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This book comprehensively describes the development and practice of DNA-encoded library synthesis technology. Together, the chapters detail an approach to drug discovery that offers an attractive addition to the portfolio of existing hit generation technologies such as high-throughput screening, structure-based drug discovery and fragment-based screening. The book: Provides a valuable guide for understanding and applying DNA-encoded combinatorial chemistry Helps chemists generate and screen novel chemical libraries of large size and quality Bridges interdisciplinary areas of DNA-encoded combinatorial chemistry – synthetic and analytical chemistry, molecular biology, informatics, and biochemistry Shows medicinal and pharmaceutical chemists how to efficiently broaden available "chemical space" for drug discovery Provides expert and up-to-date summary of reported literature for DNA-encoded and DNA-directed chemistry technology and methods
This volume discusses protocols that cover synthesis, screening by selection, and analysis of DNA-encoded chemical libraries (DEL). Chapters in this book focus on methods used to practice DEL technology and include solution phase library synthesis using a variety of chemistries; DNA encoding of chemical structure; design, preparation and analysis of target proteins and tool compounds; screening of soluble protein targets by affinity selection; DEL qPCR, preparative PCR and DNA sequence analysis; computational methods used to analyze selections and choose compounds for resynthesis; and analysis of hit compounds. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Cutting-edge and comprehensive, DNA-Encoded Chemical Libraries: Methods and Protocols is a valuable resource for scientists interested in DEL technology for drug discovery, and will contribute to the continued advancement in this important field.
Techniques and methods employed in the preparation and application of DNA-Encoded Libraries. DNA Encoded Libraries (DELs) have transformed the way we explore chemical space, accelerating drug discovery and innovation. This volume contains a collection of articles, bringing together many of the leaders in the field, from both industry and academia, to explore the cutting-edge techniques, strategies, and applications that are reshaping the landscape of chemical synthesis. The volume covers many aspects of this rapidly expanding field, from DNA-compatible organic reactions to innovative encoding methods and setup strategies, selection procedures, and advanced chemoinformatic techniques. Whilst background information is provided, the focus of the articles is on the techniques and methods: experts in the field present selected procedures, showing the state of the art in each area covered. This volume is an indispensable resource for chemists, researchers, and professionals seeking to stay at the forefront of chemical synthesis and drug discovery.
This book comprehensively describes the development and practice of DNA-encoded library synthesis technology. Together, the chapters detail an approach to drug discovery that offers an attractive addition to the portfolio of existing hit generation technologies such as high-throughput screening, structure-based drug discovery and fragment-based screening. The book: Provides a valuable guide for understanding and applying DNA-encoded combinatorial chemistry Helps chemists generate and screen novel chemical libraries of large size and quality Bridges interdisciplinary areas of DNA-encoded combinatorial chemistry – synthetic and analytical chemistry, molecular biology, informatics, and biochemistry Shows medicinal and pharmaceutical chemists how to efficiently broaden available “chemical space” for drug discovery Provides expert and up-to-date summary of reported literature for DNA-encoded and DNA-directed chemistry technology and methods
An amphiphilic DNA encoding platform was developed that allows the high-throughput evaluation of a large small-molecule library for a wide assortment of catalytic reactions in organic solvents. The cornerstone of this platform is a replicable, amphiphilic DNA that encodes a chemical library. Each member of the library is uniquely identifiable via a covalent attachment of encoded DNA (genotype) and small-molecule catalyst (phenotype). The amphiphilic nature of the DNA-encoded small-molecule library stems from the development of a PEG polymer that enables solubility in both aqueous and organic solvents. In vitro selection enables catalytically active members surviving the selection pressure 0́3 intermolecular bond formation of the DNA code to an affinity tag 0́3 to be separated from inactive members, PCR amplified and identified by high-throughput DNA sequencing. We explored the solubility, stability, and thermodynamics of PEGylated ssDNA in organic solvents, investigated the compatibility of PEGylated DNA as an encoding element during catalytic reactions in organic solvents, and developed methods to generate and screen a PEGylated DNA-encoded peptide library for catalytic activity in organic solvents.
Fragment-based drug discovery is a rapidly evolving area of research, which has recently seen new applications in areas such as epigenetics, GPCRs and the identification of novel allosteric binding pockets. The first fragment-derived drug was recently approved for the treatment of melanoma. It is hoped that this approval is just the beginning of the many drugs yet to be discovered using this fascinating technique. This book is written from a Chemist's perspective and comprehensively assesses the impact of fragment-based drug discovery on a wide variety of areas of medicinal chemistry. It will prove to be an invaluable resource for medicinal chemists working in academia and industry, as well as anyone interested in novel drug discovery techniques.
In The Aptamer Handbook, leading scientists from academia as well as biotech and pharma companies introduce the revolutionary concept of designing RNA and DNA oligonucleotides with novel functions by in vitro selection. These functions comprise high affinity binding (aptamers), catalytic activity (ribozymes and deoxyribozymes) or combinations of binding and catalytic properties (aptazymes). Basic concepts and technologies describing in detail how these functional oligonucleotides can be identified are presented. Numerous examples demonstrate the versatility of in vitro selected oligonucleotides. Special emphasis has been put on a section that shows the broad applicability of aptamers, e. g. in target validation, for analytics, or as new therapeutics. This first overview in the field is of prime interest for a broad audience of scientists both in academia and in industry who wish to expand their knowledge on the potential of new oligonucleotide functions and their applications.
Edited by a leading authority in the field, the first book on this important and emerging topic provides an overview of the latest trends in sequence-controlled polymers. Following a brief introduction, the book goes on to discuss various synthetic approaches to sequence-controlled polymers, including template polymerization, genetic engineering and solid-phase chemistry. Moreover, monomer sequence regulation in classical polymerization techniques such as step-growth polymerization, living ionic polymerizations and controlled radical polymerizations are explained, before concluding with a look at the future for sequence-controlled polymers. With its unique coverage of this interdisciplinary field, the text will prove invaluable to polymer and environmental chemists, as well as biochemists and bioengineers.