Altered structural fluctuations in duplex RNA versus DNA: a conformational switch involving base pair opening

DNA and RNA are known to have different structural properties. In the present study, molecular dynamics (MD) simulations on a series of RNA and DNA duplexes indicate differential structural flexibility for the two classes of oligonucleotides. In duplex RNA, multiple base pairs experienced local opening events into the major groove on the nanosecond time scale, while such events were not observed in the DNA simulations. Three factors are indicated to be responsible for the base opening events in RNA: solvent-base interactions, 2'OH(n)-O4'(n+1) intra-strand hydrogen bonding, and enhanced rigid body motion of RNA at the nucleoside level. Water molecules in the major groove of RNA contribute to initiation of base pair opening. Stabilization of the base pair open state is due to a 'conformational switch' comprised of 2'OH(n)-O4'(n+1) hydrogen bonding and a rigid body motion of the nucleoside moiety in RNA. This rigid body motion is associated with decreased flexibility of the glycosyl linkage and sugar moieties in A-form structures. The observed opening rates in RNA are consistent with the imino proton exchange experiments for AU base pairs, although not for GC base pairs, while structural and flexibility changes associated with the proposed conformational switch are consistent with survey data of RNA and DNA crystal structures. The possible relevance of base pair opening events in RNA to its many biological functions is discussed.     

Synthesis of N-isobutylnoroxymorphone from naltrexone by a selective cyclopropane ring opening reaction

Selective ring opening reaction of the N-cyclopropylmethyl group in naltrexone (1d) was effected in the presence of platinum (IV) oxide and hydrobromic acid under a hydrogen atmosphere at rt to selectively afford N-isobutyl derivative 10. The binding affinity of N-i-Bu derivative 10 for opioid receptors was 11-17 times less than that of the corresponding N-CPM compound, naltrexone (1d). However, compound 10 showed dose-dependent analgesic effects. Contrary to expectations based on previous structure-activity relationship studies for a series of N-substituted naltrexone derivatives that compound 10 would be an opioid antagonist, 10 showed dose-dependent analgesia in the mouse acetic acid writhing test (ED(50): 5.05 mg/kg, sc), indicating it was an opioid agonist. This finding may have a great influence on the drug design of opioid agonists.     

Recent developments in ring opening polymerization of lactones for biomedical applications

Aliphatic polyesters prepared by ring-opening polymerization of lactones are now used worldwide as bioresorbable devices in surgery (orthopaedic devices, sutures, stents, tissue engineering, and adhesion barriers) and in pharmacology (control drug delivery). This review presents the various methods of the synthesis of polyesters and tailoring the properties by proper control of molecular weight, composition, and architecture so as to meet the stringent requirements of devices in the medical field. The effect of structure on properties and degradation has been discussed. The applications of these polymers in the biomedical field are described in detail.     

Altered balance of half-reactions in p-hydroxybenzoate hydroxylase caused by substituting the 2'-carbon of FAD with fluorine

Apo-p-hydroxybenzoate hydroxylase was reconstituted using 2'-fluoro-2'-deoxy-arabino-FAD, a synthetic flavin in which the hydroxyl of the 2'-center of the ribityl chain was replaced with fluorine in an inverted configuration. The absorbance spectral changes caused by the binding of either p-hydroxybenzoate (pOHB) or 2,4-dihydroxybenzoate (2,4-diOHB) indicated that the isoalloxazine of the artificial flavin adopts the more solvent-exposed "out" conformation rather than the partially buried "in" conformation near the aromatic substrate. In contrast, the flavin of the natural enzyme adopts the in conformation when pOHB is bound. Much of the behavior of the artificial enzyme can be rationalized in light of the preference of the flavin for the out conformation, including the weaker binding of pOHB, the tighter binding of 2,4-diOHB, and the slower reactions involved in the hydroxylation of pOHB and 2,4-diOHB. Particularly noteworthy is the enhancement of the reduction of the flavin by NADPH when pOHB is bound to the active site, consistent with the recent finding that the reaction occurs when the flavin adopts the out conformation (Palfey, B. A., Moran, G. R., Entsch, B., Ballou, D. P., and Massey, V. (1999) Biochemistry 38, 1153-1158). Thus, whereas the change that induces the out conformation is detrimental to the oxidative half-reaction, it improves the reductive half-reaction, showing that the control of the flavin position in p-hydroxybenzoate hydroxylase represents a compromise between the conflicting needs of two chemically disparate half-reactions, and demonstrating that the 2'-hydroxyl of FAD can serve as a critical control element in flavoenzyme catalysis.     

Mechanical analysis of the ring opening test applied to human ascending aortas

This work presents experiments, modelling and numerical simulation aimed at describing the mechanical response of human ascending aortas in the ring opening test. The objective is to quantify, from the opening angles measured in the test, the residual stress distribution along the artery wall and, afterwards, how this stress pattern changes when the artery is subjected to standard physiological pressures. The cases studied correspond to four groups including both healthy and pathological arteries. The tissues are characterized via tensile test measurements that enable to derive the material parameters of two constitutive models adopted in the present analysis. Overall, the numerical results obtained for all groups were found to be a useful data that allow to estimate the residual stress and their influence on the vessels under normal and hypertension physiological conditions.     

Enantio- and regioselectivity in the epoxide-hydrolase-catalyzed ring opening of simple aliphatic oxiranes: Part I: Monoalkylsubstituted oxiranes.

The in vitro conversion of chiral aliphatic monoalkylsubstituted oxiranes into 1,2-diols catalyzed by epoxide hydrolase of rat liver microsomes occurs with substrate enantioselectivity and regioselectivity. Substrate enantioselectivity is generally low, and has the same sense, for methyloxirane, vinyloxirane, epichloro-, and epibromohydrin. In the hydrolysis of t-butyloxirane inhibitory effects are involved leading to a complex pattern of enantioselectivity. All investigated monosubstituted aliphatic oxiranes are hydrolyzed with high regioselectivity by nucleophilic attack of water at the unsubstituted ring carbon atom. The enantiomeric excess of the unreacted oxirane substrates and the diol metabolites formed were determined by complexation and inclusion gas chromatography.     

Facile ring opening of 2,3-epoxy-steroids with aromatic amines in ionic liquids

Efficient ring opening of steroidal 2,3-epoxides with stoichiometric amount of aromatic amines has been carried out using an ionic liquid ([bmim](+)[BF(4)](-)) both as solvent and catalyst. The reactions were completely regio- and stereoselective in each case. The aminoalcohol products have chair conformations in ring A. The ionic liquid-mediated ring opening can efficiently be carried out with aliphatic amines like morpholine as well.     

Enantio- and regioselectivity in the epoxide-hydrolase-catalyzed ring opening of aliphatic oxiranes: Part II: Dialkyl- and trialkylsubstituted oxiranes.

The extent of substrate enantioselectivity and regioselectivity of a series of aliphatic 2,3-dialkyl- and trialkylsubstituted oxiranes in their in vitro epoxide-hydrolase-catalyzed hydrolysis depends on the size of the alkyl residues and on the substitution pattern of the oxirane ring. The enzyme-catalyzed hydrolysis of cis-oxiranes, containing at least one methyl substituent, shows complete or nearly complete substrate enantioselectivity and regioselectivity with nucleophilic attack by water occurring with inversion of configuration at the methylsubstituted ring carbon atom of (S)-configuration. In the hydrolysis of the isomeric trans-oxiranes, both enantiomers are metabolized with a higher rate for the (2S;3S)-enantiomer. The conversion of trimethyloxirane occurs with high substrate enantioselectivity in favor of the (S)-enantiomer and with complete regioselectivity at the monomethylsubstituted ring carbon atom. The differentiation of the enantiotopic ring carbon atoms (product enantioselectivity) in the smallest aliphatic meso-oxirane, cis-2,3-dimethyloxirane, leads to (2R;3R)-butane-2,3-diol with ee = 86%. cis-2-Ethyl-3-propyloxirane, possessing alkyl residues larger than methyl, represents an extremely poor substrate in the epoxide-hydrolase-catalyzed hydrolysis process.     

Theoretical investigation of the ring opening process of verdoheme to biliverdin in the presence of dioxygen

The conversion of ferrous verdoheme to ferric biliverdin in the presence of O₂ was investigated using the B3LYP method. Both 6-31G and 6-31G (d) basis sets were employed for geometry optimization calculation as well as energy stabilization estimation. Three possible pathways for the conversion of iron verdoheme to iron biliverdin were considered. In the first route oxygen and reducing electron were employed. In this path formation of ferrous verdoheme-O₂ complex was followed by the addition of one electron to the ferrous-oxycomplex to produce ferric peroxide intermediate. The ferric peroxide intermediate experienced an intramolecular nucleophilic attack to the most positive position at 5-oxo carbons on the ring to form a closed ring biliverdin. Subsequently the ring opening process took place and the iron (III) biliverdin complex was formed. Closed ring iron biliverdin intermediate and open ring iron biliverdin formed as a product of verdoheme cleavage were respectively 13.20 and 32.70 kcal mol⁻¹ more stable than ferric peroxide intermediate. Barrier energy for conversion of ferric peroxide to closed ring Fe (III) biliverdin and from the latter to Fe (III) biliverdin were respectively 8.67 and 3.35 kcal mol⁻¹. In this path spin ground states are doublet except for iron (III) biliverdin in which spin state is quartet. In the second path a ferrous-O₂ complex was formed and, without going to a one electron reduction process, nucleophilic attack of iron superoxide complex took place followed by the formation of iron (III) biliverdin. This path is thermodynamically and kinetically less favorable than the first one. In addition, iron hydro peroxy complex or direct attack of O₂ to macrocycle to form an isoporphyrin type intermediate have shown energy surfaces less favorable than aforementioned routes.     

Synthesis of a novel inhibitor against MRSA and VRE: preparation from zerumbone ring opening material showing histidine-kinase inhibition

Zerumbone ring-opening derivative 2 inhibited autophosphorylation of the essential histidine protein kinase (HPK), YycG, existing in Bacillus subtilis constituting a two-component system (TCS). However, it did not inhibit drug-resistant bacterium such as MRSA and VRE. Tryptophan derivative 34 also could be regulated by a TCS system like 2. In addition, 34 showed good inhibition against MRSA and VRE.     

Effect of the axial ligands on the structure and reactivity of tin verdoheme in the ring opening process

Conversion of tin(IV) verdoheme complex to tin(IV) biliverdin complex in the presence of hydroxide ion as a nucleophile and various axial ligands has been investigated using the B3LYP method. Our calculations show that in the six coordinate tin(IV) verdoheme complex with imidazole and hydroxyl axial ligands, conversion of tin(IV) verdoheme to open chain macrocycle is favorable thermodynamically but not kinetically. It has been determined that ring opening is prevented through a ligand-centered mechanism. Whereas, in other six coordinate complexes, formation of open chain macrocycles is favorable from both thermodynamics and kinetics point of views. On the contrary, in the five and four coordinate verdoheme complexes of tin(IV) binding of hydroxide to tin terminates the reaction at verdoheme stage and the ring opening is blocked. In fact, in the two latter coordination states, metal-centered inhibition is the proposed mechanism for blocking the ring opening. NBO analysis has shown that in the six coordinate verdoheme complexes internal hydrogen bonding has a key role in inhibition or facilitation of ring opening. These key findings have been confirmed with the results obtained from MO analysis. The presented results could be a hint for the possible implications or coordination for the competitive inhibition of degradation of verdoheme to biliverdin by hydrolysis reaction.     

Immobilized Candida antarctica lipase B: Hydration, stripping off and application in ring opening polyester synthesis

This work reviews the stripping off, role of water molecules in activity, and flexibility of immobilized Candida antarctica lipase B (CALB). Employment of CALB in ring opening polyester synthesis emphasizing on a polylactide is discussed in detail. Execution of enzymes in place of inorganic catalysts is the most green alternative for sustainable and environment friendly synthesis of products on an industrial scale. Robust immobilization and consequently performance of enzyme is the essential objective of enzyme application in industry. Water bound to the surface of an enzyme (contact class of water molecules) is inevitable for enzyme performance; it controls enzyme dynamics via flexibility changes and has intensive influence on enzyme activity. The value of pH during immobilization of CALB plays a critical role in fixing the active conformation of an enzyme. Comprehensive selection of support and protocol can develop a robust immobilized enzyme thus enhancing its performance. Organic solvents with a log P value higher than four are more suitable for enzymatic catalysis as these solvents tend to strip away very little of the enzyme surface bound water molecules. Alternatively ionic liquid can work as a more promising reaction media. Covalent immobilization is an exclusively reliable technique to circumvent the leaching of enzymes and to enhance stability. Activated polystyrene nanoparticles can prove to be a practical and economical support for chemical immobilization of CALB. In order to reduce the E-factor for the synthesis of biodegradable polymers; enzymatic ring opening polyester synthesis (eROPS) of cyclic monomers is a more sensible route for polyester synthesis. Synergies obtained from ionic liquids and immobilized enzyme can be much effective eROPS.     

Fatty acids,part 21: ring opening reactions of synthetic and natural furanoid fatty esters

Methyl 2,5-disubstituted C₁₈ furanoid fatty ester (viz. methyl 9,12-epoxyoctadeca-9,11-dienoate) was readily converted to methyl 9,12-dioxostearate using mineral or maleic acid. Conversion of the naturally occurring 2,3,5-trisubstituted furanoid fatty ester (viz. methyl 10,13-epoxy-11-methyloctadeca-10,12-dienoate) to the corresponding methyl 10,13-dioxo-11-methylstearate was much slower in rate under similar reaction conditions. The case of separating the dioxo derivatives from a mixture of other common fatty esters was demonstrated and the cyclodehydration of the isolated dioxo derivatives to the parent furanoid ester was rapidly achieved using dilute BF₃-methanol complex.     

Mechanism of inhibition of the GluA2 AMPA receptor channel opening: consequences of adding an N-3 methylcarbamoyl group to the diazepine ring of 2,3-benzodiazepine derivatives

2,3-Benzodiazepine derivatives are AMPA receptor inhibitors, and they are potential drugs for treating some neurological diseases caused by excessive activity of AMPA receptors. Using a laser-pulse photolysis and rapid solution flow techniques, we characterized the mechanism of action of a 2,3-benzodiazepine derivative, termed BDZ-f, by measuring its inhibitory effect on the channel-opening and channel-closing rate constants as well as the whole-cell current amplitude of the homomeric GluA2Q AMPA receptor channels. We also investigated whether BDZ-f competes with GYKI 52466 for binding to the same site on GluA2Q(flip). GYKI 52466 is the prototypic 2,3-benzodiazepine compound, and BDZ-f is the N-3 methylcarbamoyl derivative. We found that BDZ-f is a noncompetitive inhibitor with a slight preference for the closed-channel state of both the flip and the flop variants of GluA2Q. Similar to other 2,3-benzodiazepine compounds that we have previously characterized, BDZ-f inhibits GluA2Q(flip) by forming an initial, loose intermediate that is partially conducting; however, this intermediate rapidly isomerizes into a tighter, fully inhibitory receptor-inhibitor complex. BDZ-f binds to the same noncompetitive site as GYKI 52466 does. Together, our results show that the addition of an N-3 methylcarbamoyl group to the diazepine ring with the azomethine feature (i.e., GYKI 52466) is what makes BDZ-f more potent and more selective toward the closed-channel conformation than the original GYKI 52466. Our results have useful implications for the structure-activity relationship of the 2,3-benzodiazepine series.     

GluR3 flip and flop: differences in channel opening kinetics

Ample evidence from earlier studies of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors, GluR3 included, suggests that alternative splicing not only enriches AMPA receptor diversity but also, more importantly, creates receptor variants that are functionally different. However, it is not known whether alternative splicing affects the receptor channel opening that occurs in the microsecond time domain. Using a laser-pulse photolysis technique combined with whole-cell recording, we characterized the channel opening rate process for two alternatively spliced variants of GluR3, i.e., GluR3flip and GluR3flop. We show that the alternative splicing that generates flip and flop variants of GluR3 receptors regulates the channel opening process by controlling the rate of channel closing but not the rate of channel opening or the glutamate binding affinity. Specifically, the flop variant closes its channel almost 4-fold faster than the flip variant. We therefore propose that the function of the flip-flop sequence module in the channel opening process of AMPA receptors is to stabilize the open channel conformation, presumably by its pivotal structural location. Furthermore, a comparison of the flip isoform among all AMPA receptor subunits, based on the magnitude of the channel opening rate constant, suggests that GluR3 is kinetically more similar to GluR2 and GluR4 than to GluR1.     

Pleuromutilin derivatives having a purine ring. Part 3: Synthesis and antibacterial activity of novel compounds possessing a piperazine ring spacer

SAR studies on the water-soluble thioether pleuromutilin analogue 6, which has excellent in vitro and in vivo antibacterial activities, led to discovery of the novel pleuromutilin derivatives having a piperazine ring spacer. These derivatives displayed potent and well-balanced in vitro antibacterial activity against various drug-susceptible and -resistant Gram-positive bacteria. In particular, the promising pleuromutilin analogues 37 and 40 were found to exhibit strong in vivo efficacy against Staphylococcus aureus Smith.     

Enzymatic ring opening of an iron corrole by plant-type heme oxygenases: unexpected substrate and protein selectivities

Heme oxygenases are widely distributed enzymes involved in the oxidative cleavage of the heme macrocycle that yields the open-chain tetrapyrrole biliverdin IX, CO, and iron. For the first time, two regioisomeric iron corroles [α-CH- and γ-CH-Fe(cor)] have been utilized as artificial substrate and cofactor analogues to mammalian, plant, cyanobacterial, and bacterial heme oxygenases. The non-natural enzymatic cleavage of γ-CH-Fe(cor), catalyzed by plant-type heme oxygenases from Arabidopsis thaliana and Synechocystis sp., happens selectively at the unexpected bipyrrolic position and yields a biomimetic biliverdin-like product. The reaction is selective for this corrole regioisomer and for plant-type heme oxygenases and is the first report of an enzymatic corrole ring opening.