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Management of Chemical and Biological Samples for Screening Applications

Mark Wigglesworth (Editor), Terry Wood (Editor)
ISBN: 978-3-527-32822-2
432 pages
April 2012
Management of Chemical and Biological Samples for Screening Applications (352732822X) cover image
Filling an obvious gap in the scientific literature, this practice-oriented reference is the first to tie together the working knowledge of large
screening centers in the pharmaceutical and biotechnological field. It spans the entire fi eld of this emerging discipline, from compound
acquisition to collection optimization for specific purposes, to technology and quality control. In so doing, it applies two decades of expertise gathered by several large pharmaceutical companies to current and future challenges in high-throughput screening. With its treatment of libraries of small molecules as well as biobanks containing biomolecules, microorganisms and tissue samples, this reference is universally applicable for any molecular scientist involved in a large screening program.
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Preface XIX

List of Contributors XXIII

1 Introduction to Sample Management 1
William P. Janzen and Andy Zaayenga

References 6

2 Generating a High-Quality Compound Collection 9
Philip B. Cox and Anil Vasudevan

2.1 Defining Current Screening Collections 9

2.2 Design Criteria for Enriching a Compound Collection with Drug-Like Compounds 10

2.3 Concluding Remarks 20

References 20

3 Assessing Compound Quality 23
Ioana Popa-Burke, Stephen Besley, and Zoe Blaxill

3.1 Introduction 23

3.2 Process Quality and Analytical Quality in Compound Management 24

3.3 Identity 28

3.4 Purity/Stability 32

3.5 Concentration/Solubility 39

3.6 Conclusions 41

Acknowledgments 41

References 42

Further Reading 44

4 Delivering and Maintaining Quality within Compound Management 45
Isabel Charles

4.1 Introduction 45

4.2 What is Quality from a Compound Management Perspective? 46

4.3 Storage and Delivery of Samples in Solution 47

4.4 Intercepting Low Purity 49

4.5 Storage and Delivery of Solids 51

4.6 Automation Quality Control and Reliability 52

4.7 High-Quality Data Management 54

4.8 Conclusion 55

Acknowledgments 56

References 56

5 Obtaining and Maintaining High-Quality Tissue Samples: Scientific and Technical Considerations to Promote Evidence-Based Biobanking Practice (EBBP) 59
Lisa B. Miranda

5.1 Introduction 59

5.2 The Path toward Integration of Evidence-based Biobanking Practice 62

5.3 Integrating Evidence-based Biobanking Practice into Sample Protocols 66

5.4 Final Thoughts and Recommendations 74

References 79

6 Thinking Lean in Compound Management Laboratories 83
Michael Allen

6.1 The Emergence of ‘Lean Thinking’ 83

6.2 The Application of ‘Lean Thinking’ 83

6.3 Lean Thinking in Drug Discovery 86

6.4 A Lean Laboratory Toolbox 87

6.5 Streamlining Compound Processing –An Example 101

6.6 Summary 103

References 105

7 Application of Supply Management Principles in Sample Management 107
Paul A. Gosnell

7.1 Introduction 107

7.2 Common Pitfalls of Sample Management 107

7.2.1 One Size Does Not Fit All 108

7.3 Sample Management and Supply Chain Concepts 108

7.4 Implementing the Sample Management Strategy 111

7.5 Sample Management Organization 111

7.6 Sample Management Informatics 113

7.7 Avoid Monolithic Silos of Excellence 114

7.8 Position and Synchronize Inventory 115

7.9 Expand the Sample Management Boundary 117

7.10 Measuring and Assessing Effectiveness and Quality 118

7.11 Conclusions 119

References 120

8 Solid Sample Weighing and Distribution 121
Michael Gray and Snehal Bhatt

8.1 The Practicalities and Technology of Weighing Solid Compounds 121

8.2 Logistical Challenges of Transportation of Small Molecules 127

References 142

9 Managing a Global Biological Resource of Cells and Cellular Derivatives 143
Frank P. Simione and Raymond H. Cypess

9.1 Introduction 143

9.2 Diversity of Collections 144

9.3 Sourcing and Acquisition 148

9.4 Authentication and Characterization 149

9.5 Cryopreservation, Storage, and Production 153

9.6 Data Management 154

9.7 Quality and Standards 155

9.8 Order Fulfillment and Distribution 157

9.9 Offsite Biorepository Management 158

9.10 Regulatory and Legal Compliance 159

9.11 Ownership and Intellectual Property Management 160

9.12 Collaborations 161

9.13 Conclusion 162

References 163

10 Development of Automation in Sample Management 165
Gregory J. Wendel

10.1 Introduction 165

10.2 Historical Background 165

10.3 Automation of Sample Management Today 167

10.4 System Building Blocks 169

10.5 Storage Systems 171

10.6 Liquid Handler 175

10.7 Accessories 180

10.8 Plate Handling, Integration 184

10.9 Case Study: Evolution of a Compound Management Group 186

10.10 Results 196

References 197

11 Applications of Acoustic Technology 199
Eric Tang, Colin Bath, and Sue Holland-Crimmin

11.1 Introduction 199

11.2 Compound-Handling Challenges in Drug Discovery 201

11.3 Acoustic Drop Ejection –Performance, Quality Assurance, and Platform Validation 203

11.4 Acoustic-Assisted Compound Solubilization and Mixing 206

11.5 Acoustic Applications in Drug Discovery 209

11.6 Emerging Applications 216

References 218

12 Enhancing Biorepository Sample Integrity with Automated Storage and Retrieval 221
Johann van Niekerk

12.1 The Emerging Growth of Biobanking 221

12.2 Automated Storage and Retrieval in a Biorepository 225

12.3 Configuration of an Automated Biorepository 236

12.4 Conclusions 241

References 241

13 Information Technology Systems for Sample Management 243
Brian Brooks

13.1 Sample Registration 243

13.2 Intellectual Property and Laboratory Notebooks 253

13.3 Some Observations on Information Technology 254

13.4 Biological Data Management 255

Dedication and Acknowledgments 263

14 Key Features of a Compound Management System 265
Clive Battle

14.1 Why Do We Need Compound Management Information Technology Systems? 265

14.2 Compound Management Software 266

14.3 Benefits of Commercially Available Compound Management Systems 272

References 273

15 What Does an HTS File of the Future Look Like? 275
François Bertelli

15.1 Introduction 275

15.2 History of Compounds Collection for HTS 276

15.3 Impact of High-Throughput Chemistry on Corporate Files 277

15.4 Chemical Library Management 278

15.5 The Concept of Drug-Likeness and the Lipinski Rules 279

15.6 Quality versus Quantity 283

15.7 The Emergence of the Subsets: Fragment, G-Protein-Coupled Receptor (GPCR), Ion Channel, Kinase, Protein–Protein Interaction, Chemogenomics, Library Of Pharmacologically Active Compounds (LOPAC), Central Nervous System (CNS), and Diversity 285

15.8 Re-designing the Corporate File for the Future 291

15.9 Future Routes for Hit Identification 299

References 301

16 New Enabling Technology 305
Neil Hardy, Ji Yi Khoo, Shoufeng Yang, Holger Eickhoff, Joe Olechno, and Richard Ellson

16.1 Introduction 305

16.2 A Drop-On-Demand Printer for Dry Powder Dispensing 307

16.3 Piezo Dispense Pens: Integrated Storage and Dispensing Devices and their Potential in Secondary Screening and Diagnostic Manufacturing 312

16.4 Future Directions in Acoustic Droplet Ejection Technology 323

16.5 Closing Remarks 347

References 347

17 The Impact of Future Technologies within Biobanking 351
Manuel M. Morente, Laura Cereceda, and Mar´ıa J. Artiga

17.1 Introduction 351

17.2 The Role of Biobanks in Biomedical Research 351

17.3 The Increasing Complexity of Biobanking 354

17.4 Future Technologies and Biobanking: How Could New Technologies Affect the Daily Activities of Biobanks? 356

17.5 The Future of Biobanking Does Not Depend on Technological Developments Alone 363

17.6 Conclusions 364

Acknowledgments 364

References 364

18 Outsourcing Sample Management 367
Sylviane Boucharens and Amelia Wall Warner

18.1 Outsourcing in the Pharmaceutical Industry 367

18.2 Outsourcing Biological Specimen Collections 374

18.3 Conclusions 378

Acknowledgments 378

References 378

19 Sample Management Yesterday and Tomorrow 381
Terry Wood and Mark Wigglesworth

19.1 The Role of Sample Management 381

19.2 Automation of Compound Management 382

19.3 Compound Integrity 384

19.4 Reduction of Redundancy 386

19.5 The Future of Sample Management? 387

19.6 Concluding Remarks 390

References 391

Index 393

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Mark Wigglesworth manages the UK Lead Optimization area of Sample Management Technologies for GlaxoSmith-Kline. Over the past 10 years Mark has managed large and small compound stores, assay ready plate production and compound set provision, as well as interacting with many areas of drug discovery. Additionally, he has led several drug discovery programs and overseen multiple screening platforms providing structure activity relationship data within GlaxoSmithKline?s screening organizations.

Now a freelance business consultant, Terry Wood retired in 2011 as the manager of the Liquid Store Centre of Emphasis at Pfizer?s world-wide R&D department, based in Sandwich (UK). He has been involved in the high-throughput screening process for the whole of his 25 year career with Pfizer. This has given him a first hand and broad knowledge about the challenges and caveats of assay design, development and
prosecution. His prime responsibility focused on the management of Pfizer?s extensive compound file, using a range of automated systems for sample preparation, storage and delivery.
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“In the same vein, the chapters on new and enabling technologies, as well as how best to approach the options for outsourcing samples serve to provide a complete overview of all aspects of this discipline and complete the overall picture for the reader.”  (ChemBioChem, 1 January 2013)

“The book is a useful tool for any sample management organization, and will be particularly helpful as a guide for both updating the already existing structures and for planning future infrastructures dedicated to sample management.”  (Annali, 2012)

 

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