Metal Fluorides as Analogues for Studies on Phosphoryl Transfer Enzymes.

The 1994 structure of a transition-state analogue with AlF and GDP complexed to G1α, a small G protein, heralded a new field of research into the structure and mechanism of enzymes that manipulate the transfer of phosphoryl (PO ) groups. The number of enzyme structures in the PDB containing metal fluorides (MF ) as ligands that imitate either a phosphoryl or a phosphate group was 357 at the end of 2016. They fall into three distinct geometrical classes: 1) Tetrahedral complexes based on BeF that mimic ground-state phosphates; 2) octahedral complexes, primarily based on AlF , which mimic "in-line" anionic transition states for phosphoryl transfer; and 3) trigonal bipyramidal complexes, represented by MgF and putative AlF moieties, which mimic the geometry of the transition state.

Synthesis of macromolecular systems via lipase catalyzed biocatalytic reactions: applications and future perspectives.

Enzymes, being remarkable catalysts, are capable of accepting a wide range of complex molecules as substrates and catalyze a variety of reactions with a high degree of chemo-, stereo- and regioselectivity in most of the reactions. Biocatalysis can be used in both simple and complex chemical transformations without the need for tedious protection and deprotection chemistry that is very common in traditional organic synthesis. This current review highlights the applicability of one class of biocatalysts viz.

Gas phase RDX decomposition pathways using coupled cluster theory.

Electronic and free energy barriers for a series of gas-phase RDX decomposition mechanisms have been obtain using coupled cluster singles, doubles, and perturbative triples with complete basis set (CCSD(T)/CBS) electronic energies for MBPT(2)/cc-pVTZ structures. Importantly, we have located a well-defined transition state for NN homolysis, in the initial RDX decomposition step, thereby obtaining a true barrier for this reaction. These calculations support the view that HONO elimination is preferred at STP over other proposed mechanisms, including NN homolysis, "triple whammy" and NONO isomerization.

Synthesis and anti-inflammatory activity evaluation of novel triazolyl-isatin hybrids.

New isatin-triazole based hybrids have been synthesized and evaluated for their inhibitory activity of TNF-α induced expression of Intercellular Adhesion Molecule-1 (ICAM-1) on the surface of human endothelial cells. Structure-activity relationship (SAR) studies revealed that the presence of the electron-attracting bromo substituent at position-5 of the isatin moiety played an important role in enhancing the anti-inflammatory potential of the synthesized compounds. Z-1-[3-(1H-1,2,4-Triazol-1-yl)propyl]-5-bromo-3-[2-(4-methoxyphenyl)hydrazono]indolin-2-one (19) with an IC50 = 20 μM and 89% ICAM-1 inhibition with MTD at 200 μM was found to be the most potent of all the synthesized derivatives.

Substrate Binding Mode and Molecular Basis of a Specificity Switch in Oxalate Decarboxylase.

Oxalate decarboxylase (OxDC) catalyzes the conversion of oxalate into formate and carbon dioxide in a remarkable reaction that requires manganese and dioxygen. Previous studies have shown that replacing an active-site loop segment Ser(161)-Glu(162)-Asn(163)-Ser(164) in the N-terminal domain of OxDC with the cognate residues Asp(161)-Ala(162)-Ser-(163)-Asn(164) of an evolutionarily related, Mn-dependent oxalate oxidase gives a chimeric variant (DASN) that exhibits significantly increased oxidase activity. The mechanistic basis for this change in activity has now been investigated using membrane inlet mass spectrometry (MIMS) and isotope effect (IE) measurements.

(19)F NMR and DFT Analysis Reveal Structural and Electronic Transition State Features for RhoA-Catalyzed GTP Hydrolysis.

Molecular details for RhoA/GAP catalysis of the hydrolysis of GTP to GDP are poorly understood. We use (19)F NMR chemical shifts in the MgF3(-) transition state analogue (TSA) complex as a spectroscopic reporter to indicate electron distribution for the γ-PO3(-) oxygens in the corresponding TS, implying that oxygen coordinated to Mg has the greatest electron density. This was validated by QM calculations giving a picture of the electronic properties of the transition state (TS) for nucleophilic attack of water on the γ-PO3(-) group based on the structure of a RhoA/GAP-GDP-MgF3(-) TSA complex.

Formation of Hexacoordinate Mn(III) in Bacillus subtilis Oxalate Decarboxylase Requires Catalytic Turnover.

Oxalate decarboxylase (OxDC) catalyzes the disproportionation of oxalic acid monoanion into CO2 and formate. The enzyme has long been hypothesized to utilize dioxygen to form mononuclear Mn(III) or Mn(IV) in the catalytic site during turnover. Recombinant OxDC, however, contains only tightly bound Mn(II), and direct spectroscopic detection of the metal in higher oxidation states under optimal catalytic conditions (pH 4.

Substrate Distortion and the Catalytic Reaction Mechanism of 5-Carboxyvanillate Decarboxylase.

5-Carboxyvanillate decarboxylase (LigW) catalyzes the conversion of 5-carboxyvanillate to vanillate in the biochemical pathway for the degradation of lignin. This enzyme was shown to require Mn(2+) for catalytic activity and the kinetic constants for the decarboxylation of 5-carboxyvanillate by the enzymes from Sphingomonas paucimobilis SYK-6 (kcat = 2.2 s(-1) and kcat/Km = 4.

Functional genomic screening reveals asparagine dependence as a metabolic vulnerability in sarcoma.

Current therapies for sarcomas are often inadequate. This study sought to identify actionable gene targets by selective targeting of the molecular networks that support sarcoma cell proliferation. Silencing of asparagine synthetase (ASNS), an amidotransferase that converts aspartate into asparagine, produced the strongest inhibitory effect on sarcoma growth in a functional genomic screen of mouse sarcomas generated by oncogenic Kras and disruption of Cdkn2a.

Structural basis for a six nucleotide genetic alphabet.

Expanded genetic systems are most likely to work with natural enzymes if the added nucleotides pair with geometries that are similar to those displayed by standard duplex DNA. Here, we present crystal structures of 16-mer duplexes showing this to be the case with two nonstandard nucleobases (Z, 6-amino-5-nitro-2(1H)-pyridone and P, 2-amino-imidazo[1,2-a]-1,3,5-triazin-4(8H)one) that were designed to form a Z:P pair with a standard "edge on" Watson-Crick geometry, but joined by rearranged hydrogen bond donor and acceptor groups. One duplex, with four Z:P pairs, was crystallized with a reverse transcriptase host and adopts primarily a B-form.

Facile C(sp(2))-C(sp(2)) bond cleavage in oxalic acid-derived radicals.

Oxalate decarboxylase (OxDC) catalyzes the Mn-dependent conversion of the oxalate monoanion into CO2 and formate. Many questions remain about the catalytic mechanism of OxDC although it has been proposed that the reaction proceeds via substrate-based radical intermediates. Using coupled cluster theory combined with implicit solvation models we have examined the effects of radical formation on the structure and reactivity of oxalic acid-derived radicals in aqueous solution.

Observation of superoxide production during catalysis of Bacillus subtilis oxalate decarboxylase at pH 4.

This contribution describes the trapping of the hydroperoxyl radical at a pH of 4 during turnover of wild-type oxalate decarboxylase and its T165V mutant using the spin-trap BMPO. Radicals were detected and identified by a combination of EPR and mass spectrometry. Superoxide, or its conjugate acid, the hydroperoxyl radical, is expected as an intermediate in the decarboxylation and oxidation reactions of the oxalate monoanion, both of which are promoted by oxalate decarboxylase.

Rhodium-catalyzed direct synthesis of unprotected NH-sulfoximines from sulfoxides.

A novel rhodium-catalyzed imination of sulfoxides using O-(2,4-dinitrophenyl)hydroxylamine is developed under mild conditions with good functional group tolerance. This method provides an efficient access to free NH-sulfoximines, an important structural unit in a variety of biologically active compounds.

A mechanochemical switch to control radical intermediates.

B₁₂-dependent enzymes employ radical species with exceptional prowess to catalyze some of the most chemically challenging, thermodynamically unfavorable reactions. However, dealing with highly reactive intermediates is an extremely demanding task, requiring sophisticated control strategies to prevent unwanted side reactions. Using hybrid quantum mechanical/molecular mechanical simulations, we follow the full catalytic cycle of an AdoB₁₂-dependent enzyme and present the details of a mechanism that utilizes a highly effective mechanochemical switch.

Assigning the EPR fine structure parameters of the Mn(II) centers in Bacillus subtilis oxalate decarboxylase by site-directed mutagenesis and DFT/MM calculations.

Oxalate decarboxylase (OxDC) catalyzes the Mn-dependent conversion of the oxalate monoanion into CO2 and formate. EPR-based strategies for investigating the catalytic mechanism of decarboxylation are complicated by the difficulty of assigning the signals associated with the two Mn(II) centers located in the N- and C-terminal cupin domains of the enzyme. We now report a mutational strategy that has established the assignment of EPR fine structure parameters to each of these Mn(II) centers at pH 8.

Optimized CGenFF force-field parameters for acylphosphate and N-phosphonosulfonimidoyl functional groups.

We report an optimized set of CGenFF parameters that can be used to model small molecules containing acylphosphate and N-phosphonosulfonimidoyl functional groups in combination with the CHARMM force field. Standard CGenFF procedures were followed to obtain bonded interaction parameters, which were validated by geometry optimizations, comparison to the results of calculations at the MP2/6-31+G(d) level of theory, and molecular dynamics simulations. In addition, partial atomic charges were assigned so that the energy of hydrogen bonding of the model compounds with water was correctly reproduced.

Computational, structural, and kinetic evidence that Vibrio vulnificus FrsA is not a cofactor-independent pyruvate decarboxylase.

The fermentation-respiration switch (FrsA) protein in Vibrio vulnificus was recently reported to catalyze the cofactor-independent decarboxylation of pyruvate. We now report quantum mechanical/molecular mechenical calculations that examine the energetics of C-C bond cleavage for a pyruvate molecule bound within the putative active site of FrsA. These calculations suggest that the barrier to C-C bond cleavage in the bound substrate is 28 kcal/mol, which is similar to that estimated for the uncatalyzed decarboxylation of pyruvate in water at 25 °C.

Rapid oxalate determination in blood and synthetic urine using a newly developed oxometer.

Blood and urine oxalate determinations have been limited to the laboratory setting because of complex sample storage and processing methods as well as the need for color spectrophotometry and ion chromatography. We hypothesized that glucometer test strips, impregnated with glucose oxidase and dyes that measure secondary hydrogen peroxide production, could be infused with oxalate oxidase and produce enhanced color changes in the presence of oxalate. By increasing the amount of sodium oxalate in fresh blood, we found that glucometer-measured oxalate increased on a linear scale.

A sulfoximine-based inhibitor of human asparagine synthetase kills L-asparaginase-resistant leukemia cells.

An adenylated sulfoximine transition-state analogue 1, which inhibits human asparagine synthetase (hASNS) with nanomolar potency, has been reported to suppress the proliferation of an l-asparagine amidohydrolase (ASNase)-resistant MOLT-4 leukemia cell line (MOLT-4R) when l-asparagine is depleted in the medium. We now report the synthesis and biological activity of two new sulfoximine analogues of 1 that have been studied as part of systematic efforts to identify compounds with improved cell permeability and/or metabolic stability. One of these new analogues, an amino sulfoximine 5 having no net charge at cellular pH, is a better hASNS inhibitor (K(I)(∗)=8 nM) than 1 and suppresses proliferation of MOLT-4R cells at 10-fold lower concentration (IC(50)=0.

A structural element that facilitates proton-coupled electron transfer in oxalate decarboxylase.

The conformational properties of an active-site loop segment, defined by residues Ser(161)-Glu(162)-Asn(163)-Ser(164), have been shown to be important for modulating the intrinsic reactivity of Mn(II) in the active site of Bacillus subtilis oxalate decarboxylase. We now detail the functional and structural consequences of removing a conserved Arg/Thr hydrogen-bonding interaction by site-specific mutagenesis. Hence, substitution of Thr-165 by a valine residue gives an OxDC variant (T165V) that exhibits impaired catalytic activity.

Membrane inlet for mass spectrometric measurement of catalysis by enzymatic decarboxylases.

Membrane inlet mass spectrometry (MIMS) uses diffusion across a permeable membrane to detect in solution uncharged molecules of small molecular weight. We point out here the application of MIMS to determine catalytic properties of decarboxylases using as an example catalysis by oxalate decarboxylase (OxDC) from Bacillus subtilis. The decarboxylase activity generates carbon dioxide and formate from the nonoxidative reaction but is accompanied by a concomitant oxidase activity that consumes oxalate and oxygen and generates CO(2) and hydrogen peroxide.

Enzymatic dissolution of calcium and struvite crystals: in vitro evaluation of biochemical requirements.

Objective: To evaluate the factors that affect the enzymatic dissolution rate of calcium oxalate monohydrate (COM), calcium phosphate (brushite), and magnesium ammonium phosphate (struvite) crystals as enzymatic digestion of kidney stones could enhance lithotripsy or provide alternatives to surgical removal.

Methods: At pH 4.2, pelleted COM crystals were combined with oxalate decarboxylase (ODC from Bacillus subtilis), oxalate oxidase (from Hordeum vulgare), or control.

Synthetic studies on the solanacol ABC ring system by cation-initiated cascade cyclization: implications for strigolactone biosynthesis.

We report a new method for constructing the ABC ring system of strigolactones, in a single step from a simple linear precursor by acid-catalyzed double cyclization. The reaction proceeds with a high degree of stereochemical control, which can be qualitatively rationalized using DFT calculations. Our concise synthetic approach offers a new model for thinking about the (as yet) unknown chemistry that is employed in the biosynthetic pathways leading to this class of plant hormones.

Characterization of Ceriporiopsis subvermispora bicupin oxalate oxidase expressed in Pichia pastoris.

Oxalate oxidase (E.C. 1.

EPR spin trapping of an oxalate-derived free radical in the oxalate decarboxylase reaction.

EPR spin trapping experiments on bacterial oxalate decarboxylase from Bacillus subtilis under turn-over conditions are described. The use of doubly (13)C-labeled oxalate leads to a characteristic splitting of the observed radical adducts using the spin trap N-tert-butyl-α-phenylnitrone linking them directly to the substrate. The radical was identified as the carbon dioxide radical anion which is a key intermediate in the hypothetical reaction mechanism of both decarboxylase and oxidase activities.