Targeting the Substrate Binding Site of E. coli Nitrile Reductase QueF by Modeling,Substrate and Enzyme Engineering

Nitrile reductase QueF catalyzes the reduction of 2‐amino‐5‐cyanopyrrolo[2,3‐d]pyrimidin‐4‐one (preQ₀) to 2‐amino‐5‐aminomethylpyrrolo[2,3‐d]pyrimidin‐4‐one (preQ₁) in the biosynthetic pathway of the hypermodified nucleoside queuosine. It is the only enzyme known to catalyze a reduction of a nitrile to its corresponding primary amine and could therefore expand the toolbox of biocatalytic reactions of nitriles. To evaluate this new oxidoreductase for application in biocatalytic reactions, investigation of its substrate scope is prerequisite. We report here an investigation of the active site binding properties and the substrate scope of nitrile reductase QueF from Escherichia coli. Screenings with simple nitrile structures revealed high substrate specificity. Consequently, binding interactions of the substrate to the active site were identified based on a new homology model of E. coli QueF and modeled complex structures of the natural and non‐natural substrates. Various structural analogues of the natural substrate preQ₀ were synthesized and screened with wild‐type QueF from E. coli and several active site mutants. Two amino acid residues Cys190 and Asp197 were shown to play an essential role in the catalytic mechanism. Three non‐natural substrates were identified and compared to the natural substrate regarding their specific activities by using wild‐type and mutant nitrile reductase.     

Einem Leib‐ und Magenfeind zum Abschied

More than half of the world population is infected with Helicobacter pylori. Mostly this uninvited guest lives a quiet life in our stomachs but can still cause a lot of trouble. In order to survive at pH = 1 it has developed a superb strategy to deal with the superior strength of hydrochloric acid. Its main weapons are the acid‐base theory and a potent urease. This enzyme hydrolyzes urea to ammonia and carbon dioxide which helps H. pylori keep the pH in its direct vicinity at a comfortable value. To get rid of H. pylori we also use acid‐base‐theory plus antibiotics and clever ways to double‐check the therapeutic success. Even after winning the battle we have to admit that H. pylori is a remarkable chemist and deserves our full respect.     

A Photoactivatable Platinum(IV) Anticancer Complex Conjugated to the RNA Ligand Guanidinoneomycin

A photoactivatable platinum(IV) complex, trans,trans,trans‐[Pt(N₃)₂(OH)(succ)(py)₂] (succ=succinylate, py=pyridine), has been conjugated to guanidinoneomycin to study the effect of this guanidinum‐rich compound on the photoactivation, intracellular accumulation and phototoxicity of the pro‐drug. Surprisingly, trifluoroacetic acid treatment causes the replacement of an azido ligand and the axial hydroxide ligand by trifluoroacetate, as shown by NMR spectroscopy, MS and X‐ray crystallography. Photoactivation of the platinum–guanidinoneomycin conjugate in the presence of 5′‐guanosine monophosphate (5′‐GMP) led to the formation of trans‐[Pt(N₃)(py)₂(5′‐GMP)]⁺, as does the parent platinum(IV) complex. Binding of the platinum(II) photoproduct {PtN₃(py)₂}⁺ to guanine nucleobases in a short single‐stranded oligonucleotide was also observed. Finally, cellular uptake studies showed that guanidinoneomycin conjugation improved the intracellular accumulation of the platinum(IV) pro‐drug in two cancer cell lines, particularly in SK‐MEL‐28 cells. Notably, the higher phototoxicity of the conjugate in SK‐MEL‐28 cells than in DU‐145 cells suggests a degree of selectivity towards the malignant melanoma cell line.     

A rapid assay for angiotensin‐converting enzyme activity using ultra‐performance liquid chromatography–mass spectrometry

Angiotensin‐converting enzyme (ACE) plays an important role in the renin–angiotensin system and ACE activity is usually assayed in vitro by monitoring the transformation from a substrate to the product catalyzed by ACE. A rapid and sensitive analysis method or ACE activity by quantifying simultaneously the substrate hippuryl–histidyl–leucine and its product hippuric acid using an ultra‐performance liquid chromatography coupled with electrospray ionization‐mass spectrometry (UPLC‐MS) was first developed and applied to assay the inhibitory activities against ACE of several natural phenolic compounds. The established UPLC‐MS method showed obvious advantages over the conventional HPLC analysis in shortened running time (3.5 min), lower limit of detection (5 pg) and limit of quantification (18 pg), and high selectivity aided by MS detection in selected ion monitoring (SIM) mode. Among the six natural products screened, five compounds, caffeic acid, caffeoyl acetate, ferulic acid, chlorogenic acid and resveratrol indicated potent in vitro ACE inhibitory activity with IC₅₀ values of 2.527 ± 0.032, 3.129 ± 0.016, 10.898 ± 0.430, 15.076 ± 1.211 and 6.359 ± 0.086 mm , respectively. A structure–activity relationship estimation suggested that the number and the situation of the hydroxyls on the benzene rings and the acrylic acid groups may play the most predominant role in their ACE inhibitory activity. Copyright © 2009 John Wiley & Sons, Ltd.     

Homology Modeling and Molecular Docking Studies of (S)‐Scoulerine 9‐O‐Methyltransferase from Coptis chinensis

(S)‐Scoulerine 9‐O‐methyltransferase (SMT), belonging to the S‐adenosyl‐L‐methionine (SAM)‐dependent O‐methyltransferase family, is an essential enzyme in the berberine biosynthetic pathways. In order to study the interactions of SMT with its substrate and further to understand the catalytic mechanism and substrate specificity, a three dimensional model of SMT from Coptis chinensis was constructed by homology modeling using the crystal structure of caffeic acid/5‐hydroxyferulic acid 3/5‐O‐methyltransferase (COMT) as a template. The three dimensional structure of SMT, which was mainly composed of α‐helices and some β‐sheets, was similar to that of COMT. In contrast with COMT, the non‐conserved residues in the substrate binding pocket of SMT might be responsible for their differences in the substrate specificity. Val119 and Asp254 in SMT were the key residues for orienting substrate for methylation as both residues had H‐bonds with (S)‐scoulerine. The methylation of (S)‐scoulerine involved deprotonation of the 9‐hydroxyl group by His253 and Asp254 in SMT followed by a nucleophilic attack on the SAM‐methyl resulting in the product, (S)‐tetrahydrocolumbamine.     

Improvement of a Stereoselective Biocatalytic Synthesis by Substrate and Enzyme Engineering: 2‐Hydroxy‐(4′‐oxocyclohexyl)acetonitrile as the Model

Even if biocatalysis is finding increasing application, it still has to gain widespread use in synthetic chemistry. Reasons for this are limitations that enzymes have with regard to substrate range, reaction scope, and insufficient selectivity with unnatural compounds. These shortcomings can be challenged by enzyme and/or substrate engineering, which are employed to alter substrate specificity and enhance the enzyme selectivity toward unnatural substrates. Herein, these two approaches are coupled to improve the hydroxynitrile lyase catalyzed synthesis of 2‐hydroxy‐(4′‐oxocyclohexyl)acetonitrile ( 4 ). The ketone functionality is masked as an enol ether, and the oxynitrilase of Hevea brasiliensis is engineered towards this masked substrate to give the product with a high optical purity and to drastically lower the amount of enzyme needed.     

Evolved Aliphatic Halogenases Enable Regiocomplementary C−H Functionalization of a Pharmaceutically Relevant Compound

Non‐heme iron halogenases are synthetically valuable biocatalysts that are capable of halogenating unactivated sp³‐hybridized carbon centers with high stereo‐ and regioselectivity. The reported substrate scope of these enzymes, however, is limited primarily to the natural substrates and their analogues. We engineered the halogenase WelO5* for chlorination of a martinelline‐derived fragment. Using structure‐guided evolution, a halogenase variant with a more than 290‐fold higher total turnover number and a 400‐fold higher apparent k_cat compared to the wildtype enzyme was generated. Moreover, we identified key positions in the active site that allow direction of the halogen to different positions in the target substrate. This is the first example of enzyme engineering to expand the substrate scope of a non‐heme iron halogenase beyond the native indole‐alkaloid‐type substrates. The highly evolvable nature of WelO5* underscores the usefulness of this enzyme family for late‐stage halogenation.     

Structural Elucidation of the Bispecificity of A Domains as a Basis for Activating Non‐natural Amino Acids

Many biologically active peptide secondary metabolites of bacteria are produced by modular enzyme complexes, the non‐ribosomal peptide synthetases. Substrate selection occurs through an adenylation (A) domain, which activates the cognate amino acid with high fidelity. The recently discovered A domain of an Anabaenopeptin synthetase from Planktothrix agardhii (ApnA A₁) is capable of activating two chemically distinct amino acids (Arg and Tyr). Crystal structures of the A domain reveal how both substrates fit into to binding pocket of the enzyme. Analysis of the binding pocket led to the identification of three residues that are critical for substrate recognition. Systematic mutagenesis of these residues created A domains that were monospecific, or changed the substrate specificity to tryptophan. The non‐natural amino acid 4‐azidophenylalanine is also efficiently activated by a mutant A domain, thus enabling the production of diversified non‐ribosomal peptides for bioorthogonal labeling.     

Investigation of the Substrate Range of CYP199A4: Modification of the Partition between Hydroxylation and Desaturation Activities by Substrate and Protein Engineering

The cytochrome P450 enzyme CYP199A4, from Rhodopseudomonas palustris HaA2, can efficiently demethylate 4‐methoxybenzoic acid. It is also capable of oxidising a range of other related substrates. By investigating substrates with different substituents and ring systems we have been able to show that the carboxylate group and the nature of the ring system and the substituent are all important for optimal substrate binding and activity. The structures of the veratric acid, 2‐naphthoic acid and indole‐6‐carboxylic acid substrate‐bound CYP199A4 complexes reveal the substrate binding modes and the side‐chain conformational changes of the active site residues to accommodate these larger substrates. They also provide a rationale for the selectivity of product oxidation. The oxidation of alkyl substituted benzoic acids by CYP199A4 is more complex, with desaturation reactions competing with hydroxylation activity. The structure of 4‐ethylbenzoic acid‐bound CYP199A4 revealed that the substrate is held in a similar position to 4‐methoxybenzoic acid, and that the C^β C? H bonds of the ethyl group are closer to the heme iron than those of the C^α (3.5 vs. 4.8 Å). This observation, when coupled to the relative energies of the reaction intermediates, indicates that the positioning of the alkyl group relative to the heme iron may be critical in determining the amount of desaturation that is observed. By mutating a single residue in the active site of CYP199A4 (Phe185) we were able to convert the enzyme into a 4‐ethylbenzoic acid desaturase.     

Study of the Phosphoryl‐Transfer Mechanism of Shikimate Kinase by NMR Spectroscopy

The phosphoryl‐transfer mechanism of shikimate kinase from Mycobacterium tuberculosis and Helicobacter pylori, which is an attractive target for antibiotic drug discovery, has been studied by 1D ¹H and ³¹P NMR spectroscopy. Metaphosphoric acid proved to be a good mimetic of the metaphosphate intermediate and facilitated the ready and rapid evaluation by NMR spectroscopic analysis of a dissociative mechanism. The required closed form of the active site for catalysis was achieved by the use of ADP (product) or two synthetic ADP analogues (AMPNP, AMPCP). Molecular dynamics simulation studies reported here also revealed that the essential arginine (Arg116/Arg117 in H. pylori and M. tuberculosis, respectively), which activates the γ‐phosphate group of ATP for catalysis and triggers the release of the product for turnover, would also be involved in the stabilisation of the metaphosphate intermediate during catalysis. We believe that the studies reported here will be helpful for future structure‐based design of inhibitors of this attractive target. The approach is also expected be useful for studies on the possible dissociative mechanism of other kinase enzymes.     

Synthesis of 2,4‐diaminopyrido[2,3‐d]pyrimidines and 2,4‐diamino‐quinazolines with bulky dibenz[b,f]azepine and dibenzo[a,d]‐cycloheptene substituents at the 6‐position as inhibitors of dihydrofolate reductases from pneumocystis carinii,toxoplasma gondii,and mycobacterium avium

The synthesis of four previously undescribed 2,4‐diaminopyrido[2,3‐d]pyrimidines ( 3,4 ) and 2,4‐diaminoquinazolines ( 5,6 ) with a bulky tricyclic aromatic group at the 6‐position is described. Condensation of dibenz[b,f]azepine with 2,4‐diamino‐6‐bromomethylpyrido[2,3‐d]pyrimidine ( 8 ) and 2,4‐diamino‐6‐bromomethylquinazoline ( 17 ) in the presence of sodium hydride afforded N‐[(2,4‐diaminopyrido[2,3‐d]‐pyrimidin‐6‐yl)methyl]dibenz[b,f]azepine ( 3 ) and N‐[(2,4‐diaminoquinazolin‐6‐yl)methyl]dibenz[b,f]‐azepine ( 4 ), respectively. Condensation of 5‐chlorodibenzo[a,d]cycloheptene ( 19 ) and 5‐chloro‐10,11‐dihydrodibenzo[a,d]cycloheptene ( 20 ) with 2,4,6‐triaminoquinazoline ( 13 ) afforded 5‐[(2,4‐diamino‐quinazolin‐6‐yl)amino]‐5H‐dibenzo[a,d]cycloheptene ( 5 ) and the corresponding 10,11‐dihydro derivative ( 6 ), respectively. The bromides 8 and 17 , as hydrobromic acid salts, were obtained from the corresponding nitriles according to a standard three‐step sequence consisting of treatment with Raney nickel in formic acid followed by reduction with sodium borohydride and bromination with dry hydrogen bromide in glacial acetic acid. Compounds 3–6 were evaluated in vitro for the ability to inhibit dihydrofolate reductase from Pneumocystis carinii, Toxoplasma gondii, Mycobacterium avium, and rat liver. Compounds 3 and 4 were potent inhibitors of all four enzymes, with IC₅₀ values in the 0.03–0.1 μM range, whereas 5 was less potent. However the selectivity of all four compounds for the parasite enzymes relative to the rat enzyme was<10‐fold, whereas the recently reported lead compound in this series, N‐[(2,4‐diaminopteridin‐6‐yl)methyl]dibenz[b,f]azepine ( 1 ) has > 100‐fold selectivity for the T. gondii and M. avium enzyme and 21‐fold selectivity for the P carinii enzyme.     

Experimental and Computational Exploration of para‐Selective Silylation with a Hydrogen‐Bonded Template

The regioselective conversion of C−H bonds into C−Si bonds is extremely important owing to the natural abundance and non‐toxicity of silicon. Classical silylation reactions often suffer from poor functional group compatibility, low atom economy, and insufficient regioselectivity. Herein, we disclose a template‐assisted method for the regioselective para silylation of toluene derivatives. A new template was designed, and the origin of selectivity was analyzed experimentally and computationally. An interesting substrate–solvent hydrogen‐bonding interaction was observed. Kinetic, spectroscopic, and computational studies shed light on the reaction mechanism. The synthetic significance of this strategy was highlighted by the generation of a precursor of a potential lipophilic bioisostere of γ‐aminobutyric acid (GABA), various late‐stage diversifications, and by mimicking enzymatic transformations.     

Insight into the Mechanism of Hydrogenation of Amino Acids to Amino Alcohols Catalyzed by a Heterogeneous MoOx‐Modified Rh Catalyst

Hydrogenation of amino acids to amino alcohols is a promising utilization of natural amino acids. We found that MoO_x‐modified Rh/SiO₂ (Rh–MoO_x/SiO₂) is an efficient heterogeneous catalyst for the reaction at low temperature (323 K) and the addition of a small amount of MoO_x drastically increases the activity and selectivity. Here, we report the catalytic potential of Rh–MoO_x/SiO₂ and the results of kinetic and spectroscopic studies to elucidate the reaction mechanism of Rh–MoO_x/SiO₂ catalyzed hydrogenation of amino acids to amino alcohols. Rh–MoO_x/SiO₂ is superior to previously reported catalysts in terms of activity and substrate scope. This reaction proceeds by direct formation of an aldehyde intermediate from the carboxylic acid moiety, which is different from the reported reaction mechanism. This mechanism can be attributed to the reactive hydride species and substrate adsorption caused by MoO_x modification of Rh metal, which results in high activity, selectivity, and enantioselectivity.     

Theoretical Studies on the Diastereoselectivity in the Lewis Acid Catalyzed Carbonyl?Ene Reaction: A Fundamental Role of Electrostatic Interaction

Lewis acids affect reactivity, selectivity, and mechanism in the carbonyl‐ene reaction. The diastereoselectivity in the glyoxylate‐ene reaction depends on Lewis acids. While the SnCl₄‐promoted reaction can be achieved with a high level of anti‐selectivity, the use of Al reagents leads to a high syn‐selectivity. The origin of the Lewis acid dependency of the diastereoselectivity in the carbonyl? ene reaction of (E)‐but‐2‐ene with glyoxylate was theoretically studied (HF/6‐31G*) from the point of view of differences and similarities between the ene and the Diels–Alder reactions. Though it has been widely accepted that the endo‐preference would be less obvious in the ene reaction than in the Diels–Alder reaction, our ab initio molecular studies showed that the electrostatic interaction between carbonyl O‐atom lone pair and cationic allylic central C‐atom of ene component exists in the Lewis acid‐promoted carbonyl–ene reaction to affect the transition‐state conformation. It is illustrated that such an electrostatic interaction is essential to control the exo/endo‐selectivity, which provides the diastereoselectivity of the product in the transition state of the Lewis acid promoted carbonyl? ene reaction.     

Identification of the Key Enzyme of Roseoflavin Biosynthesis

The bacteria Streptomyces davawensis and Streptomyces cinnabarinus produce roseoflavin, the only known natural riboflavin (vitamin B₂) analogue with antibiotic activity. Roseoflavin can be considered a natural antimetabolite and has been postulated to be biosynthesized from riboflavin via the key intermediate 8‐demethyl‐8‐aminoriboflavin (AF). The required site‐specific substitution of one of the methyl groups on the dimethylbenzene ring of riboflavin by an amino group (to give AF) is challenging. The pathway from riboflavin to AF has remained elusive, and the corresponding enzyme/s was/were unknown. Herein, we show by systematic gene deletion, heterologous gene expression, and biochemical studies that the enzyme specified by the gene BN159_7989 from S. davawensis is able to carry out a whole set of chemical reactions starting from riboflavin‐5′‐phosphate to give the final product 8‐demethyl‐8‐aminoriboflavin‐5′‐phosphate (AFP).     

Application of matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry for the study of Helicobacter pylori

The characteristics of matrix‐assisted laser desorption/ionization time‐of‐flight (MALDI‐TOF) mass spectrometry based investigation of extremely variable bacteria such as Helicobacter pylori were studied. H. pylori possesses a very high natural variability. Accurate tools for species identification and epidemiological characterization could help the scientific community to better understand the transmission pathways and virulence mechanisms of these bacteria. Seventeen clinical as well as two laboratory strains of H. pylori were analyzed by the MALDI Biotyper method for rapid species identification. Mass spectra collected were found containing 7–13 significant peaks per sample, and only six protein signals were identical for more than half of the strains. Four of them could be assigned to ribosomal proteins RL32, RL33, RL34, and RL36. The reproducible peak with m/z 6948 was identified as a histidine‐rich metal‐binding polypeptide by tandem mass spectrometry (MS/MS). In spite of the evident protein heterogeneity of H. pylori the mass spectra collected for a particular strain under several cultivations were highly reproducible. Moreover, all clinical strains were perfectly identified as H. pylori species through comparative analysis using the MALDI Biotyper software (Bruker Daltonics, Germany) by pattern matching against a database containing mass spectra from different microbial strains (n = 3287) including H. pylori 26695 and J99. The results of this study allow the conclusion that the MALDI‐TOF direct bacterial profiling is suited for H. pylori identification and could be supported by mass spectra fragmentation of the observed polypeptide if necessary. Copyright © 2010 John Wiley & Sons, Ltd.     

Asymmetric C‐Alkylation by the S‐Adenosylmethionine‐Dependent Methyltransferase SgvM

S ‐Adenosylmethionine‐dependent methyltransferases (MTs) play a decisive role in the biosynthesis of natural products and in epigenetic processes. MTs catalyze the methylation of heteroatoms and even of carbon atoms, which, in many cases, is a challenging reaction in conventional synthesis. However, C‐MTs are often highly substrate‐specific. Herein, we show that SgvM from Streptomyces griseoviridis features an extended substrate scope with respect to the nucleophile as well as the electrophile. Aside from its physiological substrate 4‐methyl‐2‐oxovalerate, SgvM catalyzes the (di)methylation of pyruvate, 2‐oxobutyrate, 2‐oxovalerate, and phenylpyruvate at the β‐carbon atom. Chiral‐phase HPLC analysis revealed that the methylation of 2‐oxovalerate occurs with R selectivity while the ethylation of 2‐oxobutyrate with S ‐adenosylethionine results in the S enantiomer of 3‐methyl‐2‐oxovalerate. Thus SgvM could be a valuable tool for asymmetric biocatalytic C‐alkylation reactions.     

Improved Cyclopropanation Activity of Histidine‐Ligated Cytochrome P450 Enables the Enantioselective Formal Synthesis of Levomilnacipran

Engineering enzymes capable of modes of activation unprecedented in nature will increase the range of industrially important molecules that can be synthesized through biocatalysis. However, low activity for a new function is often a limitation in adopting enzymes for preparative‐scale synthesis, reaction with demanding substrates, or when a natural substrate is also present. By mutating the proximal ligand and other key active‐site residues of the cytochrome P450 enzyme from Bacillus megaterium (P450‐BM3), a highly active His‐ligated variant of P450‐BM3 that can be employed for the enantioselective synthesis of the levomilnacipran core was engineered. This enzyme, BM3‐Hstar, catalyzes the cyclopropanation of N,N‐diethyl‐2‐phenylacrylamide with an estimated initial rate of over 1000 turnovers per minute and can be used under aerobic conditions. Cyclopropanation activity is highly dependent on the electronic properties of the P450 proximal ligand, which can be used to tune this non‐natural enzyme activity.     

Donor Promiscuity of a Thermostable Transketolase by Directed Evolution: Efficient Complementation of 1‐Deoxy‐d‐xylulose‐5‐phosphate Synthase Activity

Enzymes catalyzing asymmetric carboligation reactions typically show very high substrate specificity for their nucleophilic donor substrate components. Structure‐guided engineering of the thermostable transketolase from Geobacillus stearothermophilus by directed in vitro evolution yielded new enzyme variants that are able to utilize pyruvate and higher aliphatic homologues as nucleophilic components for acyl transfer instead of the natural polyhydroxylated ketose phosphates or hydroxypyruvate. The single mutant H102T proved the best hit toward 3‐methyl‐2‐oxobutyrate as donor, while the double variant H102L/H474S showed highest catalytic efficiency toward pyruvate as donor. The latter variant was able to complement the auxotrophic deficiency of Escherichia coli cells arising from a deletion of the dxs gene, which encodes for activity of the first committed step into the terpenoid biosynthesis, offering the chance to employ a growth selection test for further enzyme optimization.