Occurrence, characteristics, and applications of fructosyl amine oxidases (amadoriases)

Amadori compounds, formed by the Maillard reaction between reducing sugars (e.g., glucose) and amines (e.g., lysine residues in proteins), are ubiquitous in nature and have been implicated in aging and several chronic diseases. Fructosyl amine oxidases (FAOXs) are a relatively new class of enzymes that cleave amadori compounds and have been found in fungi, yeast, and bacteria. This mini-review summarizes over a dozen of FAOXs with different substrate specificities have been isolated, characterized, and engineered to date. All known FAOX sequences except one have the consensus motif for the ADP-binding βαβ-fold common to all FAD and NAD enzymes, and a recently solved crystal structure provides important clues for this class of enzymes. FAOXs have been explored for applications in diabetes diagnosis, detergents, and food processing. Given that naturally occurring FAOXs can only react directly with small glycated amino acids or short peptides, it is of great interest to engineer and expand the accessibility of the substrate binding sites of these enzymes.     

Organization of enzymes on subcellular structures: relay at the surface

There is a large body of evidence that soluble cytoplasmic enzymes of eukaryotic cells, e.g., glycolytic enzymes and proteins of the translational machinery, are organized in some way in space and in time. The following features of such organization emerge from the experimental data: (1) metabolites are transferred between enzymes directly "from hand to hand" in short-living enzyme-enzyme complexes rather than by diffusion in aqueous media; (2) enzymes show a tendency to be absorbed on surfaces of subcellular structures, such as membranes, cytoskeleton and polyribosomes; (3) enzymes are desorbed from a surface of a subcellular structure after binding specific metabolites, i.e., substrates and/or products of the reactions catalyzed by these enzymes. These features are suggestive of a relay mechanism for the enzyme systems functioning in a cell; an enzyme adsorbed on a surface of a subcellular structure is desorbed after binding its substrate or in the course of the catalytic act. Within a complex with its product the enzyme diffuses into the environment, until it reaches the next enzyme adsorbed on the same surface; then a short-living enzyme-enzyme complex is formed, and a direct "from hand to hand" transfer of the metabolite takes place. As a result, the overall metabolic process appears to be localized near the surface. We termed this mechanism as a "relay at the surface".     

Involvement of nitrogen-containing compounds in beta-lactam biosynthesis and its control

Biosynthesis of beta-lactam antibiotics by fungi and actinomycetes is markedly affected by compounds containing nitrogen. The different processes employed by the spectrum of microbes capable of making these valuable compounds are affected differently by particular compounds. Ammonium ions, except at very low concentrations, exert negative effects via nitrogen metabolite repression, sometimes involving the nitrogen regulatory gene nre. Certain amino acids are precursors or inducers, whereas others are involved in repression and, in certain cases, as inhibitors of biosynthetic enzymes and of enzymes supplying precursors. The most important amino acids from the viewpoint of regulation are lysine, methionine, glutamate and valine. Surprisingly, diamines such as diaminopropane, putrescine and cadaverine induce cephamycin production by actinomycetes. In addition to penicillins and cephalosporins made by fungi and cephamycins made by actinomycetes, other beta-lactams are made by actinomycetes and unicellular bacteria. These include clavams (e.g., clavulanic acid), carbapenems (e.g., thienamycin), nocardicins and monobactams. Here also, amino acids are precursors and inhibitors, but only little is known about regulation. In the case of the simplest carbapenem made by unicellular bacteria, i.e., 1-carba-2-em-3-carboxylic acid, quorum sensors containing homoserine lactone are inducers.     

The Use of Baker's Yeast in the Generation of Asymmetric Centers to Produce Chiral Drugs and Other Compounds

ABSTRACT:?

This review gives a general idea about the importance of chiral carbon in medicine and a way to obtain chiral building blocks with Baker's yeast (Saccharomyces cerevisiae) or synthesis of medicaments and other organic compounds. Reactions with these microorganisms are cheaper and easier to be executed than with chemicals (e.g., organometallics). Examples of important and practical reactions catalyzed by enzymes inside Saccharomyces cerevisiae are given and probable mechanisms of action of these enzymes are shown. Although these microbes have advantages such as low cost and availability, there are some concerns that are necessary to be resolved, such as NAD(P)H dosage to choose strains more adequate for reduction reactions.     

Immobilization of small molecules and proteins by radio-derivatized polystyrene

When molded polystyrene (PS) products (e.g., microtiter plates) or latex particles are irradiated with high-energy (1-10 Mrads) gamma rays in the presence of nonpolymerizable small molecules such as aromatic amines, some of these molecules incorporate into PS, which leads to the formation of radio-derivatized PS (RDPS). Two classes of RDPS can be identified regarding their ability for immobilization of biologically important molecules: 1) reactive RDPS that are able to form covalent bonds with molecules such as proteins without the help of cross-linkers, and 2) functionalized RDPS that can be used for the immobilization of molecules with activators (e.g., carbodiimides) or cross-linkers. The method can be used for the production of low-noise supports for binding assays. Most of the RDPS can be produced without impairment of the optical quality of PS, making derivatized microtiter plates suitable for colorimetric assays. The principle can be applied for the preparation of affinity sorbents, e.g., for high-performance affinity chromatography and for the immobilization of enzymes using latex PS particles.     

Analysis of the functional coupling between calmodulin's calcium binding and peptide recognition properties

The enhancement of calmodulin's (CaM) calcium binding activity by an enzyme or a recognition site peptide and its diminution by key point mutations at the protein recognition interface (e.g., E84K-CaM), which is more than 20 A away from the nearest calcium ligation structure, can be described by an expanded version of the Adair-Klotz equation for multiligand binding. The expanded equation can accurately describe the calcium binding events and their variable linkage to protein recognition events can be extended to other CaM-regulated enzymes and can potentially be applied to a diverse array of ligand binding systems with allosteric regulation of ligand binding, whether by other ligands or protein interaction. The 1.9 A resolution X-ray crystallographic structure of the complex between E84K-CaM and RS20 peptide, the CaM recognition site peptide from vertebrate smooth muscle and nonmuscle forms of myosin light chain kinase, provides insight into the structural basis of the functional communication between CaM's calcium ligation structures and protein recognition surfaces. The structure reveals that the complex adapts to the effect of the functional mutation by discrete adjustments in the helix that contains E84. This helix is on the amino-terminal side of the helix-loop-helix structural motif that is the first to be occupied in CaM's calcium binding mechanism. The results reported here are consistent with a sequential and cooperative model of CaM's calcium binding activity in which the two globular and flexible central helix domains are functionally linked, and provide insight into how CaM's calcium binding activity and peptide recognition properties are functionally coupled.     

Environmental injury of the lung: role of humoral mediators.

Environmental lung injury may take the form of acute tracheobronchitis, asthma, pulmonary edema, chronic bronchitis, emphysema, allergic pneumonitis, fibrosing alveolitis, pleurisy, and neoplastic disease. Environmental factors eliciting these responses include irritant gases and fumes, oxidants, organic allergens, inorganic dust, bacterial enzymes, and high partial pressures of oxygen. The basic pulmonary reactions to these toxic agents--bronchoconstriction, vasoconstriction, increased vascular permeability, inflammation, carcinogenesis--may be mediated, aggravated, or modulated by biologically active substances. These humoral agents include biogenic amines (e.g. histamine): peptides (e.g., bradykinin, vasoactive intestinal peptide, and spasmogenic lung peptide); enzymes (e.g., proteases, superoxide dismutase, and mixed function oxidases); and acidic lipids (e.g., prostaglandins, prostaglandin endoperoxides, and thromboxanes).     

Some thoughts on the evolutionary basis for the prominent role of ATP and ADP in cellular energy metabolism

The predominance of the adenosine triphosphate/adenosine diphosphate (ATP/ADP) couple in cellular phosphorylation reactions, including those that form the basis for cellular energy metabolism, cannot be explained on thermodynamic grounds since a variety of "high energy phosphate" compounds (including ADP itself) found in the cell would, based on thermodynamic considerations, be at least as effective as ATP in serving as a phosphoryl donor. How then did present-day organisms come to rely on the ATP/ADP couple as the principal mediator of phosphorylation reactions? The early appearance of adenine compounds in the prebiotic environment is suggested by experiments indicating that, relative to other purine or pyridimine compounds, adenine derivatives are preferentially synthesized under simulated prebiotic conditions (Ponnamperuma et al., 1963). In addition to the roles of adenine nucleotides in phosphorylation reactions, other adenine derivatives (e.g. Coenzyme A, flavin adenine dinucleotide, puridine nucleotides) are employed in a variety of metabolic roles. The principal function of the adenine moiety in these latter cases is in the binding of these derivatives to the relevant enzyme. The capability for binding of the adenine moiety appears to have arisen early in evolution and been exploited in a multitude of contexts, a suggestion consistent with observed similarities between the binding sites of several enzymes employing adenine derivatives as substrate. The early availability of suitable adenine compounds in the biosphere and development of complementary binding sites on cellular proteins, coupled with the expected advantages in having a limited number of metabolites as central mediators of endergonic and exergonic metabolism could readily have led to the observed pre-eminence of adenine nucleotides in cellular energy metabolism.(ABSTRACT TRUNCATED AT 250 WORDS)     

N-substituted derivatives of 4-piperidinyl benzilate: affinities for brain muscarinic acetylcholine receptors

N-Substituted derivatives of 4-piperidinyl benzilate were synthesized and their affinities for central muscarinic cholinergic receptors determined using an in vitro radioligand binding assay. 4-Piperidinyl benzilate exhibited a Ki value of 2.0 nM. N-Substitution with a methyl or an ethyl group increased the affinity to 0.2 nM, whereas substitution with a n-propyl or isopropyl group decreased the binding affinity over 100 fold. Compounds with aralkyl substitutions at the nitrogen atom of piperidinyl benzilate were also synthesized and evaluated. The Ki values (nM) obtained for these compounds were: benzyl, 0.2; p-nitrobenzyl, 13.0; p-fluorobenzyl, 3.0; phenethyl, 8.0; p-nitrophenethyl, 15.0. These data suggest that a binding region near the piperidinyl nitrogen may tolerate bulky aromatic substitutions (e.g., benzyl or phenethyl) as well or better than straight chain or branched alkyl substitutions (e.g., n-propyl or isopropyl).     

Involvement of Nitrogen-Containing Compounds in β -Lactam Biosynthesis and its Control

ABSTRACT

Biosynthesis of β -lactam antibiotics by fungi and actinomycetes is markedly affected by compounds containing nitrogen. The different processes employed by the spectrum of microbes capable of making these valuable compounds are affected differently by particular compounds. Ammonium ions, except at very low concentrations, exert negative effects via nitrogen metabolite repression, sometimes involving the nitrogen regulatory gene nre. Certain amino acids are precursors or inducers, whereas others are involved in repression and, in certain cases, as inhibitors of biosynthetic enzymes and of enzymes supplying precursors. The most important amino acids from the viewpoint of regulation are lysine, methionine, glutamate and valine. Surprisingly, diamines such as diaminopropane, putrescine and cadaverine induce cephamycin production by actinomycetes. In addition to penicillins and cephalosporins made by fungi and cephamycins made by actinomycetes, other β-lactams are made by actinomycetes and unicellular bacteria. These include clavams (e.g., clavulanic acid), carbapenems (e.g., thienamycin), nocardicins and monobactams. Here also, amino acids are precursors and inhibitors, but only little is known about regulation. In the case of the simplest carbapenem made by unicellular bacteria, i.e., 1-carba-2-em-3-carboxylic acid, quorum sensors containing homoserine lactone are inducers.     

Rapid-scanning cryospectroscopy of enzyme-substrate-inhibitor complexes of cobalt carboxypeptidase A

Rapid-scanning cryospectroscopy of cobalt(II)-substituted carboxypeptidase A serves to identify and characterize ternary enzyme-substrate-inhibitor (IES) complexes formed by the interaction between the enzyme, a peptide substrate, and a noncompetitive inhibitor. A cobalt absorption spectrum distinct from any induced by peptide or inhibitor alone signals formation of the IES complex. Tight-binding noncompetitive inhibitors containing an aromatic ring, e.g., beta-phenylpropionate, cause the IES complex to form much more slowly than simple binary complexes of the enzyme with either peptide or inhibitor. An inhibitor such as acetate, which binds more weakly and is less bulky, permits the IES complex to form relatively quickly. Remarkably, the cobalt spectra of the IES complexes match those previously found for the steady-state ester (depsipeptide) intermediates. Chemical quenching studies have demonstrated that in these ester intermediates the scissile bond is broken [Galdes, A., Auld, D. S., & Vallee, B. L. (1986) Biochemistry 25, 646-651]. This finding, in conjunction with the present studies, implies that a peptide and a noncompetitive inhibitor of its hydrolysis occupy the same binding loci as the hydrolytic products of a depsipeptide and further indicates that breakdown of an enzyme-biproduct complex is rate-determining for the turnover of depsipeptides.     

Strategies for the identification and purification of ligands for orphan biomolecules

Summary The isolation of related genes with evolutionary conserved motifs by the application of polymerase chain reaction-based molecular biology techniques, or from database searching strategies, has facilitated the identification of new members of protein families. Many of these protein molecules will be involved in protein-protein interactions (e.g. growth factors, receptors, adhesion molecules), since such interactions are intrinsic to virtually every cellular process. However, the precise biological function and specific binding partners of these novel proteins are frequently unknown, hence they are known as ‘orphan’ molecules. Complementary technologies are required for the identification of the specific ligands or receptors for these and other orphan proteins (e.g., antibodies raised against crude biological extracts or whole cells). We describe herein several alternative strategies for the identification, purification and characterisation of orphan peptide and protein molecules, specifically the synergistic use of micropreparative HPLC and biosensor techniques. These authors made equivalent contributions.     

Discovery of selective small-molecule CD80 inhibitors

Protein-protein interactions are widely found in biological systems controlling diverse cellular events. Because these interactions are implicated in many diseases such as autoimmunity and cancer, regulation of protein-protein interactions provides ideal targets for drug intervention. The CD80-CD28 costimulatory pathway plays a critical role in regulation of the immune response and thus constitutes an attractive target for therapeutic manipulation of autoimmune diseases. The objective of this study is to identify small compounds disrupting these pivotal protein-protein interactions. Compounds that specifically blocked binding of CD80 to CD28 were identified using a strategy involving a cell-based scintillation proximity assay as the initial step. Secondary screening (e.g., by analyzing the direct binding of these compounds to the target immobilized on a biosensor surface) revealed that these compounds are highly selective CD80 binders. Screening of structurally related derivatives led to the identification of the chemical features required for inhibition of the CD80-CD28 interaction. In addition, the optimization process led to a 10-fold increase in binding affinity of the CD80 inhibitors. Using this approach, the authors identify low-molecular-weight compounds that specifically and with high potency inhibit the interaction between CD80 and CD28. These compounds serve as promising starting points for further development of CD80 inhibitors as potential immunomodulatory drugs.     

Mono-oxime bisquaternary acetylcholinesterase reactivators with prop-1,3-diyl linkage-Preparation, in vitro screening and molecular docking

The treatment of organophosphorus (OP) poisoning consists of the administration of a parasympatholytic agent (e.g., atropine), an anticonvulsant (e.g., diazepam) and an acetylcholinesterase (AChE) reactivator (e.g., obidoxime). The AChE reactivator is the causal treatment of OP exposure, because it cleaves the OP moiety covalently bound to the AChE active site. In this paper, fourteen novel AChE reactivators are described. Their design originated from a former promising compound K027. These compounds were synthesized, evaluated in vitro on human AChE (hAChE) inhibited by tabun, paraoxon, methylparaoxon and DFP and then compared to commercial hAChE reactivators (pralidoxime, HI-6, trimedoxime, obidoxime, methoxime) or previously prepared compounds (K027, K203). Three of these novel compounds showed a promising ability to reactivate hAChE comparable or better than the used standards. Consequently, a molecular docking study was performed for three of these promising novel compounds. The docking results confirmed the apparent influence of π-π or cation-π interactions and hydrogen bonding for reactivator binding within the hAChE active site cleft. The SAR features concerning the non-oxime part of the reactivator molecule are also discussed.     

Phosphorylated Derivatives That Activate or Inhibit Mammalian Adenosine Kinase Provide Insights into the Role of Pentavalent Ions in AK Catalysis

The enzyme adenosine kinase (AK) exhibits a nearly complete dependency on the presence of pentavalent ions (PVI) such as phosphate, arsenate, and vanadate. To understand its basis, the effect of a large number of phosphorylated compounds on AK activity was examined. Several compounds, such as phosphoribosyl pyrophosphate, phosphoenol pyruvate, creatine phosphate, phosphorous acid, phosphonoformic acid, and inorganic pyrophosphate, were found to substitute for PVI in stimulating AK activity. Similar to PVI, these compounds lowered the Km of AK for adenosine. In contrast, many other structurally related compounds (i.e., phosphonoacetic acid, 2-carboxyethyl phosphonic acid, N-phosphonomethyl glycine, N-phosphonomethyl iminodiacetic acid) inhibited AK activity. These compounds seemed to compete with the activators for binding to AK. Structural comparisons of different compounds indicate that all activating compounds contain a net positive charge on the pentavalent atom (e.g., phosphorous), which should enable it to act as an acceptor for a nucleophilic group. We suggest that a phosphate (or other activator) bound near the active site participates in AK catalysis by forming a transient pentavalent intermediate with a nonbridging oxygen of the beta-phosphate in ATP. This interaction likely facilitates the transfer of gamma-phosphate from ATP to adenosine, thus accounting for the stimulating role of PVI in AK catalysis. The insight provided by these studies concerning the structural features of activators and inhibitors should also prove helpful in the design of more potent inhibitors of AK.     

8-Nitroxanthine,a product of myeloperoxidase,peroxynitrite, and activated human neutrophils,enhances generation of superoxide by xanthine oxidase

In biology, chiral recognition usually implies the ability of a protein, such as an enzyme or a drug receptor, to distinguish between the two enantiomeric forms of a chiral substrate or drug. Both diastereoisomerism and specific contacts between enzyme/receptor and substrate/drug are necessary. The minimum requirement is for four contact points including four nonplanar atoms (or groups of atoms) in both probe and target. The molecular models described by Easson and Stedman and by Ogston require three binding sites in a plane. A modified model with three binding sites in three dimensions is described. Under certain circumstances this model allows binding of both enantiomeric forms of a substrate or a drug. Enantiomer superposition of two enantiomers at an active site occurs in some specific cases (e.g., phenylalanine ammonia-lyase, isocitrate dehydrogenase) and is likely in others. The nature of enantiomer binding to racemase enzymes is discussed.     

Biochemical association of poly(ADP-ribose) polymerase-1 and its apoptotic peptide fragments with DNA polymerase beta

We have characterized the biochemical association of two DNA damage-dependent enzymes, poly(ADP-ribose) polymerase-1 (PARP-1) [EC 2.4.2.30] and DNA polymerase beta (pol beta) [2.7.7.7]. We reproducibly observed that pol beta is an efficient covalent target for ADP-ribose polymers under standard conditions of enzymatically catalyzed ADP-ribosylation of betaNAD+ as a substrate. The efficiency of poly(ADP-ribosyl)ation increased as a function of the pol beta and betaNAD+ concentrations. To further characterize the molecular interactions between these two unique polymerases, we also subjected human recombinant PARP-1 to peptide-specific enzymatic degradation with either caspase-3 or caspase-7 in vitro. This proteolytic treatment, commonly referred to as 'a hallmark of apoptosis', generated the two physiologically relevant peptide fragments of PARP-1, e.g., a 24-kDa amino-terminus and an 89-kDa carboxy-terminal domain. Interestingly, co-incubation of the two peptide fragments of PARP-1 with full-length pol beta resulted in their domain-specific molecular association as determined by co-immunoprecipitation and reciprocal immunoblotting. Therefore, our data strongly suggest that, once PARP-1 is proteolyzed by either caspase-3 or caspase-7 during cell death, the specific association of its apoptotic fragments with DNA repair enzymes, such as pol beta, may serve a regulatory molecular role in the execution phase of apoptosis.     

Caloric restriction mimetics: natural/physiological pharmacological autophagy inducers

Nutrient depletion, which is one of the physiological triggers of autophagy, results in the depletion of intracellular acetyl coenzyme A (AcCoA) coupled to the deacetylation of cellular proteins. We surmise that there are 3 possibilities to mimic these effects, namely (i) the depletion of cytosolic AcCoA by interfering with its biosynthesis, (ii) the inhibition of acetyltransferases, which are enzymes that transfer acetyl groups from AcCoA to other molecules, mostly leucine residues in cellular proteins, or (iii) the stimulation of deacetylases, which catalyze the removal of acetyl groups from leucine residues. There are several examples of rather nontoxic natural compounds that act as AcCoA depleting agents (e.g., hydroxycitrate), acetyltransferase inhibitors (e.g., anacardic acid, curcumin, epigallocatechin-3-gallate, garcinol, spermidine) or deacetylase activators (e.g., nicotinamide, resveratrol), and that are highly efficient inducers of autophagy in vitro and in vivo, in rodents. Another common characteristic of these agents is their capacity to reduce aging-associated diseases and to confer protective responses against ischemia-induced organ damage. Hence, we classify them as “caloric restriction mimetics” (CRM). Here, we speculate that CRM may mediate their broad health-improving effects by triggering the same molecular pathways that usually are elicited by long-term caloric restriction or short-term starvation and that imply the induction of autophagy as an obligatory event conferring organismal, organ- or cytoprotection.