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Foreword: DNA-Encoded Chemical Libraries: Past, Present, and Future

DOI: 10.1055/sos-SD-241-00256

Neri, D.Science of Synthesis: DNA-Encoded Libraries, (202411.

It is a great pleasure and honor for me to write a foreword to this volume, edited by long-term collaborators and friends, PD Dr. Jörg Scheuermann and Prof. Dr. Yizhou Li. A comprehensive volume, covering key concepts and technologies focused on DNA-encoded chemical libraries (DELs), is extremely timely, considering the relevance that DELs have gained both in industry and in academia.

The discovery of ligands that bind to target proteins of interest with sufficiently high affinity and specificity is a fundamental problem and challenge in chemistry, with profound implications and applications for pharmaceutical sciences, biology, medicine, and material sciences. Indeed, protein ligands represent the basis for the discovery and development of drugs, for the mechanistic investigation of biological processes, and for the generation of novel affinity capture supports, to mention just a few important fields of application. DEL technology has already revolutionized the ligand-discovery field and promises to play an even more important role in the future.

DNA-encoded chemical libraries are collections of organic compounds, individually tagged with DNA fragments that serve as amplifiable identification barcodes. As each library member can be identified and quantified by means of the cognate DNA tag, compounds can be stored and screened as a mixture, without a need for the complex and expensive logistics and instrumentation that are characteristic of high-throughput screening (HTS) of traditional chemical libraries. While it is difficult (even for the largest pharmaceutical companies) to perform HTS discovery campaigns with more than one million molecules, DEL technology allows the construction and screening of compound libraries with more than one billion library members. As the late Richard A. Lerner used to say, the “Chemistry of Big Numbers” facilitates the discovery of protein ligands, as the experimental interrogation of many compounds increases the probability of discovering one or more molecules that selectively recognize the target protein of interest.

DEL technology was certainly inspired by advances in peptide and antibody phage display libraries (for which George P. Smith and Sir Gregory P. Winter shared the Nobel Prize in Chemistry in 2018, along with Frances H. Arnold for her work on directed evolution). The display of polypeptides on filamentous phage allows the creation of bacterial viruses, which may contain a binding moiety on their surface (“phenotype”) and, at the same time, the corresponding genetic information (i.e., the coding DNA) inside the phage particle. By constructing combinatorial libraries comprising billions of different binding specificities (each intimately associated with the corresponding DNA information), one enables the selection of phage particles specific to the target of choice by means of affinity capture procedures, using protein coated on a solid support, such as magnetic beads. DEL technology applies a conceptually similar procedure to the realm of small organic molecules.

DEL technology was first described in 1992 in a seminal theoretical paper by Richard A. Lerner and Sidney Brenner, which envisaged the construction of peptide libraries on beads, which simultaneously carried a DNA fragment serving as barcode.[‌1‌] The technology was experimentally enabled by the synthesis and screening of model compounds of known binding specificities. However, the practical construction and de novo selection of DELs had to wait 12 years, when both our laboratory at ETH Zürich[‌2‌,‌3‌] and the laboratory of David R. Liu at Harvard University[‌4‌] published articles describing this. Other companies were working on DEL at the same time (e.g., NuEvolution and Praecis), but their publications emerged a few years later.[‌5‌] Collectively, however, these efforts and articles facilitated the implementation of DEL technology in many academic and industrial groups. It became rapidly obvious that DELs can be constructed and screened in a variety of different ways, as beautifully illustrated by the articles presented in this volume.

Much of the popularity of DEL technology is due to the fact that library construction and screening activities are much cheaper and faster, compared to conventional HTS procedures. Hundreds of protein targets have been successfully screened using DEL technology, yielding ligands which have been used in basic research or which have been moved (after medicinal chemistry optimization) to industrial development programs (e.g., clinical trials). These success stories should not make us believe that DEL research has reached its level of maturity and that we can now stop. There are still proteins for which the discovery of high-affinity ligands is not possible. Moreover, certain aspects of the technology (e.g., use of DNA barcodes in single-stranded or double-stranded format, screening by affinity-capture or by alternative methodologies) have not yet been studied in a sufficiently large number of comparative evaluations, in order to make definitive statements regarding “best practices” that should be followed. Even a simple (but important) issue, such as the impact of the number of copies of individual compounds in a library on DEL selection performance, has been described in only few publications, and more work on this topic is urgently needed.

At this moment in time, it is fair to say that DELs of good quality have been created and that ligands with potency in the subnanomolar concentration range can be found for a large proportion of target proteins of interest. Where will the field evolve from here? What are the most important open issues? Without having the ambition to present a comprehensive list, I believe that the following topics will continue to keep researchers occupied for a number of years, contributing to continuous improvements in DEL performance:

• The discovery and validation of DNA-compatible chemical reactions and methods

• The development of novel library screening methods

• The design and construction of high-performance libraries

• The use of DEL technology for affinity-maturation/lead expansion strategies

• The encoding of novel chemical matter (e.g., polypeptides and other polymers)

• The use of DEL technology for novel applications

On this last topic, it is intriguing to see that DNA barcodes have been used for a variety of ingenious applications, such as the characterization of T-cell specificities by means of DNA-encoded MHC/peptide multimers[‌6‌] and the barcoding of expensive goods (e.g., oil, jewelry, clothes, accessories) to prevent forgery or theft.[‌7‌]

This volume provides the interested reader with accurate accounts and detailed experimental procedures that will enable repetition and improvements anywhere in the world. I am convinced that the pages of this volume will inspire the design and implementation of many new and important experimental schemes. Jörg and Yizhou, as well as all the contributors of individual chapters, should be commended for their excellent work.