Mechanistic consequences of charge transfer systems in serine proteases and angiotensin: semiempirical computations

Structures and relative energies for the triads of interacting groups in the serine charge relay system of serine proteases and the proposed tyrosine charge relay system of angiotensin II, respectively, were computed according to the standard MNDOC procedure. The most stable configuration obtained for both systems was one in which the histidine residue was negatively charged. These findings indicate that the histidine ring and not the serine hydroxyl group at the active site of serine proteases would be the nucleophilic center which is acylated by substrate. Similarly, the extreme nucleophilicity of the imidazole anion produced by the proposed triad of interacting groups in angiotensin could provoke the formation of a transient covalent bond (acyl intermediate) between receptor and peptide in the receptor activation mechanism.     

3-Acylamino-azetidin-2-one as a novel class of cysteine proteases inhibitors

A new class of inhibitors for cysteine proteases cathepsin B, L, K and S is described. These inhibitors are based on the beta-lactam ring designed to interact with the nucleophilic thiol of the cysteine in the active site of cysteine proteases. Some 3-acylamino-azetidin-2-one derivatives showed very potent inhibition activities for cathepsins L, K and S at the nanomolar or subnanomolar IC(50) values.     

Protein damage and degradation by oxygen radicals. IV. Degradation of denatured protein

Proteolytic degradation of oxidatively damaged [3H] bovine serum albumin [( 3H]BSA) was studied during incubation with cell-free erythrocyte extracts and a wide variety (14) of purified proteases. [3H]BSA was pretreated by exposure (60Co radiation) to the hydroxyl radical (.OH), the superoxide anion radical (O2-), or the combination of .OH + O2- + oxygen. Treated (and untreated) samples were dialyzed and then incubated with erythrocyte extract or proteases for measurements of proteolytic susceptibility (release of acid-soluble counts). Both .OH and .OH + O2- + caused severalfold increases in proteolytic susceptibility (with extract and proteases), but O2- alone had no effect. Proteolytic susceptibility reached a maximum at 15 nmol of .OH/nmol of BSA and declined thereafter. In contrast, proteolytic susceptibility was still increasing at an .OH + O2-/BSA molar ratio of 100 (50% .OH + 50% O2-). Degradation in erythrocyte extracts was conducted by a novel ATP- and Ca2+-independent pathway, with maximal activity at pH 7.8. Inhibitor profiles indicate that this pathway may involve metalloproteases and serine proteases. Comparisons of proteolytic susceptibility with multiple modifications to BSA primary, secondary, and tertiary structure revealed a high correlation (r = 0.98) with denaturation/increased hydrophobicity by low concentrations of .OH. Covalent aggregation reactions (BSA cross-linking) may explain the declining proteolytic susceptibility observed at .OH/BSA molar ratios greater than 20. Protein denaturation may also have caused the increased proteolytic susceptibility induced by .OH + O2- + O2, but no simple correlation could be obtained. Results with .OH + O2- + O2 appear to have been complicated by direct BSA fragmentation reactions involving (.OH-induced) protein radicals and oxygen. These data indicate a direct and quantitative relationship between protein damage by oxygen radicals and increased proteolytic susceptibility. Oxidative denaturation may exemplify a simple, yet effective inherent mechanism for intracellular proteolysis.     

Enzymic oxidation of 3-hydroxyxanthine to 3-hydroxyuric acid.

1. Bovine milk xanthine oxidase (xanthine:oxygen oxidoreductase, EC 1.2.3.2) oxidises 3-hydroxyxanthine slowly to 3-hydroxyuric acid; the 1-methyl derivative of 3-hydroxyxanthine is attacked about twice as fast. 2. The pH optimum for the reaction of 2-hydroxyxanthine is near 5, i.e. the neutral form of this substrate is attacked much faster than the anion. Probably in the "active" form of the latter, the negative charge is located mainly in the imidazole ring, thus inhibiting nucleophilic attack at C-8.     

Autoxidation of oxymyoglobin. An overall stoichiometry including subsequent side reactions

Oxymyoglobin (MbO2) is oxidized easily to metmyoglobin (metMb) with generation of the superoxide anion, which can be converted by the spontaneous dismutation into H2O2, this being also a potent oxidant of MbO2. In the presence of sodium azide in stoichiometric amounts, however, the rate of autoxidation of MbO2 increased rapidly with increasing concentration of the anion, but soon reached a saturating level, the extent of which was about twice that of the normal autoxidation in buffer alone. Quantitative analysis has revealed that this enhancement is not due to the nucleophilic displacement of O2- from MbO2 by the anion (Satoh, Y., and Shikama, K. (1981) J. Biol. Chem. 256, 10272-10275), but is due to the additional oxidation of MbO2 by H2O2 freed from the metMb being occupied by the anion at the sixth coordination position. Based on these novel results and stoichiometric considerations, it is possible to propose a new view that H2O2 produced from O2- can be eliminated or decomposed mostly, if not completely, by the metMb resulting from the normal autoxidation reaction of MbO2, presumably via the formation of the ferryl species.     

Synthesis of cationic single-isomer cyclodextrins for the chiral separation of amino acids and anionic pharmaceuticals

We describe a protocol for the synthesis of mono-6(A)-(1-butyl-3-imidazolium)-6(A)-deoxy-beta-cyclodextrin chloride (BIMCD), a cationic, water-soluble cyclodextrin used in the chiral separation of amino acids and anionic pharmaceuticals by capillary electrophoresis. Starting from commercially available chemicals, BIMCD is synthesized in five steps. The first step involves a nucleophilic substitution between p-toluenesulfonyl chloride and imidazole to afford 1-(p-toluenesulfonyl)imidazole (A). In the second step, a nucleophilic substitution between beta-cyclodextrin and A affords mono-6(A)-(p-toluenesulfonyl)-6(A)-deoxy-beta-cyclodextrin (B). In the third step, a nucleophilic substitution between 1-bromobutane and imidazole affords 1-butylimidazole (C). In the fourth step, a nucleophilic addition between A and C affords BIMCD tosylate. In the final step, anion exchange using an ion-exchange resin yields BIMCD as a highly water-soluble solid. Each step takes up to 2 d, including the time required for product purification. The overall protocol requires approximately 6 d.     

Crystal structure of an actinidin-E-64 complex.

E-64, 1-(L-trans-epoxysuccinylleucylamino)-4-guanidinobutane, is a potent and highly selective irreversible inhibitor of cysteine proteases. The crystal structure of a complex of actinidin and E-64 has been determined at 1.86-A resolution by using the difference Fourier method and refined to an R-factor of 14.5%. The electron density map clearly shows that the C2 atom of the E-64 epoxide ring is covalently bonded to the S atom of the active-site cysteine 25. The charged carboxyl group of E-64 forms four H-bonds with the protein and thus may play an important role in favorably positioning the inhibitor molecule for nucleophilic attack by the active-site thiolate anion. The interaction features between E-64 and actinidin are very similar to those seen in the papain-E-64 complex; however, the amino-4-guanidinobutane group orients differently. The crystals of the actinidin-E-64 complex diffracted much better than the papain-E-64 complex, and consequently the present study provides more precise geometrical information on the binding of the inhibitor. Moreover, this study provides yet another confirmation that the binding of E-64 is at the S subsites and not at the S' subsites as has been previously proposed. The original actinidin structure has been revised using the new cDNA sequence information.     

Recognition of nucleophile-treated alpha 2-macroglobulin by the alveolar macrophage alpha-macroglobulin . protease complex receptor

Rabbit alveolar macrophages exhibit high affinity surface receptors which recognize alpha 2-macroglobulin . protease complexes but not native alpha 2- macroglobulin. Binding of alpha 2-macroglobulin . protease complexes to surface receptors is independent of the protease used to form the complex. In this communication, we demonstrate that treatment of human alpha 2-macroglobulin with nucleophilic agents (methyl amine, ammonium salts) converts native alpha 2-macroglobulin into a form recognized by the surface receptor for alpha 2-macroglobulin protease complexes. Analysis of the concentration dependency of ligand binding revealed that the surface receptor did not distinguish between nucleophile-treated alpha 2-macroglobulin and alpha 2-macroglobulin . protease complexes. These results are consistent with the hypothesis that proteases or nucleophilic agents effect the hydrolysis of an internal thiol-ester bond (Tack, B. F., Harrison, R. A., Janatova, J., Thomas, M. L., and Prahl, J. W. (1980) Proc. Natl. Acad. Sci. U. S. A. 77, 5764-5768), leading to an alteration in alpha 2-macroglobulin conformation. The altered conformation results in recognition of the alpha 2-macroglobulin by surface receptors.     

How pyridoxal 5'-phosphate could function in glycogen phosphorylase catalysis.

A mechanism for the phosphorylase reaction is proposed which offers a plausible explanation for the essential role of pyridoxal 5'-phosphate in glycogen phosphorylases: in the forward direction, phosphorolysis of alpha-1,4-glycosidic bonds in oligo- or polysaccharides is started by protonation of the glycosidic oxygen by the substrate orthophosphate followed by stabilization of the incipient oxocarbonium ion and subsequent covalent binding to form alpha-glucose 1-phosphate. In the reverse direction, protonation of the phosphate of glucose 1-phosphate destabilizes the glycosidic bond and promotes formation of a glucosyl oxocarbonium ion-phosphate anion pair. In the subsequent step the phosphate anion facilitates the nucleophilic attack of a terminal glucosyl residue on the carbonium ion bringing about alpha-1,4-glycosidic bond formation and primer elongation. Both in the forward and reverse reactions, the phosphate of the cofactor pyridoxal 5'-phosphate acts as a general acid (PL-OPO3H- or PL-OPO3(2-) and protonates the substrate phosphate functioning as proton shuttle. Thus in glycogen phosphorylases, phosphates which directly interact with each other have replaced a pair of amino acid carboxyl groups functioning in catalysis of carbohydrases.     

The synthesis of some fluoro derivatives of sucrose

2,3,1',3'4',6'-Hexa-O-benzylsucrose was obtained by mild acid-catalysed hydrolysis of the 4,6-O-isopropylidene derivative and then converted into its 4,6-di-O-mesyl derivative. Selective displacement of this disulphonate with fluoride anion (from tetrabutylammonium fluoride) then afforded the 6-fluoro-4-mesylate. Removal of the protecting groups yielded 6-deoxy-6-fluorosucrose, which was characterised as its crystalline hepta-acetate. A derivative of 6-deoxy-6-fluoro-galacto-sucrose was formed when the above 6-fluoro-4-mesylate was subjected to nucleophilic displacement with benzoate anion.     

A Mechanistic Study of the Dihydroflavin Reductive Cleavage of the Dihydroflavin-Tetrahydronaphthalene Epoxide Adducts

Dihydroflavins are facile reducing agents and potent nucleophiles. The dihydroflavin nucleophilic reactivity, as measured by the rate of covalent flavin adduct formation with tetrahydronaphthalene epoxides, is comparable to that of the thiolate anion (Y. T. Lee and J. F. Fisher (1993) J. Org. Chem. 58, 3712). In these reactions there appears subsequent to the nucleophilic cleavage of the epoxide by the dihydroflavin the product corresponding to formal hydride reduction product (at the benzylic carbon) of these epoxides. Thus the reaction of (+/-)-1a,2,3, 7b-tetrahydro-(1aalpha,2alpha,3beta,7balpha)-naphth[1,2-b]oxirene-2,3-diol (1), (+/-)-1a,2,3,7b-tetrahydro-(1aalpha,2beta,3alpha,7balpha)-naphth[1,2-b]oxirene-2,3-diol (2), and (+/-)-1a,2,3,7b-tetrahydro-(1aalpha,7balpha)-naphth[1,2-b]oxirene (3) in 9:1 (v/v) aqueous Tris buffer-dioxane, at both acidic and neutral pH, with FMNH(2) and 1,5-dihydrolumiflavin (LFH(2)) gave (following covalent flavin-epoxide adduct formation) the products having a methylene group at the benzylic position. The reduction product yield was proportional to the yield of the N(5) flavin-epoxide adduct intermediate, and the rate of the reaction was proportional to the dihydroflavin concentration. These observations are consistent with these reduction products resulting from bimolecular reaction between the dihydroflavin-epoxide adduct and a second molecule of dihydroflavin. Copyright 2000 Academic Press.     

Catalytic role of proton transfers in the formation of a tetrahedral adduct in a serine carboxyl peptidase

Quantum mechanical/molecular mechanical molecular dynamics and 2D free energy simulations are performed to study the formation of a tetrahedral adduct by an inhibitor N-acetyl-isoleucyl-prolyl-phenylalaninal (AcIPF) in a serine-carboxyl peptidase (kumamolisin-As) and elucidate the role of proton transfers during the nucleophilic attack by the Ser278 catalytic residue. It is shown that although the serine-carboxyl peptidases have a fold resembling that of subtilisin, the proton transfer processes during the nucleophilic attack by the Ser residue are likely to be more complex for these enzymes compared to the case in classical serine proteases. The computer simulations demonstrate that both general base and acid catalysts are required for the formation and stabilization of the tetrahedral adduct. The 2D free energy maps further demonstrate that the proton transfer from Ser278 to Glu78 (the general base catalyst) is synchronous with the nucleophilic attack, whereas the proton transfer from Asp164 (the general acid catalyst) to the inhibitor is not. The dynamics of the protons at the active site in different stages of the nucleophilic attack as well as the motions of the corresponding functional groups are also studied. It is found that the side chain of Glu78 is generally rather flexible, consistent with its possible multifunctional role during catalysis. The effects of proton shuffling from Asp82 to Glu78 and from Glu32 to Asp82 are examined, and the results indicate that such proton shuffling may not play an important role in the stabilization of the tetrahedral intermediate analogue.     

Preparation and receptor binding affinities of cyclic C-terminal neurotensin (8-13) and (9-13) analogues.

Cyclic analogues of neurotensin (NT) C-terminal fragments NT(8-13) and NT(9-13) were produced via intramolecular nucleophilic substitution of the Tyr(11) phenoxide anion on a 6-bromohexanoyl side chain substituted at position 8 or 9 and tested for NT receptor binding affinity.     

Quantum chemistry analysis of the mechanism of action of proteolytic enzymes. III. Proton transport in serine proteases

The model system for the proton transfer on the amide atom of the substrate leaving group based on the existence of "charge relay system" in the serine type proteases was analysed by the CNDO/2 method. The unfitness of this model to explain the action mechanism of serine proteases was shown. The model system for proton transfer with the water molecule as the intermediate acceptor of the Ser-195 proton was suggested and analysed by the same method. The acylation activation barrier of this system was shown to localize on the stage of synchronous transfer of the Ser-195 alcoholic proton and the water molecule proton hydrogen bound to the His-57 N epsilon 2-atom on the water molecule oxygen atom and the N epsilon 2-atom, respectively. The protonation of substrate in the case of the model system with the water molecule as the intermediate acceptor of proton was demonstrated to begin before the completion of the tetrahedral intermediate substance and the protonated from of the tetrahedral intermediate was shown to form only. A hypothesis considering the role of this water molecule as the nucleophilic reagent on the deacylation stage is presented.     

Crystal structure of a novel viral protease with a serine/lysine catalytic dyad mechanism

The blotched snakehead virus (BSNV), an aquatic birnavirus, encodes a polyprotein (NH2-pVP2-X-VP4-VP3-COOH) that is processed through the proteolytic activity of its own protease (VP4) to liberate itself and the viral proteins pVP2, X and VP3. The protein pVP2 is further processed by VP4 to give rise to the capsid protein VP2 and four structural peptides. We report here the crystal structure of a VP4 protease from BSNV, which displays a catalytic serine/lysine dyad in its active site. This is the first crystal structure of a birnavirus protease and the first crystal structure of a viral protease that utilizes a lysine general base in its catalytic mechanism. The topology of the VP4 substrate binding site is consistent with the enzymes substrate specificity and a nucleophilic attack from the si-face of the substrates scissile bond. Despite low levels of sequence identity, VP4 shows similarities in its active site to other characterized Ser/Lys proteases such as signal peptidase, LexA protease and Lon protease. Together, the structure of VP4 provides insights into the mechanism of a recently characterized clan of serine proteases that utilize a lysine general base and reveals the structure of potential targets for antiviral therapy, especially for other related and economically important viruses, such as infectious bursal disease virus in poultry and infectious pancreatic necrosis virus in aquaculture.     

2-Chloro-2′-deoxyadenosine: Synthesis and Antileukemic Activity of 8-Substituted Derivatives

Abstract

A series of 8-substituted 2-chloro-2′-deoxyadenosine (2-CdA, 1) derivatives were prepared as potential anticancer agents. They were synthesized stereoselectively by the anion glycosylation of 2,6,8-trichloropurine or obtained by nucleophilic displacement reactions on 8-bromo-2-chloro-2′-deoxyadenosine (3). Within the 8-substituted CdA derivatives the 8-thioxo compound 11 was cytotoxic to several leukemia cell lines.     

The function of lymphocyte proteases. Inhibition and restoration of granule-mediated lysis with isocoumarin serine protease inhibitors.

To kill other cells, lymphocytes can exocytose granules that contain serine proteases and pore-forming proteins (perforins). We report that mechanism-based isocoumarin inhibitors inhibited the proteases and inactivated lysis. When inhibited proteases were restored, lysis was also restored, indicating that the proteases were essential for lysis. We found three new lymphocyte protease activities, "Asp-ase,"Met-ase," and "Ser-ase," which in addition to ly-tryptase and ly-chymase, comprise five different protease activities in rat RNK-16 granules. The general serine protease inhibitor 3,4-dichloroisocoumarin (DCI) inhibited all five protease activities. Essentially all protease molecules were inactivated by DCI before lysis was reduced, as determined from DCI's second order inhibition rate constants for the proteases, the DCI concentrations, and the times of pretreatment needed to block lysis. The pH favoring DCI inhibition of lysis was the pH optimum for protease activity. Isocoumarin reagents acylate, and may sometimes secondarily alkylate, serine protease active sites. Granule proteases, inhibited by DCI acylation, were deacylated with hydroxylamine, restoring both the protease and lytic activities. Hydroxylamine does not restore alkylated proteases and did not restore the lytic activities after inhibition with 4-chloro-7-guanidino-3-(2-phenylethoxy)-isocoumarin, a more alkylating mechanism-based inhibitor designed to react with tryptases. It is improbable that isocoumarin reagents directly inactivated pore-forming proteins because 1) these reagents require protease activation, 2) their nonspecific effects are alkylating, and 3) alkylated proteins are not restored by hydroxylamine. We conclude that serine proteases participate in lysis when lysis is mediated by the complete assembly of granule proteins.     

The SUMO-Specific Protease Senp2 Regulates SUMOylation,Expression and Function of Human Organic Anion Transporter 3

Organic anion transporter 3 (OAT3) plays a vital role in removing a broad array of anionic drugs from kidney, thereby avoiding their possibly toxic side effects in the body. We earlier demonstrated that OAT3 is subjected to a specific type of post-translational modification called SUMOylation. SUMOylation is a dynamic event, where de-SUMOylation is catalyzed by a class of SUMO-specific proteases. In the present investigation, we assessed the role of SUMO-specific protease Senp2 in OAT3 SUMOylation, expression and function. We report here that overexpression of Senp2 in COS-7 cells led to a reduced OAT3 SUMOylation, which correlated well with a decreased OAT3 expression and transport activity. Such phenomenon was not observed in cells overexpressing an inactive mutant of Senp2. Furthermore, transfection of cells with Senp2-specific siRNA to knockdown the endogenous Senp2 resulted in an increased OAT3 SUMOylation, which correlated well with an enhanced OAT3 expression and transport activity. Coimmunoprecipitation experiments showed that Senp2 directly interacted with OAT3 in the kidneys of rats. Together these results provided first demonstration that Senp2 is a significant regulator for OAT3-mediated organic anion/drug transport.     

Mechanism of hydrolyses of phenyl alpha-maltosides catalyzed by taka-amylase A.

Michaelis constants (Kms) and molecular activities (kos) of phenyl, p-nitrophenyl and p-methylphenyl alpha-maltoside for taka-amylase A catalyzed hydrolyses were determined in H2O and in D2O at pH or pD 5.3 and at 25 degrees C. Production of alpha-maltose in the hydrolysis was confirmed by 1H NMR. Neither substituent nor solvent deuterium isotope effects on Kms for phenyl, p-nitrophenyl and p-methylphenyl alpha-maltosides were detected. On the other hand, substituent effects on kos of these compounds were evident, but the isotope effects on kos were not marked, so that protonation of the substrate in the catalytic reaction might not be rate-limiting. The result indicates that nucleophilic attack of a carboxylate anion of the enzyme upon the protonated substrate is the rate-limiting step in the hydrolysis proceeding through the nucleophilic double displacement mechanism, which involves a covalently bonded glycosyl intermediate. The molecular orbitals of phenyl alpha-D-glucosides as model compounds of phenyl alpha-maltosides were calculated by the AM1 method. From the results, it was concluded that the lowering of the lowest unoccupied molecular orbital (LUMO) energy levels and the increase of distribution of LUMO on the anomeric carbon, C-1, of the compounds are caused by protonation at the glycosidic oxygen from the protonated carboxyl group of the enzyme. This causes acceleration of the hydrolysis of a substrate by the enzyme.