Diazoacetyl groups have been shown to undergo spontaneous cycloaddition reactions with strained alkenes and alkynes. The rates of reaction are similar to the equivalent reactions of azide groups. This allows diazo groups to be used as bioorthogonal reporter groups. This is demonstrated by fluorescent labelling of a diazoacetylated protein and of cell-surface glycans via metabolic incorporation of a diazoacetylated sugar.

We report the first account of metabolically labelling N-acetylglucosamine, in conjunction with either N-acetylgalactosamine or N-acetylmannosamine using a combination of isonitrile- and azide-based chemistries. With the appropriately labelled fluorescent probe molecules, that react with either the azido or isonitrile groups, the method enabled co-visualisation of cancer cell glycoproteins.

PigC and HapC catalyse the condensation of 4-methoxy-2,2′-bipyrrole-5-carbaldehyde (MBC) with 2-methyl-3-amylpyrrole (MAP) to give the bright red tripyrrolic prodigiosin, which has potent anticancer activity. We have cloned and over-expressed both enzymes and characterised their enzymic activity in vitro using both the natural substrates, MBC and MAP, and analogues of these substrates. Thus a range of prodigiosin analogues have been produced. Both PigC and HapC are membrane-associated enzymes and attempts to fully solubilise them using detergents led to inactivation. The enzymes are ATP-dependent but, unlike the enzymes to which they show the greatest similarity, the by-product is ADP not AMP. Two different slowly interconverting rotamers of prodigiosin exist and the spectral changes with time are consistent with isomerisation of the E,Z (or α) rotamer to the Z,Z (or β) rotameric form.

The Escherichia coli thiM riboswitch forms specific contacts with its natural ligand, thiamine pyrophosphate (TPP or thiamine diphosphate), allowing it to generate not only nanomolar binding affinity, but also a high degree of discrimination against similar small molecules. A range of synthetic TPP analogues have been used to probe each of the riboswitch–ligand interactions. The results show that the pyrimidine-sensing helix of thiM is exquisitely tuned to select for TPP by recognising the H-bonding donor and acceptors around its aminopyrimidine ring and also by forming π-stacking interactions that may be sensitive to the electronics of the ring. The central thiazolium ring of TPP appears to be more important for ligand recognition than previously thought. It may contribute to binding via long-range electrostatic interactions and/or by exerting an electron withdrawing effect on the pyrimidine ring, allowing its presence to be sensed indirectly and thereby allowing discrimination between thiamine (and its phosphate esters) and other aminopyrimidines found in vivo. The pyrophosphate moiety is essential for submicromolar binding affinity, but unexpectedly, it does not appear to be strictly necessary for modulation of gene expression.

The synthesis of a number of 3,4-fused cycloalkanopyrroles bearing substituents on the cycloalkane ring was accomplished by 1,3-dipolar cycloaddition. The yield of the cyclization appeared to depend on the base-sensitivity of the Michael acceptor, but the method is applicable across a broad range of cyclic α,β-unsaturated ketone esters. Functional group transformations can be undertaken following pyrrole synthesis to increase the diversity of cycloalkanopyrroles accessible by this method. One pyrrole thus made is a diester of a conformationally-constrained analogue of porphobilinogen, the precursor of the natural tetrapyrroles.

Two reagents have been synthesized for selective labeling of cell surface azidoglycans, an unusually stable version of a dibenzo cyclooctyne (TMDIBO) and a third-generation difluorinated cyclooctyne (DIFO3). Both syntheses are efficient with minimal purification, and the dibenzo cyclooctyne is stable under basic and acidic conditions. Flow cytometric measurements with azidosugar labeled cancer cells, in which these reagents were linked to the fluorophore Alexa Fluor 647, gave a signal-to-background ratio of up to 35 with TMDIBO as compared to ≈10 for DIFO3 and ≈5 for a phosphine reagent. TMDIBO-based probes should have applications in molecular imaging of cell surface glycans in vivo.

Two in one—We show here that the highly strained trans,trans-diolefin (E,E)-1,5-cyclooctadiene can perform efficiently two different click reactions at fast reaction rates. It is capable of first undergoing [3+2] cycloadditions with 1,3-dipoles at a reaction rate comparable to that of strained cyclooctynes. The resulting cycloadduct can then perform a much faster inverse-electron-demand Diels–Alder reaction with tetrazines, effectively linking an azide to a tetrazine. Thus, (E,E)-1,5-cyclooctadiene could have many applications in chemical biology and polymer chemistry.

We show here that isonitriles can perform click reactions with tetrazines in aqueous media, making them promising candidates for ligation reactions in chemical biology and polymer chemistry. This is the first time that a [4+1] cycloaddition has been used as a biocompatible ligation reaction.

Pyruvate decarboxylase (PDC) uses thiamine diphosphate as an essential cofactor to catalyze the formation of acetaldehyde on the pathway of ethanol synthesis. Here we report the crystallographic image of a prereaction intermediate of a bacterial pyruvate decarboxylase prepared by cocrystallizing the enzyme with pyruvate and a stable analogue of the cofactor’s activated ylid form. A second crystal structure of PDC in complex with fluoride shows that the ion organizes a water molecule that occludes the pyruvate binding site, accounting for the inhibitory effect of the halide. Also reported is a structure of the cofactor-free apo form, which when compared to the structure of the holo form indicates how thiamine diphosphate organizes the active site pocket of pyruvate decarboxylase to support catalysis. Guided by the structural and enzymatic data, we propose roles for several key residues in the catalytic mechanism.

Analogues of prodigiosin, a tripyrrolic pigment produced by Serratia species with potent immunosuppressive and anticancer activities, have been produced by feeding synthetic analogues of the normal precursor MBC to mutants of Serratia sp. ATCC 39006 or to engineered strains of Escherichia coli; in this way it has been shown that the prodigiosin synthesising enzyme, PigC, has a relaxed substrate-specificity.

Replacement of the thiazolium ring of thiamine pyrophosphate with a triazole gives extremely potent inhibitors of pyruvate decarboxylase from Z. mobilis, with KI values down to 20 pM; this system was used to explore pyrophosphate mimics and several effective analogues were discovered.

(3R)- and (3S)-Deuteriated forms of 5-aminolaevulinic acid have been synthesised and the (3R)-form shows a significantly larger isotope effect when incubated with porphobilinogen synthase from bovine liver and from Bacillus subtilis; based on this and on available crystal structures, a modified mechanism for the enzymic reaction is proposed.

Two analogues of porphobilinogen, the 6-methyl and 6,11-ethano derivatives, have been made by a new synthetic route and the 6-methyl analogue has proved to be the most potent inhibitor of hydroxymethylbilane synthase yet reported (Ki = 3 µM).

Analogues of prodigiosin, a tripyrrolic pigment produced by Serratia species with potent immunosuppressive and anticancer activities, have been produced by feeding synthetic analogues of the normal precursor MBC to mutants of Serratia sp. ATCC 39006 or to engineered strains of Escherichia coli; in this way it has been shown that the prodigiosin synthesising enzyme, PigC, has a relaxed substrate-specificity.

Two reagents have been synthesized for selective labeling of cell surface azidoglycans, an unusually stable version of a dibenzo cyclooctyne (TMDIBO) and a third-generation difluorinated cyclooctyne (DIFO3). Both syntheses are efficient with minimal purification, and the dibenzo cyclooctyne is stable under basic and acidic conditions. Flow cytometric measurements with azidosugar labeled cancer cells, in which these reagents were linked to the fluorophore Alexa Fluor 647, gave a signal-to-background ratio of up to 35 with TMDIBO as compared to ≈10 for DIFO3 and ≈5 for a phosphine reagent. TMDIBO-based probes should have applications in molecular imaging of cell surface glycans in vivo.

We show here that isonitriles can perform click reactions with tetrazines in aqueous media, making them promising candidates for ligation reactions in chemical biology and polymer chemistry. This is the first time that a [4+1] cycloaddition has been used as a biocompatible ligation reaction.

Two in one—We show here that the highly strained trans,trans-diolefin (E,E)-1,5-cyclooctadiene can perform efficiently two different click reactions at fast reaction rates. It is capable of first undergoing [3+2] cycloadditions with 1,3-dipoles at a reaction rate comparable to that of strained cyclooctynes. The resulting cycloadduct can then perform a much faster inverse-electron-demand Diels–Alder reaction with tetrazines, effectively linking an azide to a tetrazine. Thus, (E,E)-1,5-cyclooctadiene could have many applications in chemical biology and polymer chemistry.

The Escherichia coli thiM riboswitch forms specific contacts with its natural ligand, thiamine pyrophosphate (TPP or thiamine diphosphate), allowing it to generate not only nanomolar binding affinity, but also a high degree of discrimination against similar small molecules. A range of synthetic TPP analogues have been used to probe each of the riboswitch–ligand interactions. The results show that the pyrimidine-sensing helix of thiM is exquisitely tuned to select for TPP by recognising the H-bonding donor and acceptors around its aminopyrimidine ring and also by forming π-stacking interactions that may be sensitive to the electronics of the ring. The central thiazolium ring of TPP appears to be more important for ligand recognition than previously thought. It may contribute to binding via long-range electrostatic interactions and/or by exerting an electron withdrawing effect on the pyrimidine ring, allowing its presence to be sensed indirectly and thereby allowing discrimination between thiamine (and its phosphate esters) and other aminopyrimidines found in vivo. The pyrophosphate moiety is essential for submicromolar binding affinity, but unexpectedly, it does not appear to be strictly necessary for modulation of gene expression.

Replacement of the thiazolium ring of thiamine pyrophosphate with a triazole gives extremely potent inhibitors of pyruvate decarboxylase from Z. mobilis, with KI values down to 20 pM; this system was used to explore pyrophosphate mimics and several effective analogues were discovered.

Novel triazole-based pyrophosphate analogues of thiamine pyrophosphate (TPP) have been synthesised and tested for inhibition of pyruvate decarboxylase (PDC) from Zymomonas mobilis. The thiazolium ring of thiamine was replaced by a triazole in an efficient two-step procedure. Pyrophosphorylation then gave extremely potent triazole inhibitors with KI values down to 20 pM, compared to a KD value of 0.35 μM for TPP. This triazole scaffold was used for further investigation and six analogues containing mimics of the pyrophosphate group were synthesised and tested for inhibition of PDC. Several effective analogues were found with KI values down to around 1 nM.

PigC and HapC catalyse the condensation of 4-methoxy-2,2′-bipyrrole-5-carbaldehyde (MBC) with 2-methyl-3-amylpyrrole (MAP) to give the bright red tripyrrolic prodigiosin, which has potent anticancer activity. We have cloned and over-expressed both enzymes and characterised their enzymic activity in vitro using both the natural substrates, MBC and MAP, and analogues of these substrates. Thus a range of prodigiosin analogues have been produced. Both PigC and HapC are membrane-associated enzymes and attempts to fully solubilise them using detergents led to inactivation. The enzymes are ATP-dependent but, unlike the enzymes to which they show the greatest similarity, the by-product is ADP not AMP. Two different slowly interconverting rotamers of prodigiosin exist and the spectral changes with time are consistent with isomerisation of the E,Z (or α) rotamer to the Z,Z (or β) rotameric form.

We report the first account of metabolically labelling N-acetylglucosamine, in conjunction with either N-acetylgalactosamine or N-acetylmannosamine using a combination of isonitrile- and azide-based chemistries. With the appropriately labelled fluorescent probe molecules, that react with either the azido or isonitrile groups, the method enabled co-visualisation of cancer cell glycoproteins.