Chemical and Biological Synthesis

Enabling Approaches for Understanding Biology

Nick J Westwood, Adam Nelson

• Publisher: Royal Society of Chemistry
• Year: 2018
• eBook ISBN: 9781788015073
• Edition: 1
• Topic: Physical Sciences
• Subtopic: Biochemistry

Synthetic chemistry plays a central role in many areas of chemical biology; utilising recent case studies, the goal of Chemical and Biological Synthesis is to highlight the full impact that the preparation of novel reagents can have in chemical biology. Covering the synthetic approaches that can be applied across the whole field of chemical biology, this book provides synthetic chemists with the broader context to which their work contributes and the biological questions that can be addressed through it. An ideal guide for postgraduate students and researchers in synthetic organic chemistry and chemical biology, Chemical and Biological Synthesis introduces synthetic techniques and methods to those who wish to incorporate synthesis for the first time in their biology-focused research programmes.

Section 1:
Synthetic Approaches to Enable
Small-molecule Probe Discovery

CHAPTER 1

Synthetic Tools for the Elucidation of Biological Mechanisms

NICHOLAS WESTWOOD^*a,b AND ADAM NELSON,^*c,d

^a School of Chemistry, University of St Andrews, North Haugh, St Andrews KY16 9ST, UK;

^b Biomolecular Sciences Research Complex, University of St Andrews, North Haugh, St Andrews KY16 9ST, UK;

^c School of Chemistry, University of Leeds, Leeds LS2 9JT, UK;

^d Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
*Email: [email protected]; [email protected]

1.1 Context

The elucidation of the molecular basis of biological mechanisms is an enduring theme in biomedical science. Although there are as few as approximately 19 000 protein-coding human genes,¹ whose corresponding proteins have been mapped in many tissue types,² biological mechanisms are remarkably complex. This complexity arises, in part, from the functional relevance of macromolecular complexes: the number of pairwise protein–protein interactions in humans has been estimated to be approximately 650 000,³ the vast majority of which have not been functionally annotated. Moreover, biological macromolecules and processes are highly dynamic,⁴ operating across many different timescales, and are often physically separated via compartmentalisation. In addition, the regulation of biological mechanisms is often achieved through many different post-translational modifications of the participating proteins.⁵

Against this backdrop, increased innovation⁶ and productivity⁷ have been framed as major challenges for the pharmaceutical sector. Despite spiralling investment, the rate of drug discovery has remained roughly constant over the past 60 years.⁸ Future innovation in drug discovery is likely to rely on the identification and validation of new protein targets (and classes of target) that may then be translated into drugs with novel mechanisms of action. However, the biology of proteins has historically been investigated in a highly uneven and unsystematic manner.⁹ For example, across three protein classes that are central to disease—protein kinases, ion channels and nuclear hormone receptors—biologists’ favourite proteins have remained broadly the same for the last 50 years! Crucially, the use of high-quality chemical probes^10–12 has been shown to be one of the few approaches that can change which proteins are the subject of biomedical research.

This book focuses on synthetic approaches that can facilitate the elucidation of biological mechanisms. The nature of the biomolecules that may be prepared using these approaches is extremely wide-ranging: from small-molecule probes through to large site-specifically modified macromolecular complexes. A wide-ranging toolkit is therefore featured, including synthetic and enzymatic approaches, both in isolation and in combination. Throughout, the power of the synthetic approaches is showcased in the context of the elucidation of specific biological mechanisms.

1.2 Synthetic Approaches to Enable Small-molecule Probe Discovery

The availability of high-quality small-molecule probes can have a disruptive effect on which proteins are the subject of fundamental biomedical research.^10–12 The key characteristics of high-quality probes include high in vitro potency and selectivity, a defined mechanism of action and demonstrated utility in cells. In addition, it is important that physical samples of probes are readily available, ideally together with structurally-related controls. The Chemical Probes Portal has been established to assist biomedical scientists to identify appropriate small-molecule probes for specific biological investigations.

The challenge of discovering new small-molecule probes is heightened because chemical space is vast, but has been historically explored very unevenly and unsystematically.¹³ However, despite consensus on the vastness of chemical space, estimates of the number of possible drug-like molecules vary extremely widely. In one study,¹⁴ extrapolation from GDB-17 (a database¹⁵ of approximately 10¹¹ enumerated molecules with up to 17 heavy atoms) led to an estimation of approximately 10³³ drug-like small molecules with up to 36 heavy atoms. How, then, can chemical space be explored productively in the quest for novel chemical probes? Section 1 of the book covers a range of strategies that has been devised to address this problem.

Chapter 2 opens by introducing different types of molecular diversity, as well as diversity-oriented synthesis strategies that enable the exploration of diverse regions within chemical space. Alternative approaches that can improve the productivity of exploration of chemical space are then covered. For example, in biology-oriented synthesis (Chapter 3), the focus is placed on scaffolds related to the (necessarily) biologically-relevant frameworks that are found in natural products. In contrast, the searching problem may be reduced by focusing on specific molecular property space (e.g. fragment- or lead-like chemical space) relevant to the specific discovery application (Chapter 4). In Chapter 5, the practice of harnessing fragment-based approaches in the discovery of high-quality chemical probes is showcased through a series of case studies. Chapter 6 then describes recently-disclosed discovery approaches in which diverse chemical space is explored in a structure-blind manner, with bioactive ligands emerging (together with associated syntheses) on the basis of function alone. Two complementary technologies that can enable bioactive molecular discovery are then covered: DNA-encoded synthesis, in which the resultant very large libraries of small molecules are attached to a DNA “barcode” (Chapter 7) and automated synthetic approaches, including those that may be integrated with functional evaluation (Chapter 8; the automated synthesis of carbohydrates is covered in Chapter 10). Each of these complementary approaches can provide useful starting points for the discovery of novel chemical probes for interrogating specific biological mechanisms.

1.3 Synthetic Approaches to Classes of Modified Biomolecule

Section 2 of this book introduces complementary approaches for the synthesis of modified analogues of different classes of biomolecule. Here, focus is placed on amino-acid- and sugar-based biomacromolecules; more detailed reports on the chemistry of nucleic acids are reported elsewhere in the RSC Chemical Biology series. The first part of Section 2 focuses on technologies that enable the discovery of biomolecules that reside in beyond-rule-of-five chemical space. Chapter 9 describes platforms for preparing and screening libraries of genetically-encoded cyclic peptides, including split-intein-mediated cyclization of peptides and proteins (SICLOPPS), phage display and mRNA display technologies. The reader is also referred to a related book¹⁶ in this series that is specifically focused on the synthesis and applications of cyclic peptides. In Chapter 10, a comprehensive review of carbohydrate-based compounds is provided, including an up-to-date assessment on the state of automated synthetic approaches. Chapter 11 provides an overview of the modification of biosynthetic pathways to deliver novel compounds that are derivatives of natural products. This chapter is complementary to the synthetic approaches to explore natural-product-related chemical space that are featured in Chapter 3.

Section 2 concludes with an overview of approaches that enable the preparation of site-specifically modified proteins (and their complexes). In Chapter 12, the toolkit of methods that enables the site-specific chemical modification of proteins—both in vitro and in a cellular context—is introduced. This toolkit can be exploited in a wide range of applications, for example in the discovery and validation of protein targets using chemical proteomics. In contrast, site-specifically modified anal...

Table of contents

• Cover
• Title
• Copyright Page
• Contents
• Section 1: Synthetic Approaches to Enable Small-molecule Probe Discovery
• Section 2: Synthetic Approaches to Classes of Modified Biomolecule
• Subject Index