Natural products version 2.0: connecting genes to molecules

Abstract

Natural products have played a prominent role in the history of organic chemistry, and they continue to be important as drugs, biological probes, and targets of study for synthetic and analytical chemists. In this Perspective, we explore how connecting Nature's small molecules to the genes that encode them has sparked a renaissance in natural product research, focusing primarily on the biosynthesis of polyketides and non-ribosomal peptides. We survey monomer biogenesis, coupling chemistries from templated and non-templated pathways, and the broad set of tailoring reactions and hybrid pathways that give rise to the diverse scaffolds and functionalization patterns of natural products. We conclude by considering two questions: What would it take to find all natural product scaffolds? What kind of scientists will be studying natural products in the future?

Figure 1

The erythromycin synthase., The three proteins of the erythromycin synthase harbor 28 domains organized into seven modules; each module is responsible for inserting a building block into the growing chain. Following macrocyclization and concomitant release from DEBS 3, 6dEB undergoes two hydroxylations and two glycosylations (highlighted in red) to yield erythromycin A.

Figure 2

Biosynthetic genes are physically clustered in bacterial genomes. The gene cluster for the enediyne C-1027 is shown. Genes are color coded according to the portion of the molecule their protein products contribute to synthesizing, with unassigned ORFs in gray.

Figure 3

Core vs. auxiliary metabolites. Bacillus subtilis NCIB 3610 and Bacillus cereus ATCC 14579 both harbor the bacillibactin gene cluster and produce this iron-binding molecule (siderophore); however, only B. subtilis NCIB 3610 encodes and produces bacillaene, while only B. cereus ATCC 14579 encodes and produces thiocillin., Thus, with respect to these two bacterial strains, bacillibactin is a core metabolite while bacillaene and thiocillin are auxiliary metabolites.

Figure 4

Natural product building blocks. (A) Highlighted are the two- and three-carbon building blocks of the polyketide tetronomycin, the amino acid building blocks of the nonribosomal peptide trapoxin B, the five-carbon building blocks of the polyketide cyclooctatin, and the hexose building blocks of the oligosaccharide gentamicin. (B). Glucose-1-phosphate is the precursor for two of the building blocks of rubradirin, 3-amino-5-hydroxybenzoate and TDP-D-rubraminose.

Figure 5

Proline and its derivatives as a building block for natural products. (A) Lysine gets converted to pipecolate during FK506 biosynthesis. (B) Tyrosine gets converted to propylproline during lincomycin biosynthesis. (C) The proposed pathways to piperazate and 3-hydroxy-3-methylproline, both of which are building blocks of polyoxypeptin A.

Figure 6

Solid-phase natural product synthesis by assembly line enzymes. (A) An amide bond-forming condensation reaction during the proposed pathway for SW-163D biosynthesis. (B) The NRPS that constructs SW-163D, showing the nascent intermediates tethered to each thiolation domain. C = condensation, A = adenylation, T= thiolation, E = epimerization, MT = methyltransferase, TE = thioesterase.

Figure 7

Unconventional modes of chain termination. (A) Oligomerization and subsequent macrocyclication catalyzed by the enterobactin TE. (B) Claisen condensations catalyzed by the terrequinone TE. (C) Reductase-catalyzed release during lyngbyatoxin biosynthesis. (D) A proposed alpha-oxoamine synthase-catalyzed chain release during saxitoxin biosynthesis. Bonds formed or modified during chain release are colored red, and post-assembly modifications are highlighted in blue. R = reductase, OS = alpha-oxoamine synthase.

Figure 8

Oligosaccharide pathways. (A) A schematic view of the streptomycin pathway. (B) Iteratively acting glycosyltransferases from the landomycin pathway., GTF = glycosyltransferase.

Figure 9

Isoprenoid biosynthesis. In the biosynthetic pathways for terpenoids such as taxol and phenalinolactone,, a linear polyisoprenoid precursor is cyclized to a hydrophobic scaffold, which is then tailored by the addition of oxygen-based functional groups. These oxygen-based functionalities are sometimes further tailored by group transfer reactions.

Figure 10

Amide ligases form the amide bonds of hydroxamate siderophores such as desferrioxamine E.

Figure 11

Pictet-Spengler reactions in widely distributed plant pathways.,

Figure 12

Oxidative coupling reactions in biosynthetic pathways. (A) Lignin and lignan pathways in plants begin with the oxidative coupling of coniferyl alcohol. (B) The pathway to indolocarbazoles such as staurosporine involves the coupling of two tryptophan-derived monomers., (C) Intramolecular crosslinking of aryl monomers forms the cup-like shape of glycopeptides such as chloroeremomycin and vancomycin.–

Figure 13

Hybrid natural products. (A) Examples of hybrid natural products. Nonribosomal peptide-derived monomers are colored blue, polyketide monomers are colored red, oligosaccharide monomers are colored green, and isoprenoid monomers are colored pink. (B) A condensation reaction links a nonribosomal peptide monomer to a polyketide monomer during the proposed pathway for salinosporamide.

Figure 14

Oxidative tailoring reactions from β-lactam pathways. (A) IPNS catalyzes two successive two-electron oxidations to form the 4,5-ring system of the penicillins. Following an epimerization reaction in the acyl chain, DAOCS (expandase) catalyzes the conversion of the 5-membered ring to a 6-membered ring to form the 4,6-ring system of the cephalosporins. The portion of the aminoadipoyl-Cys-Val tripeptide that becomes the β-lactam core is highlighted in green, the bonds formed by oxidation are colored red, and post-assembly modifications are shown in blue. (B) CarC catalyzes both the epimerization and the desaturation of the carbapenem core; both modifications are shown in red. (C) CAS catalyzes three different oxidative transformations during clavulanate biosynthesis, each of which is shown in red.

Figure 15

Baeyer-Villigerase action remodels the mithramycin scaffold by effecting C-C bond cleavage.

Figure 16

Converting a ribosomally synthesized peptide into a natural product. A schematic view of the thiostrepton pathway is shown., The C-terminal 17 amino acids of the structural peptide TsrH undergo 14 posttranslational modifications, including cleavage of the leader peptide, to become thiostrepton.

Figure 17

Oxidation control in iterative PKS pathways. The regiochemistry of cyclization is controlled by regiospecific reduction or oxidation reactions, leading to widely divergent outcomes.,

Figure 18

Oxidative chemistry that converts polyenes into polycyclic scaffolds. (A) The pathways to polyether polyketides involve the epoxidation of a polyolefinic precursor, followed by an epoxide-opening cascade that constructs the tetrahydropyran and tetrahydrofuran rings., (B) Polyenes are the precursors of enediynes.– Additional oxidation reactions may occur out of the sequence shown in the figure.

Figure 19

Cascade reactions for polycyclic ring systems. (A) Proposed [4+2]-like cyclizations during the biosynthesis of lovastatin and indanomycin. (B) Proposed intramolecular cyclizations during the coronatine and anatoxin-a pathways.

Figure 20

Examples of common natural product scaffolds.