Peptide-cleaving agents for human islet amyloid polypeptide containing substrate recognition site based on quinoxaline: cleavage efficiency enhanced by lowering substrate concentration.

Oligomers of human islet amyloid polypeptide (h-IAPP) are believed to be the pathogenic species for type 2 diabetes mellitus. Peptide-cleaving agents selective for oligomers of h-IAPP were synthesized by using quinoxaline derivatives as recognition sites attached to the Co(III) complex of cyclen in this study. When the initial concentration of h-IAPP was lowered from 4.0 to 0.20 µM, cleavage yield of the new agents was enhanced by 3 times reaching 16-22 mol%. This shows that the agents would have significant activities at subnano molar concentrations if the concentration of h-IAPP is lowered to the in vivo values. This further indicates that the peptide-cleaving agents prepared previously in this laboratory possess sufficiently high activity for application as a new therapeutic option for Alzheimer's disease, type 2 diabetes mellitus, and Parkinson's disease.

A Co(III) complex cleaving soluble oligomers of h-IAPP in the presence of polymeric aggregates of h-IAPP.

Soluble oligomers of human islet amyloid polypeptide (h-IAPP) are believed to be the pathogenic species for type 2 diabetes mellitus. In search of the peptide-cleavage agent cleaving oligomers of h-IAPP with low affinity for polymeric aggregates of h-IAPP, a chemical library was constructed by using the Ugi condensation. From the library, a Co(III) complex was discovered to cleave soluble oligomers of h-IAPP in the presence of polymeric aggregates of h-IAPP without being captured by the aggregates considerably. The peptide-cleavage agent inhibited apoptosis of INS-1 cell by h-IAPP even in the presence of preformed polymeric aggregates of h-IAPP. This suggests that target-selective peptide-cleavage agents may be applied clinically not only to diabetes but also to various other amyloid diseases.

New chelating ligands for Co(III)-based peptide-cleaving catalysts selective for pathogenic proteins of amyloidoses.

The Co(III) complex of 1,4,7,10-tetraazacyclododecane has been employed as the catalytic center of target-selective peptide-cleaving catalysts in previous studies. As new chelating ligands for the Co(III) ion in the peptide-cleaving catalysts, 1-oxo-4,7,10-triazacyclodedecane, 1-aryl-1,4,7,10-tetraazacyclodecane, and 7-aryl-1-oxo-4,7,10-triazacyclodecane were examined in the present study. A chemical library comprising 612 derivatives of the Co(III) complex of the new chelating ligands was constructed. The catalyst candidates were tested for their activity to cleave the soluble oligomers of amyloidogenic peptides amyloid ß-42 and human islet amyloid polypeptide (h-IAPP), which are believed to be the pathogenic species for Alzheimer's disease and type 2 diabetes mellitus, respectively. One derivative of the Co(III) complex of 1-aryl-1,4,7,10-tetraazacyclodecane was found to cleave the oligomers of h-IAPP. Cleavage products were identified and cleavage yields were measured at various catalyst concentrations for the action of the new catalyst. The present results reveal that effective catalytic drugs for amyloidoses may be obtained by using Co(III) complexes of various chelating ligands.

Soluble artificial metalloproteases with broad substrate selectivity, high reactivity, and high thermal and chemical stabilities.

To design soluble artificial proteases that cleave peptide backbones of a wide range of proteins with high reactivity, artificial active sites comprising the Cu(II) complex of 1-oxa-4,7,10-triazacyclodedecane (oxacyclen) and the aldehyde group were synthesized. The aldehyde group was employed as the binding site in view of its ability to reversibly form imine bonds with ammonium groups exposed on the surfaces of proteins, and Cu(II) oxacyclen was exploited as the catalytic group for peptide hydrolysis. The artificial metalloproteases synthesized in the present study cleaved all of the protein substrates examined (albumin, gamma-globulin, myoglobin, and lysozyme). In addition, the activity of the best soluble artificial protease was enhanced by up to 190-fold in terms of kcat/Km. When the temperature was raised to 80 degrees C, the activities of the artificial proteases were significantly enhanced. The activity of the artificial protease was not greatly affected by surfactants, including sodium dodecyl sulfate. The intermediacy of the imine complex formed between the artificial protease and the protein substrate was supported by an experiment using sodium cyanoborohydride. Soluble artificial metalloproteases with broad substrate selectivity, high reactivity, high thermal and chemical stabilities, and small molecular weights were thus synthesized by positioning the aldehyde group in proximity to Cu(II) oxacyclen.

Cell-penetration by Co(III)cyclen-based peptide-cleaving catalysts selective for pathogenic proteins of amyloidoses.

Derivatives of the Co(III) complex of 1,4,7,10-tetraazacyclododecane (cyclen) with various organic pendants have been reported as target-selective peptide-cleaving catalysts, which can be exploited as catalytic drugs. In order to provide a firm basis for the catalytic drugs based on Co(III)cyclen, the ability of the Co(III)cyclen-containing peptide-cleaving catalysts to penetrate animal cells such as mouse fibroblast NIH-3T 3 or human embryonic kidney (HEK) 293 cells is demonstrated in the present study. Since the catalysts destroy pathogenic proteins for amyloidoses, results of the present study are expected to initiate extensive efforts to obtain therapeutically safe catalytic drugs for amyloidoses such as Alzheimer's disease, type 2 diabetes mellitus, Parkinson's disease, Huntington's disease, mad cow disease, and so on.

Mechanical capping of silica nanotubes for encapsulation of molecules.

Multifunctional silica nanotubes (SNTs) are being widely used for many biomedical applications due to their structural benefits. Controlling the structure of the open end of an SNT is a crucial step for drug/gene delivery and for fabrication of multifunctional SNTs. We developed a mechanical capsulation method to fabricate caps at the ends of SNTs. A thin layer of malleable capping materials (Au, Ag, PLGA) was deposited onto the surface of an SNT-grown AAO template. Capped SNTs were then obtained by hammering with alumina microbeads. For a proof-of-concept experiment, we demonstrated dye-encapsulated SNTs without any chemical functionalizations. Since a mechanical approach is free of the issue of chemical compatibility between cargo molecules and capping materials, the method can provide an effective platform for the preparation of smart multifunctional nanotubes for biomedical applications.

A bifunctional molecule as an artificial flavin mononucleotide cyclase and a chemosensor for selective fluorescent detection of flavins.

Flavins, comprising flavin mononucleotide (FMN), flavin adenine dinucleotide (FAD), and riboflavin (RF, vitamin B(2)), play important roles in numerous redox reactions such as those taking place in the electron-transfer chains of mitochondria in all eukaryotes and of plastids in plants. A selective chemosensor for flavins would be useful not only in the investigation of metabolic processes but also in the diagnosis of diseases related to flavins; such a sensor is presently unavailable. Herein, we report the first bifunctional chemosensor (PTZ-DPA) for flavins. PTZ-DPA consists of bis(Zn(2+)-dipicolylamine) and phenothiazine. Bis(Zn(2+)-dipicolylamine) (referred to here as XyDPA) was found to be an excellent catalyst in the conversion of FAD into cyclic FMN (riboflavin 4',5'-cyclic phosphate, cFMN) under physiological conditions, even at pH 7.4 and 27 degrees C, with less than 1 mol % of substrate. Utilizing XyDPA's superior function as an artificial FMN cyclase and phenothiazine as an electron donor able to quench the fluorescence of an isoalloxazine ring, PTZ-DPA enabled selective fluorescent discrimination of flavins (FMN, FAD, and RF): FAD shows ON(+), FMN shows OFF(-), and RF shows NO(0) fluorescence changes upon the addition of PTZ-DPA. With this selective sensing property, PTZ-DPA is applicable to real-time fluorescent monitoring of riboflavin kinase (RF to FMN), alkaline phosphatase (FMN to RF), and FAD synthetase (FMN to FAD).

Metal complexes as artificial proteases: toward catalytic drugs.

Catalytic cleavage of the backbone of a protein related to a disease may cure the disease. Owing to the catalytic nature of the protein inactivation, the drug dosage and the side effects can be reduced with the catalytic drugs. Catalytic drugs can be designed even for proteins lacking active sites. Effective artificial proteases have been designed for proteins or oligomers of oligopeptides. The Co(III) complex of cyclen has been used as the catalytic center for peptide hydrolysis. Binding sites of the catalysts that recognize the targets have been searched by using various kinds of chemical libraries. Some of the artificial metalloproteases reported till date offer a new therapeutic option for amyloidoses (e.g. Alzheimer's disease, type 2 diabetes mellitus, Parkinson's disease, mad cow's disease, etc.).

Proteolytic activity of Co(III) complex of 1-oxa-4,7,10-triazacyclododecane: a new catalytic center for peptide-cleavage agents.

Catalytic drugs based on target-selective artificial proteases have been proposed as a new paradigm in drug design. Peptide-cleavage agents selective for pathogenic proteins of Alzheimer's disease, type 2 diabetes mellitus or Parkinson's disease have been prepared using the Co(III) aqua complex (Co(III)cyclen) of 1,4,7,10-tetraazacyclododecane as the catalytic center. In the present study, the Co(III) aqua complex (Co(III)oxacyclen) of 1-oxa-4,7,10-triazacyclododecane was examined in search of an improved catalytic center for peptide-cleavage agents. An X-ray crystallographic study of [Co(oxacyclen)(CO(3))](ClO(4)), titration of Co(III)oxacyclen, and kinetic studies on the cleavage of albumin, gamma-globulin, lysozyme, and myoglobin by Co(III)oxacyclen were carried out. Considerably higher proteolytic activity was observed for Co(III)oxacyclen in comparison with Co(III)cyclen, indicating that better target-selective artificial metalloproteases would be obtained using Co(III)oxacyclen as the catalytic center. The improved proteolytic activity was attributed to either steric effects or the increased Lewis acidity of the Co(III) center. The kinetic data also predicted that side effects due to the cleavage of nontarget proteins by a catalytic drug based on Co(III)oxacyclen would be insignificant.

Proteolytic activity of Cu(II) complex of 1-oxa-4,7,10-triazacyclododecane.

Proteolytic activity of the Cu(II) complex of 1-oxa-4,7,10-triazacyclododecane (oxacyclen) was compared with that of the Cu(II) complex of 1,4,7,10-tetraazacyclododecane by using albumin, gamma-globulin, and myoglobin as substrates. Values of kcat/Km were greater for Cu(II)oxacyclen by 40-80 times. The enhanced activity is attributed to the increased Lewis acidity of Cu(II) due to substitution of one nitrogen donor atom with oxygen.

Protein-cleaving catalyst selective for protein substrate.

A protein-cleaving catalyst specific for a disease-related protein can be used as a catalytic drug. As the first protein-cleaving catalyst selective for a protein substrate, a catalyst for myoglobin was designed by attaching Cu(II) or Co(III) complex of cyclen to a binding site searched by a combinatorial method using peptide nucleic acid monomers as building units. [reaction: see text]

Kinetics of Hydrolysis of Phenyl Acetates Catalyzed by the Zinc(II) Complex of 1,5,9-Triazacyclododecane. Evidence for Attack of Water or Hydroxide Ion at the Coordinated Ester.

Rates for hydrolysis of substituted phenyl acetates were measured in the presence of the Zn(II) complex of 1,5,9-triazacyclododecane. The kinetic data are incompatible with the mechanism in which the water and hydroxide ion coordinated to the metal center makes a nucleophilic attack at the ester linkage. Instead, the results support the mechanism in which the ester is first complexed to the metal center and then water or hydroxide ion makes a nucleophilic attack at the complexed ester. The kinetic data further indicate that the electrostatic interaction between the cationic metal center and the anionic hydroxide ion facilitates the attack of hydroxide ion at the complexed ester. In addition, the C-O bond of the ester is not cleaved significantly in the rate-determining transition state for attack by both water and hydroxide ion.

Target-selective peptide-cleaving catalysts as a new paradigm in drug design.

This tutorial review describes the evolution of peptide-hydrolyzing metal catalysts towards artificial metalloproteases cleaving target proteins selectively. The catalytic cleavage of the backbone of a protein related to a disease may effect a cure. In particular, a new therapeutic option for amyloid diseases such as Alzheimer's disease, diabetes and Parkinson's disease has been presented. The new paradigm of drug design based on artificial metalloproteases should be of interest to researchers in the areas of biomimetic chemistry, as well as medicinal chemistry.

Cleavage agents for soluble oligomers of human islet amyloid polypeptide.

Soluble oligomers of human islet amyloid polypeptide (h-IAPP) are implicated in the initiation of beta-cell apoptosis leading to type 2 diabetes mellitus (T2DM). Cleavage of the h-IAPP included in an oligomer may provide a novel method for reducing the level of h-IAPP oligomers, offering a new therapeutic option for T2DM. From the combinatorial library of triazine derivatives prepared by exploiting the Co(III) complex of cyclen as the cleavage center for peptide bonds, eight compounds were selected as cleavage agents for oligomers of h-IAPP. After reaction with cleavage agents for 36 h at 37 degrees C and pH 7.50, up to 20 mol% of h-IAPP (initial concentration: 4.0 microM) was cleaved, although the target oligomers existed as transient species. Considerable activity was manifested at agent concentrations as low as 100 nM.

Peptide-cleaving catalyst selective for melanin-concentrating hormone: Oxidative decarboxylation of N-terminal aspartate catalyzed by Co(III)cyclen.

To provide a firm basis for the new paradigm of drug discovery based on catalysts for oxidative cleavage of N-terminal aspartate (Asp) residues of oligopeptides, oligopeptide-cleaving catalysts were searched by using melanin-concentrating hormone (MCH) as the substrate. MCH is a target for designing drugs to reduce obesity. Catalyst candidates containing the Co(III) complex of cyclen as the catalytic center were prepared by multicomponent condensation reactions. From three kinds of chemical libraries containing about 19,000 catalyst candidates, one compound was identified as the MCH-cleaving catalyst. On incubation with the catalyst, the N-terminal Asp residue of MCH was converted to the pyruvate residue by oxidative decarboxylation. Detailed kinetics analysis revealed the catalytic nature of the action of the catalyst. In addition, the kinetics data indicated that MCH can be cleaved with half-lives of 3 h or less with submicromolar catalyst concentrations if the structure of the catalyst is further improved.

Structural and dynamical basis of broad substrate specificity, catalytic mechanism, and inhibition of cytochrome P450 3A4.

Cytochrome P450 (CYP) 3A4 is responsible for the oxidative degradation of more than 50% of clinically used drugs. By means of molecular dynamics simulations with the newly developed force field parameters for the heme-thiolate group and its dioxygen adduct, we examine the differences in structural and dynamic properties between CYP3A4 in the resting form and its complexes with the substrate progesterone and the inhibitor metyrapone. The results indicate that the broad substrate specificity of CYP3A4 stems from the malleability of a loop (residues 211-218) that resides in the vicinity of the channel connecting the active site and bulk solvent. However, the high-amplitude motion of the flexible loop is found to be damped out upon binding of the inhibitor or the substrate in the active site. In the resting form of CYP3A4, a structural water molecule is bound to the sixth coordination position of the heme iron, stabilizing the octahedral coordination geometry. In addition to the direct coordination of metyrapone to the heme iron, the hydrogen bond interaction between the inhibitor carbonyl group and the side chain of Ser119 also contributes significantly to stabilizing the CYP3A4-metyrapone complex. On the other hand, progesterone is stabilized in the active site by the formation of two hydrogen bonds with Ser119 and Arg106, as well as by the van der Waals interactions with the heme and hydrophobic residues. The structural and dynamic features of the CYP3A4-progesterone complex indicate that the oxidative degradation of progesterone occurs through hydroxylation at the C16 position by the reactive oxygen coordinated to the heme iron.

Angiotensin-cleaving catalysts: conversion of N-terminal aspartate to pyruvate through oxidative decarboxylation catalyzed by Co(III)cyclen.

To provide a firm basis for the new paradigm of drug discovery based on peptide-cleaving catalysts, oligopeptide-cleaving catalysts were searched for by using human angiotensin I (Ang-I) and angiotensin II (Ang-II) as the substrates. Catalyst candidates containing the Co(III) complex of cyclen as the catalytic center were prepared by multicomponent condensation reactions. From two types of chemical libraries containing about 3,600 catalyst candidates, two compounds [SS-Co(III)X and S-Co(III)Y] were selected as the most active catalysts. On incubation with SS-Co(III)X and S-Co(III)Y, both Ang-I and Ang-II were cleaved by oxidative decarboxylation instead of peptide hydrolysis: the N-terminal Asp residues of Ang-I and Ang-II were converted to pyruvate residues. Catalysts for oxidative decarboxylation of the N-terminal Asp residue contained in an oligopeptide are unprecedented in both biological and chemical systems. Detailed kinetics analysis suggested that Ang-I and Ang-II can be cleaved with half-lives much less than 1 h if the structures of the chelating ligands of the catalysts are further improved. The results indicated that the concept of the peptide-cleaving catalysts can be expanded to include oligopeptides as the targets and nonhydrolytic reactions as the means for cleavage.

Artificial metalloprotease with active site comprising aldehyde group and Cu(II)cyclen complex.

To design artificial proteases that cleave peptide backbones of a wide range of proteins at selected sites, artificial active sites comprising the Cu(II) complex of cyclen (Cu(II)Cyc) and aldehyde group were synthesized on a cross-linked polystyrene. The aldehyde group was employed as the binding site in view of its ability of reversible formation of imine bonds with epsilon-amino groups of Lys residues exposed on the surface of proteins and Cu(II)Cyc as the catalytic group for peptide hydrolysis. The two polymeric artificial metalloproteases synthesized in the present study cleaved all of the protein substrates examined (myoglobin, gamma-globulin, bovine serum albumin, human serum albumin, lysozyme, and ovalbumin), manifesting saturation kinetic behavior. At 50 degrees C and pH 9.0 or 9.5, K(m) was (1.3-22) x 10(-)(4) M, comparable to those of natural proteases, and k(cat) was (6.0-25) x 10(-)(4) s(-)(1), corresponding to half-lives of 4.6-19 min. Intermediacy of the imine complexes formed between the aldehyde group of the catalyst and the epsilon-amino groups of Lys residues of the substrates was confirmed by the trapping experiment with NaB(OAc)(3)H. MALDI-TOF MS of the proteolytic reaction mixtures revealed formation of various cleavage products. Structures of some of the cleavage products were determined by using carboxypeptidase A and trypsin. Among various cleavage sites thus identified, Gln(91)-Ser(92) and Ala(94)-Thr(95) were the major initial cleavage sites in the degradation of myoglobin by the two catalysts. The selective cleavage of Gln(91)-Ser(92) and Ala(94)-Thr(95) was attributed to general acid assistance in peptide cleavage by Tyr(146) located in proximity to the two peptide bonds. Broad substrate selectivity, high cleavage-site selectivity, and high proteolytic rate are achieved, therefore, by positioning the aldehyde group in proximity to Cu(II)Cyc attached to a cross-linked polystyrene.

Peptide-cleaving catalyst selective for peptide deformylase.

A peptide-cleaving catalyst selective for peptide deformylase (PDF) was obtained from a library containing about 15 000 catalyst candidates. The catalyst cleaved the polypeptide backbone of PDF at Gln(152)-Arg(153). Docking simulations suggested multiple modes of interactions in the complex formed between the catalyst and PDF.