Preface to the 2nd Edition

During the half dozen years since the 1st edition of this book, prepared in 2016, thousands of research publications on natural product biosynthesis, from all the kingdoms of life, have appeared. Genome mining algorithms have improved biosynthetic gene cluster identification. Gene cluster expression, often in heterologous plant or microbial hosts, and new approaches to rapid structure determination, including exquisitely sensitive mass spectrometry probes along with microelectron diffraction for nanocrystals, have coalesced around de-orphanization of many biosynthetic gene clusters.

This second edition integrates many new findings into the sets of principles of the first edition that parsed categories of natural product chemistries into the underlying enzymatic mechanisms and the catalytic machinery for building the varied and complex end-product metabolites. All of the chapters have been updated with new discoveries, while three of the fifteen chapters are completely new.

Chapter 2 introduces the concept of a core set of thermodynamically activated but kinetically stable metabolites that power both primary and secondary metabolic pathways. These include a variety of different chemical functional groups from phosphoric anhydride linkages in ATP to phosphoric sulfuric anhydrides in phosphoadenosine phosphosulfate (PAPS) and acyl phosphoric anhydride linkages in carbamoyl phosphate. The acyl thioester linkage in acetyl and longer chain acyl-CoAs serve as nature's diffusible acyl transfer currencies. The dihydro oxidation state of the two nicotinamide coenzymes, NADH and NADPH, are thermodynamically poised to oxidatively re-aromatize by direct hydride transfer to cosubstrate carbonyl groups as electrophiles. Among other thermodynamically activated functional groups with sufficient kinetic stability to serve in cell metabolism are the trivalent cationic sulfonium group in S-adenosylmethionine (set up for both heterolytic (two electron) and homolytic (one electron) chemistries), the Δ²-isopentenyl diphosphate as source of allylic carbocations, and nucleoside diphosphohexoses, such as UDP-glucose, which are metabolic donors of C_1′-glycosyl oxocarbenium ion equivalents to cosubstrate nucleophiles. We also categorize molecular oxygen (O₂) in this thermodynamically activated, kinetically stable class of molecules, as a prelude to subsequent reductive metabolism by oxygenases and oxidases (see Chapter 12).

The peptide natural product chapter in the first edition has now been divided into two separate chapters, taking up ribosomally-synthesized and posttranslationally modified peptides (RiPPs) in Chapter 4 and nonribosomal peptide (NRP) assembly-line-generated natural products in Chapter 5. This division reflects the explosion of new RiPP and NRP subtypes from genome mining efforts and the identification of both two-electron and one-electron reaction modes of various groups of tailoring enzymes. In both RiPP and NRP categories, it is the morphing of both canonical and noncanonical amino acid-based floppy acyclic peptides into compact, rigidified architectures that leads to hydrolytically and oxidatively stable altered scaffolds.

The third completely new chapter, Chapter 14, deals with four classes of pericyclases, enzymes that carry out concerted reactions; conversion of substrates to products without any intermediates of discrete lifetimes. These include electrocyclizations or the reverse fragmentations (in vitamin D₃ assembly), cycloadditions (notably via enzyme catalysts such as Diels–Alderases carrying out [4 + 2]-cyclizations), sigmatropic shift enzymes, and Alder-ene H-group transfer enzymes. After decades of uncertainty about the existence of various pericyclase classes, a series of genome mining, heterologous expression, and enzymatic activity characterizations have validated a plethora of pericyclases over the past decade. The several types of pericyclases are involved in biosynthetic complexity generation of almost every major category of natural products.

In addition to the above three totally new chapters, every other chapter has been rewritten, with updates to emphasize novel reactions and biosynthetic mechanisms among the polyketide, isoprenoid, nucleoside, alkaloid, phenylpropanoid, and glycoside groups of natural products. This includes, but is not limited to, Chapter 12, on the many routes for reductive oxygen metabolism. Oxygen reductive chemical biology is all about one-electron chemistry. The modification of hydrophobic natural product scaffolds to hydrophilic products by oxygenation is perhaps the most common type of enzymatic modification in many of the natural product classes. A particularly notable cascading burst of sequential oxygenase action consumes eighteen molecules of O₂ by seven iron-based oxygenases during maturation of the C30 lanosterol metabolite to the C18 estrone female sex hormone.

Chapter 13 likewise provides a deep dive into both the heterolytic and homolytic chemical biology of S-adenosylmethionine (SAM), which makes it a central substrate/cofactor in many types of metabolite framework modifications in natural product scaffold maturations. The two-electron routes involving direct transfer of methyl groups or aminobutyryl groups from SAM to nucleophilic cosubstrate atoms are a justly celebrated hallmark of SAM-based chemical biology for modifying natural product scaffolds. However, there are now some 570 000 predicted protein open reading frames, largely in microbial genomes, that have the features of catalyzing one-electron/homolytic cleavage of SAM into methionine and the 5′-deoxyadenosyl radical (5′-dA˙) in enzyme active sites. The transient, bound 5′-dA˙ initiates a variety of substrate-based radical chemistry across every natural product group and is described in Chapters 3–10 of this second edition. The combined one-electron/two-electron chemistry open to SAM makes it the most widely used substrate/cofactor after O₂ in maturation and tailoring of natural product scaffolds.

This 2nd edition builds on the organizing principles of the 1st edition and focuses on analysis of the prolific capabilities of three major tailoring enzyme classes, oxygenases, S-adenosylmethionine-consuming transferases, and pericyclases, to build a plethora of carbocyclic and heterocyclic fused-ring scaffolds that constitute complex architectures with a wide array of chemical functional groups. The natural product biosynthetic arena, with a renaissance opened up by genome sequencing and genome mining, continues to grow exponentially and present novel structural hybrids and functional group chemistry not seen in primary metabolic pathways, and an array of bioactive novel molecular architectures.

Christopher T. Walsh

Yi Tang