Chapter 1: Major Classes of Natural Product Scaffolds and Enzymatic Biosynthetic Machinery

Natural products could be defined broadly as any molecules found in nature. More traditionally in organic and medicinal chemistry communities, natural products are defined as small organic molecules (MW < 1500 daltons) generated from conditional metabolic pathways. That is the definition used here. Conditional metabolic pathways are also known as secondary pathways, which are not present in all organisms and are not essential for life. Producer organisms include microorganisms (such as bacteria), algae, fungi, and also plants of every variety.

The natural products they generate from conditional pathways presumably confer some form of advantage or protection to the producers. The physiological functions may differ and are often not clear to the chemists who have done the isolation. On the other hand, historically many of the natural product classes isolated either have useful pharmacologic activities in human medicine or, the reverse, show mammalian toxicity through diverse mechanisms.

The adjective “natural” has a strong positive resonance in this era, with consumers of food, cosmetics, medicines, nutraceuticals, and even clothing and furnishings. In part that may be a reaction to the synthetic and abiotic materials that pervade our environments, and in part is probably a connection back to humanity's past and a time when there was a closer dependence on and harmony with what the natural world provided for carving out a simpler existence. One (incompletely examined) assumption is that humans have evolved with the plants and microorganisms that generate the natural materials and small molecules and have co-adapted. This has led, over millennia, to a learned avoidance of toxic substances and, conversely, the utilization of natural extracts for treatment of health problems.

Starting some 200 years ago, and continuing into the present, chemists have focused on isolating biologically and pharmacologically active substances, first from plants and then from fungi and bacteria, characterizing them molecularly, and producing useful molecules as pure compounds. At this point there are some 32 000 compounds tabulated from Chinese traditional medicine sources, including the antimalarial drug artemisinin (for which the 2015 Nobel Prize in Chemistry was awarded). In parallel, the Dictionary of Natural Products database, which records information on purified natural molecules, contains some 210 000 compounds.¹  Natural products have been a continuing source of architectural and synthetic inspiration²  to eight generations of chemists, since the first decades of the 19th century. It is estimated that 50% of natural products still have no synthetic counterparts and up to 80% of the natural product ring systems, which generate the constrained molecular architectures, are not mimicked by synthetic molecules.¹ 

Figure 1.1 shows the structures of eight natural products isolated and characterized by their pharmacologic activities. Ergotamine, rebeccamycin, tubocurarine, and morphine have diverse biologic roles as foreign substances in humans. All four of these molecules have amino acid-derived scaffolds and can be broadly classified in the realm of alkaloid natural products, by virtue of one or more basic nitrogens embedded in a ring system. In structural terms, morphine and the lysergic acid tetracyclic moiety of ergotamine are clearly related, but the indolocarbazole framework of the antitumor rebeccamycin and the arrow poison tubocurarine bear no obvious overlap.

Ergotamine, in addition to the tetracyclic lysergic acid starter unit, is also built from the three amino acids l-alanine, l-proline, and l-phenylalanine on a nonribosomal peptide synthetase assembly line (Chapter 5). Similarly, the nitrogen atoms in the bicyclic antibiotic penicillin derive from a nonribosomally generated tripeptide aminoadipyl-cysteinyl-d-valine.³ 

The remaining three molecules in Figure 1.1 come from three additional distinct natural product classes. The anticancer microtubule blocking agent paclitaxel (Taxol) is of diterpene origin. A late-stage hydrocarbon intermediate taxadiene (Chapter 6) is subsequently heavily oxygenated and multiply acylated to yield paclitaxel. Erythromycin is a venerable antibiotic with a 14-membered macrolactone core and a pair of deoxy sugars. The substitution pattern on the macrolactone arises from a polyketide synthase assembly line (Chapter 3). The eighth natural product shown is rotenone, a mitochondrial respiratory blocker that is a member of the plant phenylpropanoid class of natural products (Chapter 9).

Paclitaxel erythromycin, and rotenone lack any nitrogen atoms in their scaffolds, reflecting distinct building blocks and assembly logic from the alkaloids and penicillin, respectively. The presence or absence of nitrogens, particularly basic nitrogen atoms in natural product frameworks, affect the physical and functional properties of the metabolite classes and is a key factor in subclass definitions.

Natural products in general, and dozens of particular compounds that have become therapeutic agents or inspired design of structural mimics, have come to the attention of human investigators over the past 150–200 years on the basis of their diverse biologic activities. Table 1.1 summarizes a range of pharmacologic activity of just eleven of the hundreds of thousands of known natural products. Among contemporary natural products of therapeutic interest, lovastatin, which lowers cholesterol by targeting the rate-determining enzyme in cholesterol biosynthesis, and the immunosuppressives rapamycin and cyclosporine, have probably been the most significant human therapeutic leads. Lovastatin biogenesis is examined in Chapter 3 and cyclosporine and rapamycin in Chapter 5.

Estimates of the natural product inventory, defined as above, are in the range of 300 000 to 600 000 compounds. Three-quarters have been isolated from plants, indicating their prodigious commitment to secondary metabolites; the remainder are microbial metabolites. There are no good estimates on the inventory of those yet to be discovered and whether many new molecular classes will be found. In the future, as more plant genomes are sequenced, better estimates may become available.

Primary metabolites are the molecules that populate the pathways essential for life. At one limit they comprise the molecules in both the biosynthesis and degradation of the classes of biopolymers: nucleic acids, proteins, polysaccharides, and lipids. They also populate the pathways for generation and storage of energy, including glycolysis, the citrate cycle, aromatic biosyntheses, amino acid metabolism, the pentose phosphate pathways, and others.

Secondary metabolites instead populate pathways that may only be turned on in some cells or in some organisms,⁴  or in some circumstances: for example, when plants respond to predators by synthesis of defensive small molecules (phytoalexins and phytoanticipins).^5,6  They may represent specialized molecular scaffolds that are not found in primary metabolism. Often the natural products that sit as the end metabolites of secondary pathways have substantially more complex scaffolds than found in primary metabolites, reflecting C–C bond-forming reactions in their biosynthesis.

The boundaries between primary and secondary metabolic pathways often have a gatekeeper (or anchoring) enzyme, which acts to shuttle some of the flux of a primary metabolite into the secondary pathway. For example, lignan is a key structural polymer in woody plants (Chapter 9). After cellulose it is the most abundant form of plant biomass. The proteinogenic amino acid phenylalanine provides all of the carbon framework for lignan polymers. The gatekeeper enzyme, the first one committed to moving l-phenylalanine into phenylpropanoid metabolites, is phenylalanine deaminase. We will note in Chapter 9 that this enzyme has an unusual, covalently attached cofactor that allows a low-energy mechanistic path for elimination of the elements of NH₃ across C_α and C_β to produce cinnamate.

Analogously, acetyl-coenzyme A (CoA) carboxylase and propionyl-CoA carboxylase, generating malonyl-CoA and 2S-propionyl-CoA, respectively, are on the border between primary metabolism and secondary pathways that lead to polyketide natural products. Malonyl-CoA can go either way in producer organisms, to fatty acids (primary pathway) or to polyketides (conditional pathway). 2S-Methylmalonyl-CoA is not used for fatty acid synthesis but is a key elongation substrate in erythromycin assembly.

Figure 1.2 tabulates a set of primary metabolites that are building blocks for many of the structural classes of natural products discussed in Chapters 3–9. Glucose is the most common sugar in cells and the glucose-1-phosphate derivative is the entry point for commitment of glucose flux to glycosylated natural products: this is the subject of Chapter 11.

The isomeric pair of isopentenyl diphosphates, the Δ²- and Δ³-isomers, in head-to-tail alkylative couplings are progenitors to >50 000 isoprenoid natural products. When such molecules are isolated from plants they have been known, historically and even today, as terpenoid molecules.⁷  The C30 isoprenoid squalene-2,3-oxide is a secondary metabolite (triterpene) that, on directed enzymatic cyclizations, gives rise to hundreds to thousands of sterol-type natural products, as we shall note in Chapter 6.

The two aromatic amino acids l-tryptophan (Trp) and l-phenylalanine (Phe) are important building blocks for the thousands of proteins made in every free-living cell and organism. They are also utilized in nonribosomal peptide assemblies. As shown in Figure 1.2, they are also the building blocks for d-(+)-lysergic acid and the dimeric lignan pinoresinol, respectively (Chapters 7 and 9).

As noted above, the two-carbon acetyl-CoA and its three-carbon enzymatic carboxylation product malonyl-CoA are key acyl thioesters in primary metabolism and also in the genesis of the large and various natural product class of polyketides. Shown in Figure 1.2 is the antifungal ionophore monensin, which is distinguished from other polyketide subclasses by the presence of furan and pyran cyclic ethers embedded in the molecular backbone.

Figure 1.2 contains two additional molecules in the primary metabolite column: molecular oxygen (O₂) and S-adenosylmethionine (SAM). O₂ is such a pervasive cosubstrate in the tailoring of all the major natural product classes of Chapters 3–11 that a separate chapter (Chapter 12) is devoted to the chemical logic and enzymatic catalysts that have evolved for its selective reductive activation.

S-Adenosylmethionine, with its trigonal sulfonium cation interspersed between a methionine residue and an adenosyl residue is a crucial reactant in both primary and secondary metabolic pathways. We will note the iterative use of SAM as a methyl donor to a diverse array of cosubstrate oxygen, nitrogen, and carbon nucleophiles of isoprenoid, polyketide, alkaloid, peptide, and phenylpropanoid frameworks. Most of these involve transfer of a [CH₃⁺] equivalent. A significant set of methyl transfers go to substrates at unactivated carbon centers, and these are dealt with in Chapter 13 where radical intermediates, including [CH₃˙] equivalents, are emphasized.

One can parse the great bulk of the ∼500 000 identified natural product structures that have been isolated over the past two centuries into a few major classes as covered in the several chapters of Section II. Sometimes the class is defined by historical isolation protocols. The vast and diverse class of alkaloids are defined by the presence of a protonatable nitrogen group, which allows partition of the scaffold between aqueous and organic solvents, depending on the protonation state of the amine group. Otherwise, alkaloid scaffolds can be dramatically diverse (Figure 1.3). We divide the large, alkaloid natural product class into two separate chapters: the first (Chapter 7) examining the different amino acid origins of many alkaloid classes and the second (Chapter 9) dealing with the hybrid class of indole terpene scaffolds.

Other natural product categories are defined by repeating structural motifs. These include peptide-based natural products, both derived from selective proteolysis and modification of ribosomally generated protein precursors as well as nonribosomally generated peptides (Figure 1.4A) (Chapters 4 and 5). Phenylpropanoid natural products, particularly abundant in plant metabolism, all derive from the nine-carbon phenylpropanoid scaffold of the amino acid primary metabolite phenylalanine (Figure 1.4B) (Chapter 9). The 65 000 or so isoprenoid natural products⁸  (also known historically as terpenes when isolated from plants) all derive from an isomeric pair of five-carbon isopentenyl diphosphate starting metabolites (Figure 1.5) (Chapter 6).

Equally prominent, as the alkaloids and isoprenoids, are the polyketide class of natural products. We will note that while the aromatic polyketides, such as the tetracycline antibiotics, do in fact generate (highly reactive) polyketonic biosynthetic intermediates, other subsets of polyketides actually avoid the accumulation of polyketonic chains, reducing the reactive β-ketone groups during chain extensions. Major subgroupings of polyketides, explored in Chapter 3, include macrolactones, such as erythromycin, decalin-containing frameworks, such as lovastatin, and polyene antibiotics that may undergo epoxidations on the way to polyether ionophore scaffolds (Figure 1.6). All polyketides are characterized by iterative chain elongations from malonyl or methylmalonyl thioester building blocks. Chain growth occurs as a series of elongating covalent enzyme thioester adducts with initiation, elongation, and termination phases.

We take up two additional classes of natural products in Section II: purine and pyrimidine natural products (Chapter 8); and glycosylated variants of all the above natural product classes (Chapter 11). One could formally define purine and pyrimidine natural products as members of the alkaloid class, but we call them out separately both for their pharmacologic distinctions (caffeine may be the most extensively used drug globally) and the antiviral properties of nucleosides such as adenosyl-arabinoside (araA) (Figure 1.7).

Two aspects of natural product glycosides are featured. The first is the transfer of the glycosyl units from nucleoside diphospho sugars as electrophilic units at carbon one for capture by a variety of oxygen, nitrogen, sulfur, and even carbon nucleophiles in natural product cosubstrates. The ∼200 000 bioinformatically identified glucosyltransferases enable glycosyl transfers to almost any secondary metabolite with one or more nucleophilic atoms. The second feature of sugars in many bioactive natural products is the dedicated biosynthesis of deoxy- and aminodeoxy-hexoses, which provide hydrophobic/hydrophilic balance to the aglycone moieties of the glycosylated end products (see erythromycin and nystatin in Figure 1.6).

The chapters on indole terpene (Chapter 10) and glycoside (Chapter 11) explicitly address the biosynthetic convergence of different natural product classes. In the analysis of biosynthetic logics for polyketide, isoprenoid, and nonribosomal peptide chapters we also take up late-stage enzymatic combinations to generate such molecules as hyperforin (a tetraprenylated polyketide in St John's wort); the Δ⁹-tetrahydrocannabinol (prenylated aromatic polyketide) from the Cannabis plant; and the antibiotic andrimid, a polyketide-nonribosomal peptide hybrid (see Figure 3.45). The combinations reflect the underlying chemical logic and enzymatic machinery noted in the next section for capturing electrophilic groups by cosubstrate nucleophiles.

One route to deciphering the chemical logic that operates in the biosynthetic pathways to the different natural product classes starts with the distinct building blocks in each major pathway. A first mechanistic categorization is whether the energy barriers for reaction are lower for two-electron steps or one-electron steps. In Section 1.5 below we take up the two specialized routes by which organisms lower energy barriers for homolytic reaction pathways (one-electron transfers, radical intermediates). Here, we focus first on the premise that most spin-paired stable organic metabolites in metabolism react by two-electron pathways, involving carbanions and carbocations at carbon centers, alcoholate and carboxylate oxyanions, available lone pairs on basic nitrogen atoms, and thiolate anions as sulfur nucleophiles.

Chapter 2 notes a set of eight primary metabolites that serve as central molecules that power metabolic transformation by reaction with diverse cosubstrate molecules. Those eight molecules share the dual properties of thermodynamic activation and kinetic stability, and can be spent to drive otherwise unfavorable coupled equilibria.⁹  They encompass a wide range of chemical functional groups, including phosphoric anhydrides, acyl phosphates, acyl thioesters, alkyl sulfonium ions, allylic pyrophosphates, and nucleoside diphospho-hexoses (see Chapter 2). All of these groups are potentially electrophilic and can be captured by the O, N, S, and C nucleophiles noted in the previous paragraph. The capture of such electron-deficient electrophilic groups by electron-rich cosubstrate nucleophiles accounts for the common reactions of natural product methylations, acetylations, prenylations, and glycosylations.

The two outliers in the group of the eight common metabolites that drive coupled cellular equilibria are NAD(P)H and O₂. The dihydropyridine core of NAD(P)H rearomatizes by transfer of a hydride ion to electrophilic carbonyl groups. Considering a hydride ion as a hydrogen with its electron pair as a nucleophilic species, the reduced nicotinamide coenzymes differ from the other central metabolites as being a nucleophilic rather than an electrophilic reagent.

Molecular oxygen, O₂, as a stable ground-state triple (one can think of it as a diradical), is kinetically stable in the presence of organic molecules and metabolites, at 21% of the global atmosphere. Yet, its thermodynamic activation is indisputable, with an estimated K_eq of 10³⁸ for four-electron reduction by 2 NADH to H₂O (assuming a kinetic mechanism could be found for the orthogonal two-electron-only NADH and one-electron-only O₂). The indifference of O₂ to two-electron reduction mechanisms leads to the next section, to remind how both aerobic and anaerobic organisms have evolved mechanisms to carry out one-electron chemistries.

Section III of this volume takes up three enzyme classes that populate secondary metabolic pathways preferentially and carry out chemical transformations that are central to appreciation of the underlying chemical logic employed by producer organisms. The first two chapters focus on radical reaction routes, at the two ends of the aerobic/anaerobic spectrum. Chapter 12 examines oxygenases and then Chapter 13 focuses on S-adenosylmethionine (SAM) as a key molecule that can utilize its cationic sulfonium group as a source of both two-electron and one-electron transfer reactions. The third chapter (Chapter 14) is devoted to the burgeoning group of enzymes (pericyclases) that catalyze concerted pericyclic transformations of substrates into products.¹⁰ 

Organisms have evolved two separate routes to reductively activate O₂ by one-electron paths. One route is to employ redox-active transition metals, Fe^II/Fe^III or less often Cu^I/Cu^II, as one-electron conduits to O₂, producing reduced superoxide anion radical, O₂^−˙, on the way to Fe^III–OOH or Cu^II–OOH two-electron-reduced, coordinated peroxides. These may eliminate water, e.g. in the case of heme iron to generate the high-valent Fe^V=O species that is robust enough to generate carbon radicals in substrates. These carbon radicals can capture [˙OH] by radical rebound or can rearrange intramolecularly. Organisms have also evolved the redox-active organic coenzyme riboflavin as a 2e⁻/1e⁻ step-down redox agent for oxygen transfer to a suite of organic cosubstrates. Notable among these flavoenzyme oxygenases is squalene-2,3-epoxidase, which sets up the cyclization of acyclic squalene to the thousands of tetracyclic and pentacyclic sterol metabolites (Figure 1.8).

Chapter 13 examines the two universes of S-adenosylmethionine (Figure 1.9). Most familiar is its canonical role as a donor of a methyl cation that is equivalent in S_N2-type transition states to electron-rich nucleophilic atoms in cosubstrates.¹¹  The transfer of either the methyl group or the aminobutyryl side chain as C₄ carbon electrophile to nucleophiles is enabled by the positive charge on the trivalent sulfonium cation, which is the core functionality of SAM.

Orthogonal one-electron reactivity of SAM is now predicted in some 575 000 open-reading frames in protein databases where SAM will coordinate to one of the iron atoms in a redox-active [4Fe–4S] cluster at the protein-active site. Input of one electron via the [4Fe–4S] cluster leads to homolysis of the sulfonium-adenosyl bond, yielding the methionine fragment coordinated to the [4Fe–4S] cluster and the 5′-deoxyadenosyl radical (5′-dA^˙), which acts as radical initiator on bound cosubstrate molecules in a given radical SAM enzyme active site. The scope of this radical chemistry has opened up new types of physiologic chemistry in the 60 or so (out of 575 000) radical SAM enzymes examined to date, with more new chemical reactions likely to be discovered. Essentially, all known radical SAM enzymes are inactivated by oxygen in air, which is probably by redox destruction of the labile [4Fe–4S] core.

Thus, organisms have evolved two disparate routes to lower energy barriers for one-electron reactions in spin-paired organic metabolites at the two ends of the anaerobic/aerobic spectrum. Presumably the radical SAM strategy, to carbon radicals, is the more ancient. We will note in specific chapters the remarkable density of oxygenases in late stages of natural product pathways to sculpt hydrophobic secondary metabolite scaffolds into more hydrophilic frameworks by performing oxygen-based radical chemistries that are otherwise energetically inaccessible. The oxygenative carving away of the C30 framework of lanosterol to the C18 scaffold of estradiol by seven iteratively acting oxygenases is such an example in Chapter 12 (Figure 12.22).

The third chapter in Section III examines a different route to metabolite scaffold rearrangement: pericyclic reactions without any finite-lived intermediates. Concerted, pericyclic reactions have been the mainstays of organic synthetic and mechanistic chemistry since the days of Claisen, Cope, Diels, and Alder.^10,12  A masterly integration and unified interpretation of the multiple classes of pericyclic reactions was achieved by Woodward and Hoffmann in the 1960s.^13,14  In the intervening half century, evidence for the existence of enzymes that carried out such concerted reactions—the class of pericyclases—has accrued, with the literature exploding over the past decade.

Chapter 14 summarizes the four categories of known pericyclase enzymes: cycloadditions/cycloreversions (encompassing canonical Diels–Alder and hetero-Diels–Alder reactions), electrocyclization reactions, sigmatropic reactions, and Alder-ene reactions, which have been observed in natural product pathways (Figure 1.10). For decades chorismate mutase, a Claisen rearrangement catalyst, stood alone.¹⁵  In the era of genome sequencing, bioinformatic analyses, and protein expression in heterologous hosts, examples of enzymes that catalyze Diels–Alder cyclization to form the decalin core of lovastatin or the spirotetronate ring system in the antibiotic abyssomycin have been characterized, among others.

The expanding list of pericyclases, where C–C, C–O, and C–N bonds are interconverted without any detectable intermediates, completes the typologies of bond-forming and -breaking mechanisms in natural product chemical biology, to go along with nucleophilic and electrophilic catalysis in heterolytic reaction manifolds, and one-electron-based homolytic reaction manifolds.

Historically, many natural products were detected, purified, and characterized based on some particular biologic activity. Up until about 200 years ago mixtures extracted from plants or microbial ferments were the norm. The past two centuries have seen the transition to isolation and characterization of purified individual natural product molecules. The past 70 years may have been the golden age of complex natural product synthetic chemistry, in part to establish structure, in part to allow for scale-up of minute quantities of natural products, and in part for medicinal synthetic efforts to produce analogs of bioactive metabolites with improved pharmacokinetic and pharmaco-distributive properties of the naturally inspired therapeutic agents.

The final section, Section IV, contains two chapters. Chapter 15 summarizes approaches to historical isolation of some natural products that have become key molecules in human medicines by gene-independent approaches. The ability to elicit different natural products from producer microorganisms by varying media composition (one substrate, many culture conditions) and growth conditions also presaged the eventual discovery of silent biosynthetic gene clusters, once the genomic era arrived. In Chapter 15, new advances to enable rapid characterization of natural product structures, such as microcrystal electron diffraction, will also be presented.

Chapter 16 summarizes some of the approaches to natural product isolation, both from microorganisms and from plants in genome-dependent detections (Figure 1.11). Natural product science has moved from a predominantly chemical arena, populated by isolation and structure-determination chemists, to a cross-disciplinary set of efforts, heavily dependent on both genomics and genetics, on bioinformatics algorithms, to find biosynthetic gene clusters, to move them to surrogate hosts in genetic constructs amenable to controlled expression, and mass spectrometry to evaluate desired gene activities. These integrated approaches are applied both to multistep pathways from bacteria and fungi and also plant-based alkaloid and phenylpropanoid molecules, such as colchicine and epipodophyllotoxin. Because the informatics, genomics, pathway gene refactoring, heterologous host expressions, and mass spectroscopic detection methodologies are likely to change rapidly, we do not drill down on specific details.

The preceding sections in this opening chapter set the tone for the second edition of this volume on Natural Product Biosynthesis: Chemical Logic and Enzymatic Machinery.

The focus on the major classes of natural products and the chemical logic of their assembly from small molecule primary metabolites as building blocks is selective, not encyclopedic. The approach is chemocentric, examining how the functional groups of starting materials and pathway intermediates are formed and utilized in building up complexity, typically in short, efficient enzymatic pathways. In polyketide, peptide, and isoprenoid pathways much of the core reactivities are parsed in terms of nucleophilicity and electrophilicity of functional groups in partner substrates. The C–C bonds in polyketide chain growth almost always occur by thio-Claisen condensations, whereas in the head-to-tail five-carbon alkylations in isoprenoid chain growth and rearrangements, carbocation chemistry is dominant. The core inventory of alkylating metabolites (S-adenosylmethionine, Δ²-prenyl diphosphates), acylating reagents (acyl-CoAs, carbamoyl phosphate), and glycosylating reagents (e.g. UDP-glucose) provide the electrophilic groups that decorate mature natural product scaffolds.

Radical chemistry occurs much more frequently in secondary metabolic pathways than in primary metabolic ones. Oxygenases act in bunches in several natural product classes: for example, converting the C20 hydrocarbon taxadiene to the octahydroxy framework of the antimitotic drug Taxol (Chapter 6). Oxygenases are also central in late stages of steroid maturation, in phenylpropanoid radical coupling in lignol assemblies, and in converting nascent olefins to electrophilic epoxides that lead to scaffold rearrangements (Chapter 12). We will examine a large subclass of iron-based oxygenases that generate substrate carbon radicals but do not complete the oxygen transfer step. The penicillin and cephalosporin synthases are members of this enzyme category.

Those “thwarted oxygenases” have similar net effects to the anaerobic, O₂-intolerant radical SAM enzymes. The mechanism for generating cosubstrate radicals, the in situ liberation of the 5′-deoxyadenosyl radical from SAM, is fully distinct, but initiation of carbon-radical-based framework rearrangements to altered product scaffolds, often with increased complexity, is similar.

This is not a book devoted solely to enzymatic reaction mechanisms in biosynthetic pathways. Many of the enzymes carrying out C–C bond formations, amide bond formations, imine/enamine catalysis, and hydride transfers are analogs of the catalysts that function in primary metabolism. However, we do pay extra attention to the range, scope, and mechanism of oxygenases, radical SAM enzymes, and pericyclases, in part because they offer new modes of C–C bond formations and disconnections and they are clustered in biosynthetic pathways.

There are short vignettes in most chapters that illustrate a specific case or lesson relevant to the natural product or reaction type that is the focal point of a given chapter. The decision on referencing is to be parsimonious with regard to original literature citations. Review articles, often recent, rather than the original literature, are cited as gateways for an interested reader to gain entry into the specialized literature.