Heteroatom-Heteroatom Bond Formation in Natural Product Biosynthesis

Abstract

Natural products that contain functional groups with heteroatom-heteroatom linkages (X-X, where X = N, O, S, and P) are a small yet intriguing group of metabolites. The reactivity and diversity of these structural motifs has captured the interest of synthetic and biological chemists alike. Functional groups containing X-X bonds are found in all major classes of natural products and often impart significant biological activity. This review presents our current understanding of the biosynthetic logic and enzymatic chemistry involved in the construction of X-X bond containing functional groups within natural products. Elucidating and characterizing biosynthetic pathways that generate X-X bonds could both provide tools for biocatalysis and synthetic biology, as well as guide efforts to uncover new natural products containing these structural features.

Figure 1

X–X bond containing functional groups covered in this review

Figure 2

Selected bioactive natural products containing an X–X bond

Figure 3

Structures of selected siderophores, highlighting key amino acid and amine building blocks and the presence of hydroxylamines

Figure 4

A) Structure of calicheamicin (6) B) N-hydroxylation reaction catalyzed by CalE10 and substrate scope of CalE10

Figure 5

Logic of oxime installation in organic synthesis versus biosynthesis

Figure 6

Structures of caerulomycin A (38) and related analogues

Figure 7

Structure of the RiPPs azolemycin (49) and ustiloxin B (50)

Figure 8

A) Feeding experiments reveal the precursors to the N–O linkage found in L-acivicin (78). B): In vitro assays examining the biosynthesis of L-quisqualic acid (79) and BIA (76)

Figure 9

Logic of nitro group installation in organic synthesis versus biosynthesis

Figure 10

A) Proposed geometric arrangements of the peroxo-Fe₂^III/III species in several di-iron enzymes and AurF. B) Coo rdination sphere of the μ-oxo-Fe₂^III/III species from the crystal structure of AurF

Figure 11

A) Proposed geometric arrangements of the peroxo-Fe₂^III/III species in several di-iron enzymes and CmlI. B) Coordination sphere of the μ-oxo-Fe₂^III/III species from the crystal structure of CmlI

Figure 12

Depiction of a typical Rieske non-heme mononuclear iron site with the putative active oxygenating peroxo-Fe^III species

Figure 13

Structures of selected nitro sugar-containing natural products

Figure 14

Structures of malleobactins A – D

Figure 15

Structures of azoxymycin A – C

Figure 16

Logic of diazo group installation in organic synthesis versus biosynthesis

Figure 17

Structures of several kinamycins and the previously proposed, incorrect structure for kinamycin C

Figure 18

Reactive intermediates proposed to be relevant for the bioactivity of the kinamycins

Figure 19

Structures of lomaiviticin A and C

Figure 20

Comparison of putative diazo- and hydrazide-forming gene cassettes from the lomaiviticin, kinamycin, and fosfazinomycin biosynthetic gene clusters

Figure 21

Logic for hydrazide construction in organic synthesis and biosynthesis

Figure 22

Selected piperazic acid-containing hydrazide NRPS-derived natural products

Figure 23

Logic of hydrazine installation in organic synthesis versus biosynthesis

Figure 24

A) Current paradigms for N-nitrosation in living organisms. B) Mechanisms of action for nitrosamines

Figure 25

Chemical structures of gilotoxin, holomyin, and romidepsin

Figure 26

Chemical structures of the sulfadixiamycins A – C

Scheme 1

General flavin-dependent monooxygenation mechanism

Scheme 2

C_4a-hydroperoxyflavin intermediate stabilization by NADP⁺ prevents uncoupling and generation of H₂O₂

Scheme 3

Proposed mechanisms for cytochrome P450-catalyzed N-hydroxylation

Scheme 4

Proposed biosynthetic pathway for L-canavanine (32)

Scheme 5

Proposed reaction leading to the formation of oxime 43 by CrmH

Scheme 6

Involvement of an oxime intermediate in ustiloxin B (50) biosynthesis

Scheme 7

A) Mechanism of action for glucosinolates. B) Aldoxime formation catalyzed by CYP79s

Scheme 8

Structure of nocardicin A (37) and proposed mechanism of the oxidation catalyzed by NocL

Scheme 9

Proposed biosynthetic pathway for althiomycin (41). A, adenylation domain. T, thiolation domain

Scheme 10

A) Trapping of radical intermediates by nitrones. B) Mechanism of action proposed for avrainvillamide (66)

Scheme 11

The proposed biosynthetic pathway of oxaline (68) and nitrone formation catalyzed by OxaD

Scheme 12

A) The biosynthetic pathway of D-cycloserine (2). B) Reaction catalyzed by nitric oxide synthase

Scheme 13

A) Biosynthetic pathway of 4,3-HMBAm (83). B) Biosynthetic pathway of grixazone (86). C) Other substrates tested for NspF activity

Scheme 14

A) Proposed mechanism for the catecholase activity of tyrosinases. B) Proposed mechanism of C-nitrosation from Ref.

Scheme 15

Proposed peroxo-Fe₂^III/III and bis-μ-oxo Fe₂^IV/IV species involved in diverse reactions catalyzed by non-heme di-iron enzymes. We show the peroxo-Fe₂ ^III/III species as having a μ-1,2 bridging mode, although additional binding modes have been suggested

Scheme 16

Oxidation of PABA to PNBA by AurF in the biosynthesis of aureothin. T = thiolation domain

Scheme 17

A) Proposed mechanisms and B) reaction stoichiometries of the AurF-catalyzed oxidation of PABA (101) to PNBA (102)

Scheme 18

A) Proposed mechanism for the AurF-mediated N-hydroxylation of PABA to 103. B) Proposed mechanism for the AurF-mediated four-electron of oxidation of 103 to PNBA

Scheme 19

Proposed catalytic cycles for the six-electron N-oxidation of amines to nitro groups by A) AurF and B) CmlI

Scheme 20

Proposed pathway for chloramphenicol biosynthesis. A, adenylation domain; T, thiolation domain; R, reductase domain

Scheme 21

Proposed radical-based mechanism for the CmlI-mediated N-hydroxylation of 109 to 111

Scheme 22

Proposed pathway for pyrrolnitrin biosynthesis involving nitro formation as the final step

Scheme 23

Selected psychrophilins and their proposed biosynthetic pathway involved PsyC-catalyzed nitro group installation

Scheme 24

The reactions catalyzed in vitro by A) RubN8, ORF36, and DnmZ and B) KijD3

Scheme 25

Proposed biosynthetic pathway for thaxtomin A

Scheme 26

Proposed mechanisms for L-tryptophan nitration by cytochrome P450 TxtE. A) Generation of potential reactive intermediates from nitric oxide. B) Radical-based mechanism C) Electrophilic aromatic substitution mechanism

Scheme 27

Proposed biosynthetic pathway of 3-nitropropanoic acid in fungi

Scheme 28

A) Structure of hormaomycin (132) and B) Proposed mechanisms for cyclopropanation and nitration to afford 133

Scheme 29

Logic of two azoxy group installation strategies used in biosynthesis

Scheme 30

Proposed biosynthetic pathway for valanimycin

Scheme 31

Proposed pathways for azoxy group installation from putative intermediate 140

Scheme 32

A) Structures of isolated elaiomycins and B) proposed biosynthesis

Scheme 33

Structure and proposed biosynthesis of KA57-A

Scheme 34

Proposed biosynthesis of azoxymycin A – C involving coupling of amino precursors 169 and 170 potentially via AzoC

Scheme 35

Proposed mechanisms for the non-enzymatic generation of azoxy compounds from nitroso and N-hydroxyl intermediates

Scheme 36

Proposed pathway for cremeomycin biosynthesis

Scheme 37

Proposed mechanism for CreD/CreE-catalyzed nitrite formation from L-aspartate

Scheme 38

Proposed pathway for kinamycin biosynthesis

Scheme 39

Proposed biosynthesis of fosfazinomycin A (186) and B (187)

Scheme 40

Proposed pathway for hydrazido assembly in fosfazinomycin biosynthesis

Scheme 41

NRPS-catalyzed hydrazide formation using piperazic acid as an extender unit. C = condensation, A = adenylation, T = thiolation

Scheme 42

Biosynthesis of hydrazine in anammox metabolism. HZS = hydrazine synthase

Scheme 43

A) Structures of the diaxiamycins. B) Proposed biosynthesis of the dixiamycins and oxiamycin by XiaH-mediated one-electron oxidation

Scheme 44

Original biosynthetic proposal for the formation of substituted piperazic acids

Scheme 45

Characterization of KtzI in N-oxidation of ornithine and proposed biosynthesis of piperazic acid

Scheme 46

Proposed biosynthesis of pyrazole and β-pyrazol-1-alanine

Scheme 47

Proposed biosynthetic pathway involving oxidative rearrangement of the diazo intermediate to afford the pyridazine ring of azamerone

Scheme 48

Biosynthetic origins of pyridazomycin based on feeding studies

Scheme 49

Proposed biosynthetic pathway for toxoflavin

Scheme 50

Proposed biosynthesis for streptozotocin based on feeding studies

Scheme 51

Maturation of microcin C7 involves an N–P bond formation step catalyzed by MccB

Scheme 52

Proposed mechanism of MccB-mediated N–P formation in microcin C7 biosynthesis

Scheme 53

Two proposed mechanisms of action for gilotoxin

Scheme 54

Proposed mechanism of disulfide formation catalyzed by flavin-dependent disulfide oxidases GilT, HImI, and DepH

Scheme 55

EgtB and OvoA catalyze C–S bond formation coupled with formation of a sulfoxide

Scheme 56

General mechanism for α-ketoglutarate-dependent non-heme mononuclear iron enzymes

Scheme 57

Proposed mechanism for the C–S/S–O bond forming non-heme mononuclear iron enzyme EgtB

Scheme 58

Proposed biosynthetic pathway of ustiloxin H

Scheme 59

Proposed biosynthesis of allicin from precursor alliin

Scheme 60

Proposed mechanism of DNA alkylation by leinamycins

Scheme 61

Proposal for installation of a key sulfur atom in leinamycin biosynthesis

Scheme 62

Proposed mechanism for the formation of three sulfadixiamycins from xiamycin and sulfur dioxide by XiaH

Scheme 63

Proposed biosynthetic pathway for ascamycin

Scheme 64

Two-step, polyketide-mediated sulfation strategy involved in CPZ biosynthesis