Practical Workshop: Chemical Biology, Drug Discovery and Screening

Transcription

1 Practical Workshop: Chemical Biology, Drug Discovery and Screening Date: October 2013 Location: European ScreeningPort GmbH, Schnackenburgallee 114, Hamburg, Germany Course overview The emergence of chemical biology has coincided with increasing numbers of exploratory molecular targets and mechanisms, both therapeutic and non-therapeutic in origin. Screening using miniaturised microtitre plate format based assays remains the most widely utilised methodology for identifying novel chemical matter capable of modulating target function in a meaningful, biologically relevant manner 1. The first practical steps are the selection synthesis, management and subsequent screening of molecular libraries, either small molecule or biological in origin. The second critical area is the selection, development and prosecution of bio-assays for primary hit identification, validation and profiling. In the context of drug discovery projects, hits are the further optimised using multiple criteria including structure activity relationships, selectivity, physicochemical properties and liability. Automation is a key enabler to increase productivity, particularly in structural based approaches to hit identification and validation; for example, x-ray crystallography and NMR spectroscopy. Selecting assays for screening Recent years have witnessed an expansion in the disciplines encompassing drug discovery outside the pharmaceutical industry. This is most notable with a significant number of universities worldwide that now host infrastructure such as compound libraries and automated screening centres 2-4. An archetypal small molecule drug discovery project will aim to identify chemical starting points that modify the functions of genes, cells or biochemical pathways. In some but not all instances, these functions may be linked to disease processes, and an opportunity will exist to further develop the chemical starting points into novel therapeutic agents. In small molecule drug discovery, the ultimate aim is to identify new therapeutics, an activity that has, due to high risk and cost, historically been conducted within the commercial sector 5. The expansion of small molecule drug discovery outside the pharmaceutical manufacturing industry has coincided with increasing numbers of exploratory molecular targets and mechanisms, both therapeutic and non-therapeutic in origin 6. Screening using miniaturised microtitre plate formats remains the most widely utilised methodology for identifying novel

2 chemical starting points that are capable of modulating target function in a meaningful, biologically relevant manner 7. The first practical steps in drug discovery include the selection of a target (followed by its cloning, expression and purification), development of an assay to monitor the activity of the target, and the synthesis and management of molecular libraries. The second practical step includes the use of the above in screening campaigns to identify primary hits, followed by their validation. In the context of drug discovery projects that make use of biochemical assays with purified targets, the activities of selected primary hits would typically be further evaluated in biophysical assays such as surface plasmon resonance and isothermal titration calorimetry. This effort would expect to lead to the identification of validated hits with some of these selected for optimisation using multiple criteria including structure activity relationships, selectivity, physicochemical properties and liability 8,9. Despite the successes that have been reported in the literature 7 where the above approaches have led to the identification of potent and selective compounds, their activities often fail to translate in vivo and this may well be due in part to the target based assays being non-physiological in nature e.g. the target protein being a truncate of the protein and the assay using a substrate that is non-physiological. Although biochemical assays have historically been the most amenable to HTS, cell based assays are becoming the method of choice for screening activities 10. These cell-based assays are often phenotypic in nature and it is advantageous to have in place a biochemical assay in which compounds can be evaluated so as to confirm that they directly modify the activity of the target or bind to it. In addition, it can be difficult to drive medicinal chemistry and structure-activity-relationship (SAR) in the absence of the knowledge of the target(s) upon which the compounds act. Therefore, the ability to evaluate compounds in target based assays is important as it adds confidence that any measured activities are genuine and not assay format specific artefacts 11. The role of label-free assays The term label-free assay has a relatively broad meaning and it is important to be aware of its limits. The term label-free could be used to imply that it offers an improvement upon an assay that makes use of a label however, this may not be the case. Many label-free assays for soluble protein targets make use of substrates that are not physiological and therefore these are potentially as artificial as assays that require labels. It is therefore important to consider pseudo-label-free assays in which the key biological event e.g. substrate phosphorylation (by a kinase) or substrate degradation (by a protease) make use of the native target and substrate which are in essence label-free, but the detection of the extent of phosphorylation or cleaved protein are made using methods which make use of labels 12.

3 Label-free phenotypic assays We are now witnessing a resurgence of cell based assays including phenotypic assays where a particular change is monitored, in some cases without knowledge of the underlying target(s) upon which compounds are acting upon. Some of the successes using these approaches for drug discovery have been reviewed 10. It is interesting to note that in some cases where efficacious compounds were identified, the target(s) they act upon were identified subsequently. However, their efficacy may still be due to a poly-pharmacological effect that includes the effect of compounds upon additional targets that may still be unidentified. Advances in cell based assays are also being made, for example using human induced pluripotent stem (ips) cell-derived cells that better recapitulate normal human biology compared to transformed cell lines and non-human primary cells. It is in light of the above that a partnership was established between the European Pharmaceutical Review and the European ScreeningPort in order to set up a unique Practical Workshop: Chemical Biology, Drug Discovery and Screening. This workshop is being held subsequent to three successful practical workshops held in December 2012, April 2013 and June The Practical Workshop: Chemical Biology, Drug Discovery and Screening will be held on October 2013 at the European ScreeningPort facility in Hamburg and will be part lecture based with a significant practical component. References 1. Schenone M, Dančík V, Wagner BK, Clemons PA. Target identification and mechanism of action in chemical biology and drug discovery. Nat Chem Biol 2013;9: Frearson JA and Collie IT. HTS and hit finding in academia - from chemical genomics to drug discovery. Drug Discov Today 2009;14: Frye S, et al. US academic drug discovery. Drug Discov Today 2011;10: Baker M. Academic screening goes high-throughput. Nat Meth 2010;7: Goodman M. Market watch: Pharma industry performance metrics: E. Nature Rev Drug Discov 2008;7: Overington JP, et al. How many drug targets are there? Nat Rev Drug Discov 2006;5: Macarron R, et al. Impact of high-throughput screening in biomedical research. Nat Rev Drug Discov 2011;10: Bleicher KH, et al. Hit and lead generation: beyond high-throughput screening. Nat Rev Drug Discov 2003;2: Gul S. Overview of the gene-to-lead phase in drug discovery. Eur Pharm Rev Digital 2009;6:3 10. Swinney DC and Anthony J. How were new medicines discovered? Nat Rev Drug Discov 2011;10:507

4 11. Baell JB and Holloway GA. New substructure filters for removal of pan assay interference compounds (PAINS) from screening libraries and for their exclusion in bioassays. J Med Chem 2010;53: Gul S. The challenges associated with label-free technologies in drug discovery. International Drug Discov 2011;6;24 Attendee profile The Practical Workshop: Chemical Biology, Drug Discovery and Screening is designed for scientists at all levels (undergraduates, postgraduates and laboratory based scientists within academic and industrial research organisations) engaged in early stage drug discovery and have an interest in the development, validation and utilisation of cell based assays for screening against small molecule libraries. The Practical Workshop: Chemical Biology, Drug Discovery and Screening is equally well suited to technically focused staff from core facilities or contract research organisations who may wish to extend their expertise. The evening dinner on the first day will offer the opportunity for the participants to network and establish relationships that would be mutually beneficial. Learning objectives The main learning objectives of the Practical Workshop: Chemical Biology, Drug Discovery and Screening will be to examine by way of practical sessions and lectures, aspects of chemical biology, drug discovery and screening. All participants will take part in the practical sessions and these will involve the development of screening compatible assays, pharmacology of standard compounds and proof-of-concept screen. Participants in this workshop will discuss and demonstrate practically: (1) the appropriate steps in selecting suitable assays in light of the fact that a multitude of assay technologies are currently available for a given target; (2) how to select an appropriate technology; which criteria should be examined during the early stage chemical biology and drug discovery processes; (3) whether a generic, flexible set of assay methodologies or customised solutions should be applied to the targets being investigated. The specific aspects of the lectures will cover general concepts in chemical biology and drug discovery, the role of biochemical and cell based assays for drug discovery purposes, their advantages and disadvantages and how to incorporate them into a drug discovery workflow.

5 Workshop topics The Practical Workshop: Chemical Biology, Drug Discovery and Screening will include the following laboratory sessions: 1. General concepts for biochemical assays exemplified by kinase and protease targets 2. Pharmacology of standard compounds, signal stability, choice of liquid handling, Z calculation and proof-of-concept screen 3. Cell viability assays 4. Label-free cell-based assay for GPCR targets 5. Pseudo-label-free kinase assays Workshop lectures 1. Lecture: Introduction to chemical biology and drug discovery and the design and development of assays - what can be achieved and lessons from past successes and failures. chemical biology, drug discovery, screening jargon and terms The learning objectives from this lecture will be: o Appreciate that a wide range of assays are available for use in pre-clinical drug discovery o Gain an understanding of how to develop appropriate assays for use in preclinical drug discovery o Appreciate the limitations of the currently available assays that are used in pre-clinical drug discovery o Gain an understanding of appropriate data processing required to identify hits from small molecule screening campaigns o Gain an understanding of the processes involved in validating and identifying hits from small molecule screening campaigns o Gain an understanding the commonly used terms in pre-clinical drug discovery o Appreciate that these terms are used in a variety of contexts within different organisations (e.g. the pharmaceutical industry, biotech and academic) o Gain an understanding of how to prepare documents and presentations that refer to assay and compound data in a universally recognised format. 2. Case study: Phenotypic cell-based assay development and screening 3. Lecture: Reagent characterisation and selection of assays which will ensure translation of hits between formats

6 The learning objectives from this lecture will be: o Gain an understanding of the advantages of using cell-based assays for screening o Gain an understanding of the disadvantages of using cell-based assays for screening o Appreciate that additional biochemical assays and/or cell based assays are required to progress compounds for drug discovery purposes. 4. Practical: General concepts and application of chemical biology and drug discovery assays 5. Practical: Pharmacology of standard compounds, signal stability, choice of liquid handling, Z calculation and proof-of-concept screen 6. Lecture: Data analysis and reduction - going beyond the Z. Discuss methods for analysing in vitro biological assays data including false positive/negative rates, doseresponse curve fitting and correlations The learning objectives from this lecture/practical will be: o Gain an understanding that the efficient processing of screening data requires suitable software o Appreciate the need to assess both raw and processed screening data o Gain an understanding of the underlying equations used to normalise data and fit dose-response curves o Gain an understanding of the processes that should be followed in order to identify false positives/negatives in screening. 7. Case study: Analysis of assay data The learning objectives from this lecture will be: o Gain an understanding of how to use software for analysing assay data o Gain an understanding that an integrated multi-disciplinary team is required to progress compounds in pre-clinical drug discovery 8. Lecture: Integrating your research program, design of project critical paths which integrate in-vitro, in-vivo and in-silico elements The learning objectives from this lecture will be: o Gain an understanding of how to construct critical pathways for pre-clinical

7 drug discovery projects o Appreciate that a variety of tools are required to ensure the progression of the outputs of screening o Gain an understanding that an integrated multi-disciplinary team is required to progress compounds in pre-clinical drug discovery

8 Practical Workshop: Chemical Biology, Drug Discovery and Screening Agenda Day One 9:00-9:30 Introductions 9:30-10:00 Lecture: Introduction to chemical biology and drug discovery and the design and development of assays - what can be achieved and lessons from past successes and failures. Chemical biology, drug discovery, screening jargon and terms :20 Case study: Phenotypic assay development and screening 10:20-10:30 Break Lecture: Reagent characterisation and selection of assays which will ensure translation of hits between formats 11:00-12:00 Overview of practical work for day one and creation of groups for practical work: General concepts and application of chemical biology and drug discovery assays Pharmacology of standard compounds, signal stability, choice of liquid handling, Z calculation and proof-of-concept screen 12:00-12:15 Talk from Vendor (optional) 12:15-13:15 Lunch 13:15-17:00 Experimental work 17:00 Group Dinner Day Two 9:00-10:00 Discuss results from day one 10:00-10:30 Lecture: Data analysis and reduction - going beyond the Z. Discuss methods to analysing in vitro biological assays data including false positive/negative rates, dose-response curve fitting and correlations 10:30-11:00 Case study: Analysis of assay data Break 11:15-12:15 Overview of practical work for day two Continued from previous day 12:15-13:15 Lunch 13:15-13:30 Talk from Vendor (optional) 13:30-18:00 Experimental work 18:00 Free evening Day Three 9:00-10:00 Discuss results from previous day 10:00-12:00 Case study: Analysis of assay data 12:00-12:15 Talk from Vendor (optional) 12:15-13:15 Lunch Lecture: Integrating your research program, design of project critical paths which integrate in-vitro, in-vivo and in-silico elements 14:00-15:00 Each team to compare results and identify lessons from practical course, presentations from each team and wrap up

9 About the Scientific Coordinator Sheraz Gul is Head of Biology at European ScreeningPort, Hamburg, Germany where he manages the assay development and screening of academic targets. Prior to this, he worked for GlaxoSmithKline for seven years where he developed biochemical and cellular assays for high throughput screening as well as hit characterisation. In addition he has worked in academia for five years on proteases and kinases. He is the co-author of the Enzyme Assays: Essential Data Handbook. He is also involved in many European drug discovery initiatives involving government, Pharmaceutical industry and academia (e.g. EU Framework 7 and IMI). His research interests are directed towards maximising the impact of HTS for drug discovery. sheraz.gul@screeningport.com The Practical Workshop: Chemical Biology, Drug Discovery and Screening is approved by the Society of Biology for purposes of Continuing Professional Development (CPD) and may be counted as 72 CPD credits if registered on the Society of Biology CPD Scheme.

10 REGISTRATION FORM Chemical Biology, Drug Discovery & Screening October 2013 European Screening Port, Hamburg, Germany 4 EASY WAYS TO REGISTER Website: workshops@russellpublishing.com Phone: +44 (0) Fax: +44 (0) CHEMICAL BIOLOGY, DRUG DISCOVERY & SCREENING WORKSHOP PACKAGE 2,250 + VAT Pharmaceutical Industry Rate 1,500 + VAT Academic Rate 1,000 + VAT Post Graduate Rate Discount Code: Package includes: 3 days of practical sessions using the latest technology available from the top screening equipment / reagent vendors in the pharmaceutical industry 3 nights accommodation All meals and refreshments Supporting workshop materials YOUR REGISTRATION (For additional bookings please photocopy this form) Title: First Name: Family Name: Job Title: Company Name: Job Type: Company Type: Address/PO Box: Town: Postcode/Zip Code: City/State: Country: Telephone: VAT Number: Where did you hear about this event? Advert in Magazine Web Search Forwarded By A Colleague LinkedIn Facebook Twitter Other (Please specify) ARE YOU A MEMEBER OF ANY ASSOCIATIONS? (Please specify) HOW TO PAY bank transfer - full details of the bank transfer options will be given with your invoice on registration SIGNATURE: (MANDATORY) DATE: Terms and Conditions By proceeding with this registration you are committing to placing an order to attend the Workshop at the charge shown above. Payment must be received before the event in order to secure your place. Cancellations must be in writing to fwhite@ russellpublishing.com. Cancellations received 28 days before the event will be subject to an admin istration charge of 25% of the registration fee. It is regretted that cancellations made after this time will have to pay the full registration fee. Substitu tions may be made at any time. If the event is postponed, cancelled or changed, European Screening Port is not liable for any costs incurred by delegates in connection with their attendance. No refunds of the registration fee will be paid if events outside the control of European Screening Port, such as transport disruption, weather, terrorism or any other incidents of force majeure occur leading to the cancellation or disruption of the Workshop. The organisers reserve the right to charge the full rate on all unpaid bookings that are more than one month old. VAT: Under EU VAT regulations guests are required to pay VAT at the prevailing local rate on any event taking place within the EU. Guests may be entitled to reclaim this cost, which can make a significant reduction on your attendance costs. If you require help with this please contact us. Information you supply to European Screening Port may be used for publication (where you provide details for inclusion in our directories or catalogues and on our websites) and also to provide you with information about our products or services in the form of direct marketing activity by phone, fax, or post. Information may also be made available to 3rd parties on a list lease or list rental basis for the purpose of direct marketing. If at any time you no longer wish to receive anything from European Screening Port or to have your data made available to 3rd parties, please write to the Data Coordinator, European Screening Port, Court Lodge, Hogtrough Hill, Brasted, Kent TN16 1NU.