Patrick S. Mariano

Oxaloacetate Hydrolase, the C–C Bond Lyase of Oxalate Secreting Fungi

Oxalate secretion by fungi is known to be associated with fungal pathogenesis. In addition, oxalate toxicity is a concern for the commercial application of fungi in the food and drug industries. Although oxalate is generated through several different biochemical pathways, oxaloacetate acetylhydrolase (OAH)-catalyzed hydrolytic cleavage of oxaloacetate appears to be an especially important route. Below, we report the cloning of the Botrytis cinerea oahA gene and the demonstration that the disruption of this gene results in the loss of oxalate formation. In addition, through complementation we have shown that the intact B. cinerea oahA gene restores oxalate production in an Aspergillus niger mutant strain, lacking a functional oahA gene. These observations clearly indicate that oxalate production in A. niger and B. cinerea is solely dependent on the hydrolytic cleavage of oxaloacetate catalyzed by OAH. In addition, the B. cinera oahA gene was overexpressed in Escherichia coli and the purified OAH was used to define catalytic efficiency, substrate specificity, and metal ion activation. These results are reported along with the discovery of the mechanism-based, tight binding OAH inhibitor 3,3-difluorooxaloacetate (Ki = 68 nm). Finally, we propose that cellular uptake of this inhibitor could reduce oxalate production.

Studies Leading to the Development of a Single-Electron Transfer (SET) Photochemical Strategy for Syntheses of Macrocyclic Polyethers, Polythioethers, and Polyamides

Organic photochemists began to recognize in the 1970s that a new mechanistic pathway involving excited-state single-electron transfer (SET) could be used to drive unique photochemical reactions. Arnolds seminal studies demonstrated that SET photochemical reactions proceed by way of ion radical intermediates, the properties of which govern the nature of the ensuing reaction pathways. Thus, in contrast to classical photochemical reactions, SET-promoted excited-state processes are controlled by the nature and rates of secondary reactions of intermediate ion radicals. In this Account, we discuss our work in harnessing SET pathways for photochemical synthesis, focusing on the successful production of macrocyclic polyethers, polythioethers, and polyamides. One major thrust of our studies in SET photochemistry has been to develop new, efficient reactions that can be used for the preparation of important natural and non-natural substances. Our efforts with α-silyl donor-tethered phthalimides and naphthalimides have led to the discovery of efficient photochemical processes in which excited-state SET is followed by regioselective formation of carbon-centered radicals. The radical formation takes place through nucleophile-assisted desilylation of intermediate α-silyl-substituted ether-, thioether-, amine-, and amide-centered cation radicals. Early laser flash photolysis studies demonstrated that the rates of methanol- and water-promoted bimolecular desilylations of cation radicals (derived from α-silyl electron donors) exceeded the rates of other cation radical α-fragmentation processes, such as α-deprotonation. In addition, mechanistic analyses of a variety of SET-promoted photocyclization reactions of α-silyl polydonor-linked phthalimides and naphthalimides showed that the chemical and quantum efficiencies of the processes are highly dependent on the lengths and types of the chains connecting the imide acceptor and α-silyl electron donor centers. We also observed that reaction efficiencies are controlled by the rates of desilylation at the α-silyl donor cation radical moieties in intermediate zwitterionic biradicals that are formed by either direct excited-state intramolecular SET or by SET between the donor sites in the intervening chains. It is important to note that knowledge about how these factors govern product yields, regiochemical selectivities, and quantum efficiencies was crucial for the design of synthetically useful photochemical reactions of linked polydonor-acceptor substrates. The fruits of these insights are exemplified by synthetic applications in the concise preparation of cyclic peptide mimics, crown ethers and their lariat- and bis-analogs, and substances that serve as fluorescence sensors for important heavy metal cations.

Nature and kinetic analysis of carbon-carbon bond fragmentation reactions of cation radicals derived from SET-oxidation of lignin model compounds.

Features of the oxidative cleavage reactions of diastereomers of dimeric lignin model compounds, which are models of the major types of structural units found in the lignin backbone, were examined. Cation radicals of these substances were generated by using SET-sensitized photochemical and Ce(IV) and lignin peroxidase promoted oxidative processes, and the nature and kinetics of their C-C bond cleavage reactions were determined. The results show that significant differences exist between the rates of cation radical C1-C2 bond cleavage reactions of 1,2-diaryl-(β-1) and 1-aryl-2-aryloxy-(β-O-4) propan-1,3-diol structural units found in lignins. Specifically, under all conditions C1-C2 bond cleavage reactions of cation radicals of the β-1 models take place more rapidly than those of the β-O-4 counterparts. The results of DFT calculations on cation radicals of the model compounds show that the C1-C2 bond dissociation energies of the β-1 lignin model compounds are significantly lower than those of the β-O-4 models, providing clear evidence for the source of the rate differences.

Panoramic view of a superfamily of phosphatases through substrate profiling

Significance Here, we examine the activity profile of the haloalkanoic acid dehalogenase (HAD) superfamily by screening a customized library against >200 enzymes from a broad sampling of the superfamily. From this dataset, we can infer the function of nearly 35% of the superfamily. Overall, the superfamily was found to show high substrate ambiguity, with 75% of the superfamily utilizing greater than five substrates. In addition, the HAD members with the least amount of structural accessorization of the Rossmann fold were found to be the most specific, suggesting that elaboration of the core domain may have led to increased substrate range of the superfamily. Large-scale activity profiling of enzyme superfamilies provides information about cellular functions as well as the intrinsic binding capabilities of conserved folds. Herein, the functional space of the ubiquitous haloalkanoate dehalogenase superfamily (HADSF) was revealed by screening a customized substrate library against >200 enzymes from representative prokaryotic species, enabling inferred annotation of ∼35% of the HADSF. An extremely high level of substrate ambiguity was revealed, with the majority of HADSF enzymes using more than five substrates. Substrate profiling allowed assignment of function to previously unannotated enzymes with known structure, uncovered potential new pathways, and identified iso-functional orthologs from evolutionarily distant taxonomic groups. Intriguingly, the HADSF subfamily having the least structural elaboration of the Rossmann fold catalytic domain was the most specific, consistent with the concept that domain insertions drive the evolution of new functions and that the broad specificity observed in HADSF may be a relic of this process.

Characterization, Kinetics, and Crystal Structures of Fructose-1,6-bisphosphate Aldolase from the Human Parasite, Giardia lamblia

Class I and class II fructose-1,6-bisphosphate aldolases (FBPA), glycolytic pathway enzymes, exhibit no amino acid sequence homology and utilize two different catalytic mechanisms. The mammalian class I FBPA employs a Schiff base mechanism, whereas the human parasitic protozoan Giardia lamblia class II FBPA is a zinc-dependent enzyme. In this study, we have explored the potential exploitation of the Giardia FBPA as a drug target. First, synthesis of FBPA was demonstrated in Giardia trophozoites by using an antibody-based fluorescence assay. Second, inhibition of FBPA gene transcription in Giardia trophozoites suggested that the enzyme is necessary for the survival of the organism under optimal laboratory growth conditions. Third, two crystal structures of FBPA in complex with the transition state analog phosphoglycolohydroxamate (PGH) show that the enzyme is homodimeric and that its active site contains a zinc ion. In one crystal form, each subunit contains PGH, which is coordinated to the zinc ion through the hydroxamic acid hydroxyl and carbonyl oxygen atoms. The second crystal form contains PGH only in one subunit and the active site of the second subunit is unoccupied. Inspection of the two states of the enzyme revealed that it undergoes a conformational transition upon ligand binding. The enzyme cleaves d-fructose-1,6-bisphosphate but not d-tagatose-1,6-bisphosphate, which is a tight binding competitive inhibitor. The essential role of the active site residue Asp-83 in catalysis was demonstrated by amino acid replacement. Determinants of catalysis and substrate recognition, derived from comparison of the G. lamblia FBPA structure with Escherichia coli FBPA and with a closely related enzyme, E. coli tagatose-1,6-bisphosphate aldolase (TBPA), are described.

The photochemistry of iminium salts and related heteroaromatic systems

Introduction . . . . . . , . . . . . . , . . Characteristics of the lminium Cation Chromophore . . . Excited State Properties of Iminium Salts . . . . . . E-Z-Isomcrizations, elcctrocyclizations and cycloadditions . . . Electron Transfer Photochemist~ of Iminium Salts . . . . . . . . Excited state electron transfer, general concepts . . . . . . . . Electron transfer pathways in inimium salt photochemistry . . . . . Photochemistry of N-Hctcroaromatic Salts . . . . . . . . . Electron transfer induced alcohol oxidation . . . . . . . . . . Photoaddition of alcohols and ethers to N-heteroaromatic salts . . Photoreductions and photodimerization of N-heteroaromatic salts. . Electron transfer induced photoalkylations between N-heteroaromatic carboxylic acids . . . . . . . . . Electron Transfer Photochemistry of Non-Aromatic Iminium Salts. . . General overview . . . . . . . . . . . . . + . Olefin-iminium salt photoaddition reactions . , . . . , . . Sequential electron-proton transfer and related reactions . . . Allylsilane photoadditions to iminium salts. . . . . References . . . . . . . . . . . . . . I . .

Single Electron Transfer-Promoted Photocyclization Reactions of Linked Acceptor−Polydonor Systems: Effects of Chain Length and Type on the Efficiencies of Macrocyclic Ring-Forming Photoreactions of Tethered α-Silyl Ether Phthalimide Substrates

Results of an investigation, aimed at gaining information about the factors governing the efficiencies of single electron transfer (SET)-promoted photocyclization reactions of linked acceptor-polydonor systems, are described. One set of substrates used in this effort includes alpha-trimethylsilyl ether terminated, polymethylene- and polyethylenoxy-tethered phthalimides and 2,3-naphthalimides. Photocyclization reactions of the polyethylenoxy-linked phthalimides and naphthalimides were observed to take place in higher chemical yields and with larger quantum efficiencies than those of analogs containing polymethylene tethers of near equal length. These findings show that the rates of formation of 1,omega-zwitterionic biradicals that serve as key intermediates in the photocyclization processes are enhanced in substances that contain oxygen donor sites in the chain. The findings suggest that these donor sites facilitate both initial SET to acceptor excited states and ensuing intrachain SET, resulting in migration of the cation radical center to the terminal alpha-trimethylsilyl ether position. In addition, an inverse relationship was observed between the quantum yields of photocyclization reactions of the tethered phthalimides and naphthalimides and the length of the polyethylenoxy chain. Finally, the roles played by chain type and length in governing photoreaction efficiencies were investigated by using intramolecular competition in photoreactions of polyethylenoxy and polymethylene bis-tethered phthalimides. Mechanistic interpretations and synthetic consequences of the observations made in this study are discussed.

Investigation of the substrate binding and catalytic groups of the PC bond cleaving enzyme, phosphonoacetaldehyde hydrolase

Kinetic studies with substrate analogs and group-directed chemical modification agents were carried out for the purpose of identifying the enzyme-substrate interactions required for phosphonoacetaldehyde (P-Ald) binding and catalyzed hydrolysis by P-Ald hydrolase (phosphonatase). Malonic semialdehyde (Ki = 1.6 mM), phosphonoacetate (Ki = 10 mM), phosphonoethanol (Ki = 10 mM), and fluorophosphate (Ki = 20 mM) were found to be competitive inhibitors of the enzyme but not substrates. Thiophosphonoacetaldehyde and acetonyl phosphonate underwent phosphonatase-catalyzed hydrolysis but at 20-fold and 140-fold slower rates, respectively, than did P-Ald. In the presence of NaBH4, acetonyl-phosphonate inactivated phosphonatase at a rate exceeding that of its turnover. Sequence analysis of the radiolabeled tryptic peptide generated from [3-3H]acetonylphosphonate/NaBH4-treated phosphonatase revealed that Schiff base formation had occurred with the catalytic lysine. From the Vm/Km and Vm pH profiles for phosphonatase-catalyzed P-Ald hydrolysis, an optimal pH range of 6-8 was defined for substrate binding and catalysis. The pH dependence of inactivation by acetylation of the active site lysine with acetic anhydride and 2,4-dinitrophenyl acetate evidenced protonation of the active site lysine residue as the cause for activity loss below pH 6. The pH dependence of inactivation of an active site cysteine residue with methyl methanethiol-sulfonate indicated that deprotonation of this residue may be the cause for the loss of enzyme activity above pH 8.

Single electron transfer-induced photocyclization reactions of N-[(N-trimethylsilylmethyl)aminoalkyl]phthalimides

Abstract Studies have been conducted to explore single electron transfer (SET) induced photocyclization reactions of N -[( N -acetyl- N -trimethylsilylmethyl)amidoalkyl]phthalimides (alkyl≡ethyl, n -propyl, n -pentyl and n -hexyl) and N -[( N -mesyl- N -trimethylsilylmethyl)amidoethyl]phthalimide. Photocyclizations occur on irradation of these substances in methanol in modest to high yields to produce cyclized products in which the phthalimide carbonyl carbon has become bonded to the carbon of the side chain in place of the trimethylsilyl group. A mechanism for these photocyclization reactions involving intramolecular SET from nitrogen in the α-silylamido group to the singlet excited state of the phthalimide followed by desilylation of the intermediate α-silylamido cation radical and cyclization by radical coupling is proposed. Furthermore, photoreactivity of N -[( N -methyl- N -trimethylsilylmethyl)aminoethyl]phthalimide differs from the other members of this series. Here a route involving triplet hydrogen atom abstraction predominates over that involving sequential singlet SET-desilylation. A relationship between the quantum efficiencies for reactions of the phthalimides with various α-silyl- n -electron donors and the oxidation potentials of the electron donors has been noted. The results suggest that the rate of desilylation of the cation radical intermediate is an important factor in determining the quantum efficiency of the SET-induced photoreaction and that the desilylation rates are directly proportional to the oxidation potentials of the donors. The efficient and regioselective cyclization reactions observed for photolyses in methanol represent synthetically useful processes for construction of medium and large ring heterocyclic compounds.

Preparation of enantioenriched tetrahydropyridines by iminium ion-vinylsilane cyclizations

Abstract Tetrahydropyridines can be prepared from ( S )-amino acids in high enantiomeric purity as outlined in equation 1.