more from their peaks.5 Alternative
approaches, such as encoded libraries and diversity oriented synthesis,
changed the types of libraries available. Lower throughput but arguably
morebiologicallyrelevantassays,suchashighcontentimagingandactivity
profiling, changed the nature of the information available.2 In turn, this
ledtonewrequirements,asphenotypicassaysrequiredsystematicmethods
for identification of cellular targets. Overall, of course, these different
approaches have different requirements for capital and operational invest-
ment, and all scientific research remains a trade-off between available
fundingandhopedforreturnintheunderstandingofbasicbiologyandthe
impact on improvements in human health.
Given these historical and ongoing changes, no one would argue that we
are at the ideal state of HTS discovery now. This book is a snapshot of the
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Preface ix
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bs.r Figure1 TheevolutionofHTSmethods.Eachcolumnshowstheapproximatetime
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p://p fbroaomke,sbewchameneawdiddietliyonavaaliltaebchlen.iTqhueesc,oeloarcshooffthwehbicohxesisinddisiccautsesewdhiicnhtkheisy
n htt aspect of HTS the method helps to improve. Some methods involve
6 o contributions to multiple aspects of HTS, indicated by multiple colors
01 (e.g. encoded libraries are a new source of compound diversity and also
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er provideanewassaymethod).Byunderstandingthereasonsfordeveloping
mb eachnewtechnologyandthecurrentlimitations,wecantrytounderstand
ce whatimprovementsmaybenefitfutureHTSanddrugdiscovery.HC:high
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D content; PPI: protein–protein interaction; uHTS: ultra-high throughput
n 05 screening.
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blis state of the field in 2016, as well as a historical survey of how the methods
Pu presented arrived at their current state of the art. Our contributors also
highlight weaknesses and potential solutions to further improve the field.
This, then, is our hope and challenge for our readers: we seek to provide a
meansofunderstandinghowandwhywehavearrivedwhereweare,through
the above-mentioned combination of technological and societal changes.
With that understanding, we hope to illuminate the way forward—what
changes are necessary, what impact will they have, how can they be imple-
mented practically and what future challenges will those changes in turn
bring about?
Wecannotpredictorunderstandinasinglebookwrittenatasingletime
allofthetechnologies yettocome.However,byprovidingthereader witha
means of understanding how and why technological change occurs, as
illustrated by the evolution and refinement of HTS methods, we hope that
future capabilities can more readily be anticipated, developed, applied and
further improved, to the benefit of researchers and society.
Joshua Bittker and Nathan Ross
Cambridge, MA, USA
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x Preface
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2. D. C. Swinney and J. Anthony, Nat. Rev. Drug Discovery, 2011, 10, 507.
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