Preface Free

Since the development of molecular biology and the ability to study single proteins on an atomic level, it has emerged that most small-molecule drugs and many pharmacologically active natural products exert their often profound phenotypic effects on cells and organisms by modulating the function of a single or small number of protein targets critical to cellular function. This knowledge sparked the modern era of (protein) target-based drug discovery and efforts to treat human disease have since paired molecular/cellular biology (MCB) and synthetic/medicinal chemistry (Med Chem) as a means of identifying disease-causing proteins in relevant cells and tissues and correct their function with bespoke small molecules, often antagonists or inhibitors. Over the following decades, the relationship between these experimentally very different disciplines has matured and produced scores of offspring: the medicines developed since the 1980s that have had such a huge impact on human health, increased lifespan and life quality.

However, the development of small molecules as modulators of protein function has not been limited in utility to the production of new medicines. Small molecules that show an effect on a specific target with certain potency and selectivity criteria do not necessarily need to fulfil all the requirements needed to become a drug, but instead they can be used as tool compounds, or what are now called chemical probes. These chemical probes can act as the keys to unlock the elusive and fractally complex secrets of cells and entire organisms.

A variety of compound sources have led to the discovery of chemical probes. In the biopharmaceutical industry, for example, where most small-molecule medicines are discovered, the intermediate forms in drug discovery –the hits, leads and candidates of pharma jargon – designed and made en route to the final medicine are extraordinarily useful in deciphering the complex disease biology in preclinical cellular and animal models. Historically, these proto-drugs were buried in patents and obscured by incomplete disclosure of biological potency and selectivity.

In parallel with mostly industry-led drug discovery, natural product chemists, primarily in academia, were discovering their own chemical probes. From the 1980s, despite the importance of natural product synthesis in training biopharma's army of medicinal chemists, it became more and more difficult to justify funding natural product synthesis as an end in itself. Hence synthetic organic chemists looked for other means to justify their obsession with Nature's own pharmacopoeia of complex secondary metabolites. More and more natural and semi-natural products were tested for their biological activity, with many showing cytotoxicity towards cancer and other cell types. What was more intriguing than their cytotoxicity was how these compounds killed cells, shedding light on the intricacies of the cell cycle, signalling and transport. Paclitaxel stabilizes microtubules and prevents cell-cycle progression; rapamycin forms a complex with FKBP12 and inhibits mTOR to prevent cell growth; epoxomicin selectively inhibits the proteasome; and brefeldin A prevents ARF1 GTPase reactivation and thereby vesicle transport. All of these natural products highlighted the importance of their respective targets and pathways on cellular physiology. Some of them led to the development of medicines (paclitaxel to Taxol, rapamycin to Rapamune, epoxomicin to Kyprolis), but they all showed unexpected mechanisms of action for small molecules on protein targets. Another extraordinary mechanism of action was shown by Craig Crews at Yale with his synthetic proteolysis-targeting chimeras (PROTACs), designed to induce protein degradation by tagging target proteins for destruction by the ubiquitin–proteasome system.

Seminal work from Tim Wilson (GlaxoSmithKline) and Stuart Schreiber (Harvard) in the late 1990s brought these nascent chemical probe strands together. Wilson's “reverse endocrinology” with nuclear hormone receptor ligands and Schreiber's “chemical genetics” with natural product-inspired scaffolds laid out the philosophy and groundwork of the field of chemical probes as it exists today. Essentially, potent and selective small molecules are not just medicines, failed medicines or substances with curious pharmacology, but are powerful and, critically, simple-to-use chemical probes for interrogating protein targets in complex biological systems. Expanding the haphazard collection of chemical probes discovered by chance and semi-rationally by natural product and medicinal chemists to the entire druggable genome, a goal still not yet realized, would allow us to interrogate and understand cell biology in extraordinary new ways. An extremely ambitious multi-collaborative project, Target 2035, is a global federation for developing and applying new technologies with the goal of creating chemical probes or antibodies for the entire proteome. Target 2035 is notable in its ambition, but also in the membership of the consortium. The mix of industry and academia shows that big pharma is no longer just burying priceless chemical probes in patents, but actively getting them into the laboratories of researchers worldwide, including their own competitors.

In this book, the authors review and exemplify the discovery and use of chemical probes as it exists today. Chapter 1 provides a background on the utility of chemical probes and presents the criteria for high-quality probes and different probe sources and databases available to the scientific community. Chapter 2 shows how the use of DNA-encoded libraries has expanded the breadth and depth of the protein targets available to chemical probe development. Chapter 3 reviews how computational tools are critical to the discovery of chemical probes. In Chapter 4, methodologies for the discovery and unique advantages of covalent chemical probes are presented. The rapidly developing field of peptidic chemical probes, which further expands chemical probe target scope, is reviewed in Chapter 5. In Chapter 6, an elegant case study of the derivatization of a natural product is used to untangle its unusual mechanism of cytotoxicity. Chapter 7 presents the principles and discovery of PROTACs, a field that grown exponentially in the last decade and has potential for enormous impact in new medicines and chemical probes. In Chapter 8, chemical probes and drugs for kinases, a protein family of enormous interest in drug discovery, are reviewed. Chapter 9 shows how small-molecule chemical probes can interrogate RNA as well as protein function. In Chapter 10, assays to understand chemical probes in native cellular environments are reviewed. Finally, in Chapter 11, the use of chemical probe libraries in phenotypic screening in cells is presented, with a focus on cellular models of neurodegeneration. Collectively, the principles, methods and examples in this book present a comprehensive picture of how chemical probes are used in biological and medical research today and offer a glimpse of how the field will evolve to achieve true chemical genetics when we have a chemical probe for every targetable protein encoded in the genome.

Paul Brennan and Saleta Vazquez Rodriguez