Covalent modification of biological targets with natural products through Paal-Knorr pyrrole formation

Abstract

Covering: up to June 2017Natural products and endogenous metabolites engage specific targets within tissues and cells through complex mechanisms. This review examines the extent to which natural systems have adopted the Paal-Knorr reaction to engage nucleophilic amine groups within biological targets. Current understanding of this mode of reactivity is limited by only a few examples of this reaction in a biological context. This highlight is intended to stimulate the scientific community to identify potential research directions and applications of the Paal-Knorr reaction in native and engineered biological systems.

Fig. 1

The criticality of C5, C21-dicarbonyl for the antitumour activity of natural ophiobolins and their synthetic analogues.

Fig. 2

Chemical structures of exemplary sesquiterpene 1,4-dialdehydes.

Fig. 3

Golgi-apparatus-modifying properties of macfarlandin E. NRK cells were treated with (a) control (DMSO) or (b) 45 μM macfarlandin E for 1 h at 37 °C. After treatment, the cells were fixed and stained for the Golgi (green) using a fluorescently labeled antibody against man-nosidase II (green) and the nucleus (blue) with Hoechst 33342 (blue). The areas in the white boxes are enlarged (insets) to show the details of Golgi organization following each treatment.

Fig. 4

Protein labelling. (a) Modification of HEWL protein with 29 or 30 led to the formation of pyrrole adducts 37 and 38, respectively. ESI-MS spectra reconstructed from charge ladders denoting the distribution of alkylated products obtained from (b) 30 and (c) 29.

Fig. 5

MALDI-TOF MS spectrum of an HPLC fraction containing bispyrrole products 41–43 from the reaction of N-acetyl-glycyl-lysine methyl ester with iso[4]LGE₂ with air.

Fig. 6

Structures of DOPAL, N-acetyllysine (N-Ac-Lys) and DCPL.

Fig. 7

Super-resolution imaging of ophiobolin probe 51. U2OS cells cultured in an 18 mm plate at 10⁶ cells per cm² were treated with a 5 μL drop of 50 μM 51 and incubated for 1 h, fixed and stained with 80 μM Alexa 647-conjugated anti-IAF TF35 mAb for STORM imaging. (a) An image depicting the area of interest as shown by a white box. (b) An epifluorescence image within the box in (a). (c) A STORM image obtained from the same region in (b). Scale bars denote 10 μm.

Scheme 1

The mechanism of the Paal–Knorr reaction. Diketone 1 (red) condenses with an amine (blue) to generate hemiaminals 2–4. Facile double dehydration of 4 affords aromatic pyrrole 5.

Scheme 2

Trost–Doherty’s application of the Paal–Knorr reaction in the synthesis of roseophilin. The diketone and amine groups are coloured in red and blue, respectively.

Scheme 3

Commercial synthesis of atorvastatin (Lipitor). The Paal–Knorr reaction plays a central role in the condensation of diketone 8 with amine 9 to afford pyrrole 10. Atorvastatin is then delivered through acetal deprotection.

Scheme 4

Metabolic conversion of n-hexane to 2,5-hexanedione enables Paal–Knorr condensations to occur at lysine residues within proteins resulting in the corresponding 2,5-dimethylpyrrole-conjugated proteins. In neuronal cells, further oxidation and protein cross-linking lead to axonal atrophy.

Scheme 5

Proposed Paal–Knorr modification of target proteins by ophiobolin A and chemical demonstration of its feasibility.

Scheme 6

Reaction of ophiobolin A with PE and cleavage of the covalent adduct 15 with phospholipase (PLD) to produce pyrrole 16.

Scheme 7

Proposed Paal–Knorr reaction on polygodial results in two possible pyrrole products, 17 and 18.

Scheme 8

Addition of methylamine to cis-fused decalin analogue 19a results in the facile conversion to 23 via 20a–22a. Comparable reactivity with the other aldehyde isomer 19b did not lead to the observed products.

Scheme 9

Exploration of the Paal–Knorr reaction on polygodial illustrates that the stability of the resulting pyrrole adducts can be increased by using electron-withdrawing substituents on the nitrogen. The use of p-nitrophenylamine led to stable and isolable product 24c.

Scheme 10

Recent studies have shown that comparable trapping can also occur between an α,β-unsaturated ester and an aldehyde.

Scheme 11

Structures of aplyviolene and macfarlandin E and their analogues 29–30. Treatment of 29 with benzylamine leads to the formation of pyrrole 33. In the case of 30, pyrrole 34 loses acetate to give 35, which in turn undergoes a second addition of benzylamine to afford pyrrole 36.

Scheme 12

Structure of 1-palmitoyl-2-arachidonyl-phosphatidyl-choline (PAPC) and its conversion to iso[4]LGE₂-PC and isoLGE₂-PC. The R group is depicted in the box with the point of connection denoted by the wavy line (green).

Scheme 13

Reaction of iso[4]LGE₂-PC with lysine residues within proteins leads to Paal–Knorr pyrrole adduct 39, which dimerizes to 40 upon oxidation with air.

Scheme 14

Proposed mechanisms for the formation DCPL from the reaction of DOPAL with N-acetyllysine. The first option, A, arises through the oxidation of DOPAL to 44 followed by dimerization to afford dialdehyde 45. Subsequent Paal–Knorr reaction with N-acetyllysine delivers DCPL. The second option, B, occurs through sequential formation of imine 46 from DOPAL and N-acetyllysine, followed by the corresponding imine-based Paal–Knorr reaction via 48.

Scheme 15

A schematic representation of the development of an immunoaffinity fluorescent (IAF) probe 51 from ophiobolin A.